Updates from code inspection (#209)

Author: bbimber

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

@@ -49,7 +49,7 @@ public class OpenLdapSyncController extends SpringActionController
     private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(OpenLdapSyncController.class);
     public static final String NAME = "openldapsync";
 
-    private static Logger _log = LogManager.getLogger(OpenLdapSyncController.class);
+    private static final Logger _log = LogManager.getLogger(OpenLdapSyncController.class);
 
     public OpenLdapSyncController()
     {
@@ -59,6 +59,7 @@ public OpenLdapSyncController()
     @RequiresPermission(AdminOperationsPermission.class)
     public class InitiateLdapSyncAction extends MutatingApiAction<InitiateLdapSyncForm>
     {
+        @Override
         public ApiResponse execute(InitiateLdapSyncForm form, BindException errors) throws Exception
         {
             try
@@ -101,6 +102,7 @@ public void setForPreview(boolean forPreview)
     @RequiresPermission(AdminPermission.class)
     public class ListLdapGroupsAction extends ReadOnlyApiAction<LdapForm>
     {
+        @Override
         public ApiResponse execute(LdapForm form, BindException errors) throws Exception
         {
             ApiSimpleResponse resp = new ApiSimpleResponse();
@@ -495,6 +497,7 @@ public void setMemberSyncMode(String memberSyncMode)
     @RequiresPermission(AdminOperationsPermission.class)
     public class TestLdapConnectionAction extends MutatingApiAction<Object>
     {
+        @Override
         public ApiResponse execute(Object form, BindException errors) throws Exception
         {
             ApiSimpleResponse resp = new ApiSimpleResponse();
@@ -544,6 +547,7 @@ public ApiResponse execute(Object form, BindException errors) throws Exception
     @RequiresPermission(AdminOperationsPermission.class)
     public class GetLdapSettingsAction extends ReadOnlyApiAction<Object>
     {
+        @Override
         public ApiResponse execute(Object form, BindException errors)
         {
             Map<String, Object> result = new HashMap<>();
@@ -567,6 +571,7 @@ public ApiResponse execute(Object form, BindException errors)
     @RequiresPermission(AdminOperationsPermission.class)
     public class SetLdapSettingsAction extends MutatingApiAction<LdapForm>
     {
+        @Override
         public ApiResponse execute(LdapForm form, BindException errors)
         {
             Map<String, String> props = new HashMap<>();

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

@@ -74,6 +74,7 @@ protected void startupAfterSpringConfig(ModuleContext moduleContext)
     {
         DefaultSchema.registerProvider(OpenLdapSyncSchema.getInstance().getSchema().getQuerySchemaName(), new DefaultSchema.SchemaProvider(this)
         {
+            @Override
             public QuerySchema createSchema(final DefaultSchema schema, Module module)
             {
                 DbSchema dbSchema = DbSchema.get(OpenLdapSyncSchema.NAME, DbSchemaType.Module);

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

@@ -73,7 +73,6 @@ public synchronized void schedule()
         catch (LdapException e)
         {
             _log.error("LDAP sync is enabled, but the saved setting are invalid.  Sync will not start.", e);
-            return;
         }
         catch (Exception e)
         {

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

@@ -79,7 +79,7 @@ public class LdapSettings
 
     public static final String DELIM = "<>";
 
-    private Map<String, Object> _settings;
+    private final Map<String, Object> _settings;
 
     public LdapSettings()
     {
@@ -448,10 +448,6 @@ public User getLabKeyAdminUser()
         {
             ValidEmail e = new ValidEmail(email);
             User u = UserManager.getUser(e);
-            if (u == null)
-            {
-                return null;
-            }
 
             return u;
         }

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

@@ -72,13 +72,13 @@ public class LdapSyncRunner implements Job
     private static final Logger _log = LogManager.getLogger(LdapSyncRunner.class);
     private LdapSettings _settings;
     private LdapConnectionWrapper _wrapper;
-    private Map<String, LdapSyncModel> _syncedRecordMap = new HashMap<>();
+    private final Map<String, LdapSyncModel> _syncedRecordMap = new HashMap<>();
     private boolean _previewOnly = false;
-    private List<String> _messages = new ArrayList<>();
+    private final List<String> _messages = new ArrayList<>();
     private boolean _doDetailedLogging = true;
 
-    private Map<String, Integer> _usersSynced = new HashMap<>();
-    private Map<String, Integer> _groupsSynced = new HashMap<>();
+    private final Map<String, Integer> _usersSynced = new HashMap<>();
+    private final Map<String, Integer> _groupsSynced = new HashMap<>();
 
     public static final String AUDIT_EVENT_TYPE = "LdapAuditEvent";
 
@@ -98,6 +98,7 @@ public LdapSyncRunner()
 
     }
 
+    @Override
     public void execute(JobExecutionContext context) throws JobExecutionException
     {
         try
@@ -437,7 +438,7 @@ else if (_settings.getMemberSyncMode().equals(LdapSettings.MemberSyncMode.remove
                         if (u.getPrincipalType().equals(PrincipalType.GROUP))
                             continue;
 
