diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d3331a3b24145747836c0898ff852a8ade438bb4..e9b2b144f896c631cfb1129ec249c0bd35b386c1 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,10 +1,10 @@
#
-# ** 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) 2019 Henrik tom Wörden
+# Copyright (C) 2021 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
@@ -19,23 +19,45 @@
# 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
-#
variables:
DEPLOY_REF: dev
CI_REGISTRY_IMAGE: $CI_REGISTRY/caosdb/src/caosdb-server/caosdb-server-testenv:latest
+ GIT_SUBMODULE_STRATEGY: normal
+
+ DEPLOY_PIPELINE: https://gitlab.indiscale.com/api/v4/projects/14/trigger/pipeline
+
+ ## FOR DEBUGGING
+ TRIGGERED_BY_REPO: SERVER
+ TRIGGERED_BY_REF: $CI_COMMIT_REF_NAME
+ TRIGGERED_BY_HASH: $CI_COMMIT_SHORT_SHA
image: $CI_REGISTRY_IMAGE
stages:
+ - info
- setup
- test
- deploy
+.env: &env
+ - F_BRANCH="${CI_COMMIT_REF_NAME}"
+
+info:
+ tags: [cached-dind]
+ image: docker:20.10
+ stage: info
+ needs: []
+ script:
+ - *env
+ - echo "Pipeline triggered by $TRIGGERED_BY_REPO@$TRIGGERED_BY_REF ($TRIGGERED_BY_HASH)"
+ - echo "Pipeline will trigger DEPLOY with branch $DEPLOY_REF"
+ - echo "F_BRANCH = $F_BRANCH"
+
+
# Setup: Build a docker image in which tests for this repository can run
build-testenv:
tags: [ cached-dind ]
- image: docker:19.03
+ image: docker:20.10
stage: setup
timeout: 3h
only:
@@ -61,18 +83,24 @@ test:
- mvn compile
- mvn test
+
+
# Deploy: Trigger building of server image and integration tests
trigger_build:
tags: [ docker ]
stage: deploy
script:
+ - *env
+
+ - echo "Triggering pipeline ${DEPLOY_PIPELINE}@${DEPLOY_REF} with F_BRANCH=${F_BRANCH}"
- /usr/bin/curl -X POST
-F token=$CI_JOB_TOKEN
- -F "variables[F_BRANCH]=$CI_COMMIT_REF_NAME"
-F "variables[SERVER]=$CI_COMMIT_REF_NAME"
- -F "variables[TriggerdBy]=SERVER"
- -F "variables[TriggerdByHash]=$CI_COMMIT_SHORT_SHA"
- -F ref=$DEPLOY_REF https://gitlab.indiscale.com/api/v4/projects/14/trigger/pipeline
+ -F "variables[F_BRANCH]=$F_BRANCH"
+ -F "variables[TRIGGERED_BY_REPO]=$TRIGGERED_BY_REPO"
+ -F "variables[TRIGGERED_BY_REF]=$TRIGGERED_BY_REF"
+ -F "variables[TRIGGERED_BY_HASH]=$TRIGGERED_BY_HASH"
+ -F ref=$DEPLOY_REF $DEPLOY_PIPELINE
# Build the sphinx documentation and make it ready for deployment by Gitlab Pages
# Special job for serving a static website. See https://docs.gitlab.com/ee/ci/yaml/README.html#pages
@@ -85,7 +113,7 @@ pages_prepare: &pages_prepare
script:
- echo "Deploying..."
- make doc
- - cp -r build/doc/html public
+ - rm -r public || true ; cp -r build/doc/html public
artifacts:
paths:
- public
diff --git a/.gitmodules b/.gitmodules
index 7a232e00813ac832eb23f82ae0e3104738bf9b9d..175f1f1740ad20fa27dd445118ff4285c1aaec25 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -2,3 +2,6 @@
path = caosdb-webui
url = ../caosdb-webui/
branch = dev
+[submodule "caosdb-proto"]
+ path = caosdb-proto
+ url = ../caosdb-proto/
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 03a7868390523098ebe88c2d7758b6863085ee9a..ca41b8287dba890cdeadabcf4886aa3f3308bfd2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,12 +5,47 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [v0.6.0] - 2021-11-17
+(Timm Fitschen)
+
+### Added
+
+* Endpoint for CaosDB GRPC API 0.1 (see https://gitlab.com/caosdb-proto.git for
+ more).
+ Authentication is supported via a Basic scheme, using the well-known
+ "authentication" header.
+ Notable limitations of the current implementation of the API:
+ * It is currently not possible to mix retrievals
+ (caosdb.entity.v1.RetrieveRequest) with any other transaction type - so
+ transaction are either read-only or write-only. The server throws an error
+ if it finds mixed read/write transactions.
+ * It is currently not possible to have more that one query
+ (caosdb.entity.v1.Query) in a single transaction. The server throws an
+ error if it finds more than one query.
+
+
+### Changed
+
+### Deprecated
+
+* Legacy XML/HTTP API (also known as the REST API). The API will not be removed
+ until the web interface (caosdb-webui) and the python client libraries have
+ been updated and freed from any dependencies. However, new clients should not
+ implement this API anymore.
+
+### Removed
+
+### Fixed
+
+### Security
+
## [v0.5.0] - 2021-10-19
### Added
* An openAPI specification of the XML api
-* New server configuration option `SERVER_BIND_ADDRESS`, which is the address to listen to. See [server.conf](conf/core/server.conf).
+* New server configuration option `SERVER_BIND_ADDRESS`, which is the address to listen to. See
+ [server.conf](conf/core/server.conf).
### Changed
diff --git a/DEPENDENCIES.md b/DEPENDENCIES.md
index 6159dcd8f0ed2296e2f3ac992830f03659d1a131..2f2967d0e835abc882650356ab2cf0c29bd9db47 100644
--- a/DEPENDENCIES.md
+++ b/DEPENDENCIES.md
@@ -1,5 +1,30 @@
-* caosdb-mysqlbackend == 5.0.0
-* Java 11
-* Apache Maven >= 3.6.0
-* make >= 4.2.0
+# Dependencies
+
+## For Building and Running the Server
+
+* `>=caosdb-proto 0.1.0`
+* `>=caosdb-mysqlbackend 5.0.0`
+* `>=Java 11`
+* `>=Apache Maven 3.6.0`
+* `>=Make 4.2`
+* `libpam` (if PAM authentication is required)
* More dependencies are being pulled and installed automatically by Maven. See the complete list of dependencies in the [pom.xml](pom.xml)
+
+## For Deploying a Web User Interface (optional)
+
+* `>=caosdb-webui 0.4.`
+
+## For Building the Documentation (optional)
+
+* `>=Python 3.8`
+* `>=pip 21.0.0`
+
+## For Server-side Scripting (optional)
+
+* `>=Python 3.8`
+* `>=pip 21.0.0`
+* `openpyxl` (for XLS/ODS export)
+
+## Recommended Packages
+
+* `openssl` (if a custom TLS certificate is required)
diff --git a/FEATURES.md b/FEATURES.md
new file mode 100644
index 0000000000000000000000000000000000000000..a5341f355fb67d0ca05e82642840789aac43bb45
--- /dev/null
+++ b/FEATURES.md
@@ -0,0 +1,21 @@
+# Features
+
+* The CaosDB Server implements a CaosDB GRPC API Endpoint (v0.1.0)
+ Authentication is supported via a Basic scheme, using the well-known
+ "authentication" header.
+ Notable limitations of the current implementation of the API:
+ * It is currently not possible to mix retrievals
+ (caosdb.entity.v1.RetrieveRequest) with any other transaction type - so
+ transaction are either read-only or write-only. The server throws an error
+ if it finds mixed read/write transactions.
+ * It is currently not possible to have more that one query
+ (caosdb.entity.v1.Query) in a single transaction. The server throws an
+ error if it finds more than one query.
+* Legacy XML/HTTP API (Deprecated)
+* Deployment of caosdb-webui (>=v0.4.1)
+* Server-side Scripting API (v0.1)
+* CaosDB Query Language Processor
+* CaosDB FileSystem
+* User Management, Authentication and Authorization
+ * Internal authentication service
+ * Authentication via an external service.
diff --git a/Makefile b/Makefile
index 7cafdb949cc213d1468383ce7c6a280452ef9904..29b7d5a51cb110e35f999da0a7c6b366b5bd0d05 100644
--- a/Makefile
+++ b/Makefile
@@ -57,7 +57,7 @@ formatting:
# Compile into a standalone jar file
jar: print-version easy-units
- mvn package -DskipTests
+ mvn -e package -DskipTests
@pushd target ; \
ln -s caosdb-server-$(CAOSDB_SERVER_VERSION)-jar-with-dependencies.jar caosdb-server.jar; \
popd
diff --git a/README_SETUP.md b/README_SETUP.md
index d738ad13768df8878b55808e4519202fc95dbd86..5065e3383c4ac2f2d549bfedb15687d0b4124ec0 100644
--- a/README_SETUP.md
+++ b/README_SETUP.md
@@ -5,26 +5,7 @@ more.
## Requirements
-### CaosDB Packages
-
-* caosdb-webui=0.2.1
-* caosdb-mysqlbackend=3.0
-
-### Third-party Software
-
-* `>=Java 8`
-* `>=Apache Maven 3.0.4`
-* `>=Python 3.4`
-* `>=pip 9.0.1`
-* `>=git 1.9.1`
-* `>=Make 3.81`
-* `>=Screen 4.01`
-* `>=MySQL 5.5` (better `>=5.6`) or `>=MariaDB 10.1`
-* `libpam` (if PAM authentication is required)
-* `unzip`
-* `openpyxl` (for XLS/ODS export)
-* `openssl` (if a custom TLS certificate is required)
-- `easy-units` >= 0.0.1 https://gitlab.com/timm.fitschen/easy-units
+See [DEPENDENCIES.md](DEPENDENCIES.md).
#### Install the requirements on Debian
diff --git a/RELEASE_GUIDELINES.md b/RELEASE_GUIDELINES.md
index 5c1fd68d462212e9b81dbc803fc590006df36a3d..4b9185323d3b6fdafbd049e7c68273c909de5a05 100644
--- a/RELEASE_GUIDELINES.md
+++ b/RELEASE_GUIDELINES.md
@@ -31,3 +31,5 @@ guidelines of the CaosDB Project
8. Update the version property in [pom.xml](./pom.xml) for the next
developlement round (with a `-SNAPSHOT` suffix).
+
+9. Add a gitlab release in the respective repository.
diff --git a/caosdb-proto b/caosdb-proto
new file mode 160000
index 0000000000000000000000000000000000000000..533c8e7341d0659e3cc43d834793a7a965703f55
--- /dev/null
+++ b/caosdb-proto
@@ -0,0 +1 @@
+Subproject commit 533c8e7341d0659e3cc43d834793a7a965703f55
diff --git a/caosdb-webui b/caosdb-webui
index d29e9a020f67fc07f42d1a023883b697ef922a8e..ed062d621ba1b8c7c05308fe8870d8dfee4c9b1f 160000
--- a/caosdb-webui
+++ b/caosdb-webui
@@ -1 +1 @@
-Subproject commit d29e9a020f67fc07f42d1a023883b697ef922a8e
+Subproject commit ed062d621ba1b8c7c05308fe8870d8dfee4c9b1f
diff --git a/conf/core/server.conf b/conf/core/server.conf
index ac6efe9778a34c2ce1337a2eba6889ca521a5141..246be9aa9285e4434803d3a71d18c24412922bf4 100644
--- a/conf/core/server.conf
+++ b/conf/core/server.conf
@@ -95,6 +95,11 @@ INITIAL_CONNECTIONS=1
MAX_CONNECTIONS=10
+# HTTPS port of the grpc end-point
+GRPC_SERVER_PORT_HTTPS=8443
+# HTTP port of the grpc end-point
+GRPC_SERVER_PORT_HTTP=
+
# --------------------------------------------------
# HTTPS options
# --------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 19a0ef7be51c4cef216d514bf999f11e46c64b81..f9ecf89e6236921b21e670e3522927e2416eb8c5 100644
--- a/pom.xml
+++ b/pom.xml
@@ -25,12 +25,18 @@
<modelVersion>4.0.0</modelVersion>
<groupId>org.caosdb</groupId>
<artifactId>caosdb-server</artifactId>
- <version>0.5.0</version>
+ <version>0.6.0</version>
<packaging>jar</packaging>
<name>CaosDB Server</name>
+ <scm>
+ <connection>scm:git:https://gitlab.indiscale.com/caosdb/src/caosdb-server.git</connection>
+ </scm>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.build.testSourceDirectory>src/test/java</project.build.testSourceDirectory>
+ <protobuf.version>3.14.0</protobuf.version>
+ <grpc.version>1.35.0</grpc.version>
+ <netty-tcnative.version>2.0.34.Final</netty-tcnative.version>
</properties>
<repositories>
<repository>
@@ -57,7 +63,7 @@
<dependency>
<groupId>org.quartz-scheduler</groupId>
<artifactId>quartz</artifactId>
- <version>2.3.2</version>
+ <version>2.3.2</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
@@ -100,7 +106,7 @@
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
- <version>8.0.19</version>
+ <version>8.0.19</version>
</dependency>
<dependency>
<groupId>org.xerial</groupId>
@@ -177,13 +183,58 @@
<artifactId>log4j-core</artifactId>
<version>2.11.1</version>
</dependency>
+ <dependency>
+ <groupId>io.grpc</groupId>
+ <artifactId>grpc-netty</artifactId>
+ <version>${grpc.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>io.netty</groupId>
+ <artifactId>netty-tcnative</artifactId>
+ <version>${netty-tcnative.version}</version>
+ <classifier>${os.detected.classifier}</classifier>
+ <scope>runtime</scope>
+ </dependency>
+ <dependency>
+ <groupId>io.grpc</groupId>
+ <artifactId>grpc-protobuf</artifactId>
+ <version>${grpc.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>io.grpc</groupId>
+ <artifactId>grpc-stub</artifactId>
+ <version>${grpc.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>javax.annotation</groupId>
+ <artifactId>javax.annotation-api</artifactId>
+ <version>1.3.2</version>
+ </dependency>
+ <dependency>
+ <groupId>com.google.protobuf</groupId>
+ <artifactId>protobuf-java</artifactId>
+ <version>${protobuf.version}</version>
+ </dependency>
</dependencies>
<build>
+ <resources>
+ <resource>
+ <directory>${basedir}/src/main/</directory>
+ <includes><include>**/*.properties</include></includes>
+ </resource>
+ </resources>
<sourceDirectory>${basedir}/src/main/java</sourceDirectory>
<scriptSourceDirectory>${basedir}/src/main/scripts</scriptSourceDirectory>
<testSourceDirectory>${basedir}/src/test/java</testSourceDirectory>
<outputDirectory>${basedir}/target/classes</outputDirectory>
<testOutputDirectory>${basedir}/target/test-classes</testOutputDirectory>
+ <extensions>
+ <extension>
+ <groupId>kr.motd.maven</groupId>
+ <artifactId>os-maven-plugin</artifactId>
+ <version>1.7.0</version>
+ </extension>
+ </extensions>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
@@ -256,6 +307,28 @@
<forkCount>0.5C</forkCount>
</configuration>
</plugin>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>buildnumber-maven-plugin</artifactId>
+ <version>1.4</version>
+ <executions>
+ <execution>
+ <phase>generate-resources</phase>
+ <goals>
+ <goal>create-metadata</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <addOutputDirectoryToResources>true</addOutputDirectoryToResources>
+ <applicationPropertyName>project.name</applicationPropertyName>
+ <revisionPropertyName>project.revision</revisionPropertyName>
+ <versionPropertyName>project.version</versionPropertyName>
+ <timestampPropertyName>build.timestamp</timestampPropertyName>
+ <outputDirectory>${basedir}/target/classes/org/caosdb/server/</outputDirectory>
+ <outputName>build.properties</outputName>
+ </configuration>
+ </plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
@@ -320,7 +393,40 @@
<excludeArtifactIds>easy-units</excludeArtifactIds>
</configuration>
</plugin>
+ <plugin>
+ <groupId>kr.motd.maven</groupId>
+ <artifactId>os-maven-plugin</artifactId>
+ <version>1.7.0</version>
+ <executions>
+ <execution>
+ <phase>initialize</phase>
+ <goals>
+ <goal>detect</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ <!-- code generation protobuf/grpc -->
+ <plugin>
+ <groupId>org.xolstice.maven.plugins</groupId>
+ <artifactId>protobuf-maven-plugin</artifactId>
+ <version>0.6.1</version>
+ <configuration>
+ <protoSourceRoot>${basedir}/caosdb-proto/proto/</protoSourceRoot>
+ <protocArtifact>com.google.protobuf:protoc:${protobuf.version}:exe:${os.detected.classifier}</protocArtifact>
+ <pluginId>grpc-java</pluginId>
+ <pluginArtifact>io.grpc:protoc-gen-grpc-java:${grpc.version}:exe:${os.detected.classifier}</pluginArtifact>
+ </configuration>
+ <executions>
+ <execution>
+ <goals>
+ <goal>compile</goal>
+ <goal>compile-custom</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
</plugins>
</build>
- <url>bmp.ds.mpg.de</url>
+ <url>caosdb.org</url>
</project>
diff --git a/src/doc/DEPENDENCIES.md b/src/doc/DEPENDENCIES.md
new file mode 120000
index 0000000000000000000000000000000000000000..28771e4dc45403b9c9baa795f04584e5b0a283ec
--- /dev/null
+++ b/src/doc/DEPENDENCIES.md
@@ -0,0 +1 @@
+../../DEPENDENCIES.md
\ No newline at end of file
diff --git a/src/doc/conf.py b/src/doc/conf.py
index 0027ef7af1b0c53157b30db86c12715ac58c6e27..3e4e90e8c26fcc1fc709f20b82d06d21d2b5f787 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -25,9 +25,9 @@ copyright = '2020, IndiScale GmbH'
author = 'Daniel Hornung'
# The short X.Y version
-version = '0.5'
+version = '0.6'
# The full version, including alpha/beta/rc tags
-release = '0.5.0'
+release = '0.6.0'
# -- General configuration ---------------------------------------------------
diff --git a/src/doc/index.rst b/src/doc/index.rst
index 21fd891c083e7932d8b342d93992b2d02158364e..67a9e365f506009da21b3a6c00b771e751bf26c0 100644
--- a/src/doc/index.rst
+++ b/src/doc/index.rst
@@ -13,6 +13,7 @@ Welcome to caosdb-server's documentation!
Query Language <CaosDB-Query-Language>
administration
Development <development/devel>
+ Dependencies <DEPENDENCIES>
specification/index.rst
Glossary
API documentation<_apidoc/packages>
diff --git a/src/main/java/org/caosdb/server/CaosDBServer.java b/src/main/java/org/caosdb/server/CaosDBServer.java
index bd053276e08fda4a898950e476814999f9bf4156..17bb1e500ed5aeffec25cf9aa2535150ceb40b4c 100644
--- a/src/main/java/org/caosdb/server/CaosDBServer.java
+++ b/src/main/java/org/caosdb/server/CaosDBServer.java
@@ -1,21 +1,23 @@
/*
- * ** header v3.0 This file is a part of the CaosDB Project.
+ * 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) 2019-2021 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2019-2021 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/>.
- *
- * ** end header
+ * 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/>.
*/
package org.caosdb.server;
@@ -57,6 +59,7 @@ import org.caosdb.server.datatype.AbstractDatatype;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.Role;
import org.caosdb.server.entity.container.Container;
+import org.caosdb.server.grpc.GRPCServer;
import org.caosdb.server.logging.RequestErrorLogMessage;
import org.caosdb.server.resource.AuthenticationResource;
import org.caosdb.server.resource.DefaultResource;
@@ -150,7 +153,7 @@ public class CaosDBServer extends Application {
initBackend();
initWebServer();
initShutDownHook();
- } catch (Exception e1) {
+ } catch (final Exception e1) {
logger.error("Could not start the server.", e1);
System.exit(1);
}
@@ -203,7 +206,7 @@ public class CaosDBServer extends Application {
* @throws IOException
*/
public static void initTimeZone() throws InterruptedException, IOException {
- String serverProperty = getServerProperty(ServerProperties.KEY_TIMEZONE);
+ final String serverProperty = getServerProperty(ServerProperties.KEY_TIMEZONE);
if (serverProperty != null && !serverProperty.isEmpty()) {
logger.info(
"SET TIMEZONE = "
@@ -216,7 +219,7 @@ public class CaosDBServer extends Application {
return;
}
- String prop = System.getProperty("user.timezone");
+ final String prop = System.getProperty("user.timezone");
if (prop != null && !prop.isEmpty()) {
logger.info("SET TIMEZONE = " + prop + " from JVM property `user.timezone`.");
TimeZone.setDefault(TimeZone.getTimeZone(ZoneId.of(prop)));
@@ -224,7 +227,7 @@ public class CaosDBServer extends Application {
return;
}
- String envVar = System.getenv("TZ");
+ final String envVar = System.getenv("TZ");
if (envVar != null && !envVar.isEmpty()) {
logger.info("SET TIMEZONE = " + envVar + " from evironment variable `TZ`.");
TimeZone.setDefault(TimeZone.getTimeZone(ZoneId.of(envVar)));
@@ -232,7 +235,7 @@ public class CaosDBServer extends Application {
return;
}
- String fromDate = getTimeZoneFromDate();
+ final String fromDate = getTimeZoneFromDate();
if (fromDate != null && fromDate.isEmpty()) {
logger.info("SET TIMEZONE = " + fromDate + " from `date +%Z`.");
TimeZone.setDefault(TimeZone.getTimeZone(ZoneId.of(fromDate)));
@@ -298,8 +301,8 @@ public class CaosDBServer extends Application {
return config;
}
- public static void initShiro(Ini config) {
- BasicIniEnvironment env = new BasicIniEnvironment(config);
+ public static void initShiro(final Ini config) {
+ final BasicIniEnvironment env = new BasicIniEnvironment(config);
final SecurityManager securityManager = env.getSecurityManager();
SecurityUtils.setSecurityManager(securityManager);
}
@@ -345,7 +348,7 @@ public class CaosDBServer extends Application {
try {
port_redirect_https =
Integer.parseInt(getServerProperty(ServerProperties.KEY_REDIRECT_HTTP_TO_HTTPS_PORT));
- } catch (NumberFormatException e) {
+ } catch (final NumberFormatException e) {
port_redirect_https = port_https;
}
final int initialConnections =
@@ -364,6 +367,7 @@ public class CaosDBServer extends Application {
initialConnections,
maxTotalConnections);
}
+ GRPCServer.startServer();
}
private static void initDatatypes(final Access access) throws Exception {
@@ -784,10 +788,12 @@ public class CaosDBServer extends Application {
}
}
+ /** Add a shutdown hook which runs after the Restlet Server has been shut down. */
public static void addPostShutdownHook(final Thread t) {
postShutdownHooks.add(t);
}
+ /** Add a shutdown hook which runs before the Restlet Server is being shut down. */
public static void addPreShutdownHook(final Runnable runnable) {
preShutdownHooks.add(runnable);
}
@@ -827,7 +833,7 @@ public class CaosDBServer extends Application {
* @param key, the server property.
* @param value, the new value.
*/
- public static void setProperty(String key, String value) {
+ public static void setProperty(final String key, final String value) {
SERVER_PROPERTIES.setProperty(key, value);
}
@@ -835,7 +841,8 @@ public class CaosDBServer extends Application {
return SERVER_PROPERTIES;
}
- public static void scheduleJob(JobDetail job, Trigger trigger) throws SchedulerException {
+ public static void scheduleJob(final JobDetail job, final Trigger trigger)
+ throws SchedulerException {
SCHEDULER.scheduleJob(job, trigger);
}
}
@@ -865,7 +872,7 @@ class CaosDBComponent extends Component {
*/
@Override
public void handle(final Request request, final Response response) {
- long t1 = System.currentTimeMillis();
+ final long t1 = System.currentTimeMillis();
// The server request ID is just a long random number
request.getAttributes().put("SRID", UUID.randomUUID().toString());
response.setServerInfo(CaosDBServer.getServerInfo());
@@ -873,7 +880,7 @@ class CaosDBComponent extends Component {
log(request, response, t1);
}
- private void log(final Request request, final Response response, long t1) {
+ private void log(final Request request, final Response response, final long t1) {
if (response.getStatus() == Status.SERVER_ERROR_INTERNAL) {
final Object object = request.getAttributes().get("THROWN");
Throwable t = null;
diff --git a/src/main/java/org/caosdb/server/FileSystem.java b/src/main/java/org/caosdb/server/FileSystem.java
index 6bff612ca69acc24b699f8807b6969e343c60fb3..67587f3da7930dd2cbf3e76d3ed06f19508efef7 100644
--- a/src/main/java/org/caosdb/server/FileSystem.java
+++ b/src/main/java/org/caosdb/server/FileSystem.java
@@ -174,7 +174,7 @@ public class FileSystem {
tmpFile.getParentFile().mkdirs();
if (tmpFile.isDirectory()) {
// TODO this should generate an error. This means that the
- // tmpIdentifyers are inconsistent
+ // tmpIdentifiers are inconsistent
}
final OutputStream outputStream = new FileOutputStream(tmpFile);
final MessageDigest md = MessageDigest.getInstance("SHA-512");
diff --git a/src/main/java/org/caosdb/server/ServerProperties.java b/src/main/java/org/caosdb/server/ServerProperties.java
index d1df2c66587fe6377fb8293cb8b16264480e8ef0..34899f7551ccc8ac99e6f2246eeb154c37171e53 100644
--- a/src/main/java/org/caosdb/server/ServerProperties.java
+++ b/src/main/java/org/caosdb/server/ServerProperties.java
@@ -1,11 +1,10 @@
/*
- * ** 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) 2019 IndiScale GmbH
- * Copyright (C) 2019 Timm Fitschen (t.fitschen@indiscale.com)
+ * Copyright (C) 2019-2021 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2019-2021 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
@@ -19,8 +18,6 @@
*
* 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 org.caosdb.server;
@@ -28,6 +25,7 @@ import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
+import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
@@ -66,6 +64,8 @@ public class ServerProperties extends Properties {
public static final String KEY_SERVER_PORT_HTTPS = "SERVER_PORT_HTTPS";
public static final String KEY_SERVER_PORT_HTTP = "SERVER_PORT_HTTP";
public static final String KEY_REDIRECT_HTTP_TO_HTTPS_PORT = "REDIRECT_HTTP_TO_HTTPS_PORT";
+ public static final String KEY_GRPC_SERVER_PORT_HTTPS = "GRPC_SERVER_PORT_HTTPS";
+ public static final String KEY_GRPC_SERVER_PORT_HTTP = "GRPC_SERVER_PORT_HTTP";
public static final String KEY_HTTPS_ENABLED_PROTOCOLS = "HTTPS_ENABLED_PROTOCOLS";
public static final String KEY_HTTPS_DISABLED_PROTOCOLS = "HTTPS_DISABLED_PROTOCOLS";
@@ -136,6 +136,11 @@ public class ServerProperties extends Properties {
public static final String KEY_AUTHTOKEN_CONFIG = "AUTHTOKEN_CONFIG";
public static final String KEY_JOB_RULES_CONFIG = "JOB_RULES_CONFIG";
+ public static final String KEY_PROJECT_VERSION = "project.version";
+ public static final String KEY_PROJECT_NAME = "project.name";
+ public static final String KEY_PROJECT_REVISTION = "project.revision";
+ public static final String KEY_BUILD_TIMESTAMP = "build.timestamp";
+
/**
* Read the config files and initialize the server properties.
