From 8bfbf9cce092e1fbb2d03a56b8253040493015c9 Mon Sep 17 00:00:00 2001
From: Timm Fitschen <t.fitschen@indiscale.com>
Date: Fri, 22 Jan 2021 17:22:51 +0100
Subject: [PATCH] cleanup
---
.../handlers/FileUploadHandler.java | 39 --
.../handlers/GetNamesRequestHandler.java | 13 -
.../transaction/handlers/IDHandler.java | 36 --
.../transaction/handlers/RequestHandler.java | 31 --
...etrieveGlobalEntityPermissionsHandler.java | 37 --
.../handlers/RetriveOwnerRequestHandler.java | 36 --
.../handlers/SimpleDeleteRequestHandler.java | 55 ---
.../handlers/SimpleGetRequestHandler.java | 38 --
.../handlers/SimpleWriteHandler.java | 34 --
.../org/caosdb/server/transaction/Delete.java | 56 ---
.../org/caosdb/server/transaction/Insert.java | 59 ---
.../org/caosdb/server/transaction/Update.java | 401 ------------------
.../server/transaction/WriteTransaction.java | 35 +-
13 files changed, 16 insertions(+), 854 deletions(-)
delete mode 100644 src/main/java/org/caosdb/server/resource/transaction/handlers/FileUploadHandler.java
delete mode 100644 src/main/java/org/caosdb/server/resource/transaction/handlers/GetNamesRequestHandler.java
delete mode 100644 src/main/java/org/caosdb/server/resource/transaction/handlers/IDHandler.java
delete mode 100644 src/main/java/org/caosdb/server/resource/transaction/handlers/RequestHandler.java
delete mode 100644 src/main/java/org/caosdb/server/resource/transaction/handlers/RetrieveGlobalEntityPermissionsHandler.java
delete mode 100644 src/main/java/org/caosdb/server/resource/transaction/handlers/RetriveOwnerRequestHandler.java
delete mode 100644 src/main/java/org/caosdb/server/resource/transaction/handlers/SimpleDeleteRequestHandler.java
delete mode 100644 src/main/java/org/caosdb/server/resource/transaction/handlers/SimpleGetRequestHandler.java
delete mode 100644 src/main/java/org/caosdb/server/resource/transaction/handlers/SimpleWriteHandler.java
delete mode 100644 src/main/java/org/caosdb/server/transaction/Delete.java
delete mode 100644 src/main/java/org/caosdb/server/transaction/Insert.java
delete mode 100644 src/main/java/org/caosdb/server/transaction/Update.java
diff --git a/src/main/java/org/caosdb/server/resource/transaction/handlers/FileUploadHandler.java b/src/main/java/org/caosdb/server/resource/transaction/handlers/FileUploadHandler.java
deleted file mode 100644
index d04706e3..00000000
--- a/src/main/java/org/caosdb/server/resource/transaction/handlers/FileUploadHandler.java
+++ /dev/null
@@ -1,39 +0,0 @@
-/// *
-// * ** header v3.0
-// * This file is a part of the CaosDB Project.
-// *
-// * Copyright (C) 2018 Research Group Biomedical Physics,
-// * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-// *
-// * This program is free software: you can redistribute it and/or modify
-// * it under the terms of the GNU Affero General Public License as
-// * published by the Free Software Foundation, either version 3 of the
-// * License, or (at your option) any later version.
-// *
-// * This program is distributed in the hope that it will be useful,
-// * but WITHOUT ANY WARRANTY; without even the implied warranty of
-// * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// * GNU Affero General Public License for more details.
-// *
-// * You should have received a copy of the GNU Affero General Public License
-// * along with this program. If not, see <https://www.gnu.org/licenses/>.
-// *
-// * ** end header
-// */
-// package caosdb.server.resource.transaction.handlers;
-//
-// import org.restlet.data.MediaType;
-// import caosdb.server.entity.Message;
-// import caosdb.server.entity.Message.MessageType;
-// import caosdb.server.entity.container.WritableContainer;
-// import caosdb.server.resource.transaction.EntityResource;
-//
-// public class FileUploadHandler<T extends WritableContainer> extends SimpleWriteHandler<T> {
-//
-// @Override
-// public void handle(final EntityResource t, final T container) throws Exception {
-// if (!t.getRequest().getEntity().getMediaType().equals(MediaType.MULTIPART_FORM_DATA, true)) {
-// throw new Message(MessageType.Error, "Wrong MediaType");
-// }
-// }
-// }
diff --git a/src/main/java/org/caosdb/server/resource/transaction/handlers/GetNamesRequestHandler.java b/src/main/java/org/caosdb/server/resource/transaction/handlers/GetNamesRequestHandler.java
deleted file mode 100644
index 779a20b3..00000000
--- a/src/main/java/org/caosdb/server/resource/transaction/handlers/GetNamesRequestHandler.java
+++ /dev/null
@@ -1,13 +0,0 @@
-// package caosdb.server.resource.transaction.handlers;
-//
-// import caosdb.server.entity.container.RetrieveContainer;
-// import caosdb.server.resource.transaction.RetrieveEntityResource;
-//
-// public class GetNamesRequestHandler extends RequestHandler<RetrieveContainer> {
-//
-// /** Adds the `names` flag to the RetrieveContainer which triggers the RetrieveAllNames job. */
-// @Override
-// public void handle(RetrieveEntityResource t, RetrieveContainer container) throws Exception {
-// container.getFlags().put("names", null);
-// }
-// }
diff --git a/src/main/java/org/caosdb/server/resource/transaction/handlers/IDHandler.java b/src/main/java/org/caosdb/server/resource/transaction/handlers/IDHandler.java
deleted file mode 100644
index a3256ab6..00000000
--- a/src/main/java/org/caosdb/server/resource/transaction/handlers/IDHandler.java
+++ /dev/null
@@ -1,36 +0,0 @@
-/// *
-// * ** header v3.0
-// * This file is a part of the CaosDB Project.
