From 19124d74d592e7f96e35e0583203246ad782ff42 Mon Sep 17 00:00:00 2001
From: Timm Fitschen <timm.fitschen@ds.mpg.de>
Date: Mon, 10 Dec 2018 14:58:58 +0100
Subject: [PATCH] MAINT: Refactoring
---
.../server/accessControl/UserSources.java | 3 +-
.../transaction/DeleteEntityProperties.java | 5 +-
.../backend/transaction/DeleteFile.java | 2 +-
.../transaction/DeleteSparseEntity.java | 5 +-
.../backend/transaction/GetChildren.java | 2 +-
.../transaction/GetDependentEntities.java | 2 +-
.../backend/transaction/GetFileIterator.java | 2 +-
.../backend/transaction/GetIDByName.java | 2 +-
.../transaction/InsertEntityDatatype.java | 3 -
.../transaction/InsertEntityProperties.java | 6 +-
.../backend/transaction/InsertFile.java | 5 +-
.../backend/transaction/InsertLogRecord.java | 4 +-
.../transaction/InsertSparseEntity.java | 3 -
.../transaction/RegisterSubDomain.java | 2 +-
.../backend/transaction/RetrieveAll.java | 2 +-
.../RetrieveAllUncheckedFiles.java | 2 +-
.../transaction/RetrieveDatatypes.java | 2 +-
.../transaction/RetrieveFullEntity.java | 14 +-
.../transaction/RetrieveLogRecord.java | 6 +-
.../backend/transaction/RetrieveParents.java | 4 +-
.../transaction/RetrievePermissionRules.java | 4 +-
.../transaction/RetrieveProperties.java | 4 +-
.../backend/transaction/RetrieveRole.java | 2 +-
.../transaction/RetrieveSparseEntity.java | 2 +-
.../RetrieveTransactionHistory.java | 4 +-
.../backend/transaction/RetrieveUser.java | 2 +-
.../backend/transaction/RuleLoader.java | 9 +-
.../transaction/SetPermissionRules.java | 2 +-
.../backend/transaction/UpdateUserRoles.java | 2 +-
.../java/caosdb/server/entity/Entity.java | 49 +++---
.../caosdb/server/entity/EntityInterface.java | 9 +-
.../server/entity/TransactionEntity.java | 18 +--
.../entity/container/ParentContainer.java | 1 -
.../entity/container/PropertyContainer.java | 1 -
.../container/TransactionContainer.java | 8 +-
.../server/entity/wrapper/EntityWrapper.java | 25 ++-
.../java/caosdb/server/jobs/ContainerJob.java | 12 +-
src/main/java/caosdb/server/jobs/Job.java | 143 ++++++++++--------
.../caosdb/server/jobs/JobAnnotation.java | 7 +
.../java/caosdb/server/jobs/Schedule.java | 8 +-
.../java/caosdb/server/jobs/core/Atomic.java | 14 +-
.../jobs/core/CheckDatatypePresent.java | 22 +--
.../CheckNoAdditionalPropertiesPresent.java | 56 +++++++
.../jobs/core/CheckNoOverridesPresent.java | 36 +++++
.../jobs/core/CheckParOblPropPresent.java | 6 +-
.../jobs/core/CheckRefidIsaParRefid.java | 4 +-
.../server/jobs/core/CheckRefidValid.java | 1 -
.../server/jobs/core/CheckUnitPresent.java | 2 +-
.../caosdb/server/jobs/core/Inheritance.java | 4 +-
.../server/jobs/core/InsertFilesInDir.java | 3 +-
.../jobs/core/LoadContainerFlagJobs.java | 2 +-
.../java/caosdb/server/jobs/core/PickUp.java | 5 +-
.../jobs/extension/SQLiteTransaction.java | 14 +-
src/main/java/caosdb/server/query/Query.java | 4 +-
.../caosdb/server/transaction/Retrieve.java | 5 +-
.../server/transaction/Transaction.java | 28 ++--
.../caosdb/server/utils/EntityStatus.java | 1 -
.../caosdb/server/utils/ServerMessages.java | 8 +
58 files changed, 357 insertions(+), 246 deletions(-)
create mode 100644 src/main/java/caosdb/server/jobs/core/CheckNoAdditionalPropertiesPresent.java
create mode 100644 src/main/java/caosdb/server/jobs/core/CheckNoOverridesPresent.java
diff --git a/src/main/java/caosdb/server/accessControl/UserSources.java b/src/main/java/caosdb/server/accessControl/UserSources.java
index 32b851e8..d96fdf14 100644
--- a/src/main/java/caosdb/server/accessControl/UserSources.java
+++ b/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;
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/DeleteEntityProperties.java b/src/main/java/caosdb/server/database/backend/transaction/DeleteEntityProperties.java
index ff306830..addcb4e7 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/DeleteEntityProperties.java
+++ b/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;
}
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/DeleteFile.java b/src/main/java/caosdb/server/database/backend/transaction/DeleteFile.java
index 82c022be..11235995 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/DeleteFile.java
+++ b/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 {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/DeleteSparseEntity.java b/src/main/java/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
index dd563882..f777a124 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
+++ b/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;
}
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/GetChildren.java b/src/main/java/caosdb/server/database/backend/transaction/GetChildren.java
index d476345c..2952b985 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/GetChildren.java
+++ b/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 {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/GetDependentEntities.java b/src/main/java/caosdb/server/database/backend/transaction/GetDependentEntities.java
index e4e6e96f..60143ec8 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/GetDependentEntities.java
+++ b/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 {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/GetFileIterator.java b/src/main/java/caosdb/server/database/backend/transaction/GetFileIterator.java
index 7e28ff24..d8f47b18 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/GetFileIterator.java
+++ b/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 {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/GetIDByName.java b/src/main/java/caosdb/server/database/backend/transaction/GetIDByName.java
index 895cd707..1adda922 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/GetIDByName.java
+++ b/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 {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/InsertEntityDatatype.java b/src/main/java/caosdb/server/database/backend/transaction/InsertEntityDatatype.java
index 39c46583..f0f7dbe2 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/InsertEntityDatatype.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/InsertEntityDatatype.java
@@ -1,13 +1,11 @@
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;
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/InsertEntityProperties.java b/src/main/java/caosdb/server/database/backend/transaction/InsertEntityProperties.java
index 05e4dbce..d5e32df1 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/InsertEntityProperties.java
+++ b/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 {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/InsertFile.java b/src/main/java/caosdb/server/database/backend/transaction/InsertFile.java
index 7fa04fbb..fe479b20 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/InsertFile.java
+++ b/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);
}
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/InsertLogRecord.java b/src/main/java/caosdb/server/database/backend/transaction/InsertLogRecord.java
index 43a21d48..c951712a 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/InsertLogRecord.java
+++ b/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 {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/InsertSparseEntity.java b/src/main/java/caosdb/server/database/backend/transaction/InsertSparseEntity.java
index f6294483..1d11d85c 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/InsertSparseEntity.java
+++ b/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;
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RegisterSubDomain.java b/src/main/java/caosdb/server/database/backend/transaction/RegisterSubDomain.java
index 08b999d0..f5cd5604 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RegisterSubDomain.java
+++ b/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 {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveAll.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveAll.java
index 5820547c..28f8e344 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveAll.java
+++ b/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 {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveAllUncheckedFiles.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveAllUncheckedFiles.java
index b9969424..192428e7 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveAllUncheckedFiles.java
+++ b/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 {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveDatatypes.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
index 44f8427a..08eac872 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
+++ b/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 {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveFullEntity.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveFullEntity.java
index 59836abc..62edee0d 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveFullEntity.java
+++ b/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;
+ }
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveLogRecord.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveLogRecord.java
index 42211d43..a08d737f 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveLogRecord.java
+++ b/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 {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java
index 5d1545d2..0169b087 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java
+++ b/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>> {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrievePermissionRules.java b/src/main/java/caosdb/server/database/backend/transaction/RetrievePermissionRules.java
index c0daecbc..ef99a55b 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrievePermissionRules.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrievePermissionRules.java
@@ -22,6 +22,8 @@
*/
package caosdb.server.database.backend.transaction;
+import java.util.HashSet;
+import org.apache.commons.jcs.access.CacheAccess;
import caosdb.server.CaosDBServer;
import caosdb.server.ServerProperties;
import caosdb.server.database.CacheableBackendTransaction;
@@ -29,8 +31,6 @@ import caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
import caosdb.server.database.exceptions.TransactionException;
import caosdb.server.database.misc.Cache;
import caosdb.server.permissions.PermissionRule;
-import java.util.HashSet;
-import org.apache.commons.jcs.access.CacheAccess;
public class RetrievePermissionRules
extends CacheableBackendTransaction<String, HashSet<PermissionRule>> {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveProperties.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveProperties.java
index b75d91ac..98f7994c 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveProperties.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveProperties.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;
@@ -33,8 +35,6 @@ import caosdb.server.database.proto.ProtoProperty;
import caosdb.server.entity.EntityInterface;
import caosdb.server.entity.Role;
import caosdb.server.entity.wrapper.Property;
-import java.util.ArrayList;
-import org.apache.commons.jcs.access.CacheAccess;
public class RetrieveProperties
extends CacheableBackendTransaction<Integer, ArrayList<ProtoProperty>> {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveRole.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveRole.java
index e4587996..ef5a5ec6 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveRole.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveRole.java
