From f4151aa2d760f931f819f954f465ef66055bf258 Mon Sep 17 00:00:00 2001
From: Khaled196 <56037954+khaled196@users.noreply.github.com>
Date: Mon, 22 Jul 2024 13:24:11 +0100
Subject: [PATCH] add beacon import and search tools (#6028)

* add new tools

* add beacon import and search

* add the beacon import and beacon search

* update tools help and tests

* update tool version

* fix .shed text

* fix .shed text

* fix help part in gene

* fix .shed text

* fix linting

* fix ip

* remove password from parmetars

* fix linting

* fix linting

* add more query options and update the script to the latest version

* change the output file format and onother linting errors

* fix spilling

* remove config_file

* add configFile
---
 tools/beacon2-import/.shed.yml                |   18 +
 tools/beacon2-import/analyses.xml             |   83 +
 tools/beacon2-import/biosamples.xml           |  119 +
 tools/beacon2-import/bracket.xml              |   63 +
 tools/beacon2-import/cnv.xml                  |   82 +
 tools/beacon2-import/cohorts.xml              |   81 +
 tools/beacon2-import/datasets.xml             |   64 +
 tools/beacon2-import/gene.xml                 |   68 +
 tools/beacon2-import/import.xml               |   54 +
 tools/beacon2-import/individuals.xml          |   98 +
 tools/beacon2-import/macros.xml               |   55 +
 tools/beacon2-import/range.xml                |   73 +
 tools/beacon2-import/runs.xml                 |   86 +
 tools/beacon2-import/sequence.xml             |   61 +
 tools/beacon2-import/test-data/HG00096.json   | 8867 +++++++++++++++++
 .../test-data/analyses_query_findings.json    |    9 +
 .../test-data/biosamples_query_findings.json  |  162 +
 .../test-data/bracket_query_findings.json     |   30 +
 .../test-data/cnv_query_findings.json         |   13 +
 .../test-data/cohorts_query_findings.json     |    8 +
 .../test-data/datasets_query_findings.json    |   11 +
 .../test-data/gene_query_findings.json        |   11 +
 .../test-data/individuals_query_findings.json |    9 +
 tools/beacon2-import/test-data/logs.txt       |  591 ++
 .../test-data/ranged_query_findings.json      |   39 +
 .../test-data/runs_query_findings.json        |   11 +
 .../test-data/sequenced_query_findings.json   |    8 +
 27 files changed, 10774 insertions(+)
 create mode 100644 tools/beacon2-import/.shed.yml
 create mode 100644 tools/beacon2-import/analyses.xml
 create mode 100644 tools/beacon2-import/biosamples.xml
 create mode 100644 tools/beacon2-import/bracket.xml
 create mode 100644 tools/beacon2-import/cnv.xml
 create mode 100644 tools/beacon2-import/cohorts.xml
 create mode 100644 tools/beacon2-import/datasets.xml
 create mode 100644 tools/beacon2-import/gene.xml
 create mode 100644 tools/beacon2-import/import.xml
 create mode 100644 tools/beacon2-import/individuals.xml
 create mode 100644 tools/beacon2-import/macros.xml
 create mode 100644 tools/beacon2-import/range.xml
 create mode 100644 tools/beacon2-import/runs.xml
 create mode 100644 tools/beacon2-import/sequence.xml
 create mode 100644 tools/beacon2-import/test-data/HG00096.json
 create mode 100644 tools/beacon2-import/test-data/analyses_query_findings.json
 create mode 100644 tools/beacon2-import/test-data/biosamples_query_findings.json
 create mode 100644 tools/beacon2-import/test-data/bracket_query_findings.json
 create mode 100644 tools/beacon2-import/test-data/cnv_query_findings.json
 create mode 100644 tools/beacon2-import/test-data/cohorts_query_findings.json
 create mode 100644 tools/beacon2-import/test-data/datasets_query_findings.json
 create mode 100644 tools/beacon2-import/test-data/gene_query_findings.json
 create mode 100644 tools/beacon2-import/test-data/individuals_query_findings.json
 create mode 100644 tools/beacon2-import/test-data/logs.txt
 create mode 100644 tools/beacon2-import/test-data/ranged_query_findings.json
 create mode 100644 tools/beacon2-import/test-data/runs_query_findings.json
 create mode 100644 tools/beacon2-import/test-data/sequenced_query_findings.json

