Support BIGINT Primary Keys

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

@@ -57,7 +57,7 @@ public OpenLdapSyncController()
     }
 
     @RequiresPermission(AdminOperationsPermission.class)
-    public class InitiateLdapSyncAction extends MutatingApiAction<InitiateLdapSyncForm>
+    public static class InitiateLdapSyncAction extends MutatingApiAction<InitiateLdapSyncForm>
     {
         @Override
         public ApiResponse execute(InitiateLdapSyncForm form, BindException errors) throws Exception
@@ -100,7 +100,7 @@ public void setForPreview(boolean forPreview)
     }
 
     @RequiresPermission(AdminPermission.class)
-    public class ListLdapGroupsAction extends ReadOnlyApiAction<LdapForm>
+    public static class ListLdapGroupsAction extends ReadOnlyApiAction<LdapForm>
     {
         @Override
         public ApiResponse execute(LdapForm form, BindException errors) throws Exception
@@ -495,7 +495,7 @@ public void setMemberSyncMode(String memberSyncMode)
     }
 
     @RequiresPermission(AdminOperationsPermission.class)
-    public class TestLdapConnectionAction extends MutatingApiAction<Object>
+    public static class TestLdapConnectionAction extends MutatingApiAction<Object>
     {
         @Override
         public ApiResponse execute(Object form, BindException errors) throws Exception
@@ -545,7 +545,7 @@ public ApiResponse execute(Object form, BindException errors) throws Exception
     }
 
     @RequiresPermission(AdminOperationsPermission.class)
-    public class GetLdapSettingsAction extends ReadOnlyApiAction<Object>
+    public static class GetLdapSettingsAction extends ReadOnlyApiAction<Object>
     {
         @Override
         public ApiResponse execute(Object form, BindException errors)
@@ -569,7 +569,7 @@ public ApiResponse execute(Object form, BindException errors)
 
     @Marshal(Marshaller.Jackson)
     @RequiresPermission(AdminOperationsPermission.class)
-    public class SetLdapSettingsAction extends MutatingApiAction<LdapForm>
+    public static class SetLdapSettingsAction extends MutatingApiAction<LdapForm>
     {
         @Override
         public ApiResponse execute(LdapForm form, BindException errors)
@@ -668,7 +668,7 @@ public ApiResponse execute(LdapForm form, BindException errors)
             if (form.getSyncMode() != null)
                 props.put(LdapSettings.SYNC_MODE_PROP, form.getSyncMode());
 
-            if (form.getAllowedDn() != null && form.getAllowedDn().length() > 0)
+            if (form.getAllowedDn() != null && !form.getAllowedDn().isEmpty())
             {
                 String allowed = StringUtils.join(form.getAllowedDn().toList(), LdapSettings.DELIM);
                 props.put(LdapSettings.ALLOWED_DN_PROP, allowed);

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);
         }
     }
 

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

@@ -75,8 +75,8 @@ public boolean isEnabled()
 
         try
         {
-            Integer value = Integer.parseInt(a);
-            return (value.intValue() & 2) == 0;
+            int value = Integer.parseInt(a);
+            return (value & 2) == 0;
         }
         catch (NumberFormatException e)
         {

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

@@ -466,7 +466,6 @@ public Integer getFrequency()
 
     /**
      * Provides a brief sanity check of the settings, designed to identify problems if a sync will run.
-     * @throws LdapException
      */
     public void validateSettings() throws LdapException
     {
@@ -495,7 +494,7 @@ public void validateSettings() throws LdapException
 
         if (LdapSyncMode.groupWhitelist.equals(mode))
         {
-            if (getGroupWhiteList().size() == 0)
+            if (getGroupWhiteList().isEmpty())
             {
                 throw new LdapException("Cannot choose to sync based on specific groups unless you provide a list of groups to sync");
             }

