Merge 25.7 to 25.11

IDR/resources/queries/bimber_data/idrAnchorDateSource.sql

@@ -7,6 +7,7 @@ PID0 as date,
 
 FROM bimber_data.subjects
 WHERE PID0 IS NOT NULL
+AND Cohort NOT IN ('PC549', 'PC585', 'PC529') AND Cohort NOT LIKE 'W%'
 
 UNION ALL
 
@@ -18,4 +19,5 @@ D0 as date,
 'Hansen/IDR' as dataSource
 
 FROM bimber_data.subjects
-WHERE D0 IS NOT NULL
+WHERE D0 IS NOT NULL
+  AND Cohort NOT IN ('PC549', 'PC585', 'PC529') AND Cohort NOT LIKE 'W%'

IDR/resources/queries/bimber_data/idrOutcomeSource.sql

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

SivStudies/resources/etls/idr-data.xml

@@ -125,7 +125,7 @@
                     <setting name="dataSourceColumns" value="Rh,PID0"/>
                     <setting name="dataSourceColumnMapping" value="Rh=Id,PID0=date"/>
                     <setting name="dataSourceColumnDefaults" value="dataSource=Hansen/IDR;category=SIV Infection;treatment=SIV - Unknown"/>
-                    <setting name="dataSourceAdditionalFilters" value="PID0~isnonblank="/>
+                    <setting name="dataSourceAdditionalFilters" value="PID0~isnonblank=;Cohort~neqornull=PC549;Cohort~neqornull=PC585;Cohort~neqornull=W1170;Cohort~neqornull=W1173;Cohort~neqornull=PC529"/>
 
                     <setting name="targetSchema" value="study"/>
                     <setting name="targetQuery" value="treatments"/>

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

@@ -0,0 +1,25 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" hidden="false" canOverride="false">
+    <columns>
+        <column name="Id"/>
+        <column name="sex"/>
+        <column name="projects/allStudies"/>
+        <column name="projects/studyDescription"/>
+        <column name="projects/subgroups"/>
+        <column name="projects/analysisGroups"/>
+        <column name="immunizations/immunizations"/>
+        <column name="sivART/allInfections"/>
+        <column name="sivART/ageAtInfection"/>
+        <column name="sivART/allART"/>
+        <column name="sivART/artInitiationDPI"/>
+        <column name="sivART/artReleaseWPI"/>
+        <column name="interventions/allInterventions"/>
+        <column name="interventions/firstInterventionDPI"/>
+        <column name="interventions/firstInterventionPostArtReleaseWeeks"/>
+        <column name="pvlInfo/numPVL"/>
+        <column name="pvlInfo/numPVLPostArtRelease"/>
+        <column name="pvlInfo/lastPvlPostArtReleaseWeeks"/>
+    </columns>
+    <sorts>
+        <sort column="Id" descending="false"/>
+    </sorts>
+</customView>

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

@@ -0,0 +1,21 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" hidden="false" canOverride="false">
+    <columns>
+        <column name="Id"/>
+        <column name="sex"/>
+        <column name="projects/allStudies"/>
+        <column name="projects/studyDescription"/>
+        <column name="projects/subgroups"/>
+        <column name="projects/analysisGroups"/>
+        <column name="immunizations/immunizations"/>
+        <column name="sivART/allInfections"/>
+        <column name="sivART/infectionDate"/>
+        <column name="sivART/ageAtInfection"/>
+        <column name="sivART/allART"/>
+        <column name="interventions/allInterventions"/>
+        <column name="interventions/firstInterventionDPI"/>
+        <column name="pvlInfo/numPVL"/>
+    </columns>
+    <sorts>
+        <sort column="Id" descending="false"/>
+    </sorts>
+</customView>

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

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

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

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

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

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

SivStudies/resources/queries/study/demographicsChallengeAndArt.sql

@@ -5,13 +5,13 @@ FROM (
     SELECT
       t.Id,
       group_concat(DISTINCT CASE
-          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 || ')')
+          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))
           ELSE NULL
       END, char(10)) as allInfections,
       min(floor(age(t.DataSets.Demographics.birth, CASE WHEN t.category = 'SIV Infection' THEN t.date ELSE NULL END))) AS ageAtInfection,
 
       group_concat(DISTINCT CASE
-          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 || ')')
+          WHEN t.category = 'ART' THEN (t.treatment || ' (' || COALESCE(t.timePostSivChallenge.timePostInfection, 'Unk DPI') || ')')
           ELSE NULL
       END, char(10)) as allART,
       min(CASE

