diff --git a/__test__/base_transformer.test.ts b/__test__/base_transformer.test.ts index 736456f..e171248 100644 --- a/__test__/base_transformer.test.ts +++ b/__test__/base_transformer.test.ts @@ -18,9 +18,9 @@ describe("test base transformer", () => { }; }); - test("Test pairInputWithAPIResponse function", () => { + test("Test pairInputWithAPIResponse function", async () => { const tf = new base_tf(input, {}); - const res = tf.pairCurieWithAPIResponse(); + const res = await tf.pairCurieWithAPIResponse(); expect(res).toHaveProperty("DOID:9562"); expect(res["DOID:9562"]).toHaveLength(1); }); diff --git a/__test__/biolink_transformers.test.ts b/__test__/biolink_transformers.test.ts index 8af30e6..ca52dfc 100644 --- a/__test__/biolink_transformers.test.ts +++ b/__test__/biolink_transformers.test.ts @@ -1,3 +1,4 @@ +import jq_tf from "../built/transformers/jq_transformer"; import biolink_tf from "../src/transformers/biolink_transformer"; import fs from "fs"; import path from "path"; @@ -18,24 +19,24 @@ describe("test biolink transformer", () => { }; }); - test("test biolink wrapper", () => { - const tf = new biolink_tf(input, {}); - const res = tf.wrap(response); + test("test biolink wrapper", async () => { + const tf = new jq_tf(input, { type: "biolink" }); + const res = await tf.wrap(response); expect(res.associations[0].object.HGNC).toBe("10956"); expect(res.associations[0].publications[0].id).toBe("21685912"); expect(res.associations[1]).not.toHaveProperty("publications"); expect(res.associations[1]).not.toHaveProperty("provided_by"); }); - test("test biolink wrapper if no association field as root key", () => { - const tf = new biolink_tf(input, {}); - const res = tf.wrap({ data: [] }); + test("test biolink wrapper if no association field as root key", async () => { + const tf = new jq_tf(input, { type: "biolink" }); + const res = await tf.wrap({ data: [] }); expect(res).toEqual({ data: [] }); }); - test("test biolink wrapper if no object id should be prefixed", () => { - const tf = new biolink_tf(input, {}); - const res = tf.wrap({ + test("test biolink wrapper if no object id should be prefixed", async () => { + const tf = new jq_tf(input, { type: "biolink" }); + const res = await tf.wrap({ associations: [ { object: { @@ -47,8 +48,8 @@ describe("test biolink transformer", () => { expect(res.associations[0].object.MONDO).toEqual("MONDO:12345"); }); - test("test biolink wrapper if no object field present", () => { - const tf = new biolink_tf(input, {}); + test("test biolink wrapper if no object field present", async () => { + const tf = new jq_tf(input, { type: "biolink" }); const fake_response = { associations: [ { @@ -58,12 +59,12 @@ describe("test biolink transformer", () => { }, ], }; - const res = tf.wrap(fake_response); + const res = await tf.wrap(fake_response); expect(res).toEqual(fake_response); }); - test("test biolink wrapper if no object.id field present", () => { - const tf = new biolink_tf(input, {}); + test("test biolink wrapper if no object.id field present", async () => { + const tf = new jq_tf(input, { type: "biolink" }); const fake_response = { associations: [ { @@ -73,13 +74,13 @@ describe("test biolink transformer", () => { }, ], }; - const res = tf.wrap(fake_response); + const res = await tf.wrap(fake_response); expect(res).toEqual(fake_response); }); - test("test biolink jsonTransform function", () => { - const tf = new biolink_tf(input, {}); - const wrapped_response = tf.wrap(response); + test("test biolink jsonTransform function", async () => { + const tf = new jq_tf(input, { type: "biolink" }); + const wrapped_response = await tf.wrap(response); const res: JSONDoc = tf.jsonTransform(wrapped_response); expect(res).toHaveProperty("related_to"); expect(res.related_to[0].HGNC).toEqual("10956"); diff --git a/__test__/biothings_transformer.test.ts b/__test__/biothings_transformer.test.ts index d526229..e0f2273 100644 --- a/__test__/biothings_transformer.test.ts +++ b/__test__/biothings_transformer.test.ts @@ -1,3 +1,4 @@ +import jq_tf from "../src/transformers/jq_transformer"; import biothings_tf from "../src/transformers/biothings_transformer"; import fs from "fs"; import path from "path"; @@ -18,9 +19,9 @@ describe("test biothings transformer", () => { }; }); - test("test biothings wrapper", () => { - const tf = new biothings_tf(input, {}); - const res = tf.pairCurieWithAPIResponse(); + test("test biothings wrapper", async () => { + const tf = new jq_tf(input, { type: "biothings" }); + const res = await tf.pairCurieWithAPIResponse(); expect(Object.keys(res)).toHaveLength(2); expect(res).toHaveProperty("DRUGBANK:DB00188"); expect(res["DRUGBANK:DB00188"]).toHaveLength(2); @@ -43,21 +44,20 @@ describe("test biothings transformer", () => { }; }); - test("test biothings wrapper", () => { - const tf = new biothings_tf(input, {}); - const res = tf.pairCurieWithAPIResponse(); + test("test biothings wrapper", async () => { + const tf = new jq_tf(input, { type: "biothings" }); + const res = await tf.pairCurieWithAPIResponse(); expect(Object.keys(res)).toHaveLength(1); expect(res).toHaveProperty("NCBIGene:1017"); expect(res["NCBIGene:1017"]).toHaveLength(1); }); test("test biothings transform", async () => { - const tf = new biothings_tf(input, {}); + const tf = new jq_tf(input, { type: "biothings" }); const res = await tf.transform(); expect(res).toHaveLength(27); expect(res[0]).not.toHaveProperty("ref_pmid"); - // TODO: re-enable when this is handled properly - // expect(res[0]).toHaveProperty("publications", ["PMID:21873635"]); + expect(res[0]).toHaveProperty("publications", ["PMID:21873635"]); }); }); @@ -76,9 +76,9 @@ describe("test biothings transformer", () => { }; }); - test("test biothings wrapper", () => { - const tf = new biothings_tf(input, {}); - const res = tf.pairCurieWithAPIResponse(); + test("test biothings wrapper", async () => { + const tf = new jq_tf(input, { type: "biothings" }); + const res = await tf.pairCurieWithAPIResponse(); expect(Object.keys(res)).toHaveLength(1); expect(res).toHaveProperty("PUBCHEM:11373846"); expect(res["PUBCHEM:11373846"]).toHaveLength(1); diff --git a/__test__/ctd_transformer.test.ts b/__test__/ctd_transformer.test.ts index 244b61d..ee87d36 100644 --- a/__test__/ctd_transformer.test.ts +++ b/__test__/ctd_transformer.test.ts @@ -1,7 +1,6 @@ import fs from "fs"; import path from "path"; - -import ctd_tf from "../src/transformers/ctd_transformer"; +import jq_tf from "../built/transformers/jq_transformer"; describe("test ctd transformer", () => { let response; @@ -18,36 +17,36 @@ describe("test ctd transformer", () => { }; }); - test("test ctd wrapper", () => { - const tf = new ctd_tf(input, {}); - const res = tf.wrap(response); + test("test ctd wrapper", async () => { + const tf = new jq_tf(input, { type: "ctd" }); + const res = await tf.wrap(response); expect(res).toHaveProperty("data"); expect(res.data).toHaveLength(2); expect(res.data[0].PubMedIDs).toEqual(["21559390"]); - expect(res.data[0].DiseaseID).toEqual("D008545"); + expect(res.data[0].DiseaseID).toEqual("MESH:D008545"); }); - test("test ctd wrapper if pubmed id field is not string", () => { - const tf = new ctd_tf(input, {}); + test("test ctd wrapper if pubmed id field is not string", async () => { + const tf = new jq_tf(input, { type: "ctd" }); const fake = [ { DiseaseID: "MESH:D008545", }, ]; - const res = tf.wrap(fake); + const res = await tf.wrap(fake); expect(res).toHaveProperty("data"); expect(res.data).toHaveLength(1); expect(res.data[0].PubMedIDs).toBeUndefined; }); - test("test ctd wrapper if disease id field is not string", () => { - const tf = new ctd_tf(input, {}); + test("test ctd wrapper if disease id field is not string", async () => { + const tf = new jq_tf(input, { type: "ctd" }); const fake = [ { PubMedID: "12345", }, ]; - const res = tf.wrap(fake); + const res = await tf.wrap(fake); expect(res).toHaveProperty("data"); expect(res.data).toHaveLength(1); expect(res.data[0].DiseaseIDs).toBeUndefined; diff --git a/__test__/data/biolink/edge.json b/__test__/data/biolink/edge.json index 23c59cb..ae7099b 100644 --- a/__test__/data/biolink/edge.json +++ b/__test__/data/biolink/edge.json @@ -1,56 +1,44 @@ { - "input": "DOID:678", - "query_operation": { - "params": { - "disease_id": "{inputs[0]}", - "rows": 200 - }, - "path": "/bioentity/disease/{disease_id}/genes", - "path_params": [ - "disease_id" - ], - "method": "get", - "server": "https://api.monarchinitiative.org/api", - "tags": [ - "anatomy", - "disease", - "gene", - "phenotype", - "pathway", - "annotation", - "query", - "translator", - "biolink" - ], - "supportBatch": false + "input": "DOID:678", + "query_operation": { + "params": { + "disease_id": "{inputs[0]}", + "rows": 200 }, - "association": { - "input_id": "MONDO", - "input_type": "Disease", - "output_id": "HGNC", - "output_type": "Gene", - "predicate": "related_to", - "api_name": "BioLink API", - "smartapi": { - "id": "d22b657426375a5295e7da8a303b9893", - "meta": { - "ETag": "62f25b12c5457f6924db7929d91e7d5a2e70de291e7672aebf06fa08d1526d9d", - "github_username": "newgene", - "timestamp": "2020-05-28T00:02:40.483712", - "uptime_status": "good", - "uptime_ts": "2020-06-11T00:05:38.030503", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biolink/openapi.yml" - } - } - }, - "response_mapping": { - "related_to": { - "HGNC": "associations.object.HGNC", - "pubmed": "associations.publications.id", - "relation": "associations.relation.label", - "source": "associations.provided_by", - "taxid": "associations.object.taxon.id" - } - }, - "id": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b" -} \ No newline at end of file + "path": "/bioentity/disease/{disease_id}/genes", + "path_params": ["disease_id"], + "method": "get", + "server": "https://api.monarchinitiative.org/api", + "tags": ["anatomy", "disease", "gene", "phenotype", "pathway", "annotation", "query", "translator", "biolink"], + "supportBatch": false + }, + "association": { + "input_id": "MONDO", + "input_type": "Disease", + "output_id": "HGNC", + "output_type": "Gene", + "predicate": "related_to", + "api_name": "BioLink