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Add study summary columns
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‎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

‎SivStudies/resources/queries/studies/studyCohorts.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="studyCohorts" tableDbType="TABLE" useColumnOrder="false">
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<columns>
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<column columnName="cohortsSummary" 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>studyCohortSummary</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/studyCohorts/.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="studyId"/>
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<column name="studyId/description">
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<properties>
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<property name="columnTitle" value="Study Description"/>
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</properties>
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</column>
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<column name="cohortName"/>
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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="isControlGroup"/>
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<column name="sortOrder"/>
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<column name="cohortsSummary/numAnimals"/>
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<column name="cohortsSummary/sexes"/>
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<column name="cohortsSummary/challenges"/>
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<column name="cohortsSummary/artInitiationsDPI"/>
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<column name="cohortsSummary/interventions"/>
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</columns>
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<sorts>
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<sort column="studyId/studyName" descending="false"/>
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<sort column="sortOrder" descending="false"/>
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<sort column="cohortName" descending="false"/>
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</sorts>
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</customView>

‎SivStudies/src/org/labkey/sivstudies/etl/PerformManualIdrStepsTask.java‎

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updateVaccineInformation(pipelineJob);
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updateChallengeAnchorDates(pipelineJob);
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updateArtInitiationAnchorDates(pipelineJob);
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updateJS46();
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// TODO: Set other cohort-by-cohort params
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return new RecordedActionSet();
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}
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{
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_containerUser = containerUser;
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}
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private void updateJS46() throws PipelineJobException
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{
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updateTreatmentRecords("JS46", new SimpleFilter(FieldKey.fromString("treatment"), "SIV - Unknown"), Map.of("treatment", "SIVmac239", "route", "IV"));
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}
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private void updateTreatmentRecords(String cohortName, SimpleFilter treatmentFilter, final Map<String, Object> additionalProps) throws PipelineJobException
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{
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TableInfo assignments = QueryService.get().getUserSchema(_containerUser.getUser(), _containerUser.getContainer(), "study").getTable("assignment");
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List<String> ids = new TableSelector(assignments, PageFlowUtil.set("Id"), new SimpleFilter(FieldKey.fromString("study"), cohortName), null).getArrayList(String.class);
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treatmentFilter.addCondition(FieldKey.fromString("Id"), ids, CompareType.IN);
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TableInfo treatments = QueryService.get().getUserSchema(_containerUser.getUser(), _containerUser.getContainer(), "study").getTable("treatments");
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List<Map<String, Object>> toUpdate = new ArrayList<>();
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new TableSelector(treatments, PageFlowUtil.set("lsid"), treatmentFilter, null).forEachMap(rs -> {
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Map<String, Object> toAdd = new CaseInsensitiveHashMap<>(rs);
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toAdd.putAll(additionalProps);
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toUpdate.add(toAdd);
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});
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if (!toUpdate.isEmpty())
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{
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try
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{
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BatchValidationException bve = new BatchValidationException();
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List<Map<String, Object>> oldKeys = toUpdate.stream().map(x -> (Map<String, Object>)new CaseInsensitiveHashMap<>(Map.of("lsid", x.get("lsid")))).toList();
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treatments.getUpdateService().updateRows(_containerUser.getUser(), _containerUser.getContainer(), toUpdate, oldKeys, bve, null, null);
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if (bve.hasErrors())
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{
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throw bve;
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}
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}
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catch (SQLException | BatchValidationException | QueryUpdateServiceException | InvalidKeyException e)
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{
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throw new PipelineJobException(e);
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}
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}
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}
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}

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