@@ -22,6 +22,7 @@
*/
package caosdb.server.database.backend.transaction;
+import org.apache.commons.jcs.access.CacheAccess;
import caosdb.server.CaosDBServer;
import caosdb.server.ServerProperties;
import caosdb.server.accessControl.Role;
@@ -29,7 +30,6 @@ import caosdb.server.database.CacheableBackendTransaction;
import caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
import caosdb.server.database.exceptions.TransactionException;
import caosdb.server.database.misc.Cache;
-import org.apache.commons.jcs.access.CacheAccess;
public class RetrieveRole extends CacheableBackendTransaction<String, Role> {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
index df9f5867..4d533068 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
@@ -22,6 +22,7 @@
*/
package caosdb.server.database.backend.transaction;
+import org.apache.commons.jcs.access.CacheAccess;
import caosdb.server.CaosDBServer;
import caosdb.server.ServerProperties;
import caosdb.server.database.CacheableBackendTransaction;
@@ -33,7 +34,6 @@ import caosdb.server.database.proto.SparseEntity;
import caosdb.server.entity.Entity;
import caosdb.server.entity.EntityInterface;
import caosdb.server.utils.EntityStatus;
-import org.apache.commons.jcs.access.CacheAccess;
public class RetrieveSparseEntity extends CacheableBackendTransaction<Integer, SparseEntity> {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveTransactionHistory.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveTransactionHistory.java
index cb9cdd9e..795e1691 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveTransactionHistory.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveTransactionHistory.java
@@ -22,6 +22,8 @@
*/
package caosdb.server.database.backend.transaction;
+import java.util.ArrayList;
+import org.apache.commons.jcs.access.CacheAccess;
import caosdb.datetime.UTCDateTime;
import caosdb.server.database.CacheableBackendTransaction;
import caosdb.server.database.backend.interfaces.RetrieveTransactionHistoryImpl;
@@ -29,8 +31,6 @@ import caosdb.server.database.exceptions.TransactionException;
import caosdb.server.database.proto.ProtoTransactionLogMessage;
import caosdb.server.entity.EntityInterface;
import caosdb.server.utils.TransactionLogMessage;
-import java.util.ArrayList;
-import org.apache.commons.jcs.access.CacheAccess;
public class RetrieveTransactionHistory
extends CacheableBackendTransaction<Integer, ArrayList<ProtoTransactionLogMessage>> {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveUser.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveUser.java
index 7492df38..9ccc4582 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveUser.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveUser.java
@@ -22,6 +22,7 @@
*/
package caosdb.server.database.backend.transaction;
+import org.apache.commons.jcs.access.CacheAccess;
import caosdb.server.CaosDBServer;
import caosdb.server.ServerProperties;
import caosdb.server.accessControl.Principal;
@@ -30,7 +31,6 @@ import caosdb.server.database.backend.interfaces.RetrieveUserImpl;
import caosdb.server.database.exceptions.TransactionException;
import caosdb.server.database.misc.Cache;
import caosdb.server.database.proto.ProtoUser;
-import org.apache.commons.jcs.access.CacheAccess;
public class RetrieveUser extends CacheableBackendTransaction<Principal, ProtoUser> {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RuleLoader.java b/src/main/java/caosdb/server/database/backend/transaction/RuleLoader.java
index 781c2ce4..888cefc5 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RuleLoader.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RuleLoader.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;
@@ -33,13 +35,10 @@ import caosdb.server.entity.EntityInterface;
import caosdb.server.entity.container.TransactionContainer;
import caosdb.server.jobs.Job;
import caosdb.server.transaction.Transaction;
-import java.util.ArrayList;
-import org.apache.commons.jcs.access.CacheAccess;
public class RuleLoader extends CacheableBackendTransaction<String, ArrayList<Rule>> {
private final Transaction<? extends TransactionContainer> transaction;
- private final TransactionContainer container;
private final EntityInterface e;
private final Integer entity;
private final Integer domain;
@@ -49,12 +48,10 @@ public class RuleLoader extends CacheableBackendTransaction<String, ArrayList<Ru
final Integer domain,
final Integer entity,
final EntityInterface e,
- final TransactionContainer container,
final Transaction<? extends TransactionContainer> transaction) {
this.domain = domain;
this.entity = entity;
this.e = e;
- this.container = container;
this.transaction = transaction;
}
@@ -94,7 +91,7 @@ public class RuleLoader extends CacheableBackendTransaction<String, ArrayList<Ru
protected void process(final ArrayList<Rule> t) throws TransactionException {
this.jobs = new ArrayList<Job>();
for (final Rule r : t) {
- this.jobs.add(Job.getJob(r.job, r.mode, this.e, this.container, this.transaction));
+ this.jobs.add(Job.getJob(r.job, r.mode, this.e, this.transaction));
}
}
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/SetPermissionRules.java b/src/main/java/caosdb/server/database/backend/transaction/SetPermissionRules.java
index a632f299..4cb7e852 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/SetPermissionRules.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/SetPermissionRules.java
@@ -22,11 +22,11 @@
*/
package caosdb.server.database.backend.transaction;
+import java.util.Set;
import caosdb.server.database.BackendTransaction;
import caosdb.server.database.backend.interfaces.SetPermissionRulesImpl;
import caosdb.server.database.exceptions.TransactionException;
import caosdb.server.permissions.PermissionRule;
-import java.util.Set;
public class SetPermissionRules extends BackendTransaction {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/UpdateUserRoles.java b/src/main/java/caosdb/server/database/backend/transaction/UpdateUserRoles.java
index 359bbb3a..fc6abf16 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/UpdateUserRoles.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/UpdateUserRoles.java
@@ -22,11 +22,11 @@
*/
package caosdb.server.database.backend.transaction;
+import java.util.HashSet;
import caosdb.server.accessControl.Principal;
import caosdb.server.database.BackendTransaction;
import caosdb.server.database.backend.interfaces.UpdateUserRolesImpl;
import caosdb.server.database.exceptions.TransactionException;
-import java.util.HashSet;
public class UpdateUserRoles extends BackendTransaction {
diff --git a/src/main/java/caosdb/server/entity/Entity.java b/src/main/java/caosdb/server/entity/Entity.java
index ff2f95de..c18d79ec 100644
--- a/src/main/java/caosdb/server/entity/Entity.java
+++ b/src/main/java/caosdb/server/entity/Entity.java
@@ -52,6 +52,7 @@ import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
+import java.util.Set;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.AuthorizationException;
import org.apache.shiro.authz.Permission;
@@ -73,7 +74,7 @@ public class Entity extends AbstractObservable implements EntityInterface {
private AbstractDatatype datatype = null;
private final ParentContainer parents = new ParentContainer(this);
private final PropertyContainer properties = new PropertyContainer(this);
- private final ArrayList<TransactionLogMessage> history = new ArrayList<TransactionLogMessage>();
+ private final List<TransactionLogMessage> history = new ArrayList<>();
private List<Selection> selections = null;
private EntityACL entityACL = null;
@@ -118,7 +119,7 @@ public class Entity extends AbstractObservable implements EntityInterface {
@Override
public final boolean hasProperties() {
- return this.properties != null && !this.properties.isEmpty();
+ return !this.properties.isEmpty();
}
@Override
@@ -255,10 +256,7 @@ public class Entity extends AbstractObservable implements EntityInterface {
@Override
public final boolean hasDescription() {
- if (this.description == null || this.description.isEmpty() || this.description.equals("")) {
- return false;
- }
- return true;
+ return !(this.description == null || this.description.isEmpty() || this.description.equals(""));
}
@Override
@@ -304,6 +302,9 @@ public class Entity extends AbstractObservable implements EntityInterface {
if (hasEntityStatus() && getEntityStatus() == entityStatus) {
return;
}
+ if(this.entityStatus == EntityStatus.UNQUALIFIED ) {
+ throw new CaosDBException("It is not allowed to change the state again, once an UNQUALIFIED state has been reached.");
+ }
this.entityStatus = entityStatus;
notifyObservers(ENTITY_STATUS_CHANGED_EVENT);
}
@@ -599,10 +600,10 @@ public class Entity extends AbstractObservable implements EntityInterface {
}
/** Errors, Warnings and Info messages for this entity. */
- private final HashSet<ToElementable> messages = new HashSet<ToElementable>();
+ private final Set<ToElementable> messages = new HashSet<>();
@Override
- public final HashSet<ToElementable> getMessages() {
+ public final Set<ToElementable> getMessages() {
return this.messages;
}
@@ -614,11 +615,9 @@ public class Entity extends AbstractObservable implements EntityInterface {
@Override
public final boolean hasMessage(final String type) {
for (final ToElementable m : this.messages) {
- if (m instanceof Message) {
- if (((Message) m).getType().equalsIgnoreCase(type)) {
+ if (m instanceof Message && ((Message) m).getType().equalsIgnoreCase(type)) {
return true;
}
- }
}
return false;
}
@@ -629,29 +628,22 @@ public class Entity extends AbstractObservable implements EntityInterface {
}
@Override
- public final LinkedList<Message> getMessages(final String type) {
- final LinkedList<Message> ret = new LinkedList<Message>();
+ public final List<Message> getMessages(final String type) {
+ final LinkedList<Message> ret = new LinkedList<>();
for (final ToElementable m : this.messages) {
- if (m instanceof Message) {
- if (((Message) m).getType().equalsIgnoreCase(type)) {
+ if (m instanceof Message && ((Message) m).getType().equalsIgnoreCase(type)) {
ret.add((Message) m);
- }
}
}
- if (ret.isEmpty()) {
- return null;
- }
return ret;
}
@Override
public final Message getMessage(final String type, final Integer code) {
for (final ToElementable m : this.messages) {
- if (m instanceof Message) {
- if (((Message) m).getType().equalsIgnoreCase(type) && ((Message) m).getCode() == code) {
+ if (m instanceof Message&& ((Message) m).getType().equalsIgnoreCase(type) && ((Message) m).getCode() == code) {
return (Message) m;
}
- }
}
return null;
}
@@ -663,6 +655,7 @@ public class Entity extends AbstractObservable implements EntityInterface {
@Override
public final void addError(final Message m) {
+ setEntityStatus(EntityStatus.UNQUALIFIED);
if (m.getType().equalsIgnoreCase(MessageType.Error.toString())) {
addMessage(m);
} else {
@@ -755,7 +748,7 @@ public class Entity extends AbstractObservable implements EntityInterface {
this.setDatatype(element.getAttributeValue("datatype"));
} catch (final IllegalArgumentException e) {
addError(ServerMessages.UNKNOWN_DATATYPE);
- setEntityStatus(EntityStatus.UNQUALIFIED);
+
}
}
@@ -826,7 +819,7 @@ public class Entity extends AbstractObservable implements EntityInterface {
} else {
final String type = pe.getName();
Integer code = null;
- String description = null;
+ String localDescription = null;
String body = null;
// Parse MESSAGE CODE.
