| Next changeset 1:d524bd42b89e (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:
cohorts.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 8fc2c603a61f cohorts.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cohorts.xml Mon Jul 22 12:37:13 2024 +0000 |
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| @@ -0,0 +1,81 @@ +<tool id="beacon2_cohorts" name="Beacon2 Cohorts" version="1.0.0" profile="21.05"> + <description>Query the Cohorts collection in the beacon database</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creators"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"> + <![CDATA[ + beacon2-search cohorts + --db-host '$db_host' + --db-port $db_port + --database '$database' + --collection '$collection' + --advance-connection + --db-auth-config '$credentials' + #if str($advanced_settings.cohortDataTypes) + --cohortDataTypes '$advanced_settings.cohortDataTypes' + #end if + #if str($advanced_settings.cohortDesign) + --cohortDesign '$advanced_settings.cohortDesign' + #end if + #if str($advanced_settings.cohortSize) + --cohortSize $advanced_settings.cohortSize + #end if + #if str($advanced_settings.identification) + --identification '$advanced_settings.identification' + #end if + #if str($advanced_settings.cohortType) + --cohortType '$advanced_settings.cohortType' + #end if + #if str($advanced_settings.genders) and $advanced_settings.genders != "" + --genders '$advanced_settings.genders' + #end if + #if str($advanced_settings.name) + --name '$advanced_settings.name' + #end if + > cohorts_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="--cohortDataTypes" optional="true" type="text" label="COHORTDATA TYPES" value="" help="The type of data chorort, e.g. clinical history" /> + <param argument="--cohortDesign" optional="true" type="text" label="COHORTDESIGN" value="" help="A plan specification comprised of protocols that are executed as part of an investigation, e.g. longitudinal study design" /> + <param argument="--cohortSize" optional="true" type="integer" label="COHORT SIZE" value="" help="Count of unique Individuals in cohort" /> + <param argument="--cohortType" optional="true" type="text" label="COHORT TYPE" value="" help="Cohort type by its definition, e.g. study-defined" /> + <param argument="--identification" optional="true" type="text" label="ID" value="" help="Cohort identifier, e.g. cohort0001" /> + <param argument="--genders" optional="true" type="select" label="GENDERS" help=""> + <option value="male">male</option> + <option value="female">female</option> + <option value="" selected="True">non specific</option> + </param> + <param argument="--name" optional="true" type="text" label="NAME" value="" help="Name of the cohort" /> + </section> + </inputs> + <outputs> + <data name="out_cohorts_query" format="json" label="${tool.name} on ${on_string}: Cohorts Query" from_work_dir="cohorts_query_findings.json" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="database" value="beacon" /> + <param name="collection" value="cohorts" /> + <param name="db_host" value="20.108.51.167" /> + <param name="cohortType" value="study-defined" /> + <param name="cohortDataTypes" value="demographic data" /> + <param name="identification" value="refvar-668fcc22387cab4642e5f1a4" /> + <output name="out_cohorts_query"> + <assert_contents> + <has_text_matching expression="_id"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Beacon2 Cohorts queries the cohorts collection in the Beacon database to study the variants or individuals in a populations or groups that share something in common. + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 8fc2c603a61f macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jul 22 12:37:13 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 8fc2c603a61f test-data/HG00096.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HG00096.json Mon Jul 22 12:37:13 2024 +0000 |
| [ |
| 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 8fc2c603a61f 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 12:37:13 2024 +0000 |
| b |
| @@ -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'} |
| b |
| diff -r 000000000000 -r 8fc2c603a61f 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 12:37:13 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 8fc2c603a61f 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 12:37:13 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 8fc2c603a61f 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 12:37:13 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 8fc2c603a61f 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 12:37:13 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 8fc2c603a61f 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 12:37:13 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 8fc2c603a61f 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 12:37:13 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 8fc2c603a61f 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 12:37:13 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 8fc2c603a61f test-data/logs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/logs.txt Mon Jul 22 12:37:13 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 8fc2c603a61f 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 12:37:13 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 8fc2c603a61f 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 12:37:13 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 8fc2c603a61f 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 12:37:13 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'} |