*
@@ -145,6 +150,9 @@ public class ServerProperties extends Properties {
final Properties serverProperties = new Properties();
final String basepath = System.getProperty("user.dir");
+ final URL url = CaosDBServer.class.getResource("/build.properties");
+ serverProperties.load(url.openStream());
+
// load standard config
loadConfigFile(serverProperties, new File(basepath + "/conf/core/server.conf"));
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityProperties.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityProperties.java
index 7b02fbf003e49c18bc14a602f7e2f781b495c682..4072c1b2877cd9231424a98948fad32747870537 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityProperties.java
@@ -22,13 +22,12 @@
*/
package org.caosdb.server.database.backend.transaction;
-import static org.caosdb.server.transaction.Transaction.ERROR_INTEGRITY_VIOLATION;
-
import org.caosdb.server.database.BackendTransaction;
import org.caosdb.server.database.backend.interfaces.DeleteEntityPropertiesImpl;
import org.caosdb.server.database.exceptions.IntegrityException;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.utils.EntityStatus;
+import org.caosdb.server.utils.ServerMessages;
public class DeleteEntityProperties extends BackendTransaction {
@@ -50,7 +49,7 @@ public class DeleteEntityProperties extends BackendTransaction {
try {
ret.execute(this.entity.getId());
} catch (final IntegrityException exc) {
- this.entity.addError(ERROR_INTEGRITY_VIOLATION);
+ this.entity.addError(ServerMessages.ERROR_INTEGRITY_VIOLATION);
throw exc;
}
}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
index 55989d219ad738d5a866e0ef6f322368c8fc559b..e371cfe1f9caf3d4438e8801d4a6cee1119322f8 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
@@ -24,13 +24,12 @@
*/
package org.caosdb.server.database.backend.transaction;
-import static org.caosdb.server.transaction.Transaction.ERROR_INTEGRITY_VIOLATION;
-
import org.caosdb.server.database.BackendTransaction;
import org.caosdb.server.database.backend.interfaces.DeleteSparseEntityImpl;
import org.caosdb.server.database.exceptions.IntegrityException;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.utils.EntityStatus;
+import org.caosdb.server.utils.ServerMessages;
public class DeleteSparseEntity extends BackendTransaction {
@@ -54,7 +53,7 @@ public class DeleteSparseEntity extends BackendTransaction {
ret.execute(this.entity.getId());
}
} catch (final IntegrityException exc) {
- this.entity.addError(ERROR_INTEGRITY_VIOLATION);
+ this.entity.addError(ServerMessages.ERROR_INTEGRITY_VIOLATION);
throw exc;
}
}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityDatatype.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityDatatype.java
index 182874d1f1e30ed8f5249e609dbbc42a724d94af..aa139e7db565ae82073d6983915c0c53e9cd8b51 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityDatatype.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityDatatype.java
@@ -1,12 +1,11 @@
package org.caosdb.server.database.backend.transaction;
-import static org.caosdb.server.transaction.Transaction.ERROR_INTEGRITY_VIOLATION;
-
import org.caosdb.server.database.BackendTransaction;
import org.caosdb.server.database.backend.interfaces.InsertEntityDatatypeImpl;
import org.caosdb.server.database.exceptions.IntegrityException;
import org.caosdb.server.database.proto.SparseEntity;
import org.caosdb.server.entity.EntityInterface;
+import org.caosdb.server.utils.ServerMessages;
public class InsertEntityDatatype extends BackendTransaction {
@@ -25,7 +24,7 @@ public class InsertEntityDatatype extends BackendTransaction {
try {
t.execute(e);
} catch (final IntegrityException exc) {
- this.entity.addError(ERROR_INTEGRITY_VIOLATION);
+ this.entity.addError(ServerMessages.ERROR_INTEGRITY_VIOLATION);
throw exc;
}
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java
index 22720f836e5cbd4912f3aedccd25398e80a19324..213c7529766dcac4cc002f81380bf8d141cd8065 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java
@@ -22,8 +22,6 @@
*/
package org.caosdb.server.database.backend.transaction;
-import static org.caosdb.server.transaction.Transaction.ERROR_INTEGRITY_VIOLATION;
-
import org.caosdb.server.database.BackendTransaction;
import org.caosdb.server.database.backend.interfaces.InsertSparseEntityImpl;
import org.caosdb.server.database.exceptions.IntegrityException;
@@ -31,6 +29,7 @@ import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.proto.SparseEntity;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.Version;
+import org.caosdb.server.utils.ServerMessages;
import org.caosdb.server.utils.Undoable;
public class InsertSparseEntity extends BackendTransaction {
@@ -52,7 +51,7 @@ public class InsertSparseEntity extends BackendTransaction {
try {
t.execute(e);
} catch (final IntegrityException exc) {
- this.entity.addError(ERROR_INTEGRITY_VIOLATION);
+ this.entity.addError(ServerMessages.ERROR_INTEGRITY_VIOLATION);
throw exc;
}
diff --git a/src/main/java/org/caosdb/server/datatype/BooleanValue.java b/src/main/java/org/caosdb/server/datatype/BooleanValue.java
index 0abfa0c917f21d246854cabcfe437fe48cb3d59e..2bcbb48bcaf52ec0ef9a83a6d81d51190d1249ef 100644
--- a/src/main/java/org/caosdb/server/datatype/BooleanValue.java
+++ b/src/main/java/org/caosdb/server/datatype/BooleanValue.java
@@ -37,4 +37,8 @@ public class BooleanValue extends AbstractEnumValue {
public static BooleanValue valueOf(final boolean b) {
return valueOf(Boolean.toString(b));
}
+
+ public boolean getValue() {
+ return toDatabaseString().equals("TRUE");
+ }
}
diff --git a/src/main/java/org/caosdb/server/datatype/CaosEnum.java b/src/main/java/org/caosdb/server/datatype/CaosEnum.java
index 1040ab9a8114544dfd8a0d5a0a75660be4de5f07..00d8cb167a158a40417e7fddcb9fbe1cf21e7cdb 100644
--- a/src/main/java/org/caosdb/server/datatype/CaosEnum.java
+++ b/src/main/java/org/caosdb/server/datatype/CaosEnum.java
@@ -61,17 +61,17 @@ class EnumElement implements Comparable<EnumElement> {
public class CaosEnum {
- final boolean cs;
+ final boolean case_sensitive; // for string operations
public CaosEnum(final String... values) {
this(false, values);
}
- public CaosEnum(final boolean cs, final String... values) {
- this.cs = cs;
+ public CaosEnum(final boolean case_sensitive, final String... values) {
+ this.case_sensitive = case_sensitive;
int index = 0;
for (String v : values) {
- if (!cs) {
+ if (!case_sensitive) {
v = v.toUpperCase();
}
this.values.add(new EnumElement(index++, v));
@@ -82,7 +82,7 @@ public class CaosEnum {
public EnumElement valueOf(final String s) {
int hash;
- if (!this.cs) {
+ if (!this.case_sensitive) {
hash = s.toUpperCase().hashCode();
} else {
hash = s.hashCode();
diff --git a/src/main/java/org/caosdb/server/datatype/GenericValue.java b/src/main/java/org/caosdb/server/datatype/GenericValue.java
index e21841ee782a2ff86d2d993bbb0b9901a7835667..02d735abcc36297e61b08f99455f077d832a3a4b 100644
--- a/src/main/java/org/caosdb/server/datatype/GenericValue.java
+++ b/src/main/java/org/caosdb/server/datatype/GenericValue.java
@@ -58,10 +58,14 @@ public class GenericValue implements SingleValue {
this.table = Table.text_data;
}
+ public GenericValue(final long value) {
+ this((Integer) Math.toIntExact(value));
+ }
+
@Override
public void addToElement(final Element e) {
if (this.value instanceof String && ((String) this.value).isEmpty()) {
- Element empty = new Element("EmptyString");
+ final Element empty = new Element("EmptyString");
e.addContent(empty);
} else {
e.addContent(this.value.toString());
@@ -91,4 +95,8 @@ public class GenericValue implements SingleValue {
}
return false;
}
+
+ public Object getValue() {
+ return this.value;
+ }
}
diff --git a/src/main/java/org/caosdb/server/datatype/IntegerDatatype.java b/src/main/java/org/caosdb/server/datatype/IntegerDatatype.java
index b5ac2d971c7edd1eaf3947eacf1d1f94f967d808..0b1116ed5cbc135f846b5c7fbc0e1d497576380f 100644
--- a/src/main/java/org/caosdb/server/datatype/IntegerDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/IntegerDatatype.java
@@ -32,10 +32,13 @@ public class IntegerDatatype extends AbstractDatatype {
public SingleValue parseValue(final Object value) throws Message {
try {
if (value instanceof GenericValue) {
- return new GenericValue(Integer.parseInt(((GenericValue) value).toDatabaseString()));
+ return new GenericValue(Long.parseLong(((GenericValue) value).toDatabaseString()));
} else {
- return new GenericValue(Integer.parseInt(value.toString()));
+ return new GenericValue(Long.parseLong(value.toString()));
}
+
+ } catch (final ArithmeticException e) {
+ throw ServerMessages.INTEGER_OUT_OF_RANGE;
} catch (final NumberFormatException e) {
throw ServerMessages.CANNOT_PARSE_INT_VALUE;
}
diff --git a/src/main/java/org/caosdb/server/datatype/ReferenceDatatype.java b/src/main/java/org/caosdb/server/datatype/ReferenceDatatype.java
index 42f60cebc116d23137d359c11015a2978233234e..769d3ebdd109e22dcbc41f2ae7bd478b709f0482 100644
--- a/src/main/java/org/caosdb/server/datatype/ReferenceDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/ReferenceDatatype.java
@@ -27,9 +27,6 @@ import org.caosdb.server.entity.Message;
@DatatypeDefinition(name = "Reference")
public class ReferenceDatatype extends AbstractDatatype {
- public static final Message REFERENCE_ID_NOT_PARSABLE =
- new Message(217, "The reference is not parsable. It must be an integer.");
-
@Override
public ReferenceValue parseValue(final Object value) throws Message {
return ReferenceValue.parseReference(value);
diff --git a/src/main/java/org/caosdb/server/entity/Entity.java b/src/main/java/org/caosdb/server/entity/Entity.java
index 0a60f9af59f731098a0e194e4848b578094d4e68..20ef481cde3845a35fbdc3853fb12a31278dc7e3 100644
--- a/src/main/java/org/caosdb/server/entity/Entity.java
+++ b/src/main/java/org/caosdb/server/entity/Entity.java
@@ -550,79 +550,11 @@ public class Entity extends AbstractObservable implements EntityInterface {
getToElementStrategy().addToElement(this, element, strategy);
}
- /**
- * Print this entity to the standard outputs. Just for debugging.
- *
- * @throws CaosDBException
- */
- @Override
- public void print() {
- print("");
- }
-
@Override
public Integer getDomain() {
return 0;
}
- @Override
- public void print(final String indent) {
- System.out.println(
- indent
- + "+---| "
- + this.getClass().getSimpleName()
- + " |----------------------------------");
- if (getDomain() != 0) {
- System.out.println(indent + "| Domain: " + Integer.toString(getDomain()));
- }
- if (hasId()) {
- System.out.println(indent + "| ID: " + Integer.toString(getId()));
- }
- if (hasCuid()) {
- System.out.println(indent + "| Cuid: " + getCuid());
- }
- if (hasName()) {
- System.out.println(indent + "| Name: " + getName());
- }
- if (hasDescription()) {
- System.out.println(indent + "| Description: " + getDescription());
- }
- if (hasRole()) {
- System.out.println(indent + "| Role: " + getRole());
- }
- if (hasStatementStatus()) {
- System.out.println(indent + "| Statement: " + getStatementStatus().toString());
- }
- if (hasDatatype()) {
- System.out.println(indent + "| Datatype: " + getDatatype().toString());
- }
- if (hasValue()) {
- System.out.println(indent + "| Value: " + getValue().toString());
- }
- if (hasEntityStatus()) {
- System.out.println(indent + "| Entity: " + getEntityStatus().toString());
- }
- if (hasFileProperties()) {
- getFileProperties().print(indent);
- }
- System.out.println(indent + "+-----------------------------------");
- for (final ToElementable m : getMessages()) {
- if (m instanceof Message) {
- ((Message) m).print(indent + "| ");
- }
- }
- for (final EntityInterface p : getParents()) {
- // p.print(indent + "| ");
- System.out.println(indent + "| Parent: " + p.getName());
- }
- for (final EntityInterface s : getProperties()) {
- s.print(indent + "| ");
- }
- if (indent.equals("")) {
- System.out.println(indent + "+------------------------------------");
- }
- }
-
/** Errors, Warnings and Info messages for this entity. */
private final Set<ToElementable> messages = new HashSet<>();
@@ -662,18 +594,6 @@ public class Entity extends AbstractObservable implements EntityInterface {
return ret;
}
- @Override
- public final Message getMessage(final String type, final Integer code) {
- for (final ToElementable m : this.messages) {
- if (m instanceof Message
- && ((Message) m).getType().equalsIgnoreCase(type)
- && ((Message) m).getCode() == code) {
- return (Message) m;
- }
- }
- return null;
- }
-
@Override
public final void addMessage(final ToElementable m) {
this.messages.add(m);
@@ -691,7 +611,7 @@ public class Entity extends AbstractObservable implements EntityInterface {
@Override
public void addInfo(final String description) {
- final Message m = new Message(MessageType.Info, 0, description);
+ final Message m = new Message(description);
addMessage(m);
}
@@ -712,7 +632,6 @@ public class Entity extends AbstractObservable implements EntityInterface {
if (!this.isParsed) {
this.isParsed = true;
setValue(getDatatype().parseValue(getValue()));
- this.isParsed = true;
}
}
@@ -886,23 +805,23 @@ public class Entity extends AbstractObservable implements EntityInterface {
}
// Parse TMPIDENTIFYER.
- String tmpIdentifyer = null;
+ String tmpIdentifier = null;
boolean pickup = false;
if (element.getAttribute("pickup") != null && !element.getAttributeValue("pickup").equals("")) {
- tmpIdentifyer = element.getAttributeValue("pickup");
+ tmpIdentifier = element.getAttributeValue("pickup");
pickup = true;
} else if (element.getAttribute("upload") != null
&& !element.getAttributeValue("upload").equals("")) {
- tmpIdentifyer = element.getAttributeValue("upload");
+ tmpIdentifier = element.getAttributeValue("upload");
}
- if (tmpIdentifyer != null && tmpIdentifyer.endsWith("/")) {
- tmpIdentifyer = tmpIdentifyer.substring(0, tmpIdentifyer.length() - 1);
+ if (tmpIdentifier != null && tmpIdentifier.endsWith("/")) {
+ tmpIdentifier = tmpIdentifier.substring(0, tmpIdentifier.length() - 1);
}
// Store PATH, HASH, SIZE, TMPIDENTIFYER
- if (tmpIdentifyer != null || checksum != null || path != null || size != null) {
+ if (tmpIdentifier != null || checksum != null || path != null || size != null) {
setFileProperties(
- new FileProperties(checksum, path, size, tmpIdentifyer).setPickupable(pickup));
+ new FileProperties(checksum, path, size, tmpIdentifier).setPickupable(pickup));
}
// Parse flags
diff --git a/src/main/java/org/caosdb/server/entity/EntityInterface.java b/src/main/java/org/caosdb/server/entity/EntityInterface.java
index 954bcc47ca5b6117d3164ba3c9c585dbd373d4f8..46726df63dcedb651e0762f54a7b2cdafb5041d7 100644
--- a/src/main/java/org/caosdb/server/entity/EntityInterface.java
+++ b/src/main/java/org/caosdb/server/entity/EntityInterface.java
@@ -112,10 +112,6 @@ public interface EntityInterface
public abstract boolean hasDatatype();
- public abstract void print();
-
- public abstract void print(String indent);
-
public abstract FileProperties getFileProperties();
public abstract void setFileProperties(FileProperties fileProperties);
diff --git a/src/main/java/org/caosdb/server/entity/FileProperties.java b/src/main/java/org/caosdb/server/entity/FileProperties.java
index c2c2c10fae44d4d84af56a33a052f5ed589debed..eaf4246f6c16a0f7cb38964e0ffb12757a4f0373 100644
--- a/src/main/java/org/caosdb/server/entity/FileProperties.java
+++ b/src/main/java/org/caosdb/server/entity/FileProperties.java
@@ -38,7 +38,7 @@ public class FileProperties {
private String checksum = null;
private String path = null;
private Long size = null;
- private String tmpIdentifyer = null;
+ private String tmpIdentifier = null;
public FileProperties setChecksum(final String checksum) {
this.checksum = checksum;
@@ -96,26 +96,11 @@ public class FileProperties {
}
public FileProperties(
- final String checksum, final String path, final Long size, final String tmpIdentifyer) {
+ final String checksum, final String path, final Long size, final String tmpIdentifier) {
this.checksum = checksum;
this.path = (path == null ? null : path.replaceFirst("^/", ""));
this.size = size;
- this.tmpIdentifyer = tmpIdentifyer;
- }
-
- public void print(final String indent) {
- if (hasChecksum()) {
- System.out.println(indent + "| Checksum: " + this.checksum);
- }
- if (hasPath()) {
- System.out.println(indent + "| Path: " + "/" + this.path);
- }
- if (hasSize()) {
- System.out.println(indent + "| Size: " + Long.toString(this.size));
- }
- if (getFile() != null) {
- System.out.println(indent + "| File: " + getFile().getAbsolutePath());
- }
+ this.tmpIdentifier = tmpIdentifier;
}
public FileProperties setFile(final File file) {
@@ -127,13 +112,13 @@ public class FileProperties {
return this.file;
}
- public FileProperties setTmpIdentifyer(final String tmpIdentifyer) {
- this.tmpIdentifyer = tmpIdentifyer;
+ public FileProperties setTmpIdentifier(final String tmpIdentifier) {
+ this.tmpIdentifier = tmpIdentifier;
return this;
}
- public String getTmpIdentifyer() {
- return this.tmpIdentifyer;
+ public String getTmpIdentifier() {
+ return this.tmpIdentifier;
}
private String getThumbnailPath(final File target) {
@@ -291,6 +276,6 @@ public class FileProperties {
}
public boolean hasTmpIdentifier() {
- return this.tmpIdentifyer != null;
+ return this.tmpIdentifier != null;
}
}
diff --git a/src/main/java/org/caosdb/server/entity/MagicTypes.java b/src/main/java/org/caosdb/server/entity/MagicTypes.java
index cffdb0723588d3aaec31e24a39895e304aa2e18b..f17d448ca934901dc491f1d737f9122e2a67862a 100644
--- a/src/main/java/org/caosdb/server/entity/MagicTypes.java
+++ b/src/main/java/org/caosdb/server/entity/MagicTypes.java
@@ -26,6 +26,7 @@ import java.util.HashMap;
import org.caosdb.server.entity.container.RetrieveContainer;
import org.caosdb.server.transaction.Retrieve;
+/** Some types correspond to entities in the database with magic IDs. */
public enum MagicTypes {
UNIT,
NAME,
diff --git a/src/main/java/org/caosdb/server/entity/Message.java b/src/main/java/org/caosdb/server/entity/Message.java
index 91720aed492a8b1875bb5613df2aaace7df3bef5..4c89e1ee23839483f7bed1099c52e8c24a56a6a2 100644
--- a/src/main/java/org/caosdb/server/entity/Message.java
+++ b/src/main/java/org/caosdb/server/entity/Message.java
@@ -21,17 +21,41 @@
*/
package org.caosdb.server.entity;
+import java.util.HashMap;
+import java.util.Map;
+import org.caosdb.api.entity.v1.MessageCode;
import org.caosdb.server.entity.xml.ToElementable;
+import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
public class Message extends Exception implements Comparable<Message>, ToElementable {
protected final String type;
- private final Integer code;
+ private final MessageCode code;
private final String description;
private final String body;
- private static final long serialVersionUID = -3005017964769041935L;
+ @Deprecated private static final Map<String, String> legacy_codes_mapping = new HashMap<>();
+
+ static void init() {
+ legacy_codes_mapping.put(
+ ServerMessages.ENTITY_HAS_BEEN_DELETED_SUCCESSFULLY.coreToString(), "10");
+ legacy_codes_mapping.put(ServerMessages.ATOMICITY_ERROR.coreToString(), "12");
+ legacy_codes_mapping.put(ServerMessages.ENTITY_DOES_NOT_EXIST.coreToString(), "101");
+ legacy_codes_mapping.put(ServerMessages.PROPERTY_HAS_NO_DATATYPE.coreToString(), "110");
+ legacy_codes_mapping.put(
+ ServerMessages.ENTITY_HAS_UNQUALIFIED_PROPERTIES.coreToString(), "114");
+ legacy_codes_mapping.put(ServerMessages.ENTITY_HAS_UNQUALIFIED_PARENTS.coreToString(), "116");
+ legacy_codes_mapping.put(ServerMessages.WARNING_OCCURED.coreToString(), "128");
+ legacy_codes_mapping.put(ServerMessages.ENTITY_NAME_IS_NOT_UNIQUE.coreToString(), "152");
+ legacy_codes_mapping.put(ServerMessages.REQUIRED_BY_UNQUALIFIED.coreToString(), "192");
+ legacy_codes_mapping.put(ServerMessages.REFERENCED_ENTITY_DOES_NOT_EXIST.coreToString(), "235");
+ legacy_codes_mapping.put(ServerMessages.AUTHORIZATION_ERROR.coreToString(), "403");
+ legacy_codes_mapping.put(ServerMessages.ROLE_DOES_NOT_EXIST.coreToString(), "1104");
+ legacy_codes_mapping.put(ServerMessages.ENTITY_NAME_DUPLICATES.coreToString(), "0");
+ }
+
+ private static final long serialVersionUID = 1837110172902899264L;
public enum MessageType {
Warning,
@@ -44,15 +68,18 @@ public class Message extends Exception implements Comparable<Message>, ToElement
return toString().hashCode();
}
- @Override
- public String toString() {
- return this.type.toString()
- + " ("
- + (this.code != null ? Integer.toString(this.code) : "")
+ private String coreToString() {
+ return " ("
+ + (this.code != null ? this.code.toString() : "0")
+ ") - "
+ (this.description != null ? this.description : "");
}
+ @Override
+ public String toString() {
+ return this.type.toString() + coreToString();
+ }
+
@Override
public boolean equals(final Object obj) {
return obj.toString().equals(toString());
@@ -74,33 +101,33 @@ public class Message extends Exception implements Comparable<Message>, ToElement
this(type, null, description, body);
}
- public Message(final String type, final Integer code) {
+ public Message(final String type, final MessageCode code) {
this(type, code, null, null);
}
- public Message(Integer code, String description) {
+ public Message(final MessageCode code, final String description) {
this(MessageType.Info, code, description);
}
- public Message(final MessageType type, final Integer code, final String description) {
+ public Message(final MessageType type, final MessageCode code, final String description) {
this(type.toString(), code, description, null);
}
public Message(
- final MessageType type, final Integer code, final String description, final String body) {
+ final MessageType type, final MessageCode code, final String description, final String body) {
this(type.toString(), code, description, body);
}
- public Message(final String type, final Integer code, final String description) {
+ public Message(final String type, final MessageCode code, final String description) {
this(type, code, description, null);
}
- public Message(MessageType type, String description) {
- this(type.toString(), 0, description);
+ public Message(final MessageType type, final String description) {
+ this(type.toString(), MessageCode.MESSAGE_CODE_UNKNOWN, description);
}
public Message(
- final String type, final Integer code, final String description, final String body) {
+ final String type, final MessageCode code, final String description, final String body) {
this.code = code;
this.description = description;
this.body = body;
@@ -108,7 +135,7 @@ public class Message extends Exception implements Comparable<Message>, ToElement
}
public Message(
- final Integer code, final String description, final String body, final MessageType type) {
+ final MessageCode code, final String description, final String body, final MessageType type) {
this.code = code;
this.description = description;
this.body = body;
@@ -116,20 +143,29 @@ public class Message extends Exception implements Comparable<Message>, ToElement
}
public Message(final String string) {
- this.code = null;
+ this.code = MessageCode.MESSAGE_CODE_UNKNOWN;
this.description = string;
this.body = null;
this.type = MessageType.Info.toString();
}
- public Integer getCode() {
+ public MessageCode getCode() {
return this.code;
}
public Element toElement() {
+ if (legacy_codes_mapping.isEmpty()) {
+ init();
+ }
final Element e = new Element(this.type);
if (this.code != null) {
- e.setAttribute("code", Integer.toString(this.code));
+ if (legacy_codes_mapping.containsKey(this.coreToString())) {
+ e.setAttribute("code", legacy_codes_mapping.get(this.coreToString()));
+ } else if (this.code == MessageCode.MESSAGE_CODE_UNKNOWN) {
+ e.setAttribute("code", "0");
+ } else {
+ e.setAttribute("code", Integer.toString(this.code.getNumber()));
+ }
}
if (this.description != null) {
e.setAttribute("description", this.description);
@@ -146,20 +182,6 @@ public class Message extends Exception implements Comparable<Message>, ToElement
parent.addContent(e);
}
- /** Print this entity to the standard outputs. Just for debugging. */
- public final void print() {
- print("");
- }
-
- public final void print(final String indent) {
- System.out.println(indent + "+---| " + this.type + " |------------------------ ");
- System.out.println(
- indent + "| Code: " + (this.code != null ? Integer.toString(this.code) : "null"));
- System.out.println(indent + "| Description: " + this.description);
- System.out.println(indent + "| Body: " + this.body);
- System.out.println(indent + "+------------------------------------------------------ ");
- }
-
@Override
public int compareTo(final Message o) {
final int tc = this.type.compareToIgnoreCase(o.type);
diff --git a/src/main/java/org/caosdb/server/entity/TransactionEntity.java b/src/main/java/org/caosdb/server/entity/TransactionEntity.java
index 2883c076f437520581037219a724020b47893424..7dd96b7f5ba8dc71c976731fed4d91e43688f919 100644
--- a/src/main/java/org/caosdb/server/entity/TransactionEntity.java
+++ b/src/main/java/org/caosdb/server/entity/TransactionEntity.java
@@ -59,8 +59,6 @@ public interface TransactionEntity {
public abstract List<Message> getMessages(String type);
- public abstract Message getMessage(String type, Integer code);
-
public abstract void addMessage(ToElementable m);
public abstract void addError(Message m);
diff --git a/src/main/java/org/caosdb/server/entity/UpdateEntity.java b/src/main/java/org/caosdb/server/entity/UpdateEntity.java
index 221888b3da57694e5eabb64d0955cd6fca5e0b0e..c5727e8257e4826b25408f35577eee4bc588e6f5 100644
--- a/src/main/java/org/caosdb/server/entity/UpdateEntity.java
+++ b/src/main/java/org/caosdb/server/entity/UpdateEntity.java
@@ -40,12 +40,16 @@ public class UpdateEntity extends WritableEntity {
super(element);
}
+ public UpdateEntity(final Integer id, final Role role) {
+ super(id, role);
+ }
+
@Override
public boolean skipJob() {
return getEntityStatus() != EntityStatus.QUALIFIED;
}
- public void setOriginal(EntityInterface original) {
+ public void setOriginal(final EntityInterface original) {
this.original = original;
}
diff --git a/src/main/java/org/caosdb/server/entity/WritableEntity.java b/src/main/java/org/caosdb/server/entity/WritableEntity.java
index 22ffd6e869e871cf568e87363e5ead762e444400..147feb0c43de65e9fa204207b29ae27df4251721 100644
--- a/src/main/java/org/caosdb/server/entity/WritableEntity.java
+++ b/src/main/java/org/caosdb/server/entity/WritableEntity.java
@@ -29,7 +29,11 @@ public class WritableEntity extends Entity {
super(element);
}
- public WritableEntity(String name, Role role) {
+ public WritableEntity(final String name, final Role role) {
super(name, role);
}
+
+ public WritableEntity(final Integer id, final Role role) {
+ super(id, role);
+ }
}
diff --git a/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java b/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java
index 18a7837df27b39efa92abb2b16943a3476dca9ec..7e9a2ba36bc1fe7474e8dc57a9fe3e2d5e649c6f 100644
--- a/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java
@@ -114,15 +114,6 @@ public class TransactionContainer extends Container<EntityInterface>
}
}
- public void print() {
- System.out.println("*******************************************************************");
- System.out.println("*******************************************************************");
- for (final EntityInterface e : this) {
- e.print("*");
- }
- System.out.println("*******************************************************************\n\n");
- }
-
/** The files that have been uploaded. */
private HashMap<String, FileProperties> files = new HashMap<String, FileProperties>();
diff --git a/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java b/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
index c83cb67883f5a616109268fb6d62bae40cd73e6b..e5115dc219ac427e93ae87c0921ced965023f55e 100644
--- a/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
+++ b/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
@@ -290,16 +290,6 @@ public class EntityWrapper implements EntityInterface {
this.entity.addToElement(element);
}
- @Override
- public void print() {
- this.entity.print();
- }
-
- @Override
- public void print(final String indent) {
- this.entity.print(indent);
- }
-
@Override
public FileProperties getFileProperties() {
return this.entity.getFileProperties();
@@ -340,11 +330,6 @@ public class EntityWrapper implements EntityInterface {
return this.entity.getMessages(type);
}
- @Override
- public Message getMessage(final String type, final Integer code) {
- return this.entity.getMessage(type, code);
- }
-
@Override
public void addMessage(final ToElementable m) {
this.entity.addMessage(m);
diff --git a/src/main/java/org/caosdb/server/entity/wrapper/Property.java b/src/main/java/org/caosdb/server/entity/wrapper/Property.java
index b3ce45b56527e40382d3971a61b43f9bc054d21f..064e2bd31fd329477d712c723ecd6462e94d3933 100644
--- a/src/main/java/org/caosdb/server/entity/wrapper/Property.java
+++ b/src/main/java/org/caosdb/server/entity/wrapper/Property.java
@@ -50,6 +50,7 @@ public class Property extends EntityWrapper {
super(new Entity());
}
+ /** Return the Property Index, the index of a property with respect to a containing Entity. */
public int getPIdx() {
return this.pIdx;
}
@@ -58,6 +59,7 @@ public class Property extends EntityWrapper {
private EntityInterface domain = null;
private boolean isName;
+ /** Set the Property Index. */
public void setPIdx(final int i) {
this.pIdx = i;
}
diff --git a/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java b/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java
new file mode 100644
index 0000000000000000000000000000000000000000..0b359835c293a9b1ad95b296f1301de93a6fbbfa
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java
@@ -0,0 +1,145 @@
+package org.caosdb.server.grpc;
+
+import io.grpc.Context;
+import io.grpc.Contexts;
+import io.grpc.Metadata;
+import io.grpc.Metadata.Key;
+import io.grpc.ServerCall;
+import io.grpc.ServerCall.Listener;
+import io.grpc.ServerCallHandler;
+import io.grpc.ServerInterceptor;
+import io.grpc.Status;
+import java.util.Base64;
+import org.apache.shiro.SecurityUtils;
+import org.apache.shiro.authc.AuthenticationException;
+import org.apache.shiro.subject.Subject;
+import org.caosdb.server.CaosDBServer;
+import org.caosdb.server.ServerProperties;
+import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
+import org.caosdb.server.accessControl.RealmUsernamePasswordToken;
+import org.caosdb.server.accessControl.UserSources;
+
+/**
+ * ServerInterceptor for Authentication. If the authentication succeeds or if the caller is
+ * anonymous, the {@link Context} of the {@link ServerCall} is updated with a {@link Subject}
+ * instance. If the request does not succeed the call is closed with {@link Status#UNAUTHENTICATED}.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+class AuthInterceptor implements ServerInterceptor {
+
+ private static final Key<String> AUTHENTICATION_HEADER =
+ Key.of("authentication", Metadata.ASCII_STRING_MARSHALLER);
+ private static final Context.Key<Subject> SUBJECT_KEY = Context.key("subject");
+ private static final String BASIC_SCHEME_PREFIX = "Basic ";
+ /**
+ * A no-op listener. This class is used for failed authentications. We couldn't return a null
+ * instead because the documentation of the {@link ServerInterceptor} explicitely forbids it.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+ static class NoOpListener<ReqT> extends Listener<ReqT> {}
+
+ /** Whether the anonymous login is possible or not. */
+ private final boolean isAuthOptional() {
+ return CaosDBServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
+ .equalsIgnoreCase("true");
+ }
+
+ /**
+ * Login via username and password with the basic authentication scheme and return the logged-in
+ * subject.