-// *
-// * Copyright (C) 2018 Research Group Biomedical Physics,
-// * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-// *
-// * This program is free software: you can redistribute it and/or modify
-// * it under the terms of the GNU Affero General Public License as
-// * published by the Free Software Foundation, either version 3 of the
-// * License, or (at your option) any later version.
-// *
-// * This program is distributed in the hope that it will be useful,
-// * but WITHOUT ANY WARRANTY; without even the implied warranty of
-// * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// * GNU Affero General Public License for more details.
-// *
-// * You should have received a copy of the GNU Affero General Public License
-// * along with this program. If not, see <https://www.gnu.org/licenses/>.
-// *
-// * ** end header
-// */
-// package caosdb.server.resource.transaction.handlers;
-//
-// import caosdb.server.entity.container.EntityByIdContainer;
-// import caosdb.server.resource.transaction.RetrieveEntityResource;
-//
-// public class IDHandler<T extends EntityByIdContainer> extends RequestHandler<T> {
-//
-// @Override
-// public void handle(final RetrieveEntityResource t, final T container) throws Exception {
-// for (final int id : t.getRequestedIDs()) {
-// container.add(id);
-// }
-// }
-// }
diff --git a/src/main/java/org/caosdb/server/resource/transaction/handlers/RequestHandler.java b/src/main/java/org/caosdb/server/resource/transaction/handlers/RequestHandler.java
deleted file mode 100644
index 2931d526..00000000
--- a/src/main/java/org/caosdb/server/resource/transaction/handlers/RequestHandler.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/// *
-// * ** header v3.0
-// * This file is a part of the CaosDB Project.
-// *
-// * Copyright (C) 2018 Research Group Biomedical Physics,
-// * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-// *
-// * This program is free software: you can redistribute it and/or modify
-// * it under the terms of the GNU Affero General Public License as
-// * published by the Free Software Foundation, either version 3 of the
-// * License, or (at your option) any later version.
-// *
-// * This program is distributed in the hope that it will be useful,
-// * but WITHOUT ANY WARRANTY; without even the implied warranty of
-// * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// * GNU Affero General Public License for more details.
-// *
-// * You should have received a copy of the GNU Affero General Public License
-// * along with this program. If not, see <https://www.gnu.org/licenses/>.
-// *
-// * ** end header
-// */
-// package caosdb.server.resource.transaction.handlers;
-//
-// import caosdb.server.entity.container.TransactionContainer;
-// import caosdb.server.resource.transaction.RetrieveEntityResource;
-//
-// public abstract class RequestHandler<T extends TransactionContainer> {
-//
-// public abstract void handle(final RetrieveEntityResource t, T container) throws Exception;
-// }
diff --git a/src/main/java/org/caosdb/server/resource/transaction/handlers/RetrieveGlobalEntityPermissionsHandler.java b/src/main/java/org/caosdb/server/resource/transaction/handlers/RetrieveGlobalEntityPermissionsHandler.java
deleted file mode 100644
index d87f9a06..00000000
--- a/src/main/java/org/caosdb/server/resource/transaction/handlers/RetrieveGlobalEntityPermissionsHandler.java
+++ /dev/null
@@ -1,37 +0,0 @@
-/// *
-// * ** header v3.0
-// * This file is a part of the CaosDB Project.
-// *
-// * Copyright (C) 2018 Research Group Biomedical Physics,
-// * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-// *
-// * This program is free software: you can redistribute it and/or modify
-// * it under the terms of the GNU Affero General Public License as
-// * published by the Free Software Foundation, either version 3 of the
-// * License, or (at your option) any later version.
-// *
-// * This program is distributed in the hope that it will be useful,
-// * but WITHOUT ANY WARRANTY; without even the implied warranty of
-// * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// * GNU Affero General Public License for more details.
