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Merge pull request #205 from bimberlabinternal/25.11_fb_merge_25.7
Merge 25.7 to 25.11
2 parents bb108ec + 389425a commit 343fba0

19 files changed

+153
-38
lines changed

‎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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@@ -18,4 +19,5 @@ D0 as date,
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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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@@ -125,7 +125,7 @@
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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/study/demographics/Expanded ART Detail.qview.xml‎

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@@ -0,0 +1,25 @@
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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/allART"/>
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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 Vaccine Detail.qview.xml‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,21 @@
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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/infectionDate"/>
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<column name="sivART/ageAtInfection"/>
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<column name="sivART/allART"/>
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<column name="interventions/allInterventions"/>
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<column name="interventions/firstInterventionDPI"/>
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<column name="pvlInfo/numPVL"/>
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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.query.xml‎

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@@ -12,11 +12,13 @@
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<columnTitle>SIV Infection</columnTitle>
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<url>/query/executeQuery.view?schemaName=study&amp;query.queryName=treatments&amp;query.Id~eq=${Id}&amp;query.category~eq=SIV Infection</url>
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<urlTarget>_blank</urlTarget>
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<displayWidth>150</displayWidth>
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</column>
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<column columnName="allART">
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<columnTitle>ART</columnTitle>
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<columnTitle>ART Regimen</columnTitle>
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<url>/query/executeQuery.view?schemaName=study&amp;query.queryName=treatments&amp;query.Id~eq=${Id}&amp;query.category~eq=ART</url>
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<urlTarget>_blank</urlTarget>
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<displayWidth>175</displayWidth>
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</column>
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<column columnName="infectionDate">
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<columnTitle>Infection Date</columnTitle>

‎SivStudies/resources/queries/study/demographicsChallengeAndArt.sql‎

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@@ -5,13 +5,13 @@ 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,
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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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WHEN t.category = 'ART' THEN (t.treatment || ' (' || COALESCE(t.timePostSivChallenge.timePostInfection, 'Unk DPI') || ')')
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ELSE NULL
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END, char(10)) as allART,
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min(CASE

‎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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