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You should check out fs-extra (https://github.com/jprichardson/node-fs-extra) for any operations you were using wrench for. Thanks for all the usage over the years.", + "engines": { + "node": ">=0.1.97" + } + }, "node_modules/write-file-atomic": { "version": "3.0.3", "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-3.0.3.tgz", diff --git a/beaconplusWeb/node_modules/@next/swc-darwin-x64/README.md b/beaconplusWeb/node_modules/@next/swc-darwin-x64/README.md new file mode 100644 index 000000000..a0d630ddd --- /dev/null +++ b/beaconplusWeb/node_modules/@next/swc-darwin-x64/README.md @@ -0,0 +1,3 @@ +# `@next/swc-darwin-x64` + +This is the **x86_64-apple-darwin** binary for `@next/swc` diff --git a/beaconplusWeb/node_modules/@next/swc-darwin-x64/next-swc.darwin-x64.node b/beaconplusWeb/node_modules/@next/swc-darwin-x64/next-swc.darwin-x64.node new file mode 100644 index 000000000..37d7b41e2 Binary files /dev/null and b/beaconplusWeb/node_modules/@next/swc-darwin-x64/next-swc.darwin-x64.node differ diff --git a/beaconplusWeb/node_modules/@next/swc-darwin-x64/package.json b/beaconplusWeb/node_modules/@next/swc-darwin-x64/package.json new file mode 100644 index 000000000..6b706abbd --- /dev/null +++ b/beaconplusWeb/node_modules/@next/swc-darwin-x64/package.json @@ -0,0 +1,18 @@ +{ + "name": "@next/swc-darwin-x64", + "version": "12.3.4", + "os": [ + "darwin" + ], + "cpu": [ + "x64" + ], + "main": "next-swc.darwin-x64.node", + "files": [ + "next-swc.darwin-x64.node" + ], + "license": "MIT", + "engines": { + "node": ">= 10" + } +} \ No newline at end of file diff --git a/beaconplusWeb/package-lock.json b/beaconplusWeb/package-lock.json index 427d499a0..fa6954f87 100644 --- a/beaconplusWeb/package-lock.json +++ b/beaconplusWeb/package-lock.json @@ -14,6 +14,7 @@ "@tippyjs/react": "^4.2.0", "animate": "^1.0.0", "animate.css": "^4.1.1", + "build": "^0.1.4", "classnames": "^2.2.6", "env-cmd": "^10.1.0", "file-saver": "^2.0.5", @@ -471,9 +472,9 @@ } }, "node_modules/@babel/runtime": { - 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"dev": true, "dependencies": { "makeerror": "1.0.12" } @@ -14502,6 +14590,42 @@ "url": "https://github.com/sponsors/ljharb" } }, + "node_modules/winston": { + "version": "3.17.0", + "resolved": "https://registry.npmjs.org/winston/-/winston-3.17.0.tgz", + "integrity": "sha512-DLiFIXYC5fMPxaRg832S6F5mJYvePtmO5G9v9IgUFPhXm9/GkXarH/TUrBAVzhTCzAj9anE/+GjrgXp/54nOgw==", + "license": "MIT", + "dependencies": { + "@colors/colors": "^1.6.0", + "@dabh/diagnostics": "^2.0.2", + "async": "^3.2.3", + "is-stream": "^2.0.0", + "logform": "^2.7.0", + "one-time": "^1.0.0", + "readable-stream": "^3.4.0", + "safe-stable-stringify": "^2.3.1", + "stack-trace": "0.0.x", + "triple-beam": "^1.3.0", + "winston-transport": "^4.9.0" + }, + "engines": { + "node": ">= 12.0.0" + } + }, + "node_modules/winston-transport": { + "version": "4.9.0", + "resolved": "https://registry.npmjs.org/winston-transport/-/winston-transport-4.9.0.tgz", + "integrity": "sha512-8drMJ4rkgaPo1Me4zD/3WLfI/zPdA9o2IipKODunnGDcuqbHwjsbB79ylv04LCGGzU0xQ6vTznOMpQGaLhhm6A==", + "license": "MIT", + "dependencies": { + "logform": "^2.7.0", + "readable-stream": "^3.6.2", + "triple-beam": "^1.3.0" + }, + "engines": { + "node": ">= 