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remove refseq in ensembl test files
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sshugsc committed Mar 5, 2024
1 parent f4acbcc commit 2e18fe7
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10 changes: 5 additions & 5 deletions test/data/ensembl_biomart_export_ENSG00000139618.tsv
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Original file line number Diff line number Diff line change
@@ -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
325 changes: 0 additions & 325 deletions test/data/ensembl_uploadFile_requests.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand Down Expand Up @@ -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": {
Expand Down Expand Up @@ -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": {
Expand Down
9 changes: 0 additions & 9 deletions test/ensembl/ensembl.uploadFile.test.js
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Original file line number Diff line number Diff line change
Expand Up @@ -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' },
],
Expand Down Expand Up @@ -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
Expand Down

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