diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7161569a7e43017869d9bb0025c35388db6c3623..1802b5bb9fe8cd2f2a21643ee44a380ed8621c37 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -59,7 +59,7 @@ trigger_build:
-F "variables[SERVER]=$CI_COMMIT_REF_NAME"
-F "variables[TriggerdBy]=SERVER"
-F "variables[TriggerdByHash]=$CI_COMMIT_SHORT_SHA"
- -F ref=master https://gitlab.indiscale.com/api/v4/projects/14/trigger/pipeline
+ -F ref=dev https://gitlab.indiscale.com/api/v4/projects/14/trigger/pipeline
# Build a docker image in which tests for this repository can run
build-testenv:
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000000000000000000000000000000000000..4d8a87996586347cb32457bfbb06e524f380098b
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,42 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+
+- Scripting is simplified by adding a `home` directory, of which a copy is
+ created for each called script and set as the `HOME` environment variable.
+
+### Changed
+
+-
+
+
+### Deprecated
+
+-
+
+
+### Fixed
+
+- #46 - Server-side scripting failed as an unprivileged user because the was no
+ writable home directory.
+
+- NaN Double Values (see #41)
+
+
+
+### Security (in case of vulnerabilities)
+
+## [0.1.0] - 2018-10-09
+
+Tag `v0.1` - Commit 3b17b49
+
+### Added
+
+- everything
diff --git a/caosdb-webui b/caosdb-webui
index 8c43e0ed13d4e2baf34b80ac2e98d0494e3272a3..b4950db910523029c3b1f9a268e84576b2584fbf 160000
--- a/caosdb-webui
+++ b/caosdb-webui
@@ -1 +1 @@
-Subproject commit 8c43e0ed13d4e2baf34b80ac2e98d0494e3272a3
+Subproject commit b4950db910523029c3b1f9a268e84576b2584fbf
diff --git a/conf/core/cache.ccf b/conf/core/cache.ccf
index 87d1338a5cf70da9b551744bc154190965d4bb46..672c798d126e9c759e0c7a59a81702733aa4e7b3 100644
--- a/conf/core/cache.ccf
+++ b/conf/core/cache.ccf
@@ -1,3 +1,35 @@
+# default caching options
jcs.default.cacheattributes=org.apache.commons.jcs.engine.CompositeCacheAttributes
jcs.default.cacheattributes.MaxObjects=1000
-jcs.default.cacheattributes.MemoryCacheName=org.apache.commons.jcs.engine.memory.lru.LRUMemoryCache
\ No newline at end of file
+jcs.default.elementattributes=org.apache.commons.jcs.engine.ElementAttributes
+
+# Caching of the backend transactions
+jcs.region.BACKEND_UserRoles.cacheattributes.MaxObjects=100
+jcs.region.BACKEND_Users.cacheattributes.MaxObjects=100
+jcs.region.BACKEND_PermissionRules.cacheattributes.MaxObjects=1000
+
+jcs.region.BACKEND_SparseEntities.cacheattributes.MaxObjects=1000
+jcs.region.BACKEND_EntityProperties.cacheattributes.MaxObjects=1000
+jcs.region.BACKEND_EntityParents.cacheattributes.MaxObjects=1000
+jcs.region.BACKEND_SparseFileRecordsByPath.cacheattributes.MaxObjects=1000
+
+jcs.region.BACKEND_JobRules.cacheattributes.MaxObjects=100
+
+
+# PAM UserSource Caching: Cached Items expire after 60 seconds if they are not requested (idle) and after 600 seconds max.
