diff --git a/test/data/ensembl_biomart_export_ENSG00000139618.tsv b/test/data/ensembl_biomart_export_ENSG00000139618.tsv index 7d143ea0..f0aa0d0c 100644 --- a/test/data/ensembl_biomart_export_ENSG00000139618.tsv +++ b/test/data/ensembl_biomart_export_ENSG00000139618.tsv @@ -1,5 +1,5 @@ -Gene stable ID Gene stable ID version Transcript stable ID Transcript stable ID version Protein stable ID Protein stable ID version HGNC ID RefSeq mRNA ID Gene description Gene name Source of gene name -ENSG00000139618 ENSG00000139618.17 ENST00000544455 ENST00000544455.6 ENSP00000439902 ENSP00000439902.1 HGNC:1101 BRCA2 DNA repair associated [Source:HGNC Symbol;Acc:HGNC:1101] BRCA2 HGNC Symbol -ENSG00000139618 ENSG00000139618.17 ENST00000530893 ENST00000530893.6 ENSP00000499438 ENSP00000499438.2 HGNC:1101 BRCA2 DNA repair associated [Source:HGNC Symbol;Acc:HGNC:1101] BRCA2 HGNC Symbol -ENSG00000139618 ENSG00000139618.17 ENST00000380152 ENST00000380152.8 ENSP00000369497 ENSP00000369497.3 HGNC:1101 NM_000059 BRCA2 DNA repair associated [Source:HGNC Symbol;Acc:HGNC:1101] BRCA2 HGNC Symbol -ENSG00000139618 ENSG00000139618.17 ENST00000680887 ENST00000680887.1 ENSP00000505508 ENSP00000505508.1 HGNC:1101 BRCA2 DNA repair associated [Source:HGNC Symbol;Acc:HGNC:1101] BRCA2 HGNC Symbol +Gene stable ID Gene stable ID version Transcript stable ID Transcript stable ID version Protein stable ID Protein stable ID version HGNC ID Gene description Gene name Source of gene name +ENSG00000139618 ENSG00000139618.17 ENST00000544455 ENST00000544455.6 ENSP00000439902 ENSP00000439902.1 HGNC:1101 BRCA2 DNA repair associated [Source:HGNC Symbol;Acc:HGNC:1101] BRCA2 HGNC Symbol +ENSG00000139618 ENSG00000139618.17 ENST00000530893 ENST00000530893.6 ENSP00000499438 ENSP00000499438.2 HGNC:1101 BRCA2 DNA repair associated [Source:HGNC Symbol;Acc:HGNC:1101] BRCA2 HGNC Symbol +ENSG00000139618 ENSG00000139618.17 ENST00000380152 ENST00000380152.8 ENSP00000369497 ENSP00000369497.3 HGNC:1101 BRCA2 DNA repair associated [Source:HGNC Symbol;Acc:HGNC:1101] BRCA2 HGNC Symbol +ENSG00000139618 ENSG00000139618.17 ENST00000680887 ENST00000680887.1 ENSP00000505508 ENSP00000505508.1 HGNC:1101 BRCA2 DNA repair associated [Source:HGNC Symbol;Acc:HGNC:1101] BRCA2 HGNC Symbol diff --git a/test/data/ensembl_uploadFile_requests.json b/test/data/ensembl_uploadFile_requests.json index 5bdefb4a..9c0d2ccf 100644 --- a/test/data/ensembl_uploadFile_requests.json +++ b/test/data/ensembl_uploadFile_requests.json @@ -50,58 +50,6 @@ } } }, - { - "opt": { - "body": { - "filters": { - "name": "refseq" - }, - "neighbors": 1, - "target": "Source" - }, - "method": "POST", - "uri": "/query" - }, - "result": { - "metadata": { - "records": 0 - }, - "result": [] - } - }, - { - "opt": { - "body": { - "description": "A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.", - "displayName": "RefSeq", - "longName": "RefSeq: NCBI Reference Sequence Database", - "name": "refseq", - "url": "https://www.ncbi.nlm.nih.gov/refseq", - "usage": "https://www.ncbi.nlm.nih.gov/home/about/policies" - }, - "method": "POST", - "uri": "/sources" - }, - "result": { - "result": { - "@class": "Source", - "sort": 99999, - "description": "a comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.", - "displayName": "RefSeq", - "longName": "refseq: ncbi reference sequence database", - "name": "refseq", - "url": "https://www.ncbi.nlm.nih.gov/refseq", - "usage": "https://www.ncbi.nlm.nih.gov/home/about/policies", - "createdBy": "#32:0", - "updatedBy": "#32:0", - "uuid": "f319e234-13b1-4841-b049-e48aacf2644a", - "createdAt": 1653589823081, - "updatedAt": 1653589823081, - "@rid": "#42:0", - "@version": 1 - } - } - }, { "opt": { "body": { @@ -235,167 +183,6 @@ "result": [] } }, - { - "opt": { - "body": { - "filters": { - "AND": [ - { - "source": { - "filters": { - "name": "refseq" - }, - "target": "Source" - } - }, - { - "dependency": null - }, - { - "deprecated": false - } - ] - }, - "limit": 1000, - "neighbors": 0, - "returnProperties": null, - "skip": 0, - "target": "Feature" - }, - "method": "POST", - "uri": "/query" - }, - "result": { - "metadata": { - "records": 0 - }, - "result": [] - } - }, - { - "opt": { - "body": { - "filters": { - "name": "refseq" - }, - "neighbors": 1, - "target": "Source" - }, - "method": "POST", - "uri": "/query" - }, - "result": { - "metadata": { - "records": 1 - }, - "result": [ - { - "createdAt": 1653589823081, - "updatedBy": { - "createdAt": 1653589817005, - "lastLoginAt": 1653589823040, - "name": "mlemieux", - "groups": [ - "#25:0" - ], - "signedLicenseAt": 1653589817002, - "firstLoginAt": 1653589823040, - "uuid": "d3ccc0e1-a51d-4086-abd4-a35ee8f8b6fa", - "loginCount": 1, - "@rid": "#32:0", - "@class": "User" - }, - "createdBy": { - "createdAt": 1653589817005, - "lastLoginAt": 1653589823040, - "name": "mlemieux", - "groups": [ - "#25:0" - ], - "signedLicenseAt": 1653589817002, - "firstLoginAt": 1653589823040, - "uuid": "d3ccc0e1-a51d-4086-abd4-a35ee8f8b6fa", - "loginCount": 1, - "@rid": "#32:0", - "@class": "User" - }, - "displayName": "RefSeq", - "usage": "https://www.ncbi.nlm.nih.gov/home/about/policies", - "name": "refseq", - "description": "a comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.", - "sort": 99999, - "uuid": "f319e234-13b1-4841-b049-e48aacf2644a", - "url": "https://www.ncbi.nlm.nih.gov/refseq", - "longName": "refseq: ncbi reference sequence database", - "updatedAt": 1653589823081, - "@rid": "#42:0", - "@class": "Source" - } - ] - } - }, - { - "opt": { - "body": { - "filters": { - "AND": [ - { - "sourceId": "NM_000059" - }, - { - "source": "#42:0" - }, - { - "sourceIdVersion": null - } - ] - }, - "neighbors": 1, - "target": "Feature" - }, - "method": "POST", - "uri": "/query" - }, - "result": { - "metadata": { - "records": 0 - }, - "result": [] - } - }, - { - "opt": { - "body": { - "biotype": "transcript", - "displayName": "NM_000059", - "sourceId": "nm_000059", - "sourceIdVersion": null, - "source": "#42:0" - }, - "method": "POST", - "uri": "/features" - }, - "result": { - "result": { - "@class": "Feature", - "deprecated": false, - "alias": false, - "biotype": "transcript", - "displayName": "NM_000059", - "sourceId": "nm_000059", - "sourceIdVersion": null, - "source": "#42:0", - "createdBy": "#32:0", - "updatedBy": "#32:0", - "uuid": "1703537d-b15a-4a95-a3f8-575939e5c89d", - "createdAt": 1653589823632, - "updatedAt": 