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

@@ -6,6 +6,7 @@
 import org.labkey.api.audit.AuditTypeProvider;
 import org.labkey.api.audit.query.AbstractAuditDomainKind;
 import org.labkey.api.audit.query.DefaultAuditTypeTable;
+import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.MutableColumnInfo;
@@ -121,7 +122,7 @@ public <K extends AuditTypeEvent> Class<K> getEventClass()
     public static void addAuditEntry(User user, int usersAdded, int usersRemoved, int usersInactivated, int usersModified, int groupsAdded, int groupsRemoved, int membershipsAdded, int membershipsRemoved)
     {
         String comment = String.format("LDAP Sync Summary: users added: %s, users removed: %s, users inactivated: %s, users modified: %s, groups added: %s, groups removed: %s, memberships added: %s, memberships removed: %s", usersAdded, usersRemoved, usersInactivated, usersModified, groupsAdded, groupsRemoved, membershipsAdded, membershipsRemoved);
-        LdapSyncAuditProvider.LdapSyncAuditEvent event = new LdapSyncAuditProvider.LdapSyncAuditEvent(ContainerManager.getRoot().getId(), comment);
+        LdapSyncAuditProvider.LdapSyncAuditEvent event = new LdapSyncAuditProvider.LdapSyncAuditEvent(ContainerManager.getRoot(), comment);
 
         event.setTotalUsersAndGroupsAdded(usersAdded + groupsAdded);
         event.setTotalUsersAndGroupsRemoved(usersRemoved + groupsRemoved);
@@ -141,7 +142,7 @@ public LdapSyncAuditEvent()
             super();
         }
 
-        public LdapSyncAuditEvent(String container, String comment)
+        public LdapSyncAuditEvent(Container container, String comment)
         {
             super(LdapSyncRunner.AUDIT_EVENT_TYPE, container, comment);
         }

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

@@ -14,7 +14,6 @@
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.RuntimeSQLException;
-import org.labkey.api.data.Selector;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.Table;
 import org.labkey.api.data.TableInfo;
@@ -40,7 +39,6 @@
 import org.labkey.security.xml.GroupEnumType;
 import org.quartz.Job;
 import org.quartz.JobExecutionContext;
-import org.quartz.JobExecutionException;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -99,7 +97,7 @@ public LdapSyncRunner()
     }
 
     @Override
-    public void execute(JobExecutionContext context) throws JobExecutionException
+    public void execute(JobExecutionContext context)
     {
         try
         {
@@ -284,7 +282,7 @@ private void setUserActive(User u, boolean active, String reason)
         }
     }
 
-    private void handleGroupsRemovedFromLdap() throws LdapException
+    private void handleGroupsRemovedFromLdap()
     {
         //find any previously synced groups that are no longer present
         List<LdapSyncModel> records = getPreviouslySyncedRecords(PrincipalType.GROUP);
@@ -522,7 +520,7 @@ private void deactivatePrincipalsPreviouslySynced()
             previouslySynced.remove(syncedUser);
         }
 
-        if (previouslySynced.size() > 0)
+        if (!previouslySynced.isEmpty())
         {
             //TODO: determine whether to delete/deactive, etc?
             for (Integer userId : previouslySynced)
@@ -543,7 +541,7 @@ private void deactivatePrincipalsPreviouslySynced()
             previouslySyncedGroups.remove(syncedGroup);
         }
 
-        if (previouslySyncedGroups.size() > 0)
+        if (!previouslySyncedGroups.isEmpty())
         {
             //TODO: determine whether to delete/deactive, etc
             for (Integer groupId : previouslySyncedGroups)
@@ -569,14 +567,7 @@ private void initPreviouslySyncedRecords()
         SimpleFilter filter = new SimpleFilter(FieldKey.fromString("provider"), _wrapper.getProviderName(), CompareType.EQUAL);
         TableSelector ts = new TableSelector(ti, filter, null);
 
