Mercurial > repos > iuc > beacon2_biosamples
changeset 0:7cea4f9c4d8f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
| author | iuc |
|---|---|
| date | Mon, 22 Jul 2024 12:36:29 +0000 |
| parents | |
| children | 5fedf42a718b |
| files | biosamples.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 |
| diffstat | 15 files changed, 9943 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biosamples.xml Mon Jul 22 12:36:29 2024 +0000 @@ -0,0 +1,119 @@ +<tool id="beacon2_biosamples" name="Beacon2 Biosamples" version="1.0.0" profile="21.05"> + <description>Query the biosamples collection in the beacon database for samples taken from individuals</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creators"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"> + <![CDATA[ + beacon2-search biosamples + --db-host '$db_host' + --db-port $db_port + --database '$database' + --collection '$collection' + --advance-connection + --db-auth-config '$credentials' + #if str($advanced_settings.biosampleStatus) + --biosampleStatus '$advanced_settings.biosampleStatus' + #end if + #if str($advanced_settings.collectionDate) + --collectionDate '$advanced_settings.collectionDate' + #end if + #if str($advanced_settings.collectionMoment) + --collectionMoment '$advanced_settings.collectionMoment' + #end if + #if str($advanced_settings.identification) + --identification '$advanced_settings.identification' + #end if + #if str($advanced_settings.diagnosticMarkers) + --diagnosticMarkers '$advanced_settings.diagnosticMarkers' + #end if + #if str($advanced_settings.histologicalDiagnosis) + --histologicalDiagnosis '$advanced_settings.histologicalDiagnosis' + #end if + #if str($advanced_settings.obtentionProcedure) + --obtentionProcedure '$advanced_settings.obtentionProcedure' + #end if + #if str($advanced_settings.pathologicalStage) + --pathologicalStage '$advanced_settings.pathologicalStage' + #end if + #if str($advanced_settings.pathologicalTnmFinding) + --pathologicalTnmFinding '$advanced_settings.pathologicalTnmFinding' + #end if + #if str($advanced_settings.featureType) + --featureType '$advanced_settings.featureType' + #end if + #if str($advanced_settings.severity) + --severity '$advanced_settings.severity' + #end if + #if str($advanced_settings.sampleOriginDetail) + --sampleOriginDetail '$advanced_settings.sampleOriginDetail' + #end if + #if str($advanced_settings.sampleOriginType) + --sampleOriginType '$advanced_settings.sampleOriginType' + #end if + #if str($advanced_settings.sampleProcessing) + --sampleProcessing '$advanced_settings.sampleProcessing' + #end if + #if str($advanced_settings.sampleStorage) + --sampleStorage '$advanced_settings.sampleStorage' + #end if + #if str($advanced_settings.tumorGrade) + --tumorGrade '$advanced_settings.tumorGrade' + #end if + #if str($advanced_settings.tumorProgression) + --tumorProgression '$advanced_settings.tumorProgression' + #end if + > biosamples_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="--biosampleStatus" optional="true" type="text" label="BIOSAMPLE STATUS" value="" help="Ontology value for the classification of the sample in abnormal sample (EFO:0009655) or reference sample (EFO:0009654)" /> + <param argument="--collectionDate" optional="true" type="text" label="COLLECTION DATE" value="" help="Date of biosample collection in ISO8601 format" /> + <param argument="--collectionMoment" optional="true" type="text" label="COLLECTION MOMENT" value="" help="Individual's or cell culture age at the time of sample