diff --git a/tools/beacon2-import/.shed.yml b/tools/beacon2-import/.shed.yml
new file mode 100644
index 00000000000..e1dd4c69dcd
--- /dev/null
+++ b/tools/beacon2-import/.shed.yml
@@ -0,0 +1,18 @@
+categories: 
+- Variant Analysis
+description: Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants.
+long_description: Beacon Import facilitates the seamless transfer of local genetic data to the server, enhancing collaboration and knowledge sharing. Meanwhile,
+       Beacon Query empowers users to efficiently explore the server for specific genetic information, including genes, sequences, variants, cnv, and genomic ranges. The search
+       tools also search the phenopacket and other metadata B2RI collections (individuals, runs, datasets, biosamples, cohorts and analyses),
+      catalyzing genomic research and clinical applications.
+homepage_url: https://pypi.org/project/beacon2-import/
+name: Beacon2_Import
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for {{ tool_name }}."
+suite:
+  name: "suite_beacon2_import"
+  description: "A suite of Galaxy tools designed to work with the beacon2-import python library."
+  type: repository_suite_definition
\ No newline at end of file
diff --git a/tools/beacon2-import/analyses.xml b/tools/beacon2-import/analyses.xml
new file mode 100644
index 00000000000..2239baa366f
--- /dev/null
+++ b/tools/beacon2-import/analyses.xml
@@ -0,0 +1,83 @@
+<tool id="beacon2_analyses" name="Beacon2 Analyses" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>َQuery the analyses collection in the beacon database for bioinformatic procedures to identify variants</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[    
+        beacon2-search analyses
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        #if str($advanced_settings.aligner)
+            --aligner '$advanced_settings.aligner'
+        #end if
+        #if str($advanced_settings.analysisDate)
+            --analysisDate '$advanced_settings.analysisDate'
+        #end if
+        #if str($advanced_settings.biosampleId)
+            --biosampleId '$advanced_settings.biosampleId'
+        #end if
+        #if str($advanced_settings.identification)
+            --identification '$advanced_settings.identification'
+        #end if
+        #if str($advanced_settings.individualId)
+            --individualId '$advanced_settings.individualId'
+        #end if
+        #if str($advanced_settings.pipelineName)
+            --pipelineName '$advanced_settings.pipelineName'
+        #end if
+        #if str($advanced_settings.pipelineRef)
+            --pipelineRef '$advanced_settings.pipelineRef'
+        #end if
+        #if str($advanced_settings.runId)
+            --runId '$advanced_settings.runId'
+        #end if
+        #if str($advanced_settings.variantCaller)
+            --variantCaller '$advanced_settings.variantCaller'
+        #end if
+        > analyses_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="--aligner" optional="true" type="text" label="ALIGNER" value="" help="Reference to mapping/alignment software. Example bwa-0.7.8" />
+            <param argument="--analysisDate" optional="true" type="text" label="ANALYSIS DATE" value="" help="Date at which analysis was performed. Example 2021-10-17	 " />
+            <param argument="--biosampleId" optional="true" type="text" label="BIOSAMPLE ID" value="" help="Reference to the id of the biosample this analysis is reporting on. Example S0001 " />
+            <param argument="--identification" optional="true" type="text" label="ID" value="" help="Analysis reference ID (external accession or internal ID). Example GA.01234abcde" />
+            <param argument="--individualId" optional="true" type="text" label="INDIVIDUALID" value="" help="Reference to the id of the individual this analysis is reporting on.	Example P0001 " />
+            <param argument="--pipelineName" optional="true" type="text" label="PIPELINE NAME" value="" help="Analysis pipeline and version if a standardized pipeline was used. Example Pipeline-panel-0001-v1	 " />
+            <param argument="--pipelineRef" optional="true" type="text" label="PIPELINE REF" value="" help="Link to Analysis pipeline resource" />
+            <param argument="--runId" optional="true" type="text" label="RUNID" value="" help="	Run identifier (external accession or internal ID). Example SRR10903401" />
+            <param argument="--variantCaller" optional="true" type="text" label="VARIANT CALLER" value="" help="Reference to variant calling software / pipeline. Example GATK4.0 " />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_analyses_query" format="json" label="${tool.name} on ${on_string}: Analyses Query" from_work_dir="analyses_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="analyses" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="individualId" value="NA24694" />
+            <param name="biosampleId" value="S0002" />
+            <param name="aligner" value="bwa-0.7.8" />
+            <param name="pipelineName" value="GATK Pipeline 4.2.3.0" />
+            <param name="identification" value="refvar-668fc705ef8bca245c3c2185" />
+            <output name="out_analyses_query">
+                <assert_contents><has_text_matching expression="_id"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Beacon2 Analyses queries the analyses collection in the Beacon database to identify bioinformatic procedures and variants. This tool allows detailed queries using advanced settings such as aligner, analysis date, biosample ID, and more.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tools/beacon2-import/biosamples.xml b/tools/beacon2-import/biosamples.xml
new file mode 100644
index 00000000000..950e2b70651
--- /dev/null
+++ b/tools/beacon2-import/biosamples.xml
@@ -0,0 +1,119 @@
+<tool id="beacon2_biosamples" name="Beacon2 Biosamples" version="1.0.0" profile="21.05">
+    <description>Query the biosamples collection in the beacon database for samples taken from individuals</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        beacon2-search biosamples
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        #if str($advanced_settings.biosampleStatus)
+            --biosampleStatus '$advanced_settings.biosampleStatus'
+        #end if
+        #if str($advanced_settings.collectionDate)
+            --collectionDate '$advanced_settings.collectionDate'
+        #end if
+        #if str($advanced_settings.collectionMoment)
+            --collectionMoment '$advanced_settings.collectionMoment'
+        #end if
+        #if str($advanced_settings.identification)
+            --identification '$advanced_settings.identification'
+        #end if
+        #if str($advanced_settings.diagnosticMarkers)
+            --diagnosticMarkers '$advanced_settings.diagnosticMarkers'
+        #end if
+        #if str($advanced_settings.histologicalDiagnosis)
+            --histologicalDiagnosis '$advanced_settings.histologicalDiagnosis'
+        #end if
+        #if str($advanced_settings.obtentionProcedure)
+            --obtentionProcedure '$advanced_settings.obtentionProcedure'
+        #end if
+        #if str($advanced_settings.pathologicalStage)
+            --pathologicalStage '$advanced_settings.pathologicalStage'
+        #end if
+        #if str($advanced_settings.pathologicalTnmFinding)
+            --pathologicalTnmFinding '$advanced_settings.pathologicalTnmFinding'
+        #end if
+        #if str($advanced_settings.featureType)
+            --featureType '$advanced_settings.featureType'
+        #end if
+        #if str($advanced_settings.severity)
+            --severity '$advanced_settings.severity'
+        #end if
+        #if str($advanced_settings.sampleOriginDetail)
+            --sampleOriginDetail '$advanced_settings.sampleOriginDetail'
+        #end if
+        #if str($advanced_settings.sampleOriginType)
