| Next changeset 1:2e057dfe494c (2024-08-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258 |
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added:
analyses.xml macros.xml test-data/HG00096.json test-data/analyses_query_findings.json test-data/biosamples_query_findings.json test-data/bracket_query_findings.json test-data/cnv_query_findings.json test-data/cohorts_query_findings.json test-data/datasets_query_findings.json test-data/gene_query_findings.json test-data/individuals_query_findings.json test-data/logs.txt test-data/ranged_query_findings.json test-data/runs_query_findings.json test-data/sequenced_query_findings.json |
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| diff -r 000000000000 -r 5fcaabf17d8d analyses.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/analyses.xml Mon Jul 22 12:35:29 2024 +0000 |
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| @@ -0,0 +1,83 @@ +<tool id="beacon2_analyses" name="Beacon2 Analyses" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> + <description>َQuery the analyses collection in the beacon database for bioinformatic procedures to identify variants</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creators"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + beacon2-search analyses + --db-host '$db_host' + --db-port $db_port + --database '$database' + --collection '$collection' + --advance-connection + --db-auth-config '$credentials' + #if str($advanced_settings.aligner) + --aligner '$advanced_settings.aligner' + #end if + #if str($advanced_settings.analysisDate) + --analysisDate '$advanced_settings.analysisDate' + #end if + #if str($advanced_settings.biosampleId) + --biosampleId '$advanced_settings.biosampleId' + #end if + #if str($advanced_settings.identification) + --identification '$advanced_settings.identification' + #end if + #if str($advanced_settings.individualId) + --individualId '$advanced_settings.individualId' + #end if + #if str($advanced_settings.pipelineName) + --pipelineName '$advanced_settings.pipelineName' + #end if + #if str($advanced_settings.pipelineRef) + --pipelineRef '$advanced_settings.pipelineRef' + #end if + #if str($advanced_settings.runId) + --runId '$advanced_settings.runId' + #end if + #if str($advanced_settings.variantCaller) + --variantCaller '$advanced_settings.variantCaller' + #end if + > analyses_query_findings.json + ]]></command> + <expand macro="configfile"/> + <inputs> + <expand macro="Connection_to_MongoDB" /> + <expand macro="Database_Configuration" /> + <section name="advanced_settings" title="Advanced settings" expanded="false"> + <param argument="--aligner" optional="true" type="text" label="ALIGNER" value="" help="Reference to mapping/alignment software. Example bwa-0.7.8" /> + <param argument="--analysisDate" optional="true" type="text" label="ANALYSIS DATE" value="" help="Date at which analysis was performed. Example 2021-10-17 " /> + <param argument="--biosampleId" optional="true" type="text" label="BIOSAMPLE ID" value="" help="Reference to the id of the biosample this analysis is reporting on. Example S0001 " /> + <param argument="--identification" optional="true" type="text" label="ID" value="" help="Analysis reference ID (external accession or internal ID). Example GA.01234abcde" /> + <param argument="--individualId" optional="true" type="text" label="INDIVIDUALID" value="" help="Reference to the id of the individual this analysis is reporting on. Example P0001 " /> + <param argument="--pipelineName" optional="true" type="text" label="PIPELINE NAME" value="" help="Analysis pipeline and version if a standardized pipeline was used. Example Pipeline-panel-0001-v1 " /> + <param argument="--pipelineRef" optional="true" type="text" label="PIPELINE REF" value="" help="Link to Analysis pipeline resource" /> + <param argument="--runId" optional="true" type="text" label="RUNID" value="" help=" Run identifier (external accession or internal ID). Example SRR10903401" /> + <param argument="--variantCaller" optional="true" type="text" label="VARIANT CALLER" value="" help="Reference to variant calling software / pipeline. Example GATK4.0 " /> + </section> + </inputs> + <outputs> + <data name="out_analyses_query" format="json" label="${tool.name} on ${on_string}: Analyses Query" from_work_dir="analyses_query_findings.json" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="database" value="beacon" /> + <param name="collection" value="analyses" /> + <param name="db_host" value="20.108.51.167" /> + <param name="individualId" value="NA24694" /> + <param