API", + "smartapi": { + "id": "d22b657426375a5295e7da8a303b9893", + "meta": { + "ETag": "62f25b12c5457f6924db7929d91e7d5a2e70de291e7672aebf06fa08d1526d9d", + "github_username": "newgene", + "timestamp": "2020-05-28T00:02:40.483712", + "uptime_status": "good", + "uptime_ts": "2020-06-11T00:05:38.030503", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biolink/openapi.yml" + } + } + }, + "response_mapping": { + "related_to": { + "HGNC": "associations.object.HGNC", + "pubmed": "associations.publications.id", + "relation": "associations.relation.label", + "source": "associations.provided_by", + "taxid": "associations.object.taxon.id" + } + }, + "id": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b" +} diff --git a/__test__/data/biolink/response.json b/__test__/data/biolink/response.json index b707993..6d272c6 100644 --- a/__test__/data/biolink/response.json +++ b/__test__/data/biolink/response.json @@ -1,4227 +1,3303 @@ { - "associations": [ + "associations": [ + { + "id": "235d96fe-7a99-4554-8cae-ed2d04e2c0c5", + "type": null, + "subject": { + "taxon": { + "id": null, + "label": null + }, + "id": "MONDO:0019037", + "label": "progressive supranuclear palsy", + "iri": "http://purl.obolibrary.org/obo/MONDO_0019037", + "category": ["disease"] + }, + "subject_eq": null, + "subject_extensions": null, + "object": { + "taxon": { + "id": "NCBITaxon:9606", + "label": "Homo sapiens" + }, + "id": "HGNC:10956", + "label": "SLCO1A2", + "iri": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:10956", + "category": ["gene"] + }, + "object_eq": null, + "object_extensions": null, + "relation": { + "inverse": true, + "id": "RO:0003304", + "label": "contributes to condition", + "iri": "http://purl.obolibrary.org/obo/RO_0003304", + "category": null + }, + "slim": null, + "negated": false, + "qualifiers": null, + "evidence_graph": { + "nodes": [ + { + "id": "MONARCH:b8d5e5d72e9364f0e46e", + "lbl": null, + "meta": {} + }, + { + "id": "MONARCH:bff6d3cb1c2f75352e05", + "lbl": null, + "meta": {} + }, + { + "id": "RO:0003304", + "lbl": "contributes to condition", + "meta": {} + }, + { + "id": "PMID:30089514", + "lbl": null, + "meta": {} + }, + { + "id": "MONDO:0019037", + "lbl": "progressive supranuclear palsy", + "meta": {} + }, + { + "id": "ECO:0000213", + "lbl": "combinatorial evidence used in automatic assertion", + "meta": {} + }, + { + "id": "PMID:21685912", + "lbl": null, + "meta": {} + }, + { + "id": "HGNC:10956", + "lbl": "SLCO1A2", + "meta": {} + }, + { + "id": "dbSNP:rs11568563", + "lbl": "rs11568563-?", + "meta": {} + }, + { + "id": "dbSNP:rs7966334", + "lbl": "rs7966334-?", + "meta": {} + } + ], + "edges": [ + { + "sub": "MONARCH:b8d5e5d72e9364f0e46e", + "pred": "RO:0002558", + "obj": "ECO:0000213", + "meta": { + "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"], + "lbl": ["has evidence"] + } + }, + { + "sub": "MONARCH:b8d5e5d72e9364f0e46e", + "pred": "OBAN:association_has_predicate", + "obj": "RO:0003304", + "meta": { + "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"], + "lbl": ["association has predicate"] + } + }, + { + "sub": "MONARCH:bff6d3cb1c2f75352e05", + "pred": "dc:source", + "obj": "PMID:30089514", + "meta": { + "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"], + "lbl": ["source"] + } + }, + { + "sub": "MONARCH:bff6d3cb1c2f75352e05", + "pred": "OBAN:association_has_object", + "obj": "MONDO:0019037", + "meta": { + "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"], + "lbl": ["association has object"], + "equivalentOriginalNodeTarget": ["http://www.orpha.net/ORDO/Orphanet_683"] + } + }, + { + "sub": "dbSNP:rs11568563", + "pred": "RO:0003304", + 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It is involved in the metabolism of drugs such as antiarrhythmics, adrenoceptor antagonists, and tricyclic antidepressants.", - "uniprot": "P10635" - }, - { - "actions": [ - "substrate", - "inhibitor" - ], - "gene_name": "CYP1A2", - "general_function": "Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen", - "id": "BE0002433", - "known_action": "no", - "name": "Cytochrome P450 1A2", - "organism": "Humans", - "pmids": [ - 15764713 - ], - "source": "Swiss-Prot", - "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.", - "uniprot": "P05177" - }, - { - "actions": [ - "substrate", - "inhibitor" - ], - "gene_name": "CYP2C9", - "general_function": "Steroid hydroxylase activity", - "id": "BE0002793", - "known_action": "no", - "name": "Cytochrome P450 2C9", - "organism": "Humans", - "pmids": [ - 15764713, - 16443666, - 16103134 - ], - "source": "Swiss-Prot", - "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.", - "uniprot": "P11712" - } - ] + { + "query": "DB00188", + "fake": true + }, + { + "query": "DB00188", + "_id": "GXJABQQUPOEUTA-RDJZCZTQSA-N", + "_score": 6.163889, + "drugbank": { + "_license": "http://bit.ly/2PSfZTD", + "enzymes": [ + { + "actions": "substrate", + "gene_name": "CYP3A4", + "general_function": "Vitamin d3 25-hydroxylase activity", + "id": "BE0002638", + "known_action": "no", + "name": "Cytochrome P450 3A4", + "organism": "Humans", + "pmids": [22087865, 26622646, 15764713, 16443666], + "source": "Swiss-Prot", + "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide (PubMed:11159812). Catalyzes 4-beta-hydroxylation of cholesterol. May catalyze 25-hydroxylation of cholesterol in vitro (PubMed:21576599).", + "uniprot": "P08684" + }, + { + "actions": ["substrate", "inhibitor"], + "gene_name": "CYP2C19", + "general_function": "Steroid hydroxylase activity", + "id": "BE0003536", + "known_action": "no", + "name": "Cytochrome P450 2C19", + "organism": "Humans", + "pmids": [19515014, 15764713, 16103134, 16443666], + "source": "Swiss-Prot", + "specific_function": "Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.", + "uniprot": "P33261" + }, + { + "actions": "substrate", + "gene_name": "CYP2D6", + "general_function": "Steroid hydroxylase activity", + "id": "BE0002363", + "name": "Cytochrome P450 2D6", + "organism": "Humans", + "pmids": [19515014, 16103134, 15764713], + "source": "Swiss-Prot", + "specific_function": "Responsible for the metabolism of many drugs and environmental chemicals that it oxidizes. It is involved in the metabolism of drugs such as antiarrhythmics, adrenoceptor antagonists, and tricyclic antidepressants.", + "uniprot": "P10635" + }, + { + "actions": ["substrate", "inhibitor"], + "gene_name": "CYP1A2", + "general_function": "Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen", + "id": "BE0002433", + "known_action": "no", + "name": "Cytochrome P450 1A2", + "organism": "Humans", + "pmids": [15764713], + "source": "Swiss-Prot", + "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.", + "uniprot": "P05177" + }, + { + "actions": ["substrate", "inhibitor"], + "gene_name": "CYP2C9", + "general_function": "Steroid hydroxylase activity", + "id": "BE0002793", + "known_action": "no", + "name": "Cytochrome P450 2C9", + "organism": "Humans", + "pmids": [15764713, 16443666, 16103134], + "source": "Swiss-Prot", + "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.", + "uniprot": "P11712" } - }, - { - "query": "DB00184", - "_id": "SNICXCGAKADSCV-JTQLQIEISA-N", - "_score": 6.411114, - "drugbank": { - "_license": "http://bit.ly/2PSfZTD", - "enzymes": [ - { - "actions": [ - "substrate", - "inhibitor" - ], - "gene_name": "CYP2A6", - "general_function": "Steroid hydroxylase activity", - "id": "BE0003336", - "name": "Cytochrome P450 2A6", - "organism": "Humans", - "pmids": [ - 10350185, - 22869927, - 11678779, - 14757175 - ], - "source": "Swiss-Prot", - "specific_function": "Exhibits a high coumarin 7-hydroxylase activity. Can act in the hydroxylation of the anti-cancer drugs cyclophosphamide and ifosphamide. Competent in the metabolic activation of aflatoxin B1. Constitutes the major nicotine C-oxidase. Acts as a 1,4-cineole 2-exo-monooxygenase. Possesses low phenacetin O-deethylation activity.", - "uniprot": "P11509" - }, - { - "actions": [ - "substrate", - "inhibitor", - "inducer" - ], - "gene_name": "CYP2E1", - "general_function": "Steroid hydroxylase activity", - "id": "BE0003533", - "name": "Cytochrome P450 2E1", - "organism": "Humans", - "pmids": [ - 12711639, - 11719700, - 10350185, - 12750430, - 20233178, - 8328992 - ], - "source": "Swiss-Prot", - "specific_function": "Metabolizes several precarcinogens, drugs, and solvents to reactive metabolites. Inactivates a number of drugs and xenobiotics and also bioactivates many xenobiotic substrates to their hepatotoxic or carcinogenic forms.", - "uniprot": "P05181" - }, - { - "actions": "substrate", - "gene_name": "CYP2A13", - "general_function": "Steroid hydroxylase activity", - "id": "BE0003534", - "name": "Cytochrome P450 2A13", - "organism": "Humans", - "pmids": [ - 16188955, - 15196988, - 15528319 - ], - "source": "Swiss-Prot", - "specific_function": "Exhibits a coumarin 7-hydroxylase activity. Active in the metabolic activation of hexamethylphosphoramide, N,N-dimethylaniline, 2'-methoxyacetophenone, N-nitrosomethylphenylamine, and the tobacco-specific carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone. Possesses phenacetin O-deethylation activity.", - "uniprot": "Q16696" - }, - { - "actions": "substrate", - "gene_name": "CYP2B6", - "general_function": "Steroid hydroxylase activity", - "id": "BE0003549", - "name": "Cytochrome P450 2B6", - "organism": "Humans", - "pmids": [ - 10350185, - 11996015 - ], - "source": "Swiss-Prot", - "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,4-cineole 2-exo-monooxygenase.", - "uniprot": "P20813" - }, - { - "actions": [ - "substrate", - "inducer" - ], - "gene_name": "CYP1A1", - "general_function": "Vitamin d 24-hydroxylase activity", - "id": "BE0003543", - "name": "Cytochrome P450 1A1", - "organism": "Humans", - "pmids": [ - 11849738, - 10427467, - 10350185 - ], - "source": "Swiss-Prot", - "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.", - "uniprot": "P04798" - }, - { - "actions": [ - "substrate", - "inducer" - ], - "gene_name": "CYP1A2", - "general_function": "Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen", - "id": "BE0002433", - "name": "Cytochrome P450 1A2", - "organism": "Humans", - "pmids": [ - 21599724, - 10427467, - 10350185, - 20932495 - ], - "source": "Swiss-Prot", - "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.", - "uniprot": "P05177" - }, - { - "actions": "substrate", - "gene_name": "CYP2C19", - "general_function": "Steroid hydroxylase activity", - "id": "BE0003536", - "name": "Cytochrome P450 2C19", - "organism": "Humans", - "pmids": [ - 10350185 - ], - "source": "Swiss-Prot", - "specific_function": "Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.", - "uniprot": "P33261" - }, - { - "actions": "substrate", - "gene_name": "CYP2C8", - "general_function": "Steroid hydroxylase