+            --sampleOriginType '$advanced_settings.sampleOriginType'
+        #end if
+        #if str($advanced_settings.sampleProcessing)
+            --sampleProcessing '$advanced_settings.sampleProcessing'
+        #end if
+        #if str($advanced_settings.sampleStorage)
+            --sampleStorage '$advanced_settings.sampleStorage'
+        #end if
+        #if str($advanced_settings.tumorGrade)
+            --tumorGrade '$advanced_settings.tumorGrade'
+        #end if
+        #if str($advanced_settings.tumorProgression)
+            --tumorProgression '$advanced_settings.tumorProgression'
+        #end if
+        > biosamples_query_findings.json
+        ]]>
+    </command>
+    <expand macro="configfile"/>
+    <inputs>
+        <expand macro="Connection_to_MongoDB"/>
+        <expand macro="Database_Configuration"/>
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <param argument="--biosampleStatus" optional="true" type="text" label="BIOSAMPLE STATUS" value="" help="Ontology value for the classification of the sample in abnormal sample (EFO:0009655) or reference sample (EFO:0009654)" />
+            <param argument="--collectionDate" optional="true" type="text" label="COLLECTION DATE" value="" help="Date of biosample collection in ISO8601 format" />
+            <param argument="--collectionMoment" optional="true" type="text" label="COLLECTION MOMENT" value="" help="Individual's or cell culture age at the time of sample collection in the ISO8601 duration format P[n]Y[n]M[n]DT[n]H[n]M[n]S, e.g. P32Y6M1D, P7D" />
+            <param argument="--identification" optional="true" type="text" label="ID" value="" help="Biosample identifier (external accession or internal ID)" />
+            <param argument="--diagnosticMarkers" optional="true" type="text" label="DIAGNOSTIC MARKERS" value="" help="Clinically relevant bio markers, e.g. T2b Stage Finding" />
+            <param argument="--histologicalDiagnosis" optional="true" type="text" label="HISTOLOGICAL DIAGNOSIS" value="" help="Disease diagnosis that was inferred from the histological examination, e.g. Serous Cystadenocarcinoma" />
+            <param argument="--obtentionProcedure" optional="true" type="text" label="OBTENTION PROCEDURE" value="" help="Ontology value describing the procedure for sample obtention, e.g. biopsy" />
+            <param argument="--pathologicalStage" optional="true" type="text" label="PATHOLOGICAL STAGE" value="" help="Pathological stage, if applicable, e.g. Stage IIIA" />
+            <param argument="--pathologicalTnmFinding" optional="true" type="text" label="PATHOLOGICAL TNM FINDING" value="" help="T2b Stage Finding" />
+            <param argument="--featureType" optional="true" type="text" label="FEATURE TYPE" value="" help="Definition of an ontology term which describes the phenotype, e.g. Infantile spasms" />
+            <param argument="--severity" optional="true" type="text" label="SEVERITY" value="" help="Ontology class that describes the severity of the condition, e.g. Moderate" />
+            <param argument="--sampleOriginDetail" optional="true" type="text" label="SAMPLE ORIGIN DETAIL" value="" help="Tissue from which the sample was taken or sample origin matching the category set in 'sampleOriginType', e.g. wall of urinary bladder" />
+            <param argument="--sampleOriginType" optional="true" type="text" label="SAMPLE ORIGIN TYPE" value="" help="Category of sample origin. Value from Ontology for Biomedical Investigations (OBI) material entity, e.g abnormal sample" />
+            <param argument="--sampleProcessing" optional="true" type="text" label="SAMPLE PROCESSING" value="" help="Status of how the specimen was processed, e.g. mechanical dissociation" />
+            <param argument="--sampleStorage" optional="true" type="text" label="SAMPLE STORAGE" value="" help="Status of how the specimen was stored" />
+            <param argument="--tumorGrade" optional="true" type="text" label="TUMOR GRADE" value="" help="Term representing the tumor grade, e.g. Grade 3a" />
+            <param argument="--tumorProgression" optional="true" type="text" label="TUMOR PROGRESSION" value="" help="Tumor progression category indicating primary, metastatic or recurrent progression, e.g. Primary Malignant Neoplasm" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_biosamples_query" format="json" label="${tool.name} on ${on_string}: Biosamples Query" from_work_dir="biosamples_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="biosamples" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="tumorGrade" value="Grade 2 Lesion" />
+            <param name="biosampleStatus" value="abnormal sample" />
+            <param name="collectionDate" value="2021-04-23" />
+            <param name="sampleOriginDetail" value="wall of urinary bladde" />
+            <param name="tumorProgression" value="Primary Malignant Neoplasm" />
+            <output name="out_biosamples_query">
+                <assert_contents>
+                    <has_text_matching expression="_id"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Beacon2 Biosamples queries the biosamples collection in the Beacon database for samples taken from individuals. This tool allows detailed queries using advanced settings such as biosample status, collection date, diagnostic markers, and more.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tools/beacon2-import/bracket.xml b/tools/beacon2-import/bracket.xml
new file mode 100644
index 00000000000..9e69fea2c32
--- /dev/null
+++ b/tools/beacon2-import/bracket.xml
@@ -0,0 +1,63 @@
+<tool id="beacon2_bracket" name="Beacon2 Bracket" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Specifies a sequence ranges for both the start and end positions of a genomic variation</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[    
+        beacon2-search bracket
+        --db-host '$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 ${on_string}: Bracket Query" from_work_dir="bracket_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="genomicVariations" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="start_minimum" value="131836" />
+            <param name="start_maximum" value="161836" />
+            <param name="end_minimum" value="131837" />
+            <param name="end_maximum" value="151837" />
+            <param name="variantType" value="SNP" />
+            <output name="out_bracket_query">
+                <assert_contents><has_text_matching expression="_id"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Bracket Queries allow the specification of sequence ranges for both start and end positions of a genomic variation. The typical example here is the query for similar structural variants - particularly CNVs - affecting a genomic region but potentially differing in their exact base extents.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tools/beacon2-import/cnv.xml b/tools/beacon2-import/cnv.xml
new file mode 100644
index 00000000000..df3071584ac
--- /dev/null
+++ b/tools/beacon2-import/cnv.xml
@@ -0,0 +1,82 @@
+<tool id="beacon2_cnv" name="Beacon2 CNV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Retrieve the copy number varients from genomicVariations collection from the beacon database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[    
+        beacon2-search cnv
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        #if str($advanced_settings.variantInternalId)
+            --variantInternalId '$advanced_settings.variantInternalId'
+        #end if
+        #if str($advanced_settings.analysisId)
+            --analysisId '$advanced_settings.analysisId'
+        #end if
+        #if str($advanced_settings.individualId)
+            --individualId '$advanced_settings.individualId'
+        #end if
+        #if str($advanced_settings.start)
+            --start $advanced_settings.start
