Merge branch 'f-server-side-scripting' of...

Merge branch 'f-server-side-scripting' of gitlab.gwdg.de:bmp-caosdb/caosdb-server into f-server-side-scripting

src/main/java/caosdb/server/accessControl/UserSources.java

@@ -44,6 +44,7 @@ import org.apache.shiro.subject.PrincipalCollection;
 
 public class UserSources extends HashMap<String, UserSource> {
 
+  public static final String ANONYMOUS_ROLE = "anonymous";
   private static final Logger logger =
       LogManager.getLogManager().getLogger(UserSources.class.getName());
   public static final String KEY_DEAULT_REALM = "defaultRealm";
@@ -171,7 +172,7 @@ public class UserSources extends HashMap<String, UserSource> {
     if (principals.getPrimaryPrincipal() == AuthenticationUtils.ANONYMOUS_USER.getPrincipal()) {
       // anymous has one role
       Set<String> roles = new HashSet<>();
-      roles.add("anonymous");
+      roles.add(ANONYMOUS_ROLE);
       return roles;
     }
 

src/main/java/caosdb/server/database/backend/transaction/DeleteEntityProperties.java

@@ -23,11 +23,9 @@
 package caosdb.server.database.backend.transaction;
 
 import static caosdb.server.transaction.Transaction.ERROR_INTEGRITY_VIOLATION;
-
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.backend.interfaces.DeleteEntityPropertiesImpl;
 import caosdb.server.database.exceptions.IntegrityException;
-import caosdb.server.database.exceptions.TransactionException;
 import caosdb.server.entity.EntityInterface;
 import caosdb.server.utils.EntityStatus;
 
@@ -40,7 +38,7 @@ public class DeleteEntityProperties extends BackendTransaction {
   }
 
   @Override
-  public void execute() throws TransactionException {
+  public void execute() {
     RetrieveProperties.removeCached(this.entity.getId());
     RetrieveParents.removeCached(this.entity.getId());
 
@@ -52,7 +50,6 @@ public class DeleteEntityProperties extends BackendTransaction {
         ret.execute(this.entity.getId());
       } catch (final IntegrityException exc) {
         this.entity.addError(ERROR_INTEGRITY_VIOLATION);
-        this.entity.setEntityStatus(EntityStatus.CORRUPT);
         throw exc;
       }
     }

src/main/java/caosdb/server/database/backend/transaction/DeleteFile.java

@@ -22,12 +22,12 @@
  */
 package caosdb.server.database.backend.transaction;
 
+import java.io.IOException;
 import caosdb.server.CaosDBException;
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.exceptions.TransactionException;
 import caosdb.server.entity.EntityInterface;
 import caosdb.server.entity.Message;
-import java.io.IOException;
 
 public class DeleteFile extends BackendTransaction {
 

src/main/java/caosdb/server/database/backend/transaction/DeleteSparseEntity.java

@@ -23,11 +23,9 @@
 package caosdb.server.database.backend.transaction;
 
 import static caosdb.server.transaction.Transaction.ERROR_INTEGRITY_VIOLATION;
-
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.backend.interfaces.DeleteSparseEntityImpl;
 import caosdb.server.database.exceptions.IntegrityException;
-import caosdb.server.database.exceptions.TransactionException;
 import caosdb.server.entity.EntityInterface;
 import caosdb.server.utils.EntityStatus;
 
@@ -40,7 +38,7 @@ public class DeleteSparseEntity extends BackendTransaction {
   }
 
   @Override
-  protected void execute() throws TransactionException {
+  protected void execute()  {
     RetrieveSparseEntity.removeCached(this.entity.getId());
 
     final DeleteSparseEntityImpl ret = getImplementation(DeleteSparseEntityImpl.class);
@@ -51,7 +49,6 @@ public class DeleteSparseEntity extends BackendTransaction {
       }
     } catch (final IntegrityException exc) {
       this.entity.addError(ERROR_INTEGRITY_VIOLATION);
-      this.entity.setEntityStatus(EntityStatus.CORRUPT);
       throw exc;
     }
   }

src/main/java/caosdb/server/database/backend/transaction/GetChildren.java

@@ -22,10 +22,10 @@
  */
 package caosdb.server.database.backend.transaction;
 