-        ts.forEach(LdapSyncModel.class, new Selector.ForEachBlock<LdapSyncModel>()
-        {
-            @Override
-            public void exec(LdapSyncModel model)
-            {
-                _syncedRecordMap.put(model.getSourceId(), model);
-            }
-        });
+        ts.forEach(LdapSyncModel.class, model -> _syncedRecordMap.put(model.getSourceId(), model));
     }
 
     private User createUser(LdapEntry ldapEntry) throws LdapException
@@ -702,7 +693,7 @@ private Group createGroup(String groupName)
 
         if (!_previewOnly)
         {
-            return SecurityManager.createGroup(getUserGroupContainer(), groupName);
+            return SecurityManager.createGroup(getUserGroupContainer(), groupName, _settings.getLabKeyAdminUser());
         }
         else
         {
@@ -712,11 +703,11 @@ private Group createGroup(String groupName)
 
     private void deleteGroup(Group g)
     {
-        log("Deleteing LabKey group: " + g.getName());
+        log("Deleting LabKey group: " + g.getName());
         _groupsRemoved++;
 
         if (!_previewOnly)
-            SecurityManager.deleteGroup(g);
+            SecurityManager.deleteGroup(g, _settings.getLabKeyAdminUser());
     }
 
     private void deleteUser(User u) throws LdapException
@@ -894,8 +885,7 @@ public void doSetup() throws Exception
             if (project == null)
             {
                 project = ContainerManager.createContainer(ContainerManager.getRoot(), PROJECT_NAME, TestContext.get().getUser());
-                Set<Module> modules = new HashSet<>();
-                modules.addAll(project.getActiveModules());
+                Set<Module> modules = new HashSet<>(project.getActiveModules());
                 modules.add(ModuleLoader.getInstance().getModule(OpenLdapSyncModule.NAME));
                 project.setActiveModules(modules);
             }
@@ -962,7 +952,7 @@ private void cleanUsersAndGroups() throws Exception
                 _log.info("Cleaning up group: "+ groupName);
                 Group g = GroupManager.getGroup(getProject(), groupName, GroupEnumType.PROJECT);
                 if (g != null)
-                    SecurityManager.deleteGroup(g);
+                    SecurityManager.deleteGroup(g, TestContext.get().getUser());
             }
         }
 
@@ -1067,7 +1057,7 @@ public void testIndividualOperations() throws Exception
         }
 
         // This can be used to return LdapEntry objects to support some degree of automated testing without needing a functional LDAP Server
-        public class DummyConnectionWrapper extends LdapConnectionWrapper
+        public static class DummyConnectionWrapper extends LdapConnectionWrapper
         {
             private final List<LdapEntry> _users = new ArrayList<>();
             private final Map<String, MockLdapEntry> _groupMap = new HashMap<>();

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

@@ -16,14 +16,7 @@
 
 package org.labkey.queryextensions;
 
-import org.labkey.api.action.SimpleViewAction;
 import org.labkey.api.action.SpringActionController;
-import org.labkey.api.security.RequiresPermission;
-import org.labkey.api.security.permissions.ReadPermission;
-import org.labkey.api.view.JspView;
-import org.labkey.api.view.NavTree;
-import org.springframework.validation.BindException;
-import org.springframework.web.servlet.ModelAndView;
 
 public class QueryExtensionsController extends SpringActionController
 {

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);
     }
-}
+}

QueryExtensions/test/src/org/labkey/test/tests/queryextensions/QueryExtensionsTest.java

@@ -39,7 +39,7 @@ protected void doCleanup(boolean afterTest) throws TestTimeoutException
     @BeforeClass
     public static void setupProject()
     {
-        QueryExtensionsTest init = (QueryExtensionsTest)getCurrentTest();
+        QueryExtensionsTest init = getCurrentTest();
 
         init.doSetup();
     }

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

@@ -16,7 +16,6 @@
 package org.labkey.api.sequenceanalysis;
 
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.labkey.api.data.Container;
 import org.labkey.api.security.User;
 

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);
 
@@ -113,10 +113,10 @@ static public void setInstance(SequenceAnalysisService instance)
 
     abstract public void registerReadsetListener(ReadsetListener listener);
 
-    public static interface ReadsetListener
+    public interface ReadsetListener
     {
-        public void onReadsetCreate(User u, Readset rs, @Nullable Readset replacedReadset, @Nullable PipelineJob job);
+        void onReadsetCreate(User u, Readset rs, @Nullable Readset replacedReadset, @Nullable PipelineJob job);
 
-        public boolean isAvailable(Container c, User u);
+        boolean isAvailable(Container c, User u);
     }
 }