+        #end if
+        #if str($advanced_settings.end)
+            --end $advanced_settings.end
+        #end if
+        #if str($advanced_settings.chromosome)
+            --chromosome '$advanced_settings.chromosome'
+        #end if
+        #if str($advanced_settings.variantStateId)
+            --variantStateId '$advanced_settings.variantStateId'
+        #end if
+        #if str($advanced_settings.variantState)
+            --variantState '$advanced_settings.variantState'
+        #end if
+        #if str($advanced_settings.sequenceId)
+            --sequenceId '$advanced_settings.sequenceId'
+        #end if
+        > cnv_query_findings.json
+    ]]></command>
+    <expand macro="configfile"/>
+    <inputs>
+        <expand macro="Connection_to_MongoDB" />
+        <expand macro="Database_Configuration" />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <param argument="--variantInternalId" optional="true" type="text" label="VARIANT INTERNAL ID" value="" help="E.g. 11:52900000-134452384:DEL" />
+            <param argument="--analysisId" optional="true" type="text" label="ANALYSIS ID" value="" help="" />
+            <param argument="--individualId" optional="true" type="text" label="INDIVIDUAL ID" value="" help="" />
+            <param argument="--start" optional="true" type="integer" label="START" value="" help="Start position" />
+            <param argument="--end" optional="true" type="integer" label="END" value="" help="End position" />
+            <param argument="--chromosome" optional="true" type="text" label="CHROMOSOME" value="" help="Chromosome numbers (without chr)" />
+            <param argument="--variantStateId" optional="true" type="text" label="VARIANT STATE ID" value="" help="E.g EFO:0030067" />
+            <param argument="--variantState" optional="true" type="text" label="VARIANT STATE" value="" help="E.g. copy number loss" />
+            <param argument="--sequenceId" optional="true" type="text" label="SEQUENCE ID" value="" help="E.g. refseq:NC_000011.10" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_cnv_query" format="json" label="${tool.name} on ${on_string}: CNV Query" from_work_dir="cnv_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="cnv" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="chromosome" value="1" />
+            <param name="start" value="243618689" />
+            <param name="end" value="243620819" />
+            <param name="variantStateId" value="EFO:0030068" />
+            <output name="out_cnv_query">
+                <assert_contents><has_text_matching expression="_id"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Beacon CNV Queries are supposed to return matches of any copy number variants with at least partial overlap of the input parameters
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tools/beacon2-import/cohorts.xml b/tools/beacon2-import/cohorts.xml
new file mode 100644
index 00000000000..977373f3b5c
--- /dev/null
+++ b/tools/beacon2-import/cohorts.xml
@@ -0,0 +1,81 @@
+<tool id="beacon2_cohorts" name="Beacon2 Cohorts" version="1.0.0" profile="21.05">
+    <description>Query the Cohorts collection in the beacon database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        beacon2-search cohorts
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        #if str($advanced_settings.cohortDataTypes)
+            --cohortDataTypes '$advanced_settings.cohortDataTypes'
+        #end if
+        #if str($advanced_settings.cohortDesign)
+            --cohortDesign '$advanced_settings.cohortDesign'
+        #end if
+        #if str($advanced_settings.cohortSize)
+            --cohortSize $advanced_settings.cohortSize
+        #end if
+        #if str($advanced_settings.identification)
+            --identification '$advanced_settings.identification'
+        #end if
+        #if str($advanced_settings.cohortType)
+            --cohortType '$advanced_settings.cohortType'
+        #end if
+        #if str($advanced_settings.genders) and $advanced_settings.genders != ""
+            --genders '$advanced_settings.genders'
+        #end if
+        #if str($advanced_settings.name)
+            --name '$advanced_settings.name'
+        #end if
+        > cohorts_query_findings.json
+        ]]>
+    </command>
+    <expand macro="configfile"/>
+    <inputs>
+        <expand macro="Connection_to_MongoDB"/>
+        <expand macro="Database_Configuration"/>
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <param argument="--cohortDataTypes" optional="true" type="text" label="COHORTDATA TYPES" value="" help="The type of data chorort, e.g. clinical history" />
+            <param argument="--cohortDesign" optional="true" type="text" label="COHORTDESIGN" value="" help="A plan specification comprised of protocols that are executed as part of an investigation, e.g. longitudinal study design" />
+            <param argument="--cohortSize" optional="true" type="integer" label="COHORT SIZE" value="" help="Count of unique Individuals in cohort" />
+            <param argument="--cohortType" optional="true" type="text" label="COHORT TYPE" value="" help="Cohort type by its definition, e.g. study-defined" />
+            <param argument="--identification" optional="true" type="text" label="ID" value="" help="Cohort identifier, e.g. cohort0001" />
+            <param argument="--genders" optional="true" type="select" label="GENDERS" help="">
+            <option value="male">male</option>
+            <option value="female">female</option>
+            <option value="" selected="True">non specific</option>
+            </param>
+            <param argument="--name" optional="true" type="text" label="NAME" value="" help="Name of the cohort" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_cohorts_query" format="json" label="${tool.name} on ${on_string}: Cohorts Query" from_work_dir="cohorts_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="cohorts" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="cohortType" value="study-defined" />
+            <param name="cohortDataTypes" value="demographic data" />
+            <param name="identification" value="refvar-668fcc22387cab4642e5f1a4" />
+            <output name="out_cohorts_query">
+                <assert_contents>
+                    <has_text_matching expression="_id"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Beacon2 Cohorts queries the cohorts collection in the Beacon database to study the variants or individuals in a populations or  groups that share something in common.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tools/beacon2-import/datasets.xml b/tools/beacon2-import/datasets.xml
new file mode 100644
index 00000000000..d91f28ec0c0
--- /dev/null
+++ b/tools/beacon2-import/datasets.xml
@@ -0,0 +1,64 @@
+<tool id="beacon2_datasets" name="Beacon2 Datasets" version="1.0.0" profile="21.05">
+    <description>Query the datasets collection in the beacon database groupings of variants or individuals who belong to the same repository</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        beacon2-search datasets
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        #if str($advanced_settings.dataUseConditions)
+            --dataUseConditions '$advanced_settings.dataUseConditions'
+        #end if
+        #if str($advanced_settings.ontologyModifiers)
+            --ontologyModifiers '$advanced_settings.ontologyModifiers'
+        #end if
+        #if str($advanced_settings.identification)
+            --identification '$advanced_settings.identification'
+        #end if
+        #if str($advanced_settings.name)
+            --name '$advanced_settings.name'
+        #end if
+        > datasets_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="--dataUseConditions" optional="true" type="text" label="DATAUSECONDITIONS" value="" help="Data use conditions applying to this dataset, e.g. disease specific research" />