collection in the ISO8601 duration format P[n]Y[n]M[n]DT[n]H[n]M[n]S, e.g. P32Y6M1D, P7D" /> + <param argument="--identification" optional="true" type="text" label="ID" value="" help="Biosample identifier (external accession or internal ID)" /> + <param argument="--diagnosticMarkers" optional="true" type="text" label="DIAGNOSTIC MARKERS" value="" help="Clinically relevant bio markers, e.g. T2b Stage Finding" /> + <param argument="--histologicalDiagnosis" optional="true" type="text" label="HISTOLOGICAL DIAGNOSIS" value="" help="Disease diagnosis that was inferred from the histological examination, e.g. Serous Cystadenocarcinoma" /> + <param argument="--obtentionProcedure" optional="true" type="text" label="OBTENTION PROCEDURE" value="" help="Ontology value describing the procedure for sample obtention, e.g. biopsy" /> + <param argument="--pathologicalStage" optional="true" type="text" label="PATHOLOGICAL STAGE" value="" help="Pathological stage, if applicable, e.g. Stage IIIA" /> + <param argument="--pathologicalTnmFinding" optional="true" type="text" label="PATHOLOGICAL TNM FINDING" value="" help="T2b Stage Finding" /> + <param argument="--featureType" optional="true" type="text" label="FEATURE TYPE" value="" help="Definition of an ontology term which describes the phenotype, e.g. Infantile spasms" /> + <param argument="--severity" optional="true" type="text" label="SEVERITY" value="" help="Ontology class that describes the severity of the condition, e.g. Moderate" /> + <param argument="--sampleOriginDetail" optional="true" type="text" label="SAMPLE ORIGIN DETAIL" value="" help="Tissue from which the sample was taken or sample origin matching the category set in 'sampleOriginType', e.g. wall of urinary bladder" /> + <param argument="--sampleOriginType" optional="true" type="text" label="SAMPLE ORIGIN TYPE" value="" help="Category of sample origin. Value from Ontology for Biomedical Investigations (OBI) material entity, e.g abnormal sample" /> + <param argument="--sampleProcessing" optional="true" type="text" label="SAMPLE PROCESSING" value="" help="Status of how the specimen was processed, e.g. mechanical dissociation" /> + <param argument="--sampleStorage" optional="true" type="text" label="SAMPLE STORAGE" value="" help="Status of how the specimen was stored" /> + <param argument="--tumorGrade" optional="true" type="text" label="TUMOR GRADE" value="" help="Term representing the tumor grade, e.g. Grade 3a" /> + <param argument="--tumorProgression" optional="true" type="text" label="TUMOR PROGRESSION" value="" help="Tumor progression category indicating primary, metastatic or recurrent progression, e.g. Primary Malignant Neoplasm" /> + </section> + </inputs> + <outputs> + <data name="out_biosamples_query" format="json" label="${tool.name} on ${on_string}: Biosamples Query" from_work_dir="biosamples_query_findings.json" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="database" value="beacon" /> + <param name="collection" value="biosamples" /> + <param name="db_host" value="20.108.51.167" /> + <param name="tumorGrade" value="Grade 2 Lesion" /> + <param name="biosampleStatus" value="abnormal sample" /> + <param name="collectionDate" value="2021-04-23" /> + <param name="sampleOriginDetail" value="wall of urinary bladde" /> + <param name="tumorProgression" value="Primary Malignant Neoplasm" /> + <output name="out_biosamples_query"> + <assert_contents> + <has_text_matching expression="_id"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Beacon2 