@@ -843,7 +836,7 @@ public class Entity extends AbstractObservable implements EntityInterface {
// Parse MESSAGE DESCRIPTION.
if (pe.getAttribute("description") != null
&& !pe.getAttributeValue("description").equals("")) {
- description = pe.getAttributeValue("description");
+ localDescription = pe.getAttributeValue("description");
}
// Parse MESSAGE BODY.
@@ -851,7 +844,7 @@ public class Entity extends AbstractObservable implements EntityInterface {
body = pe.getTextTrim();
}
- addMessage(new Message(type, code, description, body));
+ addMessage(new Message(type, code, localDescription, body));
}
}
@@ -1027,7 +1020,7 @@ public class Entity extends AbstractObservable implements EntityInterface {
}
@Override
- public ArrayList<TransactionLogMessage> getTransactionLogMessages() {
+ public List<TransactionLogMessage> getTransactionLogMessages() {
return this.history;
}
@@ -1086,7 +1079,7 @@ public class Entity extends AbstractObservable implements EntityInterface {
public EntityInterface addSelections(final List<Selection> selections) {
if (this.selections == null) {
- this.selections = new LinkedList<Selection>();
+ this.selections = new LinkedList<>();
}
this.selections.addAll(selections);
return this;
diff --git a/src/main/java/caosdb/server/entity/EntityInterface.java b/src/main/java/caosdb/server/entity/EntityInterface.java
index 315a80e8..2bfe32a4 100644
--- a/src/main/java/caosdb/server/entity/EntityInterface.java
+++ b/src/main/java/caosdb/server/entity/EntityInterface.java
@@ -22,6 +22,9 @@
*/
package caosdb.server.entity;
+import java.util.List;
+import org.apache.shiro.authz.Permission;
+import org.apache.shiro.subject.Subject;
import caosdb.server.database.proto.SparseEntity;
import caosdb.server.database.proto.VerySparseEntity;
import caosdb.server.datatype.AbstractDatatype;
@@ -37,10 +40,6 @@ import caosdb.server.permissions.EntityACL;
import caosdb.server.utils.Observable;
import caosdb.server.utils.TransactionLogMessage;
import caosdb.unit.Unit;
-import java.util.ArrayList;
-import java.util.List;
-import org.apache.shiro.authz.Permission;
-import org.apache.shiro.subject.Subject;
public interface EntityInterface
extends JobTarget, Observable, ToElementable, WriteEntity, TransactionEntity {
@@ -148,7 +147,7 @@ public interface EntityInterface
public abstract void addTransactionLog(TransactionLogMessage transactionLogMessage);
- public abstract ArrayList<TransactionLogMessage> getTransactionLogMessages();
+ public abstract List<TransactionLogMessage> getTransactionLogMessages();
public abstract boolean hasTransactionLogMessages();
diff --git a/src/main/java/caosdb/server/entity/TransactionEntity.java b/src/main/java/caosdb/server/entity/TransactionEntity.java
index cb0782d0..36c581b5 100644
--- a/src/main/java/caosdb/server/entity/TransactionEntity.java
+++ b/src/main/java/caosdb/server/entity/TransactionEntity.java
@@ -22,16 +22,14 @@
*/
package caosdb.server.entity;
-import caosdb.server.CaosDBException;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import org.jdom2.Element;
import caosdb.server.entity.xml.ToElementStrategy;
import caosdb.server.entity.xml.ToElementable;
import caosdb.server.query.Query.Selection;
import caosdb.server.utils.EntityStatus;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import org.jdom2.Element;
public interface TransactionEntity {
@@ -45,13 +43,13 @@ public interface TransactionEntity {
public abstract String getCuid();
- public abstract void setCuid(String cuid) throws CaosDBException;
+ public abstract void setCuid(String cuid);
public abstract void setToElementStragegy(ToElementStrategy s);
public abstract Element toElement();
- public abstract HashSet<ToElementable> getMessages();
+ public abstract Set<ToElementable> getMessages();
public abstract boolean hasMessages();
@@ -59,7 +57,7 @@ public interface TransactionEntity {
public abstract void removeMessage(Message m);
- public abstract LinkedList<Message> getMessages(String type);
+ public abstract List<Message> getMessages(String type);
public abstract Message getMessage(String type, Integer code);
@@ -75,7 +73,7 @@ public interface TransactionEntity {
public abstract ToElementStrategy getToElementStrategy();
- public abstract HashMap<String, String> getFlags();
+ public abstract Map<String, String> getFlags();
public abstract void setFlag(String key, String value);
diff --git a/src/main/java/caosdb/server/entity/container/ParentContainer.java b/src/main/java/caosdb/server/entity/container/ParentContainer.java
index 64bbb6ff..461760b8 100644
--- a/src/main/java/caosdb/server/entity/container/ParentContainer.java
+++ b/src/main/java/caosdb/server/entity/container/ParentContainer.java
@@ -78,7 +78,6 @@ public class ParentContainer extends Container<Parent> {
switch (parent.getEntityStatus()) {
case UNQUALIFIED:
- case CORRUPT:
case DELETED:
case NONEXISTENT:
entity.addError(ServerMessages.ENTITY_HAS_UNQUALIFIED_PARENTS);
diff --git a/src/main/java/caosdb/server/entity/container/PropertyContainer.java b/src/main/java/caosdb/server/entity/container/PropertyContainer.java
index 8667901e..a80e2bfc 100644
--- a/src/main/java/caosdb/server/entity/container/PropertyContainer.java
+++ b/src/main/java/caosdb/server/entity/container/PropertyContainer.java
@@ -96,7 +96,6 @@ public class PropertyContainer extends Container<Property> {
}
switch (prop.getEntityStatus()) {
case UNQUALIFIED:
- case CORRUPT:
case DELETED:
case NONEXISTENT:
entity.addError(ServerMessages.ENTITY_HAS_UNQUALIFIED_PROPERTIES);
diff --git a/src/main/java/caosdb/server/entity/container/TransactionContainer.java b/src/main/java/caosdb/server/entity/container/TransactionContainer.java
index 763e1cd3..20668f54 100644
--- a/src/main/java/caosdb/server/entity/container/TransactionContainer.java
+++ b/src/main/java/caosdb/server/entity/container/TransactionContainer.java
@@ -32,6 +32,7 @@ import caosdb.server.jobs.JobTarget;
import caosdb.server.utils.EntityStatus;
import java.util.HashMap;
import java.util.LinkedList;
+import java.util.List;
import org.apache.shiro.subject.Subject;
import org.jdom2.Element;
@@ -77,7 +78,11 @@ public class TransactionContainer extends Container<Entity> implements ToElement
this.status = status;
}
- private final LinkedList<ToElementable> messages = new LinkedList<ToElementable>();
+ private final LinkedList<ToElementable> messages = new LinkedList<>();
+
+ public List<ToElementable> getMessages() {
+ return messages;
+ }
public void addMessage(final ToElementable m) {
this.messages.add(m);
@@ -177,4 +182,5 @@ public class TransactionContainer extends Container<Entity> implements ToElement
public boolean skipJob() {
return false;
}
+
}
diff --git a/src/main/java/caosdb/server/entity/wrapper/EntityWrapper.java b/src/main/java/caosdb/server/entity/wrapper/EntityWrapper.java
index 7ae648cc..8b6ec031 100644
--- a/src/main/java/caosdb/server/entity/wrapper/EntityWrapper.java
+++ b/src/main/java/caosdb/server/entity/wrapper/EntityWrapper.java
@@ -22,7 +22,12 @@
*/
package caosdb.server.entity.wrapper;
-import caosdb.server.CaosDBException;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import org.apache.shiro.authz.Permission;
+import org.apache.shiro.subject.Subject;
+import org.jdom2.Element;
import caosdb.server.database.proto.SparseEntity;
import caosdb.server.database.proto.VerySparseEntity;