activity", - "id": "BE0002887", - "name": "Cytochrome P450 2C8", - "organism": "Humans", - "pmids": [ - 10350185 - ], - "source": "Swiss-Prot", - "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. In the epoxidation of arachidonic acid it generates only 14,15- and 11,12-cis-epoxyeicosatrienoic acids. It is the principal enzyme responsible for the metabolism the anti-cancer drug paclitaxel (taxol).", - "uniprot": "P10632" - }, - { - "actions": "substrate", - "gene_name": "CYP2C9", - "general_function": "Steroid hydroxylase activity", - "id": "BE0002793", - "name": "Cytochrome P450 2C9", - "organism": "Humans", - "pmids": [ - 10350185 - ], - "source": "Swiss-Prot", - "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.", - "uniprot": "P11712" - }, - { - "actions": "substrate", - "gene_name": "CYP2D6", - "general_function": "Steroid hydroxylase activity", - "id": "BE0002363", - "name": "Cytochrome P450 2D6", - "organism": "Humans", - "pmids": [ - 10350185, - 8807663, - 26287939 - ], - "source": "Swiss-Prot", - "specific_function": "Responsible for the metabolism of many drugs and environmental chemicals that it oxidizes. It is involved in the metabolism of drugs such as antiarrhythmics, adrenoceptor antagonists, and tricyclic antidepressants.", - "uniprot": "P10635" - }, - { - "actions": "substrate", - "gene_name": "CYP3A4", - "general_function": "Vitamin d3 25-hydroxylase activity", - "id": "BE0002638", - "name": "Cytochrome P450 3A4", - "organism": "Humans", - "pmids": [ - 10350185 - ], - "source": "Swiss-Prot", - "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide (PubMed:11159812). Catalyzes 4-beta-hydroxylation of cholesterol. May catalyze 25-hydroxylation of cholesterol in vitro (PubMed:21576599).", - "uniprot": "P08684" - }, - { - "actions": "inhibitor", - "gene_name": "MAOA", - "general_function": "Serotonin binding", - "id": "BE0002198", - "name": "Amine oxidase [flavin-containing] A", - "organism": "Humans", - "pmids": [ - 21636610, - 19142115 - ], - "source": "Swiss-Prot", - "specific_function": "Catalyzes the oxidative deamination of biogenic and xenobiotic amines and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. MAOA preferentially oxidizes biogenic amines such as 5-hydroxytryptamine (5-HT), norepinephrine and epinephrine.", - "uniprot": "P21397" - }, - { - "actions": "inhibitor", - "gene_name": "MAOB", - "general_function": "Primary amine oxidase activity", - "id": "BE0002196", - "name": "Amine oxidase [flavin-containing] B", - "organism": "Humans", - "pmids": [ - 21636610 - ], - "source": "Swiss-Prot", - "specific_function": "Catalyzes the oxidative deamination of biogenic and xenobiotic amines and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. MAOB preferentially degrades benzylamine and phenylethylamine.", - "uniprot": "P27338" - } - ] + ] + } + }, + { + "query": "DB00184", + "_id": "SNICXCGAKADSCV-JTQLQIEISA-N", + "_score": 6.411114, + "drugbank": { + "_license": "http://bit.ly/2PSfZTD", + "enzymes": [ + { + "actions": ["substrate", "inhibitor"], + "gene_name": "CYP2A6", + "general_function": "Steroid hydroxylase activity", + "id": "BE0003336", + "name": "Cytochrome P450 2A6", + "organism": "Humans", + "pmids": [10350185, 22869927, 11678779, 14757175], + "source": "Swiss-Prot", + "specific_function": "Exhibits a high coumarin 7-hydroxylase activity. Can act in the hydroxylation of the anti-cancer drugs cyclophosphamide and ifosphamide. Competent in the metabolic activation of aflatoxin B1. Constitutes the major nicotine C-oxidase. Acts as a 1,4-cineole 2-exo-monooxygenase. Possesses low phenacetin O-deethylation activity.", + "uniprot": "P11509" + }, + { + "actions": ["substrate", "inhibitor", "inducer"], + "gene_name": "CYP2E1", + "general_function": "Steroid hydroxylase activity", + "id": "BE0003533", + "name": "Cytochrome P450 2E1", + "organism": "Humans", + "pmids": [12711639, 11719700, 10350185, 12750430, 20233178, 8328992], + "source": "Swiss-Prot", + "specific_function": "Metabolizes several precarcinogens, drugs, and solvents to reactive metabolites. Inactivates a number of drugs and xenobiotics and also bioactivates many xenobiotic substrates to their hepatotoxic or carcinogenic forms.", + "uniprot": "P05181" + }, + { + "actions": "substrate", + "gene_name": "CYP2A13", + "general_function": "Steroid hydroxylase activity", + "id": "BE0003534", + "name": "Cytochrome P450 2A13", + "organism": "Humans", + "pmids": [16188955, 15196988, 15528319], + "source": "Swiss-Prot", + "specific_function": "Exhibits a coumarin 7-hydroxylase activity. Active in the metabolic activation of hexamethylphosphoramide, N,N-dimethylaniline, 2'-methoxyacetophenone, N-nitrosomethylphenylamine, and the tobacco-specific carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone. Possesses phenacetin O-deethylation activity.", + "uniprot": "Q16696" + }, + { + "actions": "substrate", + "gene_name": "CYP2B6", + "general_function": "Steroid hydroxylase activity", + "id": "BE0003549", + "name": "Cytochrome P450 2B6", + "organism": "Humans", + "pmids": [10350185, 11996015], + "source": "Swiss-Prot", + "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,4-cineole 2-exo-monooxygenase.", + "uniprot": "P20813" + }, + { + "actions": ["substrate", "inducer"], + "gene_name": "CYP1A1", + "general_function": "Vitamin d 24-hydroxylase activity", + "id": "BE0003543", + "name": "Cytochrome P450 1A1", + "organism": "Humans", + "pmids": [11849738, 10427467, 10350185], + "source": "Swiss-Prot", + "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.", + "uniprot": "P04798" + }, + { + "actions": ["substrate", "inducer"], + "gene_name": "CYP1A2", + "general_function": "Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen", + "id": "BE0002433", + "name": "Cytochrome P450 1A2", + "organism": "Humans", + "pmids": [21599724, 10427467, 10350185, 20932495], + "source": "Swiss-Prot", + "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.", + "uniprot": "P05177" + }, + { + "actions": "substrate", + "gene_name": "CYP2C19", + "general_function": "Steroid hydroxylase activity", + "id": "BE0003536", + "name": "Cytochrome P450 2C19", + "organism": "Humans", + "pmids": [10350185], + "source": "Swiss-Prot", + "specific_function": "Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.", + "uniprot": "P33261" + }, + { + "actions": "substrate", + "gene_name": "CYP2C8", + "general_function": "Steroid hydroxylase activity", + "id": "BE0002887", + "name": "Cytochrome P450 2C8", + "organism": "Humans", + "pmids": [10350185], + "source": "Swiss-Prot", + "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. In the epoxidation of arachidonic acid it generates only 14,15- and 11,12-cis-epoxyeicosatrienoic acids. It is the principal enzyme responsible for the metabolism the anti-cancer drug paclitaxel (taxol).", + "uniprot": "P10632" + }, + { + "actions": "substrate", + "gene_name": "CYP2C9", + "general_function": "Steroid hydroxylase activity", + "id": "BE0002793", + "name": "Cytochrome P450 2C9", + "organism": "Humans", + "pmids": [10350185], + "source": "Swiss-Prot", + "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.", + "uniprot": "P11712" + }, + { + "actions": "substrate", + "gene_name": "CYP2D6", + "general_function": "Steroid hydroxylase activity", + "id": "BE0002363", + "name": "Cytochrome P450 2D6", + "organism": "Humans", + "pmids": [10350185, 8807663, 26287939], + "source": "Swiss-Prot", + "specific_function": "Responsible for the metabolism of many drugs and environmental chemicals that it oxidizes. It is involved in the metabolism of drugs such as antiarrhythmics, adrenoceptor antagonists, and tricyclic antidepressants.", + "uniprot": "P10635" + }, + { + "actions": "substrate", + "gene_name": "CYP3A4", + "general_function": "Vitamin d3 25-hydroxylase activity", + "id": "BE0002638", + "name": "Cytochrome P450 3A4", + "organism": "Humans", + "pmids": [10350185], + "source": "Swiss-Prot", + "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide (PubMed:11159812). Catalyzes 4-beta-hydroxylation of cholesterol. May catalyze 25-hydroxylation of cholesterol in vitro (PubMed:21576599).", + "uniprot": "P08684" + }, + { + "actions": "inhibitor", + "gene_name": "MAOA", + "general_function": "Serotonin binding", + "id": "BE0002198", + "name": "Amine oxidase [flavin-containing] A", + "organism": "Humans", + "pmids": [21636610, 19142115], + "source": "Swiss-Prot", + "specific_function": "Catalyzes the oxidative deamination of biogenic and xenobiotic amines and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. MAOA preferentially oxidizes biogenic amines such as 5-hydroxytryptamine (5-HT), norepinephrine and epinephrine.", + "uniprot": "P21397" + }, + { + "actions": "inhibitor", + "gene_name": "MAOB", + "general_function": "Primary amine oxidase activity", + "id": "BE0002196", + "name": "Amine oxidase [flavin-containing] B", + "organism": "Humans", + "pmids": [21636610], + "source": "Swiss-Prot", + "specific_function": "Catalyzes the oxidative deamination of biogenic and xenobiotic amines and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. MAOB preferentially degrades benzylamine and phenylethylamine.", + "uniprot": "P27338" } - }, - { - "query": "DBOOOO", - "notfound": true + ] } -] \ No newline at end of file + }, + { + "query": "DBOOOO", + "notfound": true + } +] diff --git a/__test__/data/biothings/mygene_example_edge.json b/__test__/data/biothings/mygene_example_edge.json index 36d44e2..0ba1e8d 100644 --- a/__test__/data/biothings/mygene_example_edge.json +++ b/__test__/data/biothings/mygene_example_edge.json @@ -1,58 +1,44 @@ { - "query_operation": { - "_params": { - "fields": "go.BP" - }, - "_requestBody": { - "body": { - "q": "{inputs[0]}", - "scopes": "entrezgene" - }, - "header": "application/x-www-form-urlencoded" - }, - "_supportBatch": true, - "_inputSeparator": ",", - "method": "post", - "_pathParams": [], - "_server": "https://mygene.info/v3", - "_path": "/query", - "_tags": [ - "gene", - "annotation", - "query", - "translator", - "biothings" - ] + "query_operation": { + "_params": { + "fields": "go.BP" }, - "association": { - "input_id": "NCBIGene", - "input_type": "Gene", - "output_id": "GO", - "output_type": "BiologicalProcess", - "predicate": "functional_association", - "source": "entrez", - "api_name": "MyGene.info API", - "smartapi": {}, - "x-translator": { - "component": "KP", - "team": [ - "Service