Merge discvr-25.7 to develop

SivStudies/resources/etls/idr-data.xml

@@ -100,8 +100,8 @@
                     <setting name="dataSourceSchema" value="bimber_data"/>
                     <setting name="dataSourceQuery" value="vacc"/>
                     <setting name="dataSourceSubjectColumn" value="Rh"/>
-                    <setting name="dataSourceColumns" value="Rh,vacc_date,name,route,dose,ag_source"/>
-                    <setting name="dataSourceColumnMapping" value="Rh=Id,vacc_date=date,name=treatment,dose=quantity,ag_source=category"/>
+                    <setting name="dataSourceColumns" value="Rh,vacc_date,name,route,dose,ag_source,backbone,vc_vector_id,orf"/>
+                    <setting name="dataSourceColumnMapping" value="Rh=Id,vacc_date=date,name=treatment,dose=quantity,ag_source=category,vc_vector_id=vectorId,orf=antigens"/>
                     <setting name="dataSourceColumnDefaults" value="dataSource=Hansen/IDR"/>
 
                     <setting name="targetSchema" value="study"/>
@@ -155,6 +155,11 @@
                 </settings>
             </taskref>
         </transform>
+        <transform id="subjects" type="TaskRefTransformStep">
+            <taskref ref="org.labkey.sivstudies.etl.PerformManualIdrStepsTask">
+
+            </taskref>
+        </transform>
     </transforms>
     <schedule>
         <cron expression="0 30 20 * * ?"/>

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

@@ -6,11 +6,14 @@
         <column name="calculated_status"/>
         <column name="birth"/>
         <column name="death"/>
+        <column name="sivART/ageAtInfection"/>
         <column name="projects/allStudies"/>
+        <column name="projects/studyDescription"/>
         <column name="projects/subgroups"/>
         <column name="immunizations/immunizations"/>
         <column name="sivART/allInfections"/>
-        <column name="sivART/allART"/>
+        <column name="sivART/artInitiationDPI"/>
+        <column name="interventions/allInterventions"/>
         <column name="outcomes/outcomes"/>
     </columns>
     <sorts>

SivStudies/resources/queries/study/demographics/Project Summary.qview.xml

@@ -9,8 +9,6 @@
         <column name="death"/>
         <column name="projects/allStudies"/>
         <column name="projects/categories"/>
-        <column name="projects/rhCmvVaccines"/>
-        <column name="projects/sivArt"/>
     </columns>
     <sorts>
         <sort column="Id" descending="false"/>

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

@@ -0,0 +1,22 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" hidden="false" canOverride="false">
+    <columns>
+        <column name="Id"/>
+        <column name="sex"/>
+        <column name="species"/>
+        <column name="calculated_status"/>
+        <column name="projects/categories"/>
+        <column name="projects/allStudies"/>
+        <column name="projects/subgroups"/>
+        <column name="sivART/allInfections"/>
+        <column name="sivART/artInitiationDate"/>
+        <column name="sivART/artReleaseDate"/>
+        <column name="sivART/artInitiationDPI"/>
+        <column name="sivART/artReleaseWPI"/>
+        <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/demographicsChallengeAndArt.query.xml

@@ -10,12 +10,31 @@
                     </column>
                     <column columnName="allInfections">
                         <columnTitle>SIV Infection</columnTitle>
+                        <url>/query/executeQuery.view?schemaName=study&amp;query.queryName=treatments&amp;query.Id~eq=${Id}&amp;query.category~eq=SIV Infection</url>
+                        <urlTarget>_blank</urlTarget>
                     </column>
                     <column columnName="allART">
                         <columnTitle>ART</columnTitle>
+                        <url>/query/executeQuery.view?schemaName=study&amp;query.queryName=treatments&amp;query.Id~eq=${Id}&amp;query.category~eq=ART</url>
+                        <urlTarget>_blank</urlTarget>
                     </column>
                     <column columnName="infectionDate">
                         <columnTitle>Infection Date</columnTitle>
+                        <formatString>Date</formatString>
+                    </column>
+                    <column columnName="artInitiationDate">
+                        <columnTitle>ART Initiation</columnTitle>
+                        <formatString>Date</formatString>
+                    </column>
+                    <column columnName="artInitiationDPI">
+                        <columnTitle>ART Initiation (DPI)</columnTitle>
+                    </column>
+                    <column columnName="artReleaseDate">
+                        <columnTitle>ART Release</columnTitle>
+                        <formatString>Date</formatString>
+                    </column>
+                    <column columnName="artReleaseWPI">
+                        <columnTitle>ART Release (WPI)</columnTitle>
                     </column>
                 </columns>
                 <titleColumn>allInfections</titleColumn>

