Mercurial > repos > iuc > beacon2_individuals
changeset 0:b648eb72552c 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 12:35:16 +0000 |
| parents | |
| children | 72d8cb0fa73f |
| files | individuals.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, 9922 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/individuals.xml Mon Jul 22 12:35:16 2024 +0000 @@ -0,0 +1,98 @@ +<tool id="beacon2_individuals" name="Beacon2 Individuals" version="1.0.0" profile="21.05"> + <description>Query the individuals 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 individuals + --db-host '$db_host' + --db-port $db_port + --database '$database' + --collection '$collection' + --advance-connection + --db-auth-config '$credentials' + #if str($advanced_settings.ageGroup) + --ageGroup '$advanced_settings.ageGroup' + #end if + #if str($advanced_settings.diseaseCode) + --diseaseCode '$advanced_settings.diseaseCode' + #end if + #if str($advanced_settings.familyHistory) and $advanced_settings.familyHistory != "" + --familyHistory '$advanced_settings.familyHistory' + #end if + #if str($advanced_settings.severity) + --severity '$advanced_settings.severity' + #end if + #if str($advanced_settings.stage) + --stage '$advanced_settings.stage' + #end if + #if str($advanced_settings.ethnicity) + --ethnicity '$advanced_settings.ethnicity' + #end if + #if str($advanced_settings.geographicOrigin) + --geographicOrigin '$advanced_settings.geographicOrigin' + #end if + #if str($advanced_settings.identification) + --identification '$advanced_settings.identification' + #end if + #if str($advanced_settings.assayCode) + --assayCode '$advanced_settings.assayCode' + #end if + #if str($advanced_settings.sex) and $advanced_settings.sex != "" + --sex '$advanced_settings.sex' + #end if + > individuals_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="--ageGroup" optional="true" type="text" label="AGE GROUP" value="" help="age af onset, e.g. Adult 18-65 Years Old" /> + <param argument="--diseaseCode" optional="true" type="text" label="DISEASE CODE" value="" help="Disease code, Spinocerebellar ataxia 1" /> + <param argument="--familyHistory" optional="true" type="select" label="FAMILY HISTORY" help=""> + <option value="true">true</option> + <option value="false">false</option> + <option value="" selected="True">unknown</option> + </param> + <param argument="--severity" optional="true" type="text" label="SEVERITY" value="" help="e.g. Profound" /> + <param argument="--stage" optional="true" type="text" label="STAGE" value="" help="e.g. acute onset" /> + <param argument="--ethnicity" optional="true" type="text" label="ETHNICITY" value="" help="e.g. European" /> + <param argument="--geographicOrigin" optional="true" type="text" label="GEOGRAPHIC ORIGIN" value="" help="e.g. Slovenia" /> + <param argument="--identification" optional="true" type="text" label="ID" value="" help="Individual identifier (internal ID)" /> + <param argument="--assayCode" optional="true" type="text" label="ASSAY CODE" value="" help="e.g. Platelets [#/volume] in Blood" /> + <param argument="--sex" optional="true" type="select" label="SEX" help=""> + <option value="male">male</option> + <option value="female">female</option> + <option value="" selected="True">non specific</option> + </param> + </section> + </inputs> + <outputs> + <data name="out_individuals_query" format="json" label="${tool.name} on ${on_string}: Individuals Query" from_work_dir="individuals_query_findings.json" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="database" value="beacon" /> + <param name="collection" value="individuals" /> + <param name="db_host" value="20.108.51.167" /> + <param name="sex" value="male" /> + <param name="geographicOrigin" value="United States of America" /> + <param name="diseaseCode" value="intolerance" /> + <param name="ethnicity" value="Han Chinese" /> + <output name="out_individuals_query"> + <assert_contents> + <has_text_matching expression="_id"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Beacon2 Individuals queries the individuals collection in the Beacon database for either patients or healthy controls whose details (including phenotypic and clinical) are stored in the repository. + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jul 22 12:35:16 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>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bracket_query_findings.json Mon Jul 22 12:35:16 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 12:35:16 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 12:35:16 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 