+# PAM_UnixUserGroups
+jcs.region.PAM_UnixUserGroups.elementattributes.IsEternal=false
+jcs.region.PAM_UnixUserGroups.elementattributes.MaxLife=600
+jcs.region.PAM_UnixUserGroups.elementattributes.IdleTime=60
+
+# PAM_UnixUserExists
+jcs.region.PAM_UnixUserExists.elementattributes.IsEternal=false
+jcs.region.PAM_UnixUserExists.elementattributes.MaxLife=600
+jcs.region.PAM_UnixUserExists.elementattributes.IdleTime=60
+
+# PAM_Authentication
+jcs.region.PAM_Authentication.elementattributes.IsEternal=false
+jcs.region.PAM_Authentication.elementattributes.MaxLife=600
+jcs.region.PAM_Authentication.elementattributes.IdleTime=60
+
+
diff --git a/conf/core/log4j2-default.properties b/conf/core/log4j2-default.properties
index ab7aed268e1e1e1a4088796d68b9e065086b5958..b1697a73fe6703850865406e1441947614d00f47 100644
--- a/conf/core/log4j2-default.properties
+++ b/conf/core/log4j2-default.properties
@@ -12,6 +12,11 @@ appender.stderr.name = stderr
appender.stderr.layout.type = PatternLayout
appender.stderr.layout.pattern = [%d{yy-MMM-dd HH:mm:ss:SSS}] [%p] [%c{1}:%L] - %m%n
appender.stderr.target = SYSTEM_ERR
+appender.stderr.filter.threshold.type = ThresholdFilter
+appender.stderr.filter.threshold.level = INFO
+appender.stderr.filter.threshold.onMatch = ACCEPT
+appender.stderr.filter.threshold.onMismatch = DENY
+
# ${LOG_DIR}/request_errors/...log
appender.request_errors.type = RollingRandomAccessFile
diff --git a/conf/core/server.conf b/conf/core/server.conf
index 8e71c561705fda384a2a87b2b45c3aa8ccfb8ea4..882c4453f1dd2f11eb36bf6a534e0ba26b249c62 100644
--- a/conf/core/server.conf
+++ b/conf/core/server.conf
@@ -3,6 +3,7 @@ SERVER_OWNER=
SERVER_NAME=CaosDB Server
SERVER_SIDE_SCRIPTING_BIN_DIR=./scripting/bin/
SERVER_SIDE_SCRIPTING_WORKING_DIR=./scripting/working/
+SERVER_SIDE_SCRIPTING_HOME_DIR=./scripting/home/
FILE_SYSTEM_ROOT=./CaosDBFileSystem/FileSystemRoot/
DROP_OFF_BOX=./CaosDBFileSystem/DropOffBox/
TMP_FILES=./CaosDBFileSystem/TMP/
@@ -49,13 +50,6 @@ BUGTRACKER_URI=
TRANSACTION_BENCHMARK_ENABLED=true
CACHE_CONF_LOC=./conf/core/cache.ccf
-RULES_CACHE_CAPACITY=100
-SPARSE_ENTITY_CACHE_CAPACITY=1000
-PROPERTIES_CACHE_CAPACITY=1000
-PARENTS_CACHE_CAPACITY=1000
-USER_ACCOUNT_CACHE_CAPACITY=100
-GROUP_CACHE_CAPACITY=100
-
INSERT_FILES_IN_DIR_ALLOWED_DIRS=
SUDO_PASSWORD=
@@ -69,4 +63,4 @@ CERTIFICATES_KEY_PASSWORD=
CERTIFICATES_KEY_STORE_PATH=
CERTIFICATES_KEY_STORE_PASSWORD=
-WEBUI_HTTP_HEADER_CACHE_MAX_AGE=28800
\ No newline at end of file
+WEBUI_HTTP_HEADER_CACHE_MAX_AGE=28800
diff --git a/doc/devel/Benchmarking.md b/doc/devel/Benchmarking.md
new file mode 100644
index 0000000000000000000000000000000000000000..a244a3a64b771060fbf025fc0ee47054b9b95b48
--- /dev/null
+++ b/doc/devel/Benchmarking.md
@@ -0,0 +1,13 @@
+# Manual Java-Side Benchmarking #
+
+Benchmarking can be done using the `TransactionBenchmark` class (in package
+`caosdb.server.database.misc`).
+
+- Single timings can be added to instances of that class via the
+ `addBenchmark(object, time)` method. Multiple benchmarks for the same object
+ (typically just strings) can be averaged.
+- Benchmarks can be serialized into XML, `Container` and `Query` objects already
+ use this with their included benchmarks to output benchmarking results.