+            <param argument="--ontologyModifiers" optional="true" type="text" label="DATA USE CONDITIONS MODIFIERS" value="" help="Modifiers that further specify the datasets, e.g. coronary artery disease" />
+            <param argument="--identification" optional="true" type="text" label="ID" value="" help="Unique identifier of the dataset" />
+            <param argument="--name" optional="true" type="text" label="NAME" value="" help="Name of the dataset" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_datasets_query" format="json" label="${tool.name} on ${on_string}: Datasets Query" from_work_dir="datasets_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="datasets" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="identification" value="refvar-668fcf57aee552bc911b966e" />
+            <param name="name" value="The Genome in a Bottle Consortium (GIAB)" />
+            <output name="out_datasets_query">
+                <assert_contents>
+                    <has_text_matching expression="_id"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Beacon2 Datasets queries the datasets collection in the Beacon database to study the variants or individuals in a populations or groups who belong to the same repository.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tools/beacon2-import/gene.xml b/tools/beacon2-import/gene.xml
new file mode 100644
index 00000000000..af6319963a2
--- /dev/null
+++ b/tools/beacon2-import/gene.xml
@@ -0,0 +1,68 @@
+<tool id="beacon2_gene" name="Beacon2 Gene" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Queries the beacon database and retrieve the genomic variants matching gene symbol</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[    
+        beacon2-search gene
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        --geneId $geneId
+        #if str($advanced_settings.alternateBases)
+            --alternateBases '$advanced_settings.alternateBases'
+        #end if
+        #if str($advanced_settings.variantType)
+            --variantType '$advanced_settings.variantType'
+        #end if
+        #if str($advanced_settings.aminoacidChange)
+            --aminoacidChange '$advanced_settings.aminoacidChange'
+        #end if
+        #if str($advanced_settings.variantMinLength)
+            --variantMinLength $advanced_settings.variantMinLength
+        #end if
+        #if str($advanced_settings.variantMaxLength)
+            --variantMaxLength $advanced_settings.variantMaxLength
+        #end if
+        > gene_query_findings.json
+    ]]></command>
+    <expand macro="configfile"/>
+    <inputs>
+        <expand macro="Connection_to_MongoDB" />
+        <expand macro="Database_Configuration" />
+        <param argument="--geneId" type="text" label="Gene Id" value="" help="" />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <param argument="--alternateBases"  optional="true" type="text" label="ALTERNATEBASES" value="" help="Targeted Alternate bases to search for" />
+            <param argument="--variantType"  optional="true" type="text" label="VARIANT TYPE" value="" help="Targeted Variant type to search for" />
+            <param argument="--aminoacidChange"  optional="true" type="text" label="AMINOACID CHANGE" value="" help="Targeted Amino acid change to search for" />
+            <param argument="--variantMinLength"  optional="true" type="integer" label="VARIANT MIN LENGTH" value="" help="Targeted Variant minimum length to search for" />
+            <param argument="--variantMaxLength"  optional="true" type="integer" label="VARIANT MAX LENGTH" value="" help="Targeted VVariant maximum length to search for" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_gene_query" format="json" label="${tool.name} on ${on_string}: Gene Query" from_work_dir="gene_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="genomicVariations" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="geneId" value="OR4F5-LOC729737" />
+            <param name="alternateBases" value="A" />
+            <param name="variantType" value="SNP" />
+            <param name="aminoacidChange" value="." />
+            <output name="out_gene_query">
+                <assert_contents><has_text_matching expression="_id"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        GeneId Queries are in essence a variation of Range Queries in which the coordinates are replaced by the HGNC gene symbol. It is left to the implementation if the matching is done on variants annotated for the gene symbol or if a positional translation is being applied.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tools/beacon2-import/import.xml b/tools/beacon2-import/import.xml
new file mode 100644
index 00000000000..24ddb2a2d79
--- /dev/null
+++ b/tools/beacon2-import/import.xml
@@ -0,0 +1,54 @@
+<tool id="beacon2_import" name="Beacon2 Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Import JSON formatted datasets to beacon database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[    
+        ln -s '$input_json_file' ./input.json &&
+        beacon2-import
+        --input_json_file ./input.json
+        --db-host $db_host
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        $advanced_settings.clearAll
+        #if $advanced_settings.clearColl:
+            $advanced_settings.clearColl
+            --removeCollection $advanced_settings.removeCollection
+        #end if 
+        > logs.txt
+    ]]></command>
+    <expand macro="configfile"/>
+    <inputs>
+        <expand macro="Connection_to_MongoDB" />
+        <expand macro="Database_Configuration" />
+        <param argument="--input_json_file" type="data" format="json" label="INPUT JSON FILE" help="Input the local path to the JSON file or its name on your Galaxy History to import to beacon" />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <param argument="--clearAll" type="boolean" checked="false" truevalue="--clearAll" falsevalue="" label="CLEAR ALL COLLECTIONS" help="Delete all data before the new import" />
+            <param argument="--clearColl" type="boolean" checked="false" truevalue="--clearColl" falsevalue="" label="CLEAR SPECIFIC COLLECTION" help="Delete specific collection before the new import" />
+            <param argument="--removeCollection"  optional="true" type="text" label="REMOVED COLLECTION NAME" value="" help="Define the collection name for deletion" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_logs" format="txt" label="${tool.name} on ${on_string}: Log file" from_work_dir="logs.txt" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_json_file" ftype="json" value="HG00096.json" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="database" value="beacon" />
+            <param name="collection" value="genomicvarients" />
+            <output name="out_logs">
+                <assert_contents><has_text_matching expression="inserted"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Import JSON formatted datasets to Beacon MongoDB
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tools/beacon2-import/individuals.xml b/tools/beacon2-import/individuals.xml
new file mode 100644
index 00000000000..ee48f65af62
--- /dev/null
+++ b/tools/beacon2-import/individuals.xml
@@ -0,0 +1,98 @@
+<tool id="beacon2_individuals" name="Beacon2 Individuals" version="1.0.0" profile="21.05">
+    <description>Query the individuals collection in the beacon database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        beacon2-search individuals
+        --db-host '$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>
diff --git a/tools/beacon2-import/macros.xml b/tools/beacon2-import/macros.xml
new file mode 100644
index 00000000000..bd088a234cf
--- /dev/null
+++ b/tools/beacon2-import/macros.xml
@@ -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 --git a/tools/beacon2-import/range.xml b/tools/beacon2-import/range.xml