12:35:16 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 12:35:16 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 12:35:16 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 12:35:16 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 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+==> 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 +==> inserted refvar-6630e15a0767459cc186e1dd +==> inserted refvar-6630e15a0767459cc186e1de +==> inserted refvar-6630e15a0767459cc186e1df +==> inserted refvar-6630e15a0767459cc186e1e0 +==> inserted refvar-6630e15a0767459cc186e1e1 +==> inserted refvar-6630e15a0767459cc186e1e2 +==> inserted refvar-6630e15a0767459cc186e1e3 +==> inserted refvar-6630e15a0767459cc186e1e4 +==> inserted refvar-6630e15a0767459cc186e1e5 +==> inserted refvar-6630e15a0767459cc186e1e6 +==> inserted refvar-6630e15a0767459cc186e1e7 +==> inserted refvar-6630e15a0767459cc186e1e8 +==> inserted refvar-6630e15a0767459cc186e1e9 +==> inserted refvar-6630e15a0767459cc186e1ea +==> inserted refvar-6630e15a0767459cc186e1eb +==> inserted refvar-6630e15a0767459cc186e1ec +==> inserted refvar-6630e15a0767459cc186e1ed +==> inserted refvar-6630e15a0767459cc186e1ee +==> inserted refvar-6630e15a0767459cc186e1ef +==> inserted refvar-6630e15a0767459cc186e1f0 +==> inserted refvar-6630e15a0767459cc186e1f1 +==> inserted refvar-6630e15a0767459cc186e1f2 +==> inserted refvar-6630e15a0767459cc186e1f3 +==> inserted refvar-6630e15a0767459cc186e1f4 +==> inserted refvar-6630e15a0767459cc186e1f5 +==> inserted refvar-6630e15a0767459cc186e1f6 +==> inserted refvar-6630e15a0767459cc186e1f7 +==> inserted refvar-6630e15a0767459cc186e1f8 +==> inserted refvar-6630e15a0767459cc186e1f9 +==> inserted refvar-6630e15a0767459cc186e1fa +==> inserted refvar-6630e15a0767459cc186e1fb +==> inserted refvar-6630e15a0767459cc186e1fc +==> inserted refvar-6630e15a0767459cc186e1fd +==> inserted refvar-6630e15a0767459cc186e1fe +==> inserted refvar-6630e15a0767459cc186e1ff +==> inserted refvar-6630e15a0767459cc186e200 +==> inserted refvar-6630e15a0767459cc186e201 +==> inserted refvar-6630e15a0767459cc186e202 +==> inserted refvar-6630e15a0767459cc186e203 +==> inserted refvar-6630e15a0767459cc186e204 +==> inserted refvar-6630e15a0767459cc186e205 +==> inserted refvar-6630e15a0767459cc186e206 +==> inserted refvar-6630e15a0767459cc186e207 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refvar-6630e15a0767459cc186e2f4 +==> inserted refvar-6630e15a0767459cc186e2f5 +==> inserted refvar-6630e15a0767459cc186e2f6 +==> inserted refvar-6630e15a0767459cc186e2f7 +==> inserted refvar-6630e15a0767459cc186e2f8 +==> inserted refvar-6630e15a0767459cc186e2f9 +==> inserted refvar-6630e15a0767459cc186e2fa +==> inserted refvar-6630e15a0767459cc186e2fb +==> inserted refvar-6630e15a0767459cc186e2fc +==> inserted refvar-6630e15a0767459cc186e2fd +==> inserted refvar-6630e15a0767459cc186e2fe +==> inserted refvar-6630e15a0767459cc186e2ff +==> inserted refvar-6630e15a0767459cc186e300 +==> inserted refvar-6630e15a0767459cc186e301 +==> inserted refvar-6630e15a0767459cc186e302 +==> inserted refvar-6630e15a0767459cc186e303 +==> inserted refvar-6630e15a0767459cc186e304 +==> inserted refvar-6630e15a0767459cc186e305 +==> inserted refvar-6630e15a0767459cc186e306 +==> inserted refvar-6630e15a0767459cc186e307 +==> inserted refvar-6630e15a0767459cc186e308 +==> inserted refvar-6630e15a0767459cc186e309 +==> inserted refvar-6630e15a0767459cc186e30a +==> inserted refvar-6630e15a0767459cc186e30b +==> inserted refvar-6630e15a0767459cc186e30c +==> inserted refvar-6630e15a0767459cc186e30d +==> inserted refvar-6630e15a0767459cc186e30e +==> inserted refvar-6630e15a0767459cc186e30f +==> inserted refvar-6630e15a0767459cc186e310 +==> inserted refvar-6630e15a0767459cc186e311 +==> inserted refvar-6630e15a0767459cc186e312 +==> inserted refvar-6630e15a0767459cc186e313 +==> inserted refvar-6630e15a0767459cc186e314 +==> inserted refvar-6630e15a0767459cc186e315 +==> inserted refvar-6630e15a0767459cc186e316 +==> inserted refvar-6630e15a0767459cc186e317 +==> inserted refvar-6630e15a0767459cc186e318 +==> inserted refvar-6630e15a0767459cc186e319 +==> inserted refvar-6630e15a0767459cc186e31a +==> inserted refvar-6630e15a0767459cc186e31b +==> inserted refvar-6630e15a0767459cc186e31c +==> inserted refvar-6630e15a0767459cc186e31d +==> inserted refvar-6630e15a0767459cc186e31e +==> inserted 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 12:35:16 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 12:35:16 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 12:35:16 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'}