From 0ed4a23df77054e682e051926ffcc424595e8268 Mon Sep 17 00:00:00 2001 From: s-paquett Date: Tue, 12 Mar 2019 15:15:21 -0700 Subject: [PATCH 01/17] -> Drop annotations --- .../isb_cgc_api_TCGA/aliquots_annotations.py | 72 ------------- api_3/isb_cgc_api_TCGA/annotations_api.py | 100 ------------------ api_3/isb_cgc_api_TCGA/message_classes.py | 30 ------ .../isb_cgc_api_TCGA/patients_annotations.py | 72 ------------- api_3/isb_cgc_api_TCGA/samples_annotations.py | 74 ------------- 5 files changed, 348 deletions(-) delete mode 100644 api_3/isb_cgc_api_TCGA/aliquots_annotations.py delete mode 100755 api_3/isb_cgc_api_TCGA/annotations_api.py delete mode 100644 api_3/isb_cgc_api_TCGA/patients_annotations.py delete mode 100644 api_3/isb_cgc_api_TCGA/samples_annotations.py diff --git a/api_3/isb_cgc_api_TCGA/aliquots_annotations.py b/api_3/isb_cgc_api_TCGA/aliquots_annotations.py deleted file mode 100644 index e4b64fea..00000000 --- a/api_3/isb_cgc_api_TCGA/aliquots_annotations.py +++ /dev/null @@ -1,72 +0,0 @@ -""" - -Copyright 2015, Institute for Systems Biology - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this file except in compliance with the License. -You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - -""" -import logging - -import endpoints -from protorpc import messages - -from api_3.isb_cgc_api_TCGA.annotations_api import AnnotationAPI, MetadataAnnotationList -from api_3.isb_cgc_api_TCGA.isb_cgc_api_helpers import ISB_CGC_TCGA_Endpoints - -logger = logging.getLogger(__name__) - -class AliquotsAnnotationsQueryBuilder(object): - - @staticmethod - def build_query(entity_types=None): - query_str = 'select * ' \ - 'from TCGA_metadata_annotation ' \ - 'where aliquot_barcode=%s and status = "Approved" ' - if len(entity_types) > 0: - query_str += 'and entity_type in (' + ', '.join(['%s']*len(entity_types)) + ')' - - return query_str - - @staticmethod - def build_metadata_query(): - return 'select * from TCGA_metadata_data_HG19 where aliquot_barcode=%s ' - -@ISB_CGC_TCGA_Endpoints.api_class(resource_name='aliquots') -class TCGAAliquotsAnnotationAPI(AnnotationAPI): - - GET_RESOURCE = endpoints.ResourceContainer(aliquot_barcode=messages.StringField(1, required=True), - entity_type=messages.StringField(2, repeated=True)) - - @endpoints.method(GET_RESOURCE, MetadataAnnotationList, - path='aliquots/{aliquot_barcode}/annotations', http_method='GET') - def annotations(self, request): - """ - Returns TCGA annotations about a specific aliquot, - Takes an aliquot barcode (of length 28, *eg* TCGA-01-0628-11A-01D-0356-01) as a required parameter. - User does not need to be authenticated. - """ - return self.process_annotations(request, 'aliquot_barcode', AliquotsAnnotationsQueryBuilder(), logger) - - - def validate_barcode(self, aliquot_barcode): - # check to make sure aliquot_barcode is in correct form - parts = aliquot_barcode.split('-') - assert len(parts) == 7 - assert len(parts[0]) == 4 - assert len(parts[1]) == 2 - assert len(parts[2]) == 4 - assert len(parts[3]) == 3 - assert len(parts[4]) in [2, 3] - assert len(parts[5]) == 4 - assert len(parts[6]) == 2 - diff --git a/api_3/isb_cgc_api_TCGA/annotations_api.py b/api_3/isb_cgc_api_TCGA/annotations_api.py deleted file mode 100755 index 3f9bef9e..00000000 --- a/api_3/isb_cgc_api_TCGA/annotations_api.py +++ /dev/null @@ -1,100 +0,0 @@ -''' -Created on Mar 23, 2017 - -Copyright 2017, Institute for Systems Biology - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this file except in compliance with the License. -You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - -@author: michael -''' -import MySQLdb - -import endpoints -from django.core.signals import request_finished -from protorpc import remote, messages - -from api_3.cohort_endpoint_helpers import build_constructor_dict_for_message -from api_3.isb_cgc_api_TCGA.message_classes import AnnotationMetadataItem -from api_3.api_helpers import sql_connection - -class MetadataAnnotationList(messages.Message): - items = messages.MessageField(AnnotationMetadataItem, 1, repeated=True) - count = messages.IntegerField(2, variant=messages.Variant.INT32) - -class AnnotationAPI(remote.Service): - def process_annotations(self, request, barcode_type, annotationQueryBuilder, logger): - """ - Base class method to return TCGA annotations about a specific case, sample, or aliquot, - Takes a barcode as a required parameter. User does not need to be authenticated. - """ - try: - cursor = None - db = None - request_barcode = request.get_assigned_value(barcode_type) - query_tuple = str(request_barcode), - try: - self.validate_barcode(request_barcode) - except AssertionError: - raise endpoints.BadRequestException( - '{0} is not the correct format for the {1} barcode.'.format(request_barcode, barcode_type)) - entity_types = request.get_assigned_value('entity_type') - - # check to make sure each entity type is valid - if len(entity_types) > 0: - for itm in entity_types: - itm = itm.strip() - if itm.lower() not in ['case', 'aliquot', 'analyte', 'portion', 'slide', 'sample']: - raise endpoints.BadRequestException("'{}' is not a valid entry for entity_type. " - "Valid entries are 'case', 'aliquot', 'analyte', 'portion', 'slide', and 'sample'". - format(itm)) - query_tuple += itm, - - query_str = annotationQueryBuilder.build_query(entity_types=entity_types) - metadata_query_str = annotationQueryBuilder.build_metadata_query() - db = sql_connection() - cursor = db.cursor(MySQLdb.cursors.DictCursor) - # build annotation message - cursor.execute(query_str, query_tuple) - rows = cursor.fetchall() - cursor.execute(metadata_query_str, (str(request_barcode), )) - metadata_rows = cursor.fetchall() - if len(rows) == 0: - cursor.close() - db.close() - if len(metadata_rows) == 0: - msg = "{} {} not found in the database.".format(barcode_type, request_barcode) - logger.info(msg) - else: - msg = "No annotations found for {} {}".format(barcode_type, request_barcode) - if entity_types is not None and 0 < len(entity_types): - msg += " and entity_type {}. entity_type name must be one of the following: "\ - "'case', 'aliquot', 'analyte', 'portion', 'slide', 'sample'.".format(entity_types) - logger.info(msg) - raise endpoints.NotFoundException(msg) - items = [] - for row in rows: - constructor_dict = build_constructor_dict_for_message(AnnotationMetadataItem(), row) - items.append(AnnotationMetadataItem(**constructor_dict)) - - return MetadataAnnotationList(items=items, count=len(items)) - - except (IndexError, TypeError), e: - logger.info("{} {} not found. Error: {}".format(barcode_type, request_barcode, e)) - raise endpoints.NotFoundException("{} {} not found.".format(barcode_type, request_barcode)) - except MySQLdb.ProgrammingError as e: - logger.warn("Error retrieving {} data: {}".format(barcode_type, e)) - raise endpoints.BadRequestException("Error retrieving {} data: {}".format(barcode_type, e)) - finally: - if cursor: cursor.close() - if db and db.open: db.close() - request_finished.send(self) diff --git a/api_3/isb_cgc_api_TCGA/message_classes.py b/api_3/isb_cgc_api_TCGA/message_classes.py index 3fba55c9..f5daa31c 100644 --- a/api_3/isb_cgc_api_TCGA/message_classes.py +++ b/api_3/isb_cgc_api_TCGA/message_classes.py @@ -499,34 +499,4 @@ class MetadataItem(messages.Message): Biospecimen = messages.MessageField(BiospecimenMetadataItem, 3) Data_HG19 = messages.MessageField(Data_HG19MetadataItem, 4) Data_HG38 = messages.MessageField(Data_HG38MetadataItem, 5) - -class AnnotationMetadataRangesItem(messages.Message): - aliquot_barcode = messages.StringField(1, repeated=True) - annotation_gdc_id = messages.StringField(2, repeated=True) - annotation_submitter_id = messages.StringField(3, repeated=True) - case_barcode = messages.StringField(4, repeated=True) - case_gdc_id = messages.StringField(5, repeated=True) - category = messages.StringField(6, repeated=True) - classification = messages.StringField(7, repeated=True) - entity_barcode = messages.StringField(8, repeated=True) - entity_gdc_id = messages.StringField(9, repeated=True) - entity_type = messages.StringField(10, repeated=True) - notes = messages.StringField(11, repeated=True) - sample_barcode = messages.StringField(12, repeated=True) - status = messages.StringField(13, repeated=True) - -class AnnotationMetadataItem(messages.Message): - aliquot_barcode = messages.StringField(1) - annotation_gdc_id = messages.StringField(2) - annotation_submitter_id = messages.StringField(3) - case_barcode = messages.StringField(4) - case_gdc_id = messages.StringField(5) - category = messages.StringField(6) - classification = messages.StringField(7) - entity_barcode = messages.StringField(8) - entity_gdc_id = messages.StringField(9) - entity_type = messages.StringField(10) - notes = messages.StringField(11) - sample_barcode = messages.StringField(12) - status = messages.StringField(13) diff --git a/api_3/isb_cgc_api_TCGA/patients_annotations.py b/api_3/isb_cgc_api_TCGA/patients_annotations.py deleted file mode 100644 index a8a9f9be..00000000 --- a/api_3/isb_cgc_api_TCGA/patients_annotations.py +++ /dev/null @@ -1,72 +0,0 @@ -""" - -Copyright 2015, Institute for Systems Biology - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this file except in compliance with the License. -You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - -""" -import logging - -import endpoints -from protorpc import messages - -from api_3.isb_cgc_api_TCGA.annotations_api import AnnotationAPI, MetadataAnnotationList -from api_3.isb_cgc_api_TCGA.isb_cgc_api_helpers import ISB_CGC_TCGA_Endpoints - -logger = logging.getLogger(__name__) - - -class CasesAnnotationsQueryBuilder(object): - - @staticmethod - def build_query(entity_types=None): - query_str = 'select * ' \ - 'from TCGA_metadata_annotation ' \ - 'where case_barcode=%s and status = "Approved" ' - if len(entity_types) > 0: - query_str += 'and entity_type in (' + ', '.join(['%s']*len(entity_types)) + ')' - - return query_str - - @staticmethod - def build_metadata_query(): - query_str = 'select case_barcode ' \ - 'from TCGA_metadata_clinical ' \ - 'where case_barcode=%s ' - - return query_str - -@ISB_CGC_TCGA_Endpoints.api_class(resource_name='cases') -class TCGACasesAnnotationAPI(AnnotationAPI): - - GET_RESOURCE = endpoints.ResourceContainer(case_barcode=messages.StringField(1, required=True), - entity_type=messages.StringField(2, repeated=True)) - - @endpoints.method(GET_RESOURCE, MetadataAnnotationList, - path='cases/{case_barcode}/annotations', http_method='GET') - def annotations(self, request): - """ - Returns TCGA annotations about a specific sample, - Takes a case barcode (of length 12, *eg* TCGA-01-0628) as a required parameter. - User does not need to be authenticated. - """ - return self.process_annotations(request, 'case_barcode', CasesAnnotationsQueryBuilder(), logger) - - - def validate_barcode(self, case_barcode): - # check to make sure case_barcode is in correct form - parts = case_barcode.split('-') - assert len(parts) == 3 - assert len(parts[0]) == 4 - assert len(parts[1]) == 2 - assert len(parts[2]) == 4 diff --git a/api_3/isb_cgc_api_TCGA/samples_annotations.py b/api_3/isb_cgc_api_TCGA/samples_annotations.py deleted file mode 100644 index 1d4ec3c3..00000000 --- a/api_3/isb_cgc_api_TCGA/samples_annotations.py +++ /dev/null @@ -1,74 +0,0 @@ -""" - -Copyright 2015, Institute for Systems Biology - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this file except in compliance with the License. -You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - -""" -import logging - -import endpoints -from protorpc import messages - -from api_3.isb_cgc_api_TCGA.annotations_api import AnnotationAPI, MetadataAnnotationList -from api_3.isb_cgc_api_TCGA.isb_cgc_api_helpers import ISB_CGC_TCGA_Endpoints - -logger = logging.getLogger(__name__) - - -class SamplesAnnotationsQueryBuilder(object): - - @staticmethod - def build_query(entity_types=None): - query_str = 'select * ' \ - 'from TCGA_metadata_annotation ' \ - 'where sample_barcode=%s and status = "Approved" ' - if len(entity_types) > 0: - query_str += 'and entity_type in (' + ', '.join(['%s']*len(entity_types)) + ')' - - return query_str - - @staticmethod - def build_metadata_query(): - query_str = 'select sample_barcode ' \ - 'from TCGA_metadata_biospecimen ' \ - 'where sample_barcode=%s ' - - return query_str - - -@ISB_CGC_TCGA_Endpoints.api_class(resource_name='samples') -class TCGASamplesAnnotationAPI(AnnotationAPI): - - GET_RESOURCE = endpoints.ResourceContainer(sample_barcode=messages.StringField(1, required=True), - entity_type=messages.StringField(2, repeated=True)) - - @endpoints.method(GET_RESOURCE, MetadataAnnotationList, - path='samples/{sample_barcode}/annotations', http_method='GET') - def annotations(self, request): - """ - Returns TCGA annotations about a specific sample, - Takes a sample barcode (of length 16, *eg* TCGA-01-0628-11A) as a required parameter. - User does not need to be authenticated. - """ - return self.process_annotations(request, 'sample_barcode', SamplesAnnotationsQueryBuilder(), logger) - - - def validate_barcode(self, sample_barcode): - # check to make sure sample_barcode is in correct form - parts = sample_barcode.split('-') - assert len(parts) == 4 - assert len(parts[0]) == 4 - assert len(parts[1]) == 2 - assert len(parts[2]) == 4 - assert len(parts[3]) == 3 From e603276f82b0ac7d4e0ae20a6143d069849d46a1 Mon Sep 17 00:00:00 2001 From: s-paquett Date: Mon, 1 Apr 2019 13:14:15 -0700 Subject: [PATCH 02/17] -> Fix table names for new metadata_data tables (patch) --- api_3/cloudstoragefilepaths_helper.py | 2 +- api_3/cohort_create_preview_helper.py | 4 ++-- api_3/isb_cgc_api/cohorts_cloudstoragefilepaths.py | 2 +- api_3/isb_cgc_api/files_get_file_paths.py | 2 +- api_3/message_generator.py | 4 ++-- api_3/patients_get_helper.py | 2 +- api_3/samples_get_helper.py | 4 ++-- 7 files changed, 10 insertions(+), 10 deletions(-) diff --git a/api_3/cloudstoragefilepaths_helper.py b/api_3/cloudstoragefilepaths_helper.py index f6d47139..0b52d6f5 100755 --- a/api_3/cloudstoragefilepaths_helper.py +++ b/api_3/cloudstoragefilepaths_helper.py @@ -122,7 +122,7 @@ def build_query(self, param_map, program): query_tuple = [] for build in builds: query_str = 'SELECT md.file_name_key, md.access ' \ - 'FROM {}_metadata_data_{} md '.format(program, build) + 'FROM {}_metadata_data_{}_r14 md '.format(program, build) query_str += 'WHERE sample_barcode=%s ' query_tuple += [param_map['sample_barcode']] diff --git a/api_3/cohort_create_preview_helper.py b/api_3/cohort_create_preview_helper.py index 86b0e252..227656d3 100755 --- a/api_3/cohort_create_preview_helper.py +++ b/api_3/cohort_create_preview_helper.py @@ -134,8 +134,8 @@ def query(self, request): ret_gte_query_dict = {} ret_rows = None - for table in ('Clinical', 'Biospecimen', 'Data_HG19', 'Data_HG38'): - if 'CCLE' == self.program and 'Data_HG38' == table: + for table in ('Clinical', 'Biospecimen', 'data_HG19_r14', 'data_HG38_r14'): + if 'CCLE' == self.program and 'data_HG38_r14' == table: continue fields = request.get_assigned_value(table) diff --git a/api_3/isb_cgc_api/cohorts_cloudstoragefilepaths.py b/api_3/isb_cgc_api/cohorts_cloudstoragefilepaths.py index 26fc5df1..ed47aaf4 100755 --- a/api_3/isb_cgc_api/cohorts_cloudstoragefilepaths.py +++ b/api_3/isb_cgc_api/cohorts_cloudstoragefilepaths.py @@ -25,7 +25,7 @@ class CohortsCloudStorageFilePathsAPI(CohortsCloudStorageFilePathsHelper): def build_program_query(self, final_query_str, query_tuple, program, param_map, build): query_str = 'SELECT md.file_name_key, md.access '\ - 'FROM {}_metadata_data_{} md '.format(program, build) + 'FROM {}_metadata_data_{}_r14 md '.format(program, build) query_str += 'JOIN cohorts_samples cs ON md.sample_barcode=cs.sample_barcode WHERE cs.cohort_id=%s ' query_tuple += [param_map['cohort_id']] query_str += 'AND file_name_key != "" AND file_name_key is not null ' diff --git a/api_3/isb_cgc_api/files_get_file_paths.py b/api_3/isb_cgc_api/files_get_file_paths.py index b6d94d1f..f110bbbe 100755 --- a/api_3/isb_cgc_api/files_get_file_paths.py +++ b/api_3/isb_cgc_api/files_get_file_paths.py @@ -44,7 +44,7 @@ def get(self, request): in_clause = in_clause[:-2] uuid2paths = {} - sql = 'select file_gdc_id, file_name_key from {}_metadata_data_{} where file_gdc_id in ({}) order by 1, 2' + sql = 'select file_gdc_id, file_name_key from {}_metadata_data_{}_r14 where file_gdc_id in ({}) order by 1, 2' programs = ['CCLE', 'TARGET', 'TCGA'] db = sql_connection() for program in programs: diff --git a/api_3/message_generator.py b/api_3/message_generator.py index e35e1f9a..31644464 100755 --- a/api_3/message_generator.py +++ b/api_3/message_generator.py @@ -208,11 +208,11 @@ def main(args): create_metadata_file(cursor, program[0], 'Clinical', path_template % (program[0]), column_filter, True, False, write_file) column_filter += ["disease_code", "endpoint_type", "program_name", "project_short_name"] create_metadata_file(cursor, program[0], 'Biospecimen', path_template % (program[0]), column_filter, True, False, write_file) - table_list = ['Common', 'Clinical', 'Biospecimen', 'Data_HG19'] + table_list = ['Common', 'Clinical', 'Biospecimen', 'data_HG19_r14'] create_metadata_file(cursor, program[0], 'Data_HG19', path_template % (program[0]), column_filter, True, True if 'CCLE' == program[0] else False, write_file) if 'CCLE' != program[0]: create_metadata_file(cursor, program[0], 'Data_HG38', path_template % (program[0]), column_filter, True, False if program[1] else True, write_file) - table_list += ['Data_HG38'] + table_list += ['data_HG38_r14'] create_nesting_class(table_list, path_template % (program[0]), write_file) if program[1]: create_metadata_file(cursor, program[0], 'Annotation', path_template % (program[0]), column_filter, True, True, write_file) diff --git a/api_3/patients_get_helper.py b/api_3/patients_get_helper.py index 1b664228..f9f5186b 100755 --- a/api_3/patients_get_helper.py +++ b/api_3/patients_get_helper.py @@ -53,7 +53,7 @@ def build_queries(self, program, genomic_builds, count=1): aliquot_query_str = '' for genomic_build in genomic_builds: part_aliquot_query_str = 'select aliquot_barcode ' \ - 'from {}_metadata_data_{} ' \ + 'from {}_metadata_data_{}_r14 ' \ 'where {} and aliquot_barcode is not null ' \ 'group by aliquot_barcode '.format(program, genomic_build, case_clause) if 0 < len(aliquot_query_str): diff --git a/api_3/samples_get_helper.py b/api_3/samples_get_helper.py index 735ac6ed..6a74d79c 100755 --- a/api_3/samples_get_helper.py +++ b/api_3/samples_get_helper.py @@ -38,7 +38,7 @@ def build_aliquot_query(self, program, param_list, count=1): aliquot_query_str = '' for genomic_build in genomic_builds: part_aliquot_query_str = 'select sample_barcode, case_barcode, aliquot_barcode, aliquot_gdc_id ' \ - 'from {}_metadata_data_{} ' \ + 'from {}_metadata_data_{}_r14 ' \ 'where file_name_key is not null and file_name_key !="" '.format(program, genomic_build) for column in param_list: if column == 'sample_barcode' and count>1: @@ -72,7 +72,7 @@ def build_data_query(self, program, datadict_class, param_list, count=1): data_query_str = '' for genomic_build in genomic_builds: part_data_query_str = 'select {0} ' \ - 'from {1}_metadata_data_{2} ' \ + 'from {1}_metadata_data_{2}_r14 ' \ 'where file_name_key is not null and file_name_key !="" '.format(', '.join(field.name for field in datadict_class.all_fields()), program, genomic_build) for column in param_list: if column == 'sample_barcode' and count > 1: From 636d7c17490f6a16e44df8caaeee8e88202a7513 Mon Sep 17 00:00:00 2001 From: s-paquett Date: Mon, 1 Apr 2019 14:57:56 -0700 Subject: [PATCH 03/17] -> More annotation removal --- cgc_api.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/cgc_api.py b/cgc_api.py index bb05e37e..ba06bf73 100644 --- a/cgc_api.py +++ b/cgc_api.py @@ -27,11 +27,8 @@ from api_3.isb_cgc_api_TCGA.cohorts_preview import TCGACohortsPreviewAPI from api_3.isb_cgc_api_TCGA.cohorts_create import TCGACohortsCreateAPI from api_3.isb_cgc_api_TCGA.patients_get import TCGACasesGetAPI -from api_3.isb_cgc_api_TCGA.patients_annotations import TCGACasesAnnotationAPI from api_3.isb_cgc_api_TCGA.samples_get import TCGASamplesGetAPI from api_3.isb_cgc_api_TCGA.samples_cloudstoragefilepaths import TCGASamplesCloudStorageFilePathsAPI -from api_3.isb_cgc_api_TCGA.samples_annotations import TCGASamplesAnnotationAPI -from api_3.isb_cgc_api_TCGA.aliquots_annotations import TCGAAliquotsAnnotationAPI from api_3.isb_cgc_api_TCGA.users_get import TCGAUserGetAPI from api_3.isb_cgc_api_TARGET.cohorts_preview import TARGETCohortsPreviewAPI From 7236db77492eddea5bcdae4de1c6074a9a88113d Mon Sep 17 00:00:00 2001 From: s-paquett Date: Tue, 2 Apr 2019 12:56:25 -0700 Subject: [PATCH 04/17] -> Remove check for 'expected' datasets, since we don't know that anymore. --- api_3/users_get_common.py | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/api_3/users_get_common.py b/api_3/users_get_common.py index 91aa9e61..8f410237 100755 --- a/api_3/users_get_common.py +++ b/api_3/users_get_common.py @@ -68,21 +68,6 @@ def get(self, program): if program in dataset.name: authorized = True allowed = True - if not allowed: - das = DatasetAccessSupportFactory.from_webapp_django_settings() - authorized_datasets = das.get_datasets_for_era_login(nih_user.NIH_username) - for dataset in authorized_datasets: - try: - ad = AuthorizedDataset.objects.get(whitelist_id=dataset.dataset_id) - if program in ad.name: - allowed = True - except (ObjectDoesNotExist) as e: - logger.exception('didn\'t find an expected authorized dataset for {}: {}'.format(dataset, e)) - raise - except (MultipleObjectsReturned) as e: - authdatasets = AuthorizedDataset.objects.filter(whitelist_id=dataset.dataset_id).values_list('name',flat=True) - logger.exception('found more than one expected authorized dataset for {} named {}: {}'.format(dataset, ", ".join(authdatasets), e)) - raise if not allowed: return UserGetAPIReturnJSON(message="{} is not on the controlled-access google group.".format(user_email), From b6b871a3bef2e7ce6945948b0a5f5455ad355ba0 Mon Sep 17 00:00:00 2001 From: s-paquett Date: Tue, 2 Apr 2019 14:43:16 -0700 Subject: [PATCH 05/17] -> Remove check for 'expected' datasets, since we don't know that anymore. --- api_3/users_get_common.py | 1 - 1 file changed, 1 deletion(-) diff --git a/api_3/users_get_common.py b/api_3/users_get_common.py index 8f410237..aea70154 100755 --- a/api_3/users_get_common.py +++ b/api_3/users_get_common.py @@ -24,7 +24,6 @@ from django.core.exceptions import ObjectDoesNotExist, MultipleObjectsReturned from accounts.models import AuthorizedDataset, NIH_User, UserAuthorizedDatasets -from dataset_utils.dataset_access_support_factory import DatasetAccessSupportFactory logger = logging.getLogger(__name__) From 7fad34013f801aacbc3415cda6c249d9a8118ea1 Mon Sep 17 00:00:00 2001 From: s-paquett Date: Fri, 5 Apr 2019 14:38:10 -0700 Subject: [PATCH 06/17] -> Still trying to remove annotations... --- api/isb_cgc_api/aliquots_annotations.py | 149 - api/isb_cgc_api/message_classes.py | 16 - api/isb_cgc_api/message_generator.py | 18 - api/isb_cgc_api/patients_annotations.py | 144 - api/isb_cgc_api/samples_annotations.py | 145 - .../allowed_values_v3_TCGA.json | 55 - api_3/message_generator.py | 2 - cgc_api.py | 3 - isb_cgc_apiv3_openapiv2.json | 500 -- isb_cgc_apiv3_openapiv3.json | 571 --- isb_cgc_ccle_apiv3_openapiv2.json | 4083 ---------------- isb_cgc_ccle_apiv3_openapiv3.json | 4140 ----------------- isb_cgc_target_apiv3_openapiv2.json | 3612 -------------- isb_cgc_target_apiv3_openapiv3.json | 3672 --------------- isb_cgc_tcga_apiv3_openapiv2.json | 2819 ----------- isb_cgc_tcga_apiv3_openapiv3.json | 2907 ------------ 16 files changed, 22836 deletions(-) delete mode 100644 api/isb_cgc_api/aliquots_annotations.py delete mode 100644 api/isb_cgc_api/patients_annotations.py delete mode 100644 api/isb_cgc_api/samples_annotations.py delete mode 100644 isb_cgc_apiv3_openapiv2.json delete mode 100644 isb_cgc_apiv3_openapiv3.json delete mode 100644 isb_cgc_ccle_apiv3_openapiv2.json delete mode 100644 isb_cgc_ccle_apiv3_openapiv3.json delete mode 100644 isb_cgc_target_apiv3_openapiv2.json delete mode 100644 isb_cgc_target_apiv3_openapiv3.json delete mode 100644 isb_cgc_tcga_apiv3_openapiv2.json delete mode 100644 isb_cgc_tcga_apiv3_openapiv3.json diff --git a/api/isb_cgc_api/aliquots_annotations.py b/api/isb_cgc_api/aliquots_annotations.py deleted file mode 100644 index 890bcd82..00000000 --- a/api/isb_cgc_api/aliquots_annotations.py +++ /dev/null @@ -1,149 +0,0 @@ -""" - -Copyright 2015, Institute for Systems Biology - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this file except in compliance with the License. -You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - -""" - -import endpoints -import logging -import MySQLdb - -from django.core.signals import request_finished -from protorpc import remote, messages - -from isb_cgc_api_helpers import ISB_CGC_Endpoints, build_constructor_dict_for_message -from message_classes import MetadataAnnotationItem -from api.api_helpers import sql_connection - -logger = logging.getLogger(__name__) - - -class MetadataAnnotationList(messages.Message): - items = messages.MessageField(MetadataAnnotationItem, 1, repeated=True) - count = messages.IntegerField(2, variant=messages.Variant.INT32) - - -class AliquotsAnnotationsQueryBuilder(object): - - @staticmethod - def build_query(item_type_name=None): - query_str = 'select * ' \ - 'from metadata_annotation ' \ - 'where AliquotBarcode=%s ' - if len(item_type_name) > 0: - query_str += 'and itemTypeName in (' + ', '.join(['%s']*len(item_type_name)) + ')' - - - return query_str - - @staticmethod - def build_metadata_samples_query(): - query_str = 'select * ' \ - 'from metadata_data ' \ - 'where AliquotBarcode=%s ' - - return query_str - -@ISB_CGC_Endpoints.api_class(resource_name='aliquots') -class AliquotsAnnotationAPI(remote.Service): - - GET_RESOURCE = endpoints.ResourceContainer(aliquot_barcode=messages.StringField(1, required=True), - item_type_name=messages.StringField(2, repeated=True)) - - @endpoints.method(GET_RESOURCE, MetadataAnnotationList, - path='aliquots/{aliquot_barcode}/annotations', http_method='GET') - def annotations(self, request): - """ - Returns TCGA annotations about a specific aliquot, - Takes a aliquot barcode (of length 28 *eg* TCGA-01-0628-11A-01D-0358-06) as a required parameter. - User does not need to be authenticated. - """ - - cursor = None - db = None - - aliquot_barcode = request.get_assigned_value('aliquot_barcode') - query_tuple = (str(aliquot_barcode),) - # check to make sure aliquot_barcode is in correct form - try: - parts = aliquot_barcode.split('-') - assert len(parts) == 7 - assert len(parts[0]) == 4 - assert len(parts[1]) == 2 - assert len(parts[2]) == 4 - assert len(parts[3]) == 3 - assert len(parts[4]) in [2, 3] - assert len(parts[5]) == 4 - assert len(parts[6]) == 2 - except AssertionError: - raise endpoints.BadRequestException('{} is not the correct format for a aliquot barcode. ' - 'Aliquot barcodes must be of the form XXXX-XX-XXXX-XXX-XXX-XXXX-XX ' - 'or XXXX-XX-XXXX-XXX-XX-XXXX-XX.'.format(aliquot_barcode)) - - item_type_name = request.get_assigned_value('item_type_name') - - # check to make sure each item_type_name is valid - if len(item_type_name) > 0: - for itm in item_type_name: - itm = itm.strip() - if itm.lower() not in ['patient', 'aliquot', 'analyte', 'shipped portion', 'portion', 'slide', 'sample']: - raise endpoints.BadRequestException("'{}' is not a valid entry for item_type_name. " - "Valid entries include 'Patient', 'Aliquot', 'Analyte', 'Shipped Portion', " - "'Portion', 'Slide', and 'Sample'".format(itm)) - query_tuple += (itm,) - - query_str = AliquotsAnnotationsQueryBuilder().build_query(item_type_name=item_type_name) - metadata_samples_query_str = AliquotsAnnotationsQueryBuilder().build_metadata_samples_query() - - try: - db = sql_connection() - cursor = db.cursor(MySQLdb.cursors.DictCursor) - - # build annotation message - cursor.execute(query_str, query_tuple) - rows = cursor.fetchall() - cursor.execute(metadata_samples_query_str, (str(aliquot_barcode),)) - metadata_sample_rows = cursor.fetchall() - if len(rows) == 0: - cursor.close() - db.close() - if len(metadata_sample_rows) == 0: - msg = "Aliquot barcode {} not found in the database.".format(aliquot_barcode) - logger.info(msg) - else: - msg = "No annotations found for aliquot barcode {}".format(aliquot_barcode) - if item_type_name is not None: - msg += " and item type name {}. Item type name must be one of the following: " \ - "'Patient', 'Aliquot', 'Analyte', 'Shipped Portion', 'Portion', 'Slide', 'Sample'.".format(item_type_name) - logger.info(msg) - raise endpoints.NotFoundException(msg) - - items = [] - for row in rows: - constructor_dict = build_constructor_dict_for_message(MetadataAnnotationItem(), row) - items.append(MetadataAnnotationItem(**constructor_dict)) - - return MetadataAnnotationList(items=items, count=len(items)) - - except (IndexError, TypeError), e: - logger.info("Aliquot {} not found. Error: {}".format(aliquot_barcode, e)) - raise endpoints.NotFoundException("Aliquot {} not found.".format(aliquot_barcode)) - except MySQLdb.ProgrammingError as e: - logger.warn("Error retrieving aliquot data: {}".format(e)) - raise endpoints.BadRequestException("Error retrieving aliquot data: {}".format(e)) - finally: - if cursor: cursor.close() - if db and db.open: db.close() - request_finished.send(self) \ No newline at end of file diff --git a/api/isb_cgc_api/message_classes.py b/api/isb_cgc_api/message_classes.py index 2a60db14..420b7b6c 100644 --- a/api/isb_cgc_api/message_classes.py +++ b/api/isb_cgc_api/message_classes.py @@ -348,19 +348,3 @@ class MetadataItem(messages.Message): weight = messages.IntegerField(101, variant=messages.Variant.INT32) weiss_venous_invasion = messages.StringField(102) year_of_initial_pathologic_diagnosis = messages.IntegerField(103, variant=messages.Variant.INT32) - - -class MetadataAnnotationItem(messages.Message): - AliquotBarcode = messages.StringField(1) - annotationCategoryId = messages.IntegerField(2, variant=messages.Variant.INT32) - annotationCategoryName = messages.StringField(3) - annotationClassification = messages.StringField(4) - annotationClassificationId = messages.IntegerField(5, variant=messages.Variant.INT32) - annotationId = messages.IntegerField(6, variant=messages.Variant.INT32) - annotationNoteText = messages.StringField(7) - itemBarcode = messages.StringField(8) - itemTypeId = messages.IntegerField(9, variant=messages.Variant.INT32) - itemTypeName = messages.StringField(10) - case_barcode = messages.StringField(11) - sample_barcode = messages.StringField(12) - disease_code = messages.StringField(13) \ No newline at end of file diff --git a/api/isb_cgc_api/message_generator.py b/api/isb_cgc_api/message_generator.py index dfefbf6b..9063a0a1 100644 --- a/api/isb_cgc_api/message_generator.py +++ b/api/isb_cgc_api/message_generator.py @@ -70,24 +70,6 @@ def write_metadata_file(rows, write_file=False): print item_text -def write_annotation_file(rows, write_file=False): - item_text = '\nclass MetadataAnnotationItem(messages.Message):\n ' - i = 1 - for row in rows: - field_type = FIELD_TYPES.get(row['DATA_TYPE']) - if field_type.lower() == 'datetime': continue - item_text += '%-30s = messages.