+ */
+ private Subject basicAuth(final String base64) {
+ final String plain = new String(Base64.getDecoder().decode(base64));
+ final String[] split = plain.split(":", 2);
+ final String username = split[0];
+ final String password = split[1];
+ final RealmUsernamePasswordToken token =
+ new RealmUsernamePasswordToken(UserSources.getDefaultRealm(), username, password);
+ final org.apache.shiro.subject.Subject subject = SecurityUtils.getSubject();
+ subject.login(token);
+ return subject;
+ }
+
+ @Override
+ public <ReqT, RespT> Listener<ReqT> interceptCall(
+ final ServerCall<ReqT, RespT> call,
+ final Metadata headers,
+ final ServerCallHandler<ReqT, RespT> next) {
+ final String authentication = headers.get(AUTHENTICATION_HEADER);
+ Status status =
+ Status.UNKNOWN.withDescription(
+ "An unknown error occured during authentication. Please report a bug.");
+ if (authentication == null && isAuthOptional()) {
+ return anonymous(call, headers, next);
+ } else if (authentication == null) {
+ status = Status.UNAUTHENTICATED.withDescription("Please login.");
+ } else if (authentication.startsWith(BASIC_SCHEME_PREFIX)) {
+ return basicAuth(authentication.substring(BASIC_SCHEME_PREFIX.length()), call, headers, next);
+ } else {
+ status =
+ Status.UNAUTHENTICATED.withDescription(
+ "Unsupported authentication scheme: " + authentication.split(" ", 2)[0]);
+ }
+ call.close(status, new Metadata());
+ return new NoOpListener<ReqT>();
+ }
+
+ /**
+ * Login via username and password with the basic authentication scheme and add the resulting
+ * subject to the call context.
+ *
+ * @see #updateContext(Subject, ServerCall, Metadata, ServerCallHandler) for more information.
+ */
+ private <ReqT, RespT> Listener<ReqT> basicAuth(
+ final String base64,
+ final ServerCall<ReqT, RespT> call,
+ final Metadata headers,
+ final ServerCallHandler<ReqT, RespT> next) {
+ try {
+ final Subject subject = basicAuth(base64);
+ return updateContext(subject, call, headers, next);
+ } catch (final AuthenticationException e) {
+ final Status status =
+ Status.UNAUTHENTICATED.withDescription(
+ "Authentication failed. Username or password wrong.");
+ call.close(status, new Metadata());
+ return new NoOpListener<ReqT>();
+ }
+ }
+
+ /**
+ * Login as anonymous and add the anonymous subject to the call context.
+ *
+ * @see #updateContext(Subject, ServerCall, Metadata, ServerCallHandler) for more information.
+ */
+ private <ReqT, RespT> Listener<ReqT> anonymous(
+ final ServerCall<ReqT, RespT> call,
+ final Metadata headers,
+ final ServerCallHandler<ReqT, RespT> next) {
+ final Subject subject = anonymous();
+ return updateContext(subject, call, headers, next);
+ }
+
+ /** Login as anonymous. */
+ private Subject anonymous() {
+ final Subject anonymous = SecurityUtils.getSubject();
+ anonymous.login(AnonymousAuthenticationToken.getInstance());
+ return anonymous;
+ }
+
+ /**
+ * Add the subject to the call context. This is done the grpcic way by returning a listener which
+ * does exactly that.
+ */
+ private <ReqT, RespT> Listener<ReqT> updateContext(
+ final Subject subject,
+ final ServerCall<ReqT, RespT> call,
+ final Metadata headers,
+ final ServerCallHandler<ReqT, RespT> next) {
+ final Context context = Context.current();
+ context.withValue(SUBJECT_KEY, subject);
+ return Contexts.interceptCall(Context.current(), call, headers, next);
+ }
+}
diff --git a/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java b/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java
new file mode 100644
index 0000000000000000000000000000000000000000..aa6a260dfb52b5e36520d130219632d26095b0d1
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java
@@ -0,0 +1,441 @@
+package org.caosdb.server.grpc;
+
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import org.caosdb.api.entity.v1.AtomicDataType;
+import org.caosdb.api.entity.v1.CollectionValues;
+import org.caosdb.api.entity.v1.DataType;
+import org.caosdb.api.entity.v1.Entity;
+import org.caosdb.api.entity.v1.Entity.Builder;
+import org.caosdb.api.entity.v1.EntityResponse;
+import org.caosdb.api.entity.v1.EntityRole;
+import org.caosdb.api.entity.v1.Importance;
+import org.caosdb.api.entity.v1.ListDataType;
+import org.caosdb.api.entity.v1.MessageCode;
+import org.caosdb.api.entity.v1.Parent;
+import org.caosdb.api.entity.v1.ReferenceDataType;
+import org.caosdb.api.entity.v1.ScalarValue;
+import org.caosdb.api.entity.v1.SpecialValue;
+import org.caosdb.api.entity.v1.Version;
+import org.caosdb.datetime.DateTimeInterface;
+import org.caosdb.server.datatype.AbstractCollectionDatatype;
+import org.caosdb.server.datatype.AbstractDatatype;
+import org.caosdb.server.datatype.BooleanDatatype;
+import org.caosdb.server.datatype.BooleanValue;
+import org.caosdb.server.datatype.CollectionValue;
+import org.caosdb.server.datatype.DateTimeDatatype;
+import org.caosdb.server.datatype.DoubleDatatype;
+import org.caosdb.server.datatype.FileDatatype;
+import org.caosdb.server.datatype.GenericValue;
+import org.caosdb.server.datatype.IndexedSingleValue;
+import org.caosdb.server.datatype.IntegerDatatype;
+import org.caosdb.server.datatype.ReferenceDatatype;
+import org.caosdb.server.datatype.ReferenceDatatype2;
+import org.caosdb.server.datatype.ReferenceValue;
+import org.caosdb.server.datatype.TextDatatype;
+import org.caosdb.server.datatype.Value;
+import org.caosdb.server.entity.EntityInterface;
+import org.caosdb.server.entity.MagicTypes;
+import org.caosdb.server.entity.Message;
+import org.caosdb.server.entity.Role;
+import org.caosdb.server.entity.StatementStatus;
+import org.caosdb.server.entity.container.ParentContainer;
+import org.caosdb.server.entity.container.PropertyContainer;
+import org.caosdb.server.entity.wrapper.Property;
+
+public class CaosDBToGrpcConverters {
+
+ /** Get the unit as string. */
+ public String getStringUnit(final EntityInterface entity) {
+ final Iterator<Property> iterator = entity.getProperties().iterator();
+ while (iterator.hasNext()) {
+ final Property p = iterator.next();
+ if (MagicTypes.UNIT.getId() == p.getId()) {
+ iterator.remove();
+ return p.getValue().toString();
+ }
+ }
+ return null;
+ }
+
+ public EntityResponse.Builder convert(final EntityInterface from) {
+
+ final Builder entityBuilder = Entity.newBuilder();
+
+ if (from.hasId()) {
+ entityBuilder.setId(Integer.toString(from.getId()));
+ }
+ if (from.getRole() != null) {
+ entityBuilder.setRole(convert(from.getRole()));
+ }
+ if (from.hasName()) {
+ entityBuilder.setName(from.getName());
+ }
+ if (from.hasDescription()) {
+ entityBuilder.setDescription(from.getDescription());
+ }
+ if (from.hasDatatype()) {
+ entityBuilder.setDataType(convert(from.getDatatype()));
+ }
+ if (from.hasValue()) {
+ try {
+ from.parseValue();
+ } catch (final Message e) {
+ // ignore. This problem should be handled elsewhere because this is
+ // only for the serialization of the data and not for the validation.
+ // In any case, the string representation can be used.
+ }
+ entityBuilder.setValue(convert(from.getValue()));
+ }
+ final String unit = getStringUnit(from);
+ if (unit != null) {
+ entityBuilder.setUnit(unit);
+ }
+ if (from.hasProperties()) {
+ entityBuilder.addAllProperties(convert(from.getProperties()));
+ }
+ if (from.hasParents()) {
+ entityBuilder.addAllParents(convert(from.getParents()));
+ }
+
+ final EntityResponse.Builder responseBuilder = EntityResponse.newBuilder();
+ responseBuilder.setEntity(entityBuilder);
+
+ appendMessages(from, responseBuilder);
+
+ return responseBuilder;
+ }
+
+ private EntityRole convert(final Role role) {
+ switch (role) {
+ case RecordType:
+ return EntityRole.ENTITY_ROLE_RECORD_TYPE;
+ case Record:
+ return EntityRole.ENTITY_ROLE_RECORD;
+ case Property:
+ return EntityRole.ENTITY_ROLE_PROPERTY;
+ case File:
+ return EntityRole.ENTITY_ROLE_FILE;
+ default:
+ return EntityRole.ENTITY_ROLE_UNSPECIFIED;
+ }
+ }
+
+ public Iterable<? extends org.caosdb.api.entity.v1.Message> convert(
+ final List<Message> messages) {
+ final List<org.caosdb.api.entity.v1.Message> result = new LinkedList<>();
+ for (final Message m : messages) {
+ result.add(convert(m));
+ }
+ return result;
+ }
+
+ public org.caosdb.api.entity.v1.Message convert(final Message m) {
+ final org.caosdb.api.entity.v1.Message.Builder builder =
+ org.caosdb.api.entity.v1.Message.newBuilder();
+ final MessageCode code = getMessageCode(m);
+ builder.setCode(code.getNumber());
+ builder.setDescription(m.getDescription());
+ return builder.build();
+ }
+
+ public static MessageCode getMessageCode(final Message m) {
+ return m.getCode();
+ }
+
+ public Version convert(final org.caosdb.server.entity.Version from) {
+ final org.caosdb.api.entity.v1.Version.Builder builder = Version.newBuilder();
+
+ builder.setId(from.getId());
+ return builder.build();
+ }
+
+ public Parent convert(final org.caosdb.server.entity.wrapper.Parent from) {
+ final org.caosdb.api.entity.v1.Parent.Builder builder = Parent.newBuilder();
+ if (from.hasId()) {
+ builder.setId(from.getId().toString());
+ }
+ if (from.hasName()) {
+ builder.setName(from.getName());
+ }
+ if (from.hasDescription()) {
+ builder.setDescription(from.getDescription());
+ }
+
+ return builder.build();
+ }
+
+ public org.caosdb.api.entity.v1.Property convert(final Property from) {
+ final org.caosdb.api.entity.v1.Property.Builder builder =
+ org.caosdb.api.entity.v1.Property.newBuilder();
+
+ if (from.hasId()) {
+ builder.setId(from.getId().toString());
+ }
+ if (from.hasName()) {
+ builder.setName(from.getName());
+ }
+ if (from.hasDescription()) {
+ builder.setDescription(from.getDescription());
+ }
+ if (from.hasDatatype()) {
+ builder.setDataType(convert(from.getDatatype()));
+ }
+ final String unit = getStringUnit(from);
+ if (unit != null) {
+ builder.setUnit(unit);
+ }
+ if (from.hasValue()) {
+ try {
+ from.parseValue();
+ } catch (final Message e) {
+ // ignore. This problem should be handled elsewhere because this is
+ // only for the serialization of the data and not for the validation.
+ // In any case, the string representation can be used.
+ }
+ builder.setValue(convert(from.getValue()));
+ }
+ builder.setImportance(convert(from.getStatementStatus()));
+ return builder.build();
+ }
+
+ private org.caosdb.api.entity.v1.Value.Builder convert(final Value value) {
+ if (value instanceof CollectionValue) {
+ return convertCollectionValue((CollectionValue) value);
+ }
+ final org.caosdb.api.entity.v1.Value.Builder builder =
+ org.caosdb.api.entity.v1.Value.newBuilder();
+ builder.setScalarValue(convertScalarValue(value));
+ return builder;
+ }
+
+ private ScalarValue.Builder convertScalarValue(final Value value) {
+
+ if (value instanceof BooleanValue) {
+ return convertBooleanValue((BooleanValue) value);
+
+ } else if (value instanceof ReferenceValue) {
+ return convertReferenceValue((ReferenceValue) value);
+
+ } else if (value instanceof DateTimeInterface) {
+ return convertDateTimeInterface((DateTimeInterface) value);
+
+ } else if (value instanceof GenericValue) {
+ return convertGenericValue((GenericValue) value);
+ }
+ return null;
+ }
+
+ private ScalarValue.Builder convertGenericValue(final GenericValue value) {
+ final Object wrappedValue = value.getValue();
+ if (wrappedValue instanceof Double) {
+ return ScalarValue.newBuilder().setDoubleValue((Double) wrappedValue);
+ } else if (wrappedValue instanceof Integer) {
+ return ScalarValue.newBuilder().setIntegerValue((Integer) wrappedValue);
+ } else {
+ return convertStringValue(value);
+ }
+ }
+
+ private org.caosdb.api.entity.v1.ScalarValue.Builder convertStringValue(final Value value) {
+ if (value.toString().isEmpty()) {
+ return ScalarValue.newBuilder().setSpecialValue(SpecialValue.SPECIAL_VALUE_EMPTY_STRING);
+ }
+ return ScalarValue.newBuilder().setStringValue(value.toString());
+ }
+
+ private org.caosdb.api.entity.v1.ScalarValue.Builder convertDateTimeInterface(
+ final DateTimeInterface value) {
+ return convertStringValue(value);
+ }
+
+ private org.caosdb.api.entity.v1.ScalarValue.Builder convertBooleanValue(
+ final BooleanValue value) {
+ return ScalarValue.newBuilder().setBooleanValue(value.getValue());
+ }
+
+ private ScalarValue.Builder convertReferenceValue(final ReferenceValue value) {
+ return convertStringValue(value);
+ }
+
+ private org.caosdb.api.entity.v1.Value.Builder convertCollectionValue(
+ final CollectionValue value) {
+
+ final org.caosdb.api.entity.v1.Value.Builder builder =
+ org.caosdb.api.entity.v1.Value.newBuilder();
+ final List<ScalarValue> values = new LinkedList<>();
+ value.forEach(
+ (v) -> {
+ values.add(convertScalarValue(v));
+ });
+ builder.setListValues(CollectionValues.newBuilder().addAllValues(values));
+ return builder;
+ }
+
+ private ScalarValue convertScalarValue(final IndexedSingleValue v) {
+ return convertScalarValue(v.getWrapped()).build();
+ }
+
+ private Importance convert(final StatementStatus statementStatus) {
+ switch (statementStatus) {
+ case FIX:
+ return Importance.IMPORTANCE_FIX;
+ case OBLIGATORY:
+ return Importance.IMPORTANCE_OBLIGATORY;
+ case RECOMMENDED:
+ return Importance.IMPORTANCE_RECOMMENDED;
+ case SUGGESTED:
+ return Importance.IMPORTANCE_SUGGESTED;
+ default:
+ return null;
+ }
+ }
+
+ private org.caosdb.api.entity.v1.DataType.Builder convert(final AbstractDatatype datatype) {
+ if (datatype instanceof ReferenceDatatype2) {
+ return DataType.newBuilder()
+ .setReferenceDataType(convertReferenceDatatype((ReferenceDatatype2) datatype));
+ } else if (datatype instanceof FileDatatype) {
+ return DataType.newBuilder()
+ .setReferenceDataType(convertReferenceDatatype((FileDatatype) datatype));
+ } else if (datatype instanceof ReferenceDatatype) {
+ return DataType.newBuilder()
+ .setReferenceDataType(convertReferenceDatatype((ReferenceDatatype) datatype));
+ } else if (datatype instanceof AbstractCollectionDatatype) {
+ return DataType.newBuilder()
+ .setListDataType(
+ convertAbstractCollectionDatatype((AbstractCollectionDatatype) datatype));
+ } else if (datatype instanceof BooleanDatatype) {
+ return DataType.newBuilder()
+ .setAtomicDataType(convertBooleanDatatype((BooleanDatatype) datatype));
+
+ } else if (datatype instanceof DateTimeDatatype) {
+ return DataType.newBuilder()
+ .setAtomicDataType(convertDateTimeDatatype((DateTimeDatatype) datatype));
+
+ } else if (datatype instanceof DoubleDatatype) {
+ return DataType.newBuilder()
+ .setAtomicDataType(convertDoubleDatatype((DoubleDatatype) datatype));
+
+ } else if (datatype instanceof IntegerDatatype) {
+ return DataType.newBuilder()
+ .setAtomicDataType(convertIntegerDatatype((IntegerDatatype) datatype));
+
+ } else if (datatype instanceof TextDatatype) {
+ return DataType.newBuilder().setAtomicDataType(convertTextDatatype((TextDatatype) datatype));
+ }
+ return null;
+ }
+
+ private AtomicDataType convertTextDatatype(final TextDatatype datatype) {
+ return AtomicDataType.ATOMIC_DATA_TYPE_TEXT;
+ }
+
+ private AtomicDataType convertIntegerDatatype(final IntegerDatatype datatype) {
+ return AtomicDataType.ATOMIC_DATA_TYPE_INTEGER;
+ }
+
+ private AtomicDataType convertDoubleDatatype(final DoubleDatatype datatype) {
+ return AtomicDataType.ATOMIC_DATA_TYPE_DOUBLE;
+ }
+
+ private AtomicDataType convertDateTimeDatatype(final DateTimeDatatype datatype) {
+ return AtomicDataType.ATOMIC_DATA_TYPE_DATETIME;
+ }
+
+ private AtomicDataType convertBooleanDatatype(final BooleanDatatype datatype) {
+ return AtomicDataType.ATOMIC_DATA_TYPE_BOOLEAN;
+ }
+
+ private org.caosdb.api.entity.v1.ListDataType.Builder convertAbstractCollectionDatatype(
+ final AbstractCollectionDatatype collectionDatatype) {
+
+ final org.caosdb.api.entity.v1.ListDataType.Builder listBuilder = ListDataType.newBuilder();
+ final AbstractDatatype datatype = collectionDatatype.getDatatype();
+ if (datatype instanceof ReferenceDatatype) {
+ listBuilder.setReferenceDataType(convertReferenceDatatype((ReferenceDatatype) datatype));
+ } else if (datatype instanceof BooleanDatatype) {
+ return listBuilder.setAtomicDataType(convertBooleanDatatype((BooleanDatatype) datatype));
+
+ } else if (datatype instanceof DateTimeDatatype) {
+ return listBuilder.setAtomicDataType(convertDateTimeDatatype((DateTimeDatatype) datatype));
+
+ } else if (datatype instanceof DoubleDatatype) {
+ return listBuilder.setAtomicDataType(convertDoubleDatatype((DoubleDatatype) datatype));
+
+ } else if (datatype instanceof IntegerDatatype) {
+ return listBuilder.setAtomicDataType(convertIntegerDatatype((IntegerDatatype) datatype));
+
+ } else if (datatype instanceof TextDatatype) {
+ return listBuilder.setAtomicDataType(convertTextDatatype((TextDatatype) datatype));
+ }
+ return listBuilder;
+ }
+
+ private org.caosdb.api.entity.v1.ReferenceDataType.Builder convertReferenceDatatype(
+ final ReferenceDatatype datatype) {
+ return ReferenceDataType.newBuilder().setName(datatype.getName());
+ }
+
+ public Iterable<? extends org.caosdb.api.entity.v1.Property> convert(
+ final PropertyContainer from) {
+ final Iterator<org.caosdb.server.entity.wrapper.Property> iterator = from.iterator();
+ return () ->
+ new Iterator<>() {
+
+ @Override
+ public boolean hasNext() {
+ return iterator.hasNext();
+ }
+
+ @Override
+ public org.caosdb.api.entity.v1.Property next() {
+ return convert(iterator.next());
+ }
+ };
+ }
+
+ public Iterable<? extends Parent> convert(final ParentContainer from) {
+ final Iterator<org.caosdb.server.entity.wrapper.Parent> iterator = from.iterator();
+ return () ->
+ new Iterator<>() {
+
+ @Override
+ public boolean hasNext() {
+ return iterator.hasNext();
+ }
+
+ @Override
+ public Parent next() {
+ return convert(iterator.next());
+ }
+ };
+ }
+
+ public void appendMessages(
+ final EntityInterface from, final org.caosdb.api.entity.v1.EntityResponse.Builder builder) {
+ if (from.hasMessage(Message.MessageType.Error.toString())) {
+ builder.addAllErrors(convert(from.getMessages(Message.MessageType.Error.toString())));
+ }
+ if (from.hasMessage(Message.MessageType.Warning.toString())) {
+ builder.addAllWarnings(convert(from.getMessages(Message.MessageType.Warning.toString())));
+ }
+ if (from.hasMessage(Message.MessageType.Info.toString())) {
+ builder.addAllInfos(convert(from.getMessages(Message.MessageType.Info.toString())));
+ }
+ }
+
+ public void appendMessages(
+ final EntityInterface from, final org.caosdb.api.entity.v1.IdResponse.Builder builder) {
+ if (from.hasMessage(Message.MessageType.Error.toString())) {
+ builder.addAllErrors(convert(from.getMessages(Message.MessageType.Error.toString())));
+ }
+ if (from.hasMessage(Message.MessageType.Warning.toString())) {
+ builder.addAllWarnings(convert(from.getMessages(Message.MessageType.Warning.toString())));
+ }
+ if (from.hasMessage(Message.MessageType.Info.toString())) {
+ builder.addAllInfos(convert(from.getMessages(Message.MessageType.Info.toString())));
+ }
+ }
+}
diff --git a/src/main/java/org/caosdb/server/grpc/DownloadBuffer.java b/src/main/java/org/caosdb/server/grpc/DownloadBuffer.java
new file mode 100644
index 0000000000000000000000000000000000000000..06c387624c887f5ceeb73efb3ee7b042519a1a6f
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/DownloadBuffer.java
@@ -0,0 +1,72 @@
+package org.caosdb.server.grpc;
+
+import com.google.protobuf.ByteString;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.nio.MappedByteBuffer;
+import java.nio.channels.FileChannel;
+import java.nio.channels.FileChannel.MapMode;
+import org.caosdb.api.entity.v1.FileChunk;
+import org.caosdb.api.entity.v1.FileDownloadResponse;
+import org.caosdb.api.entity.v1.TransmissionStatus;
+import org.caosdb.server.entity.FileProperties;
+
+public class DownloadBuffer {
+
+ private final FileProperties file_properties;
+ private FileInputStream fileInputStream;
+ private FileChannel fileChannel;
+
+ public DownloadBuffer(final FileProperties file_properties) {
+ this.file_properties = file_properties;
+ this.fileInputStream = null;
+ }
+
+ public FileProperties getFileProperties() {
+ return file_properties;
+ }
+
+ public FileDownloadResponse getNextChunk() throws FileNotFoundException, IOException {
+ if (fileChannel == null) {
+ fileInputStream = new FileInputStream(file_properties.getFile());
+ fileChannel = fileInputStream.getChannel();
+ }
+ final long position = fileChannel.position();
+ final long unread_bytes = fileChannel.size() - position;
+ final long next_chunk_size = Math.min(unread_bytes, getChunkSize());
+
+ final MappedByteBuffer map = fileChannel.map(MapMode.READ_ONLY, position, next_chunk_size);
+ fileChannel.position(position + next_chunk_size);
+
+ final FileChunk.Builder builder = FileChunk.newBuilder();
+ builder.setData(ByteString.copyFrom(map));
+
+ final TransmissionStatus status;
+ if (fileInputStream.available() > 0) {
+ status = TransmissionStatus.TRANSMISSION_STATUS_GO_ON;
+ } else {
+ status = TransmissionStatus.TRANSMISSION_STATUS_SUCCESS;
+ cleanUp();
+ }
+ return FileDownloadResponse.newBuilder().setChunk(builder).setStatus(status).build();
+ }
+
+ public void cleanUp() {
+ try {
+ if (fileChannel != null && fileChannel.isOpen()) {
+ fileChannel.close();
+ }
+ if (fileInputStream != null) {
+ fileInputStream.close();
+ }
+ } catch (final IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ private int getChunkSize() {
+ // 16kB
+ return 16384;
+ }
+}
diff --git a/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java b/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java
new file mode 100644
index 0000000000000000000000000000000000000000..7062defe36121177976d43bc58355f87f235ff8a
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java
@@ -0,0 +1,376 @@
+package org.caosdb.server.grpc;
+
+import io.grpc.stub.StreamObserver;
+import java.util.HashMap;
+import java.util.UUID;
+import org.apache.shiro.SecurityUtils;
+import org.caosdb.api.entity.v1.DeleteRequest;
+import org.caosdb.api.entity.v1.DeleteResponse;
+import org.caosdb.api.entity.v1.Entity;
+import org.caosdb.api.entity.v1.EntityRequest;
+import org.caosdb.api.entity.v1.EntityResponse;
+import org.caosdb.api.entity.v1.EntityTransactionServiceGrpc.EntityTransactionServiceImplBase;
+import org.caosdb.api.entity.v1.IdResponse;
+import org.caosdb.api.entity.v1.InsertRequest;
+import org.caosdb.api.entity.v1.InsertResponse;
+import org.caosdb.api.entity.v1.MultiTransactionRequest;
+import org.caosdb.api.entity.v1.MultiTransactionResponse;
+import org.caosdb.api.entity.v1.RetrieveResponse;
+import org.caosdb.api.entity.v1.TransactionRequest;
+import org.caosdb.api.entity.v1.TransactionRequest.WrappedRequestsCase;
+import org.caosdb.api.entity.v1.TransactionResponse;
+import org.caosdb.api.entity.v1.UpdateRequest;
+import org.caosdb.api.entity.v1.UpdateResponse;
+import org.caosdb.server.CaosDBException;
+import org.caosdb.server.entity.DeleteEntity;
+import org.caosdb.server.entity.EntityInterface;
+import org.caosdb.server.entity.FileProperties;
+import org.caosdb.server.entity.InsertEntity;
+import org.caosdb.server.entity.RetrieveEntity;
+import org.caosdb.server.entity.UpdateEntity;
+import org.caosdb.server.entity.container.RetrieveContainer;
+import org.caosdb.server.entity.container.WritableContainer;
+import org.caosdb.server.transaction.Retrieve;
+import org.caosdb.server.transaction.WriteTransaction;
+import org.caosdb.server.utils.ServerMessages;
+
+public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBase {
+
+ private final CaosDBToGrpcConverters caosdbToGrpc = new CaosDBToGrpcConverters();
+ private final GrpcToCaosDBConverters grpcToCaosdb = new GrpcToCaosDBConverters();
+ private final FileTransmissionServiceImpl fileTransmissionService;
+
+ public EntityTransactionServiceImpl(final FileTransmissionServiceImpl fileTransmissionService) {
+ this.fileTransmissionService = fileTransmissionService;
+ }
+
+ /**
+ * Handle read-only transactions. Of these only one may be a query at the moment, the others must
+ * be ID retrieves.
