Merge branch '25.3_fb_studydef' of github.com:BimberLab/DiscvrLabKeyModules into 25.3_fb_studydef

Author: Sebastian Benjamin

SequenceAnalysis/build.gradle

@@ -44,6 +44,7 @@ dependencies {
     BuildUtils.addLabKeyDependency(project: project, config: "apiImplementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile")
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
     BuildUtils.addLabKeyDependency(project: project, config: "apiImplementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
+    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:discvrcore", depProjectConfig: "apiJarFile")
     BuildUtils.addExternalDependency(
             project,
             new ExternalDependency(

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java

@@ -72,6 +72,7 @@
 import org.labkey.api.data.Table;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
+import org.labkey.api.discvrcore.annotation.UtilityAction;
 import org.labkey.api.exceptions.OptimisticConflictException;
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.exp.api.DataType;
@@ -501,6 +502,7 @@ public void export(ConvertTextToFileForm form, HttpServletResponse response, Bin
         }
     }
 
+    @UtilityAction(label = "Find Orphan Files", description = "This will start a pipeline job that will inspect all files in this folder to identify potential orphan or otherwise unnecessary files")
     @RequiresPermission(ReadPermission.class)
     public static class FindOrphanFilesAction extends ConfirmAction<Object>
     {
@@ -5065,6 +5067,7 @@ public void setOutputFileIds(Integer[] outputFileIds)
         }
     }
 
+    @UtilityAction(label = "Update ExpData Path", description = "This will update the DataFileUrl on the selected ExpData to the path provided")
     @RequiresSiteAdmin
     public static class UpdateExpDataPathAction extends ConfirmAction<UpdateExpDataPathForm>
     {

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceProvider.java

@@ -236,17 +236,17 @@ public List<TabbedReportItem> getTabbedReportItems(Container c, User u)
         TabbedReportItem analyses = new QueryTabbedReportItem(cache, this, SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_ANALYSES, "Sequence Analyses", category);
         analyses.setSubjectIdFieldKey(FieldKey.fromString("readset/subjectid"));
         analyses.setSampleDateFieldKey(FieldKey.fromString("readset/sampledate"));
-        analyses.setAllProjectsFieldKey(FieldKey.fromString("readset/allProjectsPivot"));
-        analyses.setOverlappingProjectsFieldKey(FieldKey.fromString("readset/overlappingProjectsPivot"));
+        analyses.setKeyOverride("allProjectsFieldName", FieldKey.fromString("readset/allProjectsPivot"));
+        analyses.setKeyOverride("overlappingProjectsFieldName", FieldKey.fromString("readset/overlappingProjectsPivot"));
         analyses.setOwnerKey(owner.getPropertyManagerKey());
         analyses.setVisible(owner.isVisible(c, u));
         items.add(analyses);
 
         TabbedReportItem outputs = new QueryTabbedReportItem(cache, this, SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_OUTPUTFILES, "Sequence Outputs", category);
         outputs.setSubjectIdFieldKey(FieldKey.fromString("readset/subjectid"));
         outputs.setSampleDateFieldKey(FieldKey.fromString("readset/sampledate"));
-        outputs.setAllProjectsFieldKey(FieldKey.fromString("readset/allProjectsPivot"));
-        outputs.setOverlappingProjectsFieldKey(FieldKey.fromString("readset/overlappingProjectsPivot"));
+        outputs.setKeyOverride("allProjectsFieldName", FieldKey.fromString("readset/allProjectsPivot"));
+        outputs.setKeyOverride("overlappingProjectsFieldName", FieldKey.fromString("readset/overlappingProjectsPivot"));
         outputs.setOwnerKey(owner.getPropertyManagerKey());
         outputs.setVisible(owner.isVisible(c, u));
         items.add(outputs);

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java

@@ -344,6 +344,8 @@ public void getOrphanFilesForContainer(Container c, User u, Set<File> orphanFile
                 return;
             }
 
