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Merge pull request #193 from bimberlabinternal/25.7_fb_merge
Merge discvr-25.3 to discvr-25.7
2 parents d2cde06 + 4cf34f1 commit dbe3cdc

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‎GenotypeAssays/test/src/org/labkey/test/tests/external/labModules/GenotypeAssaysTest.java‎

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@@ -182,6 +182,7 @@ private void beadStudioImportTest()
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Ext4FieldRef.getForLabel(this, "Run Description").setValue("Description");
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waitForElement(Ext4Helper.Locators.ext4Button("Download Example Data"));
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File exampleData = clickAndWaitForDownload(Ext4Helper.Locators.ext4Button("Download Example Data"));
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waitAndClick(Ext4Helper.Locators.radiobutton(this, "File Upload"));

‎SivStudies/resources/data/reports.tsv‎

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@@ -7,7 +7,8 @@ query Clinical study hematologyPivot CBC/Hematology
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query Study Design study assignment Project/Study Assignment
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query Research study flow Flow Cytometry
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query Research study outcomes Study Outcomes/Phenotypes
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query Research study genetics Genetic Data / MHC
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query Research study pvl_outcomes Study PVL-Based Outcomes
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query Research study genetics Genetic Data / MHC
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query Clinical study procedures Procedures
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query Research study viralLoads Viral Loads
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query General study samples Samples

‎SivStudies/resources/queries/study/duplicateInfectionDates.query.xml‎

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<query xmlns="http://labkey.org/data/xml/query">
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<metadata>
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<tables xmlns="http://labkey.org/data/xml">
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<table tableName="duplicateInfectionDates" tableDbType="NOT_IN_DB">
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<tableTitle>Duplicate Infection Dates</tableTitle>
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<columns>
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</columns>
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</table>
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</tables>
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</metadata>
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</query>

‎SivStudies/resources/queries/study/duplicateInfectionDates.sql‎

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SELECT
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t.Id,
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t.date,
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'SIV Infection' as category
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FROM study.treatments t
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WHERE t.category = 'SIV Infection'
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GROUP BY t.Id, t.date
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HAVING count(*) > 1

‎SivStudies/resources/queries/study/infectionAnchorDateDiscordance.query.xml‎

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<query xmlns="http://labkey.org/data/xml/query">
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<metadata>
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<tables xmlns="http://labkey.org/data/xml">
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<table tableName="infectionAnchorDateDiscordance" tableDbType="NOT_IN_DB">
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<tableTitle>Discordant Infection Dates</tableTitle>
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<columns>
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<column columnName="treatmentTableDate">
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<columnTitle>Date (Treatments Table)</columnTitle>
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</column>
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<column columnName="subjectAnchorDatesTableDate">
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<columnTitle>Date (Anchor Dates Table)</columnTitle>
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</column>
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</columns>
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</table>
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</tables>
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</metadata>
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</query>

‎SivStudies/resources/queries/study/infectionAnchorDateDiscordance.sql‎

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SELECT
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t.Id,
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'SIV Infection' as category,
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t.date as treatmentTableDate,
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t2.date as subjectAnchorDatesTableDate
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FROM study.treatments t
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FULL JOIN studies.subjectAnchorDates t2 ON (
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t2.subjectId = t.Id AND
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t2.eventLabel = 'SIV Infection'
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)
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WHERE t.category = 'SIV Infection' AND t2.date != t.date

‎SivStudies/resources/queries/study/pvl_outcomes.query.xml‎

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<query xmlns="http://labkey.org/data/xml/query">
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<metadata>
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<tables xmlns="http://labkey.org/data/xml">
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<table tableName="pvl_outcomes" tableDbType="TABLE" useColumnOrder="true">
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<columns>
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<column columnName="Id"/>
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<column columnName="date">
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<columnTitle>Date</columnTitle>
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<formatString>Date</formatString>
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</column>
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<column columnName="outcome">
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<columnTitle>Outcome/Phenotype</columnTitle>
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</column>
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<column columnName="numeric_value">
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<columnTitle>Numeric Value</columnTitle>
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</column>
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<column columnName="string_value">
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<columnTitle>String Value</columnTitle>
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</column>
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<column columnName="comments">
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<columnTitle>Comments</columnTitle>
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</column>
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<column columnName="dataSource">
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<columnTitle>Data Source</columnTitle>
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</column>
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</columns>
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</table>
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</tables>
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</metadata>
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</query>

‎SivStudies/resources/queries/study/pvl_outcomes/.qview.xml‎

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<customView xmlns="http://labkey.org/data/xml/queryCustomView" hidden="false" canOverride="false">
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<columns>
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<column name="Id"/>
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<column name="date"/>
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<column name="outcome"/>
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<column name="numeric_value"/>
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<column name="string_value"/>
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<column name="comments"/>
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<column name="dataSource"/>
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</columns>
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<sorts>
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<sort column="Id" descending="false"/>
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<sort column="outcome" descending="true"/>
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</sorts>
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</customView>

‎SivStudies/resources/referenceStudy/study/datasets/datasets_manifest.xml‎

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<dataset name="outcomes" showByDefault="true" category="Research" type="Standard" id="15">
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<tags/>
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</dataset>
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<dataset name="pvl_outcomes" showByDefault="true" category="Research" type="Standard" id="16">
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<tags/>
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</dataset>
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</datasets>
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</datasets>

‎SivStudies/resources/referenceStudy/study/datasets/datasets_metadata.xml‎

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</columns>
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<tableTitle>Outcomes/Phenotypes</tableTitle>
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</table>
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<table tableName="pvl_outcomes" tableDbType="TABLE">
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<columns>
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<column columnName="Id">
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<datatype>varchar</datatype>
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<conceptURI>http://cpas.labkey.com/Study#ParticipantId</conceptURI>
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</column>
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<column columnName="date">
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<datatype>timestamp</datatype>
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<conceptURI>http://cpas.labkey.com/laboratory#sampleDate</conceptURI>
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</column>
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<column columnName="dataSource">
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<datatype>varchar</datatype>
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</column>
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<column columnName="objectId">
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<datatype>entityid</datatype>
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<isKeyField>true</isKeyField>
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</column>
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<column columnName="outcome">
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<datatype>varchar</datatype>
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</column>
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<column columnName="numeric_value">
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<datatype>double</datatype>
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</column>
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<column columnName="string_value">
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<datatype>varchar</datatype>
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</column>
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<column columnName="comments">
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<datatype>varchar</datatype>
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</column>
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</columns>
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<tableTitle>PVL Outcomes</tableTitle>
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</table>
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</tables>

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