+ *
+ * @param request
+ * @return
+ * @throws Exception
+ */
+ public MultiTransactionResponse retrieve(final MultiTransactionRequest request) throws Exception {
+ final MultiTransactionResponse.Builder builder = MultiTransactionResponse.newBuilder();
+ final RetrieveContainer container =
+ new RetrieveContainer(
+ SecurityUtils.getSubject(), getTimestamp(), getSRID(), new HashMap<>());
+ FileDownload fileDownload = null;
+
+ for (final TransactionRequest sub_request : request.getRequestsList()) {
+ if (sub_request.getWrappedRequestsCase() != WrappedRequestsCase.RETRIEVE_REQUEST) {
+ throw new CaosDBException(
+ "Cannot process a "
+ + sub_request.getWrappedRequestsCase().name()
+ + " in a read-only request.");
+ }
+ final boolean isFileDownload = sub_request.getRetrieveRequest().getRegisterFileDownload();
+ if (sub_request.getRetrieveRequest().hasQuery() // Retrieves are either queries...
+ && !sub_request.getRetrieveRequest().getQuery().getQuery().isBlank()) {
+ final String query = sub_request.getRetrieveRequest().getQuery().getQuery();
+ if (container.getFlags().containsKey("query")) { // Check for more than one query request.
+ throw new CaosDBException("Cannot process more than one query request.");
+ }
+ container.getFlags().put("query", query);
+ if (isFileDownload) {
+ container.getFlags().put("download_files", "true");
+ }
+ } else { // or ID retrieves.
+ final String id = sub_request.getRetrieveRequest().getId();
+ if (!id.isBlank()) {
+ try {
+ final RetrieveEntity entity = new RetrieveEntity(grpcToCaosdb.getId(id));
+ if (isFileDownload) {
+ entity.setFlag("download_files", "true");
+ }
+ container.add(entity);
+ } catch (final NumberFormatException e) {
+ // We handle this after the retrieval
+ }
+ }
+ }
+ }
+
+ final Retrieve transaction = new Retrieve(container);
+ transaction.execute();
+ if (container.getFlags().containsKey("query_count_result")) {
+ final int count = Integer.parseInt(container.getFlags().get("query_count_result"));
+ builder
+ .addResponsesBuilder()
+ .setRetrieveResponse(RetrieveResponse.newBuilder().setCountResult(count));
+ } else {
+ final boolean download_files_container = container.getFlags().containsKey("download_files");
+ for (final EntityInterface entity : container) {
+ final EntityResponse.Builder entityResponse = caosdbToGrpc.convert(entity);
+ if ((download_files_container || entity.getFlags().containsKey("download_files"))
+ && entity.hasFileProperties()) {
+ if (fileDownload == null) {
+ fileDownload = fileTransmissionService.registerFileDownload(null);
+ }
+ entity.getFileProperties().retrieveFromFileSystem();
+ entityResponse.setDownloadId(
+ fileTransmissionService.registerFileDownload(
+ fileDownload.getId(), entity.getFileProperties()));
+ }
+ builder
+ .addResponsesBuilder()
+ .setRetrieveResponse(RetrieveResponse.newBuilder().setEntityResponse(entityResponse));
+ }
+ }
+
+ // Add those entities which have not been retrieved because they have a string id
+ for (final TransactionRequest sub_request : request.getRequestsList()) {
+ final String id = sub_request.getRetrieveRequest().getId();
+ if (!id.isBlank()) {
+ try {
+ grpcToCaosdb.getId(id);
+ } catch (final NumberFormatException e) {
+ // ID wasn't an integer - the server doesn't support string ids yet, so that entity
+ // cannot exist.
+ builder.addResponses(
+ TransactionResponse.newBuilder()
+ .setRetrieveResponse(
+ RetrieveResponse.newBuilder().setEntityResponse(entityDoesNotExist(id))));
+ }
+ }
+ }
+ return builder.build();
+ }
+
+ private EntityResponse entityDoesNotExist(final String id) {
+ return EntityResponse.newBuilder()
+ .addErrors(caosdbToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST))
+ .setEntity(Entity.newBuilder().setId(id))
+ .build();
+ }
+
+ private String getSRID() {
+ return UUID.randomUUID().toString();
+ }
+
+ private Long getTimestamp() {
+ return System.currentTimeMillis();
+ }
+
+ /**
+ * Handle all entity transactions.
+ *
+ * <p>Currently either all requests must be read-only/retrieve requests, or none of the requests.
+ *
+ * @param request
+ * @return
+ * @throws Exception
+ */
+ public MultiTransactionResponse transaction(final MultiTransactionRequest request)
+ throws Exception {
+ if (request.getRequestsCount() > 0) {
+ // We only test the first request and raise errors when subsequent sub-transactions do not fit
+ // into the retrieve context. Currently this means that either all or none of the requests
+ // must be retrieve requests.
+ final WrappedRequestsCase requestCase = request.getRequests(0).getWrappedRequestsCase();
+ switch (requestCase) {
+ case RETRIEVE_REQUEST:
+ // Handle read-only transactions.
+ return retrieve(request);
+ default:
+ // Handle mixed-writed transactions.
+ return write(request);
+ }
+ } else {
+ // empty request, empty response.
+ return MultiTransactionResponse.newBuilder().build();
+ }
+ }
+
+ /**
+ * Handle mixed-write transactions.
+ *
+ * <p>The current implementation fails fast, without attempts to execute a single request, if
+ * there are requests with non-integer IDs. This will change in the near future, once string IDs
+ * are supported by the server.
+ *
+ * @param requests
+ * @return
+ * @throws Exception
+ */
+ private MultiTransactionResponse write(final MultiTransactionRequest requests) throws Exception {
+ final MultiTransactionResponse.Builder builder = MultiTransactionResponse.newBuilder();
+ final WritableContainer container =
+ new WritableContainer(
+ SecurityUtils.getSubject(), getTimestamp(), getSRID(), new HashMap<String, String>());
+
+ // put entities into the transaction object
+ for (final TransactionRequest subRequest : requests.getRequestsList()) {
+ switch (subRequest.getWrappedRequestsCase()) {
+ case INSERT_REQUEST:
+ {
+ final InsertRequest insertRequest = subRequest.getInsertRequest();
+ final Entity insertEntity = insertRequest.getEntityRequest().getEntity();
+
+ final InsertEntity entity =
+ new InsertEntity(
+ insertEntity.getName().isEmpty() ? null : insertEntity.getName(),
+ grpcToCaosdb.convert(insertEntity.getRole()));
+ grpcToCaosdb.convert(insertEntity, entity);
+ addFileUpload(container, entity, insertRequest.getEntityRequest());
+ container.add(entity);
+ }
+ break;
+ case UPDATE_REQUEST:
+ final UpdateRequest updateRequest = subRequest.getUpdateRequest();
+ final Entity updateEntity = updateRequest.getEntityRequest().getEntity();
+
+ try {
+ final UpdateEntity entity =
+ new UpdateEntity(
+ grpcToCaosdb.getId(updateEntity.getId()), // ID is not handled by grpc convert
+ grpcToCaosdb.convert(updateEntity.getRole()));
+ grpcToCaosdb.convert(updateEntity, entity);
+ addFileUpload(container, entity, updateRequest.getEntityRequest());
+ container.add(entity);
+ } catch (final NumberFormatException e) {
+ // ID wasn't an integer
+ return failedWriteDueToStringId(requests);
+ }
+ break;
+ case DELETE_REQUEST:
+ final DeleteRequest deleteRequest = subRequest.getDeleteRequest();
+ try {
+ final DeleteEntity entity = new DeleteEntity(grpcToCaosdb.getId(deleteRequest.getId()));
+ container.add(entity);
+
+ } catch (final NumberFormatException e) {
+ // ID wasn't an integer
+ return failedWriteDueToStringId(requests);
+ }
+ break;
+ default:
+ throw new CaosDBException(
+ "Cannot process a "
+ + subRequest.getWrappedRequestsCase().name()
+ + " in a write request.");
+ }
+ }
+
+ // execute the transaction
+ final WriteTransaction transaction = new WriteTransaction(container);
+ transaction.setNoIdIsError(false);
+ transaction.execute();
+
+ // put inserted/updated/deleted entities back into the response
+ for (final EntityInterface entity : container) {
+ final IdResponse.Builder idResponse = IdResponse.newBuilder();
+ if (entity.getId() != null) {
+ idResponse.setId(entity.getId().toString());
+ }
+ caosdbToGrpc.appendMessages(entity, idResponse);
+
+ if (entity instanceof InsertEntity) {
+ builder
+ .addResponsesBuilder()
+ .setInsertResponse(InsertResponse.newBuilder().setIdResponse(idResponse));
+ } else if (entity instanceof UpdateEntity) {
+ builder
+ .addResponsesBuilder()
+ .setUpdateResponse(UpdateResponse.newBuilder().setIdResponse(idResponse));
+ } else {
+ builder
+ .addResponsesBuilder()
+ .setDeleteResponse(DeleteResponse.newBuilder().setIdResponse(idResponse));
+ }
+ }
+ return builder.build();
+ }
+
+ /**
+ * Handle a request which contains string id (which cannot be converted to integer ids) and return
+ * a response which has the "ENTITY_DOES_NOT_EXIST" error for all entities with affected ids.
+ *
+ * <p>This does not attempt to execute a single request.
+ *
+ * @param request
+ * @return
+ */
+ private MultiTransactionResponse failedWriteDueToStringId(final MultiTransactionRequest request) {
+ final org.caosdb.api.entity.v1.MultiTransactionResponse.Builder builder =
+ MultiTransactionResponse.newBuilder();
+ for (final TransactionRequest subRequest : request.getRequestsList()) {
+ final IdResponse.Builder idResponse = IdResponse.newBuilder();
+ switch (subRequest.getWrappedRequestsCase()) {
+ case INSERT_REQUEST:
+ builder
+ .addResponsesBuilder()
+ .setInsertResponse(InsertResponse.newBuilder().setIdResponse(idResponse));
+
+ break;
+ case UPDATE_REQUEST:
+ final UpdateRequest updateRequest = subRequest.getUpdateRequest();
+ final Entity updateEntity = updateRequest.getEntityRequest().getEntity();
+
+ idResponse.setId(updateEntity.getId());
+ try {
+ grpcToCaosdb.getId(updateEntity.getId());
+ } catch (final NumberFormatException e) {
+ // ID wasn't an integer
+ idResponse.addErrors(caosdbToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST));
+ }
+ builder
+ .addResponsesBuilder()
+ .setUpdateResponse(UpdateResponse.newBuilder().setIdResponse(idResponse));
+ break;
+ case DELETE_REQUEST:
+ final DeleteRequest deleteRequest = subRequest.getDeleteRequest();
+ idResponse.setId(deleteRequest.getId());
+ try {
+ grpcToCaosdb.getId(deleteRequest.getId());
+ } catch (final NumberFormatException e) {
+ // ID wasn't an integer
+ idResponse.addErrors(caosdbToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST));
+ }
+ builder
+ .addResponsesBuilder()
+ .setDeleteResponse(DeleteResponse.newBuilder().setIdResponse(idResponse));
+ break;
+ default:
+ throw new CaosDBException(
+ "Cannot process a "
+ + subRequest.getWrappedRequestsCase().name()
+ + " in a write request.");
+ }
+ }
+ return builder.build();
+ }
+
+ private void addFileUpload(
+ final WritableContainer container,
+ final EntityInterface entity,
+ final EntityRequest entityRequest) {
+ if (entityRequest.hasUploadId()) {
+ final FileProperties uploadFile =
+ fileTransmissionService.getUploadFile(entityRequest.getUploadId());
+ if (uploadFile == null) {
+ entity.addError(ServerMessages.FILE_HAS_NOT_BEEN_UPLOAED);
+ } else {
+ container.addFile(uploadFile.getTmpIdentifier(), uploadFile);
+ entity.getFileProperties().setTmpIdentifier(uploadFile.getTmpIdentifier());
+ }
+ }
+ }
+
+ @Override
+ public void multiTransaction(
+ final MultiTransactionRequest request,
+ final StreamObserver<MultiTransactionResponse> responseObserver) {
+ try {
+ final MultiTransactionResponse response = transaction(request);
+ responseObserver.onNext(response);
+ responseObserver.onCompleted();
+
+ } catch (final Exception e) {
+ e.printStackTrace();
+ responseObserver.onError(e);
+ }
+ }
+}
diff --git a/src/main/java/org/caosdb/server/grpc/FileDownload.java b/src/main/java/org/caosdb/server/grpc/FileDownload.java
new file mode 100644
index 0000000000000000000000000000000000000000..2f3c79899dac73174c65b14e01dbc08c71f1a243
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/FileDownload.java
@@ -0,0 +1,59 @@
+package org.caosdb.server.grpc;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+import org.caosdb.api.entity.v1.FileDownloadResponse;
+import org.caosdb.api.entity.v1.FileTransmissionSettings;
+import org.caosdb.server.entity.FileProperties;
+import org.caosdb.server.utils.Utils;
+
+public class FileDownload extends FileTransmission {
+
+ Map<String, DownloadBuffer> buffers = new HashMap<>();
+ private final FileTransmissionSettings settings;
+
+ public FileDownload(final FileTransmissionSettings settings, final String id) throws Exception {
+ super(id);
+ this.settings = settings;
+ }
+
+ @Override
+ public void cleanUp() {
+ buffers.forEach(
+ (id, buffer) -> {
+ buffer.cleanUp();
+ });
+ }
+
+ @Override
+ public FileProperties getFile(final String fileId) {
+ synchronized (lock) {
+ touch();
+ return buffers.get(fileId).getFileProperties();
+ }
+ }
+
+ @Override
+ public FileTransmissionSettings getTransmissionSettings() {
+ return settings;
+ }
+
+ public String append(final FileProperties fp) {
+ synchronized (lock) {
+ touch();
+ final String id = Utils.getUID();
+ buffers.put(id, new DownloadBuffer(fp));
+ return id;
+ }
+ }
+
+ public FileDownloadResponse getNextChunk(final String fileId)
+ throws FileNotFoundException, IOException {
+ synchronized (lock) {
+ touch();
+ return buffers.get(fileId).getNextChunk();
+ }
+ }
+}
diff --git a/src/main/java/org/caosdb/server/grpc/FileDownloadRegistration.java b/src/main/java/org/caosdb/server/grpc/FileDownloadRegistration.java
new file mode 100644
index 0000000000000000000000000000000000000000..5130404024e52ec0ac36745452a609b01764dc0d
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/FileDownloadRegistration.java
@@ -0,0 +1,71 @@
+package org.caosdb.server.grpc;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import org.caosdb.api.entity.v1.FileDownloadResponse;
+import org.caosdb.api.entity.v1.FileTransmissionId;
+import org.caosdb.api.entity.v1.FileTransmissionSettings;
+import org.caosdb.server.entity.FileProperties;
+import org.caosdb.server.utils.Utils;
+
+public class FileDownloadRegistration {
+
+ private final Map<String, FileDownload> registeredDownloads = new HashMap<>();
+
+ public FileTransmissionId registerFileDownload(
+ final String registration_id, final FileProperties fp) {
+ synchronized (registeredDownloads) {
+ final String file_id = registeredDownloads.get(registration_id).append(fp);
+ return FileTransmissionId.newBuilder()
+ .setRegistrationId(registration_id)
+ .setFileId(file_id)
+ .build();
+ }
+ }
+
+ public FileDownload registerFileDownload(final FileTransmissionSettings settings)
+ throws Exception {
+ final FileDownload result = new FileDownload(settings, Utils.getUID());
+ register(result);
+ return result;
+ }
+
+ private void register(final FileDownload fileTransmission) {
+ synchronized (registeredDownloads) {
+ registeredDownloads.put(fileTransmission.getId(), fileTransmission);
+ }
+ }
+
+ public FileDownloadResponse downloadNextChunk(final FileTransmissionId fileTransmissionId)
+ throws FileNotFoundException, IOException {
+ FileDownload next;
+ synchronized (registeredDownloads) {
+ next = registeredDownloads.get(fileTransmissionId.getRegistrationId());
+ }
+ return next.getNextChunk(fileTransmissionId.getFileId());
+ }
+
+ public void cleanUp(final boolean all) {
+ synchronized (registeredDownloads) {
+ final List<String> cleanUp = new LinkedList<>();
+ for (final Entry<String, FileDownload> entry : registeredDownloads.entrySet()) {
+ if (all || entry.getValue().isExpired()) {
+ cleanUp.add(entry.getKey());
+ }
+ }
+ for (final String key : cleanUp) {
+ registeredDownloads.get(key).cleanUp();
+ registeredDownloads.remove(key);
+ }
+ }
+ }
+
+ public void cleanUp() {
+ cleanUp(false);
+ }
+}
diff --git a/src/main/java/org/caosdb/server/grpc/FileTransmission.java b/src/main/java/org/caosdb/server/grpc/FileTransmission.java
new file mode 100644
index 0000000000000000000000000000000000000000..67eca23a8f3deb557e0d773e6de7ff0ee38821a2
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/FileTransmission.java
@@ -0,0 +1,62 @@
+package org.caosdb.server.grpc;
+
+import java.util.concurrent.locks.ReentrantLock;
+import org.caosdb.api.entity.v1.FileTransmissionSettings;
+import org.caosdb.api.entity.v1.RegistrationStatus;
+import org.caosdb.server.entity.FileProperties;
+
+public abstract class FileTransmission {
+
+ protected ReentrantLock lock = new ReentrantLock();
+ protected final String id;
+ protected final long createdTimestamp;
+ protected long touchedTimestamp;
+ protected final RegistrationStatus status;
+
+ public FileTransmission(final String id) {
+ this.id = id;
+ this.status = RegistrationStatus.REGISTRATION_STATUS_ACCEPTED;
+ this.createdTimestamp = System.currentTimeMillis();
+ this.touchedTimestamp = createdTimestamp;
+ }
+
+ public abstract void cleanUp();
+
+ public long getCreatedTimestamp() {
+ return createdTimestamp;
+ }
+
+ public long getTouchedTimestamp() {
+ return this.touchedTimestamp;
+ }
+
+ public void touch() {
+ this.touchedTimestamp = System.currentTimeMillis();
+ }
+
+ public String getId() {
+ return this.id;
+ }
+
+ public RegistrationStatus getRegistrationStatus() {
+ return status;
+ }
+
+ public long getMaxChunkSize() {
+ // 2^24, 16.78 MB
+ return 16777216;
+ }
+
+ public long getMaxFileSize() {
+ // 2^30, 1.074 GB
+ return 1073741824;
+ }
+
+ public abstract FileProperties getFile(final String fileId);
+
+ public abstract FileTransmissionSettings getTransmissionSettings();
+
+ public boolean isExpired() {
+ return System.currentTimeMillis() - touchedTimestamp > 10 * 60 * 1000; // older than 10 min
+ }
+}
diff --git a/src/main/java/org/caosdb/server/grpc/FileTransmissionServiceImpl.java b/src/main/java/org/caosdb/server/grpc/FileTransmissionServiceImpl.java
new file mode 100644
index 0000000000000000000000000000000000000000..0b0c4b50e0851f3298a61c02c5e38e08c29b2601
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/FileTransmissionServiceImpl.java
@@ -0,0 +1,150 @@
+package org.caosdb.server.grpc;
+
+import io.grpc.stub.StreamObserver;
+import java.io.IOException;
+import org.caosdb.api.entity.v1.FileChunk;
+import org.caosdb.api.entity.v1.FileDownloadRequest;
+import org.caosdb.api.entity.v1.FileDownloadResponse;
+import org.caosdb.api.entity.v1.FileTransmissionId;
+import org.caosdb.api.entity.v1.FileTransmissionServiceGrpc.FileTransmissionServiceImplBase;
+import org.caosdb.api.entity.v1.FileTransmissionSettings;
+import org.caosdb.api.entity.v1.FileUploadRequest;
+import org.caosdb.api.entity.v1.FileUploadResponse;
+import org.caosdb.api.entity.v1.RegisterFileUploadRequest;
+import org.caosdb.api.entity.v1.RegisterFileUploadResponse;
+import org.caosdb.api.entity.v1.RegisterFileUploadResponse.Builder;
+import org.caosdb.api.entity.v1.RegistrationStatus;
+import org.caosdb.api.entity.v1.TransmissionStatus;
+import org.caosdb.server.CaosDBServer;
+import org.caosdb.server.entity.FileProperties;
+import org.caosdb.server.utils.CronJob;
+import org.caosdb.server.utils.Utils;
+
+public class FileTransmissionServiceImpl extends FileTransmissionServiceImplBase {
+
+ public class FileUploadStreamObserver implements StreamObserver<FileUploadRequest> {
+
+ private FileUpload fileUpload = null;
+ private FileTransmissionId fileTransmissionId = null;
+ private final StreamObserver<FileUploadResponse> outputStreamObserver;
+ private TransmissionStatus status;
+
+ public FileUploadStreamObserver(final StreamObserver<FileUploadResponse> outputStreamObserver) {
+ this.outputStreamObserver = outputStreamObserver;
+ }
+
+ @Override
+ public void onError(final Throwable throwable) {}
+
+ @Override
+ public void onCompleted() {
+ final FileUploadResponse response = FileUploadResponse.newBuilder().setStatus(status).build();
+ outputStreamObserver.onNext(response);
+ outputStreamObserver.onCompleted();
+ }
+
+ @Override
+ public void onNext(final FileUploadRequest request) {
+ final FileChunk chunk = request.getChunk();
+ if (chunk.hasFileTransmissionId()) {
+ fileUpload =
+ fileUploadRegistration.getFileUpload(chunk.getFileTransmissionId().getRegistrationId());
+ fileTransmissionId = chunk.getFileTransmissionId();
+ if (fileTransmissionId.getFileId().isBlank()) {
+ fileTransmissionId =
+ FileTransmissionId.newBuilder(fileTransmissionId).setFileId(Utils.getUID()).build();
+ }
+ } else {
+
+ try {
+ status = fileUpload.uploadChunk(fileTransmissionId.getFileId(), chunk);
+ } catch (final IOException e) {
+ status = TransmissionStatus.TRANSMISSION_STATUS_ERROR;
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
+ public FileTransmissionServiceImpl() {
+ CaosDBServer.addPreShutdownHook(
+ () -> {
+ fileDownloadRegistration.cleanUp(true);
+ fileUploadRegistration.cleanUp(true);
+ });
+ }
+
+ FileUploadRegistration fileUploadRegistration = new FileUploadRegistration();
+ FileDownloadRegistration fileDownloadRegistration = new FileDownloadRegistration();
+ CronJob cleanUp =
+ new CronJob(
+ "FileTransmissionCleanUp",
+ () -> {
+ fileUploadRegistration.cleanUp();
+ fileDownloadRegistration.cleanUp();
+ },
+ 60,
+ false);
+
+ FileTransmissionId registerFileDownload(final String registration_id, final FileProperties fp)
+ throws Exception {
+ return fileDownloadRegistration.registerFileDownload(registration_id, fp);
+ }
+
+ FileDownload registerFileDownload(final FileTransmissionSettings settings) throws Exception {
+ return fileDownloadRegistration.registerFileDownload(settings);
+ }
+
+ public FileProperties getUploadFile(final FileTransmissionId uploadId) {
+ return fileUploadRegistration.getUploadFile(uploadId);
+ }
+
+ @Override
+ public void registerFileUpload(
+ final RegisterFileUploadRequest request,
+ final StreamObserver<RegisterFileUploadResponse> responseObserver) {
+ try {
+ final FileTransmission result = fileUploadRegistration.registerFileUpload();
+ final Builder builder = RegisterFileUploadResponse.newBuilder();
+ builder.setStatus(result.getRegistrationStatus());
+ if (result.getRegistrationStatus() == RegistrationStatus.REGISTRATION_STATUS_ACCEPTED) {
+ builder.setRegistrationId(result.getId());
+ builder.setUploadSettings(result.getTransmissionSettings());
+ }
+
+ final RegisterFileUploadResponse response = builder.build();
+ responseObserver.onNext(response);
+ responseObserver.onCompleted();
+
+ } catch (final Exception e) {
+ e.printStackTrace();
+ responseObserver.onError(e);
+ }
+ }
+
+ @Override
+ public StreamObserver<FileUploadRequest> fileUpload(
+ final StreamObserver<FileUploadResponse> responseObserver) {
+ return new FileUploadStreamObserver(responseObserver);
+ }
+
+ @Override
+ public void fileDownload(
+ final FileDownloadRequest request,
+ final StreamObserver<FileDownloadResponse> responseObserver) {
+ try {
+ FileDownloadResponse response =
+ fileDownloadRegistration.downloadNextChunk(request.getFileTransmissionId());
+ responseObserver.onNext(response);
+
+ while (response.getStatus() == TransmissionStatus.TRANSMISSION_STATUS_GO_ON) {
+ response = fileDownloadRegistration.downloadNextChunk(request.getFileTransmissionId());
+ responseObserver.onNext(response);
+ }
+ responseObserver.onCompleted();
+ } catch (final Exception e) {
+ e.printStackTrace();
+ responseObserver.onError(e);
+ }
+ }
+}
diff --git a/src/main/java/org/caosdb/server/grpc/FileUpload.java b/src/main/java/org/caosdb/server/grpc/FileUpload.java
new file mode 100644
index 0000000000000000000000000000000000000000..2ec4ca3de3d5d7ad5b9c44ec16deade8725d9145
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/FileUpload.java
@@ -0,0 +1,79 @@
+package org.caosdb.server.grpc;
+
+import com.google.protobuf.ByteString;
+import java.io.File;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+import org.caosdb.api.entity.v1.FileChunk;
+import org.caosdb.api.entity.v1.FileTransmissionSettings;
+import org.caosdb.api.entity.v1.FileTransmissionSettings.Builder;
+import org.caosdb.api.entity.v1.TransmissionStatus;
+import org.caosdb.server.FileSystem;
+import org.caosdb.server.entity.FileProperties;
+
+public class FileUpload extends FileTransmission {
+
+ Map<String, UploadBuffer> buffers = new HashMap<>();
+
+ File tmpDir;
+
+ public FileUpload(final String id) {
+ super(id);
+ this.tmpDir = null;
+ }
+
+ @Override
+ public void cleanUp() {
+ if (tmpDir != null) {
+ org.apache.commons.io.FileUtils.deleteQuietly(tmpDir);
+ }
+ }
+
+ File getTmpDir() {
+ if (tmpDir == null) {
+ tmpDir = new File(FileSystem.getTmp() + id + "/");
+ tmpDir.mkdirs();
+ }
+ return tmpDir;
+ }
+
+ public TransmissionStatus upload(final String fileId, final ByteString data) throws IOException {
+ synchronized (lock) {
+ touch();
+ return getFileBuffer(fileId).write(data);
+ }
+ }
+
+ protected UploadBuffer getFileBuffer(final String fileId) {
+ touch();
+ if (!buffers.containsKey(fileId)) {
+ buffers.put(fileId, new UploadBuffer(getTmpDir().toPath().resolve(fileId).toFile()));
+ }
+ return buffers.get(fileId);
+ }
+
+ @Override
+ public FileProperties getFile(final String fileId) {
+ synchronized (lock) {
+ touch();
+ if (buffers.containsKey(fileId)) {
+ return buffers.get(fileId).toFileProperties(fileId);
+ }
+ return null;
+ }
+ }
+
+ @Override
+ public FileTransmissionSettings getTransmissionSettings() {
+ final Builder builder = FileTransmissionSettings.newBuilder();
+ builder.setMaxChunkSize(getMaxChunkSize());
+ builder.setMaxFileSize(getMaxFileSize());
+ return builder.build();
+ }
+
+ public TransmissionStatus uploadChunk(final String fileId, final FileChunk chunk)
+ throws IOException {
+ return upload(fileId, chunk.getData());
+ }
+}
diff --git a/src/main/java/org/caosdb/server/grpc/FileUploadRegistration.java b/src/main/java/org/caosdb/server/grpc/FileUploadRegistration.java
new file mode 100644
index 0000000000000000000000000000000000000000..bfb25be2ec91cda450be282b89f08ace26a16409
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/FileUploadRegistration.java
@@ -0,0 +1,64 @@
+package org.caosdb.server.grpc;
+
+import java.util.HashMap;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import org.caosdb.api.entity.v1.FileTransmissionId;
+import org.caosdb.server.entity.FileProperties;
+import org.caosdb.server.utils.Utils;
+
+public class FileUploadRegistration {
+
+ private final Map<String, FileUpload> registeredUploads = new HashMap<>();
+
+ public FileTransmission registerFileUpload() {
+ final FileUpload result = new FileUpload(Utils.getUID());
+ register(result);
+ return result;
+ }
+
+ private void register(final FileUpload fileTransmission) {
+
+ synchronized (registeredUploads) {
+ registeredUploads.put(fileTransmission.getId(), fileTransmission);
+ }
+ }
+
+ public FileProperties getUploadFile(final FileTransmissionId uploadId) {
+ final String fileId = uploadId.getFileId();
+ final String registrationId = uploadId.getRegistrationId();
+ final FileTransmission fileTransmission;
+
+ synchronized (registeredUploads) {
+ fileTransmission = registeredUploads.get(registrationId);
+ }
+ return fileTransmission.getFile(fileId);
+ }
+
+ public FileUpload getFileUpload(final String registrationId) {
+ synchronized (registeredUploads) {
+ return registeredUploads.get(registrationId);
+ }
+ }
+
+ public void cleanUp(final boolean all) {
+ synchronized (registeredUploads) {
+ final List<String> cleanUp = new LinkedList<>();
+ for (final Entry<String, FileUpload> entry : registeredUploads.entrySet()) {
+ if (all || entry.getValue().isExpired()) {
+ cleanUp.add(entry.getKey());
+ }
+ }
+ for (final String key : cleanUp) {
+ registeredUploads.get(key).cleanUp();
+ registeredUploads.remove(key);
+ }
+ }
+ }
+
+ public void cleanUp() {
+ cleanUp(false);
+ }
+}
diff --git a/src/main/java/org/caosdb/server/grpc/GRPCServer.java b/src/main/java/org/caosdb/server/grpc/GRPCServer.java
new file mode 100644
index 0000000000000000000000000000000000000000..469e4b1048b6139c58d41a46b36c738603e536cf
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/GRPCServer.java
@@ -0,0 +1,228 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2021 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/>.
