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(-) [+]
line wrap: on
line diff
--- /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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HG00096.json	Mon Jul 22 12:35:16 2024 +0000
@@ -0,0 +1,8867 @@
+[
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
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+        "variantType": "DEL",
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+        "end": 2651463,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:2650428-2651463",
+            "cnCount": 0,
+            "cnValue": 1.00369e-09
+        }
+    },
+    {
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+        "assemblyId": "GRCh38",
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+        "variantType": "DEL",
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+            "cnCount": 1,
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+        }
+    },
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+        }
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+        "end": 129368317,
+        "referenceName": "X",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chrX:129366305-129368317",
+            "cnCount": 0,
+            "cnValue": 1.00369e-09
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
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+        "variantId": "EFO:0030069",
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+        "end": 141384533,
+        "referenceName": "X",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chrX:141382260-141384533",
+            "cnCount": 0,
+            "cnValue": 1.00369e-09
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrX:143652805-143659126:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 143652805,
+        "end": 143659126,
+        "referenceName": "X",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chrX:143652806-143659126",
+            "cnCount": 0,
+            "cnValue": 0.144084
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrX:145340613-145342783:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 145340613,
+        "end": 145342783,
+        "referenceName": "X",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chrX:145340614-145342783",
+            "cnCount": 0,
+            "cnValue": 1.00369e-09
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrX:150759112-150760112:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 150759112,
+        "end": 150760112,
+        "referenceName": "X",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chrX:150759113-150760112",
+            "cnCount": 0,
+            "cnValue": 0.0295694
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrX:151124830-151127394:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 151124830,
+        "end": 151127394,
+        "referenceName": "X",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chrX:151124831-151127394",
+            "cnCount": 0,
+            "cnValue": 0.224926
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrX:155688504-155692183:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 155688504,
+        "end": 155692183,
+        "referenceName": "X",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chrX:155688505-155692183",
+            "cnCount": 0,
+            "cnValue": 1.00369e-09
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrY:3844269-3854396:EFO:0030070",
+        "variantType": "DUP",
+        "variantId": "EFO:0030070",
+        "start": 3844269,
+        "end": 3854396,
+        "referenceName": "Y",
+        "info": {
+            "legacyId": "DRAGEN:GAIN:chrY:3844270-3854396",
+            "cnCount": 2,
+            "cnValue": 1.85714
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrY:10659024-10693717:EFO:0030070",