Biosamples queries the biosamples collection in the Beacon database for samples taken from individuals. This tool allows detailed queries using advanced settings such as biosample status, collection date, diagnostic markers, and more. + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jul 22 12:36:29 2024 +0000 @@ -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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HG00096.json Mon Jul 22 12:36:29 2024 +0000 @@ -0,0 +1,8867 @@ +[ + { + "biosampleId": "HG00096", + "assemblyId": "GRCh38", + "variantInternalId": "chr1:2650427-2651463:EFO:0030069", + "variantType": "DEL", + "variantId": "EFO:0030069", + "start": 2650427, + "end": 2651463, + "referenceName": "1", + "info": { + "legacyId": "DRAGEN:LOSS:chr1:2650428-2651463", + "cnCount": 0, + "cnValue": 1.00369e-09 + } + }, + { + "biosampleId": "HG00096", + "assemblyId": "GRCh38", + "variantInternalId": "chr1:2651463-2653075:EFO:0030068", + "variantType": "DEL", + "variantId": "EFO:0030068", + "start": 2651463, + "end": 2653075, + "referenceName": "1", + "info": { + "legacyId": "DRAGEN:LOSS:chr1:2651464-2653075", + "cnCount": 1, + "cnValue": 0.395524 + } + }, + { + "biosampleId": "HG00096", + "assemblyId": "GRCh38", + "variantInternalId": "chr1:4063594-4067475:EFO:0030068", + "variantType": "DEL", + "variantId": "EFO:0030068", + "start": 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'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'}, + 'pathologicalTnmFinding': [{'id': 'NCIT:C48726', + 'label': 'T2b Stage Finding'}], + 'sampleOriginDetail': {'id': 'UBERON:0001256', + 'label': 'wall of urinary bladde'}, + 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'}, + 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'}, + 'tumorProgression': {'id': 'NCIT:C84509', + 'label': 'Primary Malignant Neoplasm'}} +{'_id': ObjectId('668fb721ae6c452887afb69e'), + 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'}, + 'collectionDate': '2021-04-23', + 'collectionMoment': 'P32Y6M1D', + 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}], + 'histologicalDiagnosis': {'id': 'NCIT:C39853', + 'label': 'Infiltrating Urothelial Carcinoma'}, + 'id': 'refvar-668fb721ae6c452887afb69e', + 'individualId': 'NA24694', + 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'}, + 'pathologicalTnmFinding': [{'id': 'NCIT:C48726', + 'label': 'T2b Stage Finding'}], + 'sampleOriginDetail': {'id': 'UBERON:0001256', + 'label': 'wall of urinary bladde'}, + 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'}, + 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'}, + 'tumorProgression': {'id': 'NCIT:C84509', + 'label': 'Primary Malignant Neoplasm'}} +{'_id': ObjectId('668fb721ae6c452887afb69f'), + 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'}, + 'collectionDate': '2021-04-23', + 'collectionMoment': 'P32Y6M1D', + 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}], + 'histologicalDiagnosis': {'id': 'NCIT:C39853', + 'label': 'Infiltrating Urothelial Carcinoma'}, + 'id': 'refvar-668fb721ae6c452887afb69f', + 'individualId': 'NA24695', + 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'}, + 'pathologicalTnmFinding': [{'id': 'NCIT:C48726', + 'label': 'T2b Stage Finding'}], + 'sampleOriginDetail': {'id': 'UBERON:0001256', + 'label': 'wall of urinary bladde'}, + 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'}, + 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'}, + 'tumorProgression': {'id': 'NCIT:C84509', + 'label': 'Primary Malignant