diff --git a/src/api/mehari/client.spec.ts b/src/api/mehari/client.spec.ts index c40c57c..ebc38a7 100644 --- a/src/api/mehari/client.spec.ts +++ b/src/api/mehari/client.spec.ts @@ -3,7 +3,7 @@ import path from 'path' import { beforeEach, describe, expect, it, vi } from 'vitest' import createFetchMock from 'vitest-fetch-mock' -import { GenomeBuild } from '@/pbs/mehari/txs' +import { GenomeBuild } from '../../pbs/mehari/txs' import { SeqvarImpl } from '../../lib/genomicVars' import { LinearStrucvarImpl } from '../../lib/genomicVars' diff --git a/src/api/mehari/client.ts b/src/api/mehari/client.ts index 0dbeb94..ed85f50 100644 --- a/src/api/mehari/client.ts +++ b/src/api/mehari/client.ts @@ -92,7 +92,7 @@ export class MehariClient { ): Promise { const urlGenomeBuild = GenomeBuild[genomeBuild] const url = - `${this.apiBaseUrl}/transcripts?hgncId=${hgncId}&` + + `${this.apiBaseUrl}/genes/txs?hgncId=${hgncId}&` + `genomeBuild=${urlGenomeBuild}&pageSize=${pageSize}` + (nextPageToken ? `&next_page_token=${nextPageToken}` : '') diff --git a/src/stores/geneInfo/__snapshots__/store.spec.ts.snap b/src/stores/geneInfo/__snapshots__/store.spec.ts.snap index dab848a..792665c 100644 --- a/src/stores/geneInfo/__snapshots__/store.spec.ts.snap +++ b/src/stores/geneInfo/__snapshots__/store.spec.ts.snap @@ -24224,5316 +24224,1011 @@ exports[`geneInfo Store > should load data 2`] = ` `; exports[`geneInfo Store > should load data 3`] = ` -{ - "transcripts": [ - { - "alignments": [ - { - "assembly": "GRCh37", - "cdsEnd": 41246659, - "cdsStart": 41197694, - "contig": "NC_000017.10", - "exons": [ - { - "alignment": null, - "exonNo": 21, - "refEnd": 41197819, - "refStart": 41196312, - "txEnd": 7114, - "txStart": 5608, - }, - { - "alignment": null, - "exonNo": 20, - "refEnd": 41199720, - "refStart": 41199659, - "txEnd": 5607, - "txStart": 5547, - }, - { - "alignment": null, - "exonNo": 19, - "refEnd": 41201211, - "refStart": 41201137, - "txEnd": 5546, - "txStart": 5473, - }, - { - "alignment": null, - "exonNo": 18, - "refEnd": 41203134, - "refStart": 41203079, - "txEnd": 5472, - "txStart": 5418, - }, - { - "alignment": null, - "exonNo": 17, - "refEnd": 41209152, - "refStart": 41209068, - "txEnd": 5417, - "txStart": 5334, - }, - { - "alignment": null, - "exonNo": 16, - "refEnd": 41215390, - "refStart": 41215349, - "txEnd": 5333, - "txStart": 5293, - }, - { - "alignment": null, - "exonNo": 15, - "refEnd": 41215968, - "refStart": 41215890, - "txEnd": 5292, - "txStart": 5215, - }, - { - "alignment": null, - "exonNo": 14, - "refEnd": 41219712, - "refStart": 41219624, - "txEnd": 5214, - "txStart": 5127, - }, - { - "alignment": null, - "exonNo": 13, - "refEnd": 41223255, - "refStart": 41222944, - "txEnd": 5126, - "txStart": 4816, - }, - { - "alignment": null, - "exonNo": 12, - "refEnd": 41226538, - "refStart": 41226347, - "txEnd": 4815, - "txStart": 4625, - }, - { - "alignment": null, - "exonNo": 11, - "refEnd": 41228631, - "refStart": 41228504, - "txEnd": 4624, - "txStart": 4498, - }, - { - "alignment": null, - "exonNo": 10, - "refEnd": 41234592, - "refStart": 41234420, - "txEnd": 4497, - "txStart": 4326, - }, - { - "alignment": null, - "exonNo": 9, - "refEnd": 41243049, - "refStart": 41242960, - "txEnd": 4325, - "txStart": 4237, - }, - { - "alignment": null, - "exonNo": 8, - "refEnd": 41246877, - "refStart": 41243451, - "txEnd": 