+- To work with the benchmarks of often used objects, use these methods:
+ - `Container.getTransactionBenchmark().addBenchmark()`
+ - `Query.addBenchmark()`
diff --git a/makefile b/makefile
index 642e31c538a98b39fdb07aeaed5b8a2515adf947..53c822deac4faaa058d7b1a04329abf2eb03d0bb 100644
--- a/makefile
+++ b/makefile
@@ -4,6 +4,8 @@
#
# 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)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -22,6 +24,7 @@
#
SHELL:=/bin/bash
+JPDA_PORT ?= 9000
compile: easy-units
mvn compile
@@ -32,8 +35,8 @@ runserver:
run: compile
mvn exec:java@run
-run-debug:
- java -Dcaosdb.debug=true -jar target/caosdb-server-0.1-SNAPSHOT-jar-with-dependencies.jar
+run-debug: jar
+ java -Xrunjdwp:transport=dt_socket,address=0.0.0.0:$(JPDA_PORT),server=y,suspend=n -Dcaosdb.debug=true -jar target/caosdb-server-0.1-SNAPSHOT-jar-with-dependencies.jar
run-single:
java -jar target/caosdb-server-0.1-SNAPSHOT-jar-with-dependencies.jar
@@ -42,15 +45,15 @@ formatting:
mvn fmt:format
# Compile into a standalone jar file
-jar: compile
- mvn clean compile assembly:single
-# mvn assembly:single
+jar: easy-units
+ mvn package -DskipTests
antlr:
mvn antlr4:antlr4
test: easy-units
- mvn test
+ MAVEN_DEBUG_OPTS="-Xdebug -Xnoagent -Djava.compiler=NONE -Dcaosdb.debug=true -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=0.0.0.0:9000"
+ mvn test -X
clean: clean-antlr
mvn clean
@@ -105,4 +108,5 @@ stop-debug-screen:
mkdir .m2-local
easy-units: .m2-local
+ mvn clean
mvn deploy:deploy-file -DgroupId=de.timmfitschen -DartifactId=easy-units -Dversion=0.0.1-SNAPSHOT -Durl=file:./.m2-local/ -DrepositoryId=local-maven-repo -DupdateReleaseInfo=true -Dfile=./lib/easy-units-0.0.1-SNAPSHOT-jar-with-dependencies.jar
diff --git a/pom.xml b/pom.xml
index 42e44ca49b82963a16ac655755ccf29b8fcde6e0..ada3403287a657f7684ba8984c57cc80a51820a9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -49,16 +49,6 @@
</repository>
</repositories>
<dependencies>
- <dependency>
- <groupId>org.apache.logging.log4j</groupId>
- <artifactId>log4j-slf4j18-impl</artifactId>
- <version>2.11.2</version>
- </dependency>
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-api</artifactId>
- <version>1.8.0-beta4</version>
- </dependency>
<dependency>
<groupId>de.timmfitschen</groupId>
<artifactId>easy-units</artifactId>
@@ -67,7 +57,7 @@
<dependency>
<groupId>org.apache.shiro</groupId>
<artifactId>shiro-core</artifactId>
- <version>1.3.2</version>
+ <version>1.4.1</version>
</dependency>
<dependency>
<groupId>junit</groupId>
@@ -162,15 +152,25 @@
<artifactId>jetty-util-ajax</artifactId>
<version>9.2.14.v20151106</version>
</dependency>
+ <dependency>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-slf4j-impl</artifactId>
+ <version>2.11.1</version>
+ </dependency>
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-api</artifactId>
+ <version>1.7.21</version>
+ </dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
- <version>2.11.2</version>
+ <version>2.11.1</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
- <version>2.11.2</version>
+ <version>2.11.1</version>
</dependency>
</dependencies>
<build>
@@ -180,6 +180,35 @@
<outputDirectory>${basedir}/target/classes</outputDirectory>
<testOutputDirectory>${basedir}/target/test-classes</testOutputDirectory>
<plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-shade-plugin</artifactId>
+ <version>2.4.3</version>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>shade</goal>
+ </goals>
+ <configuration>
+ <finalName>${project.artifactId}-${project.version}-jar-with-dependencies</finalName>
+ <transformers>
+ <transformer implementation="com.github.edwgiz.mavenShadePlugin.log4j2CacheTransformer.PluginsCacheFileTransformer"></transformer>
+ <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+ <mainClass>caosdb.server.CaosDBServer</mainClass>
+ </transformer>