12.0.0" + } + }, "node_modules/word-wrap": { "version": "1.2.5", "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.5.tgz", @@ -14564,6 +14688,15 @@ "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==", "dev": true }, + "node_modules/wrench": { + "version": "1.3.9", + "resolved": "https://registry.npmjs.org/wrench/-/wrench-1.3.9.tgz", + "integrity": "sha512-srTJQmLTP5YtW+F5zDuqjMEZqLLr/eJOZfDI5ibfPfRMeDh3oBUefAscuH0q5wBKE339ptH/S/0D18ZkfOfmKQ==", + "deprecated": "wrench.js is deprecated! You should check out fs-extra (https://github.com/jprichardson/node-fs-extra) for any operations you were using wrench for. Thanks for all the usage over the years.", + "engines": { + "node": ">=0.1.97" + } + }, "node_modules/write-file-atomic": { "version": "3.0.3", "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-3.0.3.tgz", @@ -14577,9 +14710,9 @@ } }, "node_modules/ws": { - "version": "7.5.10", - "resolved": "https://registry.npmjs.org/ws/-/ws-7.5.10.tgz", - "integrity": "sha512-+dbF1tHwZpXcbOJdVOkzLDxZP1ailvSxM6ZweXTegylPny803bFhA+vqBYw4s31NSAk4S2Qz+AKXK9a4wkdjcQ==", + "version": "7.5.9", + "resolved": "https://registry.npmjs.org/ws/-/ws-7.5.9.tgz", + "integrity": "sha512-F+P9Jil7UiSKSkppIiD94dN07AwvFixvLIj1Og1Rl9GGMuNipJnV9JzjD6XuqmAeiswGvUmNLjr5cFuXwNS77Q==", "dev": true, "engines": { "node": ">=8.3.0" diff --git a/beaconplusWeb/package.json b/beaconplusWeb/package.json index 22e03b32b..215c8fc10 100644 --- a/beaconplusWeb/package.json +++ b/beaconplusWeb/package.json @@ -20,6 +20,7 @@ "@tippyjs/react": "^4.2.0", "animate": "^1.0.0", "animate.css": "^4.1.1", + "build": "^0.1.4", "classnames": "^2.2.6", "env-cmd": "^10.1.0", "file-saver": "^2.0.5", diff --git a/bycon/config/variant_request_definitions.yaml b/bycon/config/variant_request_definitions.yaml index 091b159d1..2bcbbbbaa 100644 --- a/bycon/config/variant_request_definitions.yaml +++ b/bycon/config/variant_request_definitions.yaml @@ -17,11 +17,6 @@ request_pars: - mate_end - variant_min_length - variant_max_length - # - gene_id - # - aminoacid_change - # - genomic_allele_short_form - # - cyto_bands - # - variant_query_digests # BeaconPlus multi_request_pars: diff --git a/bycon/lib/beacon_response_generation.py b/bycon/lib/beacon_response_generation.py index feecb575a..7b829c5f5 100644 --- a/bycon/lib/beacon_response_generation.py +++ b/bycon/lib/beacon_response_generation.py @@ -537,7 +537,7 @@ def __filtering_terms_query(self): if BYC["TEST_MODE"] is True: query = mongo_test_mode_query(self.ds_id, f_coll) - prdbug(f'filtering_terms_query: {query}') + # prdbug(f'filtering_terms_query: {query}') self.filtering_terms_query = query diff --git a/bycon/lib/query_generation.py b/bycon/lib/query_generation.py index 4f60d7896..ea1103c4e 100644 --- a/bycon/lib/query_generation.py +++ b/bycon/lib/query_generation.py @@ -3,7 +3,7 @@ from os import environ from pymongo import MongoClient -from bycon_helpers import days_from_iso8601duration, prdbug, return_paginated_list +from bycon_helpers import days_from_iso8601duration, prdbug, prjsonnice, return_paginated_list from config import * from cytoband_parsing import Cytobands from genome_utils import ChroNames, GeneInfo, VariantTypes @@ -189,23 +189,31 @@ def __preprocess_variant_pars(self): v_p_s = self.variant_request_definitions.get("request_pars", []) v_mp_s = self.variant_request_definitions.get("multi_request_pars", []) + vips = [] + # standard pars + s_q_p_0 = {} if (v_s_s := v_p_s & BYC_PARS.keys()): - s_q_p_0 = {} for v_p in v_s_s: v_v = BYC_PARS.get(v_p) s_q_p_0.update({ v_p: v_v }) BYC_VARGS.update({ v_p: v_v }) prdbug(f'...