+        "variantType": "DUP",
+        "variantId": "EFO:0030070",
+        "start": 10659024,
+        "end": 10693717,
+        "referenceName": "Y",
+        "info": {
+            "legacyId": "DRAGEN:GAIN:chrY:10659025-10693717",
+            "cnCount": 2,
+            "cnValue": 1.96766
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrY:11108561-11117868:EFO:0030070",
+        "variantType": "DUP",
+        "variantId": "EFO:0030070",
+        "start": 11108561,
+        "end": 11117868,
+        "referenceName": "Y",
+        "info": {
+            "legacyId": "DRAGEN:GAIN:chrY:11108562-11117868",
+            "cnCount": 4,
+            "cnValue": 3.54352
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrY:11289947-11296309:EFO:0030071",
+        "variantType": "DUP",
+        "variantId": "EFO:0030071",
+        "start": 11289947,
+        "end": 11296309,
+        "referenceName": "Y",
+        "info": {
+            "legacyId": "DRAGEN:GAIN:chrY:11289948-11296309",
+            "cnCount": 26,
+            "cnValue": 26.0609
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrY:11296309-11330116:EFO:0030070",
+        "variantType": "DUP",
+        "variantId": "EFO:0030070",
+        "start": 11296309,
+        "end": 11330116,
+        "referenceName": "Y",
+        "info": {
+            "legacyId": "DRAGEN:GAIN:chrY:11296310-11330116",
+            "cnCount": 2,
+            "cnValue": 1.84192
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrY:11530585-11539539:EFO:0030071",
+        "variantType": "DUP",
+        "variantId": "EFO:0030071",
+        "start": 11530585,
+        "end": 11539539,
+        "referenceName": "Y",
+        "info": {
+            "legacyId": "DRAGEN:GAIN:chrY:11530586-11539539",
+            "cnCount": 17,
+            "cnValue": 16.6986
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrY:11744914-11748800:EFO:0030070",
+        "variantType": "DUP",
+        "variantId": "EFO:0030070",
+        "start": 11744914,
+        "end": 11748800,
+        "referenceName": "Y",
+        "info": {
+            "legacyId": "DRAGEN:GAIN:chrY:11744915-11748800",
+            "cnCount": 2,
+            "cnValue": 2.03175
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrY:12512335-12514483:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 12512335,
+        "end": 12514483,
+        "referenceName": "Y",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chrY:12512336-12514483",
+            "cnCount": 0,
+            "cnValue": 0.284822
+        }
+    }
+]
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/analyses_query_findings.json	Mon Jul 22 12:35:16 2024 +0000
@@ -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'}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/biosamples_query_findings.json	Mon Jul 22 12:35:16 2024 +0000
@@ -0,0 +1,162 @@
+{'_id': ObjectId('668fb4eb8ed056280039f1bd'),
+ '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-668fb4eb8ed056280039f1bd',
+ 'individualId': 'NA24631',
+ '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('668fb4eb8ed056280039f1be'),
+ '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-668fb4eb8ed056280039f1be',
+ '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('668fb4eb8ed056280039f1bf'),
+ '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-668fb4eb8ed056280039f1bf',
+ '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'}}
+{'_id': ObjectId('668fb7125d00a890d911aa69'),
+ '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-668fb7125d00a890d911aa69',
+ 'individualId': 'NA24631',
+ '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('668fb7125d00a890d911aa6a'),
+ '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-668fb7125d00a890d911aa6a',
+ '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('668fb7125d00a890d911aa6b'),
