# HG changeset patch
# User iuc
# Date 1721651701 0
# Node ID 2e60de9f50466cf9484b84d9596dfefa49d121e6

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258

diff -r 000000000000 -r 2e60de9f5046 bracket.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bracket.xml	Mon Jul 22 12:35:01 2024 +0000
@@ -0,0 +1,63 @@
+<tool id="beacon2_bracket" name="Beacon2 Bracket" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Specifies a sequence ranges for both the start and end positions of a genomic variation</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[    
+        beacon2-search bracket
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        --start-minimum $start_minimum
+        --start-maximum $start_maximum
+        --end-minimum $end_minimum
+        --end-maximum $end_maximum
+        #if str($advanced_settings.variantType)
+            --variantType '$advanced_settings.variantType'
+        #end if
+        #if str($advanced_settings.referenceName)
+            --referenceName '$advanced_settings.referenceName'
+        #end if
+        > bracket_query_findings.json
+    ]]></command>
+    <expand macro="configfile"/>
+    <inputs>
+        <expand macro="Connection_to_MongoDB" />
+        <expand macro="Database_Configuration" />
+        <param argument="--start-minimum" type="integer" label="Start minimum position" value="" help="" />
+        <param argument="--start-maximum" type="integer" label="Start maximum position" value="" help="" />
+        <param argument="--end-minimum" type="integer" label="End minimum position" value="" help="" />
+        <param argument="--end-maximum" type="integer" label="End maximum position" value="" help="" />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <param argument="--referenceName" optional="true" type="text" label="Reference Name" value="" help="Reference name in numbers chr1/1, chr2/2, chr3/3, etc." />
+            <param argument="--variantType"  optional="true" type="text" label="VARIANT TYPE" value="" help="Targeted Variant type to search for" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_bracket_query" format="json" label="${tool.name} on ${on_string}: Bracket Query" from_work_dir="bracket_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="genomicVariations" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="start_minimum" value="131836" />
+            <param name="start_maximum" value="161836" />
+            <param name="end_minimum" value="131837" />
+            <param name="end_maximum" value="151837" />
+            <param name="variantType" value="SNP" />
+            <output name="out_bracket_query">
+                <assert_contents><has_text_matching expression="_id"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Bracket Queries allow the specification of sequence ranges for both start and end positions of a genomic variation. The typical example here is the query for similar structural variants - particularly CNVs - affecting a genomic region but potentially differing in their exact base extents.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r 2e60de9f5046 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Jul 22 12:35:01 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>
diff -r 000000000000 -r 2e60de9f5046 test-data/HG00096.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HG00096.json	Mon Jul 22 12:35:01 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": 4063594,
+        "end": 4067475,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:4063595-4067475",
+            "cnCount": 1,
+            "cnValue": 0.429788
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:6377770-6385660:EFO:0030068",
+        "variantType": "DEL",
+        "variantId": "EFO:0030068",
+        "start": 6377770,
+        "end": 6385660,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:6377771-6385660",
+            "cnCount": 1,
+            "cnValue": 0.543097
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:8143311-8150440:EFO:0030071",
+        "variantType": "DUP",
+        "variantId": "EFO:0030071",
+        "start": 8143311,
+        "end": 8150440,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:GAIN:chr1:8143312-8150440",
+            "cnCount": 3,
+            "cnValue": 1.42495
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
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+        "variantType": "DUP",
+        "variantId": "EFO:0030071",
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+        "end": 13242034,
+        "referenceName": "1",
+        "info": {
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+            "cnCount": 3,
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+        }
+    },
+    {
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+        "variantType": "DUP",
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+        "end": 16646293,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:GAIN:chr1:16605062-16646293",
+            "cnCount": 7,
+            "cnValue": 3.3289
+        }
+    },
+    {
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+        "referenceName": "1",
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+        }
+    },
+    {
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+        }
+    },
+    {
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+        "variantType": "DEL",
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+        }
+    },
+    {
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+        }
+    },
+    {
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+        }
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+        }
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+        }
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+        }
+    },
+    {
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+        }
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+        }
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+        }
+    },
+    {
+        "biosampleId": "HG00096",
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+        "variantInternalId": "chr1:112148880-112161897:EFO:0030069",
+        "variantType": "DEL",
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+        }
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+        }
+    },
+    {
+        "biosampleId": "HG00096",
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+        "variantInternalId": "chr1:152787112-152798062:EFO:0030068",
+        "variantType": "DEL",
+        "variantId": "EFO:0030068",
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+    {
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+    },
+    {
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+        "variantInternalId": "chr1:153710046-153720849:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
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+    },
+    {
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+        "assemblyId": "GRCh38",
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+            "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
diff -r 000000000000 -r 2e60de9f5046 test-data/analyses_query_findings.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/analyses_query_findings.json	Mon Jul 22 12:35:01 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'}
diff -r 000000000000 -r 2e60de9f5046 test-data/biosamples_query_findings.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/biosamples_query_findings.json	Mon Jul 22 12:35:01 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'}}
diff -r 000000000000 -r 2e60de9f5046 test-data/bracket_query_findings.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bracket_query_findings.json	Mon Jul 22 12:35:01 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'}
diff -r 000000000000 -r 2e60de9f5046 test-data/cnv_query_findings.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cnv_query_findings.json	Mon Jul 22 12:35:01 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'}}
diff -r 000000000000 -r 2e60de9f5046 test-data/cohorts_query_findings.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cohorts_query_findings.json	Mon Jul 22 12:35:01 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'}
diff -r 000000000000 -r 2e60de9f5046 test-data/datasets_query_findings.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/datasets_query_findings.json	Mon Jul 22 12:35:01 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'}
diff -r 000000000000 -r 2e60de9f5046 test-data/gene_query_findings.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_query_findings.json	Mon Jul 22 12:35:01 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'}
diff -r 000000000000 -r 2e60de9f5046 test-data/individuals_query_findings.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/individuals_query_findings.json	Mon Jul 22 12:35:01 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'}}
diff -r 000000000000 -r 2e60de9f5046 test-data/logs.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/logs.txt	Mon Jul 22 12:35:01 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
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+==> inserted refvar-6630e15a0767459cc186e341
diff -r 000000000000 -r 2e60de9f5046 test-data/ranged_query_findings.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ranged_query_findings.json	Mon Jul 22 12:35:01 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'}
diff -r 000000000000 -r 2e60de9f5046 test-data/runs_query_findings.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/runs_query_findings.json	Mon Jul 22 12:35:01 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'}
diff -r 000000000000 -r 2e60de9f5046 test-data/sequenced_query_findings.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sequenced_query_findings.json	Mon Jul 22 12:35:01 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'}