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

@@ -22,6 +22,9 @@
                     <column columnName="firstInterventionWPI">
                         <columnTitle>First Intervention (WPI)</columnTitle>
                     </column>
+                    <column columnName="firstInterventionPostArtReleaseWeeks">
+                        <columnTitle>First Intervention Relative to ART Release (Weeks)</columnTitle>
+                    </column>
                 </columns>
                 <titleColumn>allInterventions</titleColumn>
             </table>

SivStudies/resources/queries/study/demographicsInterventions.sql

@@ -1,20 +1,10 @@
 SELECT
     t.Id,
-    group_concat(DISTINCT CASE
-      WHEN t.category = 'Intervention' THEN (t.treatment || ' (' || t.timePostSivChallenge.timePostInfection || ')')
-      ELSE NULL
-  END, char(10)) as allInterventions,
-    min(CASE
-            WHEN t.category = 'Intervention' THEN t.date
-            ELSE NULL
-        END) as firstInterventionDate,
-    min(CASE
-            WHEN t.category = 'Intervention' THEN t.timePostSivChallenge.daysPostInfection
-            ELSE NULL
-        END) as firstInterventionDPI,
-    min(CASE
-            WHEN t.category = 'Intervention' THEN t.timePostSivChallenge.weeksPostInfection
-            ELSE NULL
-        END) as firstInterventionWPI
+    group_concat(DISTINCT (t.treatment || ' (' || COALESCE(t.timePostSivChallenge.timePostInfection, 'Unk DPI') || ')'), char(10)) as allInterventions,
+    min(t.date) as firstInterventionDate,
+    min(t.timePostSivChallenge.daysPostInfection) as firstInterventionDPI,
+    min(t.timePostSivChallenge.weeksPostInfection) as firstInterventionWPI,
+    min(t.timePostSivChallenge.weeksPostInfection) - min(t.sivART.artReleaseWPI) as firstInterventionPostArtReleaseWeeks
 FROM study.treatments t
+WHERE t.category = 'Intervention'
 GROUP BY t.Id

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

@@ -12,7 +12,16 @@
                         <columnTitle>Study Categories</columnTitle>
                     </column>
                     <column columnName="allStudies">
-                        <columnTitle>All Studies</columnTitle>
+                        <columnTitle>Studies</columnTitle>
+                        <url>/query/executeQuery.view?schemaName=study&amp;query.queryName=assignment&amp;query.Id~eq=${Id}</url>
+                        <urlTarget>_blank</urlTarget>
+                    </column>
+                    <column columnName="allStudiesAndAnalyses">
+                        <columnTitle>Studies and Analyses</columnTitle>
+                    </column>
+                    <column columnName="analysisGroups">
+                        <columnTitle>Analysis Groups</columnTitle>
+                        <displayWidth>150</displayWidth>
                     </column>
                     <column columnName="subgroups">
                         <columnTitle>Subgroups/Treatments</columnTitle>

SivStudies/resources/queries/study/demographicsProjects.sql

@@ -1,7 +1,9 @@
 SELECT
   s.Id,
   count(s.Id) as totalProjects,
-  group_concat(DISTINCT s.study, char(10)) as allStudies,
+  group_concat(DISTINCT s.study, char(10)) as allStudiesAndAnalyses,
+  group_concat(DISTINCT CASE WHEN s.category = 'Analysis Cohorts' THEN NULL ELSE s.study END, char(10)) as allStudies,
+  group_concat(DISTINCT CASE WHEN s.category = 'Analysis Cohorts' THEN s.study ELSE NULL END, char(10)) as analysisGroups,
   group_concat(DISTINCT s.cohortId.studyId.description, char(10)) as studyDescription,
   group_concat(DISTINCT s.category, char(10)) as categories,
   group_concat(DISTINCT s.subgroup, char(10)) as subgroups

SivStudies/resources/queries/study/infectionAnchorDateDiscordance.sql

@@ -1,16 +1,15 @@
 SELECT
-    t.Id,
+    coalesce(t.Id, t2.subjectId) as Id,
     'SIV Infection' as category,
     t.date as treatmentTableDate,
     t2.date as subjectAnchorDatesTableDate
 
 FROM study.treatments t
 FULL JOIN studies.subjectAnchorDates t2 ON (
-    t.category = 'SIV Infection' AND
-    t2.subjectId = t.Id AND
-    t2.eventLabel = 'SIV Infection'
+    t.category = t2.eventLabel AND
+    t2.subjectId = t.Id
 )
 