+ '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-668fb7125d00a890d911aa6b',
+ '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'}}
+{'_id': ObjectId('668fb721ae6c452887afb69d'),
+ '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-668fb721ae6c452887afb69d',
+ 'individualId': 'NA24631',
+ '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 12:35:16 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
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+==> inserted refvar-6630e1590767459cc186e0fe
+==> inserted refvar-6630e1590767459cc186e0ff
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+==> inserted refvar-6630e1590767459cc186e102
+==> inserted refvar-6630e1590767459cc186e103
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+==> inserted refvar-6630e1590767459cc186e106
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+==> inserted refvar-6630e1590767459cc186e108
+==> inserted refvar-6630e1590767459cc186e109
+==> inserted refvar-6630e1590767459cc186e10a
+==> inserted refvar-6630e1590767459cc186e10b
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+==> inserted refvar-6630e1590767459cc186e10d
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+==> inserted refvar-6630e1590767459cc186e115
+==> inserted refvar-6630e1590767459cc186e116
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+==> inserted refvar-6630e1590767459cc186e118
+==> inserted refvar-6630e1590767459cc186e119
+==> inserted refvar-6630e1590767459cc186e11a
+==> inserted refvar-6630e1590767459cc186e11b
+==> inserted refvar-6630e1590767459cc186e11c
+==> inserted refvar-6630e1590767459cc186e11d
+==> inserted refvar-6630e1590767459cc186e11e
+==> inserted refvar-6630e1590767459cc186e11f
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+==> inserted refvar-6630e1590767459cc186e121
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+==> inserted refvar-6630e1590767459cc186e123
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+==> inserted refvar-6630e1590767459cc186e125
+==> inserted refvar-6630e1590767459cc186e126
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+==> inserted refvar-6630e1590767459cc186e129
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+==> inserted refvar-6630e1590767459cc186e12d
+==> inserted refvar-6630e1590767459cc186e12e
+==> inserted refvar-6630e1590767459cc186e12f
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+==> inserted refvar-6630e15a0767459cc186e13d
+==> inserted refvar-6630e15a0767459cc186e13e
+==> inserted refvar-6630e15a0767459cc186e13f
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+==> inserted refvar-6630e15a0767459cc186e14b
+==> inserted refvar-6630e15a0767459cc186e14c
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+==> inserted refvar-6630e15a0767459cc186e14e
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+==> inserted refvar-6630e15a0767459cc186e158
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+==> inserted refvar-6630e15a0767459cc186e15a
+==> inserted refvar-6630e15a0767459cc186e15b
+==> inserted refvar-6630e15a0767459cc186e15c
+==> inserted refvar-6630e15a0767459cc186e15d
+==> inserted refvar-6630e15a0767459cc186e15e
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+==> inserted refvar-6630e15a0767459cc186e160
+==> inserted refvar-6630e15a0767459cc186e161
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+==> inserted refvar-6630e15a0767459cc186e163
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+==> inserted refvar-6630e15a0767459cc186e16b
+==> inserted refvar-6630e15a0767459cc186e16c
+==> inserted refvar-6630e15a0767459cc186e16d
+==> inserted refvar-6630e15a0767459cc186e16e
+==> inserted refvar-6630e15a0767459cc186e16f
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+==> inserted refvar-6630e15a0767459cc186e171
