Merge branch 'discvr-25.11' into 25.11_fb_25.7_merge

Author: bbimber

.github/dependabot.yml

@@ -4,4 +4,4 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "daily"
+      interval: "weekly"

.github/workflows/branch_release.yml

@@ -8,6 +8,10 @@ on:
     tags:
       - '*'
 
+permissions:
+  pull-requests: write
+  contents: write
+
 jobs:
   branch_release:
     if: github.event.created && github.event.sender.login == 'labkey-teamcity'

.github/workflows/merge_release.yml

@@ -8,6 +8,10 @@ on:
     types:
       - submitted
 
+permissions:
+  pull-requests: write
+  contents: write
+
 jobs:
   merge_release:
     if: >

.github/workflows/validate_pr.yml

@@ -10,6 +10,9 @@ on:
       - reopened
       - ready_for_review
 
+permissions:
+  pull-requests: write
+
 jobs:
   validate_pr:
     if: github.event.pull_request.head.repo.owner.login == 'LabKey'

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

@@ -23,6 +23,7 @@
 import org.labkey.api.data.DbSchemaType;
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleContext;
+import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.module.SpringModule;
 import org.labkey.api.query.DefaultSchema;
 import org.labkey.api.query.DetailsURL;
@@ -100,7 +101,8 @@ public boolean isAvailable(DefaultSchema schema, Module module)
         {
             modules = new HashSet<>(modules);
             modules.add(this);
-            ContainerManager.getSharedContainer().setActiveModules(modules);
+            if (ModuleLoader.getInstance().shouldInsertData())
+                ContainerManager.getSharedContainer().setActiveModules(modules);
         }
     }
 
@@ -117,7 +119,7 @@ public boolean isAvailable(DefaultSchema schema, Module module)
     }
 
     @Override
-    public @NotNull Set<Class> getIntegrationTests()
+    public @NotNull Set<Class<?>> getIntegrationTests()
     {
         return PageFlowUtil.set(LdapSyncRunner.TestCase.class);
     }

OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSyncAuditProvider.java

@@ -36,8 +36,8 @@ public class LdapSyncAuditProvider extends AbstractAuditTypeProvider implements
 
     static final List<FieldKey> defaultVisibleColumns = new ArrayList<>();
 
-    static {
-
+    static
+    {
         defaultVisibleColumns.add(FieldKey.fromParts(COLUMN_NAME_CREATED));
         defaultVisibleColumns.add(FieldKey.fromParts(COLUMN_NAME_CREATED_BY));
         defaultVisibleColumns.add(FieldKey.fromParts(COLUMN_NAME_IMPERSONATED_BY));
@@ -47,6 +47,11 @@ public class LdapSyncAuditProvider extends AbstractAuditTypeProvider implements
         defaultVisibleColumns.add(FieldKey.fromParts(COLUMN_NAME_COMMENT));
     }
 
+    public LdapSyncAuditProvider()
+    {
+        super(new LdapSyncAuditDomainKind());
+    }
+
     @Override
     public String getEventName()
     {
@@ -68,7 +73,7 @@ public String getDescription()
     @Override
     public TableInfo createTableInfo(UserSchema userSchema, ContainerFilter cf)
     {
-        DefaultAuditTypeTable table = new DefaultAuditTypeTable(this, createStorageTableInfo(), userSchema, cf, defaultVisibleColumns)
+        return new DefaultAuditTypeTable(LdapSyncAuditProvider.this, createStorageTableInfo(), userSchema, cf, defaultVisibleColumns)
         {
             @Override
             protected void initColumn(MutableColumnInfo col)
@@ -87,7 +92,6 @@ else if (COLUMN_NAME_MEMBERSHIPS_CHANGED.equalsIgnoreCase(col.getName()))
                 }
             }
         };
-        return table;
     }
 
     @Override
@@ -96,12 +100,6 @@ public List<FieldKey> getDefaultVisibleColumns()
         return defaultVisibleColumns;
     }
 
-    @Override
-    protected AbstractAuditDomainKind getDomainKind()
-    {
-        return new LdapSyncAuditDomainKind();
-    }
-
     @Override
     public Map<FieldKey, String> legacyNameMap()
     {