new file mode 100644
index 00000000000..ca0e63a1f11
--- /dev/null
+++ b/tools/beacon2-import/range.xml
@@ -0,0 +1,73 @@
+<tool id="beacon2_range" name="Beacon2 Range" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Retrieve the genomic variants from the beacon database by specifying start and end positions</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[    
+        beacon2-search range
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials'
+        --start $start
+        --end $end
+        #if str($advanced_settings.referenceName)
+            --referenceName '$advanced_settings.referenceName'
+        #end if
+        #if str($advanced_settings.alternateBases)
+            --alternateBases '$advanced_settings.alternateBases'
+        #end if
+        #if str($advanced_settings.variantType)
+            --variantType '$advanced_settings.variantType'
+        #end if
+        #if str($advanced_settings.aminoacidChange)
+            --aminoacidChange '$advanced_settings.aminoacidChange'
+        #end if
+        #if str($advanced_settings.variantMinLength)
+            --variantMinLength $advanced_settings.variantMinLength
+        #end if
+        #if str($advanced_settings.variantMaxLength)
+            --variantMaxLength $advanced_settings.variantMaxLength
+        #end if
+        > ranged_query_findings.json
+    ]]></command>
+    <expand macro="configfile"/>
+    <inputs>
+        <expand macro="Connection_to_MongoDB" />
+        <expand macro="Database_Configuration" />
+        <param argument="--start" type="integer" label="START" value="" help="Start position" />
+        <param argument="--end" type="integer" label="END" value="" help="End position" />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <param argument="--referenceName" optional="true" type="text" label="REFERENCENAME" value="" help="Reference name in numbers chr1/1, chr2/2, chr3/3, etc." />
+            <param argument="--alternateBases"  optional="true" type="text" label="ALTERNATEBASES" value="" help="Targeted Alternate bases to search for" />
+            <param argument="--variantType"  optional="true" type="text" label="VARIANT TYPE" value="" help="Targeted Variant type to search for" />
+            <param argument="--aminoacidChange"  optional="true" type="text" label="AMINOACID CHANGE" value="" help="Targeted Amino acid change to search for" />
+            <param argument="--variantMinLength"  optional="true" type="integer" label="VARIANT MIN LENGTH" value="" help="Targeted Variant minimum length to search for" />
+            <param argument="--variantMaxLength"  optional="true" type="integer" label="VARIANT MAX LENGTH" value="" help="Targeted VVariant maximum length to search for" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_ranged_query" format="json" label="${tool.name} on ${on_string}: Range Query" from_work_dir="ranged_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="genomicVariations" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="start" value="131836" />
+            <param name="end" value="131837" />
+            <param name="variantType" value="SNP" />
+            <output name="out_ranged_query">
+                <assert_contents><has_text_matching expression="_id"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Beacon Range Queries are supposed to return matches of any variant with at least partial overlap of the sequence range specified by reference_name, start and end parameters
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tools/beacon2-import/runs.xml b/tools/beacon2-import/runs.xml
new file mode 100644
index 00000000000..9ffe878b3ab
--- /dev/null
+++ b/tools/beacon2-import/runs.xml
@@ -0,0 +1,86 @@
+<tool id="beacon2_runs" name="Beacon2 Runs" version="1.0.0" profile="21.05">
+    <description>Query the runs collection in the beacon database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        beacon2-search runs
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        #if str($advanced_settings.identification)
+            --identification '$advanced_settings.identification'
+        #end if
+        #if str($advanced_settings.individualId)
+            --individualId '$advanced_settings.individualId'
+        #end if
+        #if str($advanced_settings.libraryLayout)
+            --libraryLayout '$advanced_settings.libraryLayout'
+        #end if
+        #if str($advanced_settings.librarySelection)
+            --librarySelection '$advanced_settings.librarySelection'
+        #end if
+        #if str($advanced_settings.librarySource)
+            --librarySource '$advanced_settings.librarySource'
+        #end if
+        #if str($advanced_settings.libraryStrategy)
+            --libraryStrategy '$advanced_settings.libraryStrategy'
+        #end if
+        #if str($advanced_settings.platform)
+            --platform '$advanced_settings.platform'
+        #end if
+        #if str($advanced_settings.platformModel)
+            --platformModel '$advanced_settings.platformModel'
+        #end if
+        #if str($advanced_settings.runDate)
+            --runDate '$advanced_settings.runDate'
+        #end if
+        > runs_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="--identification" optional="true" type="text" label="ID" value="" help="Run ID" />
+            <param argument="--individualId" optional="true" type="text" label="INDIVIDUAL ID" value="" help="Reference to the individual ID, e.g. TCGA-AO-A0JJ" />
+            <param argument="--libraryLayout" optional="true" type="text" label="LIBRARY LAYOUT" value="" help="Ontology value for the library layout e.g 'PAIRED', 'SINGLE'" />
+            <param argument="--librarySelection" optional="true" type="text" label="LIBRARY SELECTION" value="" help="Selection method for library preparation, e.g 'RANDOM', 'RT-PCR'" />
+            <param argument="--librarySource" optional="true" type="text" label="LIBRARY SOURCE" value="" help="Ontology value for the source of the sequencing or hybridization library, e.g 'genomic source', 'transcriptomic source'" />
+            <param argument="--libraryStrategy" optional="true" type="text" label="LIBRARY STRATEGY" value="" help="Library strategy, e.g. 'WGS'" />
+            <param argument="--platform" optional="true" type="text" label="PLATFORM" value="" help="General platform technology label where the specific model is not relevant, e.g. Illumina" />
+            <param argument="--platformModel" optional="true" type="text" label="PLATFORM MODEL" value="" help="Ontology value for experimental platform or methodology used, e.g. 'Illumina HiSeq 3000'" />
+            <param argument="--runDate" optional="true" type="text" label="RUN DATE" value="" help="Date at which the experiment was performed" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_runs_query" format="json" label="${tool.name} on ${on_string}: Runs Query" from_work_dir="runs_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="runs" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="platform" value="Illumina " />
+            <param name="platformModel" value="2017-04-30" />
+            <param name="librarySource" value="KAPA library quantification kit" />
+            <param name="libraryLayout" value="PAIRED" />
+            <output name="out_runs_query">
+                <assert_contents>
+                    <has_text_matching expression="_id"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Beacon2 Runs queries the runs collection in the Beacon database for details on procedures used for sequencing a biosample. 
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tools/beacon2-import/sequence.xml b/tools/beacon2-import/sequence.xml
new file mode 100644
index 00000000000..90f4ae8561b
--- /dev/null
+++ b/tools/beacon2-import/sequence.xml
@@ -0,0 +1,61 @@
