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Expand SIV study queries
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9 files changed

+68
-22
lines changed

9 files changed

+68
-22
lines changed
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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="sex"/>
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<column name="projects/allStudies"/>
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<column name="projects/studyDescription"/>
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<column name="projects/subgroups"/>
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<column name="projects/analysisGroups"/>
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<column name="immunizations/immunizations"/>
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<column name="sivART/allInfections"/>
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<column name="sivART/ageAtInfection"/>
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<column name="sivART/artInitiationDPI"/>
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<column name="sivART/artReleaseWPI"/>
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<column name="interventions/allInterventions"/>
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<column name="interventions/firstInterventionDPI"/>
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<column name="interventions/firstInterventionPostArtReleaseWeeks"/>
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<column name="pvlInfo/numPVL"/>
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<column name="pvlInfo/numPVLPostArtRelease"/>
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<column name="pvlInfo/lastPvlPostArtReleaseWeeks"/>
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</columns>
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<sorts>
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<sort column="Id" descending="false"/>
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</sorts>
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</customView>

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

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@@ -4,8 +4,6 @@
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<column name="sex"/>
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<column name="species"/>
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<column name="calculated_status"/>
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<column name="birth"/>
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<column name="death"/>
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<column name="sivART/ageAtInfection"/>
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<column name="projects/allStudies"/>
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<column name="projects/studyDescription"/>

SivStudies/resources/queries/study/demographics/SIV and ART Info.qview.xml

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@@ -4,7 +4,7 @@
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<column name="sex"/>
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<column name="species"/>
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<column name="calculated_status"/>
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<column name="projects/categories"/>
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<column name="projects/studyDescription"/>
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<column name="projects/allStudies"/>
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<column name="projects/subgroups"/>
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<column name="sivART/allInfections"/>

SivStudies/resources/queries/study/demographicsChallengeAndArt.sql

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@@ -5,7 +5,7 @@ FROM (
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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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WHEN t.category = 'SIV Infection' THEN (t.treatment || (CASE WHEN t.route IS NULL then '' ELSE (', ' || t.route) END) || (CASE WHEN t.amount IS NULL then '' ELSE (', ' || CAST(t.amount as VARCHAR) || ' ' || t.amount_units) END))
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ELSE NULL
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END, char(10)) as allInfections,
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min(floor(age(t.DataSets.Demographics.birth, CASE WHEN t.category = 'SIV Infection' THEN t.date ELSE NULL END))) AS ageAtInfection,

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

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@@ -22,6 +22,9 @@
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<column columnName="firstInterventionWPI">
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<columnTitle>First Intervention (WPI)</columnTitle>
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</column>
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<column columnName="firstInterventionPostArtReleaseWeeks">
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<columnTitle>First Intervention Relative to ART Release (Weeks)</columnTitle>
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</column>
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</columns>
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<titleColumn>allInterventions</titleColumn>
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</table>
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Original file line numberDiff line numberDiff line change
@@ -1,20 +1,10 @@
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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 = 'Intervention' THEN (t.treatment || ' (' || t.timePostSivChallenge.timePostInfection || ')')
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ELSE NULL
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END, char(10)) as allInterventions,
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min(CASE
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WHEN t.category = 'Intervention' THEN t.date
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ELSE NULL
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END) as firstInterventionDate,
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min(CASE
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WHEN t.category = 'Intervention' THEN t.timePostSivChallenge.daysPostInfection
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ELSE NULL
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END) as firstInterventionDPI,
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min(CASE
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WHEN t.category = 'Intervention' THEN t.timePostSivChallenge.weeksPostInfection
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ELSE NULL
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END) as firstInterventionWPI
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group_concat(DISTINCT (t.treatment || ' (' || t.timePostSivChallenge.timePostInfection || ')'), char(10)) as allInterventions,
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min(t.date) as firstInterventionDate,
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min(t.timePostSivChallenge.daysPostInfection) as firstInterventionDPI,
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min(t.timePostSivChallenge.weeksPostInfection) as firstInterventionWPI,
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min(t.timePostSivChallenge.weeksPostInfection) - min(t.sivART.artReleaseWPI) as firstInterventionPostArtReleaseWeeks
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FROM study.treatments t
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WHERE t.category = 'Intervention'
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GROUP BY t.Id

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

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@@ -12,7 +12,13 @@
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<columnTitle>Study Categories</columnTitle>
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</column>
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<column columnName="allStudies">
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<columnTitle>All Studies</columnTitle>
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<columnTitle>Studies</columnTitle>
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</column>
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<column columnName="allStudiesAndAnalyses">
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<columnTitle>Studies and Analyses</columnTitle>
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</column>
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<column columnName="analysisGroups">
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<columnTitle>Analyses</columnTitle>
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</column>
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<column columnName="subgroups">
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<columnTitle>Subgroups/Treatments</columnTitle>

SivStudies/resources/queries/study/demographicsProjects.sql

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@@ -1,7 +1,9 @@
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SELECT
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s.Id,
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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.study, char(10)) as allStudiesAndAnalyses,
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group_concat(DISTINCT CASE WHEN s.category = 'Analysis Cohorts' THEN NULL ELSE s.study END, char(10)) as allStudies,
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group_concat(DISTINCT CASE WHEN s.category = 'Analysis Cohorts' THEN s.study ELSE NULL END, char(10)) as analysisGroups,
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group_concat(DISTINCT s.cohortId.studyId.description, char(10)) as studyDescription,
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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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<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="enddate"/>
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<column name="category"/>
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<column name="treatment"/>
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<column name="route"/>
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<column name="amount"/>
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<column name="amount_units"/>
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<column name="comments"/>
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<column name="dataSource"/>
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<column name="viralLoad"/>
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<column name="timePostSivChallenge/weeksPostInfection"/>
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<column name="artInformation/daysPostArtInitiation"/>
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<column name="artInformation/daysPostArtRelease"/>
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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="date" descending="true"/>
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</sorts>
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</customView>

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