Merge pull request #267 from isb-cgc/prod-sp

Sprint 33
isb-cgc · Apr 29, 2019 · e205014 · e205014
2 parents 5e9711c + 01d6266
commit e205014
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Showing 34 changed files with 67 additions and 23,376 deletions.
diff --git a/api/isb_cgc_api/aliquots_annotations.py b/api/isb_cgc_api/aliquots_annotations.py
diff --git 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)
diff --git 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
diff --git 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)