-// *
-// * You should have received a copy of the GNU Affero General Public License
-// * along with this program. If not, see <https://www.gnu.org/licenses/>.
-// *
-// * ** end header
-// */
-// package caosdb.server.resource.transaction.handlers;
-//
-// import caosdb.server.entity.container.RetrieveContainer;
-// import caosdb.server.permissions.EntityPermission;
-// import caosdb.server.resource.transaction.RetrieveEntityResource;
-//
-// public class RetrieveGlobalEntityPermissionsHandler extends SimpleGetRequestHandler {
-//
-// @Override
-// public void handle(final RetrieveEntityResource t, final RetrieveContainer container) throws
-// Exception {
-// super.handle(t, container);
-// container.addMessage(EntityPermission.getAllEntityPermissions());
-// }
-// }
diff --git a/src/main/java/org/caosdb/server/resource/transaction/handlers/RetriveOwnerRequestHandler.java b/src/main/java/org/caosdb/server/resource/transaction/handlers/RetriveOwnerRequestHandler.java
deleted file mode 100644
index cd059526..00000000
--- a/src/main/java/org/caosdb/server/resource/transaction/handlers/RetriveOwnerRequestHandler.java
+++ /dev/null
@@ -1,36 +0,0 @@
-/// *
-// * ** header v3.0
-// * This file is a part of the CaosDB Project.
-// *
-// * Copyright (C) 2018 Research Group Biomedical Physics,
-// * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-// *
-// * This program is free software: you can redistribute it and/or modify
-// * it under the terms of the GNU Affero General Public License as
-// * published by the Free Software Foundation, either version 3 of the
-// * License, or (at your option) any later version.
-// *
-// * This program is distributed in the hope that it will be useful,
-// * but WITHOUT ANY WARRANTY; without even the implied warranty of
-// * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// * GNU Affero General Public License for more details.
-// *
-// * You should have received a copy of the GNU Affero General Public License
-// * along with this program. If not, see <https://www.gnu.org/licenses/>.
-// *
-// * ** end header
-// */
-// package caosdb.server.resource.transaction.handlers;
-//
-// import caosdb.server.entity.EntityInterface;
-// import caosdb.server.entity.container.RetrieveContainer;
-// import caosdb.server.resource.transaction.RetrieveEntityResource;
-//
-// public class RetriveOwnerRequestHandler extends SimpleGetRequestHandler {
-//
-// @Override
-// public void handle(final RetrieveEntityResource t, final RetrieveContainer container) throws
-// Exception {
-// super.handle(t, container);
-// }
-// }
diff --git a/src/main/java/org/caosdb/server/resource/transaction/handlers/SimpleDeleteRequestHandler.java b/src/main/java/org/caosdb/server/resource/transaction/handlers/SimpleDeleteRequestHandler.java
deleted file mode 100644
index 02e6cfd1..00000000
--- a/src/main/java/org/caosdb/server/resource/transaction/handlers/SimpleDeleteRequestHandler.java
+++ /dev/null
@@ -1,55 +0,0 @@
-/// *
-// * ** header v3.0
-// * This file is a part of the CaosDB Project.
-// *
-// * Copyright (C) 2018 Research Group Biomedical Physics,
-// * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-// * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
-// * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
-// *
-// * This program is free software: you can redistribute it and/or modify
-// * it under the terms of the GNU Affero General Public License as
-// * published by the Free Software Foundation, either version 3 of the
-// * License, or (at your option) any later version.
-// *
-// * This program is distributed in the hope that it will be useful,
-// * but WITHOUT ANY WARRANTY; without even the implied warranty of
-// * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// * GNU Affero General Public License for more details.
-// *
-// * You should have received a copy of the GNU Affero General Public License
-// * along with this program. If not, see <https://www.gnu.org/licenses/>.
-// *
-// * ** end header
-// */
-// package caosdb.server.resource.transaction.handlers;
-//
-// import caosdb.server.entity.container.DeleteContainer;
-// import caosdb.server.resource.transaction.EntityResource;
-//
-// public class SimpleDeleteRequestHandler extends RequestHandler<DeleteContainer> {
-//
-// @Override
-// public void handle(final EntityResource t, final DeleteContainer container) throws Exception {
-// // TODO a lot of code duplication, see SimpleGetRequestHandle#handle.
-// // However, this is about to be changed again when string ids are
-// // introduced, anyways. So we just leave it.
-// for (final String item : t.getRequestedItems()) {
-// String[] elem = item.split("@", 1);
-// Integer id = null;
-// String version = null;
-// try {
-// id = Integer.parseInt(elem[0]);
-// } catch (NumberFormatException e) {
-// // pass
-// }
-// if (elem.length > 1) {
-// version = elem[1];
-// }
-//
-// if (id != null) {
-// container.add(id, version);
-// }
-// }
-// }
-// }
diff --git a/src/main/java/org/caosdb/server/resource/transaction/handlers/SimpleGetRequestHandler.java b/src/main/java/org/caosdb/server/resource/transaction/handlers/SimpleGetRequestHandler.java
deleted file mode 100644
index 0e127d0e..00000000
--- a/src/main/java/org/caosdb/server/resource/transaction/handlers/SimpleGetRequestHandler.java
+++ /dev/null
@@ -1,38 +0,0 @@
-/// *
-// * ** header v3.0
-// * This file is a part of the CaosDB Project.
