More query improvements

Author: bbimber

SivStudies/resources/queries/study/demographicsChallengeAndArt.sql

@@ -11,7 +11,7 @@ FROM (
       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 (t.treatment || ' (' || t.timePostSivChallenge.timePostInfection || ')')
+          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.sql

@@ -1,6 +1,6 @@
 SELECT
     t.Id,
-    group_concat(DISTINCT (t.treatment || ' (' || t.timePostSivChallenge.timePostInfection || ')'), char(10)) as allInterventions,
+    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,

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/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);