Merge remote-tracking branch 'origin/develop' into fb_filesystemlike

Author: labkey-matthewb

PMR/resources/queries/study/demographicsParents.sql

@@ -34,26 +34,27 @@ SELECT
 
   (CASE WHEN p3.parent IS NOT NULL THEN 1 ELSE 0 END +
   CASE WHEN coalesce(p2.parent, b.dam) IS NOT NULL THEN 1 ELSE 0 END +
-  CASE WHEN coalesce(p1.parent, b.sire) IS NOT NULL THEN 1 ELSE 0 END) as numParents
+  CASE WHEN coalesce(p1.parent, b.sire) IS NOT NULL THEN 1 ELSE 0 END) as numParents,
+  greatest(d.modified, p1.modified, p2.modified, p3.modified, b.modified) as modified
 
 FROM  study.demographics d
 
 LEFT JOIN (
-  select p1.id, min(p1.method) as method, max(p1.parent) as parent
+  select p1.id, min(p1.method) as method, max(p1.parent) as parent, max(p1.modified) as modified
   FROM study.parentage p1
   WHERE (p1.method = 'Genetic' OR p1.method = 'Provisional Genetic') AND p1.relationship = 'Sire' AND p1.enddate IS NULL
   GROUP BY p1.Id
 ) p1 ON (d.Id = p1.id)
 
 LEFT JOIN (
-  select p2.id, min(p2.method) as method, max(p2.parent) as parent
+  select p2.id, min(p2.method) as method, max(p2.parent) as parent, max(p2.modified) as modified
   FROM study.parentage p2
   WHERE (p2.method = 'Genetic' OR p2.method = 'Provisional Genetic') AND p2.relationship = 'Dam' AND p2.enddate IS NULL
   GROUP BY p2.Id
 ) p2 ON (d.Id = p2.id)
 
 LEFT JOIN (
-  select p3.id, min(p3.method) as method, max(p3.parent) as parent
+  select p3.id, min(p3.method) as method, max(p3.parent) as parent, max(p3.modified) as modified
   FROM study.parentage p3
   WHERE p3.relationship = 'Foster Dam' AND p3.enddate IS NULL
   GROUP BY p3.Id

PMR/resources/queries/study/pedigree.sql

@@ -23,7 +23,8 @@ AS status,
 d.id.demographics.calculated_status as status_code,
 d.id.demographics.species,
 '' as Display,
-'Demographics' as source
+'Demographics' as source,
+d.modified
 
 FROM study.demographicsParents d
 WHERE d.numParents > 0 and d.id.demographics.species IS NOT NULL

mcc/resources/queries/study/pedigree.sql

@@ -23,7 +23,8 @@ AS status,
 d.id.demographics.calculated_status as status_code,
 d.id.demographics.species,
 '' as Display,
-'Demographics' as source
+'Demographics' as source,
+d.modified
 
 FROM study.demographicsParents d
 WHERE d.numParents > 0 and d.id.demographics.species IS NOT NULL

mcc/src/org/labkey/mcc/etl/ZimsImportTask.java

@@ -7,6 +7,7 @@
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
@@ -231,7 +232,7 @@ private void insertDatasetRecords(PipelineJob job, List<Map<String, Object>> toI
 
     public static void saveLastRun(Container container, Date jobStart)
     {
-        PropertyManager.PropertyMap map = PropertyManager.getWritableProperties(container, PROP_CATEGORY, true);
+        WritablePropertyMap map = PropertyManager.getWritableProperties(container, PROP_CATEGORY, true);
         if (jobStart != null)
         {
             map.put(lastRunTime, String.valueOf(jobStart.getTime()));

primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java

@@ -168,8 +168,8 @@ public Integer getMaxRequestMemory(PipelineJob job)
         // NOTE: STAR in particular needs more memory
         if (isCacheAlignerIndexesTask(job))
         {
-            job.getLogger().debug("setting memory to 24");
-            return 24;
+            job.getLogger().debug("setting memory to 36");
+            return 36;
         }
 
         if (isLuceneIndexJob(job))