+ */
+package org.caosdb.server.grpc;
+
+import io.grpc.Server;
+import io.grpc.ServerInterceptors;
+import io.grpc.ServerServiceDefinition;
+import io.grpc.netty.GrpcSslContexts;
+import io.grpc.netty.NettyServerBuilder;
+import io.netty.handler.ssl.ApplicationProtocolConfig;
+import io.netty.handler.ssl.ApplicationProtocolConfig.Protocol;
+import io.netty.handler.ssl.ApplicationProtocolConfig.SelectedListenerFailureBehavior;
+import io.netty.handler.ssl.ApplicationProtocolConfig.SelectorFailureBehavior;
+import io.netty.handler.ssl.SslContext;
+import io.netty.handler.ssl.SslContextBuilder;
+import java.io.File;
+import java.io.IOException;
+import java.security.KeyStore;
+import java.security.KeyStoreException;
+import java.security.NoSuchAlgorithmException;
+import java.security.UnrecoverableKeyException;
+import java.security.cert.CertificateException;
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+import javax.net.ssl.KeyManagerFactory;
+import org.caosdb.server.CaosDBServer;
+import org.caosdb.server.ServerProperties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * This is the main class of the gRPC end-point.
+ *
+ * <p>Here, the http and https servers are startet.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public class GRPCServer {
+ private static GRPCServer instance = new GRPCServer();
+
+ private static String getServerProperty(final String key) {
+ return CaosDBServer.getServerProperty(key);
+ }
+
+ private static final Logger logger = LoggerFactory.getLogger(GRPCServer.class.getName());
+
+ private final AuthInterceptor authInterceptor = new AuthInterceptor();
+ private final LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
+
+ /**
+ * Create an ssl context.
+ *
+ * <p>Read the server certificate from the Java Key Store. Also, use the server properties for
+ * enabling desired TLS protocols and cipher suites.
+ *
+ * @return An SslContext for a https grpc end-point.
+ * @throws NoSuchAlgorithmException
+ * @throws UnrecoverableKeyException
+ * @throws KeyStoreException
+ * @throws CertificateException
+ * @throws IOException
+ */
+ private SslContext buildSslContext()
+ throws NoSuchAlgorithmException, UnrecoverableKeyException, KeyStoreException,
+ CertificateException, IOException {
+ final KeyManagerFactory kmf =
+ KeyManagerFactory.getInstance(KeyManagerFactory.getDefaultAlgorithm());
+ final char[] password =
+ getServerProperty(ServerProperties.KEY_CERTIFICATES_KEY_STORE_PASSWORD).toCharArray();
+ kmf.init(
+ KeyStore.getInstance(
+ new File(getServerProperty(ServerProperties.KEY_CERTIFICATES_KEY_STORE_PATH)),
+ password),
+ password);
+
+ final String[] protocols =
+ getServerProperty(ServerProperties.KEY_HTTPS_ENABLED_PROTOCOLS).split("\\s*,\\s*|\\s+");
+ final List<String> ciphers =
+ Arrays.asList(
+ getServerProperty(ServerProperties.KEY_HTTPS_ENABLED_CIPHER_SUITES)
+ .split("\\s*,\\s*|\\s+"));
+ final ApplicationProtocolConfig config =
+ new ApplicationProtocolConfig(
+ Protocol.NPN_AND_ALPN,
+ SelectorFailureBehavior.FATAL_ALERT,
+ SelectedListenerFailureBehavior.FATAL_ALERT,
+ protocols);
+ final SslContextBuilder builder =
+ GrpcSslContexts.configure(
+ SslContextBuilder.forServer(kmf).applicationProtocolConfig(config).ciphers(ciphers));
+
+ return builder.build();
+ }
+
+ /** @return A list of services which should be added to the gRPC end-point. */
+ private List<ServerServiceDefinition> getEnabledServices() {
+ final List<ServerServiceDefinition> services = new LinkedList<>();
+
+ final GeneralInfoServiceImpl generalInfoService = new GeneralInfoServiceImpl();
+ services.add(
+ ServerInterceptors.intercept(generalInfoService, loggingInterceptor, authInterceptor));
+
+ final FileTransmissionServiceImpl fileTransmissionService = new FileTransmissionServiceImpl();
+ services.add(
+ ServerInterceptors.intercept(fileTransmissionService, loggingInterceptor, authInterceptor));
+
+ final EntityTransactionServiceImpl entityTransactionService =
+ new EntityTransactionServiceImpl(fileTransmissionService);
+ services.add(
+ ServerInterceptors.intercept(
+ entityTransactionService, loggingInterceptor, authInterceptor));
+
+ return services;
+ }
+
+ /**
+ * Create a server listening on the specified port. If `tls` is true, the server is a HTTPS
+ * server. Otherwise, HTTP.
+ *
+ * @param port
+ * @param tls indicate whether the server uses tls or not
+ * @return A new, unstarted server instance.
+ * @throws UnrecoverableKeyException
+ * @throws NoSuchAlgorithmException
+ * @throws KeyStoreException
+ * @throws CertificateException
+ * @throws IOException
+ */
+ private Server buildServer(final int port, final boolean tls)
+ throws UnrecoverableKeyException, NoSuchAlgorithmException, KeyStoreException,
+ CertificateException, IOException {
+ final NettyServerBuilder builder = NettyServerBuilder.forPort(port);
+
+ if (tls) {
+ final SslContext sslContext = buildSslContext();
+ builder.sslContext(sslContext);
+ }
+ for (final ServerServiceDefinition service : getEnabledServices()) {
+ builder.addService(service);
+ }
+
+ return builder.build();
+ }
+
+ /**
+ * Main method of the gRPC end-point which starts the server(s) with HTTP or HTTPS. Whether a
+ * server is started or not depends on the server properites {@link
+ * ServerProperties#KEY_GRPC_SERVER_PORT_HTTP} and {@link
+ * ServerProperties#KEY_GRPC_SERVER_PORT_HTTPS}.
+ *
+ * @throws IOException
+ * @throws InterruptedException
+ * @throws KeyStoreException
+ * @throws NoSuchAlgorithmException
+ * @throws CertificateException
+ * @throws UnrecoverableKeyException
+ */
+ public static void startServer()
+ throws IOException, InterruptedException, KeyStoreException, NoSuchAlgorithmException,
+ CertificateException, UnrecoverableKeyException {
+
+ boolean started = false;
+ final String port_https_str = getServerProperty(ServerProperties.KEY_GRPC_SERVER_PORT_HTTPS);
+ if (port_https_str != null && !port_https_str.isEmpty()) {
+ final Integer port_https = Integer.parseInt(port_https_str);
+ final Server server = instance.buildServer(port_https, true);
+ CaosDBServer.addPreShutdownHook(new ServerStopper(server));
+ server.start();
+ started = true;
+ logger.info("Started GRPC (HTTPS) on port {}", port_https);
+ }
+
+ final String port_http_str = getServerProperty(ServerProperties.KEY_GRPC_SERVER_PORT_HTTP);
+ if (port_http_str != null && !port_http_str.isEmpty()) {
+ final Integer port_http = Integer.parseInt(port_http_str);
+
+ final Server server = instance.buildServer(port_http, false);
+ CaosDBServer.addPreShutdownHook(new ServerStopper(server));
+ server.start();
+ logger.info("Started GRPC (HTTP) on port {}", port_http);
+ } else if (!started) {
+ logger.warn(
+ "No GRPC Server has been started. Please configure {} or {} to do so.",
+ ServerProperties.KEY_GRPC_SERVER_PORT_HTTP,
+ ServerProperties.KEY_GRPC_SERVER_PORT_HTTPS);
+ }
+ }
+
+ private static class ServerStopper implements Runnable {
+
+ private final Server server;
+
+ public ServerStopper(final Server server) {
+ this.server = server;
+ }
+
+ @Override
+ public void run() {
+ try {
+ if (!server.isShutdown()) {
+ server.shutdown();
+ server.awaitTermination(60, TimeUnit.SECONDS);
+ }
+ } catch (final InterruptedException e) {
+ logger.warn("Could not shutdown the GRPC server on port {}", server.getPort());
+ }
+ }
+ }
+}
diff --git a/src/main/java/org/caosdb/server/grpc/GeneralInfoServiceImpl.java b/src/main/java/org/caosdb/server/grpc/GeneralInfoServiceImpl.java
new file mode 100644
index 0000000000000000000000000000000000000000..17d9f4c8e17886f66bc73096487f0b194b350fe8
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/GeneralInfoServiceImpl.java
@@ -0,0 +1,68 @@
+/*
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
+ * Copyright (C) 2021 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/>.
+ */
+package org.caosdb.server.grpc;
+
+import io.grpc.stub.StreamObserver;
+import org.caosdb.api.info.v1.GeneralInfoServiceGrpc.GeneralInfoServiceImplBase;
+import org.caosdb.api.info.v1.GetVersionInfoRequest;
+import org.caosdb.api.info.v1.GetVersionInfoResponse;
+import org.caosdb.api.info.v1.VersionInfo;
+import org.caosdb.server.CaosDBServer;
+import org.caosdb.server.ServerProperties;
+
+/**
+ * Implementation of the GeneralInfoService.
+ *
+ * <p>Currently, the only functionality is {@link #getVersionInfo(GetVersionInfoRequest,
+ * StreamObserver)} which returns the current version and build metadata of this server instance to
+ * the client.
+ *
+ * @author Timm Fitschen <t.fitschen@indiscale.com>
+ */
+public class GeneralInfoServiceImpl extends GeneralInfoServiceImplBase {
+
+ @Override
+ public void getVersionInfo(
+ final GetVersionInfoRequest request,
+ final StreamObserver<GetVersionInfoResponse> responseObserver) {
+
+ final String version[] =
+ CaosDBServer.getServerProperty(ServerProperties.KEY_PROJECT_VERSION).split("[\\.-]", 4);
+ final Integer major = Integer.parseInt(version[0]);
+ final Integer minor = Integer.parseInt(version[1]);
+ final Integer patch = Integer.parseInt(version[2]);
+ final String pre_release = version.length > 3 ? version[3] : "";
+ final String build = CaosDBServer.getServerProperty(ServerProperties.KEY_PROJECT_REVISTION);
+
+ final VersionInfo versionInfo =
+ VersionInfo.newBuilder()
+ .setMajor(major)
+ .setMinor(minor)
+ .setPatch(patch)
+ .setPreRelease(pre_release)
+ .setBuild(build)
+ .build();
+ final GetVersionInfoResponse response =
+ GetVersionInfoResponse.newBuilder().setVersionInfo(versionInfo).build();
+
+ responseObserver.onNext(response);
+ responseObserver.onCompleted();
+ }
+}
diff --git a/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java b/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java
new file mode 100644
index 0000000000000000000000000000000000000000..c2007bebd52f29ce8d1a02fe9e0fcd913a8df798
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java
@@ -0,0 +1,292 @@
+package org.caosdb.server.grpc;
+
+import java.util.Collection;
+import java.util.LinkedList;
+import java.util.List;
+import org.caosdb.api.entity.v1.AtomicDataType;
+import org.caosdb.api.entity.v1.CollectionValues;
+import org.caosdb.api.entity.v1.DataType;
+import org.caosdb.api.entity.v1.Entity;
+import org.caosdb.api.entity.v1.EntityRole;
+import org.caosdb.api.entity.v1.FileDescriptor;
+import org.caosdb.api.entity.v1.Importance;
+import org.caosdb.api.entity.v1.ListDataType;
+import org.caosdb.api.entity.v1.Parent;
+import org.caosdb.api.entity.v1.ReferenceDataType;
+import org.caosdb.api.entity.v1.SpecialValue;
+import org.caosdb.server.datatype.AbstractDatatype;
+import org.caosdb.server.datatype.BooleanValue;
+import org.caosdb.server.datatype.CollectionValue;
+import org.caosdb.server.datatype.FileDatatype;
+import org.caosdb.server.datatype.GenericValue;
+import org.caosdb.server.datatype.ListDatatype;
+import org.caosdb.server.datatype.ReferenceDatatype;
+import org.caosdb.server.datatype.ReferenceDatatype2;
+import org.caosdb.server.datatype.Value;
+import org.caosdb.server.entity.EntityInterface;
+import org.caosdb.server.entity.FileProperties;
+import org.caosdb.server.entity.MagicTypes;
+import org.caosdb.server.entity.Role;
+import org.caosdb.server.entity.StatementStatus;
+import org.caosdb.server.entity.wrapper.Property;
+import org.caosdb.server.utils.EntityStatus;
+import org.caosdb.server.utils.ServerMessages;
+
+public class GrpcToCaosDBConverters {
+
+ public Integer getId(final String id) {
+ return Integer.parseInt(id);
+ }
+
+ public Role convert(final EntityRole role) {
+ switch (role) {
+ case ENTITY_ROLE_FILE:
+ return Role.File;
+ case ENTITY_ROLE_PROPERTY:
+ return Role.Property;
+ case ENTITY_ROLE_RECORD:
+ return Role.Record;
+ case ENTITY_ROLE_RECORD_TYPE:
+ return Role.RecordType;
+ default:
+ return null;
+ }
+ }
+
+ public Property getUnit(final String unitStr) {
+ final EntityInterface magicUnit = MagicTypes.UNIT.getEntity();
+ final Property unit = new Property();
+ unit.setDescription(magicUnit.getDescription());
+ unit.setName(magicUnit.getName());
+ unit.setId(magicUnit.getId());
+ unit.setDatatype(magicUnit.getDatatype());
+ unit.setStatementStatus(StatementStatus.FIX);
+ unit.setValue(new GenericValue(unitStr));
+ unit.setEntityStatus(EntityStatus.QUALIFIED);
+ return unit;
+ }
+
+ public Value getValue(final String valString) {
+ return new GenericValue(valString);
+ }
+
+ /**
+ * Set the content of {@code entity} to that of the grpc message object {@code from}. Also return
+ * {@code entity} at the end.