+ </transformers>
+ </configuration>
+ </execution>
+ </executions>
+ <dependencies>
+ <dependency>
+ <groupId>com.github.edwgiz</groupId>
+ <artifactId>maven-shade-plugin.log4j2-cachefile-transformer</artifactId>
+ <version>2.8.1</version>
+ </dependency>
+ </dependencies>
+ </plugin>
<plugin>
<groupId>org.antlr</groupId>
<artifactId>antlr4-maven-plugin</artifactId>
@@ -204,27 +233,6 @@
<target>1.8</target>
</configuration>
</plugin>
- <plugin>
- <artifactId>maven-assembly-plugin</artifactId>
- <configuration>
- <descriptorRefs>
- <descriptorRef>jar-with-dependencies</descriptorRef>
- </descriptorRefs>
- <archive>
- <manifest>
- <mainClass>caosdb.server.CaosDBServer</mainClass>
- </manifest>
- </archive>
- </configuration>
- <executions>
- <execution>
- <phase>package</phase>
- <goals>
- <goal>single</goal> <!-- Run with: mvn assembly:single -->
- </goals>
- </execution>
- </executions>
- </plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
@@ -238,8 +246,8 @@
<log4j2.debug>true</log4j2.debug>
</systemPropertyVariables>
<reuseForks>false</reuseForks>
- <!-- Start 0.5 JVMs per CPU core -->
- <!-- Higher numbers *seem* to lead to higher failure rates... :-/ -->
+ <!-- Start 0.5 JVMs per CPU core
+ Higher numbers *seem* to lead to higher failure rates... :-/ -->
<forkCount>0.5C</forkCount>
</configuration>
</plugin>
@@ -298,13 +306,11 @@
</execution>
</executions>
</plugin>
- <!-- Remove easy-units from classpath generation because of
- https://github.com/jdee-emacs/jdee/issues/125 (no sources inside
- easy-units) -->
+ <!-- Remove easy-units from classpath generation because of https://github.com/jdee-emacs/jdee/issues/125
+ (no sources inside easy-units) -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
- <version>2.8</version>
<configuration>
<excludeArtifactIds>easy-units</excludeArtifactIds>
</configuration>
diff --git a/scripting/home/readme.md b/scripting/home/readme.md
new file mode 100644
index 0000000000000000000000000000000000000000..9c9744a55cec41f33929a3953d9c582fa97f46e0
--- /dev/null
+++ b/scripting/home/readme.md
@@ -0,0 +1,3 @@
+# The `home` directory #
+This directory will be copied to a temporary directy for each server-side
+scripting invocation and set as the `HOME` environment variable.
diff --git a/src/main/java/caosdb/server/CaosDBServer.java b/src/main/java/caosdb/server/CaosDBServer.java
index 3245902d5721e00d1ae0418a33e7a5f468794ea6..2586c2df7a388061a0986a4ff3a40f94b8657f1b 100644
--- a/src/main/java/caosdb/server/CaosDBServer.java
+++ b/src/main/java/caosdb/server/CaosDBServer.java
@@ -111,7 +111,6 @@ import org.slf4j.LoggerFactory;
public class CaosDBServer extends Application {
private static Logger logger = LoggerFactory.getLogger(CaosDBServer.class);
- private static boolean DEBUG_MODE = false;
private static boolean START_GUI = true;
private static Properties SERVER_PROPERTIES = null;
private static Component component = null;
@@ -222,7 +221,26 @@ public class CaosDBServer extends Application {
INSECURE = true;
}
}
- DEBUG_MODE = Boolean.getBoolean("caosdb.debug");
+ }
+
+ public static Ini getShiroConfig() {
+ final Ini config = new Ini();
+ final Section mainSec = config.addSection("main");
+ mainSec.put("CaosDB", CaosDBDefaultRealm.class.getCanonicalName());
+ mainSec.put("SessionTokenValidator", SessionTokenRealm.class.getCanonicalName());
+ mainSec.put("OneTimeTokenValidator", OneTimeTokenRealm.class.getCanonicalName());
+ mainSec.put("CaosDBAuthorizingRealm", CaosDBAuthorizingRealm.class.getCanonicalName());
+ mainSec.put("AnonymousRealm", AnonymousRealm.class.getCanonicalName());
+ mainSec.put(
+ "securityManager.realms",
+ "$CaosDB, $SessionTokenValidator, $OneTimeTokenValidator, $CaosDBAuthorizingRealm, $AnonymousRealm");
+
+ // disable shiro's default session management. We have quasi-stateless
+ // sessions
+ // using our SessionToken class.