-                        if (_usersSynced.values().contains(u.getUserId()))
+                        if (_usersSynced.containsValue(u.getUserId()))
                         {
                             deleteMember(existingGroup, u);
                         }
@@ -1068,9 +1069,9 @@ 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
         {
-            private List<LdapEntry> _users = new ArrayList<>();
-            private Map<String, MockLdapEntry> _groupMap = new HashMap<>();
-            private Map<MockLdapEntry, List<LdapEntry>> _groupMemberMap = new HashMap<>();
+            private final List<LdapEntry> _users = new ArrayList<>();
+            private final Map<String, MockLdapEntry> _groupMap = new HashMap<>();
+            private final Map<MockLdapEntry, List<LdapEntry>> _groupMemberMap = new HashMap<>();
 
             public DummyConnectionWrapper() throws LdapException
             {
@@ -1125,9 +1126,9 @@ public List<LdapEntry> listAllUsers()
 
         private static class MockLdapEntry extends LdapEntry
         {
-            private Dn _dn;
+            private final Dn _dn;
 
-            private Map<String, String> _otherProps = new HashMap<>();
+            private final Map<String, String> _otherProps = new HashMap<>();
 
             //represents an LDAP user entry
             public MockLdapEntry(String dn, Map<String, String> otherProps, LdapSettings settings) throws LdapInvalidDnException

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

@@ -25,18 +25,18 @@
  */
 public interface GenomeTrigger
 {
-    public String getName();
+    String getName();
 
-    public void onCreate(Container c, User u, Logger log, int genomeId);
+    void onCreate(Container c, User u, Logger log, int genomeId);
 
-    public void onRecreate(Container c, User u, Logger log, int genomeId);
+    void onRecreate(Container c, User u, Logger log, int genomeId);
 
-    public void onDelete(Container c, User u, Logger log, int genomeId);
+    void onDelete(Container c, User u, Logger log, int genomeId);
 
     default void onTrackAdd(Container c, User u, Logger log, int genomeId, int trackId)
     {
 
     }
 
-    public boolean isAvailable(Container c);
+    boolean isAvailable(Container c);
 }

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

@@ -51,12 +51,7 @@ public boolean isChildOf(PedigreeRecord potentialParent)
         {
             return true;
         }
-        else if (mother != null && mother.equals(potentialParent.subjectName))
-        {
-            return true;
-        }
-
-        return false;
+        else return mother != null && mother.equals(potentialParent.subjectName);
     }
 
     public String getSubjectName()

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

@@ -22,15 +22,15 @@
  */
 public interface ReferenceLibraryHelper
 {
-    public File getReferenceFasta();
+    File getReferenceFasta();
 
-    public File getIdKeyFile();
+    File getIdKeyFile();
 
-    public File getFastaIndexFile(boolean createIfDoesntExist);
+    File getFastaIndexFile(boolean createIfDoesntExist);
 
-    public File getSequenceDictionaryFile(boolean createIfDoesntExist);
+    File getSequenceDictionaryFile(boolean createIfDoesntExist);
 
-    public Integer resolveSequenceId(String refName);
+    Integer resolveSequenceId(String refName);
 
-    public String resolveAccession(String refName);
+    String resolveAccession(String refName);
 }

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

@@ -27,9 +27,9 @@
  */
 public interface SequenceDataProvider extends DataProvider
 {
-    public List<NavItem> getSequenceNavItems(Container c, User u, SequenceNavItemCategory category);
+    List<NavItem> getSequenceNavItems(Container c, User u, SequenceNavItemCategory category);
 
-    public enum SequenceNavItemCategory
+    enum SequenceNavItemCategory
     {
         data(),
         references(),

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/model/AnalysisModel.java

@@ -31,50 +31,50 @@
  */
 public interface AnalysisModel extends Serializable
 {
-    public Integer getAnalysisId();
+    Integer getAnalysisId();
 
-    public Integer getRunId();
+    Integer getRunId();
 
-    public String getContainer();
+    String getContainer();
 
-    public Integer getReadset();
+    Integer getReadset();
 
-    public Integer getAlignmentFile();
+    Integer getAlignmentFile();
 
-    public File getAlignmentFileObject();
+    File getAlignmentFileObject();
 
-    public ExpData getAlignmentData();
+    ExpData getAlignmentData();
 
     @Deprecated
-    public Integer getReferenceLibrary();
+    Integer getReferenceLibrary();
 
-    public void setReferenceLibrary(Integer libraryId);
+    void setReferenceLibrary(Integer libraryId);
 
-    public ExpData getReferenceLibraryData(User u) throws PipelineJobException;
+    ExpData getReferenceLibraryData(User u) throws PipelineJobException;
 
-    public File getReferenceLibraryFile(User u) throws PipelineJobException;
+    File getReferenceLibraryFile(User u) throws PipelineJobException;
 
-    public String getType();
+    String getType();
 
-    public Date getModified();
+    Date getModified();
 
-    public Integer getModifiedby();
+    Integer getModifiedby();
 
-    public Date getCreated();
+    Date getCreated();
 
-    public Integer getCreatedby();
+    Integer getCreatedby();
 
-    public Integer getRowId();
+    Integer getRowId();
 
-    public String getDescription();
+    String getDescription();
 
-    public String getSynopsis();
+    String getSynopsis();
 
-    public void setSynopsis(String synopsis);
+    void setSynopsis(String synopsis);
 
-    public Integer getLibraryId();
+    Integer getLibraryId();
 
-    public void setLibraryId(Integer libraryId);
+    void setLibraryId(Integer libraryId);
 
-    public JSONObject toJSON();
+    JSONObject toJSON();
 }