+
+            getJob().updateStatusForTask();
             if (getJob().isCancelled())
             {
                 throw new CancelledException();

…udies/query/ResultsOOODisplayColumn.java …udies/query/ResultsOORDisplayColumn.javaStudies/src/org/labkey/studies/query/ResultsOOODisplayColumn.java renamed to Studies/api-src/org/labkey/api/studies/query/ResultsOORDisplayColumn.java Studies/src/org/labkey/studies/query/ResultsOOODisplayColumn.java renamed to Studies/api-src/org/labkey/api/studies/query/ResultsOORDisplayColumn.java

@@ -1,4 +1,4 @@
-package org.labkey.studies.query;
+package org.labkey.api.studies.query;
 
 import org.apache.commons.lang3.StringUtils;
 import org.labkey.api.data.ColumnInfo;
@@ -9,9 +9,9 @@
 import java.text.DecimalFormat;
 import java.util.Set;
 
-public class ResultsOOODisplayColumn extends DataColumn
+public class ResultsOORDisplayColumn extends DataColumn
 {
-    public ResultsOOODisplayColumn(ColumnInfo col)
+    public ResultsOORDisplayColumn(ColumnInfo col)
     {
         super(col);
     }
@@ -48,15 +48,15 @@ public Object getDisplayValue(RenderContext ctx)
 
     private FieldKey getOOR()
     {
-        FieldKey oor = FieldKey.fromString("resultOOOIndicator");
-        if (getBoundColumn() != null)
+        ColumnInfo col = getBoundColumn();
+        if (col == null)
         {
-            return FieldKey.fromParts(getBoundColumn().getFieldKey().getParent(), oor);
-        }
-        else
-        {
-            return oor;
+            return null;
         }
+
+        FieldKey oor = FieldKey.fromString(col.getFieldKey().getName() + "OORIndicator");
+
+        return getBoundColumn().getFieldKey().getParent() == null ? oor : FieldKey.fromParts(getBoundColumn().getFieldKey().getParent(), oor);
     }
 
     @Override

Studies/resources/schemas/dbscripts/postgresql/studies-23.002-23.003.sql

@@ -0,0 +1,15 @@
+CREATE TABLE studies.subjectAnchorDates (
+    rowid serial,
+    subjectId varchar(4000),
+    date int,
+    eventLabel varchar(1000),
+    anchorEventId int,
+
+    container entityid,
+    created timestamp,
+    createdby int,
+    modified timestamp,
+    modifiedby int,
+
+    CONSTRAINT PK_subjectAnchorDates PRIMARY KEY (rowid)
+);

Studies/resources/schemas/dbscripts/postgresql/studies-23.003-23.004.sql

@@ -0,0 +1,2 @@
+ALTER TABLE studies.subjectAnchorDates DROP COLUMN date;
+ALTER TABLE studies.subjectAnchorDates ADD COLUMN date timestamp;

Studies/resources/schemas/dbscripts/postgresql/studies-23.004-23.005.sql

@@ -0,0 +1 @@
+ALTER TABLE studies.subjectAnchorDates ADD COLUMN dataSource varchar(1000);

Studies/resources/schemas/dbscripts/sqlserver/studies-23.002-23.003.sql

@@ -0,0 +1,15 @@
+CREATE TABLE studies.subjectAnchorDates (
+    rowid int identity(1,1),
+    subjectId varchar(4000),
+    date int,
+    eventLabel varchar(1000),
+    anchorEventId int,
+
+    container entityid,
+    created datetime,
+    createdby int,
+    modified datetime,
+    modifiedby int,
+
+    CONSTRAINT PK_subjectAnchorDates PRIMARY KEY (rowid)
+);

Studies/resources/schemas/dbscripts/sqlserver/studies-23.003-23.004.sql

@@ -0,0 +1,2 @@
+ALTER TABLE studies.subjectAnchorDates DROP COLUMN date;
+ALTER TABLE studies.subjectAnchorDates ADD date datetime;