+import java.util.List;
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.backend.interfaces.GetChildrenImpl;
 import caosdb.server.database.exceptions.TransactionException;
-import java.util.List;
 
 public class GetChildren extends BackendTransaction {
 

src/main/java/caosdb/server/database/backend/transaction/GetDependentEntities.java

@@ -22,10 +22,10 @@
  */
 package caosdb.server.database.backend.transaction;
 
+import java.util.List;
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.backend.interfaces.GetDependentEntitiesImpl;
 import caosdb.server.database.exceptions.TransactionException;
-import java.util.List;
 
 public class GetDependentEntities extends BackendTransaction {
 

src/main/java/caosdb/server/database/backend/transaction/GetFileIterator.java

@@ -22,10 +22,10 @@
  */
 package caosdb.server.database.backend.transaction;
 
+import java.util.Iterator;
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.backend.interfaces.GetFileIteratorImpl;
 import caosdb.server.database.exceptions.TransactionException;
-import java.util.Iterator;
 
 public class GetFileIterator extends BackendTransaction {
 

src/main/java/caosdb/server/database/backend/transaction/GetIDByName.java

@@ -22,12 +22,12 @@
  */
 package caosdb.server.database.backend.transaction;
 
+import java.util.List;
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.backend.interfaces.GetIDByNameImpl;
 import caosdb.server.database.exceptions.EntityDoesNotExistException;
 import caosdb.server.database.exceptions.EntityWasNotUniqueException;
 import caosdb.server.database.exceptions.TransactionException;
-import java.util.List;
 
 public class GetIDByName extends BackendTransaction {
 

src/main/java/caosdb/server/database/backend/transaction/InsertEntityDatatype.java

 package caosdb.server.database.backend.transaction;
 
 import static caosdb.server.transaction.Transaction.ERROR_INTEGRITY_VIOLATION;
-
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.backend.interfaces.InsertEntityDatatypeImpl;
 import caosdb.server.database.exceptions.IntegrityException;
 import caosdb.server.database.proto.SparseEntity;
 import caosdb.server.entity.EntityInterface;
-import caosdb.server.utils.EntityStatus;
 
 public class InsertEntityDatatype extends BackendTransaction {
 
@@ -27,7 +25,6 @@ public class InsertEntityDatatype extends BackendTransaction {
       t.execute(e);
     } catch (final IntegrityException exc) {
       this.entity.addError(ERROR_INTEGRITY_VIOLATION);
-      this.entity.setEntityStatus(EntityStatus.CORRUPT);
       throw exc;
     }
 

src/main/java/caosdb/server/database/backend/transaction/InsertEntityProperties.java

@@ -22,6 +22,9 @@
  */
 package caosdb.server.database.backend.transaction;
 
+import java.util.ArrayList;
+import java.util.Deque;
+import java.util.List;
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.DatabaseUtils;
 import caosdb.server.database.backend.interfaces.InsertEntityPropertiesImpl;
@@ -35,9 +38,6 @@ import caosdb.server.entity.EntityInterface;
 import caosdb.server.entity.Role;
 import caosdb.server.entity.StatementStatus;
 import caosdb.server.entity.wrapper.Property;
-import java.util.ArrayList;
-import java.util.Deque;
-import java.util.List;
 
 public class InsertEntityProperties extends BackendTransaction {
 

src/main/java/caosdb/server/database/backend/transaction/InsertFile.java

@@ -22,12 +22,12 @@
  */
 package caosdb.server.database.backend.transaction;
 