name="biosampleId" value="S0002" /> + <param name="aligner" value="bwa-0.7.8" /> + <param name="pipelineName" value="GATK Pipeline 4.2.3.0" /> + <param name="identification" value="refvar-668fc705ef8bca245c3c2185" /> + <output name="out_analyses_query"> + <assert_contents><has_text_matching expression="_id"/></assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Beacon2 Analyses queries the analyses collection in the Beacon database to identify bioinformatic procedures and variants. This tool allows detailed queries using advanced settings such as aligner, analysis date, biosample ID, and more. + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 5fcaabf17d8d macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jul 22 12:35:29 2024 +0000 |
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| @@ -0,0 +1,55 @@ +<macros> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">2.2.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">beacon2-import</requirement> + </requirements> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">ga4gh_beacon</xref> + </xrefs> + </xml> + <xml name="creators"> + <creator> + <person givenName="Khaled" familyName="Jum'ah" url="https://github.com/khaled196" /> + <person givenName="Björn" familyName="Grüning" url="https://github.com/bgruening" /> + <person givenName="Katarzyna" familyName="Kamieniecka" url="https://github.com/kkamieniecka" /> + <person givenName="Krzysztof" familyName="Poterlowicz" url="https://github.com/poterlowicz-lab" /> + <organization name="poterlowicz-lab" url="https://github.com/poterlowicz-lab" /> + </creator> + </xml> + <xml name="Connection_to_MongoDB"> + <param argument="--db-host" type="text" label="DATABASE HOST" value="127.0.0.1" help="Hostname/IP of the beacon database" /> + <param argument="--db-port" type="integer" label="DATABASE PORT" value="27017" help="Port of the beacon database" /> + </xml> + <xml name="Database_Configuration"> + <param argument="--database" type="text" label="DATABASE" value="" help="The targeted beacon database" /> + <param argument="--collection" type="text" label="COLLECTION" value="" help="The targeted beacon collection from the desired database" /> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1002/humu.24369</citation> + </citations> + </xml> + <xml name="configfile"> + <configfiles> + <configfile name="credentials"><![CDATA[ + #set $db_auth_source = $__user__.extra_preferences.get('beacon2_account|db_auth_source', "") + #set $db_user = $__user__.extra_preferences.get('beacon2_account|db_user', "") + #set $db_password = $__user__.extra_preferences.get('beacon2_account|db_password', "") + #if $db_user == "" or $db_password == "" or $db_auth_source == "": + #set $db_auth_source = "admin" + #set $db_user = "root" + #set $db_password = "example" + #end if + { + "db_auth_source": "$db_auth_source", + "db_user": "$db_user", + "db_password": "$db_password" + } + ]]></configfile> + </configfiles> + </xml> +</macros> |
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| diff -r 000000000000 -r 5fcaabf17d8d test-data/HG00096.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HG00096.json Mon Jul 22 12:35:29 2024 +0000 |
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| b'@@ -0,0 +1,8867 @@\n+[\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chr1:2650427-2651463:EFO:0030069",\n+ "variantType": "DEL",\n+ "variantId": "EFO:0030069",\n+ "start": 2650427,\n+ "end": 2651463,\n+ "referenceName": "1",\n+ "info": {\n+ "legacyId": "DRAGEN:LOSS:chr1:2650428-2651463",\n+ "cnCount": 0,\n+ "cnValue": 1.00369e-09\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chr1:2651463-2653075:EFO:0030068",\n+ "variantType": "DEL",\n+ "variantId": "EFO:0030068",\n+ "start": 2651463,\n+ "end": 2653075,\n+ "referenceName": "1",\n+ "info": {\n+ "legacyId": "DRAGEN:LOSS:chr1:2651464-2653075",\n+ "cnCount": 1,\n+ "cnValue": 0.395524\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chr1:4063594-4067475:EFO:0030068",\n+ "variantType": "DEL",\n+ "variantId": "EFO:0030068",\n+ "start": 4063594,\n+ "end": 4067475,\n+ "referenceName": "1",\n+ "info": {\n+ "legacyId": "DRAGEN:LOSS:chr1:4063595-4067475",\n+ "cnCount": 1,\n+ "cnValue": 0.429788\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chr1:6377770-6385660:EFO:0030068",\n+ "variantType": "DEL",\n+ "variantId": "EFO:0030068",\n+ "start": 6377770,\n+ "end": 6385660,\n+ "referenceName": "1",\n+ "info": {\n+ "legacyId": "DRAGEN:LOSS:chr1:6377771-6385660",\n+ "cnCount": 1,\n+ "cnValue": 0.543097\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chr1:8143311-8150440:EFO:0030071",\n+ "variantType": "DUP",\n+ "variantId": "EFO:0030071",\n+ "start": 8143311,\n+ "end": 8150440,\n+ "referenceName": "1",\n+ "info": {\n+ "legacyId": "DRAGEN:GAIN:chr1:8143312-8150440",\n+ "cnCount": 3,\n+ "cnValue": 1.42495\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chr1:13224579-13242034:EFO:0030071",\n+ "variantType": "DUP",\n+ "variantId": "EFO:0030071",\n+ "start": 13224579,\n+ "end": 13242034,\n+ "referenceName": "1",\n+ "info": {\n+ "legacyId": "DRAGEN:GAIN:chr1:13224580-13242034",\n+ "cnCount": 3,\n+ "cnValue": 1.49181\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chr1:16605061-16646293:EFO:0030071",\n+ "variantType": "DUP",\n+ "variantId": "EFO:0030071",\n+ "start": 16605061,\n+ "end": 16646293,\n+ "referenceName": "1",\n+ "info": {\n+ "legacyId": "DRAGEN:GAIN:chr1:16605062-16646293",\n+ "cnCount": 7,\n+ "cnValue": 3.3289\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chr1:16716711-16728256:EFO:0030071",\n+ "variantType": "DUP",\n+ "variantId": "EFO:0030071",\n+ "start": 16716711,\n+ "end": 16728256,\n+ "referenceName": "1",\n+ "info": {\n+ "legacyId": "DRAGEN:GAIN:chr1:16716712-16728256",\n+ "cnCount": 5,\n+ "cnValue": 2.68822\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chr1:16879751-16950196:EFO:0030071",\n+ "variantType": "DUP",\n+ "variantId": "EFO:0030071",\n+ "start": 16879751,\n+ "end": 16950196,\n+ "referenceName": "1",\n+ "info": {\n+ "legacyId": "DRAGEN:GAIN:'..b'",\n+ "variantType": "DEL",\n+ "variantId": "EFO:0030069",\n+ "start": 155688504,\n+ "end": 155692183,\n+ "referenceName": "X",\n+ "info": {\n+ "legacyId": "DRAGEN:LOSS:chrX:155688505-155692183",\n+ "cnCount": 0,\n+ "cnValue": 1.00369e-09\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chrY:3844269-3854396:EFO:0030070",\n+ "variantType": "DUP",\n+ "variantId": "EFO:0030070",\n+ "start": 3844269,\n+ "end": 3854396,\n+ "referenceName": "Y",\n+ "info": {\n+ "legacyId": "DRAGEN:GAIN:chrY:3844270-3854396",\n+ "cnCount": 2,\n+ "cnValue": 1.85714\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chrY:10659024-10693717:EFO:0030070",\n+ "variantType": "DUP",\n+ "variantId": "EFO:0030070",\n+ "start": 10659024,\n+ "end": 10693717,\n+ "referenceName": "Y",\n+ "info": {\n+ "legacyId": "DRAGEN:GAIN:chrY:10659025-10693717",\n+ "cnCount": 2,\n+ "cnValue": 1.96766\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chrY:11108561-11117868:EFO:0030070",\n+ "variantType": "DUP",\n+ "variantId": "EFO:0030070",\n+ "start": 11108561,\n+ "end": 11117868,\n+ "referenceName": "Y",\n+ "info": {\n+ "legacyId": "DRAGEN:GAIN:chrY:11108562-11117868",\n+ "cnCount": 4,\n+ "cnValue": 3.54352\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chrY:11289947-11296309:EFO:0030071",\n+ "variantType": "DUP",\n+ "variantId": "EFO:0030071",\n+ "start": 11289947,\n+ "end": 11296309,\n+ "referenceName": "Y",\n+ "info": {\n+ "legacyId": "DRAGEN:GAIN:chrY:11289948-11296309",\n+ "cnCount": 26,\n+ "cnValue": 26.0609\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chrY:11296309-11330116:EFO:0030070",\n+ "variantType": "DUP",\n+ "variantId": "EFO:0030070",\n+ "start": 11296309,\n+ "end": 11330116,\n+ "referenceName": "Y",\n+ "info": {\n+ "legacyId": "DRAGEN:GAIN:chrY:11296310-11330116",\n+ "cnCount": 2,\n+ "cnValue": 1.84192\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chrY:11530585-11539539:EFO:0030071",\n+ "variantType": "DUP",\n+ "variantId": "EFO:0030071",\n+ "start": 11530585,\n+ "end": 11539539,\n+ "referenceName": "Y",\n+ "info": {\n+ "legacyId": "DRAGEN:GAIN:chrY:11530586-11539539",\n+ "cnCount": 17,\n+ "cnValue": 16.6986\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chrY:11744914-11748800:EFO:0030070",\n+ "variantType": "DUP",\n+ "variantId": "EFO:0030070",\n+ "start": 11744914,\n+ "end": 11748800,\n+ "referenceName": "Y",\n+ "info": {\n+ "legacyId": "DRAGEN:GAIN:chrY:11744915-11748800",\n+ "cnCount": 2,\n+ "cnValue": 2.03175\n+ }\n+ },\n+ {\n+ "biosampleId": "HG00096",\n+ "assemblyId": "GRCh38",\n+ "variantInternalId": "chrY:12512335-12514483:EFO:0030069",\n+ "variantType": "DEL",\n+ "variantId": "EFO:0030069",\n+ "start": 12512335,\n+ "end": 12514483,\n+ "referenceName": "Y",\n+ "info": {\n+ "legacyId": "DRAGEN:LOSS:chrY:12512336-12514483",\n+ "cnCount": 0,\n+ "cnValue": 0.284822\n+ }\n+ }\n+]\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 5fcaabf17d8d test-data/analyses_query_findings.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/analyses_query_findings.json Mon Jul 22 12:35:29 2024 +0000 |