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+==> 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
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+==> 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
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+==> inserted refvar-6630e15a0767459cc186e19d
+==> inserted refvar-6630e15a0767459cc186e19e
+==> inserted refvar-6630e15a0767459cc186e19f
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+==> inserted refvar-6630e15a0767459cc186e1a2
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+==> inserted refvar-6630e15a0767459cc186e1a8
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+==> 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
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+==> inserted refvar-6630e15a0767459cc186e204
+==> inserted refvar-6630e15a0767459cc186e205
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+==> inserted refvar-6630e15a0767459cc186e208
+==> inserted refvar-6630e15a0767459cc186e209
+==> inserted refvar-6630e15a0767459cc186e20a
+==> inserted refvar-6630e15a0767459cc186e20b
+==> inserted refvar-6630e15a0767459cc186e20c
+==> inserted refvar-6630e15a0767459cc186e20d
+==> inserted refvar-6630e15a0767459cc186e20e
+==> inserted refvar-6630e15a0767459cc186e20f
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+==> inserted refvar-6630e15a0767459cc186e218
+==> inserted refvar-6630e15a0767459cc186e219
+==> inserted refvar-6630e15a0767459cc186e21a
+==> inserted refvar-6630e15a0767459cc186e21b
+==> inserted refvar-6630e15a0767459cc186e21c
+==> inserted refvar-6630e15a0767459cc186e21d
+==> inserted refvar-6630e15a0767459cc186e21e
+==> inserted refvar-6630e15a0767459cc186e21f
+==> inserted refvar-6630e15a0767459cc186e220
+==> inserted refvar-6630e15a0767459cc186e221
+==> inserted refvar-6630e15a0767459cc186e222
+==> inserted refvar-6630e15a0767459cc186e223
+==> inserted refvar-6630e15a0767459cc186e224
+==> inserted refvar-6630e15a0767459cc186e225
+==> inserted refvar-6630e15a0767459cc186e226
+==> inserted refvar-6630e15a0767459cc186e227
+==> inserted refvar-6630e15a0767459cc186e228
+==> inserted refvar-6630e15a0767459cc186e229
+==> inserted refvar-6630e15a0767459cc186e22a
+==> inserted refvar-6630e15a0767459cc186e22b
+==> inserted refvar-6630e15a0767459cc186e22c
+==> inserted refvar-6630e15a0767459cc186e22d
+==> inserted refvar-6630e15a0767459cc186e22e
+==> inserted refvar-6630e15a0767459cc186e22f
+==> inserted refvar-6630e15a0767459cc186e230
+==> inserted refvar-6630e15a0767459cc186e231
+==> inserted refvar-6630e15a0767459cc186e232
+==> inserted refvar-6630e15a0767459cc186e233
+==> inserted refvar-6630e15a0767459cc186e234
+==> inserted refvar-6630e15a0767459cc186e235
+==> inserted refvar-6630e15a0767459cc186e236
+==> inserted refvar-6630e15a0767459cc186e237
+==> inserted refvar-6630e15a0767459cc186e238
+==> inserted refvar-6630e15a0767459cc186e239
+==> inserted refvar-6630e15a0767459cc186e23a
+==> inserted refvar-6630e15a0767459cc186e23b
+==> inserted refvar-6630e15a0767459cc186e23c
+==> inserted refvar-6630e15a0767459cc186e23d
+==> inserted refvar-6630e15a0767459cc186e23e
+==> inserted refvar-6630e15a0767459cc186e23f
+==> inserted refvar-6630e15a0767459cc186e240
+==> inserted refvar-6630e15a0767459cc186e241
+==> inserted refvar-6630e15a0767459cc186e242
+==> inserted refvar-6630e15a0767459cc186e243
+==> inserted refvar-6630e15a0767459cc186e244
+==> inserted refvar-6630e15a0767459cc186e245
+==> inserted refvar-6630e15a0767459cc186e246
+==> inserted refvar-6630e15a0767459cc186e247
+==> inserted refvar-6630e15a0767459cc186e248
+==> inserted refvar-6630e15a0767459cc186e249
+==> inserted refvar-6630e15a0767459cc186e24a
+==> inserted refvar-6630e15a0767459cc186e24b
+==> inserted refvar-6630e15a0767459cc186e24c
+==> inserted refvar-6630e15a0767459cc186e24d
+==> inserted refvar-6630e15a0767459cc186e24e