Provider" - ] - } + "_requestBody": { + "body": { + "q": "{inputs[0]}", + "scopes": "entrezgene" + }, + "header": "application/x-www-form-urlencoded" }, - "response_mapping": { - "functional_association": { - "evidence": "go.BP.evidence", - "GO": "go.BP.id", - "pubmed": "go.BP.pubmed", - "term": "go.BP.term" - } - }, - "tags": [ - "gene", - "annotation", - "query", - "translator", - "biothings" - ] -} \ No newline at end of file + "_supportBatch": true, + "_inputSeparator": ",", + "_method": "post", + "_pathParams": [], + "_server": "https://mygene.info/v3", + "_path": "/query", + "_tags": ["gene", "annotation", "query", "translator", "biothings"] + }, + "association": { + "input_id": "NCBIGene", + "input_type": "Gene", + "output_id": "GO", + "output_type": "BiologicalProcess", + "predicate": "functional_association", + "source": "entrez", + "api_name": "MyGene.info API", + "smartapi": {}, + "x-translator": { + "component": "KP", + "team": ["Service Provider"] + } + }, + "response_mapping": { + "functional_association": { + "evidence": "go.BP.evidence", + "GO": "go.BP.id", + "pubmed": "go.BP.pubmed", + "term": "go.BP.term" + } + }, + "tags": ["gene", "annotation", "query", "translator", "biothings"] +} diff --git a/__test__/data/biothings/mygene_post.json b/__test__/data/biothings/mygene_post.json index 2fb6c5c..3d3c897 100644 --- a/__test__/data/biothings/mygene_post.json +++ b/__test__/data/biothings/mygene_post.json @@ -1,196 +1,193 @@ [ - { - "query": "1017", - "_id": "1017", - "_score": 23.263514, - "go": { - "BP": [ - { - "evidence": "IBA", - "gocategory": "BP", - "id": "GO:0000082", - "pubmed": 21873635, - "term": "G1/S transition of mitotic cell cycle" - }, - { - "evidence": "TAS", - "gocategory": "BP", - "id": "GO:0000082", - "term": "G1/S transition of mitotic cell cycle" - }, - { - "evidence": "NAS", - "gocategory": "BP", - "id": "GO:0000086", - "pubmed": 1653904, - "term": "G2/M transition of mitotic cell cycle" - }, - { - "evidence": "TAS", - "gocategory": "BP", - "id": "GO:0000086", - "term": "G2/M transition of mitotic cell cycle" - }, - { - "evidence": "TAS", - "gocategory": "BP", - "id": "GO:0006260", - "pubmed": 19238148, - "term": "DNA replication" - }, - { - "evidence": "IEA", - "gocategory": "BP", - "id": "GO:0006281", - "term": "DNA repair" - }, - { - "evidence": "IBA", - "gocategory": "BP", - "id": "GO:0006468", - "pubmed": 21873635, - "term": "protein phosphorylation" - }, - { - "evidence": "IDA", - "gocategory": "BP", - "id": "GO:0006468", - "pubmed": [ - 12944431, - 28666995 - ], - "term": "protein phosphorylation" - }, - { - "evidence": "IMP", - "gocategory": "BP", - "id": "GO:0006468", - "pubmed": 29203878, - "term": "protein phosphorylation" - }, - { - "evidence": "TAS", - "gocategory": "BP", - "id": "GO:0006977", - "term": "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" - }, - { - "evidence": "IMP", - "gocategory": "BP", - "id": "GO:0007099", - "pubmed": 26297806, - "term": "centriole replication" - }, - { - "evidence": "IBA", - "gocategory": "BP", - "id": "GO:0007165", - "pubmed": 21873635, - "term": "signal transduction" - }, - { - "evidence": "IEP", - "gocategory": "BP", - "id": "GO:0007265", - "pubmed": 9054499, - "term": "Ras protein signal transduction" - }, - { - "evidence": "IBA", - "gocategory": "BP", - "id": "GO:0008284", - "pubmed": 21873635, - "term": "positive regulation of cell population proliferation" - }, - { - "evidence": "IDA", - "gocategory": "BP", - "id": "GO:0008284", - "pubmed": 10767298, - "term": "positive regulation of cell population proliferation" - }, - { - "evidence": "IBA", - "gocategory": "BP", - "id": "GO:0010389", - "pubmed": 21873635, - "term": "regulation of G2/M transition of mitotic cell cycle" - }, - { - "evidence": "IBA", - "gocategory": "BP", - "id": "GO:0010468", - "pubmed": 21873635, - "term": "regulation of gene expression" - }, - { - "evidence": "IDA", - "gocategory": "BP", - "id": "GO:0016572", - "pubmed": 11746698, - "term": "histone phosphorylation" - }, - { - "evidence": "IDA", - "gocategory": "BP", - "id": "GO:0018105", - "pubmed": 23184662, - "term": "peptidyl-serine phosphorylation" - }, - { - "evidence": "TAS", - "gocategory": "BP", - "id": "GO:0031145", - "term": "anaphase-promoting complex-dependent catabolic process" - }, - { - "evidence": "TAS", - "gocategory": "BP", - "id": "GO:0031571", - "pubmed": 21319273, - "term": "mitotic G1 DNA damage checkpoint" - }, - { - "evidence": "TAS", - "gocategory": "BP", - "id": "GO:0051298", - "pubmed": 19238148, - "term": "centrosome duplication" - }, - { - "evidence": "IEA", - "gocategory": "BP", - "id": "GO:0051301", - "term": "cell division" - }, - { - "evidence": "TAS", - "gocategory": "BP", - "id": "GO:0051321", - "pubmed": 19238148, - "term": "meiotic cell cycle" - }, - { - "evidence": "IDA", - "gocategory": "BP", - "id": "GO:0060968", - "pubmed": 20935635, - "term": "regulation of gene silencing" - }, - { - "evidence": "TAS", - "gocategory": "BP", - "id": "GO:0071732", - "pubmed": 20079829, - "term": "cellular response to nitric oxide" - }, - { - "evidence": "TAS", - "gocategory": "BP", - "id": "GO:1901796", - "term": "regulation of signal transduction by p53 class mediator" - } - ] + { + "query": "1017", + "_id": "1017", + "_score": 23.263514, + "go": { + "BP": [ + { + "evidence": "IBA", + "gocategory": "BP", + "id": "GO:0000082", + "pubmed": 21873635, + "term": "G1/S transition of mitotic cell cycle" + }, + { + "evidence": "TAS", + "gocategory": "BP", + "id": "GO:0000082", + "term": "G1/S transition of mitotic cell cycle" + }, + { + "evidence": "NAS", + "gocategory": "BP", + "id": "GO:0000086", + "pubmed": 1653904, + "term": "G2/M transition of mitotic cell cycle" + }, + { + "evidence": "TAS", + "gocategory": "BP", + "id": "GO:0000086", + "term": "G2/M transition of mitotic cell cycle" + }, + { + "evidence": "TAS", + "gocategory": "BP", + "id": "GO:0006260", + "pubmed": 19238148, + "term": "DNA replication" + }, + { + "evidence": "IEA", + "gocategory": "BP", + "id": "GO:0006281", + "term": "DNA repair" + }, + { + "evidence": "IBA", + "gocategory": "BP", + "id": "GO:0006468", + "pubmed": 21873635, + "term": "protein phosphorylation" + }, + { + "evidence": "IDA", + "gocategory": "BP", + "id": "GO:0006468", + "pubmed": [12944431, 28666995], + "term": "protein phosphorylation" + }, + { + "evidence": "IMP", + "gocategory": "BP", + "id": "GO:0006468", + "pubmed": 29203878, + "term": "protein phosphorylation" + }, + { + "evidence": "TAS", + "gocategory": "BP", + "id": "GO:0006977", + "term": "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" + }, + { + "evidence": "IMP", + "gocategory": "BP", + "id": "GO:0007099", + "pubmed": 26297806, + "term": "centriole replication" + }, + { + "evidence": "IBA", + "gocategory": "BP", + "id": "GO:0007165", + "pubmed": 21873635, + "term": "signal transduction" + }, + { + "evidence": "IEP", + "gocategory": "BP", + "id": "GO:0007265", + "pubmed": 9054499, + "term": "Ras protein signal transduction" + }, + { + "evidence": "IBA", + "gocategory": "BP", + "id": "GO:0008284", + "pubmed": 21873635, + "term": "positive regulation of cell population proliferation" + }, + { + "evidence": "IDA", + "gocategory": "BP", + "id": "GO:0008284", + "pubmed": 10767298, + "term": "positive regulation of cell population proliferation" + }, + { + "evidence": "IBA", + "gocategory": "BP", + "id": "GO:0010389", + "pubmed": 21873635, + "term": "regulation of G2/M transition of mitotic cell cycle" + }, + { + "evidence": "IBA", + "gocategory": "BP", + "id": "GO:0010468", + "pubmed": 21873635, + "term": "regulation of gene expression" + }, + { + "evidence": "IDA", + "gocategory": "BP", + "id": "GO:0016572", + "pubmed": 11746698, + "term": "histone phosphorylation" + }, + { + "evidence": "IDA", + "gocategory": "BP", + "id": "GO:0018105", + "pubmed": 23184662, + "term": "peptidyl-serine phosphorylation" + }, + { + "evidence": "TAS", + "gocategory": "BP", + "id": "GO:0031145", + "term": "anaphase-promoting complex-dependent catabolic process" + }, + { + "evidence": "TAS", + "gocategory": "BP", + "id": "GO:0031571", + "pubmed": 21319273, + "term": "mitotic G1 DNA damage checkpoint" + }, + { + "evidence": "TAS", + "gocategory": "BP", + "id": "GO:0051298", + "pubmed": 19238148, + "term": "centrosome duplication" + }, + { + "evidence": "IEA", + "gocategory": "BP", + "id": "GO:0051301", + "term": "cell division" + }, + { + "evidence": "TAS", + "gocategory": "BP", + "id": "GO:0051321", + "pubmed": 19238148, + "term": "meiotic cell cycle" + }, + { + "evidence": "IDA", + "gocategory": "BP", + "id": "GO:0060968", + "pubmed": 20935635, + "term": "regulation of gene silencing" + }, + { + "evidence": "TAS", + "gocategory": "BP", + "id": "GO:0071732", + "pubmed": 20079829, + "term": "cellular response to nitric oxide" + }, + { + "evidence": "TAS", + "gocategory": "BP", + "id": "GO:1901796", + "term": "regulation of signal transduction by p53 class mediator" } + ] } -] \ No newline at end of file + } +] diff --git a/__test__/data/ctd/edge.json b/__test__/data/ctd/edge.json index 992f360..9eaa93a 100644 --- a/__test__/data/ctd/edge.json +++ b/__test__/data/ctd/edge.json @@ -1,47 +1,39 @@ { - "input": "1017", - "query_operation": { - "_params": { - "inputType": "gene", - "report": "diseases_curated", - "format": "json", - "inputTerms": "{inputs[0]}" - }, - "_supportBatch": false, - "method": "get", - "_pathParams": [], - "_server": "http://ctdbase.org/tools", - "_path": "/batchQuery.go", - "_tags": [ - "translator", - "ctd" - ] + "input": "1017", + "query_operation": { + "_params": { + "inputType": "gene", + "report": "diseases_curated", + "format": "json", + "inputTerms": "{inputs[0]}" }, - "association": { - "input_id": "NCBIGene", - "input_type": "Gene", - "output_id": "MESH", - "output_type": "Disease", - "predicate": "related_to", - "source": "CTD", - "api_name": "CTD API", - "smartapi": {}, - "x-translator": { - "component": "KP", - "team": [ - "Service Provider" - ] - } - }, - "response_mapping": { - "related_to": { - "MESH": "data.DiseaseID", - "name": "data.DiseaseName", - "pubmed": "data.PubMedIDs" - } - }, - "tags": [ - "translator", - "ctd" - ] -} \ No newline at end of file + "_supportBatch": false, + "method": "get", + "_pathParams": [], + "_server": "http://ctdbase.org/tools", + "_path": "/batchQuery.go", + "_tags": ["translator", "ctd"] + }, + "association": { + "input_id": "NCBIGene", + "input_type": "Gene", + "output_id": "MESH", + "output_type": "Disease", + "predicate": "related_to", + "source": "CTD", + "api_name": "CTD