4236, - "txStart": 811, - }, - { - "alignment": null, - "exonNo": 7, - "refEnd": 41247939, - "refStart": 41247862, - "txEnd": 810, - "txStart": 734, - }, - { - "alignment": null, - "exonNo": 6, - "refEnd": 41249306, - "refStart": 41249260, - "txEnd": 733, - "txStart": 688, - }, - { - "alignment": null, - "exonNo": 5, - "refEnd": 41251897, - "refStart": 41251791, - "txEnd": 687, - "txStart": 582, - }, - { - "alignment": null, - "exonNo": 4, - "refEnd": 41256278, - "refStart": 41256138, - "txEnd": 581, - "txStart": 442, - }, - { - "alignment": null, - "exonNo": 3, - "refEnd": 41256973, - "refStart": 41256884, - "txEnd": 441, - "txStart": 353, - }, - { - "alignment": null, - "exonNo": 2, - "refEnd": 41258550, - "refStart": 41258472, - "txEnd": 352, - "txStart": 275, - }, - { - "alignment": null, - "exonNo": 1, - "refEnd": 41276132, - "refStart": 41276033, - "txEnd": 274, - "txStart": 176, - }, - { - "alignment": null, - "exonNo": 0, - "refEnd": 41277468, - "refStart": 41277293, - "txEnd": 175, - "txStart": 1, - }, - ], - }, - ], - "hgncId": "HGNC:1100", - "hgncSymbol": "BRCA1", - "id": "ENST00000309486.4", - }, - { - "alignments": [ - { - "assembly": "GRCh37", - "cdsEnd": 41276113, - "cdsStart": 41197694, - "contig": "NC_000017.10", - "exons": [ - { - "alignment": null, - "exonNo": 18, - "refEnd": 41197819, - "refStart": 41196312, - "txEnd": 6451, - "txStart": 4945, - }, - { - "alignment": null, - "exonNo": 17, - "refEnd": 41199720, - "refStart": 41199659, - "txEnd": 4944, - "txStart": 4884, - }, - { - "alignment": null, - "exonNo": 16, - "refEnd": 41201211, - "refStart": 41201137, - "txEnd": 4883, - "txStart": 4810, - }, - { - "alignment": null, - "exonNo": 15, - "refEnd": 41203134, - "refStart": 41203079, - "txEnd": 4809, - "txStart": 4755, - }, - { - "alignment": null, - "exonNo": 14, - "refEnd": 41209152, - "refStart": 41209068, - "txEnd": 4754, - "txStart": 4671, - }, - { - "alignment": null, - "exonNo": 13, - "refEnd": 41215390, - "refStart": 41215349, - "txEnd": 4670, - "txStart": 4630, - }, - { - "alignment": null, - "exonNo": 12, - "refEnd": 41215968, - "refStart": 41215890, - "txEnd": 4629, - "txStart": 4552, - }, - { - "alignment": null, - "exonNo": 11, - "refEnd": 41234592, - "refStart": 41234420, - "txEnd": 4551, - "txStart": 4380, - }, - { - "alignment": null, - "exonNo": 10, - "refEnd": 41243049, - "refStart": 41242960, - "txEnd": 4379, - "txStart": 4291, - }, - { - "alignment": null, - "exonNo": 9, - "refEnd": 41246877, - "refStart": 41243451, - "txEnd": 4290, - "txStart": 865, - }, - { - "alignment": null, - "exonNo": 8, - "refEnd": 41247939, - "refStart": 41247862, - "txEnd": 864, - "txStart": 788, - }, - { - "alignment": null, - "exonNo": 7, - "refEnd": 41249306, - "refStart": 41249260, - "txEnd": 787, - "txStart": 742, - }, - { - "alignment": null, - "exonNo": 6, - "refEnd": 41251897, - "refStart": 41251791, - "txEnd": 741, - "txStart": 636, - }, - { - "alignment": null, - "exonNo": 5, - "refEnd": 41256278, - "refStart": 41256138, - "txEnd": 635, - "txStart": 496, - }, - { - "alignment": null, - "exonNo": 4, - "refEnd": 41256973, - "refStart": 41256884, - "txEnd": 495, - "txStart": 407, - }, - { - "alignment": null, - "exonNo": 3, - "refEnd": 41258550, - "refStart": 41258472, - "txEnd": 406, - "txStart": 329, - }, - { - "alignment": null, - "exonNo": 2, - "refEnd": 