%s(%d' % (row['COLUMN_NAME'], field_type, i) - item_text += ')\n ' if field_type is not 'IntegerField' else ', variant=messages.Variant.INT32)\n ' - i += 1 - - if write_file is True: - with open('message_classes.py', 'a') as f: - f.write('\n\n\n') - f.write(item_text) - else: - print item_text - - def main(args): db = get_sql_connection(args) cursor = db.cursor(MySQLdb.cursors.DictCursor) diff --git a/api/isb_cgc_api/patients_annotations.py b/api/isb_cgc_api/patients_annotations.py deleted file mode 100644 index c8231a16..00000000 --- a/api/isb_cgc_api/patients_annotations.py +++ /dev/null @@ -1,144 +0,0 @@ -""" - -Copyright 2015, Institute for Systems Biology - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this file except in compliance with the License. -You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - -""" - -import endpoints -import logging -import MySQLdb - -from django.core.signals import request_finished -from protorpc import remote, messages - -from isb_cgc_api_helpers import ISB_CGC_Endpoints, build_constructor_dict_for_message -from message_classes import MetadataAnnotationItem -from api.api_helpers import sql_connection - -logger = logging.getLogger(__name__) - - -class MetadataAnnotationList(messages.Message): - items = messages.MessageField(MetadataAnnotationItem, 1, repeated=True) - count = messages.IntegerField(2, variant=messages.Variant.INT32) - - -class PatientsAnnotationsQueryBuilder(object): - - @staticmethod - def build_query(item_type_name=None): - query_str = 'select * ' \ - 'from metadata_annotation ' \ - 'where case_barcode=%s ' - if len(item_type_name) > 0: - query_str += 'and itemTypeName in (' + ', '.join(['%s']*len(item_type_name)) + ')' - - - return query_str - - @staticmethod - def build_metadata_samples_query(): - query_str = 'select * ' \ - 'from metadata_samples ' \ - 'where case_barcode=%s ' - - return query_str - -@ISB_CGC_Endpoints.api_class(resource_name='patients') -class PatientsAnnotationAPI(remote.Service): - - GET_RESOURCE = endpoints.ResourceContainer(patient_barcode=messages.StringField(1, required=True), - item_type_name=messages.StringField(2, repeated=True)) - - @endpoints.method(GET_RESOURCE, MetadataAnnotationList, - path='patients/{patient_barcode}/annotations', http_method='GET') - def annotations(self, request): - """ - Returns TCGA annotations about a specific patient, - Takes a patient barcode (of length 12, *eg* TCGA-B9-7268) as a required parameter. - User does not need to be authenticated. - """ - - cursor = None - db = None - - patient_barcode = request.get_assigned_value('patient_barcode') - query_tuple = (str(patient_barcode),) - # check to make sure patient_barcode is in correct form - try: - parts = patient_barcode.split('-') - assert len(parts) == 3 - assert len(parts[0]) == 4 - assert len(parts[1]) == 2 - assert len(parts[2]) == 4 - except AssertionError: - raise endpoints.BadRequestException('{} is not the correct format for a patient barcode. ' - 'Patient barcodes must be of the form XXXX-XX-XXXX'.format(patient_barcode)) - - item_type_name = request.get_assigned_value('item_type_name') - - # check to make sure each item_type_name is valid - if len(item_type_name) > 0: - for itm in item_type_name: - itm = itm.strip() - if itm.lower() not in ['patient', 'aliquot', 'analyte', 'shipped portion', 'portion', 'slide', 'sample']: - raise endpoints.BadRequestException("'{}' is not a valid entry for item_type_name. " - "Valid entries include 'Patient', 'Aliquot', 'Analyte', 'Shipped Portion', " - "'Portion', 'Slide', and 'Sample'".format(itm)) - query_tuple += (itm,) - - query_str = PatientsAnnotationsQueryBuilder().build_query(item_type_name=item_type_name) - metadata_samples_query_str = PatientsAnnotationsQueryBuilder().build_metadata_samples_query() - - try: - db = sql_connection() - cursor = db.cursor(MySQLdb.cursors.DictCursor) - - # build annotation message - cursor.execute(query_str, query_tuple) - rows = cursor.fetchall() - cursor.execute(metadata_samples_query_str, (str(patient_barcode),)) - metadata_sample_rows = cursor.fetchall() - if len(rows) == 0: - cursor.close() - db.close() - if len(metadata_sample_rows) == 0: - msg = "Patient barcode {} not found in the database.".format(patient_barcode) - logger.info(msg) - else: - msg = "No annotations found for patient barcode {}".format(patient_barcode) - if item_type_name is not None: - msg += " and item type name {}. Item type name must be one of the following: " \ - "'Patient', 'Aliquot', 'Analyte', 'Shipped Portion', 'Portion', 'Slide', 'Sample'.".format(item_type_name) - logger.info(msg) - raise endpoints.NotFoundException(msg) - - items = [] - for row in rows: - constructor_dict = build_constructor_dict_for_message(MetadataAnnotationItem(), row) - items.append(MetadataAnnotationItem(**constructor_dict)) - - return MetadataAnnotationList(items=items, count=len(items)) - - except (IndexError, TypeError), e: - logger.info("Patient {} not found. Error: {}".format(patient_barcode, e)) - raise endpoints.NotFoundException("Patient {} not found.".format(patient_barcode)) - except MySQLdb.ProgrammingError as e: - logger.warn("Error retrieving patient data: {}".format(e)) - raise endpoints.BadRequestException("Error retrieving patient data: {}".format(e)) - finally: - if cursor: cursor.close() - if db and db.open: db.close() - request_finished.send(self) \ No newline at end of file diff --git a/api/isb_cgc_api/samples_annotations.py b/api/isb_cgc_api/samples_annotations.py deleted file mode 100644 index df51455b..00000000 --- a/api/isb_cgc_api/samples_annotations.py +++ /dev/null @@ -1,145 +0,0 @@ -""" - -Copyright 2015, Institute for Systems Biology - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this file except in compliance with the License. -You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - -""" - -import endpoints -import logging -import MySQLdb - -from django.core.signals import request_finished -from protorpc import remote, messages - -from isb_cgc_api_helpers import ISB_CGC_Endpoints, build_constructor_dict_for_message -from message_classes import MetadataAnnotationItem -from api.api_helpers import sql_connection - -logger = logging.getLogger(__name__) - - -class MetadataAnnotationList(messages.Message): - items = messages.MessageField(MetadataAnnotationItem, 1, repeated=True) - count = messages.IntegerField(2, variant=messages.Variant.INT32) - - -class SamplesAnnotationsQueryBuilder(object): - - @staticmethod - def build_query(item_type_name=None): - query_str = 'select * ' \ - 'from metadata_annotation ' \ - 'where SampleBarcode=%s' - if len(item_type_name) > 0: - query_str += 'and itemTypeName in (' + ', '.join(['%s']*len(item_type_name)) + ')' - - return query_str - - @staticmethod - def build_metadata_samples_query(): - query_str = 'select * ' \ - 'from metadata_samples ' \ - 'where sample_barcode=%s ' - - return query_str - - -@ISB_CGC_Endpoints.api_class(resource_name='samples') -class SamplesAnnotationAPI(remote.Service): - - GET_RESOURCE = endpoints.ResourceContainer(sample_barcode=messages.StringField(1, required=True), - item_type_name=messages.StringField(2, repeated=True)) - - @endpoints.method(GET_RESOURCE, MetadataAnnotationList, - path='samples/{sample_barcode}/annotations', http_method='GET') - def annotations(self, request): - """ - Returns TCGA annotations about a specific sample, - Takes a patient barcode (of length , *eg* TCGA-01-0628-11A) as a required parameter. - User does not need to be authenticated. - """ - - cursor = None - db = None - - sample_barcode = request.get_assigned_value('sample_barcode') - query_tuple = (str(sample_barcode),) - # check to make sure sample_barcode is in correct form - try: - parts = sample_barcode.split('-') - assert len(parts) == 4 - assert len(parts[0]) == 4 - assert len(parts[1]) == 2 - assert len(parts[2]) == 4 - assert len(parts[3]) == 3 - except AssertionError: - raise endpoints.BadRequestException('{} is not the correct format for a sample barcode. ' - 'Sample barcodes must be of the form XXXX-XX-XXXX-XXX'.format(sample_barcode)) - - item_type_name = request.get_assigned_value('item_type_name') - # check to make sure item_type_name is valid - # check to make sure each item_type_name is valid - if len(item_type_name) > 0: - for itm in item_type_name: - itm = itm.strip() - if itm.lower() not in ['patient', 'aliquot', 'analyte', 'shipped portion', 'portion', 'slide', 'sample']: - raise endpoints.BadRequestException("'{}' is not a valid entry for item_type_name. " - "Valid entries include 'Patient', 'Aliquot', 'Analyte', 'Shipped Portion', " - "'Portion', 'Slide', and 'Sample'".format(itm)) - query_tuple += (itm,) - - query_str = SamplesAnnotationsQueryBuilder().build_query(item_type_name=item_type_name) - metadata_samples_query_str = SamplesAnnotationsQueryBuilder().build_metadata_samples_query() - - try: - db = sql_connection() - cursor = db.cursor(MySQLdb.cursors.DictCursor) - - # build annotation message - cursor.execute(query_str, query_tuple) - rows = cursor.fetchall() - cursor.execute(metadata_samples_query_str, (str(sample_barcode),)) - metadata_sample_rows = cursor.fetchall() - if len(rows) == 0: - cursor.close() - db.close() - if len(metadata_sample_rows) == 0: - msg = "Sample barcode {} not found in the database.".format(sample_barcode) - logger.info(msg) - else: - msg = "No annotations found for sample barcode {}".format(sample_barcode) - if item_type_name is not None: - msg += " and item type name {}. Item type name must be one of the following: " \ - "'Patient', 'Aliquot', 'Analyte', 'Shipped Portion', 'Portion', 'Slide', 'Sample'.".format(item_type_name) - logger.info(msg) - raise endpoints.NotFoundException(msg) - - items = [] - for row in rows: - constructor_dict = build_constructor_dict_for_message(MetadataAnnotationItem(), row) - items.append(MetadataAnnotationItem(**constructor_dict)) - - return MetadataAnnotationList(items=items, count=len(items)) - - except (IndexError, TypeError), e: - logger.info("Patient {} not found. Error: {}".format(sample_barcode, e)) - raise endpoints.NotFoundException("Patient {} not found.".format(sample_barcode)) - except MySQLdb.ProgrammingError as e: - logger.warn("Error retrieving patient data: {}".format(e)) - raise endpoints.BadRequestException("Error retrieving patient data: {}".format(e)) - finally: - if cursor: cursor.close() - if db and db.open: db.close() - request_finished.send(self) \ No newline at end of file diff --git a/api_3/isb_cgc_api_TCGA/allowed_values_v3_TCGA.json b/api_3/isb_cgc_api_TCGA/allowed_values_v3_TCGA.json index 5b1bcd63..39bb1364 100755 --- a/api_3/isb_cgc_api_TCGA/allowed_values_v3_TCGA.json +++ b/api_3/isb_cgc_api_TCGA/allowed_values_v3_TCGA.json @@ -776,60 +776,5 @@ "species": [ "Homo sapiens" ] - }, - "Annotation": { - "category": [ - "Acceptable treatment for TCGA tumor", - "Administrative Compliance", - "Alternate sample pipeline", - "Barcode incorrect", - "BCR Notification", - "Case submitted is found to be a recurrence after submission", - "Center QC failed", - "Duplicate item", - "General", - "Genotype mismatch", - "History of acceptable prior treatment related to a prior/other malignancy", - "History of unacceptable prior treatment related to a prior/other malignancy", - "Item does not meet study protocol", - "Item flagged DNU", - "Item Flagged Low Quality", - "Item in special subset", - "Item is noncanonical", - "Item may not meet study protocol", - "Molecular analysis outside specification", - "Neoadjuvant therapy", - "Normal class but appears diseased", - "Normal tissue origin incorrect", - "Pathology outside specification", - "Permanently missing item or object", - "Prior malignancy", - "Qualification metrics changed", - "Qualified in error", - "Sample compromised", - "Subject withdrew consent", - "Synchronous malignancy", - "Tumor class but appears normal", - "Tumor tissue origin incorrect", - "Tumor type incorrect" - ], - "classification": [ - "CenterNotification", - "Notification", - "Observation", - "Redaction" - ], - "entity_type": [ - "aliquot", - "analyte", - "case", - "portion", - "sample", - "slide" - ], - "status": [ - "Approved", - "Rescinded" - ] } } diff --git a/api_3/message_generator.py b/api_3/message_generator.py index 31644464..77cf470a 100755 --- a/api_3/message_generator.py +++ b/api_3/message_generator.py @@ -214,8 +214,6 @@ def main(args): create_metadata_file(cursor, program[0], 'Data_HG38', path_template % (program[0]), column_filter, True, False if program[1] else True, write_file) table_list += ['data_HG38_r14'] create_nesting_class(table_list, path_template % (program[0]), write_file) - if program[1]: - create_metadata_file(cursor, program[0], 'Annotation', path_template % (program[0]), column_filter, True, True, write_file) print datetime.now(), 'finished program {}'.format(program) finally: if cursor: diff --git a/cgc_api.py b/cgc_api.py index ba06bf73..8cc0ae98 100644 --- a/cgc_api.py +++ b/cgc_api.py @@ -57,11 +57,8 @@ TCGACohortsPreviewAPI, TCGACohortsCreateAPI, TCGACasesGetAPI, - TCGACasesAnnotationAPI, TCGASamplesGetAPI, TCGASamplesCloudStorageFilePathsAPI, - TCGASamplesAnnotationAPI, - TCGAAliquotsAnnotationAPI, TCGAUserGetAPI, TARGETCohortsPreviewAPI, diff --git a/isb_cgc_apiv3_openapiv2.json b/isb_cgc_apiv3_openapiv2.json deleted file mode 100644 index 2ddbe4e0..00000000 --- a/isb_cgc_apiv3_openapiv2.json +++ /dev/null @@ -1,500 +0,0 @@ -{ - "basePath": "/_ah/api", - "consumes": [ - "application/json" - ], - "definitions": { - "Api3CloudstoragefilepathsHelperGCSFilePathList": { - "properties": { - "cloud_storage_file_paths": { - "items": { - "type": "string" - }, - "type": "array" - }, - "count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3CohortEndpointHelpersFilterDetails": { - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileDetail": { - "properties": { - "access": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_uuid": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "disease_code": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_gdc_uuid": { - "type": "string" - }, - "file_path": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "program": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "required": [ - "case_barcode", - "disease_code", - "file_path", - "program" - ], - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileManifest": { - "properties": { - "files": { - "items": { - "$ref": "#/definitions/Api3IsbCgcApiCohortFileManifestFileDetail" - }, - "type": "array" - }, - "files_retrieved": { - "format": "int32", - "type": "integer" - }, - "total_file_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "cases": { - "items": { - "type": "string" - }, - "type": "array" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/definitions/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetailsList": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "items": { - "items": { - "$ref": "#/definitions/Api3IsbCgcApiCohortGetListHelperCohortListDetails" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortListDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/definitions/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortsDeleteReturnJSON": { - "properties": { - "message": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiFilesGetFilePathsFilePaths": { - "properties": { - "paths": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - } - }, - "host": "api-dot-isb-cgc.appspot.com", - "info": { - "description": "Get information about cohorts for ISB-CGC. List, get, delete cohorts, and retrieve or export their file manifests.", - "title": "isb_cgc_api", - "version": "v3" - }, - "paths": { - "/isb_cgc_api/v3/cohorts": { - "get": { - "operationId": "CohortsListAPI_list", - "parameters": [], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiCohortGetListHelperCohortDetailsList" - } - } - } - } - }, - "/isb_cgc_api/v3/cohorts/{cohort_id}": { - "delete": { - "operationId": "CohortsDeleteAPI_delete", - "parameters": [ - { - "format": "int64", - "in": "path", - "name": "cohort_id", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiCohortsDeleteReturnJSON" - } - } - } - }, - "get": { - "operationId": "CohortsGetAPI_get", - "parameters": [ - { - "format": "int64", - "in": "path", - "name": "cohort_id", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiCohortGetListHelperCohortDetails" - } - } - } - } - }, - "/isb_cgc_api/v3/cohorts/{cohort_id}/cloud_storage_file_paths": { - "get": { - "operationId": "CohortsCloudStorageFilePathsAPI_cloudStorageFilePaths", - "parameters": [ - { - "format": "int64", - "in": "path", - "name": "cohort_id", - "required": true, - "type": "string" - }, - { - "format": "int64", - "in": "query", - "name": "limit", - "type": "string" - }, - { - "in": "query", - "name": "data_type", - "type": "string" - }, - { - "in": "query", - "name": "data_category", - "type": "string" - }, - { - "in": "query", - "name": "experimental_strategy", - "type": "string" - }, - { - "in": "query", - "name": "data_format", - "type": "string" - }, - { - "in": "query", - "name": "platform", - "type": "string" - }, - { - "in": "query", - "name": "genomic_build", - "type": "string" - }, - { - "in": "query", - "name": "analysis_workflow_type", - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3CloudstoragefilepathsHelperGCSFilePathList" - } - } - } - } - }, - "/isb_cgc_api/v3/cohorts/{cohort_id}/file_manifest": { - "get": { - "operationId": "CohortFileManifestAPI_fileManifest", - "parameters": [ - { - "format": "int64", - "in": "path", - "name": "cohort_id", - "required": true, - "type": "string" - }, - { - "format": "int64", - "in": "query", - "name": "fetch_count", - "type": "string" - }, - { - "format": "int64", - "in": "query", - "name": "offset", - "type": "string" - }, - { - "in": "query", - "name": "genomic_build", - "type": "string" - }, - { - "in": "query", - "name": "do_filter_count", - "type": "boolean" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiCohortFileManifestFileManifest" - } - } - } - }, - "post": { - "operationId": "CohortFileManifestAPI_fileManifestFiltered", - "parameters": [ - { - "format": "int64", - "in": "path", - "name": "cohort_id", - "required": true, - "type": "string" - }, - { - "format": "int64", - "in": "query", - "name": "fetch_count", - "type": "string" - }, - { - "format": "int64", - "in": "query", - "name": "offset", - "type": "string" - }, - { - "in": "query", - "name": "genomic_build", - "type": "string" - }, - { - "in": "query", - "name": "do_filter_count", - "type": "boolean" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiCohortFileManifestFileManifest" - } - } - } - } - }, - "/isb_cgc_api/v3/file_paths": { - "get": { - "operationId": "FilesGetPath_get", - "parameters": [ - { - "collectionFormat": "multi", - "in": "query", - "items": { - "type": "string" - }, - "name": "file_uuids", - "type": "array" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiFilesGetFilePathsFilePaths" - } - } - } - } - } - }, - "produces": [ - "application/json" - ], - "schemes": [ - "https" - ], - "securityDefinitions": { - "google_id_token": { - "authorizationUrl": "", - "flow": "implicit", - "type": "oauth2", - "x-google-issuer": "https://accounts.google.com", - "x-google-jwks_uri": "https://www.googleapis.com/oauth2/v3/certs" - } - }, - "swagger": "2.0" -} \ No newline at end of file diff --git a/isb_cgc_apiv3_openapiv3.json b/isb_cgc_apiv3_openapiv3.json deleted file mode 100644 index 3a32f189..00000000 --- a/isb_cgc_apiv3_openapiv3.json +++ /dev/null @@ -1,571 +0,0 @@ -{ - "openapi": "3.0.0", - "servers": [ - { - "url": "https://api-dot-isb-cgc.appspot.com/_ah/api" - } - ], - "info": { - "description": "Get information about cohorts for ISB-CGC. List, get, delete cohorts, and retrieve or export their file manifests.", - "title": "ISB-CGC API: Cohorts", - "version": "v3" - }, - "paths": { - "/isb_cgc_api/v3/cohorts": { - "get": { - "operationId": "CohortsListAPI_list", - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiCohortGetListHelperCohortDetailsList" - } - } - } - } - } - } - }, - "/isb_cgc_api/v3/cohorts/{cohort_id}": { - "delete": { - "operationId": "CohortsDeleteAPI_delete", - "parameters": [ - { - "in": "path", - "name": "cohort_id", - "required": true, - "schema": { - "type": "string", - "format": "int64" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiCohortsDeleteReturnJSON" - } - } - } - } - } - }, - "get": { - "operationId": "CohortsGetAPI_get", - "parameters": [ - { - "in": "path", - "name": "cohort_id", - "required": true, - "schema": { - "type": "string", - "format": "int64" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiCohortGetListHelperCohortDetails" - } - } - } - } - } - } - }, - "/isb_cgc_api/v3/cohorts/{cohort_id}/cloud_storage_file_paths": { - "get": { - "operationId": "CohortsCloudStorageFilePathsAPI_cloudStorageFilePaths", - "parameters": [ - { - "in": "path", - "name": "cohort_id", - "required": true, - "schema": { - "type": "string", - "format": "int64" - } - }, - { - "in": "query", - "name": "limit", - "schema": { - "type": "string", - "format": "int64" - } - }, - { - "in": "query", - "name": "data_type", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_category", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "experimental_strategy", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_format", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "platform", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "genomic_build", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "analysis_workflow_type", - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3CloudstoragefilepathsHelperGCSFilePathList" - } - } - } - } - } - } - }, - "/isb_cgc_api/v3/cohorts/{cohort_id}/file_manifest": { - "get": { - "operationId": "CohortFileManifestAPI_fileManifest", - "parameters": [ - { - "in": "path", - "name": "cohort_id", - "required": true, - "schema": { - "type": "string", - "format": "int64" - } - }, - { - "in": "query", - "name": "fetch_count", - "schema": { - "type": "string", - "format": "int64" - } - }, - { - "in": "query", - "name": "offset", - "schema": { - "type": "string", - "format": "int64" - } - }, - { - "in": "query", - "name": "genomic_build", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "do_filter_count", - "schema": { - "type": "boolean" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiCohortFileManifestFileManifest" - } - } - } - } - } - }, - "post": { - "operationId": "CohortFileManifestAPI_fileManifestFiltered", - "parameters": [ - { - "in": "path", - "name": "cohort_id", - "required": true, - "schema": { - "type": "string", - "format": "int64" - } - }, - { - "in": "query", - "name": "fetch_count", - "schema": { - "type": "string", - "format": "int64" - } - }, - { - "in": "query", - "name": "offset", - "schema": { - "type": "string", - "format": "int64" - } - }, - { - "in": "query", - "name": "genomic_build", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "do_filter_count", - "schema": { - "type": "boolean" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiCohortFileManifestFileManifest" - } - } - } - } - } - } - }, - "/isb_cgc_api/v3/file_paths": { - "get": { - "operationId": "FilesGetPath_get", - "parameters": [ - { - "in": "query", - "name": "file_uuids", - "explode": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiFilesGetFilePathsFilePaths" - } - } - } - } - } - } - } - }, - "components": { - "schemas": { - "Api3CloudstoragefilepathsHelperGCSFilePathList": { - "properties": { - "cloud_storage_file_paths": { - "items": { - "type": "string" - }, - "type": "array" - }, - "count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3CohortEndpointHelpersFilterDetails": { - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileDetail": { - "properties": { - "access": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_uuid": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "disease_code": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_gdc_uuid": { - "type": "string" - }, - "file_path": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "program": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "required": [ - "case_barcode", - "disease_code", - "file_path", - "program" - ], - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileManifest": { - "properties": { - "files": { - "items": { - "$ref": "#/components/schemas/Api3IsbCgcApiCohortFileManifestFileDetail" - }, - "type": "array" - }, - "files_retrieved": { - "format": "int32", - "type": "integer" - }, - "total_file_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "cases": { - "items": { - "type": "string" - }, - "type": "array" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/components/schemas/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetailsList": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "items": { - "items": { - "$ref": "#/components/schemas/Api3IsbCgcApiCohortGetListHelperCohortListDetails" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortListDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/components/schemas/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortsDeleteReturnJSON": { - "properties": { - "message": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiFilesGetFilePathsFilePaths": { - "properties": { - "paths": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - } - }, - "securitySchemes": { - "google_id_token": { - "type": "oauth2", - "x-google-issuer": "https://accounts.google.com", - "x-google-jwks_uri": "https://www.googleapis.com/oauth2/v3/certs", - "flows": { - "implicit": { - "authorizationUrl": "/", - "scopes": {} - } - } - } - } - } -} \ No newline at end of file diff --git a/isb_cgc_ccle_apiv3_openapiv2.json b/isb_cgc_ccle_apiv3_openapiv2.json deleted file mode 100644 index 1483b86e..00000000 --- a/isb_cgc_ccle_apiv3_openapiv2.json +++ /dev/null @@ -1,4083 +0,0 @@ -{ - "basePath": "/_ah/api", - "consumes": [ - "application/json" - ], - "definitions": { - "Api3CloudstoragefilepathsHelperGCSFilePathList": { - "properties": { - "cloud_storage_file_paths": { - "items": { - "type": "string" - }, - "type": "array" - }, - "count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperCohortCasesSamplesList": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "cases": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperCreatedCohort": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "filters": { - "items": { - "$ref": "#/definitions/Api3CohortCreatePreviewHelperFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperFilterDetails": { - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, - "Api3CohortEndpointHelpersFilterDetails": { - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesBiospecimenMetadataItem": { - "properties": { - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesBiospecimenMetadataRangesItem": { - "properties": { - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesClinicalMetadataItem": { - "properties": { - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "gender": { - "type": "string" - }, - "hist_subtype": { - "type": "string" - }, - "histology": { - "type": "string" - }, - "site_primary": { - "type": "string" - }, - "source": { - "type": "string" - }, - "summary_file_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesClinicalMetadataRangesItem": { - "properties": { - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gender": { - "items": { - "type": "string" - }, - "type": "array" - }, - "hist_subtype": { - "items": { - "type": "string" - }, - "type": "array" - }, - "histology": { - "items": { - "type": "string" - }, - "type": "array" - }, - "site_primary": { - "items": { - "type": "string" - }, - "type": "array" - }, - "source": { - "items": { - "type": "string" - }, - "type": "array" - }, - "summary_file_count": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "summary_file_count_gte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count_lte": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesCommonMetadataItem": { - "properties": { - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesCommonMetadataRangesItem": { - "properties": { - "disease_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "endpoint_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "program_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "project_short_name": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesDataHG19MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesDataHG19MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesMetadataItem": { - "properties": { - "Biospecimen": { - "$ref": "#/definitions/Api3IsbCgcApiCCLEMessageClassesBiospecimenMetadataItem" - }, - "Clinical": { - "$ref": "#/definitions/Api3IsbCgcApiCCLEMessageClassesClinicalMetadataItem" - }, - "Common": { - "$ref": "#/definitions/Api3IsbCgcApiCCLEMessageClassesCommonMetadataItem" - }, - "Data_HG19": { - "$ref": "#/definitions/Api3IsbCgcApiCCLEMessageClassesDataHG19MetadataItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesMetadataRangesItem": { - "properties": { - "Biospecimen": { - "$ref": "#/definitions/Api3IsbCgcApiCCLEMessageClassesBiospecimenMetadataRangesItem" - }, - "Clinical": { - "$ref": "#/definitions/Api3IsbCgcApiCCLEMessageClassesClinicalMetadataRangesItem" - }, - "Common": { - "$ref": "#/definitions/Api3IsbCgcApiCCLEMessageClassesCommonMetadataRangesItem" - }, - "Data_HG19": { - "$ref": "#/definitions/Api3IsbCgcApiCCLEMessageClassesDataHG19MetadataRangesItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEPatientsGetCaseDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_data": { - "$ref": "#/definitions/Api3IsbCgcApiCCLEMessageClassesMetadataItem" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLESamplesGetSampleDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "biospecimen_data": { - "$ref": "#/definitions/Api3IsbCgcApiCCLEMessageClassesMetadataItem" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "data_details": { - "items": { - "$ref": "#/definitions/Api3SamplesGetHelperDataDetails" - }, - "type": "array" - }, - "data_details_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileDetail": { - "properties": { - "access": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_uuid": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "disease_code": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_gdc_uuid": { - "type": "string" - }, - "file_path": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "program": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileManifest": { - "properties": { - "files": { - "items": { - "$ref": "#/definitions/Api3IsbCgcApiCohortFileManifestFileDetail" - }, - "type": "array" - }, - "files_retrieved": { - "format": "int32", - "type": "integer" - }, - "total_file_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "cases": { - "items": { - "type": "string" - }, - "type": "array" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/definitions/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetailsList": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "items": { - "items": { - "$ref": "#/definitions/Api3IsbCgcApiCohortGetListHelperCohortListDetails" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortListDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/definitions/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortsDeleteReturnJSON": { - "properties": { - "message": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiFilesGetFilePathsFilePaths": { - "properties": { - "paths": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataItem": { - "properties": { - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "tumor_code": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataRangesItem": { - "properties": { - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_code": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesClinicalMetadataItem": { - "properties": { - "age_at_diagnosis": { - "format": "int32", - "type": "integer" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "days_to_birth": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "type": "string" - }, - "event_free_survival": { - "format": "int32", - "type": "integer" - }, - "first_event": { - "type": "string" - }, - "gender": { - "type": "string" - }, - "protocol": { - "type": "string" - }, - "race": { - "type": "string" - }, - "summary_file_count": { - "format": "int32", - "type": "integer" - }, - "vital_status": { - "type": "string" - }, - "wbc_at_diagnosis": { - "format": "double", - "type": "number" - }, - "year_of_diagnosis": { - "format": "int32", - "type": "integer" - }, - "year_of_last_follow_up": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesClinicalMetadataRangesItem": { - "properties": { - "age_at_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_at_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "age_at_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_birth": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_birth_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_birth_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_death_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_death_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_followup_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_known_alive_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive_lte": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "items": { - "type": "string" - }, - "type": "array" - }, - "event_free_survival": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "event_free_survival_gte": { - "format": "int32", - "type": "integer" - }, - "event_free_survival_lte": { - "format": "int32", - "type": "integer" - }, - "first_event": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gender": { - "items": { - "type": "string" - }, - "type": "array" - }, - "protocol": { - "items": { - "type": "string" - }, - "type": "array" - }, - "race": { - "items": { - "type": "string" - }, - "type": "array" - }, - "summary_file_count": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "summary_file_count_gte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count_lte": { - "format": "int32", - "type": "integer" - }, - "vital_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "wbc_at_diagnosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "wbc_at_diagnosis_gte": { - "format": "double", - "type": "number" - }, - "wbc_at_diagnosis_lte": { - "format": "double", - "type": "number" - }, - "year_of_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_last_follow_up": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_last_follow_up_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_last_follow_up_lte": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesCommonMetadataItem": { - "properties": { - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesCommonMetadataRangesItem": { - "properties": { - "disease_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "endpoint_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "program_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "project_short_name": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesMetadataItem": { - "properties": { - "Biospecimen": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataItem" - }, - "Clinical": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesClinicalMetadataItem" - }, - "Common": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesCommonMetadataItem" - }, - "Data_HG19": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataItem" - }, - "Data_HG38": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesMetadataRangesItem": { - "properties": { - "Biospecimen": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataRangesItem" - }, - "Clinical": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesClinicalMetadataRangesItem" - }, - "Common": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesCommonMetadataRangesItem" - }, - "Data_HG19": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataRangesItem" - }, - "Data_HG38": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataRangesItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETPatientsGetCaseDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_data": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesMetadataItem" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETSamplesGetSampleDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "biospecimen_data": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesMetadataItem" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "data_details": { - "items": { - "$ref": "#/definitions/Api3SamplesGetHelperDataDetails" - }, - "type": "array" - }, - "data_details_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAAnnotationsApiMetadataAnnotationList": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "items": { - "items": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesAnnotationMetadataItem" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesAnnotationMetadataItem": { - "properties": { - "aliquot_barcode": { - "type": "string" - }, - "annotation_gdc_id": { - "type": "string" - }, - "annotation_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "category": { - "type": "string" - }, - "classification": { - "type": "string" - }, - "entity_barcode": { - "type": "string" - }, - "entity_gdc_id": { - "type": "string" - }, - "entity_type": { - "type": "string" - }, - "notes": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "status": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataItem": { - "properties": { - "avg_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "batch_number": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "days_to_collection": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement": { - "format": "int32", - "type": "integer" - }, - "max_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "num_portions": { - "format": "int32", - "type": "integer" - }, - "num_slides": { - "format": "int32", - "type": "integer" - }, - "pathology_report_uuid": { - "type": "string" - }, - "preservation_method": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataRangesItem": { - "properties": { - "avg_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "batch_number": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "batch_number_gte": { - "format": "int32", - "type": "integer" - }, - "batch_number_lte": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_collection": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_collection_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_collection_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_sample_procurement_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement_lte": { - "format": "int32", - "type": "integer" - }, - "max_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "num_portions": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "num_portions_gte": { - "format": "int32", - "type": "integer" - }, - "num_portions_lte": { - "format": "int32", - "type": "integer" - }, - "num_slides": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "num_slides_gte": { - "format": "int32", - "type": "integer" - }, - "num_slides_lte": { - "format": "int32", - "type": "integer" - }, - "pathology_report_uuid": { - "items": { - "type": "string" - }, - "type": "array" - }, - "preservation_method": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesClinicalMetadataItem": { - "properties": { - "age_at_diagnosis": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years": { - "format": "int32", - "type": "integer" - }, - "anatomic_neoplasm_subdivision": { - "type": "string" - }, - "batch_number": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "type": "string" - }, - "bmi": { - "format": "double", - "type": "number" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "clinical_M": { - "type": "string" - }, - "clinical_N": { - "type": "string" - }, - "clinical_T": { - "type": "string" - }, - "clinical_stage": { - "type": "string" - }, - "colorectal_cancer": { - "type": "string" - }, - "country": { - "type": "string" - }, - "days_to_birth": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "type": "string" - }, - "gender": { - "type": "string" - }, - "gleason_score_combined": { - "format": "int32", - "type": "integer" - }, - "h_pylori_infection": { - "type": "string" - }, - "height": { - "format": "int32", - "type": "integer" - }, - "histological_type": { - "type": "string" - }, - "history_of_colon_polyps": { - "type": "string" - }, - "history_of_neoadjuvant_treatment": { - "type": "string" - }, - "hpv_calls": { - "type": "string" - }, - "hpv_status": { - "type": "string" - }, - "icd_10": { - "type": "string" - }, - "icd_o_3_histology": { - "type": "string" - }, - "icd_o_3_site": { - "type": "string" - }, - "lymphatic_invasion": { - "type": "string" - }, - "lymphnodes_examined": { - "type": "string" - }, - "lymphovascular_invasion_present": { - "type": "string" - }, - "menopause_status": { - "type": "string" - }, - "mononucleotide_and_dinucleotide_marker_panel_analysis_status": { - "type": "string" - }, - "neoplasm_histologic_grade": { - "type": "string" - }, - "new_tumor_event_after_initial_treatment": { - "type": "string" - }, - "number_of_lymphnodes_examined": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked": { - "format": "int32", - "type": "integer" - }, - "other_dx": { - "type": "string" - }, - "other_malignancy_anatomic_site": { - "type": "string" - }, - "other_malignancy_histological_type": { - "type": "string" - }, - "other_malignancy_type": { - "type": "string" - }, - "pathologic_M": { - "type": "string" - }, - "pathologic_N": { - "type": "string" - }, - "pathologic_T": { - "type": "string" - }, - "pathologic_stage": { - "type": "string" - }, - "person_neoplasm_cancer_status": { - "type": "string" - }, - "pregnancies": { - "type": "string" - }, - "primary_neoplasm_melanoma_dx": { - "type": "string" - }, - "primary_therapy_outcome_success": { - "type": "string" - }, - "psa_value": { - "format": "double", - "type": "number" - }, - "race": { - "type": "string" - }, - "residual_tumor": { - "type": "string" - }, - "stopped_smoking_year": { - "format": "int32", - "type": "integer" - }, - "summary_file_count": { - "format": "int32", - "type": "integer" - }, - "tobacco_smoking_history": { - "type": "string" - }, - "tss_code": { - "type": "string" - }, - "tumor_tissue_site": { - "type": "string" - }, - "tumor_type": { - "type": "string" - }, - "venous_invasion": { - "type": "string" - }, - "vital_status": { - "type": "string" - }, - "weight": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesClinicalMetadataRangesItem": { - "properties": { - "age_at_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_at_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "age_at_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_began_smoking_in_years_gte": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years_lte": { - "format": "int32", - "type": "integer" - }, - "anatomic_neoplasm_subdivision": { - "items": { - "type": "string" - }, - "type": "array" - }, - "batch_number": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "batch_number_gte": { - "format": "int32", - "type": "integer" - }, - "batch_number_lte": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "items": { - "type": "string" - }, - "type": "array" - }, - "bmi": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "bmi_gte": { - "format": "double", - "type": "number" - }, - "bmi_lte": { - "format": "double", - "type": "number" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_M": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_N": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_T": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_stage": { - "items": { - "type": "string" - }, - "type": "array" - }, - "colorectal_cancer": { - "items": { - "type": "string" - }, - "type": "array" - }, - "country": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_birth": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_birth_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_birth_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_death_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_death_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_initial_pathologic_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_followup_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_known_alive_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_submitted_specimen_dx_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx_lte": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gender": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gleason_score_combined": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "gleason_score_combined_gte": { - "format": "int32", - "type": "integer" - }, - "gleason_score_combined_lte": { - "format": "int32", - "type": "integer" - }, - "h_pylori_infection": { - "items": { - "type": "string" - }, - "type": "array" - }, - "height": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "height_gte": { - "format": "int32", - "type": "integer" - }, - "height_lte": { - "format": "int32", - "type": "integer" - }, - "histological_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "history_of_colon_polyps": { - "items": { - "type": "string" - }, - "type": "array" - }, - "history_of_neoadjuvant_treatment": { - "items": { - "type": "string" - }, - "type": "array" - }, - "hpv_calls": { - "items": { - "type": "string" - }, - "type": "array" - }, - "hpv_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_10": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_o_3_histology": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_o_3_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphatic_invasion": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphnodes_examined": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphovascular_invasion_present": { - "items": { - "type": "string" - }, - "type": "array" - }, - "menopause_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "mononucleotide_and_dinucleotide_marker_panel_analysis_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "neoplasm_histologic_grade": { - "items": { - "type": "string" - }, - "type": "array" - }, - "new_tumor_event_after_initial_treatment": { - "items": { - "type": "string" - }, - "type": "array" - }, - "number_of_lymphnodes_examined": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_of_lymphnodes_examined_gte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_examined_lte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_of_lymphnodes_positive_by_he_gte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he_lte": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_pack_years_smoked_gte": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked_lte": { - "format": "int32", - "type": "integer" - }, - "other_dx": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_anatomic_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_histological_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_M": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_N": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_T": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_stage": { - "items": { - "type": "string" - }, - "type": "array" - }, - "person_neoplasm_cancer_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pregnancies": { - "items": { - "type": "string" - }, - "type": "array" - }, - "primary_neoplasm_melanoma_dx": { - "items": { - "type": "string" - }, - "type": "array" - }, - "primary_therapy_outcome_success": { - "items": { - "type": "string" - }, - "type": "array" - }, - "psa_value": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "psa_value_gte": { - "format": "double", - "type": "number" - }, - "psa_value_lte": { - "format": "double", - "type": "number" - }, - "race": { - "items": { - "type": "string" - }, - "type": "array" - }, - "residual_tumor": { - "items": { - "type": "string" - }, - "type": "array" - }, - "stopped_smoking_year": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "stopped_smoking_year_gte": { - "format": "int32", - "type": "integer" - }, - "stopped_smoking_year_lte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "summary_file_count_gte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count_lte": { - "format": "int32", - "type": "integer" - }, - "tobacco_smoking_history": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tss_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_tissue_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "venous_invasion": { - "items": { - "type": "string" - }, - "type": "array" - }, - "vital_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "weight": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "weight_gte": { - "format": "int32", - "type": "integer" - }, - "weight_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_tobacco_smoking_onset_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset_lte": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesCommonMetadataItem": { - "properties": { - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesCommonMetadataRangesItem": { - "properties": { - "disease_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "endpoint_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "program_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "project_short_name": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "archive_file_name": { - "type": "string" - }, - "archive_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_submitter_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "archive_file_name": { - "type": "string" - }, - "archive_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_submitter_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesMetadataItem": { - "properties": { - "Biospecimen": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataItem" - }, - "Clinical": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesClinicalMetadataItem" - }, - "Common": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesCommonMetadataItem" - }, - "Data_HG19": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataItem" - }, - "Data_HG38": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesMetadataRangesItem": { - "properties": { - "Biospecimen": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataRangesItem" - }, - "Clinical": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesClinicalMetadataRangesItem" - }, - "Common": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesCommonMetadataRangesItem" - }, - "Data_HG19": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataRangesItem" - }, - "Data_HG38": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataRangesItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAPatientsGetCaseDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_data": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesMetadataItem" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGASamplesGetSampleDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "biospecimen_data": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesMetadataItem" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "data_details": { - "items": { - "$ref": "#/definitions/Api3SamplesGetHelperDataDetails" - }, - "type": "array" - }, - "data_details_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3SamplesGetHelperDataDetails": { - "properties": { - "access": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_gdc_id": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_name_key": { - "type": "string" - }, - "file_size": { - "format": "int64", - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3UsersGetCommonUserGetAPIReturnJSON": { - "properties": { - "dbGaP_allowed": { - "type": "boolean" - }, - "dbGaP_authorized": { - "type": "boolean" - }, - "message": { - "type": "string" - } - }, - "type": "object" - } - }, - "host": "api-dot-isb-cgc.appspot.com", - "info": { - "description": "Get information about cohorts, cases, and samples for CCLE. Create cohorts.", - "title": "isb_cgc_ccle_api", - "version": "v3" - }, - "paths": { - "/isb_cgc_ccle_api/v3/ccle/cases/{case_barcode}": { - "get": { - "operationId": "CCLECasesGetAPI_get", - "parameters": [ - { - "in": "path", - "name": "case_barcode", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiCCLEPatientsGetCaseDetails" - } - } - } - } - }, - "/isb_cgc_ccle_api/v3/ccle/cohorts/create": { - "post": { - "operationId": "CCLECohortsCreateAPI_create", - "parameters": [ - { - "in": "body", - "name": "body", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiCCLEMessageClassesMetadataRangesItem" - } - }, - { - "in": "query", - "name": "name", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3CohortCreatePreviewHelperCreatedCohort" - } - } - } - } - }, - "/isb_cgc_ccle_api/v3/ccle/samples/{sample_barcode}": { - "get": { - "operationId": "CCLESamplesGetAPI_get", - "parameters": [ - { - "in": "path", - "name": "sample_barcode", - "required": true, - "type": "string" - }, - { - "in": "query", - "name": "data_type", - "type": "string" - }, - { - "in": "query", - "name": "data_category", - "type": "string" - }, - { - "in": "query", - "name": "experimental_strategy", - "type": "string" - }, - { - "in": "query", - "name": "data_format", - "type": "string" - }, - { - "in": "query", - "name": "platform", - "type": "string" - }, - { - "in": "query", - "name": "endpoint_type", - "type": "string" - }, - { - "in": "query", - "name": "analysis_workflow_type", - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiCCLESamplesGetSampleDetails" - } - } - } - } - }, - "/isb_cgc_ccle_api/v3/ccle/samples/{sample_barcode}/cloud_storage_file_paths": { - "get": { - "operationId": "CCLESamplesCloudStorageFilePathsAPI_cloudStorageFilePaths", - "parameters": [ - { - "in": "path", - "name": "sample_barcode", - "required": true, - "type": "string" - }, - { - "in": "query", - "name": "data_type", - "type": "string" - }, - { - "in": "query", - "name": "data_category", - "type": "string" - }, - { - "in": "query", - "name": "experimental_strategy", - "type": "string" - }, - { - "in": "query", - "name": "data_format", - "type": "string" - }, - { - "in": "query", - "name": "platform", - "type": "string" - }, - { - "in": "query", - "name": "genomic_build", - "type": "string" - }, - { - "in": "query", - "name": "analysis_workflow_type", - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3CloudstoragefilepathsHelperGCSFilePathList" - } - } - } - } - }, - "/isb_cgc_ccle_api/v3/tcga/cohorts/preview": { - "post": { - "operationId": "CCLECohortsPreviewAPI_preview", - "parameters": [ - { - "in": "body", - "name": "body", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiCCLEMessageClassesMetadataRangesItem" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3CohortCreatePreviewHelperCohortCasesSamplesList" - } - } - } - } - } - }, - "produces": [ - "application/json" - ], - "schemes": [ - "https" - ], - "securityDefinitions": { - "google_id_token": { - "authorizationUrl": "", - "flow": "implicit", - "type": "oauth2", - "x-google-issuer": "https://accounts.google.com", - "x-google-jwks_uri": "https://www.googleapis.com/oauth2/v3/certs" - } - }, - "swagger": "2.0" -} \ No newline at end of file diff --git a/isb_cgc_ccle_apiv3_openapiv3.json b/isb_cgc_ccle_apiv3_openapiv3.json deleted file mode 100644 index 429cc535..00000000 --- a/isb_cgc_ccle_apiv3_openapiv3.json +++ /dev/null @@ -1,4140 +0,0 @@ -{ - "openapi": "3.0.0", - "servers": [ - { - "url": "https://api-dot-isb-cgc.appspot.com/_ah/api" - } - ], - "info": { - "description": "Get information about cases and samples for CCLE; preview and create cohorts containing CCLE cases and samples.", - "title": "ISB-CGC API: CCLE", - "version": "v3" - }, - "paths": { - "/isb_cgc_ccle_api/v3/ccle/cases/{case_barcode}": { - "get": { - "operationId": "CCLECasesGetAPI_get", - "parameters": [ - { - "in": "path", - "name": "case_barcode", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiCCLEPatientsGetCaseDetails" - } - } - } - } - } - } - }, - "/isb_cgc_ccle_api/v3/ccle/cohorts/create": { - "post": { - "operationId": "CCLECohortsCreateAPI_create", - "parameters": [ - { - "in": "query", - "name": "name", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3CohortCreatePreviewHelperCreatedCohort" - } - } - } - } - }, - "requestBody": { - "$ref": "#/components/requestBodies/Api3IsbCgcApiCCLEMessageClassesMetadataRangesItem" - } - } - }, - "/isb_cgc_ccle_api/v3/ccle/samples/{sample_barcode}": { - "get": { - "operationId": "CCLESamplesGetAPI_get", - "parameters": [ - { - "in": "path", - "name": "sample_barcode", - "required": true, - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_type", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_category", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "experimental_strategy", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_format", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "platform", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "endpoint_type", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "analysis_workflow_type", - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiCCLESamplesGetSampleDetails" - } - } - } - } - } - } - }, - "/isb_cgc_ccle_api/v3/ccle/samples/{sample_barcode}/cloud_storage_file_paths": { - "get": { - "operationId": "CCLESamplesCloudStorageFilePathsAPI_cloudStorageFilePaths", - "parameters": [ - { - "in": "path", - "name": "sample_barcode", - "required": true, - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_type", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_category", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "experimental_strategy", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_format", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "platform", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "genomic_build", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "analysis_workflow_type", - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3CloudstoragefilepathsHelperGCSFilePathList" - } - } - } - } - } - } - }, - "/isb_cgc_ccle_api/v3/tcga/cohorts/preview": { - "post": { - "operationId": "CCLECohortsPreviewAPI_preview", - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3CohortCreatePreviewHelperCohortCasesSamplesList" - } - } - } - } - }, - "requestBody": { - "$ref": "#/components/requestBodies/Api3IsbCgcApiCCLEMessageClassesMetadataRangesItem" - } - } - } - }, - "components": { - "schemas": { - "Api3CloudstoragefilepathsHelperGCSFilePathList": { - "properties": { - "cloud_storage_file_paths": { - "items": { - "type": "string" - }, - "type": "array" - }, - "count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperCohortCasesSamplesList": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "cases": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperCreatedCohort": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "filters": { - "items": { - "$ref": "#/components/schemas/Api3CohortCreatePreviewHelperFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperFilterDetails": { - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, - "Api3CohortEndpointHelpersFilterDetails": { - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesBiospecimenMetadataItem": { - "properties": { - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesBiospecimenMetadataRangesItem": { - "properties": { - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesClinicalMetadataItem": { - "properties": { - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "gender": { - "type": "string" - }, - "hist_subtype": { - "type": "string" - }, - "histology": { - "type": "string" - }, - "site_primary": { - "type": "string" - }, - "source": { - "type": "string" - }, - "summary_file_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesClinicalMetadataRangesItem": { - "properties": { - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gender": { - "items": { - "type": "string" - }, - "type": "array" - }, - "hist_subtype": { - "items": { - "type": "string" - }, - "type": "array" - }, - "histology": { - "items": { - "type": "string" - }, - "type": "array" - }, - "site_primary": { - "items": { - "type": "string" - }, - "type": "array" - }, - "source": { - "items": { - "type": "string" - }, - "type": "array" - }, - "summary_file_count": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "summary_file_count_gte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count_lte": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesCommonMetadataItem": { - "properties": { - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesCommonMetadataRangesItem": { - "properties": { - "disease_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "endpoint_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "program_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "project_short_name": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesDataHG19MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesDataHG19MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesMetadataItem": { - "properties": { - "Biospecimen": { - "$ref": "#/components/schemas/Api3IsbCgcApiCCLEMessageClassesBiospecimenMetadataItem" - }, - "Clinical": { - "$ref": "#/components/schemas/Api3IsbCgcApiCCLEMessageClassesClinicalMetadataItem" - }, - "Common": { - "$ref": "#/components/schemas/Api3IsbCgcApiCCLEMessageClassesCommonMetadataItem" - }, - "Data_HG19": { - "$ref": "#/components/schemas/Api3IsbCgcApiCCLEMessageClassesDataHG19MetadataItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEMessageClassesMetadataRangesItem": { - "properties": { - "Biospecimen": { - "$ref": "#/components/schemas/Api3IsbCgcApiCCLEMessageClassesBiospecimenMetadataRangesItem" - }, - "Clinical": { - "$ref": "#/components/schemas/Api3IsbCgcApiCCLEMessageClassesClinicalMetadataRangesItem" - }, - "Common": { - "$ref": "#/components/schemas/Api3IsbCgcApiCCLEMessageClassesCommonMetadataRangesItem" - }, - "Data_HG19": { - "$ref": "#/components/schemas/Api3IsbCgcApiCCLEMessageClassesDataHG19MetadataRangesItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLEPatientsGetCaseDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_data": { - "$ref": "#/components/schemas/Api3IsbCgcApiCCLEMessageClassesMetadataItem" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCCLESamplesGetSampleDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "biospecimen_data": { - "$ref": "#/components/schemas/Api3IsbCgcApiCCLEMessageClassesMetadataItem" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "data_details": { - "items": { - "$ref": "#/components/schemas/Api3SamplesGetHelperDataDetails" - }, - "type": "array" - }, - "data_details_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileDetail": { - "properties": { - "access": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_uuid": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "disease_code": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_gdc_uuid": { - "type": "string" - }, - "file_path": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "program": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileManifest": { - "properties": { - "files": { - "items": { - "$ref": "#/components/schemas/Api3IsbCgcApiCohortFileManifestFileDetail" - }, - "type": "array" - }, - "files_retrieved": { - "format": "int32", - "type": "integer" - }, - "total_file_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "cases": { - "items": { - "type": "string" - }, - "type": "array" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/components/schemas/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetailsList": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "items": { - "items": { - "$ref": "#/components/schemas/Api3IsbCgcApiCohortGetListHelperCohortListDetails" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortListDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/components/schemas/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortsDeleteReturnJSON": { - "properties": { - "message": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiFilesGetFilePathsFilePaths": { - "properties": { - "paths": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataItem": { - "properties": { - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "tumor_code": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataRangesItem": { - "properties": { - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_code": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesClinicalMetadataItem": { - "properties": { - "age_at_diagnosis": { - "format": "int32", - "type": "integer" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "days_to_birth": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "type": "string" - }, - "event_free_survival": { - "format": "int32", - "type": "integer" - }, - "first_event": { - "type": "string" - }, - "gender": { - "type": "string" - }, - "protocol": { - "type": "string" - }, - "race": { - "type": "string" - }, - "summary_file_count": { - "format": "int32", - "type": "integer" - }, - "vital_status": { - "type": "string" - }, - "wbc_at_diagnosis": { - "format": "double", - "type": "number" - }, - "year_of_diagnosis": { - "format": "int32", - "type": "integer" - }, - "year_of_last_follow_up": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesClinicalMetadataRangesItem": { - "properties": { - "age_at_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_at_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "age_at_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_birth": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_birth_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_birth_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_death_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_death_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_followup_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_known_alive_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive_lte": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "items": { - "type": "string" - }, - "type": "array" - }, - "event_free_survival": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "event_free_survival_gte": { - "format": "int32", - "type": "integer" - }, - "event_free_survival_lte": { - "format": "int32", - "type": "integer" - }, - "first_event": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gender": { - "items": { - "type": "string" - }, - "type": "array" - }, - "protocol": { - "items": { - "type": "string" - }, - "type": "array" - }, - "race": { - "items": { - "type": "string" - }, - "type": "array" - }, - "summary_file_count": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "summary_file_count_gte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count_lte": { - "format": "int32", - "type": "integer" - }, - "vital_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "wbc_at_diagnosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "wbc_at_diagnosis_gte": { - "format": "double", - "type": "number" - }, - "wbc_at_diagnosis_lte": { - "format": "double", - "type": "number" - }, - "year_of_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_last_follow_up": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_last_follow_up_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_last_follow_up_lte": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesCommonMetadataItem": { - "properties": { - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesCommonMetadataRangesItem": { - "properties": { - "disease_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "endpoint_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "program_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "project_short_name": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesMetadataItem": { - "properties": { - "Biospecimen": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataItem" - }, - "Clinical": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesClinicalMetadataItem" - }, - "Common": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesCommonMetadataItem" - }, - "Data_HG19": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataItem" - }, - "Data_HG38": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesMetadataRangesItem": { - "properties": { - "Biospecimen": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataRangesItem" - }, - "Clinical": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesClinicalMetadataRangesItem" - }, - "Common": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesCommonMetadataRangesItem" - }, - "Data_HG19": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataRangesItem" - }, - "Data_HG38": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataRangesItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETPatientsGetCaseDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_data": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesMetadataItem" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETSamplesGetSampleDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "biospecimen_data": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesMetadataItem" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "data_details": { - "items": { - "$ref": "#/components/schemas/Api3SamplesGetHelperDataDetails" - }, - "type": "array" - }, - "data_details_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAAnnotationsApiMetadataAnnotationList": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "items": { - "items": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesAnnotationMetadataItem" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesAnnotationMetadataItem": { - "properties": { - "aliquot_barcode": { - "type": "string" - }, - "annotation_gdc_id": { - "type": "string" - }, - "annotation_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "category": { - "type": "string" - }, - "classification": { - "type": "string" - }, - "entity_barcode": { - "type": "string" - }, - "entity_gdc_id": { - "type": "string" - }, - "entity_type": { - "type": "string" - }, - "notes": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "status": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataItem": { - "properties": { - "avg_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "batch_number": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "days_to_collection": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement": { - "format": "int32", - "type": "integer" - }, - "max_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "num_portions": { - "format": "int32", - "type": "integer" - }, - "num_slides": { - "format": "int32", - "type": "integer" - }, - "pathology_report_uuid": { - "type": "string" - }, - "preservation_method": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataRangesItem": { - "properties": { - "avg_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "batch_number": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "batch_number_gte": { - "format": "int32", - "type": "integer" - }, - "batch_number_lte": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_collection": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_collection_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_collection_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_sample_procurement_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement_lte": { - "format": "int32", - "type": "integer" - }, - "max_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "num_portions": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "num_portions_gte": { - "format": "int32", - "type": "integer" - }, - "num_portions_lte": { - "format": "int32", - "type": "integer" - }, - "num_slides": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "num_slides_gte": { - "format": "int32", - "type": "integer" - }, - "num_slides_lte": { - "format": "int32", - "type": "integer" - }, - "pathology_report_uuid": { - "items": { - "type": "string" - }, - "type": "array" - }, - "preservation_method": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesClinicalMetadataItem": { - "properties": { - "age_at_diagnosis": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years": { - "format": "int32", - "type": "integer" - }, - "anatomic_neoplasm_subdivision": { - "type": "string" - }, - "batch_number": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "type": "string" - }, - "bmi": { - "format": "double", - "type": "number" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "clinical_M": { - "type": "string" - }, - "clinical_N": { - "type": "string" - }, - "clinical_T": { - "type": "string" - }, - "clinical_stage": { - "type": "string" - }, - "colorectal_cancer": { - "type": "string" - }, - "country": { - "type": "string" - }, - "days_to_birth": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "type": "string" - }, - "gender": { - "type": "string" - }, - "gleason_score_combined": { - "format": "int32", - "type": "integer" - }, - "h_pylori_infection": { - "type": "string" - }, - "height": { - "format": "int32", - "type": "integer" - }, - "histological_type": { - "type": "string" - }, - "history_of_colon_polyps": { - "type": "string" - }, - "history_of_neoadjuvant_treatment": { - "type": "string" - }, - "hpv_calls": { - "type": "string" - }, - "hpv_status": { - "type": "string" - }, - "icd_10": { - "type": "string" - }, - "icd_o_3_histology": { - "type": "string" - }, - "icd_o_3_site": { - "type": "string" - }, - "lymphatic_invasion": { - "type": "string" - }, - "lymphnodes_examined": { - "type": "string" - }, - "lymphovascular_invasion_present": { - "type": "string" - }, - "menopause_status": { - "type": "string" - }, - "mononucleotide_and_dinucleotide_marker_panel_analysis_status": { - "type": "string" - }, - "neoplasm_histologic_grade": { - "type": "string" - }, - "new_tumor_event_after_initial_treatment": { - "type": "string" - }, - "number_of_lymphnodes_examined": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked": { - "format": "int32", - "type": "integer" - }, - "other_dx": { - "type": "string" - }, - "other_malignancy_anatomic_site": { - "type": "string" - }, - "other_malignancy_histological_type": { - "type": "string" - }, - "other_malignancy_type": { - "type": "string" - }, - "pathologic_M": { - "type": "string" - }, - "pathologic_N": { - "type": "string" - }, - "pathologic_T": { - "type": "string" - }, - "pathologic_stage": { - "type": "string" - }, - "person_neoplasm_cancer_status": { - "type": "string" - }, - "pregnancies": { - "type": "string" - }, - "primary_neoplasm_melanoma_dx": { - "type": "string" - }, - "primary_therapy_outcome_success": { - "type": "string" - }, - "psa_value": { - "format": "double", - "type": "number" - }, - "race": { - "type": "string" - }, - "residual_tumor": { - "type": "string" - }, - "stopped_smoking_year": { - "format": "int32", - "type": "integer" - }, - "summary_file_count": { - "format": "int32", - "type": "integer" - }, - "tobacco_smoking_history": { - "type": "string" - }, - "tss_code": { - "type": "string" - }, - "tumor_tissue_site": { - "type": "string" - }, - "tumor_type": { - "type": "string" - }, - "venous_invasion": { - "type": "string" - }, - "vital_status": { - "type": "string" - }, - "weight": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesClinicalMetadataRangesItem": { - "properties": { - "age_at_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_at_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "age_at_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_began_smoking_in_years_gte": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years_lte": { - "format": "int32", - "type": "integer" - }, - "anatomic_neoplasm_subdivision": { - "items": { - "type": "string" - }, - "type": "array" - }, - "batch_number": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "batch_number_gte": { - "format": "int32", - "type": "integer" - }, - "batch_number_lte": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "items": { - "type": "string" - }, - "type": "array" - }, - "bmi": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "bmi_gte": { - "format": "double", - "type": "number" - }, - "bmi_lte": { - "format": "double", - "type": "number" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_M": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_N": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_T": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_stage": { - "items": { - "type": "string" - }, - "type": "array" - }, - "colorectal_cancer": { - "items": { - "type": "string" - }, - "type": "array" - }, - "country": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_birth": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_birth_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_birth_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_death_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_death_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_initial_pathologic_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_followup_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_known_alive_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_submitted_specimen_dx_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx_lte": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gender": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gleason_score_combined": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "gleason_score_combined_gte": { - "format": "int32", - "type": "integer" - }, - "gleason_score_combined_lte": { - "format": "int32", - "type": "integer" - }, - "h_pylori_infection": { - "items": { - "type": "string" - }, - "type": "array" - }, - "height": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "height_gte": { - "format": "int32", - "type": "integer" - }, - "height_lte": { - "format": "int32", - "type": "integer" - }, - "histological_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "history_of_colon_polyps": { - "items": { - "type": "string" - }, - "type": "array" - }, - "history_of_neoadjuvant_treatment": { - "items": { - "type": "string" - }, - "type": "array" - }, - "hpv_calls": { - "items": { - "type": "string" - }, - "type": "array" - }, - "hpv_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_10": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_o_3_histology": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_o_3_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphatic_invasion": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphnodes_examined": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphovascular_invasion_present": { - "items": { - "type": "string" - }, - "type": "array" - }, - "menopause_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "mononucleotide_and_dinucleotide_marker_panel_analysis_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "neoplasm_histologic_grade": { - "items": { - "type": "string" - }, - "type": "array" - }, - "new_tumor_event_after_initial_treatment": { - "items": { - "type": "string" - }, - "type": "array" - }, - "number_of_lymphnodes_examined": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_of_lymphnodes_examined_gte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_examined_lte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_of_lymphnodes_positive_by_he_gte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he_lte": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_pack_years_smoked_gte": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked_lte": { - "format": "int32", - "type": "integer" - }, - "other_dx": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_anatomic_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_histological_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_M": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_N": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_T": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_stage": { - "items": { - "type": "string" - }, - "type": "array" - }, - "person_neoplasm_cancer_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pregnancies": { - "items": { - "type": "string" - }, - "type": "array" - }, - "primary_neoplasm_melanoma_dx": { - "items": { - "type": "string" - }, - "type": "array" - }, - "primary_therapy_outcome_success": { - "items": { - "type": "string" - }, - "type": "array" - }, - "psa_value": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "psa_value_gte": { - "format": "double", - "type": "number" - }, - "psa_value_lte": { - "format": "double", - "type": "number" - }, - "race": { - "items": { - "type": "string" - }, - "type": "array" - }, - "residual_tumor": { - "items": { - "type": "string" - }, - "type": "array" - }, - "stopped_smoking_year": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "stopped_smoking_year_gte": { - "format": "int32", - "type": "integer" - }, - "stopped_smoking_year_lte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "summary_file_count_gte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count_lte": { - "format": "int32", - "type": "integer" - }, - "tobacco_smoking_history": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tss_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_tissue_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "venous_invasion": { - "items": { - "type": "string" - }, - "type": "array" - }, - "vital_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "weight": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "weight_gte": { - "format": "int32", - "type": "integer" - }, - "weight_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_tobacco_smoking_onset_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset_lte": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesCommonMetadataItem": { - "properties": { - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesCommonMetadataRangesItem": { - "properties": { - "disease_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "endpoint_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "program_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "project_short_name": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "archive_file_name": { - "type": "string" - }, - "archive_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_submitter_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "archive_file_name": { - "type": "string" - }, - "archive_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_submitter_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesMetadataItem": { - "properties": { - "Biospecimen": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataItem" - }, - "Clinical": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesClinicalMetadataItem" - }, - "Common": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesCommonMetadataItem" - }, - "Data_HG19": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataItem" - }, - "Data_HG38": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesMetadataRangesItem": { - "properties": { - "Biospecimen": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataRangesItem" - }, - "Clinical": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesClinicalMetadataRangesItem" - }, - "Common": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesCommonMetadataRangesItem" - }, - "Data_HG19": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataRangesItem" - }, - "Data_HG38": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataRangesItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAPatientsGetCaseDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_data": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesMetadataItem" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGASamplesGetSampleDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "biospecimen_data": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesMetadataItem" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "data_details": { - "items": { - "$ref": "#/components/schemas/Api3SamplesGetHelperDataDetails" - }, - "type": "array" - }, - "data_details_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3SamplesGetHelperDataDetails": { - "properties": { - "access": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_gdc_id": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_name_key": { - "type": "string" - }, - "file_size": { - "format": "int64", - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3UsersGetCommonUserGetAPIReturnJSON": { - "properties": { - "dbGaP_allowed": { - "type": "boolean" - }, - "dbGaP_authorized": { - "type": "boolean" - }, - "message": { - "type": "string" - } - }, - "type": "object" - } - }, - "requestBodies": { - "Api3IsbCgcApiCCLEMessageClassesMetadataRangesItem": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiCCLEMessageClassesMetadataRangesItem" - } - } - } - } - }, - "securitySchemes": { - "google_id_token": { - "type": "oauth2", - "x-google-issuer": "https://accounts.google.com", - "x-google-jwks_uri": "https://www.googleapis.com/oauth2/v3/certs", - "flows": { - "implicit": { - "authorizationUrl": "/", - "scopes": {} - } - } - } - } - } -} \ No newline at end of file diff --git a/isb_cgc_target_apiv3_openapiv2.json b/isb_cgc_target_apiv3_openapiv2.json deleted file mode 100644 index 76779529..00000000 --- a/isb_cgc_target_apiv3_openapiv2.json +++ /dev/null @@ -1,3612 +0,0 @@ -{ - "basePath": "/_ah/api", - "consumes": [ - "application/json" - ], - "definitions": { - "Api3CloudstoragefilepathsHelperGCSFilePathList": { - "properties": { - "cloud_storage_file_paths": { - "items": { - "type": "string" - }, - "type": "array" - }, - "count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperCohortCasesSamplesList": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "cases": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperCreatedCohort": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "filters": { - "items": { - "$ref": "#/definitions/Api3CohortCreatePreviewHelperFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperFilterDetails": { - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, - "Api3CohortEndpointHelpersFilterDetails": { - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileDetail": { - "properties": { - "access": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_uuid": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "disease_code": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_gdc_uuid": { - "type": "string" - }, - "file_path": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "program": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileManifest": { - "properties": { - "files": { - "items": { - "$ref": "#/definitions/Api3IsbCgcApiCohortFileManifestFileDetail" - }, - "type": "array" - }, - "files_retrieved": { - "format": "int32", - "type": "integer" - }, - "total_file_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "cases": { - "items": { - "type": "string" - }, - "type": "array" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/definitions/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetailsList": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "items": { - "items": { - "$ref": "#/definitions/Api3IsbCgcApiCohortGetListHelperCohortListDetails" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortListDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/definitions/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortsDeleteReturnJSON": { - "properties": { - "message": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiFilesGetFilePathsFilePaths": { - "properties": { - "paths": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataItem": { - "properties": { - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "tumor_code": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataRangesItem": { - "properties": { - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_code": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesClinicalMetadataItem": { - "properties": { - "age_at_diagnosis": { - "format": "int32", - "type": "integer" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "days_to_birth": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "type": "string" - }, - "event_free_survival": { - "format": "int32", - "type": "integer" - }, - "first_event": { - "type": "string" - }, - "gender": { - "type": "string" - }, - "protocol": { - "type": "string" - }, - "race": { - "type": "string" - }, - "summary_file_count": { - "format": "int32", - "type": "integer" - }, - "vital_status": { - "type": "string" - }, - "wbc_at_diagnosis": { - "format": "double", - "type": "number" - }, - "year_of_diagnosis": { - "format": "int32", - "type": "integer" - }, - "year_of_last_follow_up": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesClinicalMetadataRangesItem": { - "properties": { - "age_at_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_at_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "age_at_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_birth": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_birth_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_birth_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_death_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_death_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_followup_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_known_alive_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive_lte": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "items": { - "type": "string" - }, - "type": "array" - }, - "event_free_survival": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "event_free_survival_gte": { - "format": "int32", - "type": "integer" - }, - "event_free_survival_lte": { - "format": "int32", - "type": "integer" - }, - "first_event": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gender": { - "items": { - "type": "string" - }, - "type": "array" - }, - "protocol": { - "items": { - "type": "string" - }, - "type": "array" - }, - "race": { - "items": { - "type": "string" - }, - "type": "array" - }, - "summary_file_count": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "summary_file_count_gte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count_lte": { - "format": "int32", - "type": "integer" - }, - "vital_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "wbc_at_diagnosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "wbc_at_diagnosis_gte": { - "format": "double", - "type": "number" - }, - "wbc_at_diagnosis_lte": { - "format": "double", - "type": "number" - }, - "year_of_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_last_follow_up": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_last_follow_up_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_last_follow_up_lte": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesCommonMetadataItem": { - "properties": { - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesCommonMetadataRangesItem": { - "properties": { - "disease_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "endpoint_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "program_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "project_short_name": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesMetadataItem": { - "properties": { - "Biospecimen": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataItem" - }, - "Clinical": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesClinicalMetadataItem" - }, - "Common": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesCommonMetadataItem" - }, - "Data_HG19": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataItem" - }, - "Data_HG38": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesMetadataRangesItem": { - "properties": { - "Biospecimen": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataRangesItem" - }, - "Clinical": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesClinicalMetadataRangesItem" - }, - "Common": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesCommonMetadataRangesItem" - }, - "Data_HG19": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataRangesItem" - }, - "Data_HG38": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataRangesItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETPatientsGetCaseDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_data": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesMetadataItem" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETSamplesGetSampleDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "biospecimen_data": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesMetadataItem" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "data_details": { - "items": { - "$ref": "#/definitions/Api3SamplesGetHelperDataDetails" - }, - "type": "array" - }, - "data_details_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAAnnotationsApiMetadataAnnotationList": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "items": { - "items": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesAnnotationMetadataItem" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesAnnotationMetadataItem": { - "properties": { - "aliquot_barcode": { - "type": "string" - }, - "annotation_gdc_id": { - "type": "string" - }, - "annotation_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "category": { - "type": "string" - }, - "classification": { - "type": "string" - }, - "entity_barcode": { - "type": "string" - }, - "entity_gdc_id": { - "type": "string" - }, - "entity_type": { - "type": "string" - }, - "notes": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "status": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataItem": { - "properties": { - "avg_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "batch_number": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "days_to_collection": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement": { - "format": "int32", - "type": "integer" - }, - "max_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "num_portions": { - "format": "int32", - "type": "integer" - }, - "num_slides": { - "format": "int32", - "type": "integer" - }, - "pathology_report_uuid": { - "type": "string" - }, - "preservation_method": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataRangesItem": { - "properties": { - "avg_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "batch_number": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "batch_number_gte": { - "format": "int32", - "type": "integer" - }, - "batch_number_lte": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_collection": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_collection_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_collection_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_sample_procurement_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement_lte": { - "format": "int32", - "type": "integer" - }, - "max_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "num_portions": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "num_portions_gte": { - "format": "int32", - "type": "integer" - }, - "num_portions_lte": { - "format": "int32", - "type": "integer" - }, - "num_slides": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "num_slides_gte": { - "format": "int32", - "type": "integer" - }, - "num_slides_lte": { - "format": "int32", - "type": "integer" - }, - "pathology_report_uuid": { - "items": { - "type": "string" - }, - "type": "array" - }, - "preservation_method": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesClinicalMetadataItem": { - "properties": { - "age_at_diagnosis": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years": { - "format": "int32", - "type": "integer" - }, - "anatomic_neoplasm_subdivision": { - "type": "string" - }, - "batch_number": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "type": "string" - }, - "bmi": { - "format": "double", - "type": "number" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "clinical_M": { - "type": "string" - }, - "clinical_N": { - "type": "string" - }, - "clinical_T": { - "type": "string" - }, - "clinical_stage": { - "type": "string" - }, - "colorectal_cancer": { - "type": "string" - }, - "country": { - "type": "string" - }, - "days_to_birth": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "type": "string" - }, - "gender": { - "type": "string" - }, - "gleason_score_combined": { - "format": "int32", - "type": "integer" - }, - "h_pylori_infection": { - "type": "string" - }, - "height": { - "format": "int32", - "type": "integer" - }, - "histological_type": { - "type": "string" - }, - "history_of_colon_polyps": { - "type": "string" - }, - "history_of_neoadjuvant_treatment": { - "type": "string" - }, - "hpv_calls": { - "type": "string" - }, - "hpv_status": { - "type": "string" - }, - "icd_10": { - "type": "string" - }, - "icd_o_3_histology": { - "type": "string" - }, - "icd_o_3_site": { - "type": "string" - }, - "lymphatic_invasion": { - "type": "string" - }, - "lymphnodes_examined": { - "type": "string" - }, - "lymphovascular_invasion_present": { - "type": "string" - }, - "menopause_status": { - "type": "string" - }, - "mononucleotide_and_dinucleotide_marker_panel_analysis_status": { - "type": "string" - }, - "neoplasm_histologic_grade": { - "type": "string" - }, - "new_tumor_event_after_initial_treatment": { - "type": "string" - }, - "number_of_lymphnodes_examined": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked": { - "format": "int32", - "type": "integer" - }, - "other_dx": { - "type": "string" - }, - "other_malignancy_anatomic_site": { - "type": "string" - }, - "other_malignancy_histological_type": { - "type": "string" - }, - "other_malignancy_type": { - "type": "string" - }, - "pathologic_M": { - "type": "string" - }, - "pathologic_N": { - "type": "string" - }, - "pathologic_T": { - "type": "string" - }, - "pathologic_stage": { - "type": "string" - }, - "person_neoplasm_cancer_status": { - "type": "string" - }, - "pregnancies": { - "type": "string" - }, - "primary_neoplasm_melanoma_dx": { - "type": "string" - }, - "primary_therapy_outcome_success": { - "type": "string" - }, - "psa_value": { - "format": "double", - "type": "number" - }, - "race": { - "type": "string" - }, - "residual_tumor": { - "type": "string" - }, - "stopped_smoking_year": { - "format": "int32", - "type": "integer" - }, - "summary_file_count": { - "format": "int32", - "type": "integer" - }, - "tobacco_smoking_history": { - "type": "string" - }, - "tss_code": { - "type": "string" - }, - "tumor_tissue_site": { - "type": "string" - }, - "tumor_type": { - "type": "string" - }, - "venous_invasion": { - "type": "string" - }, - "vital_status": { - "type": "string" - }, - "weight": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesClinicalMetadataRangesItem": { - "properties": { - "age_at_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_at_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "age_at_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_began_smoking_in_years_gte": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years_lte": { - "format": "int32", - "type": "integer" - }, - "anatomic_neoplasm_subdivision": { - "items": { - "type": "string" - }, - "type": "array" - }, - "batch_number": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "batch_number_gte": { - "format": "int32", - "type": "integer" - }, - "batch_number_lte": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "items": { - "type": "string" - }, - "type": "array" - }, - "bmi": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "bmi_gte": { - "format": "double", - "type": "number" - }, - "bmi_lte": { - "format": "double", - "type": "number" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_M": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_N": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_T": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_stage": { - "items": { - "type": "string" - }, - "type": "array" - }, - "colorectal_cancer": { - "items": { - "type": "string" - }, - "type": "array" - }, - "country": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_birth": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_birth_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_birth_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_death_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_death_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_initial_pathologic_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_followup_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_known_alive_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_submitted_specimen_dx_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx_lte": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gender": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gleason_score_combined": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "gleason_score_combined_gte": { - "format": "int32", - "type": "integer" - }, - "gleason_score_combined_lte": { - "format": "int32", - "type": "integer" - }, - "h_pylori_infection": { - "items": { - "type": "string" - }, - "type": "array" - }, - "height": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "height_gte": { - "format": "int32", - "type": "integer" - }, - "height_lte": { - "format": "int32", - "type": "integer" - }, - "histological_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "history_of_colon_polyps": { - "items": { - "type": "string" - }, - "type": "array" - }, - "history_of_neoadjuvant_treatment": { - "items": { - "type": "string" - }, - "type": "array" - }, - "hpv_calls": { - "items": { - "type": "string" - }, - "type": "array" - }, - "hpv_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_10": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_o_3_histology": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_o_3_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphatic_invasion": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphnodes_examined": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphovascular_invasion_present": { - "items": { - "type": "string" - }, - "type": "array" - }, - "menopause_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "mononucleotide_and_dinucleotide_marker_panel_analysis_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "neoplasm_histologic_grade": { - "items": { - "type": "string" - }, - "type": "array" - }, - "new_tumor_event_after_initial_treatment": { - "items": { - "type": "string" - }, - "type": "array" - }, - "number_of_lymphnodes_examined": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_of_lymphnodes_examined_gte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_examined_lte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_of_lymphnodes_positive_by_he_gte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he_lte": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_pack_years_smoked_gte": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked_lte": { - "format": "int32", - "type": "integer" - }, - "other_dx": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_anatomic_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_histological_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_M": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_N": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_T": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_stage": { - "items": { - "type": "string" - }, - "type": "array" - }, - "person_neoplasm_cancer_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pregnancies": { - "items": { - "type": "string" - }, - "type": "array" - }, - "primary_neoplasm_melanoma_dx": { - "items": { - "type": "string" - }, - "type": "array" - }, - "primary_therapy_outcome_success": { - "items": { - "type": "string" - }, - "type": "array" - }, - "psa_value": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "psa_value_gte": { - "format": "double", - "type": "number" - }, - "psa_value_lte": { - "format": "double", - "type": "number" - }, - "race": { - "items": { - "type": "string" - }, - "type": "array" - }, - "residual_tumor": { - "items": { - "type": "string" - }, - "type": "array" - }, - "stopped_smoking_year": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "stopped_smoking_year_gte": { - "format": "int32", - "type": "integer" - }, - "stopped_smoking_year_lte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "summary_file_count_gte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count_lte": { - "format": "int32", - "type": "integer" - }, - "tobacco_smoking_history": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tss_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_tissue_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "venous_invasion": { - "items": { - "type": "string" - }, - "type": "array" - }, - "vital_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "weight": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "weight_gte": { - "format": "int32", - "type": "integer" - }, - "weight_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_tobacco_smoking_onset_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset_lte": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesCommonMetadataItem": { - "properties": { - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesCommonMetadataRangesItem": { - "properties": { - "disease_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "endpoint_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "program_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "project_short_name": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "archive_file_name": { - "type": "string" - }, - "archive_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_submitter_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "archive_file_name": { - "type": "string" - }, - "archive_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_submitter_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesMetadataItem": { - "properties": { - "Biospecimen": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataItem" - }, - "Clinical": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesClinicalMetadataItem" - }, - "Common": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesCommonMetadataItem" - }, - "Data_HG19": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataItem" - }, - "Data_HG38": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesMetadataRangesItem": { - "properties": { - "Biospecimen": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataRangesItem" - }, - "Clinical": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesClinicalMetadataRangesItem" - }, - "Common": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesCommonMetadataRangesItem" - }, - "Data_HG19": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataRangesItem" - }, - "Data_HG38": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataRangesItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAPatientsGetCaseDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_data": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesMetadataItem" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGASamplesGetSampleDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "biospecimen_data": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesMetadataItem" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "data_details": { - "items": { - "$ref": "#/definitions/Api3SamplesGetHelperDataDetails" - }, - "type": "array" - }, - "data_details_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3SamplesGetHelperDataDetails": { - "properties": { - "access": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_gdc_id": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_name_key": { - "type": "string" - }, - "file_size": { - "format": "int64", - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3UsersGetCommonUserGetAPIReturnJSON": { - "properties": { - "dbGaP_allowed": { - "type": "boolean" - }, - "dbGaP_authorized": { - "type": "boolean" - }, - "message": { - "type": "string" - } - }, - "type": "object" - } - }, - "host": "api-dot-isb-cgc.appspot.com", - "info": { - "description": "Get information about cohorts, cases, and samples for TARGET. Create cohorts.", - "title": "isb_cgc_target_api", - "version": "v3" - }, - "paths": { - "/isb_cgc_target_api/v3/target/cases/{case_barcode}": { - "get": { - "operationId": "TARGETCasesGetAPI_get", - "parameters": [ - { - "in": "path", - "name": "case_barcode", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETPatientsGetCaseDetails" - } - } - } - } - }, - "/isb_cgc_target_api/v3/target/cohorts/create": { - "post": { - "operationId": "TARGETCohortsCreateAPI_create", - "parameters": [ - { - "in": "body", - "name": "body", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesMetadataRangesItem" - } - }, - { - "in": "query", - "name": "name", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3CohortCreatePreviewHelperCreatedCohort" - } - } - } - } - }, - "/isb_cgc_target_api/v3/target/samples/{sample_barcode}": { - "get": { - "operationId": "TARGETSamplesGetAPI_get", - "parameters": [ - { - "in": "path", - "name": "sample_barcode", - "required": true, - "type": "string" - }, - { - "in": "query", - "name": "data_type", - "type": "string" - }, - { - "in": "query", - "name": "data_category", - "type": "string" - }, - { - "in": "query", - "name": "experimental_strategy", - "type": "string" - }, - { - "in": "query", - "name": "data_format", - "type": "string" - }, - { - "in": "query", - "name": "platform", - "type": "string" - }, - { - "in": "query", - "name": "endpoint_type", - "type": "string" - }, - { - "in": "query", - "name": "analysis_workflow_type", - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETSamplesGetSampleDetails" - } - } - } - } - }, - "/isb_cgc_target_api/v3/target/samples/{sample_barcode}/cloud_storage_file_paths": { - "get": { - "operationId": "TARGETSamplesCloudStorageFilePathsAPI_cloudStorageFilePaths", - "parameters": [ - { - "in": "path", - "name": "sample_barcode", - "required": true, - "type": "string" - }, - { - "in": "query", - "name": "data_type", - "type": "string" - }, - { - "in": "query", - "name": "data_category", - "type": "string" - }, - { - "in": "query", - "name": "experimental_strategy", - "type": "string" - }, - { - "in": "query", - "name": "data_format", - "type": "string" - }, - { - "in": "query", - "name": "platform", - "type": "string" - }, - { - "in": "query", - "name": "genomic_build", - "type": "string" - }, - { - "in": "query", - "name": "analysis_workflow_type", - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3CloudstoragefilepathsHelperGCSFilePathList" - } - } - } - } - }, - "/isb_cgc_target_api/v3/target/users": { - "get": { - "operationId": "TARGETUserGetAPI_get", - "parameters": [], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3UsersGetCommonUserGetAPIReturnJSON" - } - } - } - } - }, - "/isb_cgc_target_api/v3/tcga/cohorts/preview": { - "post": { - "operationId": "TARGETCohortsPreviewAPI_preview", - "parameters": [ - { - "in": "body", - "name": "body", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiTARGETMessageClassesMetadataRangesItem" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3CohortCreatePreviewHelperCohortCasesSamplesList" - } - } - } - } - } - }, - "produces": [ - "application/json" - ], - "schemes": [ - "https" - ], - "securityDefinitions": { - "google_id_token": { - "authorizationUrl": "", - "flow": "implicit", - "type": "oauth2", - "x-google-issuer": "https://accounts.google.com", - "x-google-jwks_uri": "https://www.googleapis.com/oauth2/v3/certs" - } - }, - "swagger": "2.0" -} \ No newline at end of file diff --git a/isb_cgc_target_apiv3_openapiv3.json b/isb_cgc_target_apiv3_openapiv3.json deleted file mode 100644 index cbb2cb16..00000000 --- a/isb_cgc_target_apiv3_openapiv3.json +++ /dev/null @@ -1,3672 +0,0 @@ -{ - "openapi": "3.0.0", - "servers": [ - { - "url": "https://api-dot-isb-cgc.appspot.com/_ah/api" - } - ], - "info": { - "description": "Get information about cases and samples for TARGET; preview and create cohorts containing TARGET cases and samples.", - "title": "ISB-CGC APi: TARGET", - "version": "v3" - }, - "paths": { - "/isb_cgc_target_api/v3/target/cases/{case_barcode}": { - "get": { - "operationId": "TARGETCasesGetAPI_get", - "parameters": [ - { - "in": "path", - "name": "case_barcode", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETPatientsGetCaseDetails" - } - } - } - } - } - } - }, - "/isb_cgc_target_api/v3/target/cohorts/create": { - "post": { - "operationId": "TARGETCohortsCreateAPI_create", - "parameters": [ - { - "in": "query", - "name": "name", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3CohortCreatePreviewHelperCreatedCohort" - } - } - } - } - }, - "requestBody": { - "$ref": "#/components/requestBodies/Api3IsbCgcApiTARGETMessageClassesMetadataRangesItem" - } - } - }, - "/isb_cgc_target_api/v3/target/samples/{sample_barcode}": { - "get": { - "operationId": "TARGETSamplesGetAPI_get", - "parameters": [ - { - "in": "path", - "name": "sample_barcode", - "required": true, - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_type", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_category", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "experimental_strategy", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_format", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "platform", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "endpoint_type", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "analysis_workflow_type", - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETSamplesGetSampleDetails" - } - } - } - } - } - } - }, - "/isb_cgc_target_api/v3/target/samples/{sample_barcode}/cloud_storage_file_paths": { - "get": { - "operationId": "TARGETSamplesCloudStorageFilePathsAPI_cloudStorageFilePaths", - "parameters": [ - { - "in": "path", - "name": "sample_barcode", - "required": true, - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_type", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_category", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "experimental_strategy", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_format", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "platform", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "genomic_build", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "analysis_workflow_type", - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3CloudstoragefilepathsHelperGCSFilePathList" - } - } - } - } - } - } - }, - "/isb_cgc_target_api/v3/target/users": { - "get": { - "operationId": "TARGETUserGetAPI_get", - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3UsersGetCommonUserGetAPIReturnJSON" - } - } - } - } - } - } - }, - "/isb_cgc_target_api/v3/tcga/cohorts/preview": { - "post": { - "operationId": "TARGETCohortsPreviewAPI_preview", - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3CohortCreatePreviewHelperCohortCasesSamplesList" - } - } - } - } - }, - "requestBody": { - "$ref": "#/components/requestBodies/Api3IsbCgcApiTARGETMessageClassesMetadataRangesItem" - } - } - } - }, - "components": { - "schemas": { - "Api3CloudstoragefilepathsHelperGCSFilePathList": { - "properties": { - "cloud_storage_file_paths": { - "items": { - "type": "string" - }, - "type": "array" - }, - "count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperCohortCasesSamplesList": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "cases": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperCreatedCohort": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "filters": { - "items": { - "$ref": "#/components/schemas/Api3CohortCreatePreviewHelperFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperFilterDetails": { - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, - "Api3CohortEndpointHelpersFilterDetails": { - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileDetail": { - "properties": { - "access": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_uuid": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "disease_code": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_gdc_uuid": { - "type": "string" - }, - "file_path": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "program": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileManifest": { - "properties": { - "files": { - "items": { - "$ref": "#/components/schemas/Api3IsbCgcApiCohortFileManifestFileDetail" - }, - "type": "array" - }, - "files_retrieved": { - "format": "int32", - "type": "integer" - }, - "total_file_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "cases": { - "items": { - "type": "string" - }, - "type": "array" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/components/schemas/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetailsList": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "items": { - "items": { - "$ref": "#/components/schemas/Api3IsbCgcApiCohortGetListHelperCohortListDetails" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortListDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/components/schemas/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortsDeleteReturnJSON": { - "properties": { - "message": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiFilesGetFilePathsFilePaths": { - "properties": { - "paths": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataItem": { - "properties": { - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "tumor_code": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataRangesItem": { - "properties": { - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_code": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesClinicalMetadataItem": { - "properties": { - "age_at_diagnosis": { - "format": "int32", - "type": "integer" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "days_to_birth": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "type": "string" - }, - "event_free_survival": { - "format": "int32", - "type": "integer" - }, - "first_event": { - "type": "string" - }, - "gender": { - "type": "string" - }, - "protocol": { - "type": "string" - }, - "race": { - "type": "string" - }, - "summary_file_count": { - "format": "int32", - "type": "integer" - }, - "vital_status": { - "type": "string" - }, - "wbc_at_diagnosis": { - "format": "double", - "type": "number" - }, - "year_of_diagnosis": { - "format": "int32", - "type": "integer" - }, - "year_of_last_follow_up": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesClinicalMetadataRangesItem": { - "properties": { - "age_at_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_at_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "age_at_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_birth": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_birth_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_birth_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_death_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_death_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_followup_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_known_alive_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive_lte": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "items": { - "type": "string" - }, - "type": "array" - }, - "event_free_survival": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "event_free_survival_gte": { - "format": "int32", - "type": "integer" - }, - "event_free_survival_lte": { - "format": "int32", - "type": "integer" - }, - "first_event": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gender": { - "items": { - "type": "string" - }, - "type": "array" - }, - "protocol": { - "items": { - "type": "string" - }, - "type": "array" - }, - "race": { - "items": { - "type": "string" - }, - "type": "array" - }, - "summary_file_count": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "summary_file_count_gte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count_lte": { - "format": "int32", - "type": "integer" - }, - "vital_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "wbc_at_diagnosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "wbc_at_diagnosis_gte": { - "format": "double", - "type": "number" - }, - "wbc_at_diagnosis_lte": { - "format": "double", - "type": "number" - }, - "year_of_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_last_follow_up": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_last_follow_up_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_last_follow_up_lte": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesCommonMetadataItem": { - "properties": { - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesCommonMetadataRangesItem": { - "properties": { - "disease_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "endpoint_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "program_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "project_short_name": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesMetadataItem": { - "properties": { - "Biospecimen": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataItem" - }, - "Clinical": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesClinicalMetadataItem" - }, - "Common": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesCommonMetadataItem" - }, - "Data_HG19": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataItem" - }, - "Data_HG38": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETMessageClassesMetadataRangesItem": { - "properties": { - "Biospecimen": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesBiospecimenMetadataRangesItem" - }, - "Clinical": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesClinicalMetadataRangesItem" - }, - "Common": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesCommonMetadataRangesItem" - }, - "Data_HG19": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesDataHG19MetadataRangesItem" - }, - "Data_HG38": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesDataHG38MetadataRangesItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETPatientsGetCaseDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_data": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesMetadataItem" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTARGETSamplesGetSampleDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "biospecimen_data": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesMetadataItem" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "data_details": { - "items": { - "$ref": "#/components/schemas/Api3SamplesGetHelperDataDetails" - }, - "type": "array" - }, - "data_details_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAAnnotationsApiMetadataAnnotationList": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "items": { - "items": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesAnnotationMetadataItem" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesAnnotationMetadataItem": { - "properties": { - "aliquot_barcode": { - "type": "string" - }, - "annotation_gdc_id": { - "type": "string" - }, - "annotation_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "category": { - "type": "string" - }, - "classification": { - "type": "string" - }, - "entity_barcode": { - "type": "string" - }, - "entity_gdc_id": { - "type": "string" - }, - "entity_type": { - "type": "string" - }, - "notes": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "status": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataItem": { - "properties": { - "avg_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "batch_number": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "days_to_collection": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement": { - "format": "int32", - "type": "integer" - }, - "max_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "num_portions": { - "format": "int32", - "type": "integer" - }, - "num_slides": { - "format": "int32", - "type": "integer" - }, - "pathology_report_uuid": { - "type": "string" - }, - "preservation_method": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataRangesItem": { - "properties": { - "avg_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "batch_number": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "batch_number_gte": { - "format": "int32", - "type": "integer" - }, - "batch_number_lte": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_collection": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_collection_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_collection_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_sample_procurement_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement_lte": { - "format": "int32", - "type": "integer" - }, - "max_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "num_portions": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "num_portions_gte": { - "format": "int32", - "type": "integer" - }, - "num_portions_lte": { - "format": "int32", - "type": "integer" - }, - "num_slides": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "num_slides_gte": { - "format": "int32", - "type": "integer" - }, - "num_slides_lte": { - "format": "int32", - "type": "integer" - }, - "pathology_report_uuid": { - "items": { - "type": "string" - }, - "type": "array" - }, - "preservation_method": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesClinicalMetadataItem": { - "properties": { - "age_at_diagnosis": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years": { - "format": "int32", - "type": "integer" - }, - "anatomic_neoplasm_subdivision": { - "type": "string" - }, - "batch_number": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "type": "string" - }, - "bmi": { - "format": "double", - "type": "number" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "clinical_M": { - "type": "string" - }, - "clinical_N": { - "type": "string" - }, - "clinical_T": { - "type": "string" - }, - "clinical_stage": { - "type": "string" - }, - "colorectal_cancer": { - "type": "string" - }, - "country": { - "type": "string" - }, - "days_to_birth": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "type": "string" - }, - "gender": { - "type": "string" - }, - "gleason_score_combined": { - "format": "int32", - "type": "integer" - }, - "h_pylori_infection": { - "type": "string" - }, - "height": { - "format": "int32", - "type": "integer" - }, - "histological_type": { - "type": "string" - }, - "history_of_colon_polyps": { - "type": "string" - }, - "history_of_neoadjuvant_treatment": { - "type": "string" - }, - "hpv_calls": { - "type": "string" - }, - "hpv_status": { - "type": "string" - }, - "icd_10": { - "type": "string" - }, - "icd_o_3_histology": { - "type": "string" - }, - "icd_o_3_site": { - "type": "string" - }, - "lymphatic_invasion": { - "type": "string" - }, - "lymphnodes_examined": { - "type": "string" - }, - "lymphovascular_invasion_present": { - "type": "string" - }, - "menopause_status": { - "type": "string" - }, - "mononucleotide_and_dinucleotide_marker_panel_analysis_status": { - "type": "string" - }, - "neoplasm_histologic_grade": { - "type": "string" - }, - "new_tumor_event_after_initial_treatment": { - "type": "string" - }, - "number_of_lymphnodes_examined": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked": { - "format": "int32", - "type": "integer" - }, - "other_dx": { - "type": "string" - }, - "other_malignancy_anatomic_site": { - "type": "string" - }, - "other_malignancy_histological_type": { - "type": "string" - }, - "other_malignancy_type": { - "type": "string" - }, - "pathologic_M": { - "type": "string" - }, - "pathologic_N": { - "type": "string" - }, - "pathologic_T": { - "type": "string" - }, - "pathologic_stage": { - "type": "string" - }, - "person_neoplasm_cancer_status": { - "type": "string" - }, - "pregnancies": { - "type