-// *
-// * Copyright (C) 2018 Research Group Biomedical Physics,
-// * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-// *
-// * This program is free software: you can redistribute it and/or modify
-// * it under the terms of the GNU Affero General Public License as
-// * published by the Free Software Foundation, either version 3 of the
-// * License, or (at your option) any later version.
-// *
-// * This program is distributed in the hope that it will be useful,
-// * but WITHOUT ANY WARRANTY; without even the implied warranty of
-// * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// * GNU Affero General Public License for more details.
-// *
-// * You should have received a copy of the GNU Affero General Public License
-// * along with this program. If not, see <https://www.gnu.org/licenses/>.
-// *
-// * ** end header
-// */
-// package caosdb.server.resource.transaction.handlers;
-//
-// import caosdb.server.entity.container.RetrieveContainer;
-// import caosdb.server.resource.transaction.RetrieveEntityResource;
-//
-// public class SimpleGetRequestHandler extends IDHandler<RetrieveContainer> {
-//
-// @Override
-// public void handle(final RetrieveEntityResource t, final RetrieveContainer container) throws
-// Exception {
-// super.handle(t, container);
-// for (final String name : t.getRequestedNames()) {
-// container.add(name);
-// }
-// }
-// }
diff --git a/src/main/java/org/caosdb/server/resource/transaction/handlers/SimpleWriteHandler.java b/src/main/java/org/caosdb/server/resource/transaction/handlers/SimpleWriteHandler.java
deleted file mode 100644
index a7e50270..00000000
--- a/src/main/java/org/caosdb/server/resource/transaction/handlers/SimpleWriteHandler.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/// *
-// * ** header v3.0
-// * This file is a part of the CaosDB Project.
-// *
-// * Copyright (C) 2018 Research Group Biomedical Physics,
-// * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-// *
-// * This program is free software: you can redistribute it and/or modify
-// * it under the terms of the GNU Affero General Public License as
-// * published by the Free Software Foundation, either version 3 of the
-// * License, or (at your option) any later version.
-// *
-// * This program is distributed in the hope that it will be useful,
-// * but WITHOUT ANY WARRANTY; without even the implied warranty of
-// * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// * GNU Affero General Public License for more details.
-// *
-// * You should have received a copy of the GNU Affero General Public License
-// * along with this program. If not, see <https://www.gnu.org/licenses/>.
-// *
-// * ** end header
-// */
-// package caosdb.server.resource.transaction.handlers;
-//
-// import caosdb.server.entity.container.WritableContainer;
-// import caosdb.server.resource.transaction.EntityResource;
-//
-// public class SimpleWriteHandler<T extends WritableContainer> extends RequestHandler<T> {
-//
-//
-// @Override
-// public void handle(final EntityResource t, final T container) throws Exception {
-// }
-// }
diff --git a/src/main/java/org/caosdb/server/transaction/Delete.java b/src/main/java/org/caosdb/server/transaction/Delete.java
deleted file mode 100644
index a3bf24c8..00000000
--- a/src/main/java/org/caosdb/server/transaction/Delete.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/// *
-// * ** header v3.0
-// * This file is a part of the CaosDB Project.
-// *
-// * Copyright (C) 2018 Research Group Biomedical Physics,
-// * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-// *
-// * This program is free software: you can redistribute it and/or modify
-// * it under the terms of the GNU Affero General Public License as
-// * published by the Free Software Foundation, either version 3 of the
-// * License, or (at your option) any later version.
-// *
-// * This program is distributed in the hope that it will be useful,
-// * but WITHOUT ANY WARRANTY; without even the implied warranty of
-// * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// * GNU Affero General Public License for more details.
-// *
-// * You should have received a copy of the GNU Affero General Public License
-// * along with this program. If not, see <https://www.gnu.org/licenses/>.
-// *
-// * ** end header
-// */
-// package caosdb.server.transaction;
-//
-// import caosdb.server.entity.container.WritableContainer;
-//
-// public class Delete extends WriteTransaction {
-//
-// public Delete(final WritableContainer container) {
-// super(container);
-// }
-//
-// @Override
-// protected void init() throws Exception {}
-//
-// @Override
-// protected void preCheck() throws InterruptedException, Exception {
-// }
-//
-// @Override
-// protected void postCheck() {}
-//
-// @Override
-// protected void postTransaction() {
-// }
-//
-// @Override
-// public void transaction() throws Exception {
-// }
-//
-//
-// @Override
-// public boolean logHistory() {
-// return true;
-// }
-// }
diff --git a/src/main/java/org/caosdb/server/transaction/Insert.java b/src/main/java/org/caosdb/server/transaction/Insert.java
deleted file mode 100644
index 13ef9c96..00000000
--- a/src/main/java/org/caosdb/server/transaction/Insert.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/// *
-// * ** header v3.0
-// * This file is a part of the CaosDB Project.