41267796, - "refStart": 41267742, - "txEnd": 328, - "txStart": 275, - }, - { - "alignment": null, - "exonNo": 1, - "refEnd": 41276132, - "refStart": 41276033, - "txEnd": 274, - "txStart": 176, - }, - { - "alignment": null, - "exonNo": 0, - "refEnd": 41277468, - "refStart": 41277293, - "txEnd": 175, - "txStart": 1, - }, - ], - }, - ], - "hgncId": "HGNC:1100", - "hgncSymbol": "BRCA1", - "id": "ENST00000346315.3", - }, - { - "alignments": [ - { - "assembly": "GRCh37", - "cdsEnd": 41276113, - "cdsStart": 41197694, - "contig": "NC_000017.10", - "exons": [ - { - "alignment": null, - "exonNo": 18, - "refEnd": 41197819, - "refStart": 41196312, - "txEnd": 3444, - "txStart": 1938, - }, - { - "alignment": null, - "exonNo": 17, - "refEnd": 41199720, - "refStart": 41199659, - "txEnd": 1937, - "txStart": 1877, - }, - { - "alignment": null, - "exonNo": 16, - "refEnd": 41201211, - "refStart": 41201137, - "txEnd": 1876, - "txStart": 1803, - }, - { - "alignment": null, - "exonNo": 15, - "refEnd": 41203134, - "refStart": 41203079, - "txEnd": 1802, - "txStart": 1748, - }, - { - "alignment": null, - "exonNo": 14, - "refEnd": 41209152, - "refStart": 41209068, - "txEnd": 1747, - "txStart": 1664, - }, - { - "alignment": null, - "exonNo": 13, - "refEnd": 41215390, - "refStart": 41215349, - "txEnd": 1663, - "txStart": 1623, - }, - { - "alignment": null, - "exonNo": 12, - "refEnd": 41215968, - "refStart": 41215890, - "txEnd": 1622, - "txStart": 1545, - }, - { - "alignment": null, - "exonNo": 11, - "refEnd": 41219712, - "refStart": 41219624, - "txEnd": 1544, - "txStart": 1457, - }, - { - "alignment": null, - "exonNo": 10, - "refEnd": 41223255, - "refStart": 41222944, - "txEnd": 1456, - "txStart": 1146, - }, - { - "alignment": null, - "exonNo": 9, - "refEnd": 41226538, - "refStart": 41226347, - "txEnd": 1145, - "txStart": 955, - }, - { - "alignment": null, - "exonNo": 8, - "refEnd": 41228631, - "refStart": 41228504, - "txEnd": 954, - "txStart": 828, - }, - { - "alignment": null, - "exonNo": 7, - "refEnd": 41234592, - "refStart": 41234420, - "txEnd": 827, - "txStart": 656, - }, - { - "alignment": null, - "exonNo": 6, - "refEnd": 41243049, - "refStart": 41242960, - "txEnd": 655, - "txStart": 567, - }, - { - "alignment": null, - "exonNo": 5, - "refEnd": 41251897, - "refStart": 41251791, - "txEnd": 566, - "txStart": 461, - }, - { - "alignment": null, - "exonNo": 4, - "refEnd": 41256278, - "refStart": 41256138, - "txEnd": 460, - "txStart": 321, - }, - { - "alignment": null, - "exonNo": 3, - "refEnd": 41256973, - "refStart": 41256884, - "txEnd": 320, - "txStart": 232, - }, - { - "alignment": null, - "exonNo": 2, - "refEnd": 41258550, - "refStart": 41258472, - "txEnd": 231, - "txStart": 154, - }, - { - "alignment": null, - "exonNo": 1, - "refEnd": 41267796, - "refStart": 41267742, - "txEnd": 153, - "txStart": 100, - }, - { - "alignment": null, - "exonNo": 0, - "refEnd": 41276132, - "refStart": 41276033, - "txEnd": 99, - "txStart": 1, - }, - ], - }, - ], - "hgncId": "HGNC:1100", - "hgncSymbol": "BRCA1", - "id": "ENST00000351666.3", - }, - { - "alignments": [ - { - "assembly": "GRCh37", - "cdsEnd": 41276113, - "cdsStart": 41197694, - "contig": "NC_000017.10", - "exons": [ - { - "alignment": null, - "exonNo": 21, - "refEnd": 41197819, - "refStart": 41196312, - "txEnd": 3780, - "txStart": 2274, - }, - { - "alignment": null, - "exonNo": 