__preprocess_variant_pars: {v_p} {v_v}') - self.variant_multi_pars.append(s_q_p_0) for v_mp in v_mp_s: if len(v_mp_vs := BYC_PARS.get(v_mp, [])) > 0: for v in v_mp_vs: - self.variant_multi_pars.append({v_mp: v}) + if len(s_q_p_0.keys()) > 0: + t_p = s_q_p_0.copy() + t_p.update({v_mp: v}) + vips.append(self.__parse_variant_parameters(t_p)) + else: + vips.append({v_mp: v}) + if (len(vips)) < 1: + if len(s_q_p_0.keys()) > 0: + vips.append(self.__parse_variant_parameters(s_q_p_0)) - for v_p_i, v_p_s in enumerate(self.variant_multi_pars): - self.variant_multi_pars[v_p_i] = self.__parse_variant_parameters(v_p_s) + self.variant_multi_pars = vips # -------------------------------------------------------------------------# @@ -713,7 +721,7 @@ def __query_from_filters(self): # TODO: needs a general solution; so far for the iso age w/ # pre-calculated days field... - if "alphanumeric" in f_info.get("type", "ontology"): + if "alphanumeric" in f_info.get("ft_type", "ontology"): f_class, comp, val = re.match(r'^(\w+):([<>=]+?)(\w[\w.]+?)$', f_info["id"]).group(1, 2, 3) if "iso8601duration" in f_info.get("format", "___none___"): val = days_from_iso8601duration(val) @@ -737,7 +745,7 @@ def __query_from_filters(self): if len(f_query_vals) == 1: f_s_l.append({f_field: f_query_vals[0]}) else: - if "alphanumeric" in f_infos[f_entity][f_field].get("type", "ontology"): + if "alphanumeric" in f_infos[f_entity][f_field].get("ft_type", "ontology"): q_l = [] for a_q_v in f_query_vals: q_l.append({f_field: a_q_v}) @@ -775,12 +783,16 @@ def __query_from_filter_definitions(self, f_val): f_info = { "id": f_val, "scope": "biosamples", - "type": "___undefined___", + "ft_type": "___undefined___", "db_key": "___undefined___", "child_terms": [f_val] } + prdbug(f'...__query_from_filter_definitions: {f_val}') + for f_d in f_d_s.values(): + if f_d.get("collationed", False) is True: + continue f_re = re.compile(f_d.get("pattern", "___none___")) if f_re.match(f_val): f_info = { @@ -788,7 +800,7 @@ def __query_from_filter_definitions(self, f_val): "scope": f_d.get("scope", "biosamples"), "entity": f_d.get("entity", "biosample"), "db_key": f_d["db_key"], - "type": f_d.get("type", "ontology"), + "ft_type": f_d.get("ft_type", "ontology"), "format": f_d.get("format", "___none___"), "child_terms": [f_val] } diff --git a/housekeepers/recordsSampler.py b/housekeepers/recordsSampler.py index c9c7c548a..6c0a4001d 100755 --- a/housekeepers/recordsSampler.py +++ b/housekeepers/recordsSampler.py @@ -46,7 +46,7 @@ def main(): exit() set_entities() - example_queries = BYC["dataset_definitions"]["progenetix"].get("test_queries", {}) + example_queries = BYC.get("test_queries", {}) BYC_PARS.update({"response_entity_path_id":"analyses"}) BYC_PARS.update({"inputfile":"___dummy___"}) @@ -87,7 +87,7 @@ def main(): continue f_i_ids = ds["analyses.id"].get("target_values", []) - ana_ids.update(random_samples(f_i_ids, min(50, len(f_i_ids)))) + ana_ids.update(random_samples(f_i_ids, min(BYC_PARS.get("limit", 200), len(f_i_ids)))) print(f'==> now {len(ana_ids)}') BYC_PARS.update({"analysis_ids": list(ana_ids)}) diff --git a/local/dataset_definitions.yaml