import caosdb.server.datatype.AbstractDatatype;
@@ -42,14 +47,6 @@ import caosdb.server.utils.EntityStatus;
import caosdb.server.utils.Observer;
import caosdb.server.utils.TransactionLogMessage;
import caosdb.unit.Unit;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import org.apache.shiro.authz.Permission;
-import org.apache.shiro.subject.Subject;
-import org.jdom2.Element;
public class EntityWrapper implements EntityInterface {
@@ -155,7 +152,7 @@ public class EntityWrapper implements EntityInterface {
}
@Override
- public void setCuid(final String cuid) throws CaosDBException {
+ public void setCuid(final String cuid) {
this.entity.setCuid(cuid);
}
@@ -315,7 +312,7 @@ public class EntityWrapper implements EntityInterface {
}
@Override
- public HashSet<ToElementable> getMessages() {
+ public Set<ToElementable> getMessages() {
return this.entity.getMessages();
}
@@ -335,7 +332,7 @@ public class EntityWrapper implements EntityInterface {
}
@Override
- public LinkedList<Message> getMessages(final String type) {
+ public List<Message> getMessages(final String type) {
return this.entity.getMessages(type);
}
@@ -405,7 +402,7 @@ public class EntityWrapper implements EntityInterface {
}
@Override
- public HashMap<String, String> getFlags() {
+ public Map<String, String> getFlags() {
return this.entity.getFlags();
}
@@ -450,7 +447,7 @@ public class EntityWrapper implements EntityInterface {
}
@Override
- public ArrayList<TransactionLogMessage> getTransactionLogMessages() {
+ public List<TransactionLogMessage> getTransactionLogMessages() {
return this.entity.getTransactionLogMessages();
}
diff --git a/src/main/java/caosdb/server/jobs/ContainerJob.java b/src/main/java/caosdb/server/jobs/ContainerJob.java
index 4b4a80e2..6cef06e3 100644
--- a/src/main/java/caosdb/server/jobs/ContainerJob.java
+++ b/src/main/java/caosdb/server/jobs/ContainerJob.java
@@ -22,17 +22,25 @@
*/
package caosdb.server.jobs;
+import caosdb.server.entity.Message;
import caosdb.server.entity.container.TransactionContainer;
+import caosdb.server.utils.EntityStatus;
public abstract class ContainerJob extends Job {
@Override
- protected final TransactionContainer getContainer() {
+ public
+ final TransactionContainer getContainer() {
return super.getContainer();
}
@Override
public JobTarget getTarget() {
return getContainer();
- };
+ }
+
+ public void addError(Message error) {
+ getContainer().addMessage(error);
+ getContainer().setStatus(EntityStatus.UNQUALIFIED);
+ }
}
diff --git a/src/main/java/caosdb/server/jobs/Job.java b/src/main/java/caosdb/server/jobs/Job.java
index 48a4ed75..13209335 100644
--- a/src/main/java/caosdb/server/jobs/Job.java
+++ b/src/main/java/caosdb/server/jobs/Job.java
@@ -22,9 +22,20 @@
*/
package caosdb.server.jobs;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Set;
+import org.apache.shiro.SecurityUtils;
+import org.apache.shiro.authz.Permission;
+import org.apache.shiro.subject.Subject;
+import org.reflections.Reflections;
+import caosdb.server.CaosDBException;
import caosdb.server.database.Database;
import caosdb.server.database.backend.transaction.GetIDByName;
import caosdb.server.database.backend.transaction.IsSubType;
+import caosdb.server.database.backend.transaction.RetrieveFullEntity;
import caosdb.server.database.backend.transaction.RetrieveParents;
import caosdb.server.database.backend.transaction.RetrieveSparseEntity;
import caosdb.server.database.backend.transaction.RuleLoader;
@@ -42,13 +53,6 @@ import caosdb.server.utils.EntityStatus;
import caosdb.server.utils.Observable;
import caosdb.server.utils.Observer;
import caosdb.server.utils.ServerMessages;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.LinkedList;
-import java.util.Set;
-import org.apache.shiro.SecurityUtils;
-import org.apache.shiro.authz.Permission;
-import org.reflections.Reflections;
public abstract class Job extends AbstractObservable implements Observer {
private Transaction<? extends TransactionContainer> transaction = null;
@@ -57,7 +61,6 @@ public abstract class Job extends AbstractObservable implements Observer {
public abstract JobTarget getTarget();
private EntityInterface entity = null;
- private final boolean isDone = false;
protected <S, T> HashMap<S, T> getCache(final String name) {
return getTransaction().getCache(name);
@@ -70,14 +73,18 @@ public abstract class Job extends AbstractObservable implements Observer {
protected String getRequestId() {
return getContainer().getRequestId();
}
+
+ protected Subject getUser(){
+ return getTransaction().getTransactor();
+ }
- protected void appendJob(final EntityInterface entity, final Class<? extends Job> clazz) {
+ protected ScheduledJob appendJob(final EntityInterface entity, final Class<? extends Job> clazz) {
try {
final Job job = clazz.newInstance();
- job.init(getMode(), entity, getContainer(), getTransaction());
- getTransaction().getSchedule().add(job);
+ job.init(getMode(), entity, getTransaction());
+ return getTransaction().getSchedule().add(job);
} catch (InstantiationException | IllegalAccessException e) {
- throw new RuntimeException(e);
+ throw new CaosDBException(e);
}
}
@@ -100,7 +107,6 @@ public abstract class Job extends AbstractObservable implements Observer {
public final Job init(
final Mode mode,
final EntityInterface entity,
- final TransactionContainer entities,
final Transaction<? extends TransactionContainer> transaction) {
this.mode = mode;
this.entity = entity;
@@ -108,19 +114,19 @@ public abstract class Job extends AbstractObservable implements Observer {
return this;
}
- public final boolean isDone() {
- return this.isDone;
- }
-
/** to be overridden */
protected abstract void run();
- protected void getJobFromSchedule(
+ protected void runJobFromSchedule(
final EntityInterface entity, final Class<? extends Job> jobclass) {
getTransaction().getSchedule().runJob(entity, jobclass);
}
+
+ protected void runJobFromSchedule(ScheduledJob job){
+ getTransaction().getSchedule().runJob(job);
+ }
- EntityInterface getEntity() {
+ public EntityInterface getEntity() {
return this.entity;
}
@@ -150,11 +156,11 @@ public abstract class Job extends AbstractObservable implements Observer {
}
protected final boolean isValidSubTypeNoCache(final int child, final int parent) {
- return Database.execute(new IsSubType(child, parent), getTransaction().getAccess()).isSubType();
+ return child==parent || Database.execute(new IsSubType(child, parent), getTransaction().getAccess()).isSubType();
}
protected final EntityInterface retrieveValidSparseEntityByName(final String name)
- throws TransactionException, Message {
+ throws Message {
return retrieveValidSparseEntityById(retrieveValidIDByName(name));
}
@@ -167,6 +173,9 @@ public abstract class Job extends AbstractObservable implements Observer {
return ret;
}
+ protected final EntityInterface retrieveValidEntity(Integer id){
+ return Database.execute(new RetrieveFullEntity(id), getTransaction().getAccess()).getContainer().get(0);
+ }
protected final Integer retrieveValidIDByName(final String name) {
return Database.execute(new GetIDByName(name), getTransaction().getAccess()).getId();
}
@@ -192,34 +201,24 @@ public abstract class Job extends AbstractObservable implements Observer {
}
static HashMap<String, Class<? extends Job>> allClasses = null;
+ private static List<Class<? extends Job>> loadAlways;
public static Job getJob(
final String job,
