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

.gitignore

@@ -18,3 +18,6 @@ target/
 .classpath
 .project
 .settings
+
+# logfiles
+screen*log*

caosdb-webui @ 519e9f86

-Subproject commit 32fa3b8af945d4d0bf4e98818b2456bdc8f375c0
+Subproject commit 519e9f868d299ca0d7477e423e71e3f080000a00

makefile

@@ -21,9 +21,13 @@
 # ** end header
 #
 
+<<<<<<< HEAD
 runserver:
 	mvn exec:exec
 
+=======
+SHELL:=/bin/bash
+>>>>>>> 619a505b48586e03fd34f65da12d6ff1b32138c6
 run: compile
 	mvn exec:exec
 
@@ -62,9 +66,14 @@ clean: clean-antlr
 clean-antlr:
 	rm -rf target/generated-sources/antlr4/
 
-run-debug-screen:
+.PHONY: run-server-screen
+run-server-screen:
+	@if test "$$(screen -ls | grep -c 'caosdb-screen')" -eq "1"; then \
+		echo "server is probably running. try 'screen -ls'"; \
+		exit 1 ; \
+	fi
 	# start and wait for server
-	@screen -L -S caosdb-screen -t server -d -m -A make run-debug
+	@screen -L -S caosdb-screen -t server -d -m -A make run
 	@sleep 2
 	@while [ 1 -eq 1 ] ; do \
 		screen -S caosdb-screen -X hardcopy .screen.log || break ; \
@@ -72,11 +81,33 @@ run-debug-screen:
 	done; \
 
 
-stop-debug-screen:
-	# stop screen session with debug server
+.PHONY: stop-server-screen
+stop-server-screen:
+	# stop screen session with server
 	@screen -S caosdb-screen -X hardcopy screen.log || true
 	@screen -S caosdb-screen -p server -X stuff "^C"
 
+.PHONY: run-debug-screen
+run-debug-screen:
+	@if test "$$(screen -ls | grep -c 'caosdb-debug-screen')" -eq "1"; then \
+		echo "server is probably running. try 'screen -ls'"; \
+		exit 1 ; \
+	fi
+	# start and wait for server
+	@screen -L -S caosdb-debug-screen -t server -d -m -A make run-debug
+	@sleep 2
+	@while [ 1 -eq 1 ] ; do \
+		screen -S caosdb-debug-screen -X hardcopy .screen.log || break ; \
+		[ $$(grep -c "org.restlet.ext.jetty.JettyServerHelper start" .screen.log) -eq 0 ] || break ; \
+	done; \
+
+
+.PHONY: stop-debug-screen
+stop-debug-screen:
+	# stop screen session with debug server
+	@screen -S caosdb-debug-screen -X hardcopy screen.log || true
+	@screen -S caosdb-debug-screen -p server -X stuff "^C"
+
 .m2-local:
 	mkdir .m2-local
 

misc/pam_authentication/makefile

@@ -23,5 +23,5 @@
 # Makefile for pam_authentication.c
 
 main: pam_authentication.c
-	mkdir ./bin
+	mkdir -p ./bin
 	gcc -o ./bin/pam_authentication pam_authentication.c -lpam -lpam_misc

src/main/java/caosdb/server/ServerProperties.java

@@ -117,6 +117,10 @@ public class ServerProperties extends Properties {
   public static final String KEY_SERVER_SIDE_SCRIPTING_WORKING_DIR =
       "SERVER_SIDE_SCRIPTING_WORKING_DIR";
 
+  public static final String KEY_NO_REPLY_EMAIL = "NO_REPLY_EMAIL";
+
+  public static final String KEY_NO_REPLY_NAME = "NO_REPLY_NAME";
+
   /**
    * This init_server_properties method reads the config file which contains key-value-pairs for
    * such variables like the user name of the database, the port the server will be listening on

src/main/java/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePermissionRules.java

@@ -59,7 +59,7 @@ public class MySQLRetrievePermissionRules extends MySQLTransaction
     } catch (final ConnectionException e) {
       throw new TransactionException(e);
     }
-    return null;
+    return new HashSet<>();
   }
 
   @SuppressWarnings("unchecked")

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

@@ -23,6 +23,7 @@
 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;

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

@@ -23,6 +23,7 @@
 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;

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;

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

@@ -22,9 +22,6 @@
  */
 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;
@@ -38,6 +35,9 @@ 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 {
 

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

@@ -23,6 +23,7 @@
 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;

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 {