b/local/dataset_definitions.yaml index 61f8f46af..baf18afa5 100644 --- a/local/dataset_definitions.yaml +++ b/local/dataset_definitions.yaml @@ -15,56 +15,6 @@ progenetix: - id: DUO:0000004 label: no restriction version: 2021-11-11 - # TODO: probably temporary ... - test_queries: - CDKN2AcnvQuery: - filters: - - NCIT:C3058 - reference_name: refseq:NC_000009.12 - start: - - 21000001 - - 21975098 - end: - - 21967753 - - 23000000 - variant_type: EFO:0030067 - EIF4A1snvQuery: - reference_name: refseq:NC_000017.11 - start: - - 7577120 - alternate_bases: A - reference_bases: G - EIF4A1rangeQuery: - reference_name: refseq:NC_000017.11 - start: - - 7572825 - end: - - 7579005 - variant_type: SO:0001059 - # geneMatchQuery: - # gene_id: CDK2 - # variant_min_length: 100000 - # variant_max_length: 200000 - # variant_type: EFO:0030070 - HeLaIdentifierQuery: - filters: - - cellosaurus:CVCL_0030 - CDKN2AshortFormExample: - filters: - - NCIT:C3058 - variant_query_digests: 9:21000001-21975098--21967753-24000000:DEL - fusionExample: - variant_type: SO:0000806 - reference_name: refseq:NC_000008.11 - mate_name: refseq:NC_000012.12 - start: - - 45100000 - end: - - 47300000 - mate_start: - - 26200000 - mate_end: - - 35600000 cellz: id: cellz diff --git a/local/test_queries.yaml b/local/test_queries.yaml index 2af64b6bb..f8b2c6103 100644 --- a/local/test_queries.yaml +++ b/local/test_queries.yaml @@ -1,18 +1,45 @@ -default: - CDKN2AcnvQuery: - filters: [NCIT:C3058] - reference_name: refseq:NC_000009.12 - start: [21000001 21975098] - end: [21967753 23000000] - variant_type: EFO:0030067 - EIF4A1snvQuery: - reference_name: refseq:NC_000017.11 - start: [7577120] - variant_type: SO:0001059 - alternate_bases: A - reference_bases: G - CDKN2ArangeQuery: - filters: [NCIT:C3058] - reference_name: refseq:NC_000009.12 - start: [21967753] - end: [21975098] +CDKN2AcnvQuery: + filters: + - NCIT:C3058 + reference_name: refseq:NC_000009.12 + start: [21000001,21975098] + end: [21967753,23000000] + variant_type: EFO:0030067 +EIF4A1snvQuery: + reference_name: refseq:NC_000017.11 + start: [7577120] + variant_type: SO:0001059 + alternate_bases: A + reference_bases: G +EIF4A1rangeQuery: + reference_name: refseq:NC_000017.11 + start: [7572825] + end: [7579005] + variant_type: SO:0001059 +geneMatchQuery: + gene_id: CDK2 + variant_min_length: 100000 + variant_max_length: 2000000 + variant_type: EFO:0030070 +HeLaIdentifierQuery: + filters: + - cellosaurus:CVCL_0030 +CDKN2AshortFormExample: + filters: + - NCIT:C3058 + variant_query_digests: 9:21000001-21975098--21967753-24000000:DEL +fusionExample: + variant_type: SO:0000806 + reference_name: refseq:NC_000008.11 + mate_name: refseq:NC_000012.12 + start: [45100000] + end: [47300000] + mate_start: [26200000] + mate_end: [35600000] +ClinicalFiltersQuery: + filters: + - NCIT:C48786 + - NCIT:C20197 +AgeAtDXquery: + filters: + - ageAtDiagnosis:<=P18Y diff --git a/rsrc/mongodump/_byconServicesDB.tar.gz b/rsrc/mongodump/_byconServicesDB.tar.gz index d27c9de84..52997c77f 100644 Binary files a/rsrc/mongodump/_byconServicesDB.tar.gz and b/rsrc/mongodump/_byconServicesDB.tar.gz differ diff --git a/rsrc/mongodump/examplez.tar.gz b/rsrc/mongodump/examplez.tar.gz index d971074b8..b7b50ab2e 100644 Binary files a/rsrc/mongodump/examplez.tar.gz and b/rsrc/mongodump/examplez.tar.gz differ