QueryExtensions/src/org/labkey/queryextensions/QueryExtensionsModule.java

@@ -40,7 +40,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 23.000;
+        return 25.000;
     }
 
     @Override
@@ -81,4 +81,4 @@ public Set<String> getSchemaNames()
     {
         return Collections.singleton(QueryExtensionsSchema.NAME);
     }
-}
+}

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/RefNtSequenceModel.java

@@ -61,8 +61,8 @@ public class RefNtSequenceModel implements Serializable
     private String _name;
     //deprecated
     private String _sequence;
-    private Integer _sequenceFile;
-    private Integer _jobId;
+    private Long _sequenceFile;
+    private Long _jobId;
     private String _category;
     private String _subset;
     private String _locus;
@@ -171,12 +171,12 @@ public void setSequence(String sequence)
         _sequence = sequence;
     }
 
-    public Integer getSequenceFile()
+    public Long getSequenceFile()
     {
         return _sequenceFile;
     }
 
-    public void setSequenceFile(Integer sequenceFile)
+    public void setSequenceFile(Long sequenceFile)
     {
         _sequenceFile = sequenceFile;
     }
@@ -361,12 +361,12 @@ public void setModified(Date modified)
         _modified = modified;
     }
 
-    public Integer getJobId()
+    public Long getJobId()
     {
         return _jobId;
     }
 
-    public void setJobId(Integer jobId)
+    public void setJobId(Long jobId)
     {
         _jobId = jobId;
     }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceAnalysisService.java

@@ -69,7 +69,7 @@ static public void setInstance(SequenceAnalysisService instance)
 
     abstract public ReadData getReadData(int rowId, User u);
 
-    abstract public Readset getReadset(int readsetId, User u);
+    abstract public Readset getReadset(long readsetId, User u);
 
     abstract public ReferenceGenome getReferenceGenome(int rowId, User u) throws PipelineJobException;
 
@@ -87,7 +87,7 @@ static public void setInstance(SequenceAnalysisService instance)
 
     abstract public String getUnzippedBaseName(String filename);
 
-    abstract public Integer getExpRunIdForJob(PipelineJob job, boolean throwUnlessFound) throws PipelineJobException;
+    abstract public Long getExpRunIdForJob(PipelineJob job, boolean throwUnlessFound) throws PipelineJobException;
 
     abstract public List<PedigreeRecord> generatePedigree(Collection<String> sampleNames, Container c, User u, DemographicsProvider d);
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceOutputFile.java

@@ -37,11 +37,11 @@ public class SequenceOutputFile implements Serializable
     private Integer _rowid;
     private String _name;
     private String _description;
-    private Integer _dataId;
+    private Long _dataId;
     private Integer _library_id;
-    private Integer _readset;
-    private Integer _analysis_id;
-    private Integer _runid;
+    private Long _readset;
+    private Long _analysis_id;
+    private Long _runid;
     private String _category;
     private Boolean _intermediate;
     private String _container;
@@ -86,12 +86,12 @@ public void setDescription(String description)
         _description = description;
     }
 
-    public Integer getDataId()
+    public Long getDataId()
     {
         return _dataId;
     }
 
-    public void setDataId(Integer dataId)
+    public void setDataId(Long dataId)
     {
         _dataId = dataId;
     }
@@ -106,32 +106,32 @@ public void setLibrary_id(Integer library_id)
         _library_id = library_id;
     }
 
-    public Integer getReadset()
+    public Long getReadset()
     {
         return _readset;
     }
 
-    public void setReadset(Integer readset)
+    public void setReadset(Long readset)
     {
         _readset = readset;
     }
 
-    public Integer getAnalysis_id()
+    public Long getAnalysis_id()
     {
         return _analysis_id;
     }
 
-    public void setAnalysis_id(Integer analysis_id)
+    public void setAnalysis_id(Long analysis_id)
     {
         _analysis_id = analysis_id;
     }
 
-    public Integer getRunId()
+    public Long getRunId()
     {
         return _runid;
     }
 
-    public void setRunId(Integer runid)
+    public void setRunId(Long runid)
     {
         _runid = runid;
     }