+ */
+ public EntityInterface convert(final Entity from, final EntityInterface entity) {
+ entity.setName(from.getName().isEmpty() ? null : from.getName());
+ entity.setDescription(from.getDescription().isBlank() ? null : from.getDescription());
+ if (!from.getUnit().isBlank()) {
+ entity.addProperty(getUnit(from.getUnit()));
+ }
+ if (from.hasDataType()) {
+ entity.setDatatype(convert(from.getDataType()));
+ }
+ if (from.hasValue()) {
+ entity.setValue(convert(from.getValue()));
+ }
+
+ if (from.getPropertiesCount() > 0) {
+ final StatementStatus defaultImportance =
+ entity.getRole() == Role.RecordType ? StatementStatus.RECOMMENDED : StatementStatus.FIX;
+ entity.getProperties().addAll(convertProperties(from.getPropertiesList(), defaultImportance));
+ }
+ if (from.getParentsCount() > 0) {
+ entity.getParents().addAll(convertParents(from.getParentsList()));
+ }
+ if (from.hasFileDescriptor()) {
+ entity.setFileProperties(convert(from.getFileDescriptor()));
+ }
+ return entity;
+ }
+
+ private Value convert(final org.caosdb.api.entity.v1.Value value) {
+ switch (value.getValueCase()) {
+ case LIST_VALUES:
+ return convertListValue(value.getListValues());
+ case SCALAR_VALUE:
+ return convertScalarValue(value.getScalarValue());
+ default:
+ break;
+ }
+ return null;
+ }
+
+ private CollectionValue convertListValue(final CollectionValues collectionValues) {
+ final CollectionValue result = new CollectionValue();
+ collectionValues
+ .getValuesList()
+ .forEach(
+ (v) -> {
+ result.add(convertScalarValue(v));
+ });
+ return result;
+ }
+
+ private Value convertScalarValue(final org.caosdb.api.entity.v1.ScalarValue value) {
+ switch (value.getScalarValueCase()) {
+ case BOOLEAN_VALUE:
+ return BooleanValue.valueOf(value.getBooleanValue());
+ case DOUBLE_VALUE:
+ return new GenericValue(value.getDoubleValue());
+ case INTEGER_VALUE:
+ return new GenericValue(Long.toString(value.getIntegerValue()));
+ case SPECIAL_VALUE:
+ return convertSpecial(value.getSpecialValue());
+ case STRING_VALUE:
+ return new GenericValue(value.getStringValue());
+ default:
+ break;
+ }
+ return null;
+ }
+
+ private Value convertSpecial(final SpecialValue specialValue) {
+ if (specialValue == SpecialValue.SPECIAL_VALUE_EMPTY_STRING) {
+ return new GenericValue("");
+ }
+ return null;
+ }
+
+ private AbstractDatatype convert(final DataType dataType) {
+ switch (dataType.getDataTypeCase()) {
+ case ATOMIC_DATA_TYPE:
+ return convertAtomicType(dataType.getAtomicDataType());
+ case LIST_DATA_TYPE:
+ return convertListDataType(dataType.getListDataType());
+ case REFERENCE_DATA_TYPE:
+ return convertReferenceDataType(dataType.getReferenceDataType());
+ default:
+ break;
+ }
+ return null;
+ }
+
+ private ReferenceDatatype convertReferenceDataType(final ReferenceDataType referenceDataType) {
+ final String name = referenceDataType.getName();
+ if (name.equalsIgnoreCase("REFERENCE")) {
+ return new ReferenceDatatype();
+ } else if (name.equalsIgnoreCase("FILE")) {
+ return new FileDatatype();
+ }
+ return new ReferenceDatatype2(name);
+ }
+
+ private AbstractDatatype convertAtomicType(final AtomicDataType dataType) {
+ switch (dataType) {
+ case ATOMIC_DATA_TYPE_BOOLEAN:
+ return AbstractDatatype.datatypeFactory("BOOLEAN");
+ case ATOMIC_DATA_TYPE_DATETIME:
+ return AbstractDatatype.datatypeFactory("DATETIME");
+ case ATOMIC_DATA_TYPE_DOUBLE:
+ return AbstractDatatype.datatypeFactory("DOUBLE");
+ case ATOMIC_DATA_TYPE_INTEGER:
+ return AbstractDatatype.datatypeFactory("INTEGER");
+ case ATOMIC_DATA_TYPE_TEXT:
+ return AbstractDatatype.datatypeFactory("TEXT");
+ default:
+ return null;
+ }
+ }
+
+ private AbstractDatatype convertListDataType(final ListDataType dataType) {
+ switch (dataType.getListDataTypeCase()) {
+ case ATOMIC_DATA_TYPE:
+ return new ListDatatype(convertAtomicType(dataType.getAtomicDataType()));
+ case REFERENCE_DATA_TYPE:
+ return new ListDatatype(convertReferenceDataType(dataType.getReferenceDataType()));
+ default:
+ return null;
+ }
+ }
+
+ private FileProperties convert(final FileDescriptor fileDescriptor) {
+ return new FileProperties(
+ null,
+ fileDescriptor.getPath(),
+ fileDescriptor.getSize() == 0 ? null : fileDescriptor.getSize());
+ }
+
+ private Collection<Property> convertProperties(
+ final List<org.caosdb.api.entity.v1.Property> propertiesList,
+ final StatementStatus defaultImportance) {
+ final Collection<Property> result = new LinkedList<>();
+ propertiesList.forEach(
+ prop -> {
+ result.add(convert(prop, defaultImportance));
+ });
+ return result;
+ }
+
+ private Property convert(
+ final org.caosdb.api.entity.v1.Property e, final StatementStatus defaultImportance) {
+ final Property result = new Property();
+
+ try {
+ result.setId(e.getId().isBlank() ? null : getId(e.getId()));
+ } catch (final NumberFormatException exc) {
+ result.addError(ServerMessages.ENTITY_DOES_NOT_EXIST);
+ }
+ result.setName(e.getName().isBlank() ? null : e.getName());
+ result.setDescription(e.getDescription().isBlank() ? null : e.getDescription());
+ if (!e.getUnit().isBlank()) {
+ result.addProperty(getUnit(e.getUnit()));
+ }
+ if (e.hasDataType()) {
+ result.setDatatype(convert(e.getDataType()));
+ }
+ if (e.hasValue()) {
+ result.setValue(convert(e.getValue()));
+ }
+ if (e.getImportance() != Importance.IMPORTANCE_UNSPECIFIED) {
+ result.setStatementStatus(convert(e.getImportance()));
+ } else {
+ result.setStatementStatus(defaultImportance);
+ }
+ // TODO remove this hard-coded setting when the API supports flags
+ if (result.getFlag("inheritance") == null) {
+ result.setFlag("inheritance", "fix");
+ }
+
+ return result;
+ }
+
+ private StatementStatus convert(final Importance importance) {
+ switch (importance) {
+ case IMPORTANCE_FIX:
+ return StatementStatus.FIX;
+ case IMPORTANCE_OBLIGATORY:
+ return StatementStatus.OBLIGATORY;
+ case IMPORTANCE_RECOMMENDED:
+ return StatementStatus.RECOMMENDED;
+ case IMPORTANCE_SUGGESTED:
+ return StatementStatus.SUGGESTED;
+ default:
+ return null;
+ }
+ }
+
+ private Collection<org.caosdb.server.entity.wrapper.Parent> convertParents(
+ final List<Parent> parentsList) {
+ final Collection<org.caosdb.server.entity.wrapper.Parent> result = new LinkedList<>();
+ parentsList.forEach(
+ e -> {
+ result.add(convert(e));
+ });
+ return result;
+ }
+
+ private org.caosdb.server.entity.wrapper.Parent convert(final Parent e) {
+ final org.caosdb.server.entity.wrapper.Parent result =
+ new org.caosdb.server.entity.wrapper.Parent();
+
+ try {
+ result.setId(e.getId().isBlank() ? null : getId(e.getId()));
+ } catch (final NumberFormatException exc) {
+ result.addError(ServerMessages.ENTITY_DOES_NOT_EXIST);
+ }
+ result.setName(e.getName().isBlank() ? null : e.getName());
+ return result;
+ }
+}
diff --git a/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java b/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java
new file mode 100644
index 0000000000000000000000000000000000000000..9edd35090659e908ecf7f3fb502d34c36ac7e829
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java
@@ -0,0 +1,24 @@
+package org.caosdb.server.grpc;
+
+import io.grpc.Context;
+import io.grpc.Contexts;
+import io.grpc.Metadata;
+import io.grpc.ServerCall;
+import io.grpc.ServerCall.Listener;
+import io.grpc.ServerCallHandler;
+import io.grpc.ServerInterceptor;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class LoggingInterceptor implements ServerInterceptor {
+
+ private static final Logger logger = LoggerFactory.getLogger(LoggingInterceptor.class.getName());
+
+ @Override
+ public <ReqT, RespT> Listener<ReqT> interceptCall(
+ ServerCall<ReqT, RespT> call, Metadata headers, ServerCallHandler<ReqT, RespT> next) {
+
+ logger.info(call.getMethodDescriptor().getFullMethodName() + " - " + call.getAttributes());
+ return Contexts.interceptCall(Context.current(), call, headers, next);
+ }
+}
diff --git a/src/main/java/org/caosdb/server/grpc/UploadBuffer.java b/src/main/java/org/caosdb/server/grpc/UploadBuffer.java
new file mode 100644
index 0000000000000000000000000000000000000000..b341c33cbe9e0ca911c35aad144492cc2631da63
--- /dev/null
+++ b/src/main/java/org/caosdb/server/grpc/UploadBuffer.java
@@ -0,0 +1,52 @@
+package org.caosdb.server.grpc;
+
+import com.google.protobuf.ByteString;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import org.caosdb.api.entity.v1.TransmissionStatus;
+import org.caosdb.server.entity.FileProperties;
+
+public class UploadBuffer {
+
+ TransmissionStatus status = TransmissionStatus.TRANSMISSION_STATUS_UNSPECIFIED;
+ private final File tmpFile;
+
+ public UploadBuffer(final File tmpFile) {
+ this.tmpFile = tmpFile;
+ }
+
+ public TransmissionStatus write(final ByteString data) throws IOException {
+ switch (status) {
+ case TRANSMISSION_STATUS_UNSPECIFIED:
+ status = TransmissionStatus.TRANSMISSION_STATUS_GO_ON;
+ break;
+ case TRANSMISSION_STATUS_GO_ON:
+ break;
+ default:
+ throw new RuntimeException("Wrong transmission state.");
+ }
+ try (final FileOutputStream fileOutputStream =
+ new FileOutputStream(tmpFile, tmpFile.exists())) {
+ data.writeTo(fileOutputStream);
+ }
+ return status;
+ }
+
+ public FileProperties toFileProperties(final String fileId) {
+ switch (status) {
+ case TRANSMISSION_STATUS_SUCCESS:
+ break;
+ case TRANSMISSION_STATUS_GO_ON:
+ status = TransmissionStatus.TRANSMISSION_STATUS_SUCCESS;
+ break;
+ default:
+ throw new RuntimeException("Wrong transmission state.");
+ }
+ final FileProperties result =
+ new FileProperties(null, tmpFile.getAbsolutePath(), tmpFile.length());
+ result.setFile(tmpFile);
+ result.setTmpIdentifier(fileId);
+ return result;
+ }
+}
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java
index f9c7704c8bd0ff00214b41d5793c8fdb15bcc61a..9ea7d4b3867b781ead42a50b23b5a7befff048f9 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java
@@ -29,6 +29,7 @@ import org.caosdb.server.datatype.AbstractCollectionDatatype;
import org.caosdb.server.datatype.AbstractDatatype;
import org.caosdb.server.datatype.ReferenceDatatype2;
import org.caosdb.server.entity.EntityInterface;
+import org.caosdb.server.entity.InsertEntity;
import org.caosdb.server.entity.Message;
import org.caosdb.server.entity.Role;
import org.caosdb.server.jobs.EntityJob;
@@ -52,7 +53,9 @@ public final class CheckDatatypePresent extends EntityJob {
// inherit datatype
if (!getEntity().hasDatatype()) {
- resolveId(getEntity());
+ if (!(getEntity() instanceof InsertEntity)) {
+ resolveId(getEntity());
+ }
inheritDatatypeFromAbstractEntity();
@@ -92,7 +95,7 @@ public final class CheckDatatypePresent extends EntityJob {
} else {
// finally, no data type
- throw ServerMessages.NO_DATATYPE;
+ throw ServerMessages.PROPERTY_HAS_NO_DATATYPE;
}
} catch (final Message m) {
@@ -211,7 +214,7 @@ public final class CheckDatatypePresent extends EntityJob {
} catch (final EntityDoesNotExistException exc) {
entity.addError(ServerMessages.ENTITY_DOES_NOT_EXIST);
} catch (final EntityWasNotUniqueException exc) {
- entity.addError(ServerMessages.CANNOT_IDENTIFY_ENTITY_UNIQUELY);
+ entity.addError(ServerMessages.ENTITY_NAME_DUPLICATES);
}
}
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckFileStorageConsistency.java b/src/main/java/org/caosdb/server/jobs/core/CheckFileStorageConsistency.java
index 8dc6fc0c60bc234d65f576377a89244d0a7a673e..e425649bb1bc43a9745120ed078c653f55af2e38 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckFileStorageConsistency.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckFileStorageConsistency.java
@@ -127,8 +127,6 @@ public class CheckFileStorageConsistency extends FlagJob {
getContainer()
.addMessage(
new Message(
- "Info",
- 0,
"Test took too long. The results will be written to './ConsistencyTest.xml'"));
} else {
// add info/warning/error
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java
index 9588a3056e15f7fb3847db37468bb6a628741203..e6ba9da430e6218e5c40fba968c309ed94152bf6 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java
@@ -39,9 +39,6 @@ import org.caosdb.server.utils.ServerMessages;
public class CheckParOblPropPresent extends EntityJob {
public static final String OBL_IMPORTANCE_FLAG_KEY = "force-missing-obligatory";
- public static final Message ENTITY_NOT_UNIQUE =
- new Message(
- MessageType.Error, 0, "Could not check importance. Parent was not uniquely resolvable.");
public static final Message ILLEGAL_FLAG_VALUE =
new Message(MessageType.Warning, "Illegal value for flag 'force-missing-obligatory'.");
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java b/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java
index e663874189ee0301a5b30452468391711624b606..4e6b097e66bf2e844cad34ae22f45eedf1b6cd67 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java
@@ -60,7 +60,7 @@ public class CheckParValid extends EntityJob {
// The parent has neither an id nor a name.
// Therefore it cannot be identified.
- throw ServerMessages.ENTITY_HAS_NO_NAME_AND_NO_ID;
+ throw ServerMessages.ENTITY_HAS_NO_NAME_OR_ID;
}
if (parent.hasId()) {
@@ -124,7 +124,7 @@ public class CheckParValid extends EntityJob {
} catch (final EntityDoesNotExistException exc) {
addError(parent, ServerMessages.ENTITY_DOES_NOT_EXIST);
} catch (final EntityWasNotUniqueException exc) {
- addError(parent, ServerMessages.NAME_DUPLICATES);
+ addError(parent, ServerMessages.ENTITY_NAME_DUPLICATES);
}
}
}
@@ -139,8 +139,8 @@ public class CheckParValid extends EntityJob {
if (par.getEntityStatus() != EntityStatus.IGNORE) {
for (final Parent par2 : getEntity().getParents()) {
if (par != par2 && par2.getEntityStatus() != EntityStatus.IGNORE) {
- if ((par.hasId() && par2.hasId() && par.getId().equals(par2.getId()))
- || (par.hasName() && par2.hasName() && par.getName().equals(par2.getName()))) {
+ if (par.hasId() && par2.hasId() && par.getId().equals(par2.getId())
+ || par.hasName() && par2.hasName() && par.getName().equals(par2.getName())) {
if (!Objects.equal(par.getFlag("inheritance"), par2.getFlag("inheritance"))) {
getEntity().addError(ServerMessages.PARENT_DUPLICATES_ERROR);
getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java b/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
index b9f804f519948b605a9fa8820c91495618463fba..e739ffde01a38fb1539c97166014350e9f9c61d7 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
@@ -31,7 +31,6 @@ import org.caosdb.server.datatype.ReferenceValue;
import org.caosdb.server.entity.Entity;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
import org.caosdb.server.entity.Role;
import org.caosdb.server.entity.wrapper.Parent;
import org.caosdb.server.jobs.EntityJob;
@@ -143,15 +142,13 @@ public class CheckRefidIsaParRefid extends EntityJob implements Observer {
getEntity()
.addInfo(
new Message(
- MessageType.Info,
- 0,
"Could not resolve all parents of the entity with id "
+ child.toString()
+ ". Problematic parent: "
+ (par.hasName()
? par.getName()
: (par.hasCuid() ? par.getCuid() : (par.toString())))));
- throw ServerMessages.ENTITY_HAS_INVALID_REFERENCE;
+ throw ServerMessages.ENTITY_HAS_UNQUALIFIED_REFERENCE;
}
if (isSubType(par.getId(), parent)) {
return true;
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java b/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java
index 8563ea716072602684dc1a78870392d573dc3a22..f19424b127feb3273571a7826bf05382299ea58a 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java
@@ -157,7 +157,7 @@ public class CheckRefidValid extends EntityJob implements Observer {
if (ref.getEntity().hasEntityStatus()) {
switch (ref.getEntity().getEntityStatus()) {
case UNQUALIFIED:
- getEntity().addError(ServerMessages.ENTITY_HAS_INVALID_REFERENCE);
+ getEntity().addError(ServerMessages.ENTITY_HAS_UNQUALIFIED_REFERENCE);
getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
return false;
case DELETED:
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckTargetPathValid.java b/src/main/java/org/caosdb/server/jobs/core/CheckTargetPathValid.java
index 7d06498f5d9e4fbc382e7dde025983ceac6a7fdc..28b914e61d33847e7beb46881c0dac4d9b17f9f0 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckTargetPathValid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckTargetPathValid.java
@@ -37,11 +37,6 @@ import org.caosdb.server.utils.ServerMessages;
*/
public class CheckTargetPathValid extends EntityJob {
- public static final Message TARGET_PATH_NOT_IN_USER_FOLDER =
- new Message(
- 0,
- "According to the server's configuration, your file has to be stored to ýour user folder");
-
@Override
public final void run() {
if (getEntity().hasFileProperties()) {
@@ -50,7 +45,7 @@ public class CheckTargetPathValid extends EntityJob {
if (!file.hasPath()) {
// the file doesn't have a path property at all
getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
- getEntity().addError(ServerMessages.NO_TARGET_PATH);
+ getEntity().addError(ServerMessages.FILE_HAS_NO_TARGET_PATH);
return;
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckUnitPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckUnitPresent.java
index 5e3e6120fadef8f4b519ec694ebbf7588d7c2488..85eb3259dcc17cfdfd2a03aeb3d3360fb04f3908 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckUnitPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckUnitPresent.java
@@ -42,11 +42,11 @@ public class CheckUnitPresent extends EntityJob {
if (!hasUnit(getEntity())) {
switch (getFailureSeverity()) {
case ERROR:
- getEntity().addError(ServerMessages.ENTITY_HAS_NO_UNIT);
+ getEntity().addError(ServerMessages.PROPERTY_HAS_NO_UNIT);
getEntity().setEntityStatus(EntityStatus.UNQUALIFIED);
break;
case WARN:
- getEntity().addWarning(ServerMessages.ENTITY_HAS_NO_UNIT);
+ getEntity().addWarning(ServerMessages.PROPERTY_HAS_NO_UNIT);
default:
break;
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/ExecuteQuery.java b/src/main/java/org/caosdb/server/jobs/core/ExecuteQuery.java
index 399039a072d2fd7b5f54566b2f448791169a356b..0a19977b199195610d96f887c4c538a75b491511 100644
--- a/src/main/java/org/caosdb/server/jobs/core/ExecuteQuery.java
+++ b/src/main/java/org/caosdb/server/jobs/core/ExecuteQuery.java
@@ -22,13 +22,16 @@
*/
package org.caosdb.server.jobs.core;
+import org.caosdb.api.entity.v1.MessageCode;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.Message;
+import org.caosdb.server.entity.Message.MessageType;
import org.caosdb.server.jobs.FlagJob;
import org.caosdb.server.jobs.JobAnnotation;
import org.caosdb.server.jobs.TransactionStage;
import org.caosdb.server.query.Query;
import org.caosdb.server.query.Query.ParsingException;
+import org.caosdb.server.query.Query.Type;
import org.caosdb.server.utils.EntityStatus;
import org.caosdb.server.utils.ServerMessages;
@@ -49,10 +52,15 @@ public class ExecuteQuery extends FlagJob {
} catch (final UnsupportedOperationException e) {
getContainer().addMessage(ServerMessages.QUERY_EXCEPTION);
getContainer().setStatus(EntityStatus.UNQUALIFIED);
- getContainer().addMessage(new Message(e.getMessage()));
+ getContainer().addMessage(new Message(MessageType.Info, (MessageCode) null, e.getMessage()));
}
getContainer().addMessage(queryInstance);
- for (EntityInterface entity : getContainer()) {
+ if (queryInstance.getQuery().getType() == Type.COUNT) {
+ getContainer()
+ .getFlags()
+ .put("query_count_result", Integer.toString(queryInstance.getCount()));
+ }
+ for (final EntityInterface entity : getContainer()) {
getTransaction().getSchedule().addAll(loadJobs(entity, getTransaction()));
}
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/Inheritance.java b/src/main/java/org/caosdb/server/jobs/core/Inheritance.java
index 56ac72fab9f980581cf755c5018dad48ad841f96..78e89a53593e3f112650ed81e292d0c62f071e24 100644
--- a/src/main/java/org/caosdb/server/jobs/core/Inheritance.java
+++ b/src/main/java/org/caosdb/server/jobs/core/Inheritance.java
@@ -26,6 +26,7 @@ package org.caosdb.server.jobs.core;
import java.util.ArrayList;
import java.util.List;
+import org.caosdb.api.entity.v1.MessageCode;
import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
import org.caosdb.server.entity.Entity;
import org.caosdb.server.entity.EntityInterface;
@@ -61,7 +62,7 @@ public class Inheritance extends EntityJob {
public static final Message ILLEGAL_INHERITANCE_MODE =
new Message(
MessageType.Warning,
- 0,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
"Unknown value for flag \"inheritance\". None of the parent's properties have been transfered to the child.");
@Override
diff --git a/src/main/java/org/caosdb/server/jobs/core/InsertFilesInDir.java b/src/main/java/org/caosdb/server/jobs/core/InsertFilesInDir.java
index 8133e4659d55caf29faa56eeb80ced194cd26cfc..5b5418286a81d442822aed0e7252fa4557fb21ff 100644
--- a/src/main/java/org/caosdb/server/jobs/core/InsertFilesInDir.java
+++ b/src/main/java/org/caosdb/server/jobs/core/InsertFilesInDir.java
@@ -30,6 +30,7 @@ import java.util.LinkedList;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
+import org.caosdb.api.entity.v1.MessageCode;
import org.caosdb.server.CaosDBException;
import org.caosdb.server.CaosDBServer;
import org.caosdb.server.FileSystem;
@@ -132,8 +133,6 @@ public class InsertFilesInDir extends FlagJob {
getContainer()
.addMessage(
new Message(
- MessageType.Info,
- 0,
"Files count in "
+ dir.getName()
+ "/: "
@@ -147,7 +146,12 @@ public class InsertFilesInDir extends FlagJob {
throw new TransactionException(e);
}
} else {
- getContainer().addMessage(new Message(MessageType.Error, 0, "No such directory: " + dirStr));
+ getContainer()
+ .addMessage(
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "No such directory: " + dirStr));
return;
}
}
@@ -289,7 +293,7 @@ public class InsertFilesInDir extends FlagJob {
.addMessage(
new Message(
MessageType.Warning,
- 1,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
"Not explicitly included file: " + sub.getCanonicalPath()));
return false;
}
@@ -297,7 +301,9 @@ public class InsertFilesInDir extends FlagJob {
getContainer()
.addMessage(
new Message(
- MessageType.Warning, 2, "Explicitly excluded file: " + sub.getCanonicalPath()));
+ MessageType.Warning,
+ MessageCode.MESSAGE_CODE_ENTITY_DOES_NOT_EXIST,
+ "Explicitly excluded file: " + sub.getCanonicalPath()));
return false;
}
}
@@ -305,14 +311,18 @@ public class InsertFilesInDir extends FlagJob {
getContainer()
.addMessage(
new Message(
- MessageType.Warning, 3, "Hidden directory or file: " + sub.getCanonicalPath()));
+ MessageType.Warning,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "Hidden directory or file: " + sub.getCanonicalPath()));
return false;
}
if (sub.isDirectory() && !sub.canExecute()) {
getContainer()
.addMessage(
new Message(
- MessageType.Warning, 4, "Unaccessible directory: " + sub.getCanonicalPath()));
+ MessageType.Warning,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "Unaccessible directory: " + sub.getCanonicalPath()));
return false;
}
if (!sub.canRead()) {
@@ -320,7 +330,7 @@ public class InsertFilesInDir extends FlagJob {
.addMessage(
new Message(
MessageType.Warning,
- 5,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
"Unreadable directory or file: " + sub.getCanonicalPath()));
return false;
}
@@ -329,7 +339,7 @@ public class InsertFilesInDir extends FlagJob {
.addMessage(
new Message(
MessageType.Warning,
- 6,
+ MessageCode.MESSAGE_CODE_ENTITY_HAS_UNQUALIFIED_PARENTS,
"Directory or file is symbolic link: " + sub.getAbsolutePath()));
if (!this.forceSymLinks) {
return false;
@@ -355,11 +365,15 @@ public class InsertFilesInDir extends FlagJob {
// overlaps the directory to be inserted.
if (!dir.isDirectory()) {
- throw new Message(MessageType.Error, 0, "Dir is not a directory.");
+ throw new Message(
+ MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "Dir is not a directory.");
}
if (!dir.canRead() || !dir.canExecute()) {
- throw new Message(MessageType.Error, 0, "Cannot read or enter the desired directory.");
+ throw new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "Cannot read or enter the desired directory.");
}
final File base = new File(FileSystem.getBasepath());
@@ -375,7 +389,10 @@ public class InsertFilesInDir extends FlagJob {
|| isSubDir(tmp, dir)
|| isSubDir(dir, root)
|| isSubDir(root, dir)) {
- throw new Message(MessageType.Error, 0, "Dir is not allowed: " + dir.toString());
+ throw new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "Dir is not allowed: " + dir.toString());
}
for (final File f : getAllowedFolders()) {
@@ -386,7 +403,7 @@ public class InsertFilesInDir extends FlagJob {
}
throw new Message(
MessageType.Error,
- 1,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
"Dir is not allowed: "
+ dir.toString()
+ " Allowed directories: "
diff --git a/src/main/java/org/caosdb/server/jobs/core/MatchFileProp.java b/src/main/java/org/caosdb/server/jobs/core/MatchFileProp.java
index cef8b2b8ae9764ceb1e4bd2636c2b532d7e9415b..249fc0b17ebe908a9a7ab9d13bfdb00d869ec630 100644
--- a/src/main/java/org/caosdb/server/jobs/core/MatchFileProp.java
+++ b/src/main/java/org/caosdb/server/jobs/core/MatchFileProp.java
@@ -46,7 +46,7 @@ public class MatchFileProp extends FilesJob {
// descriptiveFileProperties is how the copied/uploaded/... file
// ACTUALLY looks like. (path, checksum, size)
final FileProperties descriptiveFileProperties =
- getFile(normativeFileProperties.getTmpIdentifyer());
+ getFile(normativeFileProperties.getTmpIdentifier());
if (descriptiveFileProperties != null) {
checkChecksum(normativeFileProperties, descriptiveFileProperties);
diff --git a/src/main/java/org/caosdb/server/jobs/core/PickUp.java b/src/main/java/org/caosdb/server/jobs/core/PickUp.java
index 94a80836c863ea226a88e035201a2e2fb9fd1039..b0e04529fa059be33b5af99c47286a3d2a469cdb 100644
--- a/src/main/java/org/caosdb/server/jobs/core/PickUp.java
+++ b/src/main/java/org/caosdb/server/jobs/core/PickUp.java
@@ -46,12 +46,12 @@ public class PickUp extends EntityJob implements Observer {
if (normativeFileProperties.isPickupable()) {
try {
entity.acceptObserver(this);
- this.dropOffBoxPath = normativeFileProperties.getTmpIdentifyer();
+ this.dropOffBoxPath = normativeFileProperties.getTmpIdentifier();
final FileProperties descriptiveFileProperties =
FileSystem.pickUp(this.dropOffBoxPath, getRequestId());
normativeFileProperties.setFile(descriptiveFileProperties.getFile());
normativeFileProperties.setThumbnail(descriptiveFileProperties.getThumbnail());
- normativeFileProperties.setTmpIdentifyer(null);
+ normativeFileProperties.setTmpIdentifier(null);
if (!normativeFileProperties.hasSize()) {
normativeFileProperties.setSize(normativeFileProperties.getFile().length());
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/TestMail.java b/src/main/java/org/caosdb/server/jobs/core/TestMail.java
index fb3e87097fae44f3f1f609dd7e347c27c6d971c2..793e6fe211f18c2d576501597c1189dac2444d46 100644
--- a/src/main/java/org/caosdb/server/jobs/core/TestMail.java
+++ b/src/main/java/org/caosdb/server/jobs/core/TestMail.java
@@ -25,7 +25,6 @@ package org.caosdb.server.jobs.core;
import org.caosdb.server.CaosDBServer;
import org.caosdb.server.ServerProperties;
import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
import org.caosdb.server.jobs.FlagJob;
import org.caosdb.server.jobs.JobAnnotation;
import org.caosdb.server.utils.ServerMessages;
@@ -44,13 +43,12 @@ public class TestMail extends FlagJob {
CaosDBServer.getServerProperty(ServerProperties.KEY_NO_REPLY_EMAIL);
@Override
- protected void job(final String value) {
- if (CaosDBServer.isDebugMode() && value != null) {
- if (Utils.isRFC822Compliant(value)) {
- final Mail m = new Mail(NAME, EMAIL, null, value, "Test mail", "This is a test mail.");
+ protected void job(final String recipient) {
+ if (CaosDBServer.isDebugMode() && recipient != null) {
+ if (Utils.isRFC822Compliant(recipient)) {
+ final Mail m = new Mail(NAME, EMAIL, null, recipient, "Test mail", "This is a test mail.");
m.send();
- getContainer()
- .addMessage(new Message(MessageType.Info, 0, "A mail has been send to " + value));
+ getContainer().addMessage(new Message("A mail has been sent to " + recipient));
} else {
getContainer().addMessage(ServerMessages.EMAIL_NOT_WELL_FORMED);
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/UniqueName.java b/src/main/java/org/caosdb/server/jobs/core/UniqueName.java
index 2836ccf742ebbd1bbda5a8ed3ae95ac0d69c2fbb..0ef9792556e2b8b6e3981f66cb697ced5659c7a1 100644
--- a/src/main/java/org/caosdb/server/jobs/core/UniqueName.java
+++ b/src/main/java/org/caosdb/server/jobs/core/UniqueName.java
@@ -46,7 +46,7 @@ public class UniqueName extends FlagJob {
} catch (final EntityDoesNotExistException e) {
// ok
} catch (final EntityWasNotUniqueException e) {
- entity.addError(ServerMessages.NAME_IS_NOT_UNIQUE);
+ entity.addError(ServerMessages.ENTITY_NAME_IS_NOT_UNIQUE);
entity.setEntityStatus(EntityStatus.UNQUALIFIED);
return;
}
@@ -55,7 +55,7 @@ public class UniqueName extends FlagJob {
for (final EntityInterface e : getContainer()) {
if (entity != e && e.hasName() && e.getName().equals(entity.getName())) {
entity.setEntityStatus(EntityStatus.UNQUALIFIED);
- entity.addError(ServerMessages.NAME_IS_NOT_UNIQUE);
+ entity.addError(ServerMessages.ENTITY_NAME_IS_NOT_UNIQUE);
return;
}
}
diff --git a/src/main/java/org/caosdb/server/query/Query.java b/src/main/java/org/caosdb/server/query/Query.java
index 22a513f6775c9187a9a055cd92048c45f64c5cc4..95f853d607edffa29b69e4f84657560ba3a52a48 100644
--- a/src/main/java/org/caosdb/server/query/Query.java
+++ b/src/main/java/org/caosdb/server/query/Query.java
@@ -46,6 +46,7 @@ import org.antlr.v4.runtime.CharStreams;
import org.antlr.v4.runtime.CommonTokenStream;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
import org.apache.shiro.subject.Subject;
+import org.caosdb.api.entity.v1.MessageCode;
import org.caosdb.server.CaosDBServer;
import org.caosdb.server.ServerProperties;
import org.caosdb.server.caching.Cache;
@@ -210,7 +211,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
}
public static class IdVersionPair {
- public IdVersionPair(Integer id, String version) {
+ public IdVersionPair(final Integer id, final String version) {
this.id = id;
this.version = version;
}
@@ -227,9 +228,9 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
}
@Override
- public boolean equals(Object obj) {
+ public boolean equals(final Object obj) {
if (obj instanceof IdVersionPair) {
- IdVersionPair that = (IdVersionPair) obj;
+ final IdVersionPair that = (IdVersionPair) obj;
return this.id == that.id && this.version == that.version;
}
return false;
@@ -241,12 +242,12 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
}
}
- private boolean filterEntitiesWithoutRetrievePermisions =
+ private final boolean filterEntitiesWithoutRetrievePermisions =
!CaosDBServer.getServerProperty(
ServerProperties.KEY_QUERY_FILTER_ENTITIES_WITHOUT_RETRIEVE_PERMISSIONS)
.equalsIgnoreCase("FALSE");
- private Logger logger = org.slf4j.LoggerFactory.getLogger(getClass());
+ private final Logger logger = org.slf4j.LoggerFactory.getLogger(getClass());
List<IdVersionPair> resultSet = null;
private final String query;
private Pattern entity = null;
@@ -497,8 +498,8 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
}
}
- private String initQuery(boolean versioned) throws QueryException {
- String sql = "call initQuery(" + versioned + ")";
+ private String initQuery(final boolean versioned) throws QueryException {
+ final String sql = "call initQuery(" + versioned + ")";
try (final CallableStatement callInitQuery = getConnection().prepareCall(sql)) {
ResultSet initQueryResult = null;
initQueryResult = callInitQuery.executeQuery();
@@ -517,7 +518,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
* @param optimize whether to run optimize() immediately.