+ mainSec.put(
+ "securityManager.subjectDAO.sessionStorageEvaluator.sessionStorageEnabled", "false");
+ return config;
}
/**
@@ -248,28 +266,12 @@ public class CaosDBServer extends Application {
System.exit(1);
}
- INSECURE = INSECURE && DEBUG_MODE; // only allow insecure in debug mode
- START_BACKEND = START_BACKEND || !DEBUG_MODE; // always start backend if
+ INSECURE = INSECURE && isDebugMode(); // only allow insecure in debug mode
+ START_BACKEND = START_BACKEND || !isDebugMode(); // always start backend if
// not in debug mode
// init Shiro (user authentication/authorization and session management)
- final Ini config = new Ini();
- final Section mainSec = config.addSection("main");
- mainSec.put("CaosDB", CaosDBDefaultRealm.class.getCanonicalName());
- mainSec.put("SessionTokenValidator", SessionTokenRealm.class.getCanonicalName());
- mainSec.put("OneTimeTokenValidator", OneTimeTokenRealm.class.getCanonicalName());
- mainSec.put("CaosDBAuthorizingRealm", CaosDBAuthorizingRealm.class.getCanonicalName());
- mainSec.put("AnonymousRealm", AnonymousRealm.class.getCanonicalName());
- mainSec.put(
- "securityManager.realms",
- "$CaosDB, $SessionTokenValidator, $OneTimeTokenValidator, $CaosDBAuthorizingRealm, $AnonymousRealm");
-
- // disable shiro's default session management. We have quasi-stateless
- // sessions
- // using our SessionToken class.
- mainSec.put(
- "securityManager.subjectDAO.sessionStorageEvaluator.sessionStorageEnabled", "false");
-
+ final Ini config = getShiroConfig();
final Factory<SecurityManager> factory = new IniSecurityManagerFactory(config);
final SecurityManager securityManager = factory.getInstance();
SecurityUtils.setSecurityManager(securityManager);
@@ -829,7 +831,7 @@ public class CaosDBServer extends Application {
}
public static boolean isDebugMode() {
- return DEBUG_MODE;
+ return Boolean.getBoolean("caosdb.debug");
}
/**
diff --git a/src/main/java/caosdb/server/ServerProperties.java b/src/main/java/caosdb/server/ServerProperties.java
index 1f90b069df76760864385f6f090e123387bcbd0a..e68016894d65a3b77e38aa2f84f48ece7db05683 100644
--- a/src/main/java/caosdb/server/ServerProperties.java
+++ b/src/main/java/caosdb/server/ServerProperties.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -90,13 +92,6 @@ public class ServerProperties extends Properties {
public static final String KEY_CACHE_CONF_LOC = "CACHE_CONF_LOC";
- public static final String KEY_RULES_CACHE_CAPACITY = "RULES_CACHE_CAPACITY";
- public static final String KEY_SPARSE_ENTITY_CACHE_CAPACITY = "SPARSE_ENTITY_CACHE_CAPACITY";
- public static final String KEY_PROPERTIES_CACHE_CAPACITY = "PROPERTIES_CACHE_CAPACITY";
- public static final String KEY_PARENTS_CACHE_CAPACITY = "PARENTS_CACHE_CAPACITY";
- public static final String KEY_USER_ACCOUNT_CACHE_CAPACITY = "USER_ACCOUNT_CACHE_CAPACITY";
- public static final String KEY_GROUP_CACHE_CAPACITY = "GROUP_CACHE_CAPACITY";
-
public static final String KEY_TRANSACTION_BENCHMARK_ENABLED = "TRANSACTION_BENCHMARK_ENABLED";
public static final String KEY_INSERT_FILES_IN_DIR_ALLOWED_DIRS =
@@ -119,6 +114,7 @@ public class ServerProperties extends Properties {
public static final String KEY_SERVER_OWNER = "SERVER_OWNER";