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| @@ -0,0 +1,9 @@ +{'_id': ObjectId('668fc705ef8bca245c3c2185'), + 'aligner': 'bwa-0.7.8', + 'analysisDate': '2021-04-23', + 'biosampleId': 'S0002', + 'id': 'refvar-668fc705ef8bca245c3c2185', + 'individualId': 'NA24694', + 'pipelineName': 'GATK Pipeline 4.2.3.0', + 'runId': 'SRR10903402', + 'variantCaller': 'GATK4.0'} |
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| diff -r 000000000000 -r 5fcaabf17d8d test-data/biosamples_query_findings.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biosamples_query_findings.json Mon Jul 22 12:35:29 2024 +0000 |
| [ |
| b"@@ -0,0 +1,162 @@\n+{'_id': ObjectId('668fb4eb8ed056280039f1bd'),\n+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},\n+ 'collectionDate': '2021-04-23',\n+ 'collectionMoment': 'P32Y6M1D',\n+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],\n+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',\n+ 'label': 'Infiltrating Urothelial Carcinoma'},\n+ 'id': 'refvar-668fb4eb8ed056280039f1bd',\n+ 'individualId': 'NA24631',\n+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},\n+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',\n+ 'label': 'T2b Stage Finding'}],\n+ 'sampleOriginDetail': {'id': 'UBERON:0001256',\n+ 'label': 'wall of urinary bladde'},\n+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},\n+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},\n+ 'tumorProgression': {'id': 'NCIT:C84509',\n+ 'label': 'Primary Malignant Neoplasm'}}\n+{'_id': ObjectId('668fb4eb8ed056280039f1be'),\n+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},\n+ 'collectionDate': '2021-04-23',\n+ 'collectionMoment': 'P32Y6M1D',\n+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],\n+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',\n+ 'label': 'Infiltrating Urothelial Carcinoma'},\n+ 'id': 'refvar-668fb4eb8ed056280039f1be',\n+ 'individualId': 'NA24694',\n+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},\n+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',\n+ 'label': 'T2b Stage Finding'}],\n+ 'sampleOriginDetail': {'id': 'UBERON:0001256',\n+ 'label': 'wall of urinary bladde'},\n+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},\n+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},\n+ 'tumorProgression': {'id': 'NCIT:C84509',\n+ 'label': 'Primary Malignant Neoplasm'}}\n+{'_id': ObjectId('668fb4eb8ed056280039f1bf'),\n+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},\n+ 'collectionDate': '2021-04-23',\n+ 'collectionMoment': 'P32Y6M1D',\n+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],\n+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',\n+ 'label': 'Infiltrating Urothelial Carcinoma'},\n+ 'id': 'refvar-668fb4eb8ed056280039f1bf',\n+ 'individualId': 'NA24695',\n+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},\n+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',\n+ 'label': 'T2b Stage Finding'}],\n+ 'sampleOriginDetail': {'id': 'UBERON:0001256',\n+ 'label': 'wall of urinary bladde'},\n+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},\n+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},\n+ 'tumorProgression': {'id': 'NCIT:C84509',\n+ 'label': 'Primary Malignant Neoplasm'}}\n+{'_id': ObjectId('668fb7125d00a890d911aa69'),\n+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},\n+ 'collectionDate': '2021-04-23',\n+ 'collectionMoment': 'P32Y6M1D',\n+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],\n+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',\n+ 'label': 'Infiltrating Urothelial Carcinoma'},\n+ 'id': 'refvar-668fb7125d00a890d911aa69',\n+ 'individualId': 'NA24631',\n+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},\n+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',\n+ 'label': 'T2b Stage Finding'}],\n+ 'sampleOriginDetail': {'id': 'UBERON:0001256',\n+ 'label': 'wall of urinary bladde'},\n+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},\n+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},\n+ 'tumorProgression': {'id': 'NCIT:C84509',\n+ 'label': 'Primary Malignant Neoplasm'"..b"nt Neoplasm'}}\n+{'_id': ObjectId('668fb7125d00a890d911aa6b'),\n+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},\n+ 'collectionDate': '2021-04-23',\n+ 'collectionMoment': 'P32Y6M1D',\n+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],\n+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',\n+ 'label': 'Infiltrating Urothelial Carcinoma'},\n+ 'id': 'refvar-668fb7125d00a890d911aa6b',\n+ 'individualId': 'NA24695',\n+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},\n+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',\n+ 'label': 