* @throws ParsingException
*/
- public void parse(boolean optimize) throws ParsingException {
+ public void parse(final boolean optimize) throws ParsingException {
final long t1 = System.currentTimeMillis();
CQLLexer lexer;
lexer = new CQLLexer(CharStreams.fromString(this.query));
@@ -580,7 +581,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
}
}
- private String executeStrategy(boolean versioned) throws QueryException {
+ private String executeStrategy(final boolean versioned) throws QueryException {
if (this.entity != null) {
return sourceStrategy(initQuery(versioned));
} else if (this.role == Role.ENTITY && this.filter == null) {
@@ -603,7 +604,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
* @throws QueryException
*/
private String generateSelectStatementForResultSet(
- final String resultSetTableName, boolean versioned) {
+ final String resultSetTableName, final boolean versioned) {
if (resultSetTableName.equals("entities")) {
return "SELECT entity_id AS id"
+ (versioned ? ", version AS version" : "")
@@ -628,7 +629,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
* @return list of results of this query.
* @throws QueryException
*/
- private List<IdVersionPair> getResultSet(final String resultSetTableName, boolean versioned)
+ private List<IdVersionPair> getResultSet(final String resultSetTableName, final boolean versioned)
throws QueryException {
ResultSet finishResultSet = null;
try {
@@ -724,7 +725,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
* @param key
* @param resultSet
*/
- private void setCache(String key, List<IdVersionPair> resultSet) {
+ private void setCache(final String key, final List<IdVersionPair> resultSet) {
synchronized (cache) {
if (resultSet instanceof Serializable) {
cache.put(key, (Serializable) resultSet);
@@ -741,11 +742,11 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
* @return
*/
@SuppressWarnings("unchecked")
- private List<IdVersionPair> getCached(String key) {
+ private List<IdVersionPair> getCached(final String key) {
return (List<IdVersionPair>) cache.get(key);
}
- protected void executeNoCache(Access access) {
+ protected void executeNoCache(final Access access) {
try {
this.resultSet = getResultSet(executeStrategy(this.versioned), this.versioned);
} finally {
@@ -754,7 +755,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
}
private void addWarning(final String w) {
- this.messages.add(new Message(MessageType.Warning, 0, w));
+ this.messages.add(new Message(MessageType.Warning, MessageCode.MESSAGE_CODE_UNKNOWN, w));
}
private void cleanUp() {
@@ -835,7 +836,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
return entities;
}
- List<IdVersionPair> result = new ArrayList<>();
+ final List<IdVersionPair> result = new ArrayList<>();
final Iterator<IdVersionPair> iterator = entities.iterator();
while (iterator.hasNext()) {
final long t1 = System.currentTimeMillis();
@@ -902,11 +903,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
return;
}
ret.setAttribute("string", this.query);
- if (this.resultSet != null) {
- ret.setAttribute("results", Integer.toString(this.resultSet.size()));
- } else {
- ret.setAttribute("results", "0");
- }
+ ret.setAttribute("results", Integer.toString(getCount()));
ret.setAttribute("cached", Boolean.toString(this.cached));
ret.setAttribute("etag", cacheETag);
@@ -1007,11 +1004,19 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
* @return A Cache key.
*/
String getCacheKey() {
- StringBuilder sb = new StringBuilder();
- if (this.versioned) sb.append("versioned");
- if (this.role != null) sb.append(this.role.toString());
- if (this.entity != null) sb.append(this.entity.toString());
- if (this.filter != null) sb.append(this.filter.getCacheKey());
+ final StringBuilder sb = new StringBuilder();
+ if (this.versioned) {
+ sb.append("versioned");
+ }
+ if (this.role != null) {
+ sb.append(this.role.toString());
+ }
+ if (this.entity != null) {
+ sb.append(this.entity.toString());
+ }
+ if (this.filter != null) {
+ sb.append(this.filter.getCacheKey());
+ }
return sb.toString();
}
@@ -1034,4 +1039,12 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
public static String getETag() {
return cacheETag;
}
+
+ public int getCount() {
+ if (this.resultSet != null) {
+ return this.resultSet.size();
+ } else {
+ return -1;
+ }
+ }
}
diff --git a/src/main/java/org/caosdb/server/resource/ScriptingResource.java b/src/main/java/org/caosdb/server/resource/ScriptingResource.java
index 35885bb4376b26fc04977389f4dbf1cd7c40decd..6e7cf721cb11bf95df23396bc79d5691335708a6 100644
--- a/src/main/java/org/caosdb/server/resource/ScriptingResource.java
+++ b/src/main/java/org/caosdb/server/resource/ScriptingResource.java
@@ -96,7 +96,17 @@ public class ScriptingResource extends AbstractCaosDBServerResource {
return null;
}
} catch (Message m) {
- return error(m, Status.valueOf(m.getCode()));
+ if (m == ServerMessages.SERVER_SIDE_SCRIPT_DOES_NOT_EXIST) {
+ return error(m, Status.CLIENT_ERROR_NOT_FOUND);
+ } else if (m == ServerMessages.SERVER_SIDE_SCRIPT_MISSING_CALL) {
+ return error(m, Status.CLIENT_ERROR_BAD_REQUEST);
+ } else if (m == ServerMessages.SERVER_SIDE_SCRIPT_NOT_EXECUTABLE) {
+ return error(m, Status.CLIENT_ERROR_BAD_REQUEST);
+ } else if (m == ServerMessages.SERVER_SIDE_SCRIPT_TIMEOUT) {
+ return error(m, Status.CLIENT_ERROR_BAD_REQUEST);
+ }
+
+ return error(m, Status.SERVER_ERROR_INTERNAL);
} finally {
deleteTmpFiles();
}
@@ -142,7 +152,7 @@ public class ScriptingResource extends AbstractCaosDBServerResource {
final FileProperties file = FileSystem.upload(item, this.getSRID());
deleteTmpFileAfterTermination(file);
file.setPath(item.getName());
- file.setTmpIdentifyer(item.getFieldName());
+ file.setTmpIdentifier(item.getFieldName());
files.add(file);
form.add(
new Parameter(
diff --git a/src/main/java/org/caosdb/server/transaction/DeleteUserTransaction.java b/src/main/java/org/caosdb/server/transaction/DeleteUserTransaction.java
index 0f2f5b7fb676e436b131ca69678214c2e34b974c..dc935adc9ea0236ce3c8d54b498ed5f6b15a8c42 100644
--- a/src/main/java/org/caosdb/server/transaction/DeleteUserTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/DeleteUserTransaction.java
@@ -30,7 +30,6 @@ import org.caosdb.server.database.backend.transaction.DeletePassword;
import org.caosdb.server.database.backend.transaction.DeleteUser;
import org.caosdb.server.database.backend.transaction.RetrievePasswordValidator;
import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
@@ -64,7 +63,7 @@ public class DeleteUserTransaction extends AccessControlTransaction {
final Element ret = new Element("User");
ret.setAttribute("realm", this.realm);
ret.setAttribute("name", this.user);
- ret.addContent(new Message(MessageType.Info, 0, "This user has been deleted.").toElement());
+ ret.addContent(new Message("This user has been deleted.").toElement());
return ret;
}
}
diff --git a/src/main/java/org/caosdb/server/transaction/FileStorageConsistencyCheck.java b/src/main/java/org/caosdb/server/transaction/FileStorageConsistencyCheck.java
index ed93812d22eaad6bf448fa1dede2d92cea1d50a6..e066feb3028eb6dcb9bf645070cadefa9cc45047 100644
--- a/src/main/java/org/caosdb/server/transaction/FileStorageConsistencyCheck.java
+++ b/src/main/java/org/caosdb/server/transaction/FileStorageConsistencyCheck.java
@@ -28,6 +28,7 @@ import java.util.Iterator;
import java.util.List;
import java.util.Map.Entry;
import java.util.TimeZone;
+import org.caosdb.api.entity.v1.MessageCode;
import org.caosdb.datetime.UTCDateTime;
import org.caosdb.server.database.DatabaseAccessManager;
import org.caosdb.server.database.access.Access;
@@ -176,7 +177,13 @@ public class FileStorageConsistencyCheck extends Thread
sb.append('\n').append(t.toString());
}
- e.addContent(new Message("Error", 0, "An exception was thrown.", sb.toString()).toElement());
+ e.addContent(
+ new Message(
+ "Error",
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "An exception was thrown.",
+ sb.toString())
+ .toElement());
}
final List<Message> results2Messages = results2Messages(getResults(), this.location);
@@ -196,24 +203,36 @@ public class FileStorageConsistencyCheck extends Thread
final ArrayList<Message> ret = new ArrayList<Message>();
if (results.isEmpty()) {
if (location.length() > 0) {
- ret.add(new Message("Info", 0, "File system below " + location + " is consistent."));
+ ret.add(new Message("File system below " + location + " is consistent."));
} else {
- ret.add(new Message("Info", 0, "File system is consistent."));
+ ret.add(new Message("File system is consistent."));
}
}
for (final Entry<String, Integer> r : results.entrySet()) {
switch (r.getValue()) {
case FileConsistencyCheck.FILE_DOES_NOT_EXIST:
- ret.add(new Message("Error", 0, r.getKey() + ": File does not exist."));
+ ret.add(
+ new Message(
+ "Error",
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ r.getKey() + ": File does not exist."));
break;
case FileConsistencyCheck.FILE_MODIFIED:
- ret.add(new Message("Error", 0, r.getKey() + ": File was modified."));
+ ret.add(
+ new Message(
+ "Error", MessageCode.MESSAGE_CODE_UNKNOWN, r.getKey() + ": File was modified."));
break;
case FileConsistencyCheck.UNKNOWN_FILE:
- ret.add(new Message("Warning", 0, r.getKey() + ": Unknown file."));
+ ret.add(
+ new Message(
+ "Warning", MessageCode.MESSAGE_CODE_UNKNOWN, r.getKey() + ": Unknown file."));
break;
case FileConsistencyCheck.NONE:
- ret.add(new Message("Warning", 0, r.getKey() + ": Test result not available."));
+ ret.add(
+ new Message(
+ "Warning",
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ r.getKey() + ": Test result not available."));
break;
default:
break;
diff --git a/src/main/java/org/caosdb/server/transaction/Retrieve.java b/src/main/java/org/caosdb/server/transaction/Retrieve.java
index 250df0423869ae97a766da2fc54131e04d5257ca..45647c1d554d38ab2b90e91f9516305265d370b8 100644
--- a/src/main/java/org/caosdb/server/transaction/Retrieve.java
+++ b/src/main/java/org/caosdb/server/transaction/Retrieve.java
@@ -54,14 +54,14 @@ public class Retrieve extends Transaction<RetrieveContainer> {
{
final ResolveNames r = new ResolveNames();
r.init(JobFailureSeverity.WARN, null, this);
- ScheduledJob scheduledJob = getSchedule().add(r);
+ final ScheduledJob scheduledJob = getSchedule().add(r);
getSchedule().runJob(scheduledJob);
}
{
final RemoveDuplicates job = new RemoveDuplicates();
job.init(JobFailureSeverity.ERROR, null, this);
- ScheduledJob scheduledJob = getSchedule().add(job);
+ final ScheduledJob scheduledJob = getSchedule().add(job);
getSchedule().runJob(scheduledJob);
}
diff --git a/src/main/java/org/caosdb/server/transaction/Transaction.java b/src/main/java/org/caosdb/server/transaction/Transaction.java
index fe0b63f333e0151aed161ce3fa3914794e5f3d52..b4d63fbb293e0119cefe90db34b9cfb28f4e0ce1 100644
--- a/src/main/java/org/caosdb/server/transaction/Transaction.java
+++ b/src/main/java/org/caosdb/server/transaction/Transaction.java
@@ -33,7 +33,6 @@ import org.caosdb.server.database.exceptions.TransactionException;
import org.caosdb.server.database.misc.TransactionBenchmark;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
import org.caosdb.server.entity.container.TransactionContainer;
import org.caosdb.server.jobs.Job;
import org.caosdb.server.jobs.Schedule;
@@ -52,9 +51,6 @@ import org.caosdb.server.utils.Observer;
public abstract class Transaction<C extends TransactionContainer> extends AbstractObservable
implements TransactionInterface {
- public static final Message ERROR_INTEGRITY_VIOLATION =
- new Message(MessageType.Error, 0, "This entity caused an unexpected integrity violation.");
-
@Override
public TransactionBenchmark getTransactionBenchmark() {
return getContainer().getTransactionBenchmark();
@@ -91,7 +87,7 @@ public abstract class Transaction<C extends TransactionContainer> extends Abstra
*
* <p>E.g. in {@link Retrieve} and {@link WriteTransaction}.
*/
- protected void makeSchedule() throws Exception {
+ protected void makeSchedule() {
// load flag jobs
final Job loadContainerFlags =
Job.getJob("LoadContainerFlagJobs", JobFailureSeverity.ERROR, null, this);
diff --git a/src/main/java/org/caosdb/server/transaction/WriteTransaction.java b/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
index 62a9beea1921f34dd3646bcc78ed9086d05e6098..1540ca79fdf557c3998f4b66072b4cb5466633a1 100644
--- a/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
@@ -24,6 +24,7 @@ package org.caosdb.server.transaction;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.util.HashSet;
+import java.util.List;
import java.util.Objects;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
@@ -67,10 +68,17 @@ import org.caosdb.server.utils.ServerMessages;
public class WriteTransaction extends Transaction<WritableContainer>
implements WriteTransactionInterface {
+ private boolean noIdIsError = true;
+
public WriteTransaction(final WritableContainer container) {
super(container);
}
+ /** Set if it is an error, if an Entity has no ID but just a name upon update. */
+ public void setNoIdIsError(final boolean noIdIsError) {
+ this.noIdIsError = noIdIsError;
+ }
+
@Override
protected final void preTransaction() throws InterruptedException {
// Acquire strong access. No other thread can have access until this strong access is released.
@@ -174,7 +182,7 @@ public class WriteTransaction extends Transaction<WritableContainer>
// get file by tmpIdentifier
final FileProperties f =
- getContainer().getFiles().get(entity.getFileProperties().getTmpIdentifyer());
+ getContainer().getFiles().get(entity.getFileProperties().getTmpIdentifier());
// is it there?
if (f != null) {
@@ -187,7 +195,7 @@ public class WriteTransaction extends Transaction<WritableContainer>
final FileProperties thumbnail =
getContainer()
.getFiles()
- .get(entity.getFileProperties().getTmpIdentifyer() + ".thumbnail");
+ .get(entity.getFileProperties().getTmpIdentifier() + ".thumbnail");
if (thumbnail != null) {
entity.getFileProperties().setThumbnail(thumbnail.getFile());
} else {
@@ -243,7 +251,7 @@ public class WriteTransaction extends Transaction<WritableContainer>
&& !entity.getFileProperties().isPickupable()) {
// dereference files (file upload only)
final FileProperties f =
- getContainer().getFiles().get(entity.getFileProperties().getTmpIdentifyer());
+ getContainer().getFiles().get(entity.getFileProperties().getTmpIdentifier());
if (f != null) {
entity.getFileProperties().setFile(f.getFile());
if (f.getThumbnail() != null) {
@@ -252,7 +260,7 @@ public class WriteTransaction extends Transaction<WritableContainer>
final FileProperties thumbnail =
getContainer()
.getFiles()
- .get(entity.getFileProperties().getTmpIdentifyer() + ".thumbnail");
+ .get(entity.getFileProperties().getTmpIdentifier() + ".thumbnail");
if (thumbnail != null) {
entity.getFileProperties().setThumbnail(thumbnail.getFile());
} else {
@@ -288,7 +296,7 @@ public class WriteTransaction extends Transaction<WritableContainer>
entity.setEntityStatus(EntityStatus.UNQUALIFIED);
entity.addError(ServerMessages.AUTHORIZATION_ERROR);
entity.addInfo(exc.getMessage());
- } catch (ClassCastException exc) {
+ } catch (final ClassCastException exc) {
// not an update entity. ignore.
}
@@ -308,10 +316,10 @@ public class WriteTransaction extends Transaction<WritableContainer>
// split up the TransactionContainer into three containers, one for each
// type of writing transaction.
- TransactionContainer inserts = new TransactionContainer();
- TransactionContainer updates = new TransactionContainer();
- TransactionContainer deletes = new TransactionContainer();
- for (EntityInterface entity : getContainer()) {
+ final TransactionContainer inserts = new TransactionContainer();
+ final TransactionContainer updates = new TransactionContainer();
+ final TransactionContainer deletes = new TransactionContainer();
+ for (final EntityInterface entity : getContainer()) {
if (entity instanceof InsertEntity) {
inserts.add(entity);
} else if (entity instanceof UpdateEntity) {
@@ -354,7 +362,7 @@ public class WriteTransaction extends Transaction<WritableContainer>
* @throws IOException
* @throws NoSuchAlgorithmException
*/
- public static HashSet<Permission> deriveUpdate(
+ public HashSet<Permission> deriveUpdate(
final EntityInterface newEntity, final EntityInterface oldEntity)
throws NoSuchAlgorithmException, IOException, CaosDBException {
final HashSet<Permission> needPermissions = new HashSet<>();
@@ -461,46 +469,34 @@ public class WriteTransaction extends Transaction<WritableContainer>
}
// 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;
- }
+ for (final Property newProperty : newEntity.getProperties()) {
+
+ // find corresponding oldProperty for this new property and make a diff (existing property,
+ // same property index in this entity, equal content?).
+ final Property oldProperty = findOldEntity(newProperty, oldEntity.getProperties());
+ if (oldProperty != null) {
+ // do not check again.
+ oldEntity.getProperties().remove(oldProperty);
+
+ if (oldProperty.getPIdx() != newProperty.getPIdx()) {
+ // change order of properties
+ needPermissions.add(EntityPermission.UPDATE_ADD_PROPERTY);
+ needPermissions.add(EntityPermission.UPDATE_REMOVE_PROPERTY);
+ updatetable = true;
+ }
- continue outerLoop;
- }
+ deriveUpdate(newProperty, oldProperty);
+ if (newProperty.getEntityStatus() == EntityStatus.QUALIFIED) {
+ needPermissions.add(EntityPermission.UPDATE_ADD_PROPERTY);
+ needPermissions.add(EntityPermission.UPDATE_REMOVE_PROPERTY);
+ updatetable = true;
}
+
} 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;
}
-
- // 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
@@ -511,30 +507,20 @@ public class WriteTransaction extends Transaction<WritableContainer>
}
// 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;
- }
- }
+ final Parent oldProperty = findOldEntity(newParent, oldEntity.getParents());
+
+ if (oldProperty != null) {
+ // do not check again.
+ oldEntity.getParents().remove(oldProperty);
+
} 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;
}
-
- // 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
@@ -553,6 +539,35 @@ public class WriteTransaction extends Transaction<WritableContainer>
return needPermissions;
}
+ /**
+ * Attempt to find a (sparse) entity among a list of entities.
+ *
+ * <p>If no match by ID can be found, matching by name is attempted next, but only if noIdIsError
+ * is false.