Neoplasm'}}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bracket_query_findings.json Mon Jul 22 12:36:29 2024 +0000 @@ -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'}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cnv_query_findings.json Mon Jul 22 12:36:29 2024 +0000 @@ -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'}}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cohorts_query_findings.json Mon Jul 22 12:36:29 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'}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/datasets_query_findings.json Mon Jul 22 12:36:29 2024 +0000 @@ -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'}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_query_findings.json Mon Jul 22 12:36:29 2024 +0000 @@ -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'}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/individuals_query_findings.json Mon Jul 22 12:36:29 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'}}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/logs.txt Mon Jul 22 12:36:29 2024 +0000 @@ -0,0 +1,591 @@ +==> inserted refvar-6630e1590767459cc186e0f3 +==> inserted refvar-6630e1590767459cc186e0f4 +==> inserted refvar-6630e1590767459cc186e0f5 +==> inserted refvar-6630e1590767459cc186e0f6 +==> inserted refvar-6630e1590767459cc186e0f7 +==> inserted refvar-6630e1590767459cc186e0f8 +==> inserted refvar-6630e1590767459cc186e0f9 +==> inserted refvar-6630e1590767459cc186e0fa +==> inserted refvar-6630e1590767459cc186e0fb +==> inserted refvar-6630e1590767459cc186e0fc +==> inserted refvar-6630e1590767459cc186e0fd +==> inserted refvar-6630e1590767459cc186e0fe +==> inserted refvar-6630e1590767459cc186e0ff +==> inserted refvar-6630e1590767459cc186e100 +==> inserted refvar-6630e1590767459cc186e101 +==> inserted refvar-6630e1590767459cc186e102 +==> inserted refvar-6630e1590767459cc186e103 +==> inserted refvar-6630e1590767459cc186e104 +==> inserted refvar-6630e1590767459cc186e105 +==> inserted refvar-6630e1590767459cc186e106 +==> inserted refvar-6630e1590767459cc186e107 +==> inserted refvar-6630e1590767459cc186e108 +==> inserted refvar-6630e1590767459cc186e109 +==> inserted refvar-6630e1590767459cc186e10a +==> inserted refvar-6630e1590767459cc186e10b +==> inserted refvar-6630e1590767459cc186e10c +==> inserted refvar-6630e1590767459cc186e10d +==> inserted refvar-6630e1590767459cc186e10e +==> inserted refvar-6630e1590767459cc186e10f +==> inserted refvar-6630e1590767459cc186e110 +==> inserted refvar-6630e1590767459cc186e111 +==> inserted refvar-6630e1590767459cc186e112 +==> inserted refvar-6630e1590767459cc186e113 +==> inserted refvar-6630e1590767459cc186e114 +==> inserted refvar-6630e1590767459cc186e115 +==> inserted refvar-6630e1590767459cc186e116 +==> inserted refvar-6630e1590767459cc186e117 +==> inserted refvar-6630e1590767459cc186e118 +==> inserted refvar-6630e1590767459cc186e119 +==> inserted refvar-6630e1590767459cc186e11a +==> inserted refvar-6630e1590767459cc186e11b +==> inserted refvar-6630e1590767459cc186e11c +==> inserted refvar-6630e1590767459cc186e11d +==> inserted refvar-6630e1590767459cc186e11e +==> inserted refvar-6630e1590767459cc186e11f +==> inserted refvar-6630e1590767459cc186e120 +==> inserted refvar-6630e1590767459cc186e121 +==> inserted refvar-6630e1590767459cc186e122 +==> inserted refvar-6630e1590767459cc186e123 +==> inserted refvar-6630e1590767459cc186e124 +==> inserted refvar-6630e1590767459cc186e125 +==> inserted refvar-6630e1590767459cc186e126 +==> inserted refvar-6630e1590767459cc186e127 +==> inserted refvar-6630e1590767459cc186e128 +==> inserted refvar-6630e1590767459cc186e129 +==> inserted refvar-6630e1590767459cc186e12a +==> inserted refvar-6630e1590767459cc186e12b +==> inserted refvar-6630e1590767459cc186e12c +==> inserted refvar-6630e1590767459cc186e12d +==> inserted refvar-6630e1590767459cc186e12e +==> inserted refvar-6630e1590767459cc186e12f +==> inserted refvar-6630e1590767459cc186e130 +==> inserted refvar-6630e1590767459cc186e131 +==> inserted refvar-6630e15a0767459cc186e132 +==> inserted refvar-6630e15a0767459cc186e133 +==> inserted refvar-6630e15a0767459cc186e134 +==> inserted refvar-6630e15a0767459cc186e135 +==> inserted refvar-6630e15a0767459cc186e136 +==> inserted refvar-6630e15a0767459cc186e137 +==> inserted refvar-6630e15a0767459cc186e138 +==> inserted refvar-6630e15a0767459cc186e139 +==> inserted refvar-6630e15a0767459cc186e13a +==> inserted refvar-6630e15a0767459cc186e13b +==> inserted refvar-6630e15a0767459cc186e13c +==> inserted refvar-6630e15a0767459cc186e13d +==> inserted refvar-6630e15a0767459cc186e13e +==> inserted refvar-6630e15a0767459cc186e13f +==> inserted refvar-6630e15a0767459cc186e140 +==> inserted refvar-6630e15a0767459cc186e141 +==> inserted refvar-6630e15a0767459cc186e142 +==> inserted refvar-6630e15a0767459cc186e143 +==> inserted refvar-6630e15a0767459cc186e144 +==> inserted refvar-6630e15a0767459cc186e145 +==> inserted refvar-6630e15a0767459cc186e146 +==> inserted refvar-6630e15a0767459cc186e147 +==> inserted refvar-6630e15a0767459cc186e148 +==> inserted refvar-6630e15a0767459cc186e149 +==> inserted refvar-6630e15a0767459cc186e14a +==> inserted refvar-6630e15a0767459cc186e14b +==> inserted refvar-6630e15a0767459cc186e14c +==> inserted refvar-6630e15a0767459cc186e14d +==> inserted refvar-6630e15a0767459cc186e14e +==> inserted refvar-6630e15a0767459cc186e14f +==> inserted refvar-6630e15a0767459cc186e150 +==> inserted refvar-6630e15a0767459cc186e151 +==> inserted refvar-6630e15a0767459cc186e152 +==> inserted refvar-6630e15a0767459cc186e153 +==> inserted refvar-6630e15a0767459cc186e154 +==> inserted refvar-6630e15a0767459cc186e155 +==> inserted refvar-6630e15a0767459cc186e156 +==> inserted refvar-6630e15a0767459cc186e157 +==> inserted refvar-6630e15a0767459cc186e158 +==> inserted refvar-6630e15a0767459cc186e159 +==> inserted refvar-6630e15a0767459cc186e15a +==> inserted refvar-6630e15a0767459cc186e15b +==> inserted refvar-6630e15a0767459cc186e15c +==> inserted refvar-6630e15a0767459cc186e15d +==> inserted refvar-6630e15a0767459cc186e15e +==> inserted refvar-6630e15a0767459cc186e15f +==> inserted refvar-6630e15a0767459cc186e160 +==> inserted refvar-6630e15a0767459cc186e161 +==> inserted refvar-6630e15a0767459cc186e162 +==> inserted refvar-6630e15a0767459cc186e163 +==> inserted refvar-6630e15a0767459cc186e164 +==> inserted refvar-6630e15a0767459cc186e165 +==> inserted refvar-6630e15a0767459cc186e166 +==> inserted refvar-6630e15a0767459cc186e167 +==> inserted refvar-6630e15a0767459cc186e168 +==> inserted refvar-6630e15a0767459cc186e169 +==> inserted refvar-6630e15a0767459cc186e16a +==> inserted refvar-6630e15a0767459cc186e16b +==> inserted refvar-6630e15a0767459cc186e16c +==> inserted refvar-6630e15a0767459cc186e16d +==> inserted refvar-6630e15a0767459cc186e16e +==> inserted refvar-6630e15a0767459cc186e16f +==> inserted refvar-6630e15a0767459cc186e170 +==> inserted refvar-6630e15a0767459cc186e171 +==> inserted refvar-6630e15a0767459cc186e172 +==> inserted