-// *
-// * Copyright (C) 2018 Research Group Biomedical Physics,
-// * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-// *
-// * This program is free software: you can redistribute it and/or modify
-// * it under the terms of the GNU Affero General Public License as
-// * published by the Free Software Foundation, either version 3 of the
-// * License, or (at your option) any later version.
-// *
-// * This program is distributed in the hope that it will be useful,
-// * but WITHOUT ANY WARRANTY; without even the implied warranty of
-// * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// * GNU Affero General Public License for more details.
-// *
-// * You should have received a copy of the GNU Affero General Public License
-// * along with this program. If not, see <https://www.gnu.org/licenses/>.
-// *
-// * ** end header
-// */
-// package caosdb.server.transaction;
-//
-// import caosdb.server.entity.container.WritableContainer;
-//
-// public class Insert extends WriteTransaction {
-//
-// public Insert(final WritableContainer container) {
-// super(container);
-// }
-//
-// @Override
-// protected void init() throws Exception {
-//
-//
-// }
-//
-// @Override
-// protected void preCheck() throws InterruptedException {
-// }
-//
-// @Override
-// protected void postCheck() {}
-//
-// @Override
-// protected void postTransaction() {}
-//
-// @Override
-// public void transaction() throws Exception {
-// // write new entities to database
-// insert(getContainer(), getAccess());
-// }
-//
-// @Override
-// public boolean logHistory() {
-// return true;
-// }
-// }
diff --git a/src/main/java/org/caosdb/server/transaction/Update.java b/src/main/java/org/caosdb/server/transaction/Update.java
deleted file mode 100644
index 74fd2deb..00000000
--- a/src/main/java/org/caosdb/server/transaction/Update.java
+++ /dev/null
@@ -1,401 +0,0 @@
-/// *
-// * ** header v3.0
-// * This file is a part of the CaosDB Project.
-// *
-// * Copyright (C) 2018 Research Group Biomedical Physics,
-// * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-// *
-// * This program is free software: you can redistribute it and/or modify
-// * it under the terms of the GNU Affero General Public License as
-// * published by the Free Software Foundation, either version 3 of the
-// * License, or (at your option) any later version.
-// *
-// * This program is distributed in the hope that it will be useful,
-// * but WITHOUT ANY WARRANTY; without even the implied warranty of
-// * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// * GNU Affero General Public License for more details.
-// *
-// * You should have received a copy of the GNU Affero General Public License
-// * along with this program. If not, see <https://www.gnu.org/licenses/>.
-// *
-// * ** end header
-// */
-// package caosdb.server.transaction;
-//
-// import java.io.IOException;
-// import java.security.NoSuchAlgorithmException;
-// import java.util.HashSet;
-// import java.util.Set;
-// import org.apache.shiro.authz.AuthorizationException;
-// import com.google.common.base.Objects;
-// import caosdb.server.CaosDBException;
-// import caosdb.server.database.access.Access;
-// import caosdb.server.database.backend.transaction.RetrieveFullEntity;
-// import caosdb.server.database.backend.transaction.UpdateEntity;
-// import caosdb.server.entity.Entity;
-// import caosdb.server.entity.EntityInterface;
-// import caosdb.server.entity.FileProperties;
-// import caosdb.server.entity.RetrieveEntity;
-// import caosdb.server.entity.container.TransactionContainer;
-// import caosdb.server.entity.container.UpdateContainer;
-// import caosdb.server.entity.wrapper.Parent;
-// import caosdb.server.entity.wrapper.Property;
-// import caosdb.server.permissions.EntityPermission;
-// import caosdb.server.permissions.Permission;
-// import caosdb.server.utils.EntityStatus;
-// import caosdb.server.utils.ServerMessages;
-//
-// public class Update extends WriteTransaction {
-//
-// public Update(final UpdateContainer container) {
-// super(container);
-// }
-//
-// @Override
-// protected void preCheck() throws Exception {}
-//
-// @Override
-// protected void init() throws Exception {
-// // collect all ids of the entities which are to be updated.
-// final TransactionContainer oldContainer = new TransactionContainer();
-// for (final EntityInterface entity : getContainer()) {
-// // entity has no id -> it cannot be updated.