20, - "refEnd": 41199720, - "refStart": 41199659, - "txEnd": 2273, - "txStart": 2213, - }, - { - "alignment": null, - "exonNo": 19, - "refEnd": 41201211, - "refStart": 41201137, - "txEnd": 2212, - "txStart": 2139, - }, - { - "alignment": null, - "exonNo": 18, - "refEnd": 41203134, - "refStart": 41203079, - "txEnd": 2138, - "txStart": 2084, - }, - { - "alignment": null, - "exonNo": 17, - "refEnd": 41209152, - "refStart": 41209068, - "txEnd": 2083, - "txStart": 2000, - }, - { - "alignment": null, - "exonNo": 16, - "refEnd": 41215390, - "refStart": 41215349, - "txEnd": 1999, - "txStart": 1959, - }, - { - "alignment": null, - "exonNo": 15, - "refEnd": 41215968, - "refStart": 41215890, - "txEnd": 1958, - "txStart": 1881, - }, - { - "alignment": null, - "exonNo": 14, - "refEnd": 41219712, - "refStart": 41219624, - "txEnd": 1880, - "txStart": 1793, - }, - { - "alignment": null, - "exonNo": 13, - "refEnd": 41223255, - "refStart": 41222944, - "txEnd": 1792, - "txStart": 1482, - }, - { - "alignment": null, - "exonNo": 12, - "refEnd": 41226538, - "refStart": 41226347, - "txEnd": 1481, - "txStart": 1291, - }, - { - "alignment": null, - "exonNo": 11, - "refEnd": 41228631, - "refStart": 41228504, - "txEnd": 1290, - "txStart": 1164, - }, - { - "alignment": null, - "exonNo": 10, - "refEnd": 41234592, - "refStart": 41234420, - "txEnd": 1163, - "txStart": 992, - }, - { - "alignment": null, - "exonNo": 9, - "refEnd": 41243049, - "refStart": 41242960, - "txEnd": 991, - "txStart": 903, - }, - { - "alignment": null, - "exonNo": 8, - "refEnd": 41247939, - "refStart": 41247862, - "txEnd": 902, - "txStart": 826, - }, - { - "alignment": null, - "exonNo": 7, - "refEnd": 41249306, - "refStart": 41249260, - "txEnd": 825, - "txStart": 780, - }, - { - "alignment": null, - "exonNo": 6, - "refEnd": 41251897, - "refStart": 41251791, - "txEnd": 779, - "txStart": 674, - }, - { - "alignment": null, - "exonNo": 5, - "refEnd": 41256278, - "refStart": 41256138, - "txEnd": 673, - "txStart": 534, - }, - { - "alignment": null, - "exonNo": 4, - "refEnd": 41256973, - "refStart": 41256884, - "txEnd": 533, - "txStart": 445, - }, - { - "alignment": null, - "exonNo": 3, - "refEnd": 41258550, - "refStart": 41258472, - "txEnd": 444, - "txStart": 367, - }, - { - "alignment": null, - "exonNo": 2, - "refEnd": 41267796, - "refStart": 41267742, - "txEnd": 366, - "txStart": 313, - }, - { - "alignment": null, - "exonNo": 1, - "refEnd": 41276132, - "refStart": 41276033, - "txEnd": 312, - "txStart": 214, - }, - { - "alignment": null, - "exonNo": 0, - "refEnd": 41277500, - "refStart": 41277287, - "txEnd": 213, - "txStart": 1, - }, - ], - }, - ], - "hgncId": "HGNC:1100", - "hgncSymbol": "BRCA1", - "id": "ENST00000352993.3", - }, - { - "alignments": [ - { - "assembly": "GRCh37", - "cdsEnd": 41276113, - "cdsStart": 41197694, - "contig": "NC_000017.10", - "exons": [ - { - "alignment": null, - "exonNo": 17, - "refEnd": 41197819, - "refStart": 41196312, - "txEnd": 6411, - "txStart": 4905, - }, - { - "alignment": null, - "exonNo": 16, - "refEnd": 41199720, - "refStart": 41199659, - "txEnd": 4904, - "txStart": 4844, - }, - { - "alignment": null, - "exonNo": 15, - "refEnd": 41201211, - "refStart": 41201137, - "txEnd": 4843, - "txStart": 4770, - }, - { - "alignment": null, - "exonNo": 14, - "refEnd": 41203134, - "refStart": 41203079, - "txEnd": 4769, - "txStart": 