Merge discvr-25.11 to develop

OpenLdapSync/src/org/labkey/openldapsync/OpenLdapSyncController.java

@@ -125,7 +125,7 @@ public ApiResponse execute(LdapForm form, BindException errors) throws Exception
             }
             catch (LdapException e)
             {
-                _log.error(e);
+                _log.error(e.getMessage(), e);
                 errors.reject(ERROR_MSG, e.getMessage());
                 return null;
             }
@@ -528,7 +528,7 @@ public ApiResponse execute(Object form, BindException errors) throws Exception
             }
             catch (Exception e)
             {
-                _log.error(e);
+                _log.error(e.getMessage(), e);
                 errors.reject(ERROR_MSG, e.getMessage() == null ? "unable to connect to LDAP server" : e.getMessage());
                 return null;
             }

SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.329-12.330.sql

@@ -0,0 +1,12 @@
+CREATE INDEX IDX_haplotypes_name_date ON sequenceanalysis.haplotypes
+(
+	Name ASC,
+	datedisabled ASC
+);
+
+CREATE INDEX IDX_haplotype_sequences_name_haplotype_type ON sequenceanalysis.haplotype_sequences
+(
+	haplotype ASC,
+	name ASC,
+	type ASC
+);

SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql

@@ -0,0 +1,39 @@
+CREATE NONCLUSTERED INDEX IDX_haplotypes_name_date ON sequenceanalysis.haplotypes
+(
+	Name ASC,
+	datedisabled ASC
+);
+
+CREATE NONCLUSTERED INDEX IDX_haplotype_sequences_name_haplotype_type ON sequenceanalysis.haplotype_sequences
+(
+	haplotype ASC,
+	name ASC,
+	type ASC
+);
+
+CREATE NONCLUSTERED INDEX IDX_alignment_summary_analysis_id_rowid_container_total ON sequenceanalysis.alignment_summary
+(
+	analysis_id ASC,
+	rowid ASC,
+	container ASC
+)
+INCLUDE(total)
+
+CREATE STATISTICS STAT_ref_nt_sequence_rowid_locus_container ON sequenceanalysis.ref_nt_sequences (RowId, locus, container)
+WITH AUTO_DROP = OFF
+
+CREATE STATISTICS STAT_ref_nt_sequence_locus_container ON sequenceanalysis.ref_nt_sequences (locus, container)
+WITH AUTO_DROP = OFF
+
+CREATE STATISTICS STAT_sequence_analyses_container_readset ON sequenceanalysis.sequence_analyses (Container, readset)
+WITH AUTO_DROP = OFF
+
+CREATE STATISTICS STAT_sequence_readsets_rowid_container ON sequenceanalysis.sequence_readsets (RowId, Container)
+WITH AUTO_DROP = OFF
+
+CREATE STATISTICS STAT_asj_alignmentid_container_ref_nt_id ON sequenceanalysis.alignment_summary_junction (alignment_id, container, ref_nt_id)
+WITH AUTO_DROP = OFF
+
+CREATE STATISTICS STAT_asj_alignmentid_ref_nt_id_status_alignment_id ON sequenceanalysis.alignment_summary_junction (ref_nt_id, status, alignment_id)
+WITH AUTO_DROP = OFF
+

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

@@ -1191,7 +1191,7 @@ public ApiResponse execute(ValidateReadsetImportForm form, BindException errors)
             {
                 ExceptionUtil.logExceptionToMothership(getViewContext().getRequest(), e);
                 errors.reject(ERROR_MSG, e.getMessage());
-                _log.error(e);
+                _log.error(e.getMessage(), e);
                 return null;
             }
             return new ApiSimpleResponse(resultProperties);
@@ -4818,7 +4818,7 @@ public ApiResponse execute(ImportTracksForm form, BindException errors) throws E
                 catch (IOException e)
                 {
                     errors.reject(ERROR_MSG, e.getMessage());
-                    _log.error(e);
+                    _log.error(e.getMessage(), e);
 
                     return null;
                 }
@@ -4834,7 +4834,7 @@ public ApiResponse execute(ImportTracksForm form, BindException errors) throws E
             catch (PipelineValidationException e)
             {
                 errors.reject(ERROR_MSG, e.getMessage());
-                _log.error(e);
+                _log.error(e.getMessage(), e);
 
                 return null;
             }

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

@@ -211,7 +211,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 12.329;
+        return 12.330;
     }
 
     @Override

SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java

@@ -136,7 +136,7 @@ public String extractAASequence(int refNtId, List<List<Number>> exons, boolean i
             }
             catch (IOException e)
             {
-                _log.error(e);
+                _log.error(e.getMessage(), e);
                 return null;
             }
         }

Studies/resources/module.xml

@@ -2,4 +2,11 @@
     <clientDependencies>
         <dependency path="LDK.context"/>
     </clientDependencies>
+    <properties>
+        <propertyDescriptor name="demographicsDefaultView">
+            <description>This view is used as the default on the demographics table</description>
+            <canSetPerContainer>true</canSetPerContainer>
+            <label>Demographics Default View</label>
+        </propertyDescriptor>
+    </properties>
 </module>

Studies/resources/views/manageStudy.html

@@ -13,24 +13,57 @@
 
                 const parentDiv = $('#' + webpart.wrapperDivId)
                 parentDiv.append('<div id="' + webpart.wrapperDivId + '-studyCohorts"></div>')
+                parentDiv.append('<div id="' + webpart.wrapperDivId + '-demographics"></div>')
                 parentDiv.append('<div id="' + webpart.wrapperDivId + '-anchorEvents"></div>')
                 parentDiv.append('<div id="' + webpart.wrapperDivId + '-expectedTimepoints"></div>')
 