'T2b Stage Finding'}],\n+ 'sampleOriginDetail': {'id': 'UBERON:0001256',\n+ 'label': 'wall of urinary bladde'},\n+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},\n+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},\n+ 'tumorProgression': {'id': 'NCIT:C84509',\n+ 'label': 'Primary Malignant Neoplasm'}}\n+{'_id': ObjectId('668fb721ae6c452887afb69d'),\n+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},\n+ 'collectionDate': '2021-04-23',\n+ 'collectionMoment': 'P32Y6M1D',\n+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],\n+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',\n+ 'label': 'Infiltrating Urothelial Carcinoma'},\n+ 'id': 'refvar-668fb721ae6c452887afb69d',\n+ 'individualId': 'NA24631',\n+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},\n+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',\n+ 'label': 'T2b Stage Finding'}],\n+ 'sampleOriginDetail': {'id': 'UBERON:0001256',\n+ 'label': 'wall of urinary bladde'},\n+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},\n+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},\n+ 'tumorProgression': {'id': 'NCIT:C84509',\n+ 'label': 'Primary Malignant Neoplasm'}}\n+{'_id': ObjectId('668fb721ae6c452887afb69e'),\n+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},\n+ 'collectionDate': '2021-04-23',\n+ 'collectionMoment': 'P32Y6M1D',\n+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],\n+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',\n+ 'label': 'Infiltrating Urothelial Carcinoma'},\n+ 'id': 'refvar-668fb721ae6c452887afb69e',\n+ 'individualId': 'NA24694',\n+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},\n+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',\n+ 'label': 'T2b Stage Finding'}],\n+ 'sampleOriginDetail': {'id': 'UBERON:0001256',\n+ 'label': 'wall of urinary bladde'},\n+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},\n+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},\n+ 'tumorProgression': {'id': 'NCIT:C84509',\n+ 'label': 'Primary Malignant Neoplasm'}}\n+{'_id': ObjectId('668fb721ae6c452887afb69f'),\n+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},\n+ 'collectionDate': '2021-04-23',\n+ 'collectionMoment': 'P32Y6M1D',\n+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],\n+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',\n+ 'label': 'Infiltrating Urothelial Carcinoma'},\n+ 'id': 'refvar-668fb721ae6c452887afb69f',\n+ 'individualId': 'NA24695',\n+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},\n+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',\n+ 'label': 'T2b Stage Finding'}],\n+ 'sampleOriginDetail': {'id': 'UBERON:0001256',\n+ 'label': 'wall of urinary bladde'},\n+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},\n+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},\n+ 'tumorProgression': {'id': 'NCIT:C84509',\n+ 'label': 'Primary Malignant Neoplasm'}}\n" |
| b |
| diff -r 000000000000 -r 5fcaabf17d8d test-data/bracket_query_findings.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bracket_query_findings.json Mon Jul 22 12:35:29 2024 +0000 |
| b |
| @@ -0,0 +1,30 @@ +{'_id': ObjectId('664218d657ec62781caecec7'), + 'aminoacidChange': 'Gly to Ser', + 'end': 1800, + 'id': 'refvar-664218d657ec62781caecec7', + 'referenceName': 'chr4', + 'start': 800, + 'test_case': 'Test Case 4', + 'variantMaxLength': 10, + 'variantMinLength': 3, + 'variantType': 'Insertion'} +{'_id': ObjectId('664218d657ec62781caecec8'), + 'aminoacidChange': 'Gly to Ser', + 'end': 2000, + 'id': 'refvar-664218d657ec62781caecec8', + 'referenceName': 'chr4', + 'start': 1000, + 'test_case': 'Test Case 4', + 'variantMaxLength': 10, + 'variantMinLength': 3, + 'variantType': 'Insertion'} +{'_id': ObjectId('664218d657ec62781caecec9'), + 'aminoacidChange': 'Gly to Ser', + 'end': 1900, + 'id': 'refvar-664218d657ec62781caecec9', + 'referenceName': 'chr4', + 'start': 900, + 'test_case': 'Test Case 4', + 'variantMaxLength': 10, + 'variantMinLength': 3, + 'variantType': 'Insertion'} |
| b |
| diff -r 000000000000 -r 5fcaabf17d8d test-data/cnv_query_findings.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cnv_query_findings.json Mon Jul 22 12:35:29 2024 +0000 |
| b |
| @@ -0,0 +1,13 @@ +{'_id': ObjectId('6690160a3a936e8e0a7828e2'), + 'assemblyId': 'GRCh38', + 'biosampleId': 'HG00096', + 'definitions': {'Location': {'chromosome': '1', + 'end': 243620819, + 'start': 243618689}}, + 'id': 'refvar-6690160a3a936e8e0a7828e2', + 'info': {'cnCount': 1, + 'cnValue': 0.422353, + 'legacyId': 'DRAGEN:LOSS:chr1:243618690-243620819'}, + 'updated': '2024-07-11T17:26:27.265115', + 'variantInternalId': 'chr1:243618689-243620819:EFO:0030068', + 'variantState': {'id': 'EFO:0030068', 'label': 'low-level loss'}} |