-// if (!entity.hasId()) {
-// entity.addError(ServerMessages.ENTITY_HAS_NO_ID);
-// entity.setEntityStatus(EntityStatus.UNQUALIFIED);
-// continue;
-// }
-//
-// // add entity with this id to the updateContainer
-// if (entity.getEntityStatus() == EntityStatus.QUALIFIED) {
-// final Entity oldEntity = new RetrieveEntity(entity.getId());
-// oldContainer.add(oldEntity);
-// }
-// }
-//
-// // allocate strong (write) access. Only one thread can do this
-// // at a time. But weak access can still be acquired by other
-// // thread until the allocated strong access is actually
-// // acquired.
-// setAccess(getMonitor().allocateStrongAccess(this));
-//
-// // retrieve a container which contains all id of those entities
-// // which are to be updated.
-// execute(new RetrieveFullEntity(oldContainer), getAccess());
-//
-// // Check if any updates are to be processed.
-// for (final EntityInterface newEntity : getContainer()) {
-// if (newEntity.getEntityStatus() == EntityStatus.QUALIFIED) {
-// innerLoop:
-// for (final EntityInterface oldEntity : oldContainer) {
-// if (oldEntity.getId().equals(newEntity.getId())) {
-// if (oldEntity.getEntityStatus() == EntityStatus.NONEXISTENT) {
-// newEntity.addError(ServerMessages.ENTITY_DOES_NOT_EXIST);
-// newEntity.setEntityStatus(EntityStatus.UNQUALIFIED);
-// } else {
-// // dereference files (upload only)
-// if (newEntity.hasFileProperties() && !newEntity.getFileProperties().isPickupable())
-// {
-//
-// if (newEntity.getFileProperties().getTmpIdentifyer() != null) {
-// // get file by tmpIdentifier
-// final FileProperties f =
-// getContainer()
-// .getFiles()
-// .get(newEntity.getFileProperties().getTmpIdentifyer());
-//
-// // is it there?
-// if (f != null) {
-// newEntity.getFileProperties().setFile(f.getFile());
-//
-// // has it a thumbnail?
-// if (f.getThumbnail() != null) {
-// newEntity.getFileProperties().setThumbnail(f.getThumbnail());
-// } else {
-// final FileProperties thumbnail =
-// getContainer()
-// .getFiles()
-// .get(newEntity.getFileProperties().getTmpIdentifyer() +
-// ".thumbnail");
-// if (thumbnail != null) {
-// newEntity.getFileProperties().setThumbnail(thumbnail.getFile());
-// } else {
-// newEntity.addWarning(ServerMessages.THUMBNAIL_HAS_NOT_BEEN_UPLOAED);
-// }
-// }
-// } else {
-// newEntity.addError(ServerMessages.FILE_HAS_NOT_BEEN_UPLOAED);
-// newEntity.setEntityStatus(EntityStatus.UNQUALIFIED);
-// }
-//
-// } else {
-// // in case no file has been uploaded,
-// // the file is expected to stay
-// // unchanged. Therefore we let the file
-// // object point to the original file in
-// // the file system.
-// newEntity
-// .getFileProperties()
-// .setFile(oldEntity.getFileProperties().retrieveFromFileSystem());
-// }
-// }
-//
-// try {
-// checkPermissions(newEntity, deriveUpdate(newEntity, oldEntity));
-// } catch (final AuthorizationException exc) {
-// newEntity.setEntityStatus(EntityStatus.UNQUALIFIED);
-// newEntity.addError(ServerMessages.AUTHORIZATION_ERROR);
-// newEntity.addInfo(exc.getMessage());
-// }
-// }
-// break innerLoop;
-// }
-// }
-// }
-// }
-//
-// // make schedule of those entities which are to be updated.
-// makeSchedule();
-// }
-//
-// @Override
-// protected void postCheck() {}
-//
-// @Override
-// protected void postTransaction() {}
-//
-// @Override
-// public void transaction() throws Exception {
-// // write new entities to database
-// update(getContainer(), getAccess());
-// }
-//
-// private void update(final TransactionContainer container, final Access access) throws Exception
-// {
-// if (container.getStatus().ordinal() >= EntityStatus.QUALIFIED.ordinal()) {
-// execute(new UpdateEntity(container), access);
-// }
-// }
-//
-// /** Check if the user has all permissions */
-// @Override
-// public void checkPermissions(final EntityInterface entity, final Set<Permission> permissions) {
-// for (final Permission p : permissions) {
-// entity.checkPermission(p);
-// }
-// }
-//
-// /**
-// * The entity is set to VALID iff there are no updates to be processed. The entity is set to
-// * QUALIFIED otherwise.
-// *
-// * @param newEntity
-// * @param oldEntity
-// * @throws CaosDBException
-// * @throws IOException
-// * @throws NoSuchAlgorithmException
-// */
-// public static HashSet<Permission> deriveUpdate(
-// final EntityInterface newEntity, final EntityInterface oldEntity)
-// throws NoSuchAlgorithmException, IOException, CaosDBException {
-// final HashSet<Permission> needPermissions = new HashSet<>();
-// boolean updatetable = false;
-//
-// // new acl?