final Mode mode,
final EntityInterface entity,
- final TransactionContainer entities,
final Transaction<? extends TransactionContainer> transaction) {
scanJobClasspath();
final Class<? extends Job> jobClass = allClasses.get(job.toLowerCase());
- Job ret;
- try {
- if (jobClass != null) {
- ret = jobClass.newInstance();
- ret.init(mode, entity, entities, transaction);
- return ret;
- }
- return null;
- } catch (final InstantiationException e) {
- throw new TransactionException(e);
- } catch (final IllegalAccessException e) {
- throw new TransactionException(e);
- }
+ return getJob(jobClass, mode, entity, transaction);
}
private static void scanJobClasspath() {
- if (allClasses == null) {
- allClasses = new HashMap<String, Class<? extends Job>>();
+
+ if (allClasses == null || loadAlways == null) {
+ allClasses = new HashMap<>();
+ loadAlways = new ArrayList<>();
Reflections jobPackage = new Reflections("caosdb.server.jobs.core");
Set<Class<? extends Job>> allClassesSet = jobPackage.getSubTypesOf(Job.class);
allClassesSet.addAll(jobPackage.getSubTypesOf(FlagJob.class));
@@ -241,83 +240,105 @@ public abstract class Job extends AbstractObservable implements Observer {
if (flagName.length() > 0) {
allClasses.put(flagName.toLowerCase(), c);
}
+ if (c.getAnnotation(JobAnnotation.class).loadAlways()){
+ loadAlways.add(c);
+ }
}
}
}
}
- protected ArrayList<Job> loadDataTypeSpecificJobs() {
- return Job.loadDataTypeSpecificJobs(getEntity(), getContainer(), getTransaction());
+ protected List<Job> loadDataTypeSpecificJobs() {
+ return Job.loadDataTypeSpecificJobs(getEntity(), getTransaction());
}
- public static ArrayList<Job> loadDataTypeSpecificJobs(
+ public static List<Job> loadDataTypeSpecificJobs(
final EntityInterface entity,
- final TransactionContainer entities,
final Transaction<? extends TransactionContainer> transaction) {
- return loadDataTypeSpecificJobs(entity.getDatatype(), entity, entities, transaction);
+ return loadDataTypeSpecificJobs(entity.getDatatype(), entity, transaction);
}
- private static ArrayList<Job> loadDataTypeSpecificJobs(
+ private static List<Job> loadDataTypeSpecificJobs(
final AbstractDatatype dt,
final EntityInterface entity,
- final TransactionContainer entities,
final Transaction<? extends TransactionContainer> transaction) {
if (dt == null) {
return new ArrayList<Job>();
}
if (dt instanceof ReferenceDatatype2) {
- final RuleLoader t = new RuleLoader(0, 17, entity, entities, transaction);
+ final RuleLoader t = new RuleLoader(0, 17, entity, transaction);
return Database.execute(t, transaction.getAccess()).getJobs();
} else if (dt instanceof AbstractCollectionDatatype) {
final AbstractDatatype datatype = ((AbstractCollectionDatatype) dt).getDatatype();
- return loadDataTypeSpecificJobs(datatype, entity, entities, transaction);
+ return loadDataTypeSpecificJobs(datatype, entity, transaction);
} else if (dt.getId() != null) {
- final RuleLoader t = new RuleLoader(0, dt.getId(), entity, entities, transaction);
+ final RuleLoader t = new RuleLoader(0, dt.getId(), entity, transaction);
return Database.execute(t, transaction.getAccess()).getJobs();
} else {
return null;
}
}
- public static ArrayList<Job> loadStandardJobs(
+ public static List<Job> loadStandardJobs(
final EntityInterface entity,
- final TransactionContainer entities,
final Transaction<? extends TransactionContainer> transaction) {
- final ArrayList<Job> jobs = new ArrayList<Job>();
+ final ArrayList<Job> jobs = new ArrayList<>();
+ // load permanent jobs
+ for (Class<? extends Job> j : loadAlways) {
+ if(j.getAnnotation(JobAnnotation.class).transaction().isInstance(transaction)){
+ jobs.add(getJob(j, Mode.MUST, entity, transaction));
+ }
+ }
+
// load general rules
{
- final RuleLoader t = new RuleLoader(0, 0, entity, entities, transaction);
+ final RuleLoader t = new RuleLoader(0, 0, entity, transaction);
jobs.addAll(Database.execute(t, transaction.getAccess()).getJobs());
}
// load Role specific rules
if (entity.hasRole()) {
final RuleLoader t =
- new RuleLoader(0, entity.getRole().getId(), entity, entities, transaction);
+ new RuleLoader(0, entity.getRole().getId(), entity, transaction);
jobs.addAll(Database.execute(t, transaction.getAccess()).getJobs());
}
// load data type specific rules
- jobs.addAll(loadDataTypeSpecificJobs(entity, entities, transaction));
+ jobs.addAll(loadDataTypeSpecificJobs(entity, transaction));
return jobs;
}
- public static LinkedList<Job> loadJobs(
+ private static Job getJob(Class<? extends Job> jobClass, Mode mode, EntityInterface entity,
+ Transaction<? extends TransactionContainer> transaction) {
+ Job ret;
+ try {
+
+ if (jobClass != null) {
+ ret = jobClass.newInstance();
+ ret.init(mode, entity, transaction);
+ return ret;
+ }
+ return null;
+ } catch (final InstantiationException | IllegalAccessException e) {
+ throw new TransactionException(e);
+ }
+ }
+
+ public static List<Job> loadJobs(
final EntityInterface entity,
- final TransactionContainer entities,
final Transaction<? extends TransactionContainer> transaction) {
- final LinkedList<Job> jobs = new LinkedList<Job>();
+ final LinkedList<Job> jobs = new LinkedList<>();
// general rules, role rules, data type rules
- jobs.addAll(loadStandardJobs(entity, entities, transaction));
+ jobs.addAll(loadStandardJobs(entity, transaction));
// load flag jobs
if (!entity.getFlags().isEmpty()) {
for (final String key : entity.getFlags().keySet()) {
- final Job j = getJob(key, Mode.MUST, entity, entities, transaction);
+ final Job j = getJob(key, Mode.MUST, entity, transaction);
if (j != null) {
if (j instanceof FlagJob) {
((FlagJob) j).setValue(entity.getFlag(key));
@@ -332,7 +353,7 @@ public abstract class Job extends AbstractObservable implements Observer {
for (final EntityInterface p : entity.getParents()) {
if (!p.getFlags().isEmpty()) {
for (final String key : p.getFlags().keySet()) {
- final Job j = getJob(key, Mode.MUST, entity, entities, transaction);
+ final Job j = getJob(key, Mode.MUST, entity, transaction);
if (j != null) {
if (j instanceof FlagJob) {
((FlagJob) j).setValue(p.getFlag(key));
@@ -351,7 +372,7 @@ public abstract class Job extends AbstractObservable implements Observer {
for (final EntityInterface p : entity.getProperties()) {
if (!p.getFlags().isEmpty()) {
for (final String key : p.getFlags().keySet()) {
- final Job j = getJob(key, Mode.MUST, entity, entities, transaction);
+ final Job j = getJob(key, Mode.MUST, entity, transaction);
if (j != null) {
if (j instanceof FlagJob) {
((FlagJob) j).setValue(p.getFlag(key));
@@ -366,7 +387,7 @@ public abstract class Job extends AbstractObservable implements Observer {
// load jobs for the properties
if (entity.hasProperties()) {
for (final EntityInterface p : entity.getProperties()) {
- jobs.addAll(loadJobs(p, entities, transaction));
+ jobs.addAll(loadJobs(p, transaction));
}
}
diff --git a/src/main/java/caosdb/server/jobs/JobAnnotation.java b/src/main/java/caosdb/server/jobs/JobAnnotation.java
index 48f5d91c..97263aeb 100644
--- a/src/main/java/caosdb/server/jobs/JobAnnotation.java
+++ b/src/main/java/caosdb/server/jobs/JobAnnotation.java
@@ -47,4 +47,11 @@ public @interface JobAnnotation {
* @return true per default.
*/
boolean loadOnDefault() default true;
+
+ /**
+ * Load for every transaction that is a subclass of 'transaction'.
+ *
+ * @return false per default.