                 LDK.Utils.getBasicQWP({
                     frame: 'portal',
                     title: 'Cohorts',
-                    name: 'query',
+                    name: 'query-studies',
                     schemaName: 'studies',
                     queryName: 'studyCohorts',
                     filterArray: [LABKEY.Filter.create('studyId',studyId, LABKEY.Filter.Types.EQUAL)],
                     maxRows: 20,
                     renderTo: webpart.wrapperDivId + '-studyCohorts'
                 }).render();
 
+                if (LABKEY.getModuleContext('study')?.subject) {
+                    const hasAssignmentDataset = !!LABKEY.getModuleContext('studies')?.hasAssignmentDataset
+                    if (hasAssignmentDataset) {
+                        LABKEY.Query.selectRows({
+                            schemaName: 'studies',
+                            queryName: 'studies',
+                            columns: 'rowId,studyName',
+                            filterArray: [LABKEY.Filter.create('rowId', studyId)],
+                            failure: LDK.Utils.getErrorCallback(),
+                            success: function(results) {
+                                const studyName = results.rows?.[0].studyName;
+                                LDK.Assert.assertNotEmpty('StudyName was empty in manageStudy.view', studyName);
+
+                                const projectFieldName = 'allProjectsPivot/' + studyName + '::lastStartDate';
+                                const demographicsDefaultView = LABKEY.getModuleProperty('studies', 'demographicsDefaultView')
+                                LDK.Utils.getBasicQWP({
+                                    frame: 'portal',
+                                    title: LABKEY.moduleContext.study?.subject.nounPlural,
+                                    name: 'query-demographics',
+                                    schemaName: 'study',
+                                    queryName: 'demographics',
+                                    viewName: demographicsDefaultView,
+                                    filterArray: [LABKEY.Filter.create(projectFieldName, null, LABKEY.Filter.Types.NONBLANK)],
+                                    maxRows: 20,
+                                    renderTo: webpart.wrapperDivId + '-demographics'
+                                }).render();
+                            },
+                            scope: this
+                        });
+                    }
+                }
+
                 LDK.Utils.getBasicQWP({
                     frame: 'portal',
                     title: 'Anchor Events',
-                    name: 'query',
+                    name: 'query-anchorEvents',
                     schemaName: 'studies',
                     queryName: 'anchorEvents',
                     filterArray: [LABKEY.Filter.create('studyId',studyId, LABKEY.Filter.Types.EQUAL)],
@@ -41,7 +74,7 @@
                 LDK.Utils.getBasicQWP({
                     frame: 'portal',
                     title: 'Expected Timepoints',
-                    name: 'query',
+                    name: 'query-expectedTimepoints',
                     schemaName: 'studies',
                     queryName: 'expectedTimepoints',
                     filterArray: [LABKEY.Filter.create('studyId',studyId, LABKEY.Filter.Types.EQUAL)],
@@ -54,6 +87,4 @@
 
 </script>
 
-
-PLACEHOLDER: Make a page that accepts a studyId and renders useful UI to manage timepoints, run QC, and show data
 <br><br>

Studies/src/org/labkey/studies/StudiesModule.java

@@ -2,6 +2,7 @@
 
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
+import org.json.JSONObject;
 import org.labkey.api.data.Container;
 import org.labkey.api.laboratory.LaboratoryService;
 import org.labkey.api.ldk.ExtendedSimpleModule;
@@ -11,9 +12,9 @@
 import org.labkey.api.query.QuerySchema;
 import org.labkey.api.security.roles.RoleManager;
 import org.labkey.api.studies.StudiesService;
-import org.labkey.api.util.PageFlowUtil;
-import org.labkey.studies.query.StudiesUserSchema;
 import org.labkey.api.studies.security.StudiesDataAdminRole;
+import org.labkey.api.writer.ContainerUser;
+import org.labkey.studies.query.StudiesUserSchema;
 import org.labkey.studies.study.StudiesFilterProvider;
 import org.labkey.studies.study.StudyEnrollmentEventProvider;
 
@@ -68,6 +69,16 @@ public Set<String> getSchemaNames()
         return Collections.singleton(StudiesSchema.NAME);
     }
 
+    @Override
+    public JSONObject getPageContextJson(ContainerUser context)
+    {
+        JSONObject json = super.getPageContextJson(context);
+
+        json.put("hasAssignmentDataset", StudiesServiceImpl.get().hasAssignmentDataset(context.getContainer()));
+
+        return json;
+    }
+
     @Override
     public void registerSchemas()
     {

Studies/src/org/labkey/studies/StudiesServiceImpl.java

@@ -21,6 +21,8 @@
 import org.labkey.api.security.User;
 import org.labkey.api.studies.StudiesService;
 import org.labkey.api.studies.study.EventProvider;
+import org.labkey.api.study.Study;
+import org.labkey.api.study.StudyService;
 import org.labkey.api.util.ConfigurationException;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.Path;
@@ -173,4 +175,17 @@ public TableCustomizer getStudiesTableCustomizer()
     {
         return new StudiesTableCustomizer();
     }
+
+    public static String ASSIGNMENT_DATASET = "assignment";
+
+    public boolean hasAssignmentDataset(Container c)
+    {
+        Study s = StudyService.get().getStudy(c.isWorkbookOrTab() ? c.getParent() : c);
+        if (s == null)
+        {
+            return false;
+        }
+
+        return s.getDatasetByName(ASSIGNMENT_DATASET) != null;
+    }
 }