-// if (newEntity.hasEntityACL() && !newEntity.getEntityACL().equals(oldEntity.getEntityACL())) {
-// oldEntity.checkPermission(EntityPermission.EDIT_ACL);
-// if (!newEntity
-// .getEntityACL()
-// .getPriorityEntityACL()
-// .equals(oldEntity.getEntityACL().getPriorityEntityACL())) {
-// // priority acl is to be changed?
-// oldEntity.checkPermission(Permission.EDIT_PRIORITY_ACL);
-// }
-// updatetable = true;
-// } else if (!newEntity.hasEntityACL()) {
-// newEntity.setEntityACL(oldEntity.getEntityACL());
-// }
-//
-// // new query template definition?
-// if (!Objects.equal(
-// newEntity.getQueryTemplateDefinition(), oldEntity.getQueryTemplateDefinition())) {
-// needPermissions.add(EntityPermission.UPDATE_QUERY_TEMPLATE_DEFINITION);
-// updatetable = true;
-// }
-//
-// // new datatype?
-// if (newEntity.hasDatatype()
-// && oldEntity.hasDatatype()
-// && !newEntity.getDatatype().equals(oldEntity.getDatatype())
-// || newEntity.hasDatatype() ^ oldEntity.hasDatatype()) {
-// needPermissions.add(EntityPermission.UPDATE_DATA_TYPE);
-// updatetable = true;
-// }
-//
-// // entity role
-// if (newEntity.hasRole()
-// && oldEntity.hasRole()
-// && !newEntity.getRole().equals(oldEntity.getRole())
-// || newEntity.hasRole() ^ oldEntity.hasRole()) {
-// needPermissions.add(EntityPermission.UPDATE_ROLE);
-// updatetable = true;
-// }
-//
-// // entity value
-// if (newEntity.hasValue()
-// && oldEntity.hasValue()
-// && !newEntity.getValue().equals(oldEntity.getValue())
-// || newEntity.hasValue() ^ oldEntity.hasValue()) {
-// needPermissions.add(EntityPermission.UPDATE_VALUE);
-// updatetable = true;
-// }
-//
-// // entity name
-// if (newEntity.hasName()
-// && oldEntity.hasName()
-// && !newEntity.getName().equals(oldEntity.getName())
-// || newEntity.hasName() ^ oldEntity.hasName()) {
-// needPermissions.add(EntityPermission.UPDATE_NAME);
-// updatetable = true;
-// }
-//
-// // entity description
-// if (newEntity.hasDescription()
-// && oldEntity.hasDescription()
-// && !newEntity.getDescription().equals(oldEntity.getDescription())
-// || newEntity.hasDescription() ^ oldEntity.hasDescription()) {
-// needPermissions.add(EntityPermission.UPDATE_DESCRIPTION);
-// updatetable = true;
-// }
-//
-// // file properties
-// if (newEntity.hasFileProperties() || oldEntity.hasFileProperties()) {
-// if (newEntity.hasFileProperties() && !oldEntity.hasFileProperties()) {
-// // add a file
-// needPermissions.add(EntityPermission.UPDATE_ADD_FILE);
-// updatetable = true;
-// } else if (!newEntity.hasFileProperties() && oldEntity.hasFileProperties()) {
-// // remove a file
-// needPermissions.add(EntityPermission.UPDATE_REMOVE_FILE);
-// updatetable = true;
-// } else {
-// // change file
-// final FileProperties newFile = newEntity.getFileProperties();
-// final FileProperties oldFile = oldEntity.getFileProperties();
-//
-// // file path
-// if (newFile.hasPath() && oldFile.hasPath() && !newFile.getPath().equals(oldFile.getPath())
-// || newFile.hasPath() ^ oldFile.hasPath()) {
-// // this means, the location of the file is to be changed
-// needPermissions.add(EntityPermission.UPDATE_MOVE_FILE);
-// updatetable = true;
-// }
-//
-// // change actual file (different byte code!)
-// if (!oldFile.retrieveFromFileSystem().equals(newFile.getFile())) {
-// // CHANGE A FILE is like REMOVE AND ADD
-// needPermissions.add(EntityPermission.UPDATE_REMOVE_FILE);
-// needPermissions.add(EntityPermission.UPDATE_ADD_FILE);
-// updatetable = true;
-// }
-// }
-// }
-//
-// // properties
-// outerLoop:
-// for (final EntityInterface newProperty : newEntity.getProperties()) {
-//
-// // find corresponding oldProperty for this new property and make a
-// // diff.
-// if (newProperty.hasId()) {
-// for (final EntityInterface oldProperty : oldEntity.getProperties()) {
-// if (newProperty.getId().equals(oldProperty.getId())) {
-// // do not check again.
