Merge pull request #289 from LabKey/fb_merge_26.3_to_develop

Merge discvr-26.3 to develop

Author: bbimber

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

@@ -110,7 +110,7 @@ public void doStartupAfterSpringConfig(ModuleContext moduleContext)
 
         ContentSecurityPolicyFilter.registerAllowedSources(this.getClass().getName(), Directive.Connection, "https://code.jquery.com", "https://*.fontawesome.com");
         ContentSecurityPolicyFilter.registerAllowedSources(this.getClass().getName(), Directive.Style, "https://code.jquery.com", "https://www.gstatic.com");
-        ContentSecurityPolicyFilter.registerAllowedSources(this.getClass().getName(), Directive.Font, "https://*.fontawesome.com", "https://fonts.googleapis.com");
+        ContentSecurityPolicyFilter.registerAllowedSources(this.getClass().getName(), Directive.Font, "https://*.fontawesome.com", "https://fonts.googleapis.com", "https://fonts.gstatic.com");
         ContentSecurityPolicyFilter.registerAllowedSources(this.getClass().getName(), Directive.Connection, "https://oss.maxcdn.com");
 
         new PipelineStartup();

mcc/package-lock.json

@@ -26,7 +26,7 @@
     "google-palette": "^1.1.1"
   },
   "devDependencies": {
-    "@labkey/build": "^8.4.0",
+    "@labkey/build": "^9.1.0",
     "@types/chart.js": "^2.9.41",
     "@types/jexl": "^2.3.4",
     "@types/jquery": "^3.5.32",

mcc/package.json

@@ -14,6 +14,7 @@
                 </sourceColumns>
                 <sourceFilters>
                     <sourceFilter column="sire" operator="isnonblank" value=""/>
+                    <sourceFilter column="date" operator="isnonblank" value=""/>
                 </sourceFilters>
             </source>
             <destination schemaName="study" queryName="parentage" targetOption="truncate" bulkLoad="true">
@@ -41,6 +42,7 @@
                 </sourceColumns>
                 <sourceFilters>
                     <sourceFilter column="dam" operator="isnonblank" value=""/>
+                    <sourceFilter column="date" operator="isnonblank" value=""/>
                 </sourceFilters>
             </source>
             <destination schemaName="study" queryName="parentage" targetOption="append" bulkLoad="true">

mcc/resources/etls/snprc-parentage.xml

@@ -20,6 +20,8 @@ function onInit(event, helper){
 }
 
 function onUpsert(helper, scriptErrors, row, oldRow){
+    row.objectId = row.objectId || (oldRow ? oldRow.objectId : null) || LABKEY.Utils.generateUUID().toUpperCase()
+
     if (row.status && row.status.match(/Undetermined/)) {
         row.status = 'Unknown';
     }

mcc/resources/queries/study/demographics.js

@@ -10,6 +10,7 @@
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.DbSchemaType;
+import org.labkey.api.data.DbScope;
 import org.labkey.api.data.DbSequence;
 import org.labkey.api.data.DbSequenceManager;
 import org.labkey.api.data.SimpleFilter;
@@ -29,6 +30,7 @@
 import org.labkey.api.security.ValidEmail;
 import org.labkey.api.security.permissions.DeletePermission;
 import org.labkey.api.settings.AppProps;
+import org.labkey.api.study.StudyService;
 import org.labkey.api.util.MailHelper;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.view.UnauthorizedException;
@@ -45,6 +47,7 @@
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 import java.util.Set;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;
@@ -281,16 +284,14 @@ public void possiblySendRabNotification(int reviewerId)
         }
     }
 
-    private TableInfo _mappingTable = null;
-
     private TableInfo getMappingTable()
     {
-        if (_mappingTable == null)
+        if (_animalMapping == null)
         {
-            _mappingTable = QueryService.get().getUserSchema(_user, _container, MccSchema.NAME).getTable(MccSchema.TABLE_ANIMAL_MAPPING);
+            _animalMapping = QueryService.get().getUserSchema(_user, _container, MccSchema.NAME).getTable(MccSchema.TABLE_ANIMAL_MAPPING);
         }
 