+<tool id="beacon2_sequence" name="Beacon2 Sequence" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>َQuery for the existence of a specified sequence at a given genomic position</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[    
+        beacon2-search sequence
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        --alternateBases '$alternateBases'
+        --referenceBases '$referenceBases'
+        #if str($advanced_settings.referenceName)
+            --referenceName '$advanced_settings.referenceName'
+        #end if
+        #if str($advanced_settings.start)
+            --start $advanced_settings.start
+        #end if
+        #if str($advanced_settings.collectionIds)
+            --collectionIds '$advanced_settings.collectionIds'
+        #end if
+        > sequenced_query_findings.json
+    ]]></command>
+    <expand macro="configfile"/>
+    <inputs>
+        <expand macro="Connection_to_MongoDB" />
+        <expand macro="Database_Configuration" />
+        <param argument="--alternateBases" type="text" label="Alternate bases" value="" help="" />
+        <param argument="--referenceBases" type="text" label="Reference bases" value="" help="" />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <param argument="--referenceName" optional="true" type="text" label="REFERENCENAME" value="" help="Reference name in numbers chr1/1, chr2/2, chr3/3, etc." />
+            <param argument="--start" optional="true" type="integer" label="START" value="" help="Start position" />
+            <param argument="--collectionIds"  optional="true" type="text" label="Collection ID" value="" help="Datasets ID" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_sequence_query" format="json" label="${tool.name} on ${on_string}: Sequence Query" from_work_dir="sequenced_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" value="10176" />
+            <param name="alternateBases" value="AC" />
+            <param name="referenceBases" value="A" />
+            <output name="out_sequence_query">
+                <assert_contents><has_text_matching expression="_id"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Sequence Queries query for the existence of a specified sequence at a given genomic position. Such queries correspond to the original Beacon queries and are used to match short, precisely defined genomic variants such as SNVs and INDELs.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tools/beacon2-import/test-data/HG00096.json b/tools/beacon2-import/test-data/HG00096.json
new file mode 100644
index 00000000000..739de07d5a4
--- /dev/null
+++ b/tools/beacon2-import/test-data/HG00096.json
@@ -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",
+        "variantInternalId": "chr1:13224579-13242034:EFO:0030071",
+        "variantType": "DUP",
+        "variantId": "EFO:0030071",
+        "start": 13224579,
+        "end": 13242034,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:GAIN:chr1:13224580-13242034",
+            "cnCount": 3,
+            "cnValue": 1.49181
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:16605061-16646293:EFO:0030071",
+        "variantType": "DUP",
+        "variantId": "EFO:0030071",
+        "start": 16605061,
+        "end": 16646293,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:GAIN:chr1:16605062-16646293",
+            "cnCount": 7,
+            "cnValue": 3.3289
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:16716711-16728256:EFO:0030071",
+        "variantType": "DUP",
+        "variantId": "EFO:0030071",
+        "start": 16716711,
+        "end": 16728256,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:GAIN:chr1:16716712-16728256",
+            "cnCount": 5,
+            "cnValue": 2.68822
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:16879751-16950196:EFO:0030071",
+        "variantType": "DUP",
+        "variantId": "EFO:0030071",
+        "start": 16879751,
+        "end": 16950196,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:GAIN:chr1:16879752-16950196",
+            "cnCount": 3,
+            "cnValue": 1.53152
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:34636777-34646300:EFO:0030068",
+        "variantType": "DEL",
+        "variantId": "EFO:0030068",
+        "start": 34636777,
+        "end": 34646300,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:34636778-34646300",
+            "cnCount": 1,
+            "cnValue": 0.495288
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:36957723-36960386:EFO:0030068",
+        "variantType": "DEL",
+        "variantId": "EFO:0030068",
+        "start": 36957723,
+        "end": 36960386,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:36957724-36960386",
+            "cnCount": 1,
+            "cnValue": 0.479029
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:43593157-43594353:EFO:0030068",
+        "variantType": "DEL",
+        "variantId": "EFO:0030068",
+        "start": 43593157,
+        "end": 43594353,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:43593158-43594353",
+            "cnCount": 1,
+            "cnValue": 0.289679
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:58278107-58279217:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 58278107,
+        "end": 58279217,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:58278108-58279217",
+            "cnCount": 0,
+            "cnValue": 0.0937719
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:61647700-61655464:EFO:0030068",
+        "variantType": "DEL",
+        "variantId": "EFO:0030068",
+        "start": 61647700,
+        "end": 61655464,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:61647701-61655464",
+            "cnCount": 1,
+            "cnValue": 0.52381
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:62188614-62191346:EFO:0030068",
+        "variantType": "DEL",
+        "variantId": "EFO:0030068",
+        "start": 62188614,
+        "end": 62191346,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:62188615-62191346",
+            "cnCount": 1,
+            "cnValue": 0.483858
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:67542030-67543275:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 67542030,
+        "end": 67543275,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:67542031-67543275",
+            "cnCount": 0,
+            "cnValue": 0.0312573
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:72289205-72345923:EFO:0030068",
+        "variantType": "DEL",
+        "variantId": "EFO:0030068",
+        "start": 72289205,
+        "end": 72345923,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:72289206-72345923",
+            "cnCount": 1,
+            "cnValue": 0.486641
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:78183859-78192785:EFO:0030068",
+        "variantType": "DEL",
+        "variantId": "EFO:0030068",
+        "start": 78183859,
+        "end": 78192785,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:78183860-78192785",
+            "cnCount": 1,
+            "cnValue": 0.482922
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:89010497-89012783:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 89010497,
+        "end": 89012783,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:89010498-89012783",
+            "cnCount": 0,
+            "cnValue": 1.00369e-09
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:103362730-103365638:EFO:0030068",
+        "variantType": "DEL",
+        "variantId": "EFO:0030068",
+        "start": 103362730,
+        "end": 103365638,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:103362731-103365638",
+            "cnCount": 1,
+            "cnValue": 0.320331
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:105472899-105480377:EFO:0030068",
+        "variantType": "DEL",
+        "variantId": "EFO:0030068",