-WHERE t2.date != t.date OR
+WHERE (t2.date != t.date OR
     t2.date IS NULL OR
-    t.date IS NULL
+    t.date IS NULL) AND COALESCE(t.category, t2.eventLabel) = 'SIV Infection'

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

@@ -0,0 +1,9 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="missingAnchorDates" tableDbType="TABLE" useColumnOrder="true">
+                <tableTitle>Missing Anchor Dates</tableTitle>
+            </table>
+        </tables>
+    </metadata>
+</query>

SivStudies/resources/queries/study/missingAnchorDates.sql

@@ -0,0 +1,30 @@
+SELECT
+    dc.Id as SubjectId,
+    dc.infectionDate as date,
+    'SIV Infection' as eventLabel
+
+FROM study.demographicsChallengeAndArt dc
+LEFT JOIN studies.subjectAnchorDates ad ON (dc.Id = ad.SubjectId AND dc.infectionDate = ad.date AND ad.eventLabel = 'SIV Infection')
+WHERE ad.rowid IS NULL AND dc.infectionDate IS NOT NULL
+
+UNION ALL
+
+SELECT
+    dc.Id as SubjectId,
+    dc.artInitiationDate as date,
+    'ART Initiation' as eventLabel
+
+FROM study.demographicsChallengeAndArt dc
+         LEFT JOIN studies.subjectAnchorDates ad ON (dc.Id = ad.SubjectId AND dc.artInitiationDate = ad.date AND ad.eventLabel = 'ART Initiation')
+WHERE ad.rowid IS NULL AND dc.artInitiationDate IS NOT NULL
+
+UNION ALL
+
+SELECT
+    dc.Id as SubjectId,
+    dc.artReleaseDate as date,
+    'ART Release' as eventLabel
+
+FROM study.demographicsChallengeAndArt dc
+    LEFT JOIN studies.subjectAnchorDates ad ON (dc.Id = ad.SubjectId AND dc.artReleaseDate = ad.date AND ad.eventLabel = 'ART Release')
+WHERE ad.rowid IS NULL AND dc.artReleaseDate IS NOT NULL

SivStudies/resources/queries/study/treatments/With SIV-ART Dates.qview.xml

@@ -0,0 +1,23 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" hidden="false" canOverride="false">
+    <columns>
+        <column name="Id"/>
+        <column name="date"/>
+        <column name="enddate"/>
+        <column name="category"/>
+        <column name="treatment"/>
+        <column name="route"/>
+        <column name="amount"/>
+        <column name="amount_units"/>
+        <column name="comments"/>
+        <column name="dataSource"/>
+        <column name="viralLoad"/>
+        <column name="timePostSivChallenge/weeksPostInfection"/>
+        <column name="artInformation/daysPostArtInitiation"/>
+        <column name="artInformation/daysPostArtRelease"/>
+
+    </columns>
+    <sorts>
+        <sort column="Id" descending="false"/>
+        <sort column="date" descending="true"/>
+    </sorts>
+</customView>

SivStudies/src/org/labkey/sivstudies/query/SivStudiesCustomizer.java

@@ -382,7 +382,7 @@ public TableInfo getLookupTableInfo()
                         "JOIN studies.subjectAnchorDates ad ON (ad.subjectId = c." + idCol.getFieldKey().toSQLString() + ")\n" +
                         "WHERE ad.eventLabel = 'SIV Infection'\n" +
                         "GROUP BY c.date, c." + pkCol.getFieldKey().toString() + "\n" +
-                        "HAVING count(*) = 1) t"
+                        "HAVING count(DISTINCT c.date) = 1) t"
                 );
                 qd.setIsTemporary(true);
 
@@ -472,9 +472,10 @@ public TableInfo getLookupTableInfo()
                         "GROUP_CONCAT(DISTINCT tr.treatment) AS artTreatment,\n" +
                         "c." + pkCol.getFieldKey().toString() + "\n" +
                         "FROM \"" + schemaName + "\".\"" + queryName + "\" c " +
+                        // TODO: consider whether this should include all dates
                         "JOIN study.treatments tr ON (tr.category = 'ART' AND CAST(tr.date AS DATE) <= CAST(c." + dateCol.getFieldKey().toString() + " AS DATE) AND tr.Id = c." + idCol.getFieldKey().toSQLString() + ")\n" +
                         "GROUP BY c." + dateCol.getFieldKey().toString()  + ", c." + pkCol.getFieldKey().toString() + "\n" +
-                        "HAVING COUNT(*) = 1"
+                        "HAVING COUNT(DISTINCT tr.date) = 1"
                 );
                 qd.setIsTemporary(true);