refvar-6630e15a0767459cc186e173 +==> inserted refvar-6630e15a0767459cc186e174 +==> inserted refvar-6630e15a0767459cc186e175 +==> inserted refvar-6630e15a0767459cc186e176 +==> inserted refvar-6630e15a0767459cc186e177 +==> inserted refvar-6630e15a0767459cc186e178 +==> inserted refvar-6630e15a0767459cc186e179 +==> inserted refvar-6630e15a0767459cc186e17a +==> inserted refvar-6630e15a0767459cc186e17b +==> inserted refvar-6630e15a0767459cc186e17c +==> inserted refvar-6630e15a0767459cc186e17d +==> inserted refvar-6630e15a0767459cc186e17e +==> inserted refvar-6630e15a0767459cc186e17f +==> inserted refvar-6630e15a0767459cc186e180 +==> inserted refvar-6630e15a0767459cc186e181 +==> inserted refvar-6630e15a0767459cc186e182 +==> inserted refvar-6630e15a0767459cc186e183 +==> inserted refvar-6630e15a0767459cc186e184 +==> inserted refvar-6630e15a0767459cc186e185 +==> inserted refvar-6630e15a0767459cc186e186 +==> inserted refvar-6630e15a0767459cc186e187 +==> inserted refvar-6630e15a0767459cc186e188 +==> inserted refvar-6630e15a0767459cc186e189 +==> inserted refvar-6630e15a0767459cc186e18a +==> inserted refvar-6630e15a0767459cc186e18b +==> inserted refvar-6630e15a0767459cc186e18c +==> inserted refvar-6630e15a0767459cc186e18d +==> inserted refvar-6630e15a0767459cc186e18e +==> inserted refvar-6630e15a0767459cc186e18f +==> inserted refvar-6630e15a0767459cc186e190 +==> inserted refvar-6630e15a0767459cc186e191 +==> inserted refvar-6630e15a0767459cc186e192 +==> inserted refvar-6630e15a0767459cc186e193 +==> inserted refvar-6630e15a0767459cc186e194 +==> inserted refvar-6630e15a0767459cc186e195 +==> inserted refvar-6630e15a0767459cc186e196 +==> inserted refvar-6630e15a0767459cc186e197 +==> inserted refvar-6630e15a0767459cc186e198 +==> inserted refvar-6630e15a0767459cc186e199 +==> inserted refvar-6630e15a0767459cc186e19a +==> inserted refvar-6630e15a0767459cc186e19b +==> inserted refvar-6630e15a0767459cc186e19c +==> inserted refvar-6630e15a0767459cc186e19d +==> inserted refvar-6630e15a0767459cc186e19e +==> inserted refvar-6630e15a0767459cc186e19f +==> inserted refvar-6630e15a0767459cc186e1a0 +==> inserted refvar-6630e15a0767459cc186e1a1 +==> inserted refvar-6630e15a0767459cc186e1a2 +==> inserted refvar-6630e15a0767459cc186e1a3 +==> inserted refvar-6630e15a0767459cc186e1a4 +==> inserted refvar-6630e15a0767459cc186e1a5 +==> inserted refvar-6630e15a0767459cc186e1a6 +==> inserted refvar-6630e15a0767459cc186e1a7 +==> inserted refvar-6630e15a0767459cc186e1a8 +==> inserted refvar-6630e15a0767459cc186e1a9 +==> inserted refvar-6630e15a0767459cc186e1aa +==> inserted refvar-6630e15a0767459cc186e1ab +==> inserted refvar-6630e15a0767459cc186e1ac +==> inserted refvar-6630e15a0767459cc186e1ad +==> inserted refvar-6630e15a0767459cc186e1ae +==> inserted refvar-6630e15a0767459cc186e1af +==> inserted refvar-6630e15a0767459cc186e1b0 +==> inserted refvar-6630e15a0767459cc186e1b1 +==> inserted refvar-6630e15a0767459cc186e1b2 +==> inserted refvar-6630e15a0767459cc186e1b3 +==> inserted refvar-6630e15a0767459cc186e1b4 +==> inserted refvar-6630e15a0767459cc186e1b5 +==> inserted refvar-6630e15a0767459cc186e1b6 +==> inserted refvar-6630e15a0767459cc186e1b7 +==> inserted refvar-6630e15a0767459cc186e1b8 +==> inserted refvar-6630e15a0767459cc186e1b9 +==> inserted refvar-6630e15a0767459cc186e1ba +==> inserted refvar-6630e15a0767459cc186e1bb +==> inserted refvar-6630e15a0767459cc186e1bc +==> inserted refvar-6630e15a0767459cc186e1bd +==> inserted refvar-6630e15a0767459cc186e1be +==> inserted