4715, - }, - { - "alignment": null, - "exonNo": 13, - "refEnd": 41209152, - "refStart": 41209068, - "txEnd": 4714, - "txStart": 4631, - }, - { - "alignment": null, - "exonNo": 12, - "refEnd": 41215390, - "refStart": 41215349, - "txEnd": 4630, - "txStart": 4590, - }, - { - "alignment": null, - "exonNo": 11, - "refEnd": 41234592, - "refStart": 41234420, - "txEnd": 4589, - "txStart": 4418, - }, - { - "alignment": null, - "exonNo": 10, - "refEnd": 41243049, - "refStart": 41242960, - "txEnd": 4417, - "txStart": 4329, - }, - { - "alignment": null, - "exonNo": 9, - "refEnd": 41246877, - "refStart": 41243451, - "txEnd": 4328, - "txStart": 903, - }, - { - "alignment": null, - "exonNo": 8, - "refEnd": 41247939, - "refStart": 41247862, - "txEnd": 902, - "txStart": 826, - }, - { - "alignment": null, - "exonNo": 7, - "refEnd": 41249306, - "refStart": 41249260, - "txEnd": 825, - "txStart": 780, - }, - { - "alignment": null, - "exonNo": 6, - "refEnd": 41251897, - "refStart": 41251791, - "txEnd": 779, - "txStart": 674, - }, - { - "alignment": null, - "exonNo": 5, - "refEnd": 41256278, - "refStart": 41256138, - "txEnd": 673, - "txStart": 534, - }, - { - "alignment": null, - "exonNo": 4, - "refEnd": 41256973, - "refStart": 41256884, - "txEnd": 533, - "txStart": 445, - }, - { - "alignment": null, - "exonNo": 3, - "refEnd": 41258550, - "refStart": 41258472, - "txEnd": 444, - "txStart": 367, - }, - { - "alignment": null, - "exonNo": 2, - "refEnd": 41267796, - "refStart": 41267742, - "txEnd": 366, - "txStart": 313, - }, - { - "alignment": null, - "exonNo": 1, - "refEnd": 41276132, - "refStart": 41276033, - "txEnd": 312, - "txStart": 214, - }, - { - "alignment": null, - "exonNo": 0, - "refEnd": 41277500, - "refStart": 41277287, - "txEnd": 213, - "txStart": 1, - }, - ], - }, - ], - "hgncId": "HGNC:1100", - "hgncSymbol": "BRCA1", - "id": "ENST00000354071.3", - }, - { - "alignments": [ - { - "assembly": "GRCh37", - "cdsEnd": 41276113, - "cdsStart": 41197694, - "contig": "NC_000017.10", - "exons": [ - { - "alignment": null, - "exonNo": 22, - "refEnd": 41197819, - "refStart": 41196311, - "txEnd": 7094, - "txStart": 5587, - }, - { - "alignment": null, - "exonNo": 21, - "refEnd": 41199720, - "refStart": 41199659, - "txEnd": 5586, - "txStart": 5526, - }, - { - "alignment": null, - "exonNo": 20, - "refEnd": 41201211, - "refStart": 41201137, - "txEnd": 5525, - "txStart": 5452, - }, - { - "alignment": null, - "exonNo": 19, - "refEnd": 41203134, - "refStart": 41203079, - "txEnd": 5451, - "txStart": 5397, - }, - { - "alignment": null, - "exonNo": 18, - "refEnd": 41209152, - "refStart": 41209068, - "txEnd": 5396, - "txStart": 5313, - }, - { - "alignment": null, - "exonNo": 17, - "refEnd": 41215390, - "refStart": 41215349, - "txEnd": 5312, - "txStart": 5272, - }, - { - "alignment": null, - "exonNo": 16, - "refEnd": 41215968, - "refStart": 41215890, - "txEnd": 5271, - "txStart": 5194, - }, - { - "alignment": null, - "exonNo": 15, - "refEnd": 41219712, - "refStart": 41219624, - "txEnd": 5193, - "txStart": 5106, - }, - { - "alignment": null, - "exonNo": 14, - "refEnd": 41223255, - "refStart": 41222944, - "txEnd": 5105, - "txStart": 4795, - }, - { - "alignment": null, - "exonNo": 13, - "refEnd": 41226538, - "refStart": 41226347, - "txEnd": 4794, - "txStart": 4604, - }, - { - "alignment": null, - "exonNo": 12, - "refEnd": 