+ */
+ boolean loadAlways() default false;
}
diff --git a/src/main/java/caosdb/server/jobs/Schedule.java b/src/main/java/caosdb/server/jobs/Schedule.java
index 12c3f8e1..367fdcbd 100644
--- a/src/main/java/caosdb/server/jobs/Schedule.java
+++ b/src/main/java/caosdb/server/jobs/Schedule.java
@@ -90,8 +90,10 @@ public class Schedule {
}
}
- public void add(final Job j) {
- this.jobs.add(new ScheduledJob(j));
+ public ScheduledJob add(final Job j) {
+ ScheduledJob ret = new ScheduledJob(j);
+ this.jobs.add(ret);
+ return ret;
}
public void runJobs(final JobExecutionTime time) {
@@ -104,7 +106,7 @@ public class Schedule {
}
}
- private void runJob(final ScheduledJob scheduledJob) {
+ protected void runJob(final ScheduledJob scheduledJob) {
if (!this.jobs.contains(scheduledJob)) {
throw new RuntimeException("Job was not in schedule.");
}
diff --git a/src/main/java/caosdb/server/jobs/core/Atomic.java b/src/main/java/caosdb/server/jobs/core/Atomic.java
index d8e1a6b6..cf6d99a0 100644
--- a/src/main/java/caosdb/server/jobs/core/Atomic.java
+++ b/src/main/java/caosdb/server/jobs/core/Atomic.java
@@ -37,15 +37,11 @@ public class Atomic extends ContainerJob {
private boolean doCheck() {
if (getContainer().getStatus() == EntityStatus.QUALIFIED) {
for (final EntityInterface entity : getContainer()) {
- switch (entity.getEntityStatus()) {
- case CORRUPT:
- case UNQUALIFIED:
- getContainer().setStatus(EntityStatus.UNQUALIFIED);
- getContainer().addMessage(ServerMessages.ATOMICITY_ERROR);
- // job done. remove observer.
- return false;
- default:
- break;
+ if(entity.getEntityStatus() == EntityStatus.UNQUALIFIED) {
+ getContainer().setStatus(EntityStatus.UNQUALIFIED);
+ getContainer().addMessage(ServerMessages.ATOMICITY_ERROR);
+ // job done. remove observer.
+ return false;
}
}
// keep observer
diff --git a/src/main/java/caosdb/server/jobs/core/CheckDatatypePresent.java b/src/main/java/caosdb/server/jobs/core/CheckDatatypePresent.java
index 73297223..ca6ced6e 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckDatatypePresent.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckDatatypePresent.java
@@ -22,9 +22,9 @@
*/
package caosdb.server.jobs.core;
+import java.util.List;
import caosdb.server.database.exceptions.EntityDoesNotExistException;
import caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import caosdb.server.database.exceptions.TransactionException;
import caosdb.server.datatype.AbstractCollectionDatatype;
import caosdb.server.datatype.AbstractDatatype;
import caosdb.server.datatype.ReferenceDatatype2;
@@ -36,7 +36,6 @@ import caosdb.server.jobs.Job;
import caosdb.server.permissions.EntityPermission;
import caosdb.server.utils.EntityStatus;
import caosdb.server.utils.ServerMessages;
-import java.util.ArrayList;
/**
* Check whether the entity has a data type. Assign the data type of the abstract property if
@@ -80,7 +79,7 @@ public final class CheckDatatypePresent extends EntityJob {
}
// run jobsreturn this.entities;
- final ArrayList<Job> datatypeJobs = loadDataTypeSpecificJobs();
+ final List<Job> datatypeJobs = loadDataTypeSpecificJobs();
getTransaction().getSchedule().addAll(datatypeJobs);
for (final Job job : datatypeJobs) {
getTransaction().getSchedule().runJob(job);
@@ -97,15 +96,11 @@ public final class CheckDatatypePresent extends EntityJob {
} else {
getEntity().addError(m);
}
- getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
} catch (final EntityDoesNotExistException exc) {
getEntity().addError(ServerMessages.UNKNOWN_DATATYPE);
- getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
} catch (final EntityWasNotUniqueException exc) {
getEntity().addError(ServerMessages.DATA_TYPE_NAME_DUPLICATES);
- getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
}
- return;
}
private void checkReference2(final ReferenceDatatype2 datatype) throws Message {
@@ -152,7 +147,7 @@ public final class CheckDatatypePresent extends EntityJob {
checkPermission(datatype, EntityPermission.USE_AS_DATA_TYPE);
}
- private void checkIfOverride() throws TransactionException, Message {
+ private void checkIfOverride() throws Message {
if (getEntity().hasId() && getEntity().getId() > 0) {
// get data type from database
final EntityInterface foreign = retrieveValidSparseEntityById(getEntity().getId());
@@ -178,7 +173,7 @@ public final class CheckDatatypePresent extends EntityJob {
}
}
- private void inheritDatatypeFromAbstractEntity() throws TransactionException, Message {
+ private void inheritDatatypeFromAbstractEntity() throws Message {
// if this is a record type property or a concrete property, assign
// the data type of the corresponding abstract property.
if (getEntity().hasId() && getEntity().getId() > 0) {
@@ -207,16 +202,14 @@ public final class CheckDatatypePresent extends EntityJob {
entity.setEntityStatus(EntityStatus.VALID);
} catch (final EntityDoesNotExistException exc) {
entity.addError(ServerMessages.ENTITY_DOES_NOT_EXIST);
- entity.setEntityStatus(EntityStatus.UNQUALIFIED);
} catch (final EntityWasNotUniqueException exc) {
entity.addError(ServerMessages.CANNOT_IDENTIFY_ENTITY_UNIQUELY);
- entity.setEntityStatus(EntityStatus.UNQUALIFIED);
}
}
}
private void getDataTypeFromParent() throws Message {
- getJobFromSchedule(getEntity(), CheckParValid.class);
+ runJobFromSchedule(getEntity(), CheckParValid.class);
AbstractDatatype datatype = null;
for (final EntityInterface parent : getEntity().getParents()) {
@@ -225,12 +218,11 @@ public final class CheckDatatypePresent extends EntityJob {
parentEntity = retrieveValidSparseEntityById(parent.getId());
} else {
parentEntity = getEntityById(parent.getId());
- getJobFromSchedule(parentEntity, CheckDatatypePresent.class);
+ runJobFromSchedule(parentEntity, CheckDatatypePresent.class);
}
if (parentEntity.hasDatatype()) {
if (datatype != null && !parentEntity.getDatatype().equals(datatype)) {
- getEntity().addMessage(ServerMessages.DATATYPE_INHERITANCE_AMBIGUOUS);
- getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
+ getEntity().addError(ServerMessages.DATATYPE_INHERITANCE_AMBIGUOUS);
return;
} else {
datatype = parentEntity.getDatatype();
diff --git a/src/main/java/caosdb/server/jobs/core/CheckNoAdditionalPropertiesPresent.java b/src/main/java/caosdb/server/jobs/core/CheckNoAdditionalPropertiesPresent.java
new file mode 100644
index 00000000..1557401d
--- /dev/null
+++ b/src/main/java/caosdb/server/jobs/core/CheckNoAdditionalPropertiesPresent.java
@@ -0,0 +1,56 @@
+package caosdb.server.jobs.core;
+
+import java.util.HashSet;
+import java.util.Set;
+import caosdb.server.entity.EntityInterface;
+import caosdb.server.entity.Message;
+import caosdb.server.jobs.EntityJob;
+import caosdb.server.jobs.JobAnnotation;
+import caosdb.server.utils.EntityStatus;
+import caosdb.server.utils.ServerMessages;
+
+@JobAnnotation(flag="noAdditionalProperties", description="Fail if this entity has any property which has not been defined by the parents of this entity.")
+public class CheckNoAdditionalPropertiesPresent extends EntityJob {
+
+ private Set<EntityInterface> used = new HashSet<>();
+
+ @Override
+ protected void run() {
+
+ // validate all parents and properties
+ runJobFromSchedule(getEntity(), CheckParOblPropPresent.class);
+
+
+ if(getEntity().getEntityStatus() == EntityStatus.QUALIFIED && getEntity().hasProperties()){
+ for(EntityInterface property : getEntity().getProperties()){
+ checkProperty(property);
+ }
+ }
+
+ }
+
+ public void checkProperty(EntityInterface property){
+ for(EntityInterface parent : getEntity().getParents()){
+ for(EntityInterface parentProperty : parent.getProperties()){
+ if(sameProperty(property, parentProperty) && !used.contains(parentProperty)){
+ used .add(parentProperty);
+ }
+ }
+ // not found!
+ addMessage(property,ServerMessages.ADDITIONAL_PROPERTY);
+ }
+ }
+
+ private void addMessage(EntityInterface property, Message message) {
+ if(getMode()==Mode.MUST) {
+ property.addError(message);
+ } else {
+ property.addWarning(message);
+ }
+ }
+
+ private boolean sameProperty(EntityInterface property, EntityInterface parentProperty) {
+ return property.getId() == parentProperty.getId();
+ }
+
+}
diff --git a/src/main/java/caosdb/server/jobs/core/CheckNoOverridesPresent.java b/src/main/java/caosdb/server/jobs/core/CheckNoOverridesPresent.java
new file mode 100644
index 00000000..d640f19f
--- /dev/null
+++ b/src/main/java/caosdb/server/jobs/core/CheckNoOverridesPresent.java
@@ -0,0 +1,36 @@
+package caosdb.server.jobs.core;
+
+import caosdb.server.entity.Message;
+import caosdb.server.entity.wrapper.Property;
+import caosdb.server.jobs.EntityJob;
+import caosdb.server.jobs.JobAnnotation;
+import caosdb.server.utils.ServerMessages;
+
+@JobAnnotation(flag="noOverrides", description="Fail if this entity has any properties with overrides.")