| b |
| diff -r 000000000000 -r 5fcaabf17d8d test-data/cohorts_query_findings.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cohorts_query_findings.json Mon Jul 22 12:35:29 2024 +0000 |
| [ |
| @@ -0,0 +1,8 @@ +{'_id': ObjectId('668fcc22387cab4642e5f1a4'), + 'cohortDataTypes': [{'id': 'EFO:0004600', 'label': 'genomic data'}, + {'id': 'NCIT:C1578', 'label': 'clinical data'}, + {'id': 'NCIT:C142508', 'label': 'demographic data'}], + 'cohortId': 'GiaB', + 'cohortName': 'The Genome in a Bottle Consortium (GIAB)', + 'cohortType': 'study-defined', + 'id': 'refvar-668fcc22387cab4642e5f1a4'} |
| b |
| diff -r 000000000000 -r 5fcaabf17d8d test-data/datasets_query_findings.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/datasets_query_findings.json Mon Jul 22 12:35:29 2024 +0000 |
| b |
| @@ -0,0 +1,11 @@ +{'_id': ObjectId('668fcf57aee552bc911b966e'), + 'createDateTime': '2017-04-30T00:00:00+00:00', + 'description': 'The Genome in a Bottle Consortium, hosted by the National ' + 'Institute of Standards and Technology (NIST) is creating ' + 'reference materials and data for human genome sequencing, as ' + 'well as methods for genome comparison and benchmarking. ', + 'externalUrl': 'https://www.nature.com/articles/sdata201625, ' + 'https://jimb.stanford.edu/giab-resources', + 'id': 'refvar-668fcf57aee552bc911b966e', + 'name': 'The Genome in a Bottle Consortium (GIAB)', + 'updateDateTime': '2017-04-30T00:00:00+00:00'} |
| b |
| diff -r 000000000000 -r 5fcaabf17d8d test-data/gene_query_findings.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_query_findings.json Mon Jul 22 12:35:29 2024 +0000 |
| b |
| @@ -0,0 +1,11 @@ +{'_id': ObjectId('66420b807b0edffcf5545d85'), + 'aminoacidChange': 'Ala to Thr', + 'end': 1300, + 'geneId': 'HAL', + 'id': 'refvar-66420b807b0edffcf5545d85', + 'referenceName': 'chr5', + 'start': 300, + 'test_case': 'Test Case 5', + 'variantMaxLength': 8, + 'variantMinLength': 4, + 'variantType': 'Deletion'} |
| b |
| diff -r 000000000000 -r 5fcaabf17d8d test-data/individuals_query_findings.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/individuals_query_findings.json Mon Jul 22 12:35:29 2024 +0000 |
| [ |
| @@ -0,0 +1,9 @@ +{'_id': ObjectId('668fd04e32491a13d36d3a46'), + 'diseases': [{'diseaseCode': {'id': 'HP:000054', 'label': 'intolerance'}}], + 'ethnicity': {'id': 'HANCESTRO:0021', 'label': 'Han Chinese'}, + 'geographicOrigin': {'id': 'GAZ:00002459', + 'label': 'United States of America'}, + 'id': 'refvar-668fd04e32491a13d36d3a46', + 'phenotypicFeatures': [{'featureType': {'id': 'NCIT:C3001', + 'label': 'NCIT:C3001'}}], + 'sex': {'id': 'NCIT:C46112', 'label': 'male'}} |
| b |
| diff -r 000000000000 -r 5fcaabf17d8d test-data/logs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/logs.txt Mon Jul 22 12:35:29 2024 +0000 |
| b |
| b'@@ -0,0 +1,591 @@\n+==> inserted refvar-6630e1590767459cc186e0f3\n+==> inserted refvar-6630e1590767459cc186e0f4\n+==> inserted refvar-6630e1590767459cc186e0f5\n+==> inserted refvar-6630e1590767459cc186e0f6\n+==> inserted refvar-6630e1590767459cc186e0f7\n+==> inserted refvar-6630e1590767459cc186e0f8\n+==> inserted refvar-6630e1590767459cc186e0f9\n+==> inserted refvar-6630e1590767459cc186e0fa\n+==> inserted refvar-6630e1590767459cc186e0fb\n+==> inserted refvar-6630e1590767459cc186e0fc\n+==> inserted refvar-6630e1590767459cc186e0fd\n+==> inserted refvar-6630e1590767459cc186e0fe\n+==> inserted refvar-6630e1590767459cc186e0ff\n+==> inserted refvar-6630e1590767459cc186e100\n+==> inserted refvar-6630e1590767459cc186e101\n+==> inserted refvar-6630e1590767459cc186e102\n+==> inserted refvar-6630e1590767459cc186e103\n+==> inserted refvar-6630e1590767459cc186e104\n+==> inserted refvar-6630e1590767459cc186e105\n+==> inserted refvar-6630e1590767459cc186e106\n+==> inserted refvar-6630e1590767459cc186e107\n+==> inserted refvar-6630e1590767459cc186e108\n+==> inserted refvar-6630e1590767459cc186e109\n+==> inserted refvar-6630e1590767459cc186e10a\n+==> inserted refvar-6630e1590767459cc186e10b\n+==> inserted refvar-6630e1590767459cc186e10c\n+==> inserted refvar-6630e1590767459cc186e10d\n+==> inserted refvar-6630e1590767459cc186e10e\n+==> inserted refvar-6630e1590767459cc186e10f\n+==> inserted refvar-6630e1590767459cc186e110\n+==> inserted refvar-6630e1590767459cc186e111\n+==> inserted refvar-6630e1590767459cc186e112\n+==> inserted refvar-6630e1590767459cc186e113\n+==> inserted refvar-6630e1590767459cc186e114\n+==> inserted