+==> inserted refvar-6630e15a0767459cc186e24f
+==> inserted refvar-6630e15a0767459cc186e250
+==> inserted refvar-6630e15a0767459cc186e251
+==> inserted refvar-6630e15a0767459cc186e252
+==> inserted refvar-6630e15a0767459cc186e253
+==> inserted refvar-6630e15a0767459cc186e254
+==> inserted refvar-6630e15a0767459cc186e255
+==> inserted refvar-6630e15a0767459cc186e256
+==> inserted refvar-6630e15a0767459cc186e257
+==> inserted refvar-6630e15a0767459cc186e258
+==> inserted refvar-6630e15a0767459cc186e259
+==> inserted refvar-6630e15a0767459cc186e25a
+==> inserted refvar-6630e15a0767459cc186e25b
+==> inserted refvar-6630e15a0767459cc186e25c
+==> inserted refvar-6630e15a0767459cc186e25d
+==> inserted refvar-6630e15a0767459cc186e25e
+==> inserted refvar-6630e15a0767459cc186e25f
+==> inserted refvar-6630e15a0767459cc186e260
+==> inserted refvar-6630e15a0767459cc186e261
+==> inserted refvar-6630e15a0767459cc186e262
+==> inserted refvar-6630e15a0767459cc186e263
+==> inserted refvar-6630e15a0767459cc186e264
+==> inserted refvar-6630e15a0767459cc186e265
+==> inserted refvar-6630e15a0767459cc186e266
+==> inserted refvar-6630e15a0767459cc186e267
+==> inserted refvar-6630e15a0767459cc186e268
+==> inserted refvar-6630e15a0767459cc186e269
+==> inserted refvar-6630e15a0767459cc186e26a
+==> inserted refvar-6630e15a0767459cc186e26b
+==> inserted refvar-6630e15a0767459cc186e26c
+==> inserted refvar-6630e15a0767459cc186e26d
+==> inserted refvar-6630e15a0767459cc186e26e
+==> inserted refvar-6630e15a0767459cc186e26f
+==> inserted refvar-6630e15a0767459cc186e270
+==> inserted refvar-6630e15a0767459cc186e271
+==> inserted refvar-6630e15a0767459cc186e272
+==> inserted refvar-6630e15a0767459cc186e273
+==> inserted refvar-6630e15a0767459cc186e274
+==> inserted refvar-6630e15a0767459cc186e275
+==> inserted refvar-6630e15a0767459cc186e276
+==> inserted refvar-6630e15a0767459cc186e277
+==> inserted refvar-6630e15a0767459cc186e278
+==> inserted refvar-6630e15a0767459cc186e279
+==> inserted refvar-6630e15a0767459cc186e27a
+==> inserted refvar-6630e15a0767459cc186e27b
+==> inserted refvar-6630e15a0767459cc186e27c
+==> inserted refvar-6630e15a0767459cc186e27d
+==> inserted refvar-6630e15a0767459cc186e27e
+==> inserted refvar-6630e15a0767459cc186e27f
+==> inserted refvar-6630e15a0767459cc186e280
+==> inserted refvar-6630e15a0767459cc186e281
+==> inserted refvar-6630e15a0767459cc186e282
+==> inserted refvar-6630e15a0767459cc186e283
+==> inserted refvar-6630e15a0767459cc186e284
+==> inserted refvar-6630e15a0767459cc186e285
+==> inserted refvar-6630e15a0767459cc186e286
+==> inserted refvar-6630e15a0767459cc186e287
+==> inserted refvar-6630e15a0767459cc186e288
+==> inserted refvar-6630e15a0767459cc186e289
+==> inserted refvar-6630e15a0767459cc186e28a
+==> inserted refvar-6630e15a0767459cc186e28b
+==> inserted refvar-6630e15a0767459cc186e28c
+==> inserted refvar-6630e15a0767459cc186e28d
+==> inserted refvar-6630e15a0767459cc186e28e
+==> inserted refvar-6630e15a0767459cc186e28f
+==> inserted refvar-6630e15a0767459cc186e290
+==> inserted refvar-6630e15a0767459cc186e291
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+==> inserted refvar-6630e15a0767459cc186e293
+==> inserted refvar-6630e15a0767459cc186e294
+==> inserted refvar-6630e15a0767459cc186e295
+==> inserted refvar-6630e15a0767459cc186e296
+==> inserted refvar-6630e15a0767459cc186e297
+==> inserted refvar-6630e15a0767459cc186e298
+==> inserted refvar-6630e15a0767459cc186e299
+==> inserted refvar-6630e15a0767459cc186e29a
+==> inserted refvar-6630e15a0767459cc186e29b
+==> inserted refvar-6630e15a0767459cc186e29c
+==> inserted refvar-6630e15a0767459cc186e29d
+==> inserted refvar-6630e15a0767459cc186e29e
+==> inserted refvar-6630e15a0767459cc186e29f
+==> inserted refvar-6630e15a0767459cc186e2a0
+==> inserted refvar-6630e15a0767459cc186e2a1