41228631, - "refStart": 41228504, - "txEnd": 4603, - "txStart": 4477, - }, - { - "alignment": null, - "exonNo": 11, - "refEnd": 41234592, - "refStart": 41234420, - "txEnd": 4476, - "txStart": 4305, - }, - { 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"altCdsEndI": 783, + "altCdsStartI": 707, + "altEndI": 41247939, + "altStartI": 41247862, + "cigar": "77M", + "ord": 8, + }, + { + "altCdsEndI": 706, + "altCdsStartI": 661, + "altEndI": 41249306, + "altStartI": 41249260, + "cigar": "46M", + "ord": 7, + }, + { + "altCdsEndI": 660, + "altCdsStartI": 555, + "altEndI": 41251897, + "altStartI": 41251791, + "cigar": "106M", + "ord": 6, + }, + { + "altCdsEndI": 554, + "altCdsStartI": 415, + "altEndI": 41256278, + "altStartI": 41256138, + "cigar": "140M", + "ord": 5, + }, + { + "altCdsEndI": 414, + "altCdsStartI": 326, + "altEndI": 41256973, + "altStartI": 41256884, + "cigar": "89M", + "ord": 4, + }, + { + "altCdsEndI": 325, + "altCdsStartI": 248, + "altEndI": 41258550, + "altStartI": 41258472, + "cigar": "78M", + "ord": 3, + }, + { + "altCdsEndI": 247, + "altCdsStartI": 194, + "altEndI": 41267796, + "altStartI": 41267742, + "cigar": "54M", + "ord": 2, + }, + { + "altCdsEndI": 193, + "altCdsStartI": 95, + "altEndI": 41276132, + "altStartI": 41276033, + "cigar": "99M", + "ord": 1, + }, + { + "altCdsEndI": 94, + "altCdsStartI": 1, + "altEndI": 41277381, + "altStartI": 41277287, + "cigar": "94M", + }, + ], + "genomeBuild": "GENOME_BUILD_GRCH37", + "strand": "STRAND_MINUS", + }, + ], + "id": "NM_007300.4", + "protein": "NP_009231.2", + "startCodon": 113, + "stopCodon": 5768, + }, +] `; exports[`geneInfo Store > should not load data if gene symbol is the same 1`] = ` diff --git a/src/stores/geneInfo/store.spec.ts b/src/stores/geneInfo/store.spec.ts index f3a10ac..41f2bc0 100644 --- a/src/stores/geneInfo/store.spec.ts +++ b/src/stores/geneInfo/store.spec.ts @@ -8,9 +8,9 @@ import { StoreState } from '../types' import { useGeneInfoStore } from './store' /** Fixtures with response from API. */ -const findTranscriptsResponseBrca1 = JSON.parse( +const genesTxsResponseBrca1 = JSON.parse( fs.readFileSync( - path.resolve(__dirname, '../../api/dotty/fixture.findTranscriptsResponse.BRCA1.json'), + path.resolve(__dirname, '../../components/GeneClinvarCard/fixture.genesTxs.BRCA1.37.json'), 'utf8' ) ) @@ -80,8 +80,8 @@ describe('geneInfo Store', () => { return Promise.resolve(JSON.stringify(geneInfoResponseBrca1)) } else if (req.url.includes('clinvar')) { return Promise.resolve(JSON.stringify(geneClinvarResponseBrca1)) - } else if (req.url.includes('find-transcripts')) { - return Promise.resolve(JSON.stringify(findTranscriptsResponseBrca1)) + } else if (req.url.includes('genes/txs')) { + return Promise.resolve(JSON.stringify(genesTxsResponseBrca1)) } else if (req.url.includes('viguno')) { return Promise.resolve(JSON.stringify(hpoTermsResponseBrca1)) } else { @@ -110,8 +110,8 @@ describe('geneInfo Store', () => { return Promise.resolve(JSON.stringify(geneInfoResponseBrca1)) } else if (req.url.includes('clinvar')) { return Promise.resolve(JSON.stringify(geneClinvarResponseBrca1)) - } else if (req.url.includes('find-transcripts')) { - return Promise.resolve(JSON.stringify(findTranscriptsResponseBrca1)) + } else if (req.url.includes('genes/txs')) { + return Promise.resolve(JSON.stringify(genesTxsResponseBrca1)) } else if (req.url.includes('viguno')) { return Promise.resolve(JSON.stringify(hpoTermsResponseBrca1)) } else { @@ -140,8 +140,8 @@ describe('geneInfo Store', () => { return Promise.resolve(JSON.stringify(geneInfoResponseBrca1)) } else if (req.url.includes('clinvar')) { return Promise.resolve(JSON.stringify(geneClinvarResponseBrca1)) - } else if (req.url.includes('find-transcripts')) { - return Promise.resolve(JSON.stringify(findTranscriptsResponseBrca1)) + } else if (req.url.includes('genes/txs')) { + return Promise.resolve(JSON.stringify(genesTxsResponseBrca1)) } else if (req.url.includes('viguno')) { return Promise.resolve(JSON.stringify(hpoTermsResponseBrca1)) } else { @@ -168,8 +168,8 @@ describe('geneInfo Store', () => { return Promise.resolve(JSON.stringify(geneInfoResponseBrca1)) } else if (req.url.includes('clinvar')) { return Promise.resolve(JSON.stringify(geneClinvarResponseBrca1)) - } else if (req.url.includes('find-transcripts')) { - return Promise.resolve(JSON.stringify(findTranscriptsResponseBrca1)) + } else if (req.url.includes('genes/txs')) { + return Promise.resolve(JSON.stringify(genesTxsResponseBrca1)) } else if (req.url.includes('viguno')) { return Promise.resolve(JSON.stringify(hpoTermsResponseBrca1)) } else { diff --git a/src/stores/geneInfo/store.ts b/src/stores/geneInfo/store.ts index 4136c1d..7406ab6 100644 --- a/src/stores/geneInfo/store.ts +++ b/src/stores/geneInfo/store.ts @@ -7,12 +7,12 @@ import { defineStore } from 'pinia' import { ref } from 'vue' import { AnnonarsClient } from '../../api/annonars' -import { DottyClient, TranscriptResult } from '../../api/dotty' +import { MehariClient } from '../../api/mehari' import { type HpoTerm, VigunoClient } from '../../api/viguno' import { type GenomeBuild } from '../../lib/genomeBuilds' -import { urlConfig } from '../../lib/urlConfig' import { ClinvarPerGeneRecord } from '../../pbs/annonars/clinvar/per_gene' import { Record as GeneInfoRecord } from '../../pbs/annonars/genes/base' +import { GenomeBuild as MehariGenomeBuild, Transcript } from '../../pbs/mehari/txs' import { StoreState } from '../types' export const useGeneInfoStore = defineStore('geneInfo', () => { @@ -32,7 +32,7 @@ export const useGeneInfoStore = defineStore('geneInfo', () => { const geneClinvar = ref(undefined) /** Transcript information from dotty (unless dotty API not available). */ - const transcripts = ref(undefined) + const transcripts = ref(undefined) function clearData() { storeState.value = StoreState.Initial @@ -83,15 +83,14 @@ export const useGeneInfoStore = defineStore('geneInfo', () => { hgncId.value = hgncIdQuery storeState.value = StoreState.Active - // Only load from dotty if API base URL configured. - if (urlConfig.baseUrlDotty !== undefined) { - const dottyClient = new DottyClient() - const transcriptsData = await dottyClient.fetchTranscripts( - hgncIdQuery, - genomeBuild === 'grch37' ? 'GRCh37' : 'GRCh38' - ) - transcripts.value = transcriptsData ?? undefined - } + const mehariClient = new MehariClient() + const transcriptsData = await mehariClient.retrieveGeneTranscripts( + hgncIdQuery, + genomeBuild === 'grch37' + ? MehariGenomeBuild.GENOME_BUILD_GRCH37 + : MehariGenomeBuild.GENOME_BUILD_GRCH38 + ) + transcripts.value = transcriptsData.transcripts ?? undefined } catch (e) { console.error('There was an error loading the gene data.', e) clearData()