refvar-6630e1590767459cc186e115\n+==> inserted refvar-6630e1590767459cc186e116\n+==> inserted refvar-6630e1590767459cc186e117\n+==> inserted refvar-6630e1590767459cc186e118\n+==> inserted refvar-6630e1590767459cc186e119\n+==> inserted refvar-6630e1590767459cc186e11a\n+==> inserted refvar-6630e1590767459cc186e11b\n+==> inserted refvar-6630e1590767459cc186e11c\n+==> inserted refvar-6630e1590767459cc186e11d\n+==> inserted refvar-6630e1590767459cc186e11e\n+==> inserted refvar-6630e1590767459cc186e11f\n+==> inserted refvar-6630e1590767459cc186e120\n+==> inserted refvar-6630e1590767459cc186e121\n+==> inserted refvar-6630e1590767459cc186e122\n+==> inserted refvar-6630e1590767459cc186e123\n+==> inserted refvar-6630e1590767459cc186e124\n+==> inserted refvar-6630e1590767459cc186e125\n+==> inserted refvar-6630e1590767459cc186e126\n+==> inserted refvar-6630e1590767459cc186e127\n+==> inserted refvar-6630e1590767459cc186e128\n+==> inserted refvar-6630e1590767459cc186e129\n+==> inserted refvar-6630e1590767459cc186e12a\n+==> inserted refvar-6630e1590767459cc186e12b\n+==> inserted refvar-6630e1590767459cc186e12c\n+==> inserted refvar-6630e1590767459cc186e12d\n+==> inserted refvar-6630e1590767459cc186e12e\n+==> inserted refvar-6630e1590767459cc186e12f\n+==> inserted refvar-6630e1590767459cc186e130\n+==> inserted refvar-6630e1590767459cc186e131\n+==> inserted refvar-6630e15a0767459cc186e132\n+==> inserted refvar-6630e15a0767459cc186e133\n+==> inserted refvar-6630e15a0767459cc186e134\n+==> inserted refvar-6630e15a0767459cc186e135\n+==> inserted refvar-6630e15a0767459cc186e136\n+==> inserted refvar-6630e15a0767459cc186e137\n+==> inserted refvar-6630e15a0767459cc186e138\n+==> inserted refvar-6630e15a0767459cc186e139\n+==> inserted refvar-6630e15a0767459cc186e13a\n+==> inserted refvar-6630e15a0767459cc186e13b\n+==> inserted refvar-6630e15a0767459cc186e13c\n+==> inserted refvar-6630e15a0767459cc186e13d\n+==> inserted refvar-6630e15a0767459cc186e13e\n+==> inserted refvar-6630e15a0767459cc186e13f\n+==> inserted refvar-6630e15a0767459cc186e140\n+==> inserted refvar-6630e15a0767459cc186e141\n+==> inserted refvar-6630e15a0767459cc186e142\n+==> inserted refvar-6630e15a0767459cc186e143\n+==> inserted refvar-6630e15a0767459cc186e144\n+==> inserted refvar-6630e15a0767459cc186e145\n+==> inserted refvar-6630e15a0767459cc186e146\n+==> inserted refvar-6630e15a0767459cc186e147\n+==> inserted refvar-6630e15a0767459cc186e148\n+==> inserted refvar-6630'..b'> inserted refvar-6630e15a0767459cc186e2eb\n+==> inserted refvar-6630e15a0767459cc186e2ec\n+==> inserted refvar-6630e15a0767459cc186e2ed\n+==> inserted refvar-6630e15a0767459cc186e2ee\n+==> inserted refvar-6630e15a0767459cc186e2ef\n+==> inserted refvar-6630e15a0767459cc186e2f0\n+==> inserted refvar-6630e15a0767459cc186e2f1\n+==> inserted refvar-6630e15a0767459cc186e2f2\n+==> inserted refvar-6630e15a0767459cc186e2f3\n+==> inserted refvar-6630e15a0767459cc186e2f4\n+==> inserted refvar-6630e15a0767459cc186e2f5\n+==> inserted refvar-6630e15a0767459cc186e2f6\n+==> inserted refvar-6630e15a0767459cc186e2f7\n+==> inserted refvar-6630e15a0767459cc186e2f8\n+==> inserted refvar-6630e15a0767459cc186e2f9\n+==> inserted refvar-6630e15a0767459cc186e2fa\n+==> inserted refvar-6630e15a0767459cc186e2fb\n+==> inserted refvar-6630e15a0767459cc186e2fc\n+==> inserted refvar-6630e15a0767459cc186e2fd\n+==> inserted refvar-6630e15a0767459cc186e2fe\n+==> inserted refvar-6630e15a0767459cc186e2ff\n+==> inserted refvar-6630e15a0767459cc186e300\n+==> inserted refvar-6630e15a0767459cc186e301\n+==> inserted refvar-6630e15a0767459cc186e302\n+==> inserted refvar-6630e15a0767459cc186e303\n+==> inserted refvar-6630e15a0767459cc186e304\n+==> inserted refvar-6630e15a0767459cc186e305\n+==> inserted refvar-6630e15a0767459cc186e306\n+==> inserted refvar-6630e15a0767459cc186e307\n+==> inserted refvar-6630e15a0767459cc186e308\n+==> inserted refvar-6630e15a0767459cc186e309\n+==> inserted refvar-6630e15a0767459cc186e30a\n+==> inserted refvar-6630e15a0767459cc186e30b\n+==> inserted refvar-6630e15a0767459cc186e30c\n+==> inserted refvar-6630e15a0767459cc186e30d\n+==> inserted refvar-6630e15a0767459cc186e30e\n+==> inserted refvar-6630e15a0767459cc186e30f\n+==> inserted refvar-6630e15a0767459cc186e310\n+==> inserted refvar-6630e15a0767459cc186e311\n+==> inserted refvar-6630e15a0767459cc186e312\n+==> inserted refvar-6630e15a0767459cc186e313\n+==> inserted refvar-6630e15a0767459cc186e314\n+==> inserted refvar-6630e15a0767459cc186e315\n+==> inserted refvar-6630e15a0767459cc186e316\n+==> inserted