refvar-6630e15a0767459cc186e1bf +==> inserted refvar-6630e15a0767459cc186e1c0 +==> inserted refvar-6630e15a0767459cc186e1c1 +==> inserted refvar-6630e15a0767459cc186e1c2 +==> inserted refvar-6630e15a0767459cc186e1c3 +==> inserted refvar-6630e15a0767459cc186e1c4 +==> inserted refvar-6630e15a0767459cc186e1c5 +==> inserted refvar-6630e15a0767459cc186e1c6 +==> inserted refvar-6630e15a0767459cc186e1c7 +==> inserted refvar-6630e15a0767459cc186e1c8 +==> inserted refvar-6630e15a0767459cc186e1c9 +==> inserted refvar-6630e15a0767459cc186e1ca +==> inserted refvar-6630e15a0767459cc186e1cb +==> inserted refvar-6630e15a0767459cc186e1cc +==> inserted refvar-6630e15a0767459cc186e1cd +==> inserted refvar-6630e15a0767459cc186e1ce +==> inserted refvar-6630e15a0767459cc186e1cf +==> inserted refvar-6630e15a0767459cc186e1d0 +==> inserted refvar-6630e15a0767459cc186e1d1 +==> inserted refvar-6630e15a0767459cc186e1d2 +==> inserted refvar-6630e15a0767459cc186e1d3 +==> inserted refvar-6630e15a0767459cc186e1d4 +==> inserted refvar-6630e15a0767459cc186e1d5 +==> inserted refvar-6630e15a0767459cc186e1d6 +==> inserted refvar-6630e15a0767459cc186e1d7 +==> inserted refvar-6630e15a0767459cc186e1d8 +==> inserted refvar-6630e15a0767459cc186e1d9 +==> inserted refvar-6630e15a0767459cc186e1da +==> inserted refvar-6630e15a0767459cc186e1db +==> inserted refvar-6630e15a0767459cc186e1dc 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refvar-6630e15a0767459cc186e31f +==> inserted refvar-6630e15a0767459cc186e320 +==> inserted refvar-6630e15a0767459cc186e321 +==> inserted refvar-6630e15a0767459cc186e322 +==> inserted refvar-6630e15a0767459cc186e323 +==> inserted refvar-6630e15a0767459cc186e324 +==> inserted refvar-6630e15a0767459cc186e325 +==> inserted refvar-6630e15a0767459cc186e326 +==> inserted refvar-6630e15a0767459cc186e327 +==> inserted refvar-6630e15a0767459cc186e328 +==> inserted refvar-6630e15a0767459cc186e329 +==> inserted refvar-6630e15a0767459cc186e32a +==> inserted refvar-6630e15a0767459cc186e32b +==> inserted refvar-6630e15a0767459cc186e32c +==> inserted refvar-6630e15a0767459cc186e32d +==> inserted refvar-6630e15a0767459cc186e32e +==> inserted refvar-6630e15a0767459cc186e32f +==> inserted refvar-6630e15a0767459cc186e330 +==> inserted refvar-6630e15a0767459cc186e331 +==> inserted refvar-6630e15a0767459cc186e332 +==> inserted refvar-6630e15a0767459cc186e333 +==> inserted refvar-6630e15a0767459cc186e334 +==> inserted refvar-6630e15a0767459cc186e335 +==> inserted refvar-6630e15a0767459cc186e336 +==> inserted refvar-6630e15a0767459cc186e337 +==> inserted refvar-6630e15a0767459cc186e338 +==> inserted refvar-6630e15a0767459cc186e339 +==> inserted refvar-6630e15a0767459cc186e33a +==> inserted refvar-6630e15a0767459cc186e33b +==> inserted refvar-6630e15a0767459cc186e33c +==> inserted refvar-6630e15a0767459cc186e33d +==> inserted refvar-6630e15a0767459cc186e33e +==> inserted refvar-6630e15a0767459cc186e33f +==> inserted refvar-6630e15a0767459cc186e340 +==> inserted refvar-6630e15a0767459cc186e341
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ranged_query_findings.json Mon Jul 22 12:36:29 2024 +0000 @@ -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'}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/runs_query_findings.json Mon Jul 22 12:36:29 2024 +0000 @@ -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'}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sequenced_query_findings.json Mon Jul 22 12:36:29 2024 +0000 @@ -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'}