LabKey · bbimber · Dec 3, 2025 · Nov 25, 2025 · Nov 26, 2025 · Nov 26, 2025
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -4,4 +4,4 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "daily"
+      interval: "weekly"
diff --git a/IDR/resources/queries/bimber_data/idrAnchorDateSource.sql b/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%'
diff --git a/IDR/resources/queries/bimber_data/idrOutcomeSource.sql b/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%'
diff --git a/SivStudies/resources/etls/idr-data.xml b/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"/>

diff --git a/SivStudies/resources/queries/studies/studies.query.xml b/SivStudies/resources/queries/studies/studies.query.xml
@@ -0,0 +1,21 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="studies" tableDbType="TABLE" useColumnOrder="false">
+                <columns>
+                    <column columnName="studySummary" wrappedColumnName="rowId">
+                        <isUnselectable>true</isUnselectable>
+                        <shownInInsertView>false</shownInInsertView>
+                        <shownInUpdateView>false</shownInUpdateView>
+                        <columnTitle>Summary Information</columnTitle>
+                        <fk>
+                            <fkDbSchema>studies</fkDbSchema>
+                            <fkTable>studiesSummary</fkTable>
+                            <fkColumnName>rowId</fkColumnName>
+                        </fk>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>
diff --git a/SivStudies/resources/queries/studies/studies/.qview.xml b/SivStudies/resources/queries/studies/studies/.qview.xml
@@ -0,0 +1,18 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" hidden="false" canOverride="false">
+    <columns>
+        <column name="rowId"/>
+        <column name="studyName"/>
+        <column name="label"/>
+        <column name="category"/>
+        <column name="description"/>
+        <column name="cohorts"/>
+        <column name="studySummary/numAnimals"/>
+        <column name="studySummary/sexes"/>
+        <column name="studySummary/challenges"/>
+        <column name="studySummary/artInitiationsDPI"/>
+        <column name="studySummary/interventions"/>
+    </columns>
+    <sorts>
+        <sort column="studyName" descending="false"/>
+    </sorts>
+</customView>
diff --git a/SivStudies/resources/queries/studies/studiesSummary.query.xml b/SivStudies/resources/queries/studies/studiesSummary.query.xml
@@ -0,0 +1,38 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="studiesSummary" tableDbType="TABLE" useColumnOrder="true">
+                <tableTitle>Studies Summary</tableTitle>
+                <columns>
+                    <column columnName="rowId">
+
+                    </column>
+                    <column columnName="labelOrName">
+
+                    </column>
+                    <column columnName="description">
+
+                    </column>
+                    <column columnName="cohorts">
+
+                    </column>
+                    <column columnName="numAnimals">
+                        <columnTitle># Animals</columnTitle>
+                    </column>
+                    <column columnName="sexes">
+                        <columnTitle>Sex(es)</columnTitle>
+                    </column>
+                    <column columnName="challenges">
+                        <columnTitle>SIV Challenges</columnTitle>
+                    </column>
+                    <column columnName="artInitiationsDPI">
+                        <columnTitle>ART Initiation(s) (DPI)</columnTitle>
+                    </column>
+                    <column columnName="interventions">
+                        <columnTitle>Interventions</columnTitle>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>
diff --git a/SivStudies/resources/queries/studies/studiesSummary.sql b/SivStudies/resources/queries/studies/studiesSummary.sql
@@ -0,0 +1,16 @@
+SELECT
+    s.rowId,
+    s.labelOrName,
+    s.description,
+    group_concat(DISTINCT a.cohortId.labelOrName, char(10)) as cohorts,
+    count(DISTINCT a.Id) as numAnimals,
+    group_concat(DISTINCT a.DataSets.Demographics.sex) as sexes,
+    group_concat(DISTINCT a.sivArt.allInfections, char(10)) as challenges,
+    group_concat(DISTINCT a.sivArt.artInitiationDPI, char(10)) as artInitiationsDPI,
+    group_concat(DISTINCT a.interventions.allInterventions, char(10)) as interventions,
+
+
+FROM studies.studies s
+LEFT JOIN study.assignment a ON (a.cohortId.studyId = s.rowId)
+
+GROUP BY s.rowId, s.labelOrName, s.description
diff --git a/SivStudies/resources/queries/studies/studyCohortSummary.query.xml b/SivStudies/resources/queries/studies/studyCohortSummary.query.xml
@@ -0,0 +1,38 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="studiesSummary" tableDbType="TABLE" useColumnOrder="true">
+                <tableTitle>Study Cohort Summary</tableTitle>
+                <columns>
+                    <column columnName="rowId">
+
+                    </column>
+                    <column columnName="studyName">
+                        <columnTitle>Study Name</columnTitle>
+                    </column>
+                    <column columnName="description">
+
+                    </column>
+                    <column columnName="labelOrName">
+                        <columnTitle>Cohort Name</columnTitle>
+                    </column>
+                    <column columnName="numAnimals">
+                        <columnTitle># Animals</columnTitle>
+                    </column>
+                    <column columnName="sexes">
+                        <columnTitle>Sex(es)</columnTitle>
+                    </column>
+                    <column columnName="challenges">
+                        <columnTitle>SIV Challenges</columnTitle>
+                    </column>
+                    <column columnName="artInitiationsDPI">
+                        <columnTitle>ART Initiation(s) (DPI)</columnTitle>
+                    </column>
+                    <column columnName="interventions">
+                        <columnTitle>Interventions</columnTitle>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>
diff --git a/SivStudies/resources/queries/studies/studyCohortSummary.sql b/SivStudies/resources/queries/studies/studyCohortSummary.sql
@@ -0,0 +1,16 @@
+SELECT
+    sc.rowId,
+    sc.studyId.labelOrName as studyName,
+    sc.labelOrName,
+    sc.studyId.description,
+    count(DISTINCT a.Id) as numAnimals,
+    group_concat(DISTINCT a.DataSets.Demographics.sex) as sexes,
+    group_concat(DISTINCT a.sivArt.allInfections, char(10)) as challenges,
+    group_concat(DISTINCT a.sivArt.artInitiationDPI, char(10)) as artInitiationsDPI,
+    group_concat(DISTINCT a.interventions.allInterventions, char(10)) as interventions
+
+
+FROM studies.studyCohorts sc
+LEFT JOIN study.assignment a ON (a.cohortId = sc.rowId)
+
+GROUP BY sc.rowId, sc.labelOrName, sc.studyId.description, sc.studyId.labelOrName
diff --git a/SivStudies/resources/queries/studies/studyCohorts.query.xml b/SivStudies/resources/queries/studies/studyCohorts.query.xml
@@ -0,0 +1,21 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="studyCohorts" tableDbType="TABLE" useColumnOrder="false">
+                <columns>
+                    <column columnName="cohortsSummary" wrappedColumnName="rowId">
+                        <isUnselectable>true</isUnselectable>
+                        <shownInInsertView>false</shownInInsertView>
+                        <shownInUpdateView>false</shownInUpdateView>
+                        <columnTitle>Summary Information</columnTitle>
+                        <fk>
+                            <fkDbSchema>studies</fkDbSchema>
+                            <fkTable>studyCohortSummary</fkTable>
+                            <fkColumnName>rowId</fkColumnName>
+                        </fk>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>
diff --git a/SivStudies/resources/queries/studies/studyCohorts/.qview.xml b/SivStudies/resources/queries/studies/studyCohorts/.qview.xml
@@ -0,0 +1,27 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" hidden="false" canOverride="false">
+    <columns>
+        <column name="rowId"/>
+        <column name="studyId"/>
+        <column name="studyId/description">
+            <properties>
+                <property name="columnTitle" value="Study Description"/>
+            </properties>
+        </column>
+        <column name="cohortName"/>
+        <column name="label"/>
+        <column name="category"/>
+        <column name="description"/>
+        <column name="isControlGroup"/>
+        <column name="sortOrder"/>
+        <column name="cohortsSummary/numAnimals"/>
+        <column name="cohortsSummary/sexes"/>
+        <column name="cohortsSummary/challenges"/>
+        <column name="cohortsSummary/artInitiationsDPI"/>
+        <column name="cohortsSummary/interventions"/>
+    </columns>
+    <sorts>
+        <sort column="studyId/studyName" descending="false"/>
+        <sort column="sortOrder" descending="false"/>
+        <sort column="cohortName" descending="false"/>
+    </sorts>
+</customView>
diff --git a/SivStudies/resources/queries/study/demographics/Expanded ART Detail.qview.xml b/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>
diff --git a/SivStudies/resources/queries/study/demographics/Expanded Vaccine Detail.qview.xml b/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>
diff --git a/SivStudies/resources/queries/study/demographics/Expanded.qview.xml b/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"/>

diff --git a/SivStudies/resources/queries/study/demographics/SIV and ART Info.qview.xml b/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"/>

diff --git a/SivStudies/resources/queries/study/demographicsChallengeAndArt.query.xml b/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>

diff --git a/SivStudies/resources/queries/study/demographicsChallengeAndArt.sql b/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

diff --git a/SivStudies/resources/queries/study/demographicsInterventions.query.xml b/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>

diff --git a/SivStudies/resources/queries/study/demographicsInterventions.sql b/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