+ */
+ private <T extends EntityInterface> T findOldEntity(
+ final EntityInterface newEntity, final List<T> oldEntities) {
+ if (newEntity.hasId()) {
+ for (final T oldEntity : oldEntities) {
+ if (Objects.equals(oldEntity.getId(), newEntity.getId())) {
+ return oldEntity;
+ }
+ }
+ } else if (noIdIsError) {
+ newEntity.addError(ServerMessages.ENTITY_HAS_NO_ID);
+ newEntity.addInfo("On updates, always specify the id not just the name.");
+ } else if (newEntity.hasName()) {
+ for (final T oldEntity : oldEntities) {
+ if (oldEntity.getName().equals(newEntity.getName())) {
+ return oldEntity;
+ }
+ }
+ } else {
+ newEntity.addError(ServerMessages.ENTITY_HAS_NO_NAME_OR_ID);
+ }
+ return null;
+ }
+
public String getSRID() {
return getContainer().getRequestId();
}
diff --git a/src/main/java/org/caosdb/server/utils/ServerMessages.java b/src/main/java/org/caosdb/server/utils/ServerMessages.java
index 2801218aa47a18ec1494ee8ef76607eb9b962130..4197f2cf78cedb3fcf9dc0ea6648b6c3335a9da8 100644
--- a/src/main/java/org/caosdb/server/utils/ServerMessages.java
+++ b/src/main/java/org/caosdb/server/utils/ServerMessages.java
@@ -19,6 +19,7 @@
*/
package org.caosdb.server.utils;
+import org.caosdb.api.entity.v1.MessageCode;
import org.caosdb.server.CaosDBServer;
import org.caosdb.server.ServerProperties;
import org.caosdb.server.entity.Message;
@@ -27,325 +28,417 @@ import org.caosdb.server.entity.Message.MessageType;
public class ServerMessages {
public static final Message ENTITY_HAS_BEEN_DELETED_SUCCESSFULLY =
- new Message(MessageType.Info, 10, "This entity has been deleted successfully.");
+ new Message(
+ MessageType.Info,
+ MessageCode.MESSAGE_CODE_ENTITY_HAS_BEEN_DELETED_SUCCESSFULLY,
+ "This entity has been deleted successfully.");
public static final Message ENTITY_DOES_NOT_EXIST =
- new Message(MessageType.Error, 101, "Entity does not exist.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_ENTITY_DOES_NOT_EXIST,
+ "Entity does not exist.");
public static final Message ENTITY_HAS_UNQUALIFIED_PROPERTIES =
- new Message(MessageType.Error, 114, "Entity has unqualified properties.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_ENTITY_HAS_UNQUALIFIED_PROPERTIES,
+ "Entity has unqualified properties.");
public static final Message ENTITY_HAS_UNQUALIFIED_PARENTS =
- new Message(MessageType.Error, 116, "Entity has unqualified parents.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_ENTITY_HAS_UNQUALIFIED_PARENTS,
+ "Entity has unqualified parents.");
- public static final Message PARSING_FAILED = new Message(MessageType.Error, 2, "Parsing failed.");
+ public static final Message PARSING_FAILED =
+ new Message(MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "Parsing failed.");
public static final Message UNKNOWN_DATATYPE =
- new Message(MessageType.Error, 0, "Unknown datatype.");
+ new Message(MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "Unknown data type.");
public static final Message UNKNOWN_IMPORTANCE =
- new Message(MessageType.Error, 0, "Unknown importance.");
+ new Message(MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "Unknown importance.");
public static final Message ENTITY_HAS_NO_ID =
- new Message(MessageType.Error, 0, "Entity has no ID.");
+ new Message(
+ MessageType.Error, MessageCode.MESSAGE_CODE_ENTITY_HAS_NO_ID, "Entity has no ID.");
public static final Message REQUIRED_BY_PERSISTENT_ENTITY =
new Message(
MessageType.Error,
- 0,
+ MessageCode.MESSAGE_CODE_REQUIRED_BY_PERSISTENT_ENTITY,
"Entity is required by other entities which are not to be deleted.");
- public static final Message NO_DATATYPE =
- new Message(MessageType.Error, 110, "Property has no datatype.");
+ public static final Message PROPERTY_HAS_NO_DATATYPE =
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_PROPERTY_HAS_NO_DATA_TYPE,
+ "Property has no data type.");
public static final Message ENTITY_HAS_NO_DESCRIPTION =
- new Message(MessageType.Error, 0, "Entity has no description.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_ENTITY_HAS_NO_DESCRIPTION,
+ "Entity has no description.");
public static final Message ENTITY_HAS_NO_NAME =
- new Message(MessageType.Error, 0, "Entity has no name.");
+ new Message(
+ MessageType.Error, MessageCode.MESSAGE_CODE_ENTITY_HAS_NO_NAME, "Entity has no name.");
public static final Message OBLIGATORY_PROPERTY_MISSING =
- new Message(MessageType.Error, 0, "An obligatory property is missing.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_OBLIGATORY_PROPERTY_MISSING,
+ "An obligatory property is missing.");
public static final Message ENTITY_HAS_NO_PARENTS =
- new Message(MessageType.Error, 0, "Entity has no parents.");
-
- public static final Message NAME_DUPLICATES =
- new Message(MessageType.Error, 0, "Entity can not be identified due to name duplicates.");
-
- public static final Message ENTITY_HAS_NO_NAME_AND_NO_ID =
- new Message(MessageType.Error, 0, "Entity has no name and no ID.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_ENTITY_HAS_NO_PARENTS,
+ "Entity has no parents.");
public static final Message ENTITY_HAS_NO_PROPERTIES =
- new Message(MessageType.Error, 0, "Entity has no properties.");
-
- public static final Message REFERENCE_HAS_NO_REFID =
- new Message(MessageType.Error, 0, "Reference property has no refid.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_ENTITY_HAS_NO_PROPERTIES,
+ "Entity has no properties.");
- public static final Message NO_TARGET_PATH =
- new Message(MessageType.Error, 0, "No target path specified.");
+ public static final Message FILE_HAS_NO_TARGET_PATH =
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_FILE_HAS_NO_TARGET_PATH,
+ "No target path specified.");
public static final Message TARGET_PATH_NOT_ALLOWED =
- new Message(MessageType.Error, 0, "This target path is not allowed.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_TARGET_PATH_NOT_ALLOWED,
+ "This target path is not allowed.");
public static final Message TARGET_PATH_EXISTS =
- new Message(MessageType.Error, 0, "This target path does already exist.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_TARGET_PATH_EXISTS,
+ "This target path does already exist.");
- public static final Message ENTITY_HAS_NO_UNIT =
- new Message(MessageType.Error, 0, "Entity has no unit.");
+ public static final Message PROPERTY_HAS_NO_UNIT =
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_PROPERTY_HAS_NO_UNIT,
+ "Property has no unit.");
public static final Message CANNOT_PARSE_VALUE =
- new Message(MessageType.Error, 0, "Cannot parse value.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_CANNOT_PARSE_VALUE,
+ "Cannot parse the value.");
public static final Message CHECKSUM_TEST_FAILED =
- new Message(MessageType.Error, 0, "Checksum test failed. File is corrupted.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_CHECKSUM_TEST_FAILED,
+ "Checksum test failed. File is corrupted.");
public static final Message SIZE_TEST_FAILED =
- new Message(MessageType.Error, 0, "Size test failed. File is corrupted.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_SIZE_TEST_FAILED,
+ "Size test failed. File is corrupted.");
public static final Message CANNOT_CREATE_PARENT_FOLDER =
- new Message(MessageType.Error, 0, "Could not create parent folder in the file system.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_CANNOT_CREATE_PARENT_FOLDER,
+ "Could not create parent folder in the file system.");
public static final Message FILE_HAS_NOT_BEEN_UPLOAED =
- new Message(MessageType.Error, 0, "File has not been uploaded.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_FILE_HAS_NOT_BEEN_UPLOAED,
+ "File has not been uploaded.");
public static final Message THUMBNAIL_HAS_NOT_BEEN_UPLOAED =
- new Message(MessageType.Error, 0, "Thumbnail has not been uploaded.");
+ new Message(
+ MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "Thumbnail has not been uploaded.");
public static final Message CANNOT_MOVE_FILE_TO_TARGET_PATH =
- new Message(MessageType.Error, 0, "Could not move file to it's target folder.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_CANNOT_MOVE_FILE_TO_TARGET_PATH,
+ "Could not move file to its target folder.");
public static final Message CANNOT_PARSE_DATETIME_VALUE =
new Message(
MessageType.Error,
- 0,
+ MessageCode.MESSAGE_CODE_CANNOT_PARSE_DATETIME_VALUE,
"Cannot parse value to datetime format (yyyy-mm-dd'T'hh:mm:ss[.fffffffff][TimeZone]).");
public static final Message CANNOT_PARSE_DOUBLE_VALUE =
- new Message(MessageType.Error, 0, "Cannot parse value to double.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_CANNOT_PARSE_DOUBLE_VALUE,
+ "Cannot parse value to double.");
public static final Message CANNOT_PARSE_INT_VALUE =
- new Message(MessageType.Error, 0, "Cannot parse value to integer.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_CANNOT_PARSE_INT_VALUE,
+ "Cannot parse value to integer.");
public static final Message CANNOT_PARSE_BOOL_VALUE =
new Message(
MessageType.Error,
- 0,
- "Cannot parse value to boolean (either 'true' or 'false', ignoring case).");
+ MessageCode.MESSAGE_CODE_CANNOT_PARSE_BOOL_VALUE,
+ "Cannot parse value to boolean (either 'true' or 'false', case insensitive).");
public static final Message CANNOT_CONNECT_TO_DATABASE =
- new Message(MessageType.Error, 0, "Could not connect to MySQL server.");
-
- public static final Message REQUEST_BODY_NOT_WELLFORMED =
- new Message(MessageType.Error, 0, "Request Body was not a well-formed xml.");
-
- public static final Message REQUEST_BODY_EMPTY =
- new Message(MessageType.Error, 0, "Request body was empty.");
-
- public static final Message MYSQL_PROCEDURE_EXCEPTION =
new Message(
MessageType.Error,
- 0,
- "Please check if your MySQL has all required procedures installed.");
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "Could not connect to MySQL server.");
- public static final Message REQUEST_HAS_WRONG_ENCODING =
+ public static final Message REQUEST_BODY_NOT_WELLFORMED =
new Message(
MessageType.Error,
- 0,
- "This error occurred while parsing the xml. Probably it has a wrong encoding.");
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "Request body was not a well-formed xml.");
+
+ public static final Message REQUEST_BODY_EMPTY =
+ new Message(MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "Request body was empty.");
public static final Message REQUEST_DOESNT_CONTAIN_EXPECTED_ELEMENTS =
- new Message(MessageType.Error, 0, "Request body didn't contain the expected Elements.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "Request body didn't contain the expected elements.");
public static final Message FILE_NOT_IN_DROPOFFBOX =
- new Message(MessageType.Error, 0, "File is not in drop-off box.");
+ new Message(
+ MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "File is not in drop-off box.");
public static final Message FILE_NOT_FOUND =
- new Message(MessageType.Error, 0, "File could not be found.");
+ new Message(
+ MessageType.Error, MessageCode.MESSAGE_CODE_FILE_NOT_FOUND, "File could not be found.");
public static final Message CANNOT_MOVE_FILE_TO_TMP =
- new Message(MessageType.Error, 0, "Could not move file to tmp folder.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "Could not move file to tmp folder.");
public static final Message CANNOT_READ_FILE =
new Message(
MessageType.Error,
- 0,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
"Insufficient read permission for this file. Please make it readable.");
public static final Message CANNOT_READ_THUMBNAIL =
new Message(
MessageType.Error,
- 0,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
"Insufficient read permission for this file's thumbnail. Please make it readable.");
public static final Message NO_FILE_REPRESENTATION_SUBMITTED =
- new Message(MessageType.Error, 0, "No file representation submitted.");
+ new Message(
+ MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "No file representation submitted.");
public static final Message FORM_CONTAINS_UNSUPPORTED_CONTENT =
- new Message(MessageType.Error, 0, "The form contains unsupported content");
-
- public static final Message FILE_IS_EMPTY = new Message(MessageType.Error, 0, "File is empty.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "The form contains unsupported content");
public static final Message WARNING_OCCURED =
new Message(
MessageType.Error,
- 128,
+ MessageCode.MESSAGE_CODE_WARNING_OCCURED,
"A warning occured while processing an entity with the strict flag.");
- public static final Message UNKNOWN_JOB = new Message(MessageType.Warning, 0, "Unknown job.");
-
- public static final Message NAME_IS_NOT_UNIQUE =
+ public static final Message ENTITY_NAME_IS_NOT_UNIQUE =
new Message(
MessageType.Error,
- 152,
+ MessageCode.MESSAGE_CODE_ENTITY_NAME_IS_NOT_UNIQUE,
"Name is already in use. Choose a different name or reuse an existing entity.");
public static final Message ROLE_NAME_IS_NOT_UNIQUE =
- new Message(MessageType.Error, 1152, "Role name is already in use. Choose a different name.");
-
- public static final Message CANNOT_IDENTIFY_ENTITY_UNIQUELY =
new Message(
- MessageType.Error, 0, "This entity cannot be identified uniquely due to name dublicates");
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "Role name is already in use. Choose a different name.");
public static final Message QUERY_EXCEPTION =
- new Message(MessageType.Error, 13, "This query finished with errors.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_QUERY_EXCEPTION,
+ "This query finished with errors.");
public static final Message LOGOUT_INFO =
- new Message(MessageType.Info, 201, "You have successfully logged out.");
+ new Message(
+ MessageType.Info, MessageCode.MESSAGE_CODE_UNKNOWN, "You have successfully logged out.");
public static final Message ENTITY_IS_EMPTY =
- new Message(MessageType.Error, 0, "This entity is empty.");
+ new Message(MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "This entity is empty.");
public static final Message TRANSACTION_ROLL_BACK =
new Message(
MessageType.Error,
- 0,
+ MessageCode.MESSAGE_CODE_TRANSACTION_ROLL_BACK,
"An unknown error occured during the transaction and it was rolled back.");
public static final Message FILE_UPLOAD_FAILED =
- new Message(MessageType.Error, 0, "The file upload failed for an unknown reason.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "The file upload failed for an unknown reason.");
public static final Message ACCOUNT_CANNOT_BE_ACTIVATED =
- new Message(MessageType.Error, 0, "This account cannot be activated.");
+ new Message(
+ MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "This account cannot be activated.");
public static final Message ACCOUNT_DOES_NOT_EXIST =
- new Message(MessageType.Error, 0, "This account does not exist.");
+ new Message(
+ MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "This account does not exist.");
public static final Message ACCOUNT_CANNOT_BE_RESET =
- new Message(MessageType.Error, 0, "This account cannot be reset.");
+ new Message(
+ MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "This account cannot be reset.");
public static final Message UNKNOWN_UNIT =
new Message(
MessageType.Error,
- 0,
+ MessageCode.MESSAGE_CODE_UNKNOWN_UNIT,
"Unknown unit. Values with this unit cannot be converted to other units when used in search queries.");
public static final Message ACCOUNT_NAME_NOT_UNIQUE =
- new Message(MessageType.Error, 0, "This user name is yet in use. Please choose another one.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "This user name is yet in use. Please choose another one.");
public static final Message ACCOUNT_HAS_BEEN_DELETED =
- new Message(MessageType.Info, 10, "This user has been deleted successfully.");
+ new Message(
+ MessageType.Info,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "This user has been deleted successfully.");
public static final Message PLEASE_SET_A_PASSWORD =
- new Message(MessageType.Info, 0, "Please set a password.");
+ new Message(MessageType.Info, MessageCode.MESSAGE_CODE_UNKNOWN, "Please set a password.");
public static final Message USER_HAS_BEEN_ACTIVATED =
new Message(
MessageType.Info,
- 0,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
"User has been activated. You can now log in with your username and password.");
public static final Message UNAUTHENTICATED =
- new Message(MessageType.Error, 401, "Sign in, please.");
+ new Message(MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "Sign in, please.");
public static final Message AUTHORIZATION_ERROR =
- new Message(MessageType.Error, 403, "You are not allowed to do this.");
+ new Message(
+ MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "You are not allowed to do this.");
public static final Message REFERENCE_IS_NOT_ALLOWED_BY_DATATYPE =
new Message(
MessageType.Error,
- 0,
+ MessageCode.MESSAGE_CODE_REFERENCE_IS_NOT_ALLOWED_BY_DATA_TYPE,
"Reference not qualified. The value of this Reference Property is to be a child of its data type.");
public static final Message CANNOT_PARSE_ENTITY_ACL =
- new Message(MessageType.Error, 0, "Cannot parse EntityACL.");
+ new Message(MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "Cannot parse EntityACL.");
public static final Message ROLE_DOES_NOT_EXIST =
- new Message(MessageType.Error, 1104, "User Role does not exist.");
+ new Message(MessageType.Error, MessageCode.MESSAGE_CODE_UNKNOWN, "User role does not exist.");
public static final Message ENTITY_NAME_DUPLICATES =
- new Message(MessageType.Error, 0, "This entity cannot be identified due to name duplicates.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_ENTITY_NAME_DUPLICATES,
+ "Entity can not be identified due to name duplicates.");
public static final Message DATA_TYPE_NAME_DUPLICATES =
new Message(
- MessageType.Error, 0, "This data type cannot be identified due to name duplicates.");
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_DATA_TYPE_NAME_DUPLICATES,
+ "This data type cannot be identified due to name duplicates.");
public static final Message ENTITY_HAS_NO_NAME_OR_ID =
new Message(
MessageType.Error,
- 0,
+ MessageCode.MESSAGE_CODE_ENTITY_HAS_NO_NAME_OR_ID,
"This entity cannot be identified as it didn't come with a name or id.");
public static final Message EMAIL_NOT_WELL_FORMED =
- new Message(MessageType.Error, 0, "This email address is not RFC822 compliant.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "This email address is not RFC822 compliant.");
public static final Message PASSWORD_TOO_WEAK =
new Message(
MessageType.Error,
- 0,
- "This password is too weak. It should be longer than 8 characters and sufficiently random. ");
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "This password is too weak. It should be longer than 8 characters and sufficiently random.");
public static final Message AFFILIATION_ERROR =
new Message(
- MessageType.Error, 0, "Affiliation is not defined for this child-parent constellation.");
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_AFFILIATION_ERROR,
+ "Affiliation is not defined for this child-parent constellation.");
public static final Message QUERY_TEMPLATE_HAS_NO_QUERY_DEFINITION =
- new Message(MessageType.Error, 0, "This QueryTemplate has no query definition.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "This QueryTemplate has no query definition.");
public static final Message QUERY_TEMPLATE_WITH_COUNT =
new Message(
MessageType.Error,
- 0,
- "QueryTemplates may not be defined by 'COUNT...' queries for consistency reasons.");
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "QueryTemplates may not be defined by 'COUNT' queries for consistency reasons.");
public static final Message QUERY_TEMPLATE_WITH_SELECT =
new Message(
MessageType.Error,
- 0,
- "QueryTemplates may not be defined by 'SELECT... FROM...' queries for consistency reasons.");
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "QueryTemplates may not be defined by 'SELECT ... FROM ...' queries for consistency reasons.");
public static final Message QUERY_PARSING_ERROR =
new Message(
MessageType.Error,
- 0,
- "An error occured during the parsing of this query. Maybe you use a wrong syntax?");
+ MessageCode.MESSAGE_CODE_QUERY_PARSING_ERROR,
+ "An error occured during the parsing of this query. Maybe you were using a wrong syntax?");
public static final Message NAME_PROPERTIES_MUST_BE_TEXT =
new Message(
MessageType.Error,
- 0,
+ MessageCode.MESSAGE_CODE_NAME_PROPERTIES_MUST_BE_TEXT,
"A property which has 'name' as its parent must have a TEXT data type.");
public static final Message PARENT_DUPLICATES_WARNING =
new Message(
MessageType.Warning,
- 0,
- "This entity had parent duplicates. That is meaningless and only one parent had been inserted.");
+ MessageCode.MESSAGE_CODE_PARENT_DUPLICATES_WARNING,
+ "This entity had parent duplicates. That is meaningless and only one parent has been inserted.");
public static final Message PARENT_DUPLICATES_ERROR =
new Message(
MessageType.Error,
- 0,
+ MessageCode.MESSAGE_CODE_PARENT_DUPLICATES_ERROR,
"This entity had parent duplicates. Parent duplicates are meaningless and would be ignored (and inserted only once). But these parents had diverging inheritance instructions which cannot be processed.");
public static final Message ATOMICITY_ERROR =
new Message(
MessageType.Error,
- 12,
+ MessageCode.MESSAGE_CODE_ATOMICITY_ERROR,
"One or more entities are not qualified. None of them have been inserted/updated/deleted.");
public static final Message NO_SUCH_ENTITY_ROLE(final String role) {
- return new Message(MessageType.Error, 0, "There is no such role '" + role + "'.");
+ return new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_NO_SUCH_ENTITY_ROLE,
+ "There is no such role '" + role + "'.");
}
public static Message UNKNOWN_ERROR(final String requestID) {
@@ -366,72 +459,124 @@ public class ServerMessages {
+ " and include the SRID into your report.";
}
- return new Message(MessageType.Error, 500, description, (body.isEmpty() ? null : body));
+ return new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ description,
+ body.isEmpty() ? null : body);
}
public static final Message REQUIRED_BY_UNQUALIFIED =
new Message(
- MessageType.Error, 192, "This entity cannot be deleted due to dependency problems");
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_REQUIRED_BY_UNQUALIFIED,
+ "This entity cannot be deleted due to dependency problems");
- public static final Message ENTITY_HAS_INVALID_REFERENCE =
- new Message(MessageType.Error, 0, "This entity has an invalid reference.");
+ public static final Message ENTITY_HAS_UNQUALIFIED_REFERENCE =
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_ENTITY_HAS_UNQUALIFIED_REFERENCE,
+ "This entity has an unqualified reference.");
public static final Message REFERENCED_ENTITY_DOES_NOT_EXIST =
- new Message(MessageType.Error, 235, "Referenced entity does not exist.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_REFERENCED_ENTITY_DOES_NOT_EXIST,
+ "Referenced entity does not exist.");
public static final Message REFERENCE_NAME_DUPLICATES =
new Message(
- MessageType.Error, 0, "This reference cannot be identified due to name duplicates.");
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_REFERENCE_NAME_DUPLICATES,
+ "This reference cannot be identified due to name duplicates.");
public static final Message DATATYPE_INHERITANCE_AMBIGUOUS =
new Message(
MessageType.Error,
- 0,
- "The datatype which is to be inherited could not be detected due to divergent datatypes of at least two parents.");
+ MessageCode.MESSAGE_CODE_DATA_TYPE_INHERITANCE_AMBIGUOUS,
+ "The data type which is to be inherited could not be detected due to divergent data types of at least two parents.");
public static final Message DATA_TYPE_DOES_NOT_ACCEPT_COLLECTION_VALUES =
new Message(
MessageType.Error,
- 0,
- "This datatype does not accept collections of values (e.g. Lists).");
+ MessageCode.MESSAGE_CODE_DATA_TYPE_DOES_NOT_ACCEPT_COLLECTION_VALUES,
+ "This data type does not accept collections of values (e.g. Lists).");
public static final Message CANNOT_PARSE_UNIT =
- new Message(MessageType.Error, 0, "This unit cannot be parsed.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_CANNOT_PARSE_UNIT,
+ "This unit cannot be parsed.");
public static final Message SERVER_SIDE_SCRIPT_DOES_NOT_EXIST =
new Message(
- MessageType.Error, 404, "This server-side script does not exist. Did you install it?");
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "This server-side script does not exist. Did you install it?");
public static final Message SERVER_SIDE_SCRIPT_NOT_EXECUTABLE =
- new Message(MessageType.Error, 400, "This server-side script is not executable.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "This server-side script is not executable.");
public static final Message SERVER_SIDE_SCRIPT_ERROR =
- new Message(MessageType.Error, 500, "The invocation of this server-side script failed.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "The invocation of this server-side script failed.");
public static final Message SERVER_SIDE_SCRIPT_SETUP_ERROR =
new Message(
MessageType.Error,
- 500,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
"The setup routine for the server-side script failed. This might indicate a misconfiguration of the server. Please contact the administrator.");
public static final Message SERVER_SIDE_SCRIPT_TIMEOUT =
- new Message(MessageType.Error, 400, "This server-side script did not finish in time.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "This server-side script did not finish in time.");
public static final Message SERVER_SIDE_SCRIPT_MISSING_CALL =
- new Message(MessageType.Error, 400, "You must specify the `call` field.");
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_UNKNOWN,
+ "You must specify the `call` field.");
public static final Message ADDITIONAL_PROPERTY =
new Message(
MessageType.Warning,
- 0,
+ MessageCode.MESSAGE_CODE_ADDITIONAL_PROPERTY,
"This property is an additional property which has no corresponding property among the properties of the parents.");
public static final Message PROPERTY_WITH_DATATYPE_OVERRIDE =
- new Message(MessageType.Warning, 0, "This property overrides the datatype.");
+ new Message(
+ MessageType.Warning,
+ MessageCode.MESSAGE_CODE_PROPERTY_WITH_DATA_TYPE_OVERRIDE,
+ "This property overrides the data type.");
public static final Message PROPERTY_WITH_DESC_OVERRIDE =
- new Message(MessageType.Warning, 0, "This property overrides the description.");
+ new Message(
+ MessageType.Warning,
+ MessageCode.MESSAGE_CODE_PROPERTY_WITH_DESCRIPTION_OVERRIDE,
+ "This property overrides the description.");
public static final Message PROPERTY_WITH_NAME_OVERRIDE =
- new Message(MessageType.Warning, 0, "This property overrides the name.");
+ new Message(
+ MessageType.Warning,
+ MessageCode.MESSAGE_CODE_PROPERTY_WITH_NAME_OVERRIDE,
+ "This property overrides the name.");
+
+ public static final Message INTEGER_OUT_OF_RANGE =
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_INTEGER_VALUE_OUT_OF_RANGE,
+ "The integer value is out of range. This server only supports signed 32 bit integers.");
+
+ public static final Message ERROR_INTEGRITY_VIOLATION =
+ new Message(
+ MessageType.Error,
+ MessageCode.MESSAGE_CODE_INTEGRITY_VIOLATION,
+ "This entity caused an unexpected integrity violation. This is a strong indicator for a server bug. Please report.");
}
diff --git a/src/test/java/org/caosdb/server/database/InsertTest.java b/src/test/java/org/caosdb/server/database/InsertTest.java
index 7b00cacfe7c3454539cb6823d62bc3af9b4d7ce7..b6b535c77700e55bfba67523d6250025b6ce3360 100644
--- a/src/test/java/org/caosdb/server/database/InsertTest.java
+++ b/src/test/java/org/caosdb/server/database/InsertTest.java
@@ -224,8 +224,6 @@ public class InsertTest {
subp.setStatementStatus(StatementStatus.FIX);
p2.addProperty(subp);
- r.print();
-
final LinkedList<EntityInterface> stage1Inserts = new LinkedList<EntityInterface>();
final LinkedList<EntityInterface> stage2Inserts = new LinkedList<EntityInterface>();
@@ -254,15 +252,6 @@ public class InsertTest {
assertEquals((Integer) 2, stage2Inserts.get(0).getId());
assertEquals("V2", ((SingleValue) stage2Inserts.get(0).getValue()).toDatabaseString());
assertFalse(stage2Inserts.get(0).hasReplacement());
-
- System.out.println("######### stage 1 #########");
- for (EntityInterface e : stage1Inserts) {
- e.print();
- }
- System.out.println("######### stage 2 #########");
- for (EntityInterface e : stage2Inserts) {
- e.print();
- }
}
/**
diff --git a/src/test/java/org/caosdb/server/scripting/TestServerSideScriptingCaller.java b/src/test/java/org/caosdb/server/scripting/TestServerSideScriptingCaller.java
index 61be0c5c3a06319dbeb826a79ddf1c6e43a0d672..45b8e7f4408ca7186fbc2589b176d3c5eba113ba 100644
--- a/src/test/java/org/caosdb/server/scripting/TestServerSideScriptingCaller.java
+++ b/src/test/java/org/caosdb/server/scripting/TestServerSideScriptingCaller.java
@@ -186,7 +186,7 @@ public class TestServerSideScriptingCaller extends CaosDBTestClass {
}
/**
- * Throw {@link CaosDBException} because tmpIdentifyer is null or empty.
+ * Throw {@link CaosDBException} because tmpIdentifier is null or empty.
*
* @throws FileNotFoundException
* @throws CaosDBException
@@ -222,7 +222,7 @@ public class TestServerSideScriptingCaller extends CaosDBTestClass {
final ArrayList<FileProperties> files = new ArrayList<>();
final FileProperties f = new FileProperties(null, null, null);
- f.setTmpIdentifyer("a2s3d4f5");
+ f.setTmpIdentifier("a2s3d4f5");
f.setPath("testfile");
files.add(f);
@@ -247,7 +247,7 @@ public class TestServerSideScriptingCaller extends CaosDBTestClass {
final ArrayList<FileProperties> files = new ArrayList<>();
final FileProperties f = new FileProperties(null, null, null);
- f.setTmpIdentifyer("a2s3d4f5");
+ f.setTmpIdentifier("a2s3d4f5");
f.setFile(new File("blablabla_non_existing"));
f.setPath("bla");
files.add(f);
@@ -282,7 +282,7 @@ public class TestServerSideScriptingCaller extends CaosDBTestClass {
final ArrayList<FileProperties> files = new ArrayList<>();
final FileProperties f = new FileProperties(null, null, null);
- f.setTmpIdentifyer("a2s3d4f5");
+ f.setTmpIdentifier("a2s3d4f5");
f.setFile(testFile);
f.setPath("testfile");
files.add(f);
diff --git a/src/test/java/org/caosdb/server/transaction/UpdateTest.java b/src/test/java/org/caosdb/server/transaction/UpdateTest.java
index d22fbea8982b1f8d88c9ccdf069a0c8a816add25..fb121c260a7706e806ddc73e9005ea4a440f1510 100644
--- a/src/test/java/org/caosdb/server/transaction/UpdateTest.java
+++ b/src/test/java/org/caosdb/server/transaction/UpdateTest.java
@@ -29,22 +29,29 @@ import static org.junit.Assert.assertEquals;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import org.caosdb.server.CaosDBException;
+import org.caosdb.server.CaosDBServer;
import org.caosdb.server.datatype.GenericValue;
import org.caosdb.server.entity.Entity;
import org.caosdb.server.entity.EntityInterface;
import org.caosdb.server.entity.StatementStatus;
import org.caosdb.server.entity.wrapper.Property;
import org.caosdb.server.utils.EntityStatus;
+import org.junit.BeforeClass;
import org.junit.Test;
public class UpdateTest {
+ @BeforeClass
+ public static void setup() throws IOException {
+ CaosDBServer.initServerProperties();
+ }
+
@Test
public void testDeriveUpdate_SameName()
throws NoSuchAlgorithmException, IOException, CaosDBException {
final Entity newEntity = new Entity("Name");
final Entity oldEntity = new Entity("Name");
- WriteTransaction.deriveUpdate(newEntity, oldEntity);
+ new WriteTransaction(null).deriveUpdate(newEntity, oldEntity);
assertEquals(newEntity.getEntityStatus(), EntityStatus.VALID);
}
@@ -53,7 +60,7 @@ public class UpdateTest {
throws NoSuchAlgorithmException, IOException, CaosDBException {
final Entity newEntity = new Entity("NewName");
final Entity oldEntity = new Entity("OldName");
- WriteTransaction.deriveUpdate(newEntity, oldEntity);
+ new WriteTransaction(null).deriveUpdate(newEntity, oldEntity);
assertEquals(newEntity.getEntityStatus(), EntityStatus.QUALIFIED);
}
@@ -67,7 +74,7 @@ public class UpdateTest {
final Entity oldEntity = new Entity();
oldEntity.addProperty(oldProperty);
- WriteTransaction.deriveUpdate(newEntity, oldEntity);
+ new WriteTransaction(null).deriveUpdate(newEntity, oldEntity);
assertEquals(newEntity.getEntityStatus(), VALID);
}
@@ -83,7 +90,7 @@ public class UpdateTest {
final Entity oldEntity = new Entity();
oldEntity.addProperty(oldProperty);
- WriteTransaction.deriveUpdate(newEntity, oldEntity);
+ new WriteTransaction(null).deriveUpdate(newEntity, oldEntity);
assertEquals(newEntity.getEntityStatus(), QUALIFIED);
assertEquals(newProperty.getEntityStatus(), VALID);
assertEquals(newProperty2.getEntityStatus(), QUALIFIED);
@@ -124,7 +131,7 @@ public class UpdateTest {
oldEntity.addProperty(oldProperty);
- WriteTransaction.deriveUpdate(newEntity, oldEntity);
+ new WriteTransaction(null).deriveUpdate(newEntity, oldEntity);
assertEquals(newUnit.getEntityStatus(), VALID);
assertEquals(newProperty.getEntityStatus(), VALID);
assertEquals(newEntity.getEntityStatus(), VALID);
@@ -165,7 +172,7 @@ public class UpdateTest {
oldEntity.addProperty(oldProperty);
- WriteTransaction.deriveUpdate(newEntity, oldEntity);
+ new WriteTransaction(null).deriveUpdate(newEntity, oldEntity);
assertEquals(newEntity.getEntityStatus(), QUALIFIED);
assertEquals(newProperty.getEntityStatus(), QUALIFIED);
}