API", + "smartapi": {}, + "x-translator": { + "component": "KP", + "team": ["Service Provider"] + } + }, + "response_mapping": { + "related_to": { + "MESH": "data.DiseaseID", + "name": "data.DiseaseName", + "pubmed": "data.PubMedIDs" + } + }, + "tags": ["translator", "ctd"] +} diff --git a/__test__/data/ctd/response.json b/__test__/data/ctd/response.json index 08a9a2b..9f2b67c 100644 --- a/__test__/data/ctd/response.json +++ b/__test__/data/ctd/response.json @@ -1,22 +1,22 @@ [ - { - "DirectEvidence": "marker/mechanism", - "DiseaseCategories": "Cancer", - "DiseaseID": "MESH:D008545", - "DiseaseName": "Melanoma", - "GeneID": "1017", - "GeneSymbol": "CDK2", - "Input": "1017", - "PubMedIDs": "21559390" - }, - { - "DirectEvidence": "marker/mechanism", - "DiseaseCategories": "Cancer", - "DiseaseID": "MESH:D000077195", - "DiseaseName": "Squamous Cell Carcinoma of Head and Neck", - "GeneID": "1017", - "GeneSymbol": "CDK2", - "Input": "1017", - "PubMedIDs": "29464035" - } -] \ No newline at end of file + { + "DirectEvidence": "marker/mechanism", + "DiseaseCategories": "Cancer", + "DiseaseID": "MESH:D008545", + "DiseaseName": "Melanoma", + "GeneID": "1017", + "GeneSymbol": "CDK2", + "Input": "1017", + "PubMedIDs": "21559390" + }, + { + "DirectEvidence": "marker/mechanism", + "DiseaseCategories": "Cancer", + "DiseaseID": "MESH:D000077195", + "DiseaseName": "Squamous Cell Carcinoma of Head and Neck", + "GeneID": "1017", + "GeneSymbol": "CDK2", + "Input": "1017", + "PubMedIDs": "29464035" + } +] diff --git a/__test__/data/ctd/response2.json b/__test__/data/ctd/response2.json index 39c353e..8f0a95f 100644 --- a/__test__/data/ctd/response2.json +++ b/__test__/data/ctd/response2.json @@ -1 +1,1482 @@ -[{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Pregnancy complication","DiseaseID":"MESH:D000022","DiseaseName":"Abortion, Spontaneous","Input":"d003634","PubMedIDs":"16120699"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Cancer|Digestive system disease","DiseaseID":"MESH:D018248","DiseaseName":"Adenoma, Liver Cell","Input":"d003634","PubMedIDs":"12597452"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Occupational disease","DiseaseID":"MESH:D000382","DiseaseName":"Agricultural Workers' Diseases","Input":"d003634","PubMedIDs":"12584743|16487989|17182642|17495700|17932376|17975796|19541724|20061368|20730623|24064777"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Urogenital disease (male)","DiseaseID":"MESH:D053627","DiseaseName":"Asthenozoospermia","Input":"d003634","PubMedIDs":"19303595"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Immune system disease|Respiratory tract disease","DiseaseID":"MESH:D001249","DiseaseName":"Asthma","Input":"d003634","PubMedIDs":"17932376|19541724"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Urogenital disease (male)","DiseaseID":"MESH:D053713","DiseaseName":"Azoospermia","Input":"d003634","PubMedIDs":"31682807"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Cancer|Skin disease","DiseaseID":"MESH:D001943","DiseaseName":"Breast Neoplasms","Input":"d003634","PubMedIDs":"12709520|16792888|17938728"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Pathology (process)|Respiratory tract disease","DiseaseID":"MESH:D029481","DiseaseName":"Bronchitis, Chronic","Input":"d003634","PubMedIDs":"17495700|17975796"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Cancer|Digestive system disease","DiseaseID":"MESH:D006528","DiseaseName":"Carcinoma, Hepatocellular","Input":"d003634","PubMedIDs":"12597452|21035526|6667461"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Cardiovascular disease|Pathology (anatomical condition)","DiseaseID":"MESH:D006332","DiseaseName":"Cardiomegaly","Input":"d003634","PubMedIDs":"27325568"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Digestive system disease","DiseaseID":"MESH:D056486","DiseaseName":"Chemical and Drug Induced Liver Injury","Input":"d003634","PubMedIDs":"11272408|18675336"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Mental disorder","DiseaseID":"MESH:D002653","DiseaseName":"Child Behavior Disorders","Input":"d003634","PubMedIDs":"27466755"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Mental disorder","DiseaseID":"MESH:D003072","DiseaseName":"Cognition Disorders","Input":"d003634","PubMedIDs":"26630154"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Cancer|Digestive system disease","DiseaseID":"MESH:D003110","DiseaseName":"Colonic Neoplasms","Input":"d003634","PubMedIDs":"20730623"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Congenital abnormality","DiseaseID":"MESH:D000013","DiseaseName":"Congenital Abnormalities","Input":"d003634","PubMedIDs":"15095906"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseID":"MESH:D009358","DiseaseName":"Congenital, Hereditary, and Neonatal Diseases and Abnormalities","Input":"d003634","PubMedIDs":"31682807"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Congenital abnormality|Endocrine system disease|Urogenital disease (male)","DiseaseID":"MESH:D003456","DiseaseName":"Cryptorchidism","Input":"d003634","PubMedIDs":"16835070"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Mental disorder","DiseaseID":"MESH:D003866","DiseaseName":"Depressive Disorder","Input":"d003634","PubMedIDs":"28263910"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Endocrine system disease|Metabolic disease","DiseaseID":"MESH:D003920","DiseaseName":"Diabetes Mellitus","Input":"d003634","PubMedIDs":"31746186"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseID":"MESH:D064420","DiseaseName":"Drug-Related Side Effects and Adverse Reactions","Input":"d003634","PubMedIDs":"2370251"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Respiratory tract disease|Signs 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b/__test__/data/ebi_protein/edge.json index 4d6ff30..a83799b 100644 --- a/__test__/data/ebi_protein/edge.json +++ b/__test__/data/ebi_protein/edge.json @@ -1,51 +1,40 @@ { - "input": "Q93099", - "query_operation": { - "params": { - "accession": "{inputs[0]}" - }, - "path": "/proteins/{accession}", - "path_params": [ - "accession" - ], - "method": "get", - "server": "https://www.ebi.ac.uk/proteins/api", - "tags": [ - "anatomy", - "disease", - "gene", - "phenotype", - "pathway", - "annotation", - "query", - "translator" - ], - "supportBatch": false + "input": "Q93099", + "query_operation": { + "params": { + "accession": "{inputs[0]}" }, - "association": { - "input_id": "UniProtKB", - "input_type": "Protein", - "output_id": "RHEA", - "output_type": "MolecularActivity", - "predicate": "related_to", - "api_name": "EBI Proteins API", - "smartapi": { - "id": "d22b657426375a5295e7da8a303b9893", - "meta": { - "ETag": "62f25b12c5457f6924db7929d91e7d5a2e70de291e7672aebf06fa08d1526d9d", - "github_username": "newgene", - "timestamp": "2020-05-28T00:02:40.483712", - "uptime_status": "good", - "uptime_ts": "2020-06-11T00:05:38.030503", - "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biolink/openapi.yml" - } - } - }, - "response_mapping": { - "related_to": { - "RHEA": "comments.reaction.dbReferences.id", - "name": "comments.reaction.name" - } - }, - "id": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b" -} \ No newline at end of file + "path": "/proteins/{accession}", + "path_params": ["accession"], + "method": "get", + "server": "https://www.ebi.ac.uk/proteins/api", + "tags": ["anatomy", "disease", "gene", "phenotype", "pathway", "annotation", "query", "translator"], + "supportBatch": false + }, + "association": { + "input_id": "UniProtKB", + "input_type": "Protein", + "output_id": "RHEA", + "output_type": "MolecularActivity", + "predicate": "related_to", + "api_name": "EBI Proteins API", + "smartapi": { + "id": "d22b657426375a5295e7da8a303b9893", + "meta": { + "ETag": "62f25b12c5457f6924db7929d91e7d5a2e70de291e7672aebf06fa08d1526d9d", + "github_username": "newgene", + "timestamp": "2020-05-28T00:02:40.483712", + "uptime_status": "good", + "uptime_ts": "2020-06-11T00:05:38.030503", + "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biolink/openapi.yml" + } + } + }, + "response_mapping": { + "related_to": { + "RHEA": "comments.reaction.dbReferences.id", + "name": "comments.reaction.name" + } + }, + "id": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b" +} diff --git a/__test__/data/ebi_protein/response.json b/__test__/data/ebi_protein/response.json index 5dd49a9..2905521 100644 --- a/__test__/data/ebi_protein/response.json +++ b/__test__/data/ebi_protein/response.json @@ -1,4743 +1,4650 @@ { - "accession": "Q93099", - "id": "HGD_HUMAN", - "proteinExistence": "Evidence at protein level", - "info": { - "type": "Swiss-Prot", - "created": "1997-11-01", - "modified": "2021-04-07", - "version": 192 - }, - "organism": { - "taxonomy": 9606, - "names": [ - { - "type": "scientific", - "value": "Homo sapiens" - }, - { - "type": "common", - "value": "Human" - } + "accession": "Q93099", + "id": "HGD_HUMAN", + "proteinExistence": "Evidence at protein level", + "info": { + "type": "Swiss-Prot", + "created": "1997-11-01", + "modified": "2021-04-07", + "version": 192 + }, + "organism": { + "taxonomy": 9606, + "names": [ + { + "type": "scientific", + "value": "Homo sapiens" + }, + { + "type": "common", + "value": "Human" + } + ], + "lineage": [ + "Eukaryota", + "Metazoa", + "Chordata", + "Craniata", + "Vertebrata", + "Euteleostomi", + "Mammalia", + "Eutheria", + "Euarchontoglires", + "Primates", + "Haplorrhini", + "Catarrhini", + "Hominidae", + "Homo" + ] + }, + "secondaryAccession": ["A8K417", "B2R8Z0"], + "protein": { + "recommendedName": { + "fullName": { + "value": "Homogentisate 1,2-dioxygenase" + }, + "ecNumber": [ + { + "value": "1.13.11.5" + } + ] + }, + "alternativeName": [ + { + "fullName": { + "value": "Homogentisate oxygenase" + } + }, + { + "fullName": { + "value": "Homogentisic acid oxidase" + } + }, + { + "fullName": { + "value": "Homogentisicase" + } + } + ] + }, + "gene": [ + { + "name": { + "value": "HGD" + }, + "synonyms": [ + { + "value": "HGO" + } + ] + } + ], + "comments": [ + { + "type": "CATALYTIC_ACTIVITY", + "reaction": { + "name": "homogentisate + O2 = 4-maleylacetoacetate + H(+)", + "dbReferences": [ + { + "type": "Rhea", + "id": "RHEA:15449" + }, + { + "type": "ChEBI", + "id": "CHEBI:15378" + }, + { + "type": "ChEBI", + "id": "CHEBI:15379" + }, + { + "type": "ChEBI", + "id": "CHEBI:16169" + }, + { + "type": "ChEBI", + "id": "CHEBI:17105" + } ], - "lineage": [ - "Eukaryota", - "Metazoa", - "Chordata", - "Craniata", - "Vertebrata", - "Euteleostomi", - "Mammalia", - "Eutheria", - "Euarchontoglires", - "Primates", - "Haplorrhini", - "Catarrhini", - "Hominidae", - "Homo" - ] + "ecNumber": "1.13.11.5" + } }, - "secondaryAccession": [ - "A8K417", - "B2R8Z0" - ], - "protein": { - "recommendedName": { - "fullName": { - "value": "Homogentisate 1,2-dioxygenase" - }, - "ecNumber": [ - { - "value": "1.13.11.5" - } - ] - }, - "alternativeName": [ - { - "fullName": { - "value": "Homogentisate oxygenase" - } - }, - { - "fullName": { - "value": "Homogentisic acid oxidase" - } - }, + { + "type": "COFACTOR", + "cofactors": [ + { + "name": "Fe cation", + "dbReference": { + "type": "CHEBI", + "id": "CHEBI:24875" + } + } + ] + }, + { + "type": "PATHWAY", + "text": [ + { + "value": "Amino-acid degradation; L-phenylalanine degradation; acetoacetate and fumarate from L-phenylalanine: step 4/6" + } + ] + }, + { + "type": "SUBUNIT", + "text": [ + { + "value": "Homohexamer arranged as a dimer of trimers", + "evidences": [ { - "fullName": { - "value": "Homogentisicase" - } + "code": "ECO:0000269", + "source": { + "name": "PubMed", + "id": "10876237", + "url": "http://www.ncbi.nlm.nih.gov/pubmed/10876237", + "alternativeUrl": "https://europepmc.org/abstract/MED/10876237" + } } - ] + ] + } + ] }, - "gene": [ + { + "type": "INTERACTION", + "interactions": [ + { + "accession1": "Q93099", + "accession2": "Q93099", + "gene": "HGD", + "interactor1": "EBI-3907760", + "interactor2": "EBI-3907760", + "organismDiffer": false, + "experiments": 4 + }, + { + "accession1": "Q93099", + "accession2": "Q96HA8", + "gene": "NTAQ1", + "interactor1": "EBI-3907760", + "interactor2": "EBI-741158", + "organismDiffer": false, + "experiments": 3 + }, + { + "accession1": "Q93099", + "accession2": "P54274", + "gene": "TERF1", + "interactor1": "EBI-3907760", + "interactor2": "EBI-710997", + "organismDiffer": false, + "experiments": 2 + } + ] + }, + { + "type": "TISSUE_SPECIFICITY", + "text": [ { - "name": { - "value": "HGD" - }, - "synonyms": [ - { - "value": "HGO" - } - ] + "value": "Highest expression in the prostate, small intestine, colon, kidney and liver" } - ], - 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The clinical manifestations are urine that turns dark on standing and alkalinization, black ochronotic pigmentation of cartilage and collagenous tissues, and spine arthritis.", + "evidences": [ + { + "code": "ECO:0000269", + "source": { + "name": "PubMed", + "id": "10205262", + "url": "http://www.ncbi.nlm.nih.gov/pubmed/10205262", + "alternativeUrl": "https://europepmc.org/abstract/MED/10205262" } - }, - { - "type": "COFACTOR", - "cofactors": [ - { - "name": "Fe cation", - "dbReference": { - "type": "CHEBI", - "id": "CHEBI:24875" - } - } - ] - }, - { - "type": "PATHWAY", - "text": [ - { - "value": "Amino-acid degradation; L-phenylalanine degradation; acetoacetate and fumarate from L-phenylalanine: step 4/6" - } - ] - }, - { - "type": "SUBUNIT", - "text": [ - { - "value": "Homohexamer arranged as a dimer of trimers", - "evidences": [ - { - "code": "ECO:0000269", - "source": { - "name": "PubMed", - "id": "10876237", - "url": "http://www.ncbi.nlm.nih.gov/pubmed/10876237", - "alternativeUrl": "https://europepmc.org/abstract/MED/10876237" - } - } - ] - } - ] - }, - { - "type": "INTERACTION", - "interactions": [ - { - "accession1": "Q93099", - "accession2": "Q93099", - "gene": "HGD", - "interactor1": "EBI-3907760", - "interactor2": "EBI-3907760", - "organismDiffer": false, - "experiments": 4 - }, - { - "accession1": "Q93099", - "accession2": "Q96HA8", - "gene": "NTAQ1", - "interactor1": "EBI-3907760", - "interactor2": "EBI-741158", - "organismDiffer": false, - "experiments": 3 - }, - { - "accession1": "Q93099", - "accession2": "P54274", - "gene": "TERF1", - "interactor1": "EBI-3907760", - "interactor2": "EBI-710997", - "organismDiffer": false, - "experiments": 2 - } - ] - }, - { - "type": "TISSUE_SPECIFICITY", - "text": [ - { - "value": "Highest expression in the prostate, small intestine, colon, kidney and liver" - } - ] - }, - { - "type": "DISEASE", - "diseaseId": "Alkaptonuria", - "acronym": "AKU", - "dbReference": { - "type": "MIM", - "id": "203500" - }, - "description": { - "value": "An autosomal recessive error of metabolism characterized by an increase in the level of homogentisic acid. 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"value": "The disease is caused by variants affecting the gene represented in this entry" - } - ] - }, + }, + { + "code": "ECO:0000269", + "source": { + "name": "PubMed", + "id": "10340975", + "url": "http://www.ncbi.nlm.nih.gov/pubmed/10340975", + "alternativeUrl": "https://europepmc.org/abstract/MED/10340975" + } + }, + { + "code": "ECO:0000269", + "source": { + "name": "PubMed", + "id": "10482952", + "url": "http://www.ncbi.nlm.nih.gov/pubmed/10482952", + "alternativeUrl": "https://europepmc.org/abstract/MED/10482952" + } + }, + { + "code": "ECO:0000269", + "source": { + "name": "PubMed", + "id": "10594001", + "url": "http://www.ncbi.nlm.nih.gov/pubmed/10594001", + "alternativeUrl": "https://europepmc.org/abstract/MED/10594001" + } + }, + { + "code": "ECO:0000269", + "source": { + "name": "PubMed", + "id": "19862842", + "url": "http://www.ncbi.nlm.nih.gov/pubmed/19862842", + "alternativeUrl": "https://europepmc.org/abstract/MED/19862842" + } + }, + { + "code": "ECO:0000269", + "source": { + "name": "PubMed", + "id": "21437689", + "url": "http://www.ncbi.nlm.nih.gov/pubmed/21437689", + "alternativeUrl": "https://europepmc.org/abstract/MED/21437689" + } + }, + { + "code": "ECO:0000269", + "source": { + "name": "PubMed", + "id": "23353776", + "url": "http://www.ncbi.nlm.nih.gov/pubmed/23353776", + "alternativeUrl": "https://europepmc.org/abstract/MED/23353776" + } + }, + { + "code": "ECO:0000269", + "source": { + "name": "PubMed", + "id": "23430897", + "url": "http://www.ncbi.nlm.nih.gov/pubmed/23430897", + "alternativeUrl": "https://europepmc.org/abstract/MED/23430897" + } + }, + { + "code": "ECO:0000269", + "source": { + "name": "PubMed", + "id": "25681086", + "url": "http://www.ncbi.nlm.nih.gov/pubmed/25681086", + "alternativeUrl": "https://europepmc.org/abstract/MED/25681086" + } + }, + { + "code": "ECO:0000269", + "source": { + "name": "PubMed", + "id": "8782815", + "url": "http://www.ncbi.nlm.nih.gov/pubmed/8782815", + "alternativeUrl": 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"Matrix Metalloproteinase 9", + "pmid": ["22793053", "21306303", "26261552", "26679758"], + "umls": "C0165519" + }, + { "@type": "Gene", "name": "Janus kinase 2", "pmid": ["28544312"], "umls": "C0169661" }, + { "@type": "Gene", "name": "Mitogen Activated Protein Kinase 1", "pmid": ["20956518"], "umls": "C0170168" }, + { "@type": "Gene", "name": "Matrix Metalloproteinase 2", "pmid": ["22345572"], "umls": "C0172537" }, + { "@type": "Gene", "name": "Genes, Reporter", "pmid": ["15210854"], "umls": "C0206414" }, + { "@type": "ChemicalSubstance", "name": "Opioids", "pmid": ["25175863"], "umls": "C0242402" }, + { "@type": "ChemicalSubstance", "name": "agonists", "pmid": ["28626925", "28186979"], "umls": "C0243192" }, + { "@type": "ChemicalSubstance", "name": "docetaxel", "pmid": ["25359780"], "umls": "C0246415" }, + { + "@type": "Gene", + "name": "calmodulin-dependent protein kinase II", + "pmid": ["18220750", "14630801"], + "umls": "C0248868" + }, + { "@type": "Gene", "name": "src-Family Kinases", "pmid": ["17158356"], "umls": "C0282625" }, + { + "@type": "Gene", + "name": "RAC-Alpha Serine/Threonine Kinase", + "pmid": ["20829512", "14630801", "18840710"], + "umls": "C0285558" + }, + { "@type": "Gene", "name": "LIM Domain Kinase 1", "pmid": ["25359780"], "umls": "C0294209" }, + { "@type": "Gene", "name": "ran-binding protein 2", "pmid": ["28100513"], "umls": "C0299456" }, + { + "@type": "Gene", + "name": "Extracellular Signal Regulated Kinases", + "pmid": ["17550983", "9453574", "12444153", "17904532", "10651866", "25121739"], + "umls": "C0600388" + }, + { "@type": "ChemicalSubstance", "name": "Response Elements", "pmid": ["20007689"], "umls": "C0600508" }, + { "@type": "ChemicalSubstance", "name": "AMD 3100", "pmid": ["18384792", "17878755"], "umls": "C0662900" }, + { "@type": "Gene", "name": "NOS3 protein, human", "pmid": ["27243031"], "umls": "C0669365" }, + { + "@type": "Gene", + "name": "Mitogen-Activated Protein Kinases", + "pmid": ["18481208", "10997882", "23308188", "28687617"], + "umls": "C0752312" + }, + { "@type": "Gene", "name": "BCR gene", "pmid": ["10224286"], "umls": "C0812385" }, + { "@type": "Gene", "name": "C-KIT Gene", "pmid": ["23894420"], "umls": "C0920288" }, + { "@type": "ChemicalSubstance", "name": "MicroRNAs", "pmid": ["25536052"], "umls": "C1101610" }, + { "@type": "Gene", "name": "mitogen-activated protein kinase p38", "pmid": ["15972662"], "umls": "C1120843" }, + { "@type": "ChemicalSubstance", "name": "Microbicides", "pmid": ["18765807"], "umls": "C1136254" }, + { "@type": "Gene", "name": "BMP2 gene", "pmid": ["27725318"], "umls": "C1332424" }, + { "@type": "Gene", "name": "CXCR2 gene", "pmid": ["28481874"], "umls": "C1334126" }, + { "@type": "Gene", "name": "JAK2 gene", "pmid": ["16990584"], "umls": "C1334291" }, + { "@type": "Gene", "name": "KDR gene", "pmid": ["27388534"], "umls": "C1334306" }, + { "@type": "Gene", "name": "CXCL13 gene", "pmid": ["23773523"], "umls": "C1366572" }, + { "@type": "Gene", "name": "CD8B1 gene", "pmid": ["29232699", "12573587", "25647836"], "umls": "C1367471" }, + { "@type": "Gene", "name": "EGF gene", "pmid": ["17714434"], "umls": "C1367721" }, + { "@type": "Gene", "name": "MAPK8 gene", "pmid": ["18481208", "28584306", "25121739"], "umls": "C1367731" }, + { "@type": "Gene", "name": "MAPK14 protein, human", "pmid": ["24170200"], "umls": "C1456380" }, + { "@type": "ChemicalSubstance", "name": "AMD3451", "pmid": ["15542651"], "umls": "C1529450" } + ], + "umls": "C1332823" + }, + { + "query": "C1332824", + "_id": "C1332824", + "_score": 10.009048, + "name": "CXCR6 gene", + "positively_regulates": [ + { "@type": "Gene", "name": "CXCR6 gene", "pmid": ["17437534"], "umls": "C1332824" }, + { "@type": "Gene", "name": "AKT1 gene", "pmid": ["20848509"], "umls": "C0812228" }, + { "@type": "Gene", "name": "FLVCR1 gene", "pmid": ["18452560"], "umls": "C1836722" }, + { "@type": "Gene", "name": "CXCL16 wt