+public class CheckNoOverridesPresent extends EntityJob {
+
+ @Override
+ protected void run() {
+ runJobFromSchedule(this.getEntity(), CheckPropValid.class);
+ for(Property p : getEntity().getProperties()){
+ if(p.isDatatypeOverride()){
+ addMessage(p, ServerMessages.PROPERTY_WITH_DATATYPE_OVERRIDE);
+ }
+ if(p.isNameOverride()){
+ addMessage(p, ServerMessages.PROPERTY_WITH_NAME_OVERRIDE);
+ }
+ if(p.isDescOverride()){
+ addMessage(p, ServerMessages.PROPERTY_WITH_DESC_OVERRIDE);
+ }
+ }
+ }
+
+ private void addMessage(Property p, Message message) {
+ if(getMode()==Mode.MUST){
+ p.addError(message);
+ } else {
+ p.addWarning(message);
+ }
+ }
+
+}
diff --git a/src/main/java/caosdb/server/jobs/core/CheckParOblPropPresent.java b/src/main/java/caosdb/server/jobs/core/CheckParOblPropPresent.java
index 7ee0d218..ead4248f 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckParOblPropPresent.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckParOblPropPresent.java
@@ -41,12 +41,12 @@ public class CheckParOblPropPresent extends EntityJob {
// This test needs the valid/qualified ids of all properties.
// Thus, run a CheckPropValid first.
- getJobFromSchedule(getEntity(), CheckPropValid.class);
+ runJobFromSchedule(getEntity(), CheckPropValid.class);
// This test needs the valid/qualified parents. If a parent is only
// referenced by name it has to be translated into a (hopefully) unique
// id.
- getJobFromSchedule(getEntity(), CheckParValid.class);
+ runJobFromSchedule(getEntity(), CheckParValid.class);
if (getEntity().hasParents()) {
Database.execute(
@@ -54,7 +54,7 @@ public class CheckParOblPropPresent extends EntityJob {
}
// inherit properties
- getJobFromSchedule(getEntity(), Inheritance.class);
+ runJobFromSchedule(getEntity(), Inheritance.class);
// loop over all parents
if (getEntity().hasParents()) {
diff --git a/src/main/java/caosdb/server/jobs/core/CheckRefidIsaParRefid.java b/src/main/java/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
index 7c36b1cd..fa2b21cc 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
@@ -114,7 +114,7 @@ public class CheckRefidIsaParRefid extends EntityJob {
final ReferenceValue value, final ReferenceDatatype2 dt, final EntityInterface entity)
throws Message {
- getJobFromSchedule(entity, CheckRefidValid.class);
+ runJobFromSchedule(entity, CheckRefidValid.class);
if (entity.getEntityStatus() == EntityStatus.UNQUALIFIED) {
return;
}
@@ -135,7 +135,7 @@ public class CheckRefidIsaParRefid extends EntityJob {
final EntityInterface refEntity = getEntityById(child);
for (final Parent par : refEntity.getParents()) {
if (par.getId() == null) {
- getJobFromSchedule(refEntity, CheckParValid.class);
+ runJobFromSchedule(refEntity, CheckParValid.class);
}
if (par.getId() == null) {
getEntity()
diff --git a/src/main/java/caosdb/server/jobs/core/CheckRefidValid.java b/src/main/java/caosdb/server/jobs/core/CheckRefidValid.java
index 7dccec03..14d98962 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckRefidValid.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckRefidValid.java
@@ -149,7 +149,6 @@ public class CheckRefidValid extends EntityJob {
if (ref.getEntity().hasEntityStatus()) {
switch (ref.getEntity().getEntityStatus()) {
case UNQUALIFIED:
- case CORRUPT:
getEntity().addError(ServerMessages.ENTITY_HAS_INVALID_REFERENCE);
getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
return false;
diff --git a/src/main/java/caosdb/server/jobs/core/CheckUnitPresent.java b/src/main/java/caosdb/server/jobs/core/CheckUnitPresent.java
index 0b31806f..5b923769 100644
--- a/src/main/java/caosdb/server/jobs/core/CheckUnitPresent.java
+++ b/src/main/java/caosdb/server/jobs/core/CheckUnitPresent.java
@@ -37,7 +37,7 @@ public class CheckUnitPresent extends EntityJob {
@Override
protected void run() {
- getJobFromSchedule(getEntity(), Inheritance.class);
+ runJobFromSchedule(getEntity(), Inheritance.class);
if (!hasUnit(getEntity())) {
switch (getMode()) {
diff --git a/src/main/java/caosdb/server/jobs/core/Inheritance.java b/src/main/java/caosdb/server/jobs/core/Inheritance.java
index 1290f8a1..ed25c64c 100644
--- a/src/main/java/caosdb/server/jobs/core/Inheritance.java
+++ b/src/main/java/caosdb/server/jobs/core/Inheritance.java
@@ -72,7 +72,7 @@ public class Inheritance extends EntityJob {
break parentLoop;
}
- getJobFromSchedule(getEntity(), CheckParValid.class);
+ runJobFromSchedule(getEntity(), CheckParValid.class);
Database.execute(new RetrieveFullEntity(parent), getTransaction().getAccess());
@@ -149,7 +149,7 @@ public class Inheritance extends EntityJob {
break propertyLoop;
}
- getJobFromSchedule(getEntity(), CheckPropValid.class);
+ runJobFromSchedule(getEntity(), CheckPropValid.class);
EntityInterface validProperty = new Entity(property.getId());
if (getEntity().hasParents()) {
diff --git a/src/main/java/caosdb/server/jobs/core/InsertFilesInDir.java b/src/main/java/caosdb/server/jobs/core/InsertFilesInDir.java
index 86730b59..773ac275 100644
--- a/src/main/java/caosdb/server/jobs/core/InsertFilesInDir.java
+++ b/src/main/java/caosdb/server/jobs/core/InsertFilesInDir.java
@@ -44,6 +44,7 @@ import caosdb.server.utils.Utils;
import java.io.File;
import java.io.IOException;
import java.util.LinkedList;
+import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
@@ -299,7 +300,7 @@ public class InsertFilesInDir extends FlagJob {
}
private void loadJobs(final Entity e) {
- final LinkedList<Job> loadJobs = Job.loadJobs(e, getContainer(), getTransaction());
+ final List<Job> loadJobs = Job.loadJobs(e, getTransaction());
getTransaction().getSchedule().addAll(loadJobs);
}
diff --git a/src/main/java/caosdb/server/jobs/core/LoadContainerFlagJobs.java b/src/main/java/caosdb/server/jobs/core/LoadContainerFlagJobs.java
index f00c44cd..9df5e601 100644
--- a/src/main/java/caosdb/server/jobs/core/LoadContainerFlagJobs.java
+++ b/src/main/java/caosdb/server/jobs/core/LoadContainerFlagJobs.java
@@ -36,7 +36,7 @@ public class LoadContainerFlagJobs extends ContainerJob {
protected void run() {
if (getContainer().getFlags() != null) {
for (final Entry<String, String> flag : getContainer().getFlags().entrySet()) {
- final Job j = Job.getJob(flag.getKey(), Mode.MUST, null, getContainer(), getTransaction());
+ final Job j = Job.getJob(flag.getKey(), Mode.MUST, null, getTransaction());
if (j != null) {
if (j instanceof FlagJob) {
((FlagJob) j).setValue(flag.getValue());
diff --git a/src/main/java/caosdb/server/jobs/core/PickUp.java b/src/main/java/caosdb/server/jobs/core/PickUp.java
index 2d44f590..8d200ac5 100644
--- a/src/main/java/caosdb/server/jobs/core/PickUp.java
+++ b/src/main/java/caosdb/server/jobs/core/PickUp.java
@@ -70,14 +70,11 @@ public class PickUp extends EntityJob {
@Override
public boolean notifyObserver(final String e, final Observable o) {
- if (e == Entity.ENTITY_STATUS_CHANGED_EVENT && o == getEntity()) {
- if (this.rollBack && getEntity().getEntityStatus() == EntityStatus.UNQUALIFIED
- || getEntity().getEntityStatus() == EntityStatus.CORRUPT) {
+ if (e == Entity.ENTITY_STATUS_CHANGED_EVENT && o == getEntity() && this.rollBack && getEntity().getEntityStatus() == EntityStatus.UNQUALIFIED) {
final File target = new File(FileSystem.getDropOffBox() + this.dropOffBoxPath);
getEntity().getFileProperties().getFile().renameTo(target);
this.rollBack = false;
return false;
- }
}
return true;
}
diff --git a/src/main/java/caosdb/server/jobs/extension/SQLiteTransaction.java b/src/main/java/caosdb/server/jobs/extension/SQLiteTransaction.java
index af364e4e..17125669 100644
--- a/src/main/java/caosdb/server/jobs/extension/SQLiteTransaction.java
+++ b/src/main/java/caosdb/server/jobs/extension/SQLiteTransaction.java
@@ -22,11 +22,6 @@
*/
package caosdb.server.jobs.extension;
-import caosdb.server.CaosDBException;