+        "start": 105472899,
+        "end": 105480377,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:105472900-105480377",
+            "cnCount": 1,
+            "cnValue": 0.450727
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:109644578-109647981:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 109644578,
+        "end": 109647981,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:109644579-109647981",
+            "cnCount": 0,
+            "cnValue": 1.00369e-09
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:109647981-109650349:EFO:0030068",
+        "variantType": "DEL",
+        "variantId": "EFO:0030068",
+        "start": 109647981,
+        "end": 109650349,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:109647982-109650349",
+            "cnCount": 1,
+            "cnValue": 0.587163
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:109687569-109697444:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 109687569,
+        "end": 109697444,
+        "referenceName": "1",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chr1:109687570-109697444",
+            "cnCount": 0,
+            "cnValue": 1.00369e-09
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chr1:112148880-112161897:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 112148880,
+        "end": 112161897,
+        "referenceName": "1",
+        "info": {
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+        "start": 115735984,
+        "end": 115737909,
+        "referenceName": "X",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chrX:115735985-115737909",
+            "cnCount": 0,
+            "cnValue": 1.00369e-09
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrX:119740347-119742168:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 119740347,
+        "end": 119742168,
+        "referenceName": "X",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chrX:119740348-119742168",
+            "cnCount": 0,
+            "cnValue": 1.00369e-09
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrX:129366304-129368317:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 129366304,
+        "end": 129368317,
+        "referenceName": "X",
+        "info": {
+            "legacyId": "DRAGEN:LOSS:chrX:129366305-129368317",
+            "cnCount": 0,
+            "cnValue": 1.00369e-09
+        }
+    },
+    {
+        "biosampleId": "HG00096",
+        "assemblyId": "GRCh38",
+        "variantInternalId": "chrX:141382259-141384533:EFO:0030069",
+        "variantType": "DEL",
+        "variantId": "EFO:0030069",
+        "start": 141382259,
+        "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
diff --git a/tools/beacon2-import/test-data/analyses_query_findings.json b/tools/beacon2-import/test-data/analyses_query_findings.json
new file mode 100644
index 00000000000..dda13796785
--- /dev/null
+++ b/tools/beacon2-import/test-data/analyses_query_findings.json
@@ -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 --git a/tools/beacon2-import/test-data/biosamples_query_findings.json b/tools/beacon2-import/test-data/biosamples_query_findings.json
new file mode 100644
index 00000000000..a1de5b5d01e
--- /dev/null
+++ b/tools/beacon2-import/test-data/biosamples_query_findings.json
@@ -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 --git a/tools/beacon2-import/test-data/bracket_query_findings.json b/tools/beacon2-import/test-data/bracket_query_findings.json
new file mode 100644
index 00000000000..f143bcd7099
--- /dev/null
+++ b/tools/beacon2-import/test-data/bracket_query_findings.json
@@ -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 --git a/tools/beacon2-import/test-data/cnv_query_findings.json b/tools/beacon2-import/test-data/cnv_query_findings.json
new file mode 100644
index 00000000000..adca93f0cd4
--- /dev/null
+++ b/tools/beacon2-import/test-data/cnv_query_findings.json
@@ -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 --git a/tools/beacon2-import/test-data/cohorts_query_findings.json b/tools/beacon2-import/test-data/cohorts_query_findings.json
new file mode 100644
index 00000000000..28e3a4ccb68
--- /dev/null
+++ b/tools/beacon2-import/test-data/cohorts_query_findings.json
@@ -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 --git a/tools/beacon2-import/test-data/datasets_query_findings.json b/tools/beacon2-import/test-data/datasets_query_findings.json
new file mode 100644
index 00000000000..a1399b9dc32
--- /dev/null
+++ b/tools/beacon2-import/test-data/datasets_query_findings.json
@@ -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 --git a/tools/beacon2-import/test-data/gene_query_findings.json b/tools/beacon2-import/test-data/gene_query_findings.json
new file mode 100644
index 00000000000..9126d343797
--- /dev/null
+++ b/tools/beacon2-import/test-data/gene_query_findings.json
@@ -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 --git a/tools/beacon2-import/test-data/individuals_query_findings.json b/tools/beacon2-import/test-data/individuals_query_findings.json
new file mode 100644
index 00000000000..9eb7a46c6fb
--- /dev/null
+++ b/tools/beacon2-import/test-data/individuals_query_findings.json
@@ -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 --git a/tools/beacon2-import/test-data/logs.txt b/tools/beacon2-import/test-data/logs.txt
new file mode 100644
index 00000000000..30e9fa673a8
--- /dev/null
+++ b/tools/beacon2-import/test-data/logs.txt
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+==> inserted refvar-6630e15a0767459cc186e2bb
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+==> inserted refvar-6630e15a0767459cc186e2bd
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+==> inserted refvar-6630e15a0767459cc186e2ea
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+==> 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
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+==> inserted refvar-6630e15a0767459cc186e31b
+==> inserted refvar-6630e15a0767459cc186e31c
+==> inserted refvar-6630e15a0767459cc186e31d
+==> inserted refvar-6630e15a0767459cc186e31e
+==> inserted refvar-6630e15a0767459cc186e31f
+==> inserted refvar-6630e15a0767459cc186e320
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+==> inserted refvar-6630e15a0767459cc186e323
+==> inserted refvar-6630e15a0767459cc186e324
+==> inserted refvar-6630e15a0767459cc186e325
+==> inserted refvar-6630e15a0767459cc186e326
+==> inserted refvar-6630e15a0767459cc186e327
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+==> inserted refvar-6630e15a0767459cc186e329
+==> inserted refvar-6630e15a0767459cc186e32a
+==> inserted refvar-6630e15a0767459cc186e32b
+==> inserted refvar-6630e15a0767459cc186e32c
+==> inserted refvar-6630e15a0767459cc186e32d
+==> inserted refvar-6630e15a0767459cc186e32e
+==> inserted refvar-6630e15a0767459cc186e32f
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+==> 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
diff --git a/tools/beacon2-import/test-data/ranged_query_findings.json b/tools/beacon2-import/test-data/ranged_query_findings.json
new file mode 100644
index 00000000000..6c65e42f96f
--- /dev/null
+++ b/tools/beacon2-import/test-data/ranged_query_findings.json
@@ -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 --git a/tools/beacon2-import/test-data/runs_query_findings.json b/tools/beacon2-import/test-data/runs_query_findings.json
new file mode 100644
index 00000000000..6a52091c5f3
--- /dev/null
+++ b/tools/beacon2-import/test-data/runs_query_findings.json
@@ -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 --git a/tools/beacon2-import/test-data/sequenced_query_findings.json b/tools/beacon2-import/test-data/sequenced_query_findings.json
new file mode 100644
index 00000000000..3ba9ba41457
--- /dev/null
+++ b/tools/beacon2-import/test-data/sequenced_query_findings.json
@@ -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'}