Allele", "pmid": ["18452560"], "umls": "C3538864" }, + { "@type": "Gene", "name": "CXCL12 wt Allele", "pmid": ["18452560"], "umls": "C1704964" }, + { "@type": "Gene", "name": "CCR2 gene", "pmid": ["12480562"], "umls": "C1413188" }, + { "@type": "Gene", "name": "CD69 gene", "pmid": ["12914753"], "umls": "C1413235" }, + { "@type": "ChemicalSubstance", "name": "Haptens", "pmid": ["20972432"], "umls": "C0018593" }, + { "@type": "Gene", "name": "Proto-Oncogene Proteins c-akt", "pmid": ["20848509"], "umls": "C0164786" }, + { "@type": "Gene", "name": "Mitogen-Activated Protein Kinases", "pmid": ["20848509"], "umls": "C0752312" } + ], + "umls": "C1332824" + }, + { "query": "123", "notfound": true } +] diff --git a/__test__/ebi_protein_transformer.test.ts b/__test__/ebi_protein_transformer.test.ts index dbeb04b..b39b01d 100644 --- a/__test__/ebi_protein_transformer.test.ts +++ b/__test__/ebi_protein_transformer.test.ts @@ -1,6 +1,6 @@ import fs from "fs"; import path from "path"; -import ebi_tf from "../src/transformers/ebi_protein_transformer"; +import jq_tf from "../src/transformers/jq_transformer"; describe("test EBI Protein transformer", () => { let response; @@ -17,9 +17,9 @@ describe("test EBI Protein transformer", () => { }; }); - test("test ebi wrapper", () => { - const tf = new ebi_tf(input, {}); - const res = tf.wrap(response); + test("test ebi wrapper", async () => { + const tf = new jq_tf(input, { type: "ebi" }); + const res = await tf.wrap(response); expect(res.comments[0].reaction.dbReferences).toHaveLength(1); }); }); diff --git a/__test__/opentarget_transformer.test.ts b/__test__/opentarget_transformer.test.ts index 9ddc143..65ccc93 100644 --- a/__test__/opentarget_transformer.test.ts +++ b/__test__/opentarget_transformer.test.ts @@ -1,6 +1,6 @@ +import jq_tf from "../built/transformers/jq_transformer"; import fs from "fs"; import path from "path"; -import opentarget_tf from "../src/transformers/opentarget_transformer"; describe("test opentarget transformer", () => { let response; @@ -18,15 +18,15 @@ describe("test opentarget transformer", () => { }); // skip these tests since we're not ingesting opentargets right now - test.skip("test opentarget wrapper", () => { - const tf = new opentarget_tf(input, {}); - const res = tf.wrap(response); - expect(res).toHaveProperty("data"); + test.skip("test opentarget wrapper", async () => { + const tf = new jq_tf(input, { type: "opentarget" }); + let res = await tf.wrap(response); + const(res).toHaveProperty("data"); expect(res.data[0].drug.id).toEqual("CHEMBL220492"); }); - test.skip("test opentarget wrapper if id field is not chembl", () => { - const tf = new opentarget_tf(input, {}); + test.skip("test opentarget wrapper if id field is not chembl", async () => { + const tf = new jq_tf(input, { type: "opentarget" }); const fake = { data: [ { @@ -36,7 +36,7 @@ describe("test opentarget transformer", () => { }, ], }; - const res = tf.wrap(fake); + const res = await tf.wrap(fake); expect(res).toHaveProperty("data"); expect(res.data[0].drug.id).toEqual("http://identifiers.org/drugbank/DB0001"); }); diff --git a/__test__/semmed_transformer.test.ts b/__test__/semmed_transformer.test.ts index b604c9b..8783b89 100644 --- a/__test__/semmed_transformer.test.ts +++ b/__test__/semmed_transformer.test.ts @@ -16,9 +16,9 @@ describe("test semmed transformer", () => { }; }); - test("test semmed pairCurieWithAPIResponse", () => { + test("test semmed pairCurieWithAPIResponse", async () => { const tf = new semmed_tf(input, {}); - const res = tf.pairCurieWithAPIResponse(); + const res = await tf.pairCurieWithAPIResponse(); expect(res["UMLS:C1332823"][0]["umls"]).toBe("C1332823"); expect(res).toHaveProperty("UMLS:C1332823"); expect(res["UMLS:123"]).toBeUndefined(); @@ -38,8 +38,8 @@ describe("test semmed transformer", () => { test("add edge info", async () => { const tf = new semmed_tf(input, {}); - const res = tf.pairCurieWithAPIResponse(); - let rec = res["UMLS:C1332823"][0]; + const res = await tf.pairCurieWithAPIResponse(); + const rec = res["UMLS:C1332823"][0]; rec = tf.wrap(rec); const result = await tf.formatRecords("UMLS:C1332823", rec["positively_regulates"][0]); expect(result[0]).toHaveProperty("association"); diff --git a/__test__/transformers.test.ts b/__test__/transformers.test.ts index 8527313..3bba302 100644 --- a/__test__/transformers.test.ts +++ b/__test__/transformers.test.ts @@ -81,8 +81,8 @@ describe("test ctd transformer", () => { }); describe("test biothings transformer", () => { - let api_response; - let input; + const api_response; + const input; beforeAll(async () => { (axios as jest.MockedFunction).mockImplementation(async q => { @@ -153,9 +153,9 @@ describe("test biothings transformer", () => { }; }); - test("test biothings pairCurieWithAPIResponse", () => { + test("test biothings pairCurieWithAPIResponse", async () => { const tf = new biothings_tf(input, {}); - const res = tf.pairCurieWithAPIResponse(); + const res = await tf.pairCurieWithAPIResponse(); expect(res["UMLS:C1332823"][0]["umls"]).toBe("C1332823"); expect(res).toHaveProperty("UMLS:C1332823"); expect(res["123"]).toBeUndefined(); diff --git a/data/jq/pair/biothings.jq b/data/jq/pair/biothings.jq new file mode 100644 index 0000000..cf57f40 --- /dev/null +++ b/data/jq/pair/biothings.jq @@ -0,0 +1,22 @@ +if $edge.query_operation._method == "post" then + # if response is not an array, then use response.hits + if (.response | type) == "array" then .response else .response.hits end | + reduce .[] as $item ({}; + # if the item is notfound, then proceed to next item & keep current object + if ($item | keys | contains(["notfound"])) then + . + else + if $edge.input | type == "object" then + generateCurieWithInputs($edge.association.input_id; $item.query; $edge.input.queryInputs) as $curie | .[$curie] = .[$curie] + [$item] + else + generateCurieWithInputs($edge.association.input_id; $item.query; $edge.input | toArray) as $curie | .[$curie] = .[$curie] + [$item] + end + end + ) +else + if ($edge.input | type) == "object" then + .response as $res | generateCurie($edge.association.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = [$res] + else + .response as $res | generateCurie($edge.association.input_id; ($edge.input | toArray)[0]) as $curie | {} | .[$curie] = [$res] + end +end diff --git a/data/jq/pair/ctd.jq b/data/jq/pair/ctd.jq new file mode 100644 index 0000000..a912f1f --- /dev/null +++ b/data/jq/pair/ctd.jq @@ -0,0 +1,23 @@ +reduce .response[] as $item ( + {}; .[( + if ($edge.input | type) == "object" then + ($edge.input.queryInputs | toArray)[] + else + ($edge.input | toArray)[] + end + ) + | select(($item.Input | ascii_upcase | split(":") | last) == (. | ascii_upcase)) + | generateCurie($edge.association.input_id; .) + ] = [] + + .[( + if ($edge.input | type) == "object" then + ($edge.input.queryInputs | toArray)[] + else + ($edge.input | toArray)[] + end + ) + | select(($item.Input | ascii_upcase | split(":") | last) == (. | ascii_upcase)) + | generateCurie($edge.association.input_id; .) + ] + + [$item] +) | map_values([.]) diff --git a/data/jq/utils.jq b/data/jq/utils.jq new file mode 100644 index 0000000..220755c --- /dev/null +++ b/data/jq/utils.jq @@ -0,0 +1,48 @@ +# example increment function +def increment: . + 1; + +# converts value to array if not already +def toArray: if (. | type) == "array" then . else [.] end; + +# deletes key if empty array +def delifempty(k): (if k == [] then del(k) | . else . end); + +# sets inputted value to "empty" if empty array +def remifempty: (if . == [] then empty else . end); + +# gets first element of array (if array) +def getfirst: if (. | type) == "array" then .[0] else . end; + +# generates a curie from a type and id +def generateCurie(idType; id): id | getfirst | split(":") | last | idType + ":" + .; + +# generates a curie from a type and id [string] (by checking queryInputs) +def generateCurieWithInputs(idType; id; queryInputs): (id | getfirst) as $id | reduce (queryInputs | toArray | .[]) as $input (""; if ($id | ascii_upcase | contains($input | ascii_upcase)) then $input else . end) | idType + ":" + .; + +# getting a nested field from inputted object (seperated by ., ie. drugcentral.bioactivity) +def get_nested_field(field): +. as $obj | reduce (field | split(".") | .[]) as $subfield ($obj; .[$subfield]?); + +# checks if object meets any filter string +def any_filter(filter_strs): +. as $obj | reduce (filter_strs | .[]) as $filter_str ( + false; + . or ( + ($obj | get_nested_field($filter_str | split(":") | first)) == ($filter_str | split(":") | last) + ) +); + +# checks if object meets all filter strings +def all_filter(filter_strs): +. as $obj | reduce (filter_strs | .[]) as $filter_str ( + true; + . and ( + $obj | any_filter([$filter_str | split(":") | last | split(",") | .[] | ($filter_str | split(":") | first) + ":" + .]) + ) +); + +# filters the list that is supplied on all conditions +def list_filter_all(filter_strs): if (. | type) == "array" then [.[] | if . | all_filter(filter_strs) then . else empty end] else empty end; + +# filters the list that is supplied on any conditions +def list_filter_any(filter_strs): if (. | type) == "array" then [.[] | if . | any_filter(filter_strs) then . else empty end] else empty end; diff --git a/data/jq/wrap/biolink.jq b/data/jq/wrap/biolink.jq new file mode 100644 index 0000000..696d9d1 --- /dev/null +++ b/data/jq/wrap/biolink.jq @@ -0,0 +1,18 @@ +.associations = ( + [ + ( + # take associations that aren't null + select(.associations != null) | .associations | .[] | + # split association object ids & take last (only for CHEMBL, REACT, HGNC) + select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) | + # take publications with PMID & for IDs take last element after splitting by : + .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)] + ) + # delete publications if empty array + | delifempty(.publications) + ] + + # include associations with null object ids + [select(.associations != null) | .associations | .[] | select(.object.id == null)] +) +# delete association if empty array +| delifempty(.associations) diff --git a/data/jq/wrap/ctd.jq b/data/jq/wrap/ctd.jq new file mode 100644 index 0000000..7ffd766 --- /dev/null +++ b/data/jq/wrap/ctd.jq @@ -0,0 +1,6 @@ +# Split pubMedIDs by | +((.[] | select(.PubMedIDs != null) | .PubMedIDs) |= split("|")) | +((.[] | select(.PubMedIds != null) | .PubMedIds) |= split("|")) | +# Split Direct Evidence by | +((.