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Merge pull request #192 from bimberlabinternal/25.7_fb_merge
Merge discvr-25.3 to discvr-25.7
2 parents 5c625e5 + 47abfbd commit d2cde06

29 files changed

+389
-116
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‎SivStudies/resources/queries/study/additionalDatatypes.query.xml‎

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<table tableName="additionalDatatypes" tableDbType="TABLE">
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<columns>
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<column columnName="Id">
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<url />
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</column>
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<column columnName="date">
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‎SivStudies/resources/queries/study/demographics.query.xml‎

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<javaCustomizer class="org.labkey.sivstudies.query.SivStudiesCustomizer"/>
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<columns>
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<column columnName="Id">
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<url />
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<isKeyField>true</isKeyField>
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</column>
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<column columnName="date">

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

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<!-- </column>-->
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<column name="death"/>
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<column name="projects/allStudies"/>
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<column name="projects/categories"/>
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<column name="projects/subgroups"/>
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<column name="immunizations/immunizations"/>
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<column name="outcomes/outcomes"/>
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</columns>

‎SivStudies/resources/queries/study/demographics/Expanded.qview.xml‎

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<column name="birth"/>
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<column name="death"/>
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<column name="projects/allStudies"/>
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<column name="projects/categories"/>
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<column name="projects/subgroups"/>
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<column name="immunizations/immunizations"/>
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<column name="sivART/allInfections"/>
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<column name="sivART/allART"/>
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<column name="outcomes/outcomes"/>
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</columns>
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<sorts>

‎SivStudies/resources/queries/study/demographicsChallengeAndArt.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="" tableDbType="NOT_IN_DB">
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<tableTitle>SIV/ART Summary</tableTitle>
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<columns>
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<column columnName="Id">
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<isKeyField>true</isKeyField>
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<isHidden>true</isHidden>
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</column>
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<column columnName="allInfections">
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<columnTitle>SIV Infection</columnTitle>
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</column>
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<column columnName="allART">
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<columnTitle>ART</columnTitle>
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</column>
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<column columnName="infectionDate">
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<columnTitle>Infection Date</columnTitle>
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</column>
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</columns>
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<titleColumn>allInfections</titleColumn>
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</table>
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</tables>
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</metadata>
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</query>

‎SivStudies/resources/queries/study/demographicsChallengeAndArt.sql‎

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SELECT
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t.Id,
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group_concat(DISTINCT CASE
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WHEN t.category = 'SIV Infection' THEN (cast(month(t.date) as varchar) || '/' || cast(dayofmonth(t.date) as varchar) || '/' || cast(year(t.date) as varchar) || ' (' || t.treatment || ')')
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ELSE NULL
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END, char(10)) as allInfections,
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group_concat(DISTINCT CASE
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WHEN t.category = 'ART' THEN (cast(month(t.date) as varchar) || '/' || cast(dayofmonth(t.date) as varchar) || '/' || cast(year(t.date) as varchar) || ' (' || t.treatment || ')')
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ELSE NULL
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END, char(10)) as allART,
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min(CASE
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WHEN t.category = 'SIV Infection' THEN t.date
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ELSE NULL
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END) as infectionDate,
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FROM study.treatments t
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GROUP BY t.Id

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

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<column columnName="allStudies">
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<columnTitle>All Studies</columnTitle>
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</column>
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<column columnName="subgroups">
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<columnTitle>Subgroups/Treatments</columnTitle>
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</column>
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<column columnName="rhCmvVaccines">
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<columnTitle>RhCMV Vaccines?</columnTitle>
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</column>

‎SivStudies/resources/queries/study/demographicsProjects.sql‎

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count(s.Id) as totalProjects,
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group_concat(DISTINCT s.study, char(10)) as allStudies,
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group_concat(DISTINCT s.category, char(10)) as categories,
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group_concat(DISTINCT s.subgroup, char(10)) as subgroups,
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GROUP_CONCAT(distinct CASE WHEN s.category = 'RhCMV-Vaccines' THEN 'Yes' ELSE null END, char(10)) as rhCmvVaccines,
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GROUP_CONCAT(distinct CASE WHEN s.category = 'SIV/ART' THEN 'Yes' ELSE null END, char(10)) as sivArt

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

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<table tableName="procedures" tableDbType="TABLE">
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<columns>
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<column columnName="Id">
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<url />
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</column>
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<column columnName="date">
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‎SivStudies/resources/queries/study/studyData.query.xml‎

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<columns>
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<column columnName="Id">
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<conceptURI>http://cpas.labkey.com/Study#ParticipantId</conceptURI>
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<url>laboratory/dataBrowser.view?subjectId=${Id}</url>
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</column>
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<column columnName="date">
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<columnTitle>Date</columnTitle>
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<column columnName="AnimalVisit">
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<isHidden>true</isHidden>
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</column>
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<column columnName="DataSets">
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<isHidden>true</isHidden>
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</column>
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</columns>
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<buttonBarOptions includeStandardButtons="true">
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<item hidden="true">

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