+==> inserted refvar-6630e15a0767459cc186e2a2
+==> inserted refvar-6630e15a0767459cc186e2a3
+==> inserted refvar-6630e15a0767459cc186e2a4
+==> inserted refvar-6630e15a0767459cc186e2a5
+==> inserted refvar-6630e15a0767459cc186e2a6
+==> inserted refvar-6630e15a0767459cc186e2a7
+==> inserted refvar-6630e15a0767459cc186e2a8
+==> inserted refvar-6630e15a0767459cc186e2a9
+==> inserted refvar-6630e15a0767459cc186e2aa
+==> inserted refvar-6630e15a0767459cc186e2ab
+==> inserted refvar-6630e15a0767459cc186e2ac
+==> inserted refvar-6630e15a0767459cc186e2ad
+==> inserted refvar-6630e15a0767459cc186e2ae
+==> inserted refvar-6630e15a0767459cc186e2af
+==> inserted refvar-6630e15a0767459cc186e2b0
+==> inserted refvar-6630e15a0767459cc186e2b1
+==> inserted refvar-6630e15a0767459cc186e2b2
+==> inserted refvar-6630e15a0767459cc186e2b3
+==> inserted refvar-6630e15a0767459cc186e2b4
+==> inserted refvar-6630e15a0767459cc186e2b5
+==> inserted refvar-6630e15a0767459cc186e2b6
+==> inserted refvar-6630e15a0767459cc186e2b7
+==> inserted refvar-6630e15a0767459cc186e2b8
+==> inserted refvar-6630e15a0767459cc186e2b9
+==> inserted refvar-6630e15a0767459cc186e2ba
+==> inserted refvar-6630e15a0767459cc186e2bb
+==> inserted refvar-6630e15a0767459cc186e2bc
+==> inserted refvar-6630e15a0767459cc186e2bd
+==> inserted refvar-6630e15a0767459cc186e2be
+==> inserted refvar-6630e15a0767459cc186e2bf
+==> inserted refvar-6630e15a0767459cc186e2c0
+==> inserted refvar-6630e15a0767459cc186e2c1
+==> inserted refvar-6630e15a0767459cc186e2c2
+==> inserted refvar-6630e15a0767459cc186e2c3
+==> inserted refvar-6630e15a0767459cc186e2c4
+==> inserted refvar-6630e15a0767459cc186e2c5
+==> inserted refvar-6630e15a0767459cc186e2c6
+==> inserted refvar-6630e15a0767459cc186e2c7
+==> inserted refvar-6630e15a0767459cc186e2c8
+==> inserted refvar-6630e15a0767459cc186e2c9
+==> inserted refvar-6630e15a0767459cc186e2ca
+==> inserted refvar-6630e15a0767459cc186e2cb
+==> inserted refvar-6630e15a0767459cc186e2cc
+==> inserted refvar-6630e15a0767459cc186e2cd
+==> inserted refvar-6630e15a0767459cc186e2ce
+==> inserted refvar-6630e15a0767459cc186e2cf
+==> inserted refvar-6630e15a0767459cc186e2d0
+==> inserted refvar-6630e15a0767459cc186e2d1
+==> inserted refvar-6630e15a0767459cc186e2d2
+==> inserted refvar-6630e15a0767459cc186e2d3
+==> inserted refvar-6630e15a0767459cc186e2d4
+==> inserted refvar-6630e15a0767459cc186e2d5
+==> inserted refvar-6630e15a0767459cc186e2d6
+==> inserted refvar-6630e15a0767459cc186e2d7
+==> inserted refvar-6630e15a0767459cc186e2d8
+==> inserted refvar-6630e15a0767459cc186e2d9
+==> inserted refvar-6630e15a0767459cc186e2da
+==> inserted refvar-6630e15a0767459cc186e2db
+==> inserted refvar-6630e15a0767459cc186e2dc
+==> inserted refvar-6630e15a0767459cc186e2dd
+==> inserted refvar-6630e15a0767459cc186e2de
+==> inserted refvar-6630e15a0767459cc186e2df
+==> inserted refvar-6630e15a0767459cc186e2e0
+==> inserted refvar-6630e15a0767459cc186e2e1
+==> inserted refvar-6630e15a0767459cc186e2e2
+==> inserted refvar-6630e15a0767459cc186e2e3
+==> inserted refvar-6630e15a0767459cc186e2e4
+==> inserted refvar-6630e15a0767459cc186e2e5
+==> inserted refvar-6630e15a0767459cc186e2e6
+==> inserted refvar-6630e15a0767459cc186e2e7
+==> inserted refvar-6630e15a0767459cc186e2e8
+==> inserted refvar-6630e15a0767459cc186e2e9
+==> inserted refvar-6630e15a0767459cc186e2ea
+==> inserted refvar-6630e15a0767459cc186e2eb
+==> inserted refvar-6630e15a0767459cc186e2ec
+==> inserted refvar-6630e15a0767459cc186e2ed
+==> inserted refvar-6630e15a0767459cc186e2ee
+==> inserted refvar-6630e15a0767459cc186e2ef
+==> inserted refvar-6630e15a0767459cc186e2f0
+==> inserted refvar-6630e15a0767459cc186e2f1
+==> inserted refvar-6630e15a0767459cc186e2f2
+==> inserted refvar-6630e15a0767459cc186e2f3
+==> inserted 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'}