[] | select(.DirectEvidence != null) | .DirectEvidence) |= split("|")) | +{data: .} diff --git a/data/jq/wrap/ebi.jq b/data/jq/wrap/ebi.jq new file mode 100644 index 0000000..7494d30 --- /dev/null +++ b/data/jq/wrap/ebi.jq @@ -0,0 +1,4 @@ +# only take comments where dbReferences type is Rhea +.comments = [ + select(.comments != null) | .comments | .[] | select(.reaction != null) | .reaction.dbReferences = [.reaction.dbReferences | .[] | select(.type == "Rhea")] +] diff --git a/data/jq/wrap/opentarget.jq b/data/jq/wrap/opentarget.jq new file mode 100644 index 0000000..b437ee1 --- /dev/null +++ b/data/jq/wrap/opentarget.jq @@ -0,0 +1,2 @@ +# split drug IDs with CHEMBL by / +(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last) diff --git a/package.json b/package.json index bfe710b..8b6130a 100644 --- a/package.json +++ b/package.json @@ -64,6 +64,8 @@ "axios": "^0.21.4", "common-path-prefix": "^3.0.0", "husky": "^8.0.3", + "lodash": "^4.17.21", + "node-jq": "^2.3.4", "jsonata": "^1.8.6", "lodash": "^4.17.21" }, diff --git a/src/index.ts b/src/index.ts index 9e47a56..c0dfbe7 100644 --- a/src/index.ts +++ b/src/index.ts @@ -7,6 +7,7 @@ import OpenTargetTransformer from "./transformers/opentarget_transformer"; import BaseTransformer from "./transformers/transformer"; import TRAPITransformer from "./transformers/trapi_transformer"; import EBIProteinTransformer from "./transformers/ebi_protein_transformer"; +import JQTransformer from "./transformers/jq_transformer"; import { BTEQueryObject } from "./types"; import { Record } from "./record"; import Debug from "debug"; @@ -29,18 +30,32 @@ export default class Transformer { debug(`api name ${api}`); const tags = this.data.edge.query_operation.tags; debug(`api tags: ${tags}`); - if (tags.includes("bte-trapi")) { + + // if (!this.data.edge.query_operation.transformer) { + // console.log(`WE DONT DO THE OP ${api}, ${this.data.edge.query_operation}`) + // } + + if (this.data.edge.query_operation?.transformer?.jq) { + // console.log("WE DO THE OP", this.data.edge.query_operation.transformer) + this.tf = new JQTransformer(this.data, { + ...this.config, + wrap: this.data.edge.query_operation.transformer.jq.wrap, + pair: this.data.edge.query_operation.transformer.jq.pair, + }); + } else if (tags.includes("bte-trapi")) { this.tf = new TRAPITransformer(this.data, this.config); } else if (api.startsWith("SEMMED")) { this.tf = new SemmedTransformer(this.data, this.config); } else if (api === "BioLink API") { - this.tf = new BiolinkTransformer(this.data, this.config); + // this.tf = new BiolinkTransformer(this.data, this.config); + this.tf = new JQTransformer(this.data, { ...this.config, type: "biolink" }); } else if (api === "EBI Proteins API") { - this.tf = new EBIProteinTransformer(this.data, this.config); + // this.tf = new EBIProteinTransformer(this.data, this.config) + this.tf = new JQTransformer(this.data, { ...this.config, type: "ebi" }); } else if (tags.includes("biothings")) { - this.tf = new BioThingsTransformer(this.data, this.config); + this.tf = new JQTransformer(this.data, { ...this.config, type: "biothings" }); } else if (tags.includes("ctd")) { - this.tf = new CTDTransformer(this.data, this.config); + this.tf = new JQTransformer(this.data, { ...this.config, type: "ctd" }); } else if (tags.includes("opentarget")) { this.tf = new OpenTargetTransformer(this.data, this.config); } else { @@ -48,7 +63,7 @@ export default class Transformer { } } - async transform(): Promise { + async transform(): Promise { return await this.tf.transform(); } } diff --git a/src/jq_utils.ts b/src/jq_utils.ts new file mode 100644 index 0000000..d6c4d7b --- /dev/null +++ b/src/jq_utils.ts @@ -0,0 +1,23 @@ +import { JQVariable, BTEKGOperationObject } from "./types"; +import Path from "path"; +import fs from "fs"; + +const functions = fs.readFileSync(Path.resolve(`${__dirname}/../data/jq/utils.jq`), { encoding: "utf8" }); + +function generateVariables(variables: JQVariable[]) { + let variableString = ""; + for (const variable of variables) { + variableString += `${variable.value} as ${variable.name} | `; + } + return variableString; +} + +export function generateFilterString(filterString: string, edge: BTEKGOperationObject) { + const variables = [ + { + name: "$edge", + value: JSON.stringify(edge), + }, + ]; + return `${functions}\n${generateVariables(variables)}${filterString}`; +} diff --git a/src/json_transform/types.ts b/src/json_transform/types.ts index 99f9ac9..79c17ab 100644 --- a/src/json_transform/types.ts +++ b/src/json_transform/types.ts @@ -18,3 +18,7 @@ export interface JSONDoc { [key1: string]: any; [key2: number]: any; } + +export interface PairedResponse { + [curie: string]: JSONDoc[]; +} diff --git a/src/transformers/biothings_transformer.ts b/src/transformers/biothings_transformer.ts index 27a7db6..8676dbc 100644 --- a/src/transformers/biothings_transformer.ts +++ b/src/transformers/biothings_transformer.ts @@ -2,7 +2,7 @@ import BaseTransformer from "./transformer"; import { generateCurie } from "../utils"; export default class BioThingsTransformer extends BaseTransformer { - pairCurieWithAPIResponse() { + async pairCurieWithAPIResponse() { if (this.edge.query_operation.method === "post") { let res = {}; const mapper = item => { diff --git a/src/transformers/jq_transformer.ts b/src/transformers/jq_transformer.ts new file mode 100644 index 0000000..1489fde --- /dev/null +++ b/src/transformers/jq_transformer.ts @@ -0,0 +1,56 @@ +import BaseTransformer from "./transformer"; +import { generateFilterString } from "../jq_utils"; +import fs from "fs"; +import Path from "path"; + +import * as jq from "node-jq"; // If converted to import, ts compile breaks it (imports default as undefined) +import { JSONDoc, PairedResponse } from "../json_transform/types"; + +// Get prefab JQ strings from data/jq +const filterStringsWrap = Object.fromEntries( + fs.readdirSync(Path.resolve(`${__dirname}/../../data/jq/wrap`)).map(file => { + const filePath = Path.resolve(`${__dirname}/../../data/jq/wrap/${file}`); + return [Path.parse(filePath).name, fs.readFileSync(filePath, { encoding: "utf8" })]; + }), +); + +const filterStringsPair = Object.fromEntries( + fs.readdirSync(Path.resolve(`${__dirname}/../../data/jq/pair`)).map(file => { + const filePath = Path.resolve(`${__dirname}/../../data/jq/pair/${file}`); + return [Path.parse(filePath).name, fs.readFileSync(filePath, { encoding: "utf8" })]; + }), +); + +export default class JQTransformer extends BaseTransformer { + // TODO more specific typing? + async wrap(res: JSONDoc | JSONDoc[]): Promise { + if (this.config.wrap) + res = JSON.parse( + (await jq.run(generateFilterString(this.config.wrap, this.edge), res, { input: "json" })) as string, + ); + else if (filterStringsWrap[this.config.type]) + res = JSON.parse( + (await jq.run(generateFilterString(filterStringsWrap[this.config.type], this.edge), res, { + input: "json", + })) as string, + ); + else res = super.wrap(res); + + return res; + } + + async pairCurieWithAPIResponse(): Promise { + if (this.config.pair) + return JSON.parse( + (await jq.run(generateFilterString(this.config.pair, this.edge), this.data, { input: "json" })) as string, + ); + else if (filterStringsPair[this.config.type]) + return JSON.parse( + (await jq.run(generateFilterString(filterStringsPair[this.config.type], this.edge), this.data, { + input: "json", + })) as string, + ); + + return super.pairCurieWithAPIResponse(); + } +} diff --git a/src/transformers/opentarget_transformer.ts b/src/transformers/opentarget_transformer.ts index 5f9b6b7..7f1a605 100644 --- a/src/transformers/opentarget_transformer.ts +++ b/src/transformers/opentarget_transformer.ts @@ -1,13 +1,10 @@ import BaseTransformer from "./transformer"; +import jq from "node-jq"; export default class OpenTargetTransformer extends BaseTransformer { - wrap(res) { - res.data = res.data.map(item => { - if ("drug" in item && "id" in item.drug && typeof item.drug.id === "string" && item.drug.id.includes("CHEMBL")) { - item.drug.id = item.drug.id.split("/").slice(-1)[0]; - } - return item; - }); - return res; + async wrap(res) { + const filterString = + '(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)'; + return await jq.run(filterString, res); } } diff --git a/src/transformers/transformer.ts b/src/transformers/transformer.ts index d3bfdf7..a07b4a4 100644 --- a/src/transformers/transformer.ts +++ b/src/transformers/transformer.ts @@ -23,7 +23,7 @@ export default class BaseTransformer { /** * Create an object with key representing input, and value representing the output of API */ - pairCurieWithAPIResponse() { + async pairCurieWithAPIResponse() { let input = generateCurie( this.edge.association.input_id, this.edge.input.hasOwnProperty("queryInputs") ? this.edge.input["queryInputs"] : (this.edge.input as string), @@ -240,12 +240,12 @@ export default class BaseTransformer { */ async transform() { let transformedRecords = []; - let responses = this.pairCurieWithAPIResponse(); + let responses = await this.pairCurieWithAPIResponse(); await async.eachSeries(Object.entries(responses), async ([curie, curieResponses]) => { if (Array.isArray(curieResponses) && curieResponses.length > 0) { await async.eachSeries(curieResponses, async response => { - const predicateResponse = this.jsonTransform(this.wrap(response)); + const predicateResponse = this.jsonTransform(await this.wrap(response)); await async.eachSeries(Object.entries(predicateResponse), async ([predicate, mappedResponses]) => { if (Array.isArray(mappedResponses) && mappedResponses.length > 0) { await async.eachSeries(mappedResponses, async (mappedResponse: any[]) => { diff --git a/src/types.ts b/src/types.ts index 20b50c4..6c24101 100644 --- a/src/types.ts +++ b/src/types.ts @@ -14,6 +14,15 @@ interface XBTEParametersObject { [key: string]: string | number; } +interface TransformerObject { + wrap?: string; + pair?: string; +} + +interface TransformerSet { + [transformerPattern: string]: TransformerObject; +} + interface QueryOperationInterface { path: string; method: string; @@ -24,6 +33,7 @@ interface QueryOperationInterface { request_body: object; supportBatch: boolean; inputSeparator: string; + transformer: TransformerSet; } interface SmartAPIKGOperationObject { @@ -51,3 +61,8 @@ export interface BTEQueryObject { response: JSONDoc | JSONDoc[] | { hits: JSONDoc[] }; edge: BTEKGOperationObject; } + +export interface JQVariable { + name: string; + value: string; +}