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Merge discvr-25.11 to develop
2 parents 5f310dc + 6373564 commit fe16b3d

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+430
-41
lines changed

‎.github/dependabot.yml‎

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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "daily"
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interval: "weekly"

‎IDR/resources/queries/bimber_data/idrAnchorDateSource.sql‎

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@@ -7,6 +7,7 @@ PID0 as date,
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FROM bimber_data.subjects
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WHERE PID0 IS NOT NULL
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AND Cohort NOT IN ('PC549', 'PC585', 'PC529') AND Cohort NOT LIKE 'W%'
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UNION ALL
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'Hansen/IDR' as dataSource
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FROM bimber_data.subjects
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WHERE D0 IS NOT NULL
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WHERE D0 IS NOT NULL
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AND Cohort NOT IN ('PC549', 'PC585', 'PC529') AND Cohort NOT LIKE 'W%'

‎IDR/resources/queries/bimber_data/idrOutcomeSource.sql‎

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@@ -12,4 +12,5 @@ END as outcome,
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'Hansen/IDR' as dataSource
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FROM bimber_data.subjects
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WHERE contprog IS NOT NULL AND contprog != ''
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WHERE contprog IS NOT NULL AND contprog != ''
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AND Cohort NOT IN ('PC549', 'PC585', 'PC529') AND Cohort NOT LIKE 'W%'

‎SivStudies/resources/etls/idr-data.xml‎

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<setting name="dataSourceColumns" value="Rh,PID0"/>
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<setting name="dataSourceColumnMapping" value="Rh=Id,PID0=date"/>
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<setting name="dataSourceColumnDefaults" value="dataSource=Hansen/IDR;category=SIV Infection;treatment=SIV - Unknown"/>
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<setting name="dataSourceAdditionalFilters" value="PID0~isnonblank="/>
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<setting name="dataSourceAdditionalFilters" value="PID0~isnonblank=;Cohort~neqornull=PC549;Cohort~neqornull=PC585;Cohort~neqornull=W1170;Cohort~neqornull=W1173;Cohort~neqornull=PC529"/>
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<setting name="targetSchema" value="study"/>
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<setting name="targetQuery" value="treatments"/>

‎SivStudies/resources/queries/studies/studies.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="studies" tableDbType="TABLE" useColumnOrder="false">
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<columns>
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<column columnName="studySummary" wrappedColumnName="rowId">
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<isUnselectable>true</isUnselectable>
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<shownInInsertView>false</shownInInsertView>
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<shownInUpdateView>false</shownInUpdateView>
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<columnTitle>Summary Information</columnTitle>
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<fk>
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<fkDbSchema>studies</fkDbSchema>
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<fkTable>studiesSummary</fkTable>
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<fkColumnName>rowId</fkColumnName>
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</fk>
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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/studies/studies/.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="rowId"/>
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<column name="studyName"/>
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<column name="label"/>
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<column name="category"/>
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<column name="description"/>
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<column name="cohorts"/>
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<column name="studySummary/numAnimals"/>
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<column name="studySummary/sexes"/>
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<column name="studySummary/challenges"/>
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<column name="studySummary/artInitiationsDPI"/>
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<column name="studySummary/interventions"/>
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</columns>
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<sorts>
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<sort column="studyName" descending="false"/>
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</sorts>
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</customView>

‎SivStudies/resources/queries/studies/studiesSummary.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="studiesSummary" tableDbType="TABLE" useColumnOrder="true">
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<tableTitle>Studies Summary</tableTitle>
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<columns>
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<column columnName="rowId">
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</column>
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<column columnName="labelOrName">
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</column>
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<column columnName="description">
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</column>
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<column columnName="cohorts">
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</column>
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<column columnName="numAnimals">
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<columnTitle># Animals</columnTitle>
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</column>
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<column columnName="sexes">
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<columnTitle>Sex(es)</columnTitle>
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</column>
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<column columnName="challenges">
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<columnTitle>SIV Challenges</columnTitle>
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</column>
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<column columnName="artInitiationsDPI">
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<columnTitle>ART Initiation(s) (DPI)</columnTitle>
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</column>
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<column columnName="interventions">
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<columnTitle>Interventions</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/studies/studiesSummary.sql‎

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SELECT
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s.rowId,
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s.labelOrName,
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s.description,
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group_concat(DISTINCT a.cohortId.labelOrName, char(10)) as cohorts,
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count(DISTINCT a.Id) as numAnimals,
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group_concat(DISTINCT a.DataSets.Demographics.sex) as sexes,
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group_concat(DISTINCT a.sivArt.allInfections, char(10)) as challenges,
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group_concat(DISTINCT a.sivArt.artInitiationDPI, char(10)) as artInitiationsDPI,
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group_concat(DISTINCT a.interventions.allInterventions, char(10)) as interventions,
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FROM studies.studies s
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LEFT JOIN study.assignment a ON (a.cohortId.studyId = s.rowId)
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GROUP BY s.rowId, s.labelOrName, s.description

‎SivStudies/resources/queries/studies/studyCohortSummary.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="studiesSummary" tableDbType="TABLE" useColumnOrder="true">
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<tableTitle>Study Cohort Summary</tableTitle>
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<columns>
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<column columnName="rowId">
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</column>
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<column columnName="studyName">
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<columnTitle>Study Name</columnTitle>
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</column>
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<column columnName="description">
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</column>
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<column columnName="labelOrName">
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<columnTitle>Cohort Name</columnTitle>
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</column>
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<column columnName="numAnimals">
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<columnTitle># Animals</columnTitle>
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</column>
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<column columnName="sexes">
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<columnTitle>Sex(es)</columnTitle>
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</column>
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<column columnName="challenges">
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<columnTitle>SIV Challenges</columnTitle>
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</column>
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<column columnName="artInitiationsDPI">
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<columnTitle>ART Initiation(s) (DPI)</columnTitle>
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</column>
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<column columnName="interventions">
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<columnTitle>Interventions</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/studies/studyCohortSummary.sql‎

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SELECT
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sc.rowId,
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sc.studyId.labelOrName as studyName,
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sc.labelOrName,
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sc.studyId.description,
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count(DISTINCT a.Id) as numAnimals,
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group_concat(DISTINCT a.DataSets.Demographics.sex) as sexes,
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group_concat(DISTINCT a.sivArt.allInfections, char(10)) as challenges,
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group_concat(DISTINCT a.sivArt.artInitiationDPI, char(10)) as artInitiationsDPI,
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group_concat(DISTINCT a.interventions.allInterventions, char(10)) as interventions
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FROM studies.studyCohorts sc
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LEFT JOIN study.assignment a ON (a.cohortId = sc.rowId)
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GROUP BY sc.rowId, sc.labelOrName, sc.studyId.description, sc.studyId.labelOrName

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