-// oldEntity.getProperties().remove(oldProperty);
-//
-// if (((Property) oldProperty).getPIdx() != ((Property) newProperty).getPIdx()) {
-// // change order of properties
-// needPermissions.add(EntityPermission.UPDATE_ADD_PROPERTY);
-// needPermissions.add(EntityPermission.UPDATE_REMOVE_PROPERTY);
-// updatetable = true;
-// }
-//
-// deriveUpdate(newProperty, oldProperty);
-// if (newProperty.getEntityStatus() == EntityStatus.QUALIFIED) {
-// needPermissions.add(EntityPermission.UPDATE_ADD_PROPERTY);
-// needPermissions.add(EntityPermission.UPDATE_REMOVE_PROPERTY);
-// updatetable = true;
-// }
-//
-// continue outerLoop;
-// }
-// }
-// } else {
-// newProperty.setEntityStatus(EntityStatus.UNQUALIFIED);
-// newProperty.addError(ServerMessages.ENTITY_HAS_NO_ID);
-// newProperty.addInfo("On updates, allways specify the id not just the name.");
-// newEntity.addError(ServerMessages.ENTITY_HAS_UNQUALIFIED_PROPERTIES);
-// newEntity.setEntityStatus(EntityStatus.UNQUALIFIED);
-// return needPermissions;
-// }
-//
-// // no corresponding property found -> this property is new.
-// needPermissions.add(EntityPermission.UPDATE_ADD_PROPERTY);
-// updatetable = true;
-// }
-//
-// // some old properties left (and not matched with new ones) -> there are
-// // properties to be deleted.
-// if (!oldEntity.getProperties().isEmpty()) {
-// needPermissions.add(EntityPermission.UPDATE_REMOVE_PROPERTY);
-// updatetable = true;
-// }
-//
-// // update parents
-// outerLoop:
-// for (final Parent newParent : newEntity.getParents()) {
-//
-// // find corresponding oldParent
-// if (newParent.hasId()) {
-// for (final Parent oldParent : oldEntity.getParents()) {
-// if (oldParent.getId().equals(newParent.getId())) {
-// // still there! do not check this one again
-// oldEntity.getParents().remove(oldParent);
-// continue outerLoop;
-// }
-// }
-// } else {
-// newParent.setEntityStatus(EntityStatus.UNQUALIFIED);
-// newParent.addError(ServerMessages.ENTITY_HAS_NO_ID);
-// newParent.addInfo("On updates, allways specify the id not just the name.");
-// newEntity.addError(ServerMessages.ENTITY_HAS_UNQUALIFIED_PROPERTIES);
-// newEntity.setEntityStatus(EntityStatus.UNQUALIFIED);
-// return needPermissions;
-// }
-//
-// // no corresponding parent found -> this parent is new.
-// needPermissions.add(EntityPermission.UPDATE_ADD_PARENT);
-// updatetable = true;
-// }
-//
-// // some old parents left (and not matched with new ones) -> there are
-// // parents to be deleted.
-// if (!oldEntity.getParents().isEmpty()) {
-// needPermissions.add(EntityPermission.UPDATE_REMOVE_PARENT);
-// updatetable = true;
-// }
-//
-// // nothing to be updated
-// if (!updatetable) {
-// newEntity.setEntityStatus(EntityStatus.VALID);
-// newEntity.addInfo("Nothing to be updated.");
-// }
-//
-// return needPermissions;
-// }
-//
-// @Override
-// public boolean logHistory() {
-// return true;
-// }
-// }
diff --git a/src/main/java/org/caosdb/server/transaction/WriteTransaction.java b/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
index f57d4cab..86255f21 100644
--- a/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
@@ -1,19 +1,24 @@
/*
- * ** header v3.0 This file is a part of the CaosDB Project.
+ * ** header v3.0
+ * This file is a part of the CaosDB Project.
*
- * Copyright (C) 2018 Research Group Biomedical Physics, Max-Planck-Institute for Dynamics and
- * Self-Organization Göttingen
+ * Copyright (C) 2018 Research Group Biomedical Physics,
+ * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
*
- * This program is free software: you can redistribute it and/or modify it under the terms of the
- * GNU Affero General Public License as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
*
- * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Affero General Public License for more details.
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
*
- * You should have received a copy of the GNU Affero General Public License along with this program.
- * If not, see <https://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
*
* ** end header
*/
@@ -77,18 +82,10 @@ public class WriteTransaction extends Transaction<WritableContainer>
private void update(final TransactionContainer container, final Access access) throws Exception {
execute(new UpdateEntityTransaction(container), access);
- setVersionDates(container);
- }
-
- private void setVersionDates(TransactionContainer container) {
- for (EntityInterface e : container) {
- if (e.hasVersion()) e.getVersion().setDate(getTimestamp());
- }
}
private void insert(final TransactionContainer container, final Access access) throws Exception {
execute(new InsertEntityTransaction(container), access);
- setVersionDates(container);
}
private void delete(final TransactionContainer container, final Access access) throws Exception {
--
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