Merge pull request #284 from LabKey/fb_merge_25.11_to_develop

Merge discvr-25.11 to develop

Author: bbimber

GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java

@@ -320,7 +320,7 @@ private void processSet(String assayType, Map<Integer, List<Map<String, Object>>
                 }
                 catch (Exception e)
                 {
-                    _log.error(e);
+                    _log.error(e.getMessage(), e);
                     throw new IllegalArgumentException(e.getMessage());
                 }
             }

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

@@ -33,7 +33,7 @@
                             <fkDbSchema>studies</fkDbSchema>
                             <fkTable>studyCohorts</fkTable>
                             <fkColumnName>rowId</fkColumnName>
-                            <fkDisplayColumnName>labelOrName</fkDisplayColumnName>
+                            <fkDisplayColumnName>studyAndCohort</fkDisplayColumnName>
                         </fk>
                     </column>
                     <column columnName="description">

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

@@ -0,0 +1,12 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="duplicatePVLs" tableDbType="NOT_IN_DB">
+                <tableTitle>Duplicate PVLs</tableTitle>
+                <columns>
+
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

SivStudies/resources/queries/study/duplicatePVLs.sql

@@ -0,0 +1,21 @@
+SELECT
+    t.Id,
+    t.date,
+    t.sampleType,
+    t.assayType,
+    t.target,
+    t.result,
+    t.resultOORIndicator,
+    t.dataSource,
+    t.lsid,
+    t.created,
+    v.maxLsid,
+    CASE WHEN t.lsid = v.maxLsid THEN TRUE ELSE FALSE END as isMostRecent
+
+FROM study.viralLoads t
+         INNER JOIN (
+    SELECT v.Id, v.date, v.sampleType, v.assayType, max(v.lsid) as maxLsid
+    FROM study.viralLoads v
+    GROUP BY v.Id, v.date, v.sampleType, v.assayType
+    HAVING count(*) > 1
+) v ON (v.Id = t.Id AND v.date = t.date AND v.sampleType = t.sampleType AND v.assayType = t.assayType)

SivStudies/src/org/labkey/sivstudies/etl/PerformManualIdrStepsTask.java

@@ -95,6 +95,7 @@ private void pruneSivChallenges(PipelineJob pipelineJob) throws PipelineJobExcep
     private static final Pattern mir126_RE = Pattern.compile("miR[- ]{0,1}126",  Pattern.CASE_INSENSITIVE);
     private static final Pattern mir142_RE = Pattern.compile("miR[- ]{0,1}142",  Pattern.CASE_INSENSITIVE);
     private static final Pattern mir126_142_RE = Pattern.compile("miR[- ]{0,1}142[ ,-]{1,2}126",  Pattern.CASE_INSENSITIVE);
+    private static final Pattern pp71_RE = Pattern.compile("pp71",  Pattern.CASE_INSENSITIVE);
 
     private void updateVaccineInformation(PipelineJob pipelineJob) throws PipelineJobException
     {
@@ -133,6 +134,10 @@ else if (treatment.contains("RhCMV") && treatment.contains("d186-189"))
                 {
                     updatedRow.put("backbone", "68-1 d186-189");
                 }
+                else if (treatment.contains("RhCMV") && treatment.contains("pp71"))
+                {
+                    updatedRow.put("backbone", "68-1 delta-pp71");
+                }
             }
 
             if (treatment.toUpperCase().contains("MOCK"))

SivStudies/src/org/labkey/sivstudies/notification/SivStudiesDataValidationNotification.java

@@ -78,6 +78,7 @@ public String getEmailSubject(Container c)
         idsMissingFromDemographics(c, u, msg);
         missingArtRecord(c, u, msg);
         missingAnchorDates(c, u, msg);
+        duplicatePVLs(c, u, msg);
 
         if (!msg.isEmpty())
         {
@@ -128,7 +129,7 @@ private void genericQueryCheck(Container c, User u, StringBuilder msg, String sc
         if (count > 0)
         {
             msg.append("<b>WARNING: There are ").append(count).append(" " + message + "</b><br>\n");
-            msg.append("<p><a href='").append(getExecuteQueryUrl(c, schemaName, queryName, null)).append("'>Click here to view them</a><br>\n\n");
+            msg.append("<p><a href='").append(getExecuteQueryUrl(c, schemaName, queryName, null, filter)).append("'>Click here to view them</a><br>\n\n");
             msg.append("<hr>\n\n");
         }
     }
@@ -161,7 +162,7 @@ private void missingArtRecord(Container c, User u, StringBuilder msg)
         SimpleFilter filter = new SimpleFilter(FieldKey.fromString("projects/studyDescription"), "ART", CompareType.CONTAINS);
         filter.addCondition(FieldKey.fromString("projects/studyDescription"), "No ART", CompareType.DOES_NOT_CONTAIN);
         filter.addCondition(FieldKey.fromString("sivART/artInitiationDPI"), null, CompareType.ISBLANK);
-        genericQueryCheck(c, u, msg, "study", s.getSubjectNounSingular(), "IDs assigned to an ART study without a record of ART", filter);
+        genericQueryCheck(c, u, msg, "study", "demographics", "IDs assigned to an ART study without a record of ART", filter);
     }
 
     private void missingAnchorDates(Container c, User u, StringBuilder msg)
@@ -175,6 +176,17 @@ private void missingAnchorDates(Container c, User u, StringBuilder msg)
         genericQueryCheck(c, u, msg, "study", "missingAnchorDates", "records missing from the anchor dates table");
     }
 
+    private void duplicatePVLs(Container c, User u, StringBuilder msg)
+    {
+        Study s = StudyService.get().getStudy(getTargetContainer(c));
+        if (s == null)
+        {
+            return;
+        }
+
+        genericQueryCheck(c, u, msg, "study", "duplicatePVLs", "duplicate PVL records");
+    }
+
     protected Container getTargetContainer(Container c)
     {
         return c.isWorkbookOrTab() ? c.getParent() : c;

mGAP/src/org/labkey/mgap/mGAPController.java

@@ -877,7 +877,7 @@ public boolean handlePost(Object o, BindException errors) throws Exception
             }
             catch (Exception e)
             {
-                _log.error(e);
+                _log.error(e.getMessage(), e);
                 throw e;
             }