+import java.io.IOException;
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.exceptions.TransactionException;
 import caosdb.server.entity.EntityInterface;
 import caosdb.server.entity.Message;
 import caosdb.server.utils.EntityStatus;
-import java.io.IOException;
 
 public class InsertFile extends BackendTransaction {
 
@@ -38,7 +38,7 @@ public class InsertFile extends BackendTransaction {
   }
 
   @Override
-  public void execute() throws TransactionException {
+  public void execute(){
     try {
       if (this.entity.getEntityStatus() == EntityStatus.QUALIFIED) {
 
@@ -46,7 +46,6 @@ public class InsertFile extends BackendTransaction {
           getUndoHandler().append(this.entity.getFileProperties().storeFile());
         } catch (final Message m) {
           this.entity.addMessage(m);
-          this.entity.setEntityStatus(EntityStatus.CORRUPT);
           throw new TransactionException(m);
         }
       }

src/main/java/caosdb/server/database/backend/transaction/InsertLogRecord.java

@@ -22,11 +22,11 @@
  */
 package caosdb.server.database.backend.transaction;
 
+import java.util.List;
+import java.util.logging.LogRecord;
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.backend.interfaces.InsertLogRecordImpl;
 import caosdb.server.database.exceptions.TransactionException;
-import java.util.List;
-import java.util.logging.LogRecord;
 
 public class InsertLogRecord extends BackendTransaction {
 

src/main/java/caosdb/server/database/backend/transaction/InsertSparseEntity.java

@@ -23,14 +23,12 @@
 package caosdb.server.database.backend.transaction;
 
 import static caosdb.server.transaction.Transaction.ERROR_INTEGRITY_VIOLATION;
-
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.backend.interfaces.InsertSparseEntityImpl;
 import caosdb.server.database.exceptions.IntegrityException;
 import caosdb.server.database.exceptions.TransactionException;
 import caosdb.server.database.proto.SparseEntity;
 import caosdb.server.entity.EntityInterface;
-import caosdb.server.utils.EntityStatus;
 import caosdb.server.utils.Undoable;
 
 public class InsertSparseEntity extends BackendTransaction {
@@ -53,7 +51,6 @@ public class InsertSparseEntity extends BackendTransaction {
       t.execute(e);
     } catch (final IntegrityException exc) {
       this.entity.addError(ERROR_INTEGRITY_VIOLATION);
-      this.entity.setEntityStatus(EntityStatus.CORRUPT);
       throw exc;
     }
 

src/main/java/caosdb/server/database/backend/transaction/RegisterSubDomain.java

@@ -22,10 +22,10 @@
  */
 package caosdb.server.database.backend.transaction;
 
+import java.util.Deque;
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.backend.interfaces.RegisterSubDomainImpl;
 import caosdb.server.database.exceptions.TransactionException;
-import java.util.Deque;
 
 public class RegisterSubDomain extends BackendTransaction {
 

src/main/java/caosdb/server/database/backend/transaction/RetrieveAll.java

@@ -22,12 +22,12 @@
  */
 package caosdb.server.database.backend.transaction;
 
+import java.util.List;
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.backend.interfaces.RetrieveAllImpl;
 import caosdb.server.database.exceptions.TransactionException;
 import caosdb.server.entity.RetrieveEntity;
 import caosdb.server.entity.container.TransactionContainer;
-import java.util.List;
 
 public class RetrieveAll extends BackendTransaction {
 

src/main/java/caosdb/server/database/backend/transaction/RetrieveAllUncheckedFiles.java

@@ -22,11 +22,11 @@
  */
 package caosdb.server.database.backend.transaction;
 
+import java.util.Iterator;
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
 import caosdb.server.database.exceptions.TransactionException;
 import caosdb.server.database.proto.SparseEntity;
-import java.util.Iterator;
 
 public class RetrieveAllUncheckedFiles extends BackendTransaction {
 

src/main/java/caosdb/server/database/backend/transaction/RetrieveDatatypes.java

@@ -22,6 +22,7 @@
  */
 package caosdb.server.database.backend.transaction;
 