-import caosdb.server.entity.FileProperties;
-import caosdb.server.entity.Message;
-import caosdb.server.jobs.EntityJob;
-import caosdb.server.utils.FileUtils;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.Connection;
@@ -37,8 +32,13 @@ import java.sql.SQLException;
import java.sql.Statement;
import java.util.Collections;
import java.util.HashMap;
-import java.util.LinkedList;
+import java.util.List;
import java.util.concurrent.locks.ReentrantLock;
+import caosdb.server.CaosDBException;
+import caosdb.server.entity.FileProperties;
+import caosdb.server.entity.Message;
+import caosdb.server.jobs.EntityJob;
+import caosdb.server.utils.FileUtils;
public class SQLiteTransaction extends EntityJob {
private static HashMap<String, ReentrantLock> lockedTables = new HashMap<String, ReentrantLock>();
@@ -72,7 +72,7 @@ public class SQLiteTransaction extends EntityJob {
final Statement stmt = con.createStatement();
//
- final LinkedList<Message> msgs = getEntity().getMessages("execute");
+ final List<Message> msgs = getEntity().getMessages("execute");
Collections.sort(msgs);
for (final Message m : msgs) {
getEntity().removeMessage(m);
diff --git a/src/main/java/caosdb/server/query/Query.java b/src/main/java/caosdb/server/query/Query.java
index 9018ee0f..c9bff5a5 100644
--- a/src/main/java/caosdb/server/query/Query.java
+++ b/src/main/java/caosdb/server/query/Query.java
@@ -173,7 +173,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
ServerProperties.KEY_QUERY_FILTER_ENTITIES_WITHOUT_RETRIEVE_PERMISSIONS)
.equalsIgnoreCase("FALSE");
- private LinkedList<Integer> resultSet = null;
+ List<Integer> resultSet = null;
private final String query;
private Pattern entity = null;
private Role role = null;
@@ -600,7 +600,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
return this.query;
}
- public LinkedList<Integer> getResultSet() {
+ public List<Integer> getResultSet() {
return this.resultSet;
}
diff --git a/src/main/java/caosdb/server/transaction/Retrieve.java b/src/main/java/caosdb/server/transaction/Retrieve.java
index 07af1e6c..3110ee97 100644
--- a/src/main/java/caosdb/server/transaction/Retrieve.java
+++ b/src/main/java/caosdb/server/transaction/Retrieve.java
@@ -53,12 +53,12 @@ public class Retrieve extends Transaction<RetrieveContainer> {
// resolve names
final ResolveNames r = new ResolveNames();
- r.init(Mode.SHOULD, null, getContainer(), this);
+ r.init(Mode.SHOULD, null, this);
getSchedule().add(r);
getSchedule().runJob(r);
final RemoveDuplicates job = new RemoveDuplicates();
- job.init(Mode.MUST, null, getContainer(), this);
+ job.init(Mode.MUST, null, this);
getSchedule().add(job);
getSchedule().runJob(job);
@@ -134,7 +134,6 @@ public class Retrieve extends Transaction<RetrieveContainer> {
@Override
protected void transaction() throws Exception {
// retrieve entities from mysql database
- // retrieveFullEntities(getContainer(), getConnection());
retrieveFullEntities(getContainer(), getAccess());
}
diff --git a/src/main/java/caosdb/server/transaction/Transaction.java b/src/main/java/caosdb/server/transaction/Transaction.java
index 347e806e..396cf061 100644
--- a/src/main/java/caosdb/server/transaction/Transaction.java
+++ b/src/main/java/caosdb/server/transaction/Transaction.java
@@ -22,6 +22,9 @@
*/
package caosdb.server.transaction;
+import java.util.HashMap;
+import java.util.List;
+import org.apache.shiro.subject.Subject;
import caosdb.datetime.UTCDateTime;
import caosdb.server.accessControl.AuthenticationUtils;
import caosdb.server.accessControl.Principal;
@@ -45,9 +48,7 @@ import caosdb.server.jobs.core.Mode;
import caosdb.server.jobs.core.PickUp;
import caosdb.server.utils.AbstractObservable;
import caosdb.server.utils.Info;
-import java.util.HashMap;
-import java.util.LinkedList;
-import org.apache.shiro.subject.Subject;
+import caosdb.server.utils.Observer;
public abstract class Transaction<C extends TransactionContainer> extends AbstractObservable
implements TransactionInterface {
@@ -63,8 +64,13 @@ public abstract class Transaction<C extends TransactionContainer> extends Abstra
private final Schedule schedule = new Schedule();
protected Transaction(final C container) {
- acceptObserver(Info.getInstance());
+ this(container, Info.getInstance());
+ }
+
+ protected Transaction(C container, Observer o){
this.container = container;
+ if(o!=null)
+ acceptObserver(o);
}
public static DatabaseMonitor getMonitor() {
@@ -78,23 +84,23 @@ public abstract class Transaction<C extends TransactionContainer> extends Abstra
protected void makeSchedule() throws Exception {
// load flag jobs
final Job loadContainerFlags =
- Job.getJob("LoadContainerFlagJobs", Mode.MUST, null, getContainer(), this);
+ Job.getJob("LoadContainerFlagJobs", Mode.MUST, null, this);
this.schedule.add(loadContainerFlags);
this.schedule.runJob(loadContainerFlags);
// all transactions are atomic
this.schedule.add(
- Job.getJob(Atomic.class.getSimpleName(), Mode.MUST, null, getContainer(), this));
+ Job.getJob(Atomic.class.getSimpleName(), Mode.MUST, null, this));
// AccessControl
this.schedule.add(
- Job.getJob(AccessControl.class.getSimpleName(), Mode.MUST, null, getContainer(), this));
+ Job.getJob(AccessControl.class.getSimpleName(), Mode.MUST, null, this));
this.schedule.add(
Job.getJob(
- CheckEntityACLRoles.class.getSimpleName(), Mode.MUST, null, getContainer(), this));
+ CheckEntityACLRoles.class.getSimpleName(), Mode.MUST, null, this));
for (final EntityInterface e : getContainer()) {
- final LinkedList<Job> loadJobs = Job.loadJobs(e, getContainer(), this);
+ final List<Job> loadJobs = Job.loadJobs(e, this);
this.schedule.addAll(loadJobs);
// additionally load datatype job
@@ -108,13 +114,13 @@ public abstract class Transaction<C extends TransactionContainer> extends Abstra
}
}
if (!found) {
- this.schedule.add(new CheckDatatypePresent().init(Mode.MUST, e, getContainer(), this));
+ this.schedule.add(new CheckDatatypePresent().init(Mode.MUST, e, this));
}
}
// load pickup job if necessary
if (e.hasFileProperties() && e.getFileProperties().isPickupable()) {
- this.schedule.add(new PickUp().init(Mode.MUST, e, getContainer(), this));
+ this.schedule.add(new PickUp().init(Mode.MUST, e, this));
}
}
}
diff --git a/src/main/java/caosdb/server/utils/EntityStatus.java b/src/main/java/caosdb/server/utils/EntityStatus.java
index f7e9f002..3e906302 100644
--- a/src/main/java/caosdb/server/utils/EntityStatus.java
+++ b/src/main/java/caosdb/server/utils/EntityStatus.java
@@ -38,7 +38,6 @@ package caosdb.server.utils;
public enum EntityStatus {
IGNORE,
UNQUALIFIED,
- CORRUPT,
DELETED,
NONEXISTENT,
QUALIFIED,
diff --git a/src/main/java/caosdb/server/utils/ServerMessages.java b/src/main/java/caosdb/server/utils/ServerMessages.java
index 5d4a3c3a..d4a0f713 100644
--- a/src/main/java/caosdb/server/utils/ServerMessages.java
+++ b/src/main/java/caosdb/server/utils/ServerMessages.java
@@ -418,4 +418,12 @@ public class ServerMessages {
public static final Message SERVER_SIDE_SCRIPT_MISSING_CALL =
new Message(MessageType.Error, 400, "You must specify the `call` field.");
+
+ public static final Message ADDITIONAL_PROPERTY = new Message(MessageType.Warning,0,"This property is an additional property which has no corresponding properties among the properties of the parents.");
+
+ public static final Message PROPERTY_WITH_DATATYPE_OVERRIDE = new Message(MessageType.Warning,0,"This property overrides the datatype.");
+
+ public static final Message PROPERTY_WITH_DESC_OVERRIDE = new Message(MessageType.Warning,0,"This property overrides the description.");
+
+ public static final Message PROPERTY_WITH_NAME_OVERRIDE = new Message(MessageType.Warning,0,"This property overrides the name.");
}
--
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