public static final String KEY_SERVER_SIDE_SCRIPTING_BIN_DIR = "SERVER_SIDE_SCRIPTING_BIN_DIR";
+ public static final String KEY_SERVER_SIDE_SCRIPTING_HOME_DIR = "SERVER_SIDE_SCRIPTING_HOME_DIR";
public static final String KEY_SERVER_SIDE_SCRIPTING_WORKING_DIR =
"SERVER_SIDE_SCRIPTING_WORKING_DIR";
diff --git a/src/main/java/caosdb/server/accessControl/Pam.java b/src/main/java/caosdb/server/accessControl/Pam.java
index c222fb83dabe0e4ad4e99d096d33192bf65086a9..99f68faadc15c15d9404a504d15669f0c2604ea3 100644
--- a/src/main/java/caosdb/server/accessControl/Pam.java
+++ b/src/main/java/caosdb/server/accessControl/Pam.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -22,23 +24,38 @@
*/
package caosdb.server.accessControl;
+import caosdb.server.caching.Cache;
import java.io.File;
import java.io.IOException;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Map;
import java.util.Set;
+import org.apache.commons.jcs.access.behavior.ICacheAccess;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.apache.shiro.authz.AuthorizationException;
import org.jvnet.libpam.PAMException;
import org.jvnet.libpam.UnixUser;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+/**
+ * PAM UserSource for authenticating users via the Host's pam module.
+ *
+ * <p>A User's existence check and the retrieval of a user's groups is done by the org.jvnet.libpam
+ * library.
+ *
+ * <p>The authentication of a user via the password need root-access and is therefore done by a
+ * special shell script running with root privileges on the host.
+ *
+ * @author Timm Fitschen (t.fitschen@indiscale.com)
+ */
public class Pam implements UserSource {
+ private Logger logger = LogManager.getLogger(Pam.class);
+
public static class DefaultPamScriptCaller implements PamScriptCaller {
- private Logger logger = LoggerFactory.getLogger(getClass());
+ private Logger logger = LogManager.getLogger(Pam.class);
private final String pam_script;
@@ -64,7 +81,7 @@ public class Pam implements UserSource {
try {
pam_authentication = getProcess(username, password);
- logger.info("call pam script");
+ logger.trace("call pam script");
return pam_authentication.waitFor() == 0;
} catch (final IOException e) {
throw new RuntimeException(e);
@@ -75,6 +92,11 @@ public class Pam implements UserSource {
}
public static final String DEFAULT_PAM_SCRIPT = "./misc/pam_authentication/pam_authentication.sh";
+
+ /*
+ * following constants are the names of the configuration parameters and parts of parameters in
+ * the user_sources.ini for the pam user source.
+ */
public static final String KEY_PAM_SCRIPT = "pam_script";
public static final String KEY_DEFAULT_USER_STATUS = "default_status";
public static final String KEY_GROUP = "group";
@@ -83,8 +105,9 @@ public class Pam implements UserSource {
public static final String KEY_INCLUDE = "include";
public static final String KEY_ROLES = "roles";
public static final String SEPARATOR = ".";
+ public static final String KEY_EMAIL = "email";
public static final String REGEX_SPLIT_CSV = "\\s*,\\s*";
- private static final String KEY_EMAIL = "email";
+
private String[] EXCLUDE_USERS = null;
private String[] INCLUDE_USERS = null;
private String[] EXCLUDE_GROUPS = null;
@@ -92,16 +115,28 @@