+import java.util.ArrayList;
 import caosdb.server.database.BackendTransaction;
 import caosdb.server.database.backend.interfaces.RetrieveDatatypesImpl;
 import caosdb.server.database.exceptions.TransactionException;
@@ -30,7 +31,6 @@ import caosdb.server.entity.Entity;
 import caosdb.server.entity.EntityInterface;
 import caosdb.server.entity.RetrieveEntity;
 import caosdb.server.entity.container.Container;
-import java.util.ArrayList;
 
 public class RetrieveDatatypes extends BackendTransaction {
 

src/main/java/caosdb/server/database/backend/transaction/RetrieveFullEntity.java

@@ -23,8 +23,8 @@
 package caosdb.server.database.backend.transaction;
 
 import caosdb.server.database.BackendTransaction;
-import caosdb.server.database.exceptions.TransactionException;
 import caosdb.server.entity.EntityInterface;
+import caosdb.server.entity.RetrieveEntity;
 import caosdb.server.entity.Role;
 import caosdb.server.entity.container.Container;
 import caosdb.server.utils.EntityStatus;
@@ -34,7 +34,7 @@ public class RetrieveFullEntity extends BackendTransaction {
   private final Container<? extends EntityInterface> container;
 
   public RetrieveFullEntity(final EntityInterface entity) {
-    final Container<EntityInterface> c = new Container<EntityInterface>();
+    final Container<EntityInterface> c = new Container<>();
     c.add(entity);
     this.container = c;
   }
@@ -43,8 +43,12 @@ public class RetrieveFullEntity extends BackendTransaction {
     this.container = container;
   }
 
+  public RetrieveFullEntity(Integer id) {
+    this(new RetrieveEntity(id));
+  }
+
   @Override
-  public void execute() throws TransactionException {
+  public void execute() {
     for (final EntityInterface e : this.container) {
       if (e.hasId() && e.getId() > 0 && e.getEntityStatus() == EntityStatus.QUALIFIED) {
 
@@ -60,4 +64,8 @@ public class RetrieveFullEntity extends BackendTransaction {
       }
     }
   }
+  
+  public Container<? extends EntityInterface> getContainer() {
+    return container;
+  }
 }

src/main/java/caosdb/server/database/backend/transaction/RetrieveLogRecord.java

@@ -22,12 +22,12 @@
  */
 package caosdb.server.database.backend.transaction;
 
-import caosdb.server.database.BackendTransaction;
-import caosdb.server.database.backend.interfaces.RetrieveLogRecordImpl;
-import caosdb.server.database.exceptions.TransactionException;
 import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.LogRecord;
+import caosdb.server.database.BackendTransaction;
+import caosdb.server.database.backend.interfaces.RetrieveLogRecordImpl;
+import caosdb.server.database.exceptions.TransactionException;
 
 public class RetrieveLogRecord extends BackendTransaction {
 

src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java

@@ -22,6 +22,8 @@
  */
 package caosdb.server.database.backend.transaction;
 
+import java.util.ArrayList;
+import org.apache.commons.jcs.access.CacheAccess;
 import caosdb.server.CaosDBServer;
 import caosdb.server.ServerProperties;
 import caosdb.server.database.CacheableBackendTransaction;
@@ -31,8 +33,6 @@ import caosdb.server.database.exceptions.TransactionException;
 import caosdb.server.database.misc.Cache;
 import caosdb.server.database.proto.VerySparseEntity;
 import caosdb.server.entity.EntityInterface;
-import java.util.ArrayList;
-import org.apache.commons.jcs.access.CacheAccess;
 
 public class RetrieveParents
     extends CacheableBackendTransaction<Integer, ArrayList<VerySparseEntity>> {