refvar-6630e15a0767459cc186e317\n+==> inserted refvar-6630e15a0767459cc186e318\n+==> inserted refvar-6630e15a0767459cc186e319\n+==> inserted refvar-6630e15a0767459cc186e31a\n+==> inserted refvar-6630e15a0767459cc186e31b\n+==> inserted refvar-6630e15a0767459cc186e31c\n+==> inserted refvar-6630e15a0767459cc186e31d\n+==> inserted refvar-6630e15a0767459cc186e31e\n+==> inserted refvar-6630e15a0767459cc186e31f\n+==> inserted refvar-6630e15a0767459cc186e320\n+==> inserted refvar-6630e15a0767459cc186e321\n+==> inserted refvar-6630e15a0767459cc186e322\n+==> inserted refvar-6630e15a0767459cc186e323\n+==> inserted refvar-6630e15a0767459cc186e324\n+==> inserted refvar-6630e15a0767459cc186e325\n+==> inserted refvar-6630e15a0767459cc186e326\n+==> inserted refvar-6630e15a0767459cc186e327\n+==> inserted refvar-6630e15a0767459cc186e328\n+==> inserted refvar-6630e15a0767459cc186e329\n+==> inserted refvar-6630e15a0767459cc186e32a\n+==> inserted refvar-6630e15a0767459cc186e32b\n+==> inserted refvar-6630e15a0767459cc186e32c\n+==> inserted refvar-6630e15a0767459cc186e32d\n+==> inserted refvar-6630e15a0767459cc186e32e\n+==> inserted refvar-6630e15a0767459cc186e32f\n+==> inserted refvar-6630e15a0767459cc186e330\n+==> inserted refvar-6630e15a0767459cc186e331\n+==> inserted refvar-6630e15a0767459cc186e332\n+==> inserted refvar-6630e15a0767459cc186e333\n+==> inserted refvar-6630e15a0767459cc186e334\n+==> inserted refvar-6630e15a0767459cc186e335\n+==> inserted refvar-6630e15a0767459cc186e336\n+==> inserted refvar-6630e15a0767459cc186e337\n+==> inserted refvar-6630e15a0767459cc186e338\n+==> inserted refvar-6630e15a0767459cc186e339\n+==> inserted refvar-6630e15a0767459cc186e33a\n+==> inserted refvar-6630e15a0767459cc186e33b\n+==> inserted refvar-6630e15a0767459cc186e33c\n+==> inserted refvar-6630e15a0767459cc186e33d\n+==> inserted refvar-6630e15a0767459cc186e33e\n+==> inserted refvar-6630e15a0767459cc186e33f\n+==> inserted refvar-6630e15a0767459cc186e340\n+==> inserted refvar-6630e15a0767459cc186e341\n' |
| b |
| diff -r 000000000000 -r 5fcaabf17d8d test-data/ranged_query_findings.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ranged_query_findings.json Mon Jul 22 12:35:29 2024 +0000 |
| b |
| @@ -0,0 +1,39 @@ +{'_id': ObjectId('6632291df0e80a1345b280d9'), + 'assemblyId': 'GRCh38', + 'biosampleId': 'HG00096', + 'end': 2651463, + 'id': 'refvar-6632291df0e80a1345b280d9', + 'info': {'cnCount': 0, + 'cnValue': 1.00369e-09, + 'legacyId': 'DRAGEN:LOSS:chr1:2650428-2651463'}, + 'referenceName': '1', + 'start': 2650427, + 'variantId': 'EFO:0030069', + 'variantInternalId': 'chr1:2650427-2651463:EFO:0030069', + 'variantType': 'DEL'} +{'_id': ObjectId('6632296d551494bb7866e39a'), + 'assemblyId': 'GRCh38', + 'biosampleId': 'HG00096', + 'end': 2651463, + 'id': 'refvar-6632296d551494bb7866e39a', + 'info': {'cnCount': 0, + 'cnValue': 1.00369e-09, + 'legacyId': 'DRAGEN:LOSS:chr1:2650428-2651463'}, + 'referenceName': '1', + 'start': 2650427, + 'variantId': 'EFO:0030069', + 'variantInternalId': 'chr1:2650427-2651463:EFO:0030069', + 'variantType': 'DEL'} +{'_id': ObjectId('6632296f52df1a5f88158d58'), + 'assemblyId': 'GRCh38', + 'biosampleId': 'HG00096', + 'end': 2651463, + 'id': 'refvar-6632296f52df1a5f88158d58', + 'info': {'cnCount': 0, + 'cnValue': 1.00369e-09, + 'legacyId': 'DRAGEN:LOSS:chr1:2650428-2651463'}, + 'referenceName': '1', + 'start': 2650427, + 'variantId': 'EFO:0030069', + 'variantInternalId': 'chr1:2650427-2651463:EFO:0030069', + 'variantType': 'DEL'} |
| b |
| diff -r 000000000000 -r 5fcaabf17d8d test-data/runs_query_findings.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/runs_query_findings.json Mon Jul 22 12:35:29 2024 +0000 |
| b |
| @@ -0,0 +1,11 @@ +{'_id': ObjectId('668fb39af8fd7572a152ddd2'), + 'biosampleId': 'S0003', + 'id': 'refvar-668fb39af8fd7572a152ddd2', + 'individualId': 'NA24695', + 'libraryLayout': 'PAIRED', + 'librarySelection': 'LD-PCR', + 'librarySource': {'id': 'NNN:01', 'label': 'KAPA library quantification kit'}, + 'libraryStrategy': 'WGS', + 'platform': 'Illumina ', + 'platformModel': {'id': 'MODEL:HiSeq 2500 ', 'label': '2017-04-30'}, + 'runDate': '2017-04-30'} |
| b |
| diff -r 000000000000 -r 5fcaabf17d8d test-data/sequenced_query_findings.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sequenced_query_findings.json Mon Jul 22 12:35:29 2024 +0000 |
| b |
| @@ -0,0 +1,8 @@ +{'_id': ObjectId('6642048d834d5e4d6f90e978'), + 'alternateBases': 'A', + 'end': 1500, + 'id': 'refvar-6642048d834d5e4d6f90e978', + 'referenceBases': 'T', + 'referenceName': 'chr2', + 'start': 500, + 'test_case': 'Test Case 2'} |