1653589823632, - "name": "nm_000059", - "@rid": "#137:0", - "@version": 1 - } - } - }, { "opt": { "body": { @@ -2311,118 +2098,6 @@ } } }, - { - "opt": { - "body": { - "filters": { - "AND": [ - { - "source": "#42:0" - }, - { - "sourceId": "NM_000059" - }, - { - "sourceIdVersion": null - } - ] - }, - "neighbors": 1, - "target": "Feature" - }, - "method": "POST", - "uri": "/query" - }, - "result": { - "metadata": { - "records": 1 - }, - "result": [ - { - "biotype": "transcript", - "sourceId": "nm_000059", - "updatedBy": { - "createdAt": 1653589817005, - "lastLoginAt": 1653589823040, - "name": "mlemieux", - "groups": [ - "#25:0" - ], - "signedLicenseAt": 1653589817002, - "firstLoginAt": 1653589823040, - "uuid": "d3ccc0e1-a51d-4086-abd4-a35ee8f8b6fa", - "loginCount": 1, - "@rid": "#32:0", - "@class": "User" - }, - "displayName": "NM_000059", - "deprecated": false, - "sourceIdVersion": null, - "source": { - "createdAt": 1653589823081, - "updatedBy": "#32:0", - "createdBy": "#32:0", - "displayName": "RefSeq", - "usage": "https://www.ncbi.nlm.nih.gov/home/about/policies", - "name": "refseq", - "description": "a comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.", - "sort": 99999, - "uuid": "f319e234-13b1-4841-b049-e48aacf2644a", - "url": "https://www.ncbi.nlm.nih.gov/refseq", - "longName": "refseq: ncbi reference sequence database", - "updatedAt": 1653589823081, - "@rid": "#42:0", - "@class": "Source" - }, - "uuid": "1703537d-b15a-4a95-a3f8-575939e5c89d", - "createdAt": 1653589823632, - "createdBy": { - "createdAt": 1653589817005, - "lastLoginAt": 1653589823040, - "name": "mlemieux", - "groups": [ - "#25:0" - ], - "signedLicenseAt": 1653589817002, - "firstLoginAt": 1653589823040, - "uuid": "d3ccc0e1-a51d-4086-abd4-a35ee8f8b6fa", - "loginCount": 1, - "@rid": "#32:0", - "@class": "User" - }, - "name": "nm_000059", - "alias": false, - "updatedAt": 1653589823632, - "@rid": "#137:0", - "@class": "Feature" - } - ] - } - }, - { - "opt": { - "body": { - "in": "#137:0", - "out": "#138:4", - "source": "#41:0" - }, - "method": "POST", - "uri": "/crossreferenceof" - }, - "result": { - "result": { - "@class": "CrossReferenceOf", - "out": "#138:4", - "in": "#137:0", - "source": "#41:0", - "createdBy": "#32:0", - "uuid": "5b3d1a81-1453-4464-8cba-4ef3d660c163", - "createdAt": 1653589830261, - "@rid": "#83:0", - "@version": 1 - } - } - }, { "opt": { "body": { diff --git a/test/ensembl/ensembl.uploadFile.test.js b/test/ensembl/ensembl.uploadFile.test.js index 7165a253..15d43aee 100644 --- a/test/ensembl/ensembl.uploadFile.test.js +++ b/test/ensembl/ensembl.uploadFile.test.js @@ -107,7 +107,6 @@ describe('uploadFile in Ensembl loader', () => { { '@rid': '#138:4', edges: [ - { class: 'crossreferenceof', in: '#137:0' }, { class: 'elementof', in: '#139:0' }, { class: 'generalizationof', in: '#137:4' }, ], @@ -273,14 +272,6 @@ describe('uploadFile in Ensembl loader', () => { ], feature: { biotype: 'gene', name: 'XRCC11', source: 'hgnc' }, }, - { - '@rid': '#137:0', - edges: [], - feature: { - biotype: 'transcript', source: 'refseq', sourceId: 'NM_000059', sourceIdVersion: null, - }, - - }, ].map(el => Object.assign(el, { // Custom method - Returns the source's RID from mockDataset