-        return _mappingTable;
+        return _animalMapping;
     }
 
     public @Nullable String getMccAlias(String id) {
@@ -299,6 +300,12 @@ private TableInfo getMappingTable()
 
     public int ensureMccAliasExists(Collection<String> rawIds, Map<Object, Object> existingAliases)
     {
+        if (DbScope.getLabKeyScope().getCurrentTransaction() != null && Objects.requireNonNull(DbScope.getLabKeyScope().getCurrentTransaction()).isAborted())
+        {
+            _log.info("No active transaction, skipping MCC ensureMccAliasExists()");
+            return 0;
+        }
+
         // NOTE: The incoming object can convert numeric IDs from strings to int, so manually convert:
         // Also, CaseInsensitiveSet will convert the keys to lowercase, which is problematic for case-sensitive databases
         final CaseInsensitiveHashMap<String> idMap = new CaseInsensitiveHashMap<>();
@@ -313,7 +320,8 @@ public int ensureMccAliasExists(Collection<String> rawIds, Map<Object, Object> e
         TableInfo ti = getMappingTable();
         new TableSelector(ti, PageFlowUtil.set("subjectname", "externalAlias"), filter, null).forEachResults(rs -> {
             aliasesFound.add(rs.getString(FieldKey.fromString("subjectname")));
-            if (ciExistingAliases.containsKey(rs.getString(FieldKey.fromString("subjectname")))) {
+            if (ciExistingAliases.containsKey(rs.getString(FieldKey.fromString("subjectname"))))
+            {
                 if (!ciExistingAliases.get(rs.getString(FieldKey.fromString("subjectname"))).equalsIgnoreCase(rs.getString(FieldKey.fromString("externalAlias"))))
                 {
                     _log.error("Incoming MCC alias for: " + rs.getString(FieldKey.fromString("subjectname")) + "(" + ciExistingAliases.get(rs.getString(FieldKey.fromString("subjectname"))) + ") does not match existing: " + rs.getString(FieldKey.fromString("externalAlias")));

mcc/src/org/labkey/mcc/query/TriggerHelper.java

@@ -38,7 +38,6 @@ public List<ToolParameterDescriptor> getParams()
                 ToolParameterDescriptor.create("localDisk", "Local Disk (GB)", "Do not change this unless you are certain.  Each job requests and uses local space (/mnt/scratch) for temp files.  If your job will require more space, consider increasing this.", "ldk-integerfield", new JSONObject(){{
                     put("minValue", 512);
                 }}, 1028),
-                ToolParameterDescriptor.create("localSSD", "Request Nodes With SSD Scratch", "If selected, -C ssdscratch will be added to the submit script, which limits to node with faster SSD scratch space.  This might be important for I/O intense jobs.", "checkbox", null, null),
                 ToolParameterDescriptor.create("gpus", "GPUs", "The number of GPUs requested for this job. If non-zero, the gpu partition will be used.", "ldk-integerfield", null, null),
                 ToolParameterDescriptor.create("useExperimentalPartition", "Use RHEL 9.6 Partition", "If selected, jobs will be submitted to the experimental rhel96TESTING partition.", "checkbox", null, null)
         );

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

@@ -330,7 +330,6 @@ public void addExtraSubmitScriptLines(PipelineJob job, RemoteExecutionEngine<?>
             possiblyAddQOS(job, engine, lines);
             possiblyAddHighIO(job, engine, lines);
             possiblyAddDisk(job, engine, lines);
-            possiblyAddSSD(job, engine, lines);
             possiblyAddGpus(job, engine, lines);
             possiblyAddExclusive(job, engine, lines);
         }
@@ -490,27 +489,6 @@ private void possiblyAddExclusive(PipelineJob job, RemoteExecutionEngine<?> engi
         }
     }
 
-    private void possiblyAddSSD(PipelineJob job, RemoteExecutionEngine<?> engine, List<String> lines)
-    {
-        Map<String, String> params = ((HasJobParams)job).getJobParams();
-        String val = StringUtils.trimToNull(params.get("resourceSettings.resourceSettings.localSSD"));
-        if (val == null)
-        {
-            return;
-        }
-
-        boolean parsed = Boolean.parseBoolean(val);
-        if (parsed)
-        {
-            job.getLogger().info("Requiring local SSD scratch space");
-            String line = "#SBATCH -C ssdscratch";
-            if (!lines.contains(line))
-            {
-                lines.add(line);
-            }
-        }
-    }
-
     private void possiblyAddQOS(PipelineJob job, RemoteExecutionEngine<?> engine, List<String> lines)
     {
         //first remove existing