": "string" - }, - "primary_neoplasm_melanoma_dx": { - "type": "string" - }, - "primary_therapy_outcome_success": { - "type": "string" - }, - "psa_value": { - "format": "double", - "type": "number" - }, - "race": { - "type": "string" - }, - "residual_tumor": { - "type": "string" - }, - "stopped_smoking_year": { - "format": "int32", - "type": "integer" - }, - "summary_file_count": { - "format": "int32", - "type": "integer" - }, - "tobacco_smoking_history": { - "type": "string" - }, - "tss_code": { - "type": "string" - }, - "tumor_tissue_site": { - "type": "string" - }, - "tumor_type": { - "type": "string" - }, - "venous_invasion": { - "type": "string" - }, - "vital_status": { - "type": "string" - }, - "weight": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesClinicalMetadataRangesItem": { - "properties": { - "age_at_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_at_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "age_at_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_began_smoking_in_years_gte": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years_lte": { - "format": "int32", - "type": "integer" - }, - "anatomic_neoplasm_subdivision": { - "items": { - "type": "string" - }, - "type": "array" - }, - "batch_number": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "batch_number_gte": { - "format": "int32", - "type": "integer" - }, - "batch_number_lte": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "items": { - "type": "string" - }, - "type": "array" - }, - "bmi": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "bmi_gte": { - "format": "double", - "type": "number" - }, - "bmi_lte": { - "format": "double", - "type": "number" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_M": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_N": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_T": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_stage": { - "items": { - "type": "string" - }, - "type": "array" - }, - "colorectal_cancer": { - "items": { - "type": "string" - }, - "type": "array" - }, - "country": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_birth": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_birth_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_birth_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_death_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_death_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_initial_pathologic_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_followup_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_known_alive_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_submitted_specimen_dx_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx_lte": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gender": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gleason_score_combined": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "gleason_score_combined_gte": { - "format": "int32", - "type": "integer" - }, - "gleason_score_combined_lte": { - "format": "int32", - "type": "integer" - }, - "h_pylori_infection": { - "items": { - "type": "string" - }, - "type": "array" - }, - "height": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "height_gte": { - "format": "int32", - "type": "integer" - }, - "height_lte": { - "format": "int32", - "type": "integer" - }, - "histological_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "history_of_colon_polyps": { - "items": { - "type": "string" - }, - "type": "array" - }, - "history_of_neoadjuvant_treatment": { - "items": { - "type": "string" - }, - "type": "array" - }, - "hpv_calls": { - "items": { - "type": "string" - }, - "type": "array" - }, - "hpv_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_10": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_o_3_histology": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_o_3_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphatic_invasion": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphnodes_examined": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphovascular_invasion_present": { - "items": { - "type": "string" - }, - "type": "array" - }, - "menopause_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "mononucleotide_and_dinucleotide_marker_panel_analysis_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "neoplasm_histologic_grade": { - "items": { - "type": "string" - }, - "type": "array" - }, - "new_tumor_event_after_initial_treatment": { - "items": { - "type": "string" - }, - "type": "array" - }, - "number_of_lymphnodes_examined": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_of_lymphnodes_examined_gte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_examined_lte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_of_lymphnodes_positive_by_he_gte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he_lte": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_pack_years_smoked_gte": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked_lte": { - "format": "int32", - "type": "integer" - }, - "other_dx": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_anatomic_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_histological_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_M": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_N": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_T": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_stage": { - "items": { - "type": "string" - }, - "type": "array" - }, - "person_neoplasm_cancer_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pregnancies": { - "items": { - "type": "string" - }, - "type": "array" - }, - "primary_neoplasm_melanoma_dx": { - "items": { - "type": "string" - }, - "type": "array" - }, - "primary_therapy_outcome_success": { - "items": { - "type": "string" - }, - "type": "array" - }, - "psa_value": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "psa_value_gte": { - "format": "double", - "type": "number" - }, - "psa_value_lte": { - "format": "double", - "type": "number" - }, - "race": { - "items": { - "type": "string" - }, - "type": "array" - }, - "residual_tumor": { - "items": { - "type": "string" - }, - "type": "array" - }, - "stopped_smoking_year": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "stopped_smoking_year_gte": { - "format": "int32", - "type": "integer" - }, - "stopped_smoking_year_lte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "summary_file_count_gte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count_lte": { - "format": "int32", - "type": "integer" - }, - "tobacco_smoking_history": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tss_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_tissue_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "venous_invasion": { - "items": { - "type": "string" - }, - "type": "array" - }, - "vital_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "weight": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "weight_gte": { - "format": "int32", - "type": "integer" - }, - "weight_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_tobacco_smoking_onset_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset_lte": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesCommonMetadataItem": { - "properties": { - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesCommonMetadataRangesItem": { - "properties": { - "disease_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "endpoint_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "program_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "project_short_name": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "archive_file_name": { - "type": "string" - }, - "archive_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_submitter_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "archive_file_name": { - "type": "string" - }, - "archive_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_submitter_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesMetadataItem": { - "properties": { - "Biospecimen": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataItem" - }, - "Clinical": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesClinicalMetadataItem" - }, - "Common": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesCommonMetadataItem" - }, - "Data_HG19": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataItem" - }, - "Data_HG38": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesMetadataRangesItem": { - "properties": { - "Biospecimen": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataRangesItem" - }, - "Clinical": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesClinicalMetadataRangesItem" - }, - "Common": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesCommonMetadataRangesItem" - }, - "Data_HG19": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataRangesItem" - }, - "Data_HG38": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataRangesItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAPatientsGetCaseDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_data": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesMetadataItem" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGASamplesGetSampleDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "biospecimen_data": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesMetadataItem" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "data_details": { - "items": { - "$ref": "#/components/schemas/Api3SamplesGetHelperDataDetails" - }, - "type": "array" - }, - "data_details_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3SamplesGetHelperDataDetails": { - "properties": { - "access": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_gdc_id": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_name_key": { - "type": "string" - }, - "file_size": { - "format": "int64", - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3UsersGetCommonUserGetAPIReturnJSON": { - "properties": { - "dbGaP_allowed": { - "type": "boolean" - }, - "dbGaP_authorized": { - "type": "boolean" - }, - "message": { - "type": "string" - } - }, - "type": "object" - } - }, - "requestBodies": { - "Api3IsbCgcApiTARGETMessageClassesMetadataRangesItem": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiTARGETMessageClassesMetadataRangesItem" - } - } - } - } - }, - "securitySchemes": { - "google_id_token": { - "type": "oauth2", - "x-google-issuer": "https://accounts.google.com", - "x-google-jwks_uri": "https://www.googleapis.com/oauth2/v3/certs", - "flows": { - "implicit": { - "authorizationUrl": "/", - "scopes": {} - } - } - } - } - } -} \ No newline at end of file diff --git a/isb_cgc_tcga_apiv3_openapiv2.json b/isb_cgc_tcga_apiv3_openapiv2.json deleted file mode 100644 index 7be9694c..00000000 --- a/isb_cgc_tcga_apiv3_openapiv2.json +++ /dev/null @@ -1,2819 +0,0 @@ -{ - "basePath": "/_ah/api", - "consumes": [ - "application/json" - ], - "definitions": { - "Api3CloudstoragefilepathsHelperGCSFilePathList": { - "properties": { - "cloud_storage_file_paths": { - "items": { - "type": "string" - }, - "type": "array" - }, - "count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperCohortCasesSamplesList": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "cases": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperCreatedCohort": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "filters": { - "items": { - "$ref": "#/definitions/Api3CohortCreatePreviewHelperFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperFilterDetails": { - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, - "Api3CohortEndpointHelpersFilterDetails": { - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileDetail": { - "properties": { - "access": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_uuid": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "disease_code": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_gdc_uuid": { - "type": "string" - }, - "file_path": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "program": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileManifest": { - "properties": { - "files": { - "items": { - "$ref": "#/definitions/Api3IsbCgcApiCohortFileManifestFileDetail" - }, - "type": "array" - }, - "files_retrieved": { - "format": "int32", - "type": "integer" - }, - "total_file_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "cases": { - "items": { - "type": "string" - }, - "type": "array" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/definitions/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetailsList": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "items": { - "items": { - "$ref": "#/definitions/Api3IsbCgcApiCohortGetListHelperCohortListDetails" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortListDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/definitions/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortsDeleteReturnJSON": { - "properties": { - "message": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiFilesGetFilePathsFilePaths": { - "properties": { - "paths": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAAnnotationsApiMetadataAnnotationList": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "items": { - "items": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesAnnotationMetadataItem" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesAnnotationMetadataItem": { - "properties": { - "aliquot_barcode": { - "type": "string" - }, - "annotation_gdc_id": { - "type": "string" - }, - "annotation_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "category": { - "type": "string" - }, - "classification": { - "type": "string" - }, - "entity_barcode": { - "type": "string" - }, - "entity_gdc_id": { - "type": "string" - }, - "entity_type": { - "type": "string" - }, - "notes": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "status": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataItem": { - "properties": { - "avg_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "batch_number": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "days_to_collection": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement": { - "format": "int32", - "type": "integer" - }, - "max_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "num_portions": { - "format": "int32", - "type": "integer" - }, - "num_slides": { - "format": "int32", - "type": "integer" - }, - "pathology_report_uuid": { - "type": "string" - }, - "preservation_method": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataRangesItem": { - "properties": { - "avg_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "batch_number": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "batch_number_gte": { - "format": "int32", - "type": "integer" - }, - "batch_number_lte": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_collection": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_collection_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_collection_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_sample_procurement_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement_lte": { - "format": "int32", - "type": "integer" - }, - "max_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "num_portions": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "num_portions_gte": { - "format": "int32", - "type": "integer" - }, - "num_portions_lte": { - "format": "int32", - "type": "integer" - }, - "num_slides": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "num_slides_gte": { - "format": "int32", - "type": "integer" - }, - "num_slides_lte": { - "format": "int32", - "type": "integer" - }, - "pathology_report_uuid": { - "items": { - "type": "string" - }, - "type": "array" - }, - "preservation_method": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesClinicalMetadataItem": { - "properties": { - "age_at_diagnosis": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years": { - "format": "int32", - "type": "integer" - }, - "anatomic_neoplasm_subdivision": { - "type": "string" - }, - "batch_number": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "type": "string" - }, - "bmi": { - "format": "double", - "type": "number" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "clinical_M": { - "type": "string" - }, - "clinical_N": { - "type": "string" - }, - "clinical_T": { - "type": "string" - }, - "clinical_stage": { - "type": "string" - }, - "colorectal_cancer": { - "type": "string" - }, - "country": { - "type": "string" - }, - "days_to_birth": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "type": "string" - }, - "gender": { - "type": "string" - }, - "gleason_score_combined": { - "format": "int32", - "type": "integer" - }, - "h_pylori_infection": { - "type": "string" - }, - "height": { - "format": "int32", - "type": "integer" - }, - "histological_type": { - "type": "string" - }, - "history_of_colon_polyps": { - "type": "string" - }, - "history_of_neoadjuvant_treatment": { - "type": "string" - }, - "hpv_calls": { - "type": "string" - }, - "hpv_status": { - "type": "string" - }, - "icd_10": { - "type": "string" - }, - "icd_o_3_histology": { - "type": "string" - }, - "icd_o_3_site": { - "type": "string" - }, - "lymphatic_invasion": { - "type": "string" - }, - "lymphnodes_examined": { - "type": "string" - }, - "lymphovascular_invasion_present": { - "type": "string" - }, - "menopause_status": { - "type": "string" - }, - "mononucleotide_and_dinucleotide_marker_panel_analysis_status": { - "type": "string" - }, - "neoplasm_histologic_grade": { - "type": "string" - }, - "new_tumor_event_after_initial_treatment": { - "type": "string" - }, - "number_of_lymphnodes_examined": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked": { - "format": "int32", - "type": "integer" - }, - "other_dx": { - "type": "string" - }, - "other_malignancy_anatomic_site": { - "type": "string" - }, - "other_malignancy_histological_type": { - "type": "string" - }, - "other_malignancy_type": { - "type": "string" - }, - "pathologic_M": { - "type": "string" - }, - "pathologic_N": { - "type": "string" - }, - "pathologic_T": { - "type": "string" - }, - "pathologic_stage": { - "type": "string" - }, - "person_neoplasm_cancer_status": { - "type": "string" - }, - "pregnancies": { - "type": "string" - }, - "primary_neoplasm_melanoma_dx": { - "type": "string" - }, - "primary_therapy_outcome_success": { - "type": "string" - }, - "psa_value": { - "format": "double", - "type": "number" - }, - "race": { - "type": "string" - }, - "residual_tumor": { - "type": "string" - }, - "stopped_smoking_year": { - "format": "int32", - "type": "integer" - }, - "summary_file_count": { - "format": "int32", - "type": "integer" - }, - "tobacco_smoking_history": { - "type": "string" - }, - "tss_code": { - "type": "string" - }, - "tumor_tissue_site": { - "type": "string" - }, - "tumor_type": { - "type": "string" - }, - "venous_invasion": { - "type": "string" - }, - "vital_status": { - "type": "string" - }, - "weight": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesClinicalMetadataRangesItem": { - "properties": { - "age_at_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_at_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "age_at_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_began_smoking_in_years_gte": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years_lte": { - "format": "int32", - "type": "integer" - }, - "anatomic_neoplasm_subdivision": { - "items": { - "type": "string" - }, - "type": "array" - }, - "batch_number": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "batch_number_gte": { - "format": "int32", - "type": "integer" - }, - "batch_number_lte": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "items": { - "type": "string" - }, - "type": "array" - }, - "bmi": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "bmi_gte": { - "format": "double", - "type": "number" - }, - "bmi_lte": { - "format": "double", - "type": "number" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_M": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_N": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_T": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_stage": { - "items": { - "type": "string" - }, - "type": "array" - }, - "colorectal_cancer": { - "items": { - "type": "string" - }, - "type": "array" - }, - "country": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_birth": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_birth_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_birth_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_death_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_death_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_initial_pathologic_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_followup_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_known_alive_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_submitted_specimen_dx_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx_lte": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gender": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gleason_score_combined": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "gleason_score_combined_gte": { - "format": "int32", - "type": "integer" - }, - "gleason_score_combined_lte": { - "format": "int32", - "type": "integer" - }, - "h_pylori_infection": { - "items": { - "type": "string" - }, - "type": "array" - }, - "height": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "height_gte": { - "format": "int32", - "type": "integer" - }, - "height_lte": { - "format": "int32", - "type": "integer" - }, - "histological_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "history_of_colon_polyps": { - "items": { - "type": "string" - }, - "type": "array" - }, - "history_of_neoadjuvant_treatment": { - "items": { - "type": "string" - }, - "type": "array" - }, - "hpv_calls": { - "items": { - "type": "string" - }, - "type": "array" - }, - "hpv_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_10": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_o_3_histology": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_o_3_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphatic_invasion": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphnodes_examined": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphovascular_invasion_present": { - "items": { - "type": "string" - }, - "type": "array" - }, - "menopause_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "mononucleotide_and_dinucleotide_marker_panel_analysis_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "neoplasm_histologic_grade": { - "items": { - "type": "string" - }, - "type": "array" - }, - "new_tumor_event_after_initial_treatment": { - "items": { - "type": "string" - }, - "type": "array" - }, - "number_of_lymphnodes_examined": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_of_lymphnodes_examined_gte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_examined_lte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_of_lymphnodes_positive_by_he_gte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he_lte": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_pack_years_smoked_gte": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked_lte": { - "format": "int32", - "type": "integer" - }, - "other_dx": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_anatomic_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_histological_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_M": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_N": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_T": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_stage": { - "items": { - "type": "string" - }, - "type": "array" - }, - "person_neoplasm_cancer_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pregnancies": { - "items": { - "type": "string" - }, - "type": "array" - }, - "primary_neoplasm_melanoma_dx": { - "items": { - "type": "string" - }, - "type": "array" - }, - "primary_therapy_outcome_success": { - "items": { - "type": "string" - }, - "type": "array" - }, - "psa_value": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "psa_value_gte": { - "format": "double", - "type": "number" - }, - "psa_value_lte": { - "format": "double", - "type": "number" - }, - "race": { - "items": { - "type": "string" - }, - "type": "array" - }, - "residual_tumor": { - "items": { - "type": "string" - }, - "type": "array" - }, - "stopped_smoking_year": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "stopped_smoking_year_gte": { - "format": "int32", - "type": "integer" - }, - "stopped_smoking_year_lte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "summary_file_count_gte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count_lte": { - "format": "int32", - "type": "integer" - }, - "tobacco_smoking_history": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tss_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_tissue_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "venous_invasion": { - "items": { - "type": "string" - }, - "type": "array" - }, - "vital_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "weight": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "weight_gte": { - "format": "int32", - "type": "integer" - }, - "weight_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_tobacco_smoking_onset_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset_lte": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesCommonMetadataItem": { - "properties": { - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesCommonMetadataRangesItem": { - "properties": { - "disease_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "endpoint_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "program_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "project_short_name": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "archive_file_name": { - "type": "string" - }, - "archive_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_submitter_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "archive_file_name": { - "type": "string" - }, - "archive_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_submitter_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesMetadataItem": { - "properties": { - "Biospecimen": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataItem" - }, - "Clinical": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesClinicalMetadataItem" - }, - "Common": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesCommonMetadataItem" - }, - "Data_HG19": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataItem" - }, - "Data_HG38": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesMetadataRangesItem": { - "properties": { - "Biospecimen": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataRangesItem" - }, - "Clinical": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesClinicalMetadataRangesItem" - }, - "Common": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesCommonMetadataRangesItem" - }, - "Data_HG19": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataRangesItem" - }, - "Data_HG38": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataRangesItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAPatientsGetCaseDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_data": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesMetadataItem" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGASamplesGetSampleDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "biospecimen_data": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesMetadataItem" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "data_details": { - "items": { - "$ref": "#/definitions/Api3SamplesGetHelperDataDetails" - }, - "type": "array" - }, - "data_details_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3SamplesGetHelperDataDetails": { - "properties": { - "access": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_gdc_id": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_name_key": { - "type": "string" - }, - "file_size": { - "format": "int64", - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3UsersGetCommonUserGetAPIReturnJSON": { - "properties": { - "dbGaP_allowed": { - "type": "boolean" - }, - "dbGaP_authorized": { - "type": "boolean" - }, - "message": { - "type": "string" - } - }, - "type": "object" - } - }, - "host": "api-dot-isb-cgc.appspot.com", - "info": { - "description": "Get information about cohorts, cases, and samples for TCGA. Create cohorts.", - "title": "isb_cgc_tcga_api", - "version": "v3" - }, - "paths": { - "/isb_cgc_tcga_api/v3/aliquots/{aliquot_barcode}/annotations": { - "get": { - "operationId": "TCGAAliquotsAnnotationAPI_annotations", - "parameters": [ - { - "in": "path", - "name": "aliquot_barcode", - "required": true, - "type": "string" - }, - { - "collectionFormat": "multi", - "in": "query", - "items": { - "type": "string" - }, - "name": "entity_type", - "type": "array" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAAnnotationsApiMetadataAnnotationList" - } - } - } - } - }, - "/isb_cgc_tcga_api/v3/cases/{case_barcode}/annotations": { - "get": { - "operationId": "TCGACasesAnnotationAPI_annotations", - "parameters": [ - { - "in": "path", - "name": "case_barcode", - "required": true, - "type": "string" - }, - { - "collectionFormat": "multi", - "in": "query", - "items": { - "type": "string" - }, - "name": "entity_type", - "type": "array" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAAnnotationsApiMetadataAnnotationList" - } - } - } - } - }, - "/isb_cgc_tcga_api/v3/samples/{sample_barcode}/annotations": { - "get": { - "operationId": "TCGASamplesAnnotationAPI_annotations", - "parameters": [ - { - "in": "path", - "name": "sample_barcode", - "required": true, - "type": "string" - }, - { - "collectionFormat": "multi", - "in": "query", - "items": { - "type": "string" - }, - "name": "entity_type", - "type": "array" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAAnnotationsApiMetadataAnnotationList" - } - } - } - } - }, - "/isb_cgc_tcga_api/v3/tcga/cases/{case_barcode}": { - "get": { - "operationId": "TCGACasesGetAPI_get", - "parameters": [ - { - "in": "path", - "name": "case_barcode", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAPatientsGetCaseDetails" - } - } - } - } - }, - "/isb_cgc_tcga_api/v3/tcga/cohorts/create": { - "post": { - "operationId": "TCGACohortsCreateAPI_create", - "parameters": [ - { - "in": "body", - "name": "body", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesMetadataRangesItem" - } - }, - { - "in": "query", - "name": "name", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3CohortCreatePreviewHelperCreatedCohort" - } - } - } - } - }, - "/isb_cgc_tcga_api/v3/tcga/cohorts/preview": { - "post": { - "operationId": "TCGACohortsPreviewAPI_preview", - "parameters": [ - { - "in": "body", - "name": "body", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiTCGAMessageClassesMetadataRangesItem" - } - }, - { - "in": "query", - "name": "fields", - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3CohortCreatePreviewHelperCohortCasesSamplesList" - } - } - } - } - }, - "/isb_cgc_tcga_api/v3/tcga/samples/{sample_barcode}": { - "get": { - "operationId": "TCGASamplesGetAPI_get", - "parameters": [ - { - "in": "path", - "name": "sample_barcode", - "required": true, - "type": "string" - }, - { - "in": "query", - "name": "data_type", - "type": "string" - }, - { - "in": "query", - "name": "data_category", - "type": "string" - }, - { - "in": "query", - "name": "experimental_strategy", - "type": "string" - }, - { - "in": "query", - "name": "data_format", - "type": "string" - }, - { - "in": "query", - "name": "platform", - "type": "string" - }, - { - "in": "query", - "name": "endpoint_type", - "type": "string" - }, - { - "in": "query", - "name": "analysis_workflow_type", - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3IsbCgcApiTCGASamplesGetSampleDetails" - } - } - } - } - }, - "/isb_cgc_tcga_api/v3/tcga/samples/{sample_barcode}/cloud_storage_file_paths": { - "get": { - "operationId": "TCGASamplesCloudStorageFilePathsAPI_cloudStorageFilePaths", - "parameters": [ - { - "in": "path", - "name": "sample_barcode", - "required": true, - "type": "string" - }, - { - "in": "query", - "name": "data_type", - "type": "string" - }, - { - "in": "query", - "name": "data_category", - "type": "string" - }, - { - "in": "query", - "name": "experimental_strategy", - "type": "string" - }, - { - "in": "query", - "name": "data_format", - "type": "string" - }, - { - "in": "query", - "name": "platform", - "type": "string" - }, - { - "in": "query", - "name": "genomic_build", - "type": "string" - }, - { - "in": "query", - "name": "analysis_workflow_type", - "type": "string" - } - ], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3CloudstoragefilepathsHelperGCSFilePathList" - } - } - } - } - }, - "/isb_cgc_tcga_api/v3/tcga/users": { - "get": { - "operationId": "TCGAUserGetAPI_get", - "parameters": [], - "responses": { - "200": { - "description": "A successful response", - "schema": { - "$ref": "#/definitions/Api3UsersGetCommonUserGetAPIReturnJSON" - } - } - } - } - } - }, - "produces": [ - "application/json" - ], - "schemes": [ - "https" - ], - "securityDefinitions": { - "google_id_token": { - "authorizationUrl": "", - "flow": "implicit", - "type": "oauth2", - "x-google-issuer": "https://accounts.google.com", - "x-google-jwks_uri": "https://www.googleapis.com/oauth2/v3/certs" - } - }, - "swagger": "2.0" -} \ No newline at end of file diff --git a/isb_cgc_tcga_apiv3_openapiv3.json b/isb_cgc_tcga_apiv3_openapiv3.json deleted file mode 100644 index c5aea028..00000000 --- a/isb_cgc_tcga_apiv3_openapiv3.json +++ /dev/null @@ -1,2907 +0,0 @@ -{ - "openapi": "3.0.0", - "servers": [ - { - "url": "https://api-dot-isb-cgc.appspot.com/_ah/api" - } - ], - "info": { - "description": "Get information about cases and samples for TCGA; preview and create cohorts containing TCGA cases and samples.", - "title": "ISB-CGC API: TCGA", - "version": "v3" - }, - "paths": { - "/isb_cgc_tcga_api/v3/aliquots/{aliquot_barcode}/annotations": { - "get": { - "operationId": "TCGAAliquotsAnnotationAPI_annotations", - "parameters": [ - { - "in": "path", - "name": "aliquot_barcode", - "required": true, - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "entity_type", - "explode": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAAnnotationsApiMetadataAnnotationList" - } - } - } - } - } - } - }, - "/isb_cgc_tcga_api/v3/cases/{case_barcode}/annotations": { - "get": { - "operationId": "TCGACasesAnnotationAPI_annotations", - "parameters": [ - { - "in": "path", - "name": "case_barcode", - "required": true, - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "entity_type", - "explode": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAAnnotationsApiMetadataAnnotationList" - } - } - } - } - } - } - }, - "/isb_cgc_tcga_api/v3/samples/{sample_barcode}/annotations": { - "get": { - "operationId": "TCGASamplesAnnotationAPI_annotations", - "parameters": [ - { - "in": "path", - "name": "sample_barcode", - "required": true, - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "entity_type", - "explode": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAAnnotationsApiMetadataAnnotationList" - } - } - } - } - } - } - }, - "/isb_cgc_tcga_api/v3/tcga/cases/{case_barcode}": { - "get": { - "operationId": "TCGACasesGetAPI_get", - "parameters": [ - { - "in": "path", - "name": "case_barcode", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAPatientsGetCaseDetails" - } - } - } - } - } - } - }, - "/isb_cgc_tcga_api/v3/tcga/cohorts/create": { - "post": { - "operationId": "TCGACohortsCreateAPI_create", - "parameters": [ - { - "in": "query", - "name": "name", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3CohortCreatePreviewHelperCreatedCohort" - } - } - } - } - }, - "requestBody": { - "$ref": "#/components/requestBodies/Api3IsbCgcApiTCGAMessageClassesMetadataRangesItem" - } - } - }, - "/isb_cgc_tcga_api/v3/tcga/cohorts/preview": { - "post": { - "operationId": "TCGACohortsPreviewAPI_preview", - "parameters": [ - { - "in": "query", - "name": "fields", - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3CohortCreatePreviewHelperCohortCasesSamplesList" - } - } - } - } - }, - "requestBody": { - "$ref": "#/components/requestBodies/Api3IsbCgcApiTCGAMessageClassesMetadataRangesItem" - } - } - }, - "/isb_cgc_tcga_api/v3/tcga/samples/{sample_barcode}": { - "get": { - "operationId": "TCGASamplesGetAPI_get", - "parameters": [ - { - "in": "path", - "name": "sample_barcode", - "required": true, - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_type", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_category", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "experimental_strategy", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_format", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "platform", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "endpoint_type", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "analysis_workflow_type", - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGASamplesGetSampleDetails" - } - } - } - } - } - } - }, - "/isb_cgc_tcga_api/v3/tcga/samples/{sample_barcode}/cloud_storage_file_paths": { - "get": { - "operationId": "TCGASamplesCloudStorageFilePathsAPI_cloudStorageFilePaths", - "parameters": [ - { - "in": "path", - "name": "sample_barcode", - "required": true, - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_type", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_category", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "experimental_strategy", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "data_format", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "platform", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "genomic_build", - "schema": { - "type": "string" - } - }, - { - "in": "query", - "name": "analysis_workflow_type", - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3CloudstoragefilepathsHelperGCSFilePathList" - } - } - } - } - } - } - }, - "/isb_cgc_tcga_api/v3/tcga/users": { - "get": { - "operationId": "TCGAUserGetAPI_get", - "responses": { - "200": { - "description": "A successful response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3UsersGetCommonUserGetAPIReturnJSON" - } - } - } - } - } - } - } - }, - "components": { - "schemas": { - "Api3CloudstoragefilepathsHelperGCSFilePathList": { - "properties": { - "cloud_storage_file_paths": { - "items": { - "type": "string" - }, - "type": "array" - }, - "count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperCohortCasesSamplesList": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "cases": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperCreatedCohort": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "filters": { - "items": { - "$ref": "#/components/schemas/Api3CohortCreatePreviewHelperFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3CohortCreatePreviewHelperFilterDetails": { - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, - "Api3CohortEndpointHelpersFilterDetails": { - "properties": { - "name": { - "type": "string" - }, - "value": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileDetail": { - "properties": { - "access": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_uuid": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "disease_code": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_gdc_uuid": { - "type": "string" - }, - "file_path": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "program": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortFileManifestFileManifest": { - "properties": { - "files": { - "items": { - "$ref": "#/components/schemas/Api3IsbCgcApiCohortFileManifestFileDetail" - }, - "type": "array" - }, - "files_retrieved": { - "format": "int32", - "type": "integer" - }, - "total_file_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "cases": { - "items": { - "type": "string" - }, - "type": "array" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/components/schemas/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortDetailsList": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "items": { - "items": { - "$ref": "#/components/schemas/Api3IsbCgcApiCohortGetListHelperCohortListDetails" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortGetListHelperCohortListDetails": { - "properties": { - "case_count": { - "format": "int32", - "type": "integer" - }, - "comments": { - "type": "string" - }, - "email": { - "type": "string" - }, - "filters": { - "items": { - "$ref": "#/components/schemas/Api3CohortEndpointHelpersFilterDetails" - }, - "type": "array" - }, - "id": { - "type": "string" - }, - "last_date_saved": { - "type": "string" - }, - "name": { - "type": "string" - }, - "parent_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "permission": { - "type": "string" - }, - "sample_count": { - "format": "int32", - "type": "integer" - }, - "source_notes": { - "type": "string" - }, - "source_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiCohortsDeleteReturnJSON": { - "properties": { - "message": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiFilesGetFilePathsFilePaths": { - "properties": { - "paths": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAAnnotationsApiMetadataAnnotationList": { - "properties": { - "count": { - "format": "int32", - "type": "integer" - }, - "items": { - "items": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesAnnotationMetadataItem" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesAnnotationMetadataItem": { - "properties": { - "aliquot_barcode": { - "type": "string" - }, - "annotation_gdc_id": { - "type": "string" - }, - "annotation_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "category": { - "type": "string" - }, - "classification": { - "type": "string" - }, - "entity_barcode": { - "type": "string" - }, - "entity_gdc_id": { - "type": "string" - }, - "entity_type": { - "type": "string" - }, - "notes": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "status": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataItem": { - "properties": { - "avg_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "batch_number": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "days_to_collection": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement": { - "format": "int32", - "type": "integer" - }, - "max_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei": { - "format": "double", - "type": "number" - }, - "num_portions": { - "format": "int32", - "type": "integer" - }, - "num_slides": { - "format": "int32", - "type": "integer" - }, - "pathology_report_uuid": { - "type": "string" - }, - "preservation_method": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataRangesItem": { - "properties": { - "avg_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "avg_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "avg_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "batch_number": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "batch_number_gte": { - "format": "int32", - "type": "integer" - }, - "batch_number_lte": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_collection": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_collection_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_collection_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_sample_procurement_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_sample_procurement_lte": { - "format": "int32", - "type": "integer" - }, - "max_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "max_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "max_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "max_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "max_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_lymphocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_lymphocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_monocyte_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_monocyte_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_necrosis_gte": { - "format": "double", - "type": "number" - }, - "min_percent_necrosis_lte": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_neutrophil_infiltration_gte": { - "format": "double", - "type": "number" - }, - "min_percent_neutrophil_infiltration_lte": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_normal_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_normal_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_stromal_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_stromal_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_tumor_cells_gte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_cells_lte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "min_percent_tumor_nuclei_gte": { - "format": "double", - "type": "number" - }, - "min_percent_tumor_nuclei_lte": { - "format": "double", - "type": "number" - }, - "num_portions": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "num_portions_gte": { - "format": "int32", - "type": "integer" - }, - "num_portions_lte": { - "format": "int32", - "type": "integer" - }, - "num_slides": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "num_slides_gte": { - "format": "int32", - "type": "integer" - }, - "num_slides_lte": { - "format": "int32", - "type": "integer" - }, - "pathology_report_uuid": { - "items": { - "type": "string" - }, - "type": "array" - }, - "preservation_method": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesClinicalMetadataItem": { - "properties": { - "age_at_diagnosis": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years": { - "format": "int32", - "type": "integer" - }, - "anatomic_neoplasm_subdivision": { - "type": "string" - }, - "batch_number": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "type": "string" - }, - "bmi": { - "format": "double", - "type": "number" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "clinical_M": { - "type": "string" - }, - "clinical_N": { - "type": "string" - }, - "clinical_T": { - "type": "string" - }, - "clinical_stage": { - "type": "string" - }, - "colorectal_cancer": { - "type": "string" - }, - "country": { - "type": "string" - }, - "days_to_birth": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "type": "string" - }, - "gender": { - "type": "string" - }, - "gleason_score_combined": { - "format": "int32", - "type": "integer" - }, - "h_pylori_infection": { - "type": "string" - }, - "height": { - "format": "int32", - "type": "integer" - }, - "histological_type": { - "type": "string" - }, - "history_of_colon_polyps": { - "type": "string" - }, - "history_of_neoadjuvant_treatment": { - "type": "string" - }, - "hpv_calls": { - "type": "string" - }, - "hpv_status": { - "type": "string" - }, - "icd_10": { - "type": "string" - }, - "icd_o_3_histology": { - "type": "string" - }, - "icd_o_3_site": { - "type": "string" - }, - "lymphatic_invasion": { - "type": "string" - }, - "lymphnodes_examined": { - "type": "string" - }, - "lymphovascular_invasion_present": { - "type": "string" - }, - "menopause_status": { - "type": "string" - }, - "mononucleotide_and_dinucleotide_marker_panel_analysis_status": { - "type": "string" - }, - "neoplasm_histologic_grade": { - "type": "string" - }, - "new_tumor_event_after_initial_treatment": { - "type": "string" - }, - "number_of_lymphnodes_examined": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked": { - "format": "int32", - "type": "integer" - }, - "other_dx": { - "type": "string" - }, - "other_malignancy_anatomic_site": { - "type": "string" - }, - "other_malignancy_histological_type": { - "type": "string" - }, - "other_malignancy_type": { - "type": "string" - }, - "pathologic_M": { - "type": "string" - }, - "pathologic_N": { - "type": "string" - }, - "pathologic_T": { - "type": "string" - }, - "pathologic_stage": { - "type": "string" - }, - "person_neoplasm_cancer_status": { - "type": "string" - }, - "pregnancies": { - "type": "string" - }, - "primary_neoplasm_melanoma_dx": { - "type": "string" - }, - "primary_therapy_outcome_success": { - "type": "string" - }, - "psa_value": { - "format": "double", - "type": "number" - }, - "race": { - "type": "string" - }, - "residual_tumor": { - "type": "string" - }, - "stopped_smoking_year": { - "format": "int32", - "type": "integer" - }, - "summary_file_count": { - "format": "int32", - "type": "integer" - }, - "tobacco_smoking_history": { - "type": "string" - }, - "tss_code": { - "type": "string" - }, - "tumor_tissue_site": { - "type": "string" - }, - "tumor_type": { - "type": "string" - }, - "venous_invasion": { - "type": "string" - }, - "vital_status": { - "type": "string" - }, - "weight": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesClinicalMetadataRangesItem": { - "properties": { - "age_at_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_at_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "age_at_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "age_began_smoking_in_years_gte": { - "format": "int32", - "type": "integer" - }, - "age_began_smoking_in_years_lte": { - "format": "int32", - "type": "integer" - }, - "anatomic_neoplasm_subdivision": { - "items": { - "type": "string" - }, - "type": "array" - }, - "batch_number": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "batch_number_gte": { - "format": "int32", - "type": "integer" - }, - "batch_number_lte": { - "format": "int32", - "type": "integer" - }, - "bcr": { - "items": { - "type": "string" - }, - "type": "array" - }, - "bmi": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "bmi_gte": { - "format": "double", - "type": "number" - }, - "bmi_lte": { - "format": "double", - "type": "number" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_M": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_N": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_T": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_stage": { - "items": { - "type": "string" - }, - "type": "array" - }, - "colorectal_cancer": { - "items": { - "type": "string" - }, - "type": "array" - }, - "country": { - "items": { - "type": "string" - }, - "type": "array" - }, - "days_to_birth": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_birth_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_birth_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_death": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_death_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_death_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_initial_pathologic_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_initial_pathologic_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_followup_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_followup_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_last_known_alive_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_last_known_alive_lte": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "days_to_submitted_specimen_dx_gte": { - "format": "int32", - "type": "integer" - }, - "days_to_submitted_specimen_dx_lte": { - "format": "int32", - "type": "integer" - }, - "ethnicity": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gender": { - "items": { - "type": "string" - }, - "type": "array" - }, - "gleason_score_combined": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "gleason_score_combined_gte": { - "format": "int32", - "type": "integer" - }, - "gleason_score_combined_lte": { - "format": "int32", - "type": "integer" - }, - "h_pylori_infection": { - "items": { - "type": "string" - }, - "type": "array" - }, - "height": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "height_gte": { - "format": "int32", - "type": "integer" - }, - "height_lte": { - "format": "int32", - "type": "integer" - }, - "histological_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "history_of_colon_polyps": { - "items": { - "type": "string" - }, - "type": "array" - }, - "history_of_neoadjuvant_treatment": { - "items": { - "type": "string" - }, - "type": "array" - }, - "hpv_calls": { - "items": { - "type": "string" - }, - "type": "array" - }, - "hpv_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_10": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_o_3_histology": { - "items": { - "type": "string" - }, - "type": "array" - }, - "icd_o_3_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphatic_invasion": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphnodes_examined": { - "items": { - "type": "string" - }, - "type": "array" - }, - "lymphovascular_invasion_present": { - "items": { - "type": "string" - }, - "type": "array" - }, - "menopause_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "mononucleotide_and_dinucleotide_marker_panel_analysis_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "neoplasm_histologic_grade": { - "items": { - "type": "string" - }, - "type": "array" - }, - "new_tumor_event_after_initial_treatment": { - "items": { - "type": "string" - }, - "type": "array" - }, - "number_of_lymphnodes_examined": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_of_lymphnodes_examined_gte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_examined_lte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_of_lymphnodes_positive_by_he_gte": { - "format": "int32", - "type": "integer" - }, - "number_of_lymphnodes_positive_by_he_lte": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "number_pack_years_smoked_gte": { - "format": "int32", - "type": "integer" - }, - "number_pack_years_smoked_lte": { - "format": "int32", - "type": "integer" - }, - "other_dx": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_anatomic_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_histological_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "other_malignancy_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_M": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_N": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_T": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pathologic_stage": { - "items": { - "type": "string" - }, - "type": "array" - }, - "person_neoplasm_cancer_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "pregnancies": { - "items": { - "type": "string" - }, - "type": "array" - }, - "primary_neoplasm_melanoma_dx": { - "items": { - "type": "string" - }, - "type": "array" - }, - "primary_therapy_outcome_success": { - "items": { - "type": "string" - }, - "type": "array" - }, - "psa_value": { - "items": { - "format": "double", - "type": "number" - }, - "type": "array" - }, - "psa_value_gte": { - "format": "double", - "type": "number" - }, - "psa_value_lte": { - "format": "double", - "type": "number" - }, - "race": { - "items": { - "type": "string" - }, - "type": "array" - }, - "residual_tumor": { - "items": { - "type": "string" - }, - "type": "array" - }, - "stopped_smoking_year": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "stopped_smoking_year_gte": { - "format": "int32", - "type": "integer" - }, - "stopped_smoking_year_lte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "summary_file_count_gte": { - "format": "int32", - "type": "integer" - }, - "summary_file_count_lte": { - "format": "int32", - "type": "integer" - }, - "tobacco_smoking_history": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tss_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_tissue_site": { - "items": { - "type": "string" - }, - "type": "array" - }, - "tumor_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "venous_invasion": { - "items": { - "type": "string" - }, - "type": "array" - }, - "vital_status": { - "items": { - "type": "string" - }, - "type": "array" - }, - "weight": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "weight_gte": { - "format": "int32", - "type": "integer" - }, - "weight_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_diagnosis_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_diagnosis_lte": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset": { - "items": { - "format": "int32", - "type": "integer" - }, - "type": "array" - }, - "year_of_tobacco_smoking_onset_gte": { - "format": "int32", - "type": "integer" - }, - "year_of_tobacco_smoking_onset_lte": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesCommonMetadataItem": { - "properties": { - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesCommonMetadataRangesItem": { - "properties": { - "disease_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "endpoint_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "program_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "project_short_name": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "archive_file_name": { - "type": "string" - }, - "archive_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_submitter_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataItem": { - "properties": { - "access": { - "type": "string" - }, - "aliquot_barcode": { - "type": "string" - }, - "aliquot_gdc_id": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "archive_file_name": { - "type": "string" - }, - "archive_submitter_id": { - "type": "string" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "center_code": { - "type": "string" - }, - "center_name": { - "type": "string" - }, - "center_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_state": { - "type": "string" - }, - "file_uploaded": { - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - }, - "species": { - "type": "string" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataRangesItem": { - "properties": { - "access": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "aliquot_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "analysis_workflow_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "archive_submitter_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "case_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_code": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "center_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_category": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_format": { - "items": { - "type": "string" - }, - "type": "array" - }, - "data_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "experimental_strategy": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_state": { - "items": { - "type": "string" - }, - "type": "array" - }, - "file_uploaded": { - "items": { - "type": "string" - }, - "type": "array" - }, - "index_file_name": { - "items": { - "type": "string" - }, - "type": "array" - }, - "platform": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_barcode": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_gdc_id": { - "items": { - "type": "string" - }, - "type": "array" - }, - "sample_type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "species": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesMetadataItem": { - "properties": { - "Biospecimen": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataItem" - }, - "Clinical": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesClinicalMetadataItem" - }, - "Common": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesCommonMetadataItem" - }, - "Data_HG19": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataItem" - }, - "Data_HG38": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAMessageClassesMetadataRangesItem": { - "properties": { - "Biospecimen": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesBiospecimenMetadataRangesItem" - }, - "Clinical": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesClinicalMetadataRangesItem" - }, - "Common": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesCommonMetadataRangesItem" - }, - "Data_HG19": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesDataHG19MetadataRangesItem" - }, - "Data_HG38": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesDataHG38MetadataRangesItem" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGAPatientsGetCaseDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "clinical_data": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesMetadataItem" - }, - "samples": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "type": "object" - }, - "Api3IsbCgcApiTCGASamplesGetSampleDetails": { - "properties": { - "aliquots": { - "items": { - "type": "string" - }, - "type": "array" - }, - "biospecimen_data": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesMetadataItem" - }, - "case_barcode": { - "type": "string" - }, - "case_gdc_id": { - "type": "string" - }, - "data_details": { - "items": { - "$ref": "#/components/schemas/Api3SamplesGetHelperDataDetails" - }, - "type": "array" - }, - "data_details_count": { - "format": "int32", - "type": "integer" - } - }, - "type": "object" - }, - "Api3SamplesGetHelperDataDetails": { - "properties": { - "access": { - "type": "string" - }, - "analysis_workflow_type": { - "type": "string" - }, - "data_category": { - "type": "string" - }, - "data_format": { - "type": "string" - }, - "data_type": { - "type": "string" - }, - "disease_code": { - "type": "string" - }, - "endpoint_type": { - "type": "string" - }, - "experimental_strategy": { - "type": "string" - }, - "file_gdc_id": { - "type": "string" - }, - "file_name": { - "type": "string" - }, - "file_name_key": { - "type": "string" - }, - "file_size": { - "format": "int64", - "type": "string" - }, - "index_file_name": { - "type": "string" - }, - "platform": { - "type": "string" - }, - "program_name": { - "type": "string" - }, - "project_short_name": { - "type": "string" - }, - "sample_barcode": { - "type": "string" - }, - "sample_gdc_id": { - "type": "string" - }, - "sample_type": { - "type": "string" - } - }, - "type": "object" - }, - "Api3UsersGetCommonUserGetAPIReturnJSON": { - "properties": { - "dbGaP_allowed": { - "type": "boolean" - }, - "dbGaP_authorized": { - "type": "boolean" - }, - "message": { - "type": "string" - } - }, - "type": "object" - } - }, - "requestBodies": { - "Api3IsbCgcApiTCGAMessageClassesMetadataRangesItem": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Api3IsbCgcApiTCGAMessageClassesMetadataRangesItem" - } - } - } - } - }, - "securitySchemes": { - "google_id_token": { - "type": "oauth2", - "x-google-issuer": "https://accounts.google.com", - "x-google-jwks_uri": "https://www.googleapis.com/oauth2/v3/certs", - "flows": { - "implicit": { - "authorizationUrl": "/", - "scopes": {} - } - } - } - } - } -} \ No newline at end of file From 2ea70686f16d759351d4e87704f75cb899826e43 Mon Sep 17 00:00:00 2001 From: s-paquett Date: Fri, 5 Apr 2019 16:03:25 -0700 Subject: [PATCH 07/17] -> Aliquots were accidentally removed last time; until they're back, don't query for them. --- api_3/patients_get_helper.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/api_3/patients_get_helper.py b/api_3/patients_get_helper.py index f9f5186b..ed7712ab 100755 --- a/api_3/patients_get_helper.py +++ b/api_3/patients_get_helper.py @@ -115,8 +115,9 @@ def get(self, request, CaseDetails, MetadataItem, program): sample_list = [row['sample_barcode'] for row in cursor.fetchall()] # get list of aliquots - cursor.execute(aliquot_query_str, (query_tuple * len(genomic_builds))) - aliquot_list = [row['aliquot_barcode'] for row in cursor.fetchall()] + # cursor.execute(aliquot_query_str, (query_tuple * len(genomic_builds))) + # aliquot_list = [row['aliquot_barcode'] for row in cursor.fetchall()] + aliquot_list = None return CaseDetails(clinical_data=clinical_data_item, samples=sample_list, aliquots=aliquot_list if aliquot_list else []) except (IndexError, TypeError), e: @@ -180,8 +181,9 @@ def get_list(self, request, CaseSetDetails, CaseDetails, MetadataItem, program): sample_list = [sample_row['sample_barcode'] for sample_row in cursor.fetchall()] # get list of aliquots - cursor.execute(aliquot_query_str, ((row['case_barcode'],) * len(genomic_builds))) - aliquot_list = [aliquot_row['aliquot_barcode'] for aliquot_row in cursor.fetchall()] + # cursor.execute(aliquot_query_str, ((row['case_barcode'],) * len(genomic_builds))) + # aliquot_list = [aliquot_row['aliquot_barcode'] for aliquot_row in cursor.fetchall()] + aliquot_list = None case_details.append( CaseDetails( From 4e4ce58fb76253f7f8bf171a8860bc0ae0871d5b Mon Sep 17 00:00:00 2001 From: s-paquett Date: Mon, 8 Apr 2019 11:09:08 -0700 Subject: [PATCH 08/17] -> Final aliquot removal --- api_3/samples_get_helper.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/api_3/samples_get_helper.py b/api_3/samples_get_helper.py index 6a74d79c..1317f89b 100755 --- a/api_3/samples_get_helper.py +++ b/api_3/samples_get_helper.py @@ -196,8 +196,8 @@ def get(self, request, program, SampleDetails, MetadataItem): biospecimen_data_item = MetadataItem(**constructor_dict) # get list of aliquots - cursor.execute(aliquot_query_str, extra_query_tuple) - aliquot_list = [row['aliquot_barcode'] for row in cursor.fetchall()] + # cursor.execute(aliquot_query_str, extra_query_tuple) + # aliquot_list = [row['aliquot_barcode'] for row in cursor.fetchall()] # get case barcode (superfluous?) cursor.execute(case_query_str, query_tuple) @@ -294,12 +294,12 @@ def get_list(self, request, program, SampleSetDetails, SampleDetails, MetadataIt sample_data[row['sample_barcode']]['case_gdc_id'] = row['case_gdc_id'] # get list of aliquots - cursor.execute(aliquot_query_str, extra_query_tuple) - rows = cursor.fetchall() - for row in rows: - if 'aliquots' not in sample_data[row['sample_barcode']]: - sample_data[row['sample_barcode']]['aliquots'] = [] - sample_data[row['sample_barcode']]['aliquots'].append(row['aliquot_barcode']) + # cursor.execute(aliquot_query_str, extra_query_tuple) + # rows = cursor.fetchall() + # for row in rows: + # if 'aliquots' not in sample_data[row['sample_barcode']]: + # sample_data[row['sample_barcode']]['aliquots'] = [] + # sample_data[row['sample_barcode']]['aliquots'].append(row['aliquot_barcode']) # prepare to build list of data details messages cursor.execute(data_query_str, extra_query_tuple) From fade09d5a5f7423f5e6f85b8025fc43e1f7cd8de Mon Sep 17 00:00:00 2001 From: s-paquett Date: Mon, 8 Apr 2019 12:45:32 -0700 Subject: [PATCH 09/17] -> More removals of missing fields --- api_3/isb_cgc_api_CCLE/message_classes.py | 23 ++------ api_3/isb_cgc_api_TARGET/message_classes.py | 52 +++-------------- api_3/isb_cgc_api_TCGA/message_classes.py | 62 +++------------------ api_3/samples_get_helper.py | 3 - 4 files changed, 21 insertions(+), 119 deletions(-) diff --git a/api_3/isb_cgc_api_CCLE/message_classes.py b/api_3/isb_cgc_api_CCLE/message_classes.py index f73dbd6d..1c84757a 100755 --- a/api_3/isb_cgc_api_CCLE/message_classes.py +++ b/api_3/isb_cgc_api_CCLE/message_classes.py @@ -51,33 +51,21 @@ class BiospecimenMetadataItem(messages.Message): class Data_HG19MetadataRangesItem(messages.Message): access = messages.StringField(1, repeated=True) - aliquot_barcode = messages.StringField(2, repeated=True) - aliquot_gdc_id = messages.StringField(3, repeated=True) - analysis_workflow_type = messages.StringField(4, repeated=True) case_barcode = messages.StringField(5, repeated=True) case_gdc_id = messages.StringField(6, repeated=True) - center_code = messages.StringField(7, repeated=True) - center_name = messages.StringField(8, repeated=True) - center_type = messages.StringField(9, repeated=True) data_category = messages.StringField(10, repeated=True) data_format = messages.StringField(11, repeated=True) data_type = messages.StringField(12, repeated=True) experimental_strategy = messages.StringField(13, repeated=True) - file_name = messages.StringField(14, repeated=True) - file_state = messages.StringField(15, repeated=True) - file_uploaded = messages.StringField(16, repeated=True) - index_file_name = messages.StringField(17, repeated=True) + file_name_key = messages.StringField(14, repeated=True) + index_file_name_key = messages.StringField(17, repeated=True) platform = messages.StringField(18, repeated=True) sample_barcode = messages.StringField(19, repeated=True) sample_gdc_id = messages.StringField(20, repeated=True) sample_type = messages.StringField(21, repeated=True) - species = messages.StringField(22, repeated=True) class Data_HG19MetadataItem(messages.Message): access = messages.StringField(1) - aliquot_barcode = messages.StringField(2) - aliquot_gdc_id = messages.StringField(3) - analysis_workflow_type = messages.StringField(4) case_barcode = messages.StringField(5) case_gdc_id = messages.StringField(6) center_code = messages.StringField(7) @@ -87,15 +75,12 @@ class Data_HG19MetadataItem(messages.Message): data_format = messages.StringField(11) data_type = messages.StringField(12) experimental_strategy = messages.StringField(13) - file_name = messages.StringField(14) - file_state = messages.StringField(15) - file_uploaded = messages.StringField(16) - index_file_name = messages.StringField(17) + file_name_key = messages.StringField(14) + index_file_name_key = messages.StringField(17) platform = messages.StringField(18) sample_barcode = messages.StringField(19) sample_gdc_id = messages.StringField(20) sample_type = messages.StringField(21) - species = messages.StringField(22) class MetadataRangesItem(messages.Message): Common = messages.MessageField(CommonMetadataRangesItem, 1) diff --git a/api_3/isb_cgc_api_TARGET/message_classes.py b/api_3/isb_cgc_api_TARGET/message_classes.py index 9c895379..8a113621 100755 --- a/api_3/isb_cgc_api_TARGET/message_classes.py +++ b/api_3/isb_cgc_api_TARGET/message_classes.py @@ -100,99 +100,63 @@ class BiospecimenMetadataItem(messages.Message): class Data_HG19MetadataRangesItem(messages.Message): access = messages.StringField(1, repeated=True) - aliquot_barcode = messages.StringField(2, repeated=True) - aliquot_gdc_id = messages.StringField(3, repeated=True) - analysis_workflow_type = messages.StringField(4, repeated=True) case_barcode = messages.StringField(5, repeated=True) case_gdc_id = messages.StringField(6, repeated=True) - center_code = messages.StringField(7, repeated=True) - center_name = messages.StringField(8, repeated=True) - center_type = messages.StringField(9, repeated=True) data_category = messages.StringField(10, repeated=True) data_format = messages.StringField(11, repeated=True) data_type = messages.StringField(12, repeated=True) experimental_strategy = messages.StringField(13, repeated=True) - file_name = messages.StringField(14, repeated=True) - file_state = messages.StringField(15, repeated=True) - file_uploaded = messages.StringField(16, repeated=True) - index_file_name = messages.StringField(17, repeated=True) + file_name_key = messages.StringField(14, repeated=True) + index_file_name_key = messages.StringField(17, repeated=True) platform = messages.StringField(18, repeated=True) sample_barcode = messages.StringField(19, repeated=True) sample_gdc_id = messages.StringField(20, repeated=True) sample_type = messages.StringField(21, repeated=True) - species = messages.StringField(22, repeated=True) class Data_HG19MetadataItem(messages.Message): access = messages.StringField(1) - aliquot_barcode = messages.StringField(2) - aliquot_gdc_id = messages.StringField(3) - analysis_workflow_type = messages.StringField(4) case_barcode = messages.StringField(5) case_gdc_id = messages.StringField(6) - center_code = messages.StringField(7) - center_name = messages.StringField(8) - center_type = messages.StringField(9) data_category = messages.StringField(10) data_format = messages.StringField(11) data_type = messages.StringField(12) experimental_strategy = messages.StringField(13) - file_name = messages.StringField(14) - file_state = messages.StringField(15) - file_uploaded = messages.StringField(16) - index_file_name = messages.StringField(17) + file_name_key = messages.StringField(14) + index_file_name_key = messages.StringField(17) platform = messages.StringField(18) sample_barcode = messages.StringField(19) sample_gdc_id = messages.StringField(20) sample_type = messages.StringField(21) - species = messages.StringField(22) class Data_HG38MetadataRangesItem(messages.Message): access = messages.StringField(1, repeated=True) - aliquot_barcode = messages.StringField(2, repeated=True) - aliquot_gdc_id = messages.StringField(3, repeated=True) - analysis_workflow_type = messages.StringField(4, repeated=True) case_barcode = messages.StringField(5, repeated=True) case_gdc_id = messages.StringField(6, repeated=True) - center_code = messages.StringField(7, repeated=True) - center_name = messages.StringField(8, repeated=True) - center_type = messages.StringField(9, repeated=True) data_category = messages.StringField(10, repeated=True) data_format = messages.StringField(11, repeated=True) data_type = messages.StringField(12, repeated=True) experimental_strategy = messages.StringField(13, repeated=True) - file_name = messages.StringField(14, repeated=True) - file_state = messages.StringField(15, repeated=True) - file_uploaded = messages.StringField(16, repeated=True) - index_file_name = messages.StringField(17, repeated=True) + file_name_key = messages.StringField(14, repeated=True) + index_file_name_key = messages.StringField(17, repeated=True) platform = messages.StringField(18, repeated=True) sample_barcode = messages.StringField(19, repeated=True) sample_gdc_id = messages.StringField(20, repeated=True) sample_type = messages.StringField(21, repeated=True) - species = messages.StringField(22, repeated=True) class Data_HG38MetadataItem(messages.Message): access = messages.StringField(1) - aliquot_barcode = messages.StringField(2) - aliquot_gdc_id = messages.StringField(3) - analysis_workflow_type = messages.StringField(4) case_barcode = messages.StringField(5) case_gdc_id = messages.StringField(6) - center_code = messages.StringField(7) - center_name = messages.StringField(8) - center_type = messages.StringField(9) data_category = messages.StringField(10) data_format = messages.StringField(11) data_type = messages.StringField(12) experimental_strategy = messages.StringField(13) - file_name = messages.StringField(14) - file_state = messages.StringField(15) - file_uploaded = messages.StringField(16) - index_file_name = messages.StringField(17) + file_name_key = messages.StringField(14) + index_file_name_key = messages.StringField(17) platform = messages.StringField(18) sample_barcode = messages.StringField(19) sample_gdc_id = messages.StringField(20) sample_type = messages.StringField(21) - species = messages.StringField(22) class MetadataRangesItem(messages.Message): Common = messages.MessageField(CommonMetadataRangesItem, 1) diff --git a/api_3/isb_cgc_api_TCGA/message_classes.py b/api_3/isb_cgc_api_TCGA/message_classes.py index f5daa31c..e3d74b0e 100644 --- a/api_3/isb_cgc_api_TCGA/message_classes.py +++ b/api_3/isb_cgc_api_TCGA/message_classes.py @@ -384,107 +384,63 @@ class BiospecimenMetadataItem(messages.Message): class Data_HG19MetadataRangesItem(messages.Message): access = messages.StringField(1, repeated=True) - aliquot_barcode = messages.StringField(2, repeated=True) - aliquot_gdc_id = messages.StringField(3, repeated=True) - analysis_workflow_type = messages.StringField(4, repeated=True) - archive_file_name = messages.StringField(5, repeated=True) - archive_submitter_id = messages.StringField(6, repeated=True) case_barcode = messages.StringField(7, repeated=True) case_gdc_id = messages.StringField(8, repeated=True) - center_code = messages.StringField(9, repeated=True) - center_name = messages.StringField(10, repeated=True) - center_type = messages.StringField(11, repeated=True) data_category = messages.StringField(12, repeated=True) data_format = messages.StringField(13, repeated=True) data_type = messages.StringField(14, repeated=True) experimental_strategy = messages.StringField(15, repeated=True) - file_name = messages.StringField(16, repeated=True) - file_state = messages.StringField(17, repeated=True) - file_uploaded = messages.StringField(18, repeated=True) - index_file_name = messages.StringField(19, repeated=True) + index_file_name_key = messages.StringField(19, repeated=True) + file_name_key = messages.StringField(18, repeated=True) platform = messages.StringField(20, repeated=True) sample_barcode = messages.StringField(21, repeated=True) sample_gdc_id = messages.StringField(22, repeated=True) sample_type = messages.StringField(23, repeated=True) - species = messages.StringField(24, repeated=True) class Data_HG19MetadataItem(messages.Message): access = messages.StringField(1) - aliquot_barcode = messages.StringField(2) - aliquot_gdc_id = messages.StringField(3) - analysis_workflow_type = messages.StringField(4) - archive_file_name = messages.StringField(5) - archive_submitter_id = messages.StringField(6) case_barcode = messages.StringField(7) case_gdc_id = messages.StringField(8) - center_code = messages.StringField(9) - center_name = messages.StringField(10) - center_type = messages.StringField(11) data_category = messages.StringField(12) data_format = messages.StringField(13) data_type = messages.StringField(14) - experimental_strategy = messages.StringField(15) - file_name = messages.StringField(16) - file_state = messages.StringField(17) - file_uploaded = messages.StringField(18) - index_file_name = messages.StringField(19) + experimental_strategy = messages.StringField(15) + index_file_name_key = messages.StringField(19) + file_name_key = messages.StringField(18) platform = messages.StringField(20) sample_barcode = messages.StringField(21) sample_gdc_id = messages.StringField(22) sample_type = messages.StringField(23) - species = messages.StringField(24) class Data_HG38MetadataRangesItem(messages.Message): access = messages.StringField(1, repeated=True) - aliquot_barcode = messages.StringField(2, repeated=True) - aliquot_gdc_id = messages.StringField(3, repeated=True) - analysis_workflow_type = messages.StringField(4, repeated=True) - archive_file_name = messages.StringField(5, repeated=True) - archive_submitter_id = messages.StringField(6, repeated=True) case_barcode = messages.StringField(7, repeated=True) case_gdc_id = messages.StringField(8, repeated=True) - center_code = messages.StringField(9, repeated=True) - center_name = messages.StringField(10, repeated=True) - center_type = messages.StringField(11, repeated=True) data_category = messages.StringField(12, repeated=True) data_format = messages.StringField(13, repeated=True) data_type = messages.StringField(14, repeated=True) experimental_strategy = messages.StringField(15, repeated=True) - file_name = messages.StringField(16, repeated=True) - file_state = messages.StringField(17, repeated=True) - file_uploaded = messages.StringField(18, repeated=True) - index_file_name = messages.StringField(19, repeated=True) + index_file_name_key = messages.StringField(19, repeated=True) + file_name_key = messages.StringField(18, repeated=True) platform = messages.StringField(20, repeated=True) sample_barcode = messages.StringField(21, repeated=True) sample_gdc_id = messages.StringField(22, repeated=True) sample_type = messages.StringField(23, repeated=True) - species = messages.StringField(24, repeated=True) class Data_HG38MetadataItem(messages.Message): access = messages.StringField(1) - aliquot_barcode = messages.StringField(2) - aliquot_gdc_id = messages.StringField(3) - analysis_workflow_type = messages.StringField(4) - archive_file_name = messages.StringField(5) - archive_submitter_id = messages.StringField(6) case_barcode = messages.StringField(7) case_gdc_id = messages.StringField(8) - center_code = messages.StringField(9) - center_name = messages.StringField(10) - center_type = messages.StringField(11) data_category = messages.StringField(12) data_format = messages.StringField(13) data_type = messages.StringField(14) experimental_strategy = messages.StringField(15) - file_name = messages.StringField(16) - file_state = messages.StringField(17) - file_uploaded = messages.StringField(18) - index_file_name = messages.StringField(19) + index_file_name_key = messages.StringField(19) + file_name_key = messages.StringField(18) platform = messages.StringField(20) sample_barcode = messages.StringField(21) sample_gdc_id = messages.StringField(22) sample_type = messages.StringField(23) - species = messages.StringField(24) class MetadataRangesItem(messages.Message): Common = messages.MessageField(CommonMetadataRangesItem, 1) diff --git a/api_3/samples_get_helper.py b/api_3/samples_get_helper.py index 1317f89b..5ba23d31 100755 --- a/api_3/samples_get_helper.py +++ b/api_3/samples_get_helper.py @@ -103,7 +103,6 @@ def build_case_query(self, program, count=1): class DataDetails(messages.Message): file_gdc_id = messages.StringField(1) - file_name = messages.StringField(2) file_name_key = messages.StringField(3) file_size = messages.IntegerField(4, variant=messages.Variant.INT64) sample_gdc_id = messages.StringField(5) @@ -118,8 +117,6 @@ class DataDetails(messages.Message): data_format = messages.StringField(15) access = messages.StringField(16) platform = messages.StringField(17) - endpoint_type = messages.StringField(18) - analysis_workflow_type = messages.StringField(19) index_file_name = messages.StringField(20) From 1a3037f67050b0aa10725c79b50a57a85a1c84b3 Mon Sep 17 00:00:00 2001 From: s-paquett Date: Mon, 8 Apr 2019 12:48:34 -0700 Subject: [PATCH 10/17] -> More removals of missing fields --- api_3/samples_get_helper.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/api_3/samples_get_helper.py b/api_3/samples_get_helper.py index 5ba23d31..da0134b7 100755 --- a/api_3/samples_get_helper.py +++ b/api_3/samples_get_helper.py @@ -117,7 +117,7 @@ class DataDetails(messages.Message): data_format = messages.StringField(15) access = messages.StringField(16) platform = messages.StringField(17) - index_file_name = messages.StringField(20) + index_file_name_key = messages.StringField(20) class SampleGetListFilters(messages.Message): From e231e43d9a7b146ef211369daec2b6aaf821102e Mon Sep 17 00:00:00 2001 From: s-paquett Date: Mon, 8 Apr 2019 14:05:51 -0700 Subject: [PATCH 11/17] -> sample_type no longer in data tables... --- api_3/isb_cgc_api_CCLE/message_classes.py | 2 -- api_3/isb_cgc_api_TARGET/message_classes.py | 4 ---- api_3/isb_cgc_api_TCGA/message_classes.py | 5 ----- api_3/samples_get_helper.py | 2 -- 4 files changed, 13 deletions(-) diff --git a/api_3/isb_cgc_api_CCLE/message_classes.py b/api_3/isb_cgc_api_CCLE/message_classes.py index 1c84757a..20ff48e0 100755 --- a/api_3/isb_cgc_api_CCLE/message_classes.py +++ b/api_3/isb_cgc_api_CCLE/message_classes.py @@ -62,7 +62,6 @@ class Data_HG19MetadataRangesItem(messages.Message): platform = messages.StringField(18, repeated=True) sample_barcode = messages.StringField(19, repeated=True) sample_gdc_id = messages.StringField(20, repeated=True) - sample_type = messages.StringField(21, repeated=True) class Data_HG19MetadataItem(messages.Message): access = messages.StringField(1) @@ -80,7 +79,6 @@ class Data_HG19MetadataItem(messages.Message): platform = messages.StringField(18) sample_barcode = messages.StringField(19) sample_gdc_id = messages.StringField(20) - sample_type = messages.StringField(21) class MetadataRangesItem(messages.Message): Common = messages.MessageField(CommonMetadataRangesItem, 1) diff --git a/api_3/isb_cgc_api_TARGET/message_classes.py b/api_3/isb_cgc_api_TARGET/message_classes.py index 8a113621..fd2a9dc0 100755 --- a/api_3/isb_cgc_api_TARGET/message_classes.py +++ b/api_3/isb_cgc_api_TARGET/message_classes.py @@ -111,7 +111,6 @@ class Data_HG19MetadataRangesItem(messages.Message): platform = messages.StringField(18, repeated=True) sample_barcode = messages.StringField(19, repeated=True) sample_gdc_id = messages.StringField(20, repeated=True) - sample_type = messages.StringField(21, repeated=True) class Data_HG19MetadataItem(messages.Message): access = messages.StringField(1) @@ -126,7 +125,6 @@ class Data_HG19MetadataItem(messages.Message): platform = messages.StringField(18) sample_barcode = messages.StringField(19) sample_gdc_id = messages.StringField(20) - sample_type = messages.StringField(21) class Data_HG38MetadataRangesItem(messages.Message): access = messages.StringField(1, repeated=True) @@ -141,7 +139,6 @@ class Data_HG38MetadataRangesItem(messages.Message): platform = messages.StringField(18, repeated=True) sample_barcode = messages.StringField(19, repeated=True) sample_gdc_id = messages.StringField(20, repeated=True) - sample_type = messages.StringField(21, repeated=True) class Data_HG38MetadataItem(messages.Message): access = messages.StringField(1) @@ -156,7 +153,6 @@ class Data_HG38MetadataItem(messages.Message): platform = messages.StringField(18) sample_barcode = messages.StringField(19) sample_gdc_id = messages.StringField(20) - sample_type = messages.StringField(21) class MetadataRangesItem(messages.Message): Common = messages.MessageField(CommonMetadataRangesItem, 1) diff --git a/api_3/isb_cgc_api_TCGA/message_classes.py b/api_3/isb_cgc_api_TCGA/message_classes.py index e3d74b0e..fd030c77 100644 --- a/api_3/isb_cgc_api_TCGA/message_classes.py +++ b/api_3/isb_cgc_api_TCGA/message_classes.py @@ -395,7 +395,6 @@ class Data_HG19MetadataRangesItem(messages.Message): platform = messages.StringField(20, repeated=True) sample_barcode = messages.StringField(21, repeated=True) sample_gdc_id = messages.StringField(22, repeated=True) - sample_type = messages.StringField(23, repeated=True) class Data_HG19MetadataItem(messages.Message): access = messages.StringField(1) @@ -410,7 +409,6 @@ class Data_HG19MetadataItem(messages.Message): platform = messages.StringField(20) sample_barcode = messages.StringField(21) sample_gdc_id = messages.StringField(22) - sample_type = messages.StringField(23) class Data_HG38MetadataRangesItem(messages.Message): access = messages.StringField(1, repeated=True) @@ -425,7 +423,6 @@ class Data_HG38MetadataRangesItem(messages.Message): platform = messages.StringField(20, repeated=True) sample_barcode = messages.StringField(21, repeated=True) sample_gdc_id = messages.StringField(22, repeated=True) - sample_type = messages.StringField(23, repeated=True) class Data_HG38MetadataItem(messages.Message): access = messages.StringField(1) @@ -440,7 +437,6 @@ class Data_HG38MetadataItem(messages.Message): platform = messages.StringField(20) sample_barcode = messages.StringField(21) sample_gdc_id = messages.StringField(22) - sample_type = messages.StringField(23) class MetadataRangesItem(messages.Message): Common = messages.MessageField(CommonMetadataRangesItem, 1) @@ -455,4 +451,3 @@ class MetadataItem(messages.Message): Biospecimen = messages.MessageField(BiospecimenMetadataItem, 3) Data_HG19 = messages.MessageField(Data_HG19MetadataItem, 4) Data_HG38 = messages.MessageField(Data_HG38MetadataItem, 5) - diff --git a/api_3/samples_get_helper.py b/api_3/samples_get_helper.py index da0134b7..e4f949d0 100755 --- a/api_3/samples_get_helper.py +++ b/api_3/samples_get_helper.py @@ -107,7 +107,6 @@ class DataDetails(messages.Message): file_size = messages.IntegerField(4, variant=messages.Variant.INT64) sample_gdc_id = messages.StringField(5) sample_barcode = messages.StringField(6) - sample_type = messages.StringField(7) project_short_name = messages.StringField(8) disease_code = messages.StringField(9) program_name = messages.StringField(11) @@ -129,7 +128,6 @@ class SampleGetListFilters(messages.Message): data_type = messages.StringField(6, repeated=True) data_format = messages.StringField(7, repeated=True) project_short_name = messages.StringField(8, repeated=True) - analysis_workflow_type = messages.StringField(9, repeated=True) class SamplesGetAPI(remote.Service): From b6bea0ef80ab399a5e2813498e1ea1915b164867 Mon Sep 17 00:00:00 2001 From: s-paquett Date: Tue, 9 Apr 2019 12:56:15 -0700 Subject: [PATCH 12/17] -> More aliquot shenanigans --- api/isb_cgc_api/patients_get.py | 5 +++-- api/isb_cgc_api/samples_get.py | 7 ++++--- api_3/samples_get_helper.py | 1 + 3 files changed, 8 insertions(+), 5 deletions(-) diff --git a/api/isb_cgc_api/patients_get.py b/api/isb_cgc_api/patients_get.py index b618de22..c2bc12b9 100644 --- a/api/isb_cgc_api/patients_get.py +++ b/api/isb_cgc_api/patients_get.py @@ -97,8 +97,9 @@ def get(self, request): sample_list = [row['sample_barcode'] for row in cursor.fetchall()] # get list of aliquots - cursor.execute(aliquot_query_str, query_tuple) - aliquot_list = [row['AliquotBarcode'] for row in cursor.fetchall()] + # cursor.execute(aliquot_query_str, query_tuple) + # aliquot_list = [row['AliquotBarcode'] for row in cursor.fetchall()] + aliquot_list = [] return PatientDetails(clinical_data=clinical_data_item, samples=sample_list, aliquots=aliquot_list) diff --git a/api/isb_cgc_api/samples_get.py b/api/isb_cgc_api/samples_get.py index d6e260c4..6b7a6619 100644 --- a/api/isb_cgc_api/samples_get.py +++ b/api/isb_cgc_api/samples_get.py @@ -167,9 +167,10 @@ def get(self, request): biospecimen_data_item = MetadataItem(**constructor_dict) # get list of aliquots - cursor.execute(aliquot_query_str, extra_query_tuple) - aliquot_list = [row['AliquotBarcode'] for row in cursor.fetchall()] - + # cursor.execute(aliquot_query_str, extra_query_tuple) + # aliquot_list = [row['AliquotBarcode'] for row in cursor.fetchall()] + aliquot_list = [] + # get patient barcode (superfluous?) cursor.execute(patient_query_str, query_tuple) row = cursor.fetchone() diff --git a/api_3/samples_get_helper.py b/api_3/samples_get_helper.py index e4f949d0..0ddc34ee 100755 --- a/api_3/samples_get_helper.py +++ b/api_3/samples_get_helper.py @@ -193,6 +193,7 @@ def get(self, request, program, SampleDetails, MetadataItem): # get list of aliquots # cursor.execute(aliquot_query_str, extra_query_tuple) # aliquot_list = [row['aliquot_barcode'] for row in cursor.fetchall()] + aliquot_list = [] # get case barcode (superfluous?) cursor.execute(case_query_str, query_tuple) From c94a26db87aa00788dfa9e69ea7a538ef9b7ea3d Mon Sep 17 00:00:00 2001 From: s-paquett Date: Thu, 18 Apr 2019 14:33:32 -0700 Subject: [PATCH 13/17] -> Another fix attempt --- api_3/isb_cgc_api_CCLE/message_classes.py | 4 ++-- api_3/isb_cgc_api_TARGET/message_classes.py | 8 ++++---- api_3/isb_cgc_api_TCGA/message_classes.py | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/api_3/isb_cgc_api_CCLE/message_classes.py b/api_3/isb_cgc_api_CCLE/message_classes.py index 20ff48e0..c17da327 100755 --- a/api_3/isb_cgc_api_CCLE/message_classes.py +++ b/api_3/isb_cgc_api_CCLE/message_classes.py @@ -84,11 +84,11 @@ class MetadataRangesItem(messages.Message): Common = messages.MessageField(CommonMetadataRangesItem, 1) Clinical = messages.MessageField(ClinicalMetadataRangesItem, 2) Biospecimen = messages.MessageField(BiospecimenMetadataRangesItem, 3) - Data_HG19 = messages.MessageField(Data_HG19MetadataRangesItem, 4) + data_HG19_r14 = messages.MessageField(Data_HG19MetadataRangesItem, 4) class MetadataItem(messages.Message): Common = messages.MessageField(CommonMetadataItem, 1) Clinical = messages.MessageField(ClinicalMetadataItem, 2) Biospecimen = messages.MessageField(BiospecimenMetadataItem, 3) - Data_HG19 = messages.MessageField(Data_HG19MetadataItem, 4) + data_HG19_r14 = messages.MessageField(Data_HG19MetadataItem, 4) diff --git a/api_3/isb_cgc_api_TARGET/message_classes.py b/api_3/isb_cgc_api_TARGET/message_classes.py index fd2a9dc0..627398b1 100755 --- a/api_3/isb_cgc_api_TARGET/message_classes.py +++ b/api_3/isb_cgc_api_TARGET/message_classes.py @@ -158,13 +158,13 @@ class MetadataRangesItem(messages.Message): Common = messages.MessageField(CommonMetadataRangesItem, 1) Clinical = messages.MessageField(ClinicalMetadataRangesItem, 2) Biospecimen = messages.MessageField(BiospecimenMetadataRangesItem, 3) - Data_HG19 = messages.MessageField(Data_HG19MetadataRangesItem, 4) - Data_HG38 = messages.MessageField(Data_HG38MetadataRangesItem, 5) + data_HG19_r14 = messages.MessageField(Data_HG19MetadataRangesItem, 4) + data_HG38_r14 = messages.MessageField(Data_HG38MetadataRangesItem, 5) class MetadataItem(messages.Message): Common = messages.MessageField(CommonMetadataItem, 1) Clinical = messages.MessageField(ClinicalMetadataItem, 2) Biospecimen = messages.MessageField(BiospecimenMetadataItem, 3) - Data_HG19 = messages.MessageField(Data_HG19MetadataItem, 4) - Data_HG38 = messages.MessageField(Data_HG38MetadataItem, 5) + data_HG19_r14 = messages.MessageField(Data_HG19MetadataItem, 4) + data_HG38_r14 = messages.MessageField(Data_HG38MetadataItem, 5) diff --git a/api_3/isb_cgc_api_TCGA/message_classes.py b/api_3/isb_cgc_api_TCGA/message_classes.py index fd030c77..258fee81 100644 --- a/api_3/isb_cgc_api_TCGA/message_classes.py +++ b/api_3/isb_cgc_api_TCGA/message_classes.py @@ -442,12 +442,12 @@ class MetadataRangesItem(messages.Message): Common = messages.MessageField(CommonMetadataRangesItem, 1) Clinical = messages.MessageField(ClinicalMetadataRangesItem, 2) Biospecimen = messages.MessageField(BiospecimenMetadataRangesItem, 3) - Data_HG19 = messages.MessageField(Data_HG19MetadataRangesItem, 4) - Data_HG38 = messages.MessageField(Data_HG38MetadataRangesItem, 5) + data_HG19_r14 = messages.MessageField(Data_HG19MetadataRangesItem, 4) + data_HG38_r14 = messages.MessageField(Data_HG38MetadataRangesItem, 5) class MetadataItem(messages.Message): Common = messages.MessageField(CommonMetadataItem, 1) Clinical = messages.MessageField(ClinicalMetadataItem, 2) Biospecimen = messages.MessageField(BiospecimenMetadataItem, 3) - Data_HG19 = messages.MessageField(Data_HG19MetadataItem, 4) - Data_HG38 = messages.MessageField(Data_HG38MetadataItem, 5) + data_HG19_r14 = messages.MessageField(Data_HG19MetadataItem, 4) + data_HG38_r14 = messages.MessageField(Data_HG38MetadataItem, 5) From a69310611c794050f17664af76b9378f4dd06d44 Mon Sep 17 00:00:00 2001 From: s-paquett Date: Mon, 22 Apr 2019 13:28:26 -0700 Subject: [PATCH 14/17] -> Force cache invalidation --- shell/install-deps.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shell/install-deps.sh b/shell/install-deps.sh index 76728625..fe44db50 100644 --- a/shell/install-deps.sh +++ b/shell/install-deps.sh @@ -51,7 +51,7 @@ if [ -z "${CI}" ] || [ ! -d "google_appengine" ]; then export PATH=$PATH:${HOME}/google_appengine/ echo "Google App Engine Installed" else - echo "Using restored cache for Google App Engine." + echo "Using restored cache for Google App Engine. " fi # Install Google Cloud SDK From b82760ed070779f5cf78e3a13d0864692acf9cfa Mon Sep 17 00:00:00 2001 From: s-paquett Date: Mon, 22 Apr 2019 13:48:46 -0700 Subject: [PATCH 15/17] -> Force cache invalidation --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 0e83fdf5..5a9bd058 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,4 +16,4 @@ django-finalware==1.0.0 django-allauth==0.35.0 jsonschema==2.6.0 enum34==1.1.6 -google-endpoints==4.0.0 \ No newline at end of file +google-endpoints==4.0.0 From 1aa938d2524a6f5828f6397c01ede901afe0f0ae Mon Sep 17 00:00:00 2001 From: s-paquett Date: Mon, 22 Apr 2019 14:51:29 -0700 Subject: [PATCH 16/17] -> Try newest Endpoints --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 5a9bd058..e1a91652 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,4 +16,4 @@ django-finalware==1.0.0 django-allauth==0.35.0 jsonschema==2.6.0 enum34==1.1.6 -google-endpoints==4.0.0 +google-endpoints==4.8.0 From d6a0d3907e50de47dc1322779379708f71008c6f Mon Sep 17 00:00:00 2001 From: s-paquett Date: Mon, 22 Apr 2019 14:53:28 -0700 Subject: [PATCH 17/17] -> Update six as well... --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index e1a91652..bacec27b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -8,7 +8,7 @@ pyasn1==0.4.1 requests-oauthlib==0.7.0 rsa==3.2 simplejson==3.8.1 -six==1.11.0 +six==1.12.0 uritemplate==3.0.0 GoogleAppEngineCloudStorageClient==1.9.22.1 django-dotenv==1.4.2