SivStudies/resources/queries/study/demographicsChallengeAndArt.sql

@@ -1,17 +1,35 @@
 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 || ')')
-      ELSE NULL
-  END, char(10)) as allInfections,
-  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 || ')')
-      ELSE NULL
-  END, char(10)) as allART,
-  min(CASE
-      WHEN t.category = 'SIV Infection' THEN t.date
-      ELSE NULL
-  END) as infectionDate,
+    t.*,
+    TIMESTAMPDIFF('SQL_TSI_WEEK', t.infectionDate, t.artReleaseDate) as artReleaseWPI
+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 || ')')
+          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,
 
-FROM study.treatments t
-GROUP BY t.Id
+      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 || ')')
+          ELSE NULL
+      END, char(10)) as allART,
+      min(CASE
+          WHEN t.category = 'SIV Infection' THEN t.date
+          ELSE NULL
+      END) as infectionDate,
+      min(CASE
+              WHEN t.category = 'ART' THEN t.date
+              ELSE NULL
+          END) as artInitiationDate,
+        min(CASE
+              WHEN t.category = 'ART' THEN t.timePostSivChallenge.daysPostInfection
+              ELSE NULL
+          END) as artInitiationDPI,
+      min(CASE
+              WHEN t.category = 'ART' THEN t.artInformation.artRelease
+              ELSE NULL
+          END) as artReleaseDate
+    FROM study.treatments t
+    GROUP BY t.Id
+) t

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

@@ -10,9 +10,13 @@
                     </column>
                     <column columnName="immunizations">
                         <columnTitle>Immunizations</columnTitle>
+                        <url>/query/executeQuery.view?schemaName=study&amp;query.queryName=immunizations&amp;query.Id~eq=${Id}</url>
+                        <urlTarget>_blank</urlTarget>
                     </column>
                     <column columnName="immunizationTypes">
                         <columnTitle>Immunization Types</columnTitle>
+                        <url>/query/executeQuery.view?schemaName=study&amp;query.queryName=immunizations&amp;query.Id~eq=${Id}</url>
+                        <urlTarget>_blank</urlTarget>
                     </column>
                 </columns>
                 <titleColumn>immunizations</titleColumn>

SivStudies/resources/queries/study/demographicsImmunizations.sql

@@ -1,6 +1,6 @@
 SELECT
   s.Id,
-  group_concat(DISTINCT s.treatment, char(10)) as immunizations,
+  group_concat(DISTINCT COALESCE(s.backbone, s.treatment), char(10)) as immunizations,
   group_concat(DISTINCT s.category, char(10)) as immunizationTypes,
 
 FROM study.immunizations s

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

@@ -0,0 +1,30 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="" tableDbType="NOT_IN_DB">
+                <tableTitle>Interventions/Treatments Summary</tableTitle>
+                <columns>
+                    <column columnName="Id">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
+                    <column columnName="allInterventions">
+                        <columnTitle>Interventions/Treatments</columnTitle>
+                        <url>/query/executeQuery.view?schemaName=study&amp;query.queryName=treatments&amp;query.Id~eq=${Id}&amp;query.category~eq=Intervention</url>
+                        <urlTarget>_blank</urlTarget>
+                    </column>
+                    <column columnName="firstInterventionDate">
+                        <columnTitle>Date of First Intervention</columnTitle>
+                    </column>
+                    <column columnName="firstInterventionDPI">
+                        <columnTitle>First Intervention (DPI)</columnTitle>
+                    </column>
+                    <column columnName="firstInterventionWPI">
+                        <columnTitle>First Intervention (WPI)</columnTitle>
+                    </column>
+                </columns>
+                <titleColumn>allInterventions</titleColumn>
+            </table>
+        </tables>
+    </metadata>
+</query>

SivStudies/resources/queries/study/demographicsInterventions.sql

@@ -0,0 +1,20 @@
+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
+FROM study.treatments t
+GROUP BY t.Id

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

@@ -0,0 +1,65 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="demographicsPVL" tableDbType="NOT_IN_DB">
+                <tableTitle>PVL Summary</tableTitle>
+                <columns>
+                    <column columnName="Id">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
+                    <column columnName="sivChallenge">
+                        <columnTitle>SIV Challenge</columnTitle>
+                        <formatString>Date</formatString>
+                    </column>
+                    <column columnName="numPVL">
+                        <columnTitle># PVLs</columnTitle>
+                        <url>/query/executeQuery.view?schemaName=study&amp;query.queryName=viralLoads&amp;query.Id~eq=${Id}&amp;query.sampleType~eq=Plasma&amp;query.target~eq=SIV</url>
+                        <urlTarget>_blank</urlTarget>
+                    </column>
+                    <column columnName="dateOfFirstPvl">
+                        <columnTitle>First PVL</columnTitle>
+                    </column>
+                    <column columnName="dateOfLastPvl">
+                        <columnTitle>Last PVL</columnTitle>
+                    </column>
+                    <column columnName="firstPvlDPI">
+                        <columnTitle>DPI of First PVL</columnTitle>
+                    </column>
+                    <column columnName="lastPvlDPI">
+                        <columnTitle>DPI of Last PVL</columnTitle>
+                    </column>
+                    <column columnName="firstPvlWPI">
+                        <columnTitle>WPI of First PVL</columnTitle>
+                    </column>
+                    <column columnName="lastPvlWPI">
+                        <columnTitle>WPI of Last PVL</columnTitle>
+                    </column>
+                    <column columnName="artRelease">
+                        <columnTitle>ART Release</columnTitle>
+                        <formatString>Date</formatString>
+                    </column>
+
+                    <column columnName="numPVLPostArtRelease">
+                        <columnTitle># PVLs Post-ART Release</columnTitle>
+                        <url>/query/executeQuery.view?schemaName=study&amp;query.queryName=viralLoads&amp;query.Id~eq=${Id}&amp;query.sampleType~eq=Plasma&amp;query.target~eq=SIV&amp;query.date~dategte=${artRelease}</url>
+                        <urlTarget>_blank</urlTarget>
+                    </column>
+                    <column columnName="firstPvlPostArtReleaseWeeks">
+                        <columnTitle>First PVL Post-ART Release (Weeks)</columnTitle>
+                    </column>
+                    <column columnName="lastPvlPostArtReleaseWeeks">
+                        <columnTitle>Last PVL Post-ART Release (Weeks)</columnTitle>
+                    </column>
+                    <column columnName="firstPvlPostArtReleaseMonths">
+                        <columnTitle>First PVL Post-ART Release (Months)</columnTitle>
+                    </column>
+                    <column columnName="lastPvlPostArtReleaseMonths">
+                        <columnTitle>Last PVL Post-ART Release (Months)</columnTitle>
+                    </column>
+                </columns>
+                <titleColumn>numPVL</titleColumn>
+            </table>
+        </tables>
+    </metadata>
+</query>

SivStudies/resources/queries/study/demographicsPVL.sql

@@ -0,0 +1,32 @@
+SELECT
+    t.Id,
+    count(*) AS numPVL,
+    min(sivChallenge) as sivChallenge,
+    min(t.date) as dateOfFirstPvl,
+    max(t.date) as dateOfLastPvl,
+
+    min(CONVERT(CASE WHEN t.sivChallenge IS NULL THEN NULL WHEN t.date <= t.sivChallenge THEN NULL ELSE TIMESTAMPDIFF('SQL_TSI_DAY', t.sivChallenge, t.date) END, INTEGER)) as firstPvlDPI,
+    max(CONVERT(CASE WHEN t.sivChallenge IS NULL THEN NULL WHEN t.date <= t.sivChallenge THEN NULL ELSE TIMESTAMPDIFF('SQL_TSI_DAY', t.sivChallenge, t.date) END, INTEGER)) as lastPvlDPI,
+
+    min(CONVERT(CASE WHEN t.sivChallenge IS NULL THEN NULL WHEN t.date <= t.sivChallenge THEN NULL ELSE TIMESTAMPDIFF('SQL_TSI_WEEK', t.sivChallenge, t.date) END, INTEGER)) as firstPvlWPI,
+    max(CONVERT(CASE WHEN t.sivChallenge IS NULL THEN NULL WHEN t.date <= t.sivChallenge THEN NULL ELSE TIMESTAMPDIFF('SQL_TSI_WEEK', t.sivChallenge, t.date) END, INTEGER)) as lastPvlWPI,
+
+    min(artRelease) as artRelease,
+    sum(CASE WHEN (t.artRelease IS NOT NULL AND t.date > t.artRelease) THEN 1 ELSE 0 END) as numPVLPostArtRelease,
+
+    min(CONVERT(CASE WHEN t.artRelease IS NULL THEN NULL WHEN t.date <= t.artRelease THEN NULL ELSE age_in_months(t.artRelease, t.date) END, FLOAT)) as firstPvlPostArtReleaseMonths,
+    max(CONVERT(CASE WHEN t.artRelease IS NULL THEN NULL WHEN t.date <= t.artRelease THEN NULL ELSE age_in_months(t.artRelease, t.date) END, FLOAT)) as lastPvlPostArtReleaseMonths,
+
+    min(CONVERT(CASE WHEN t.artRelease IS NULL THEN NULL WHEN t.date <= t.artRelease THEN NULL ELSE TIMESTAMPDIFF('SQL_TSI_WEEK', t.artRelease, t.date) END, INTEGER)) as firstPvlPostArtReleaseWeeks,
+    max(CONVERT(CASE WHEN t.artRelease IS NULL THEN NULL WHEN t.date <= t.artRelease THEN NULL ELSE TIMESTAMPDIFF('SQL_TSI_WEEK', t.artRelease, t.date) END, INTEGER)) as lastPvlPostArtReleaseWeeks
+
+FROM (SELECT
+    vl.Id,
+    vl.date,
+    (SELECT min(tr.date) as sivChallenge FROM study.treatments tr WHERE tr.category = 'SIV Infection' AND tr.Id = vl.Id) as sivChallenge,
+    (SELECT max(tr.enddate) as artRelease FROM study.treatments tr WHERE tr.category = 'ART' AND tr.Id = vl.Id) as artRelease
+
+FROM study.viralLoads vl
+WHERE vl.target = 'SIV' AND vl.sampleType = 'Plasma'
+) t
+GROUP BY t.Id

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

@@ -17,12 +17,6 @@
                     <column columnName="subgroups">
                         <columnTitle>Subgroups/Treatments</columnTitle>
                     </column>
-                    <column columnName="rhCmvVaccines">
-                        <columnTitle>RhCMV Vaccines?</columnTitle>
-                    </column>
-                    <column columnName="sivArt">
-                        <columnTitle>SIV/ART Projects?</columnTitle>
-                    </column>
                 </columns>
                 <titleColumn>categories</titleColumn>
             </table>

SivStudies/resources/queries/study/demographicsProjects.sql

@@ -2,10 +2,9 @@ SELECT
   s.Id,
   count(s.Id) as totalProjects,
   group_concat(DISTINCT s.study, char(10)) as allStudies,
+  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,
+  group_concat(DISTINCT s.subgroup, char(10)) as subgroups
 
-  GROUP_CONCAT(distinct CASE WHEN s.category = 'RhCMV-Vaccines' THEN 'Yes' ELSE null END, char(10)) as rhCmvVaccines,
-  GROUP_CONCAT(distinct CASE WHEN s.category = 'SIV/ART' THEN 'Yes' ELSE null END, char(10)) as sivArt
 FROM study.assignment s
 GROUP BY s.Id

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

@@ -9,6 +9,9 @@
                         <columnTitle>Start Date</columnTitle>
                         <formatString>Date</formatString>
                     </column>
+                    <column columnName="tissue">
+                        <columnTitle>Tissue</columnTitle>
+                    </column>
                     <column columnName="sampleType">
                         <columnTitle>Sample Type</columnTitle>
                     </column>
@@ -18,8 +21,14 @@
                     <column columnName="population">
                         <columnTitle>Population</columnTitle>
                     </column>
-                    <column columnName="result">
-                        <columnTitle>Result</columnTitle>
+                    <column columnName="parentPopulation">
+                        <columnTitle>Parent Population</columnTitle>
+                    </column>
+                    <column columnName="percentOfParent">
+                        <columnTitle>% of Parent</columnTitle>
+                    </column>
+                    <column columnName="absoluteCount">
+                        <columnTitle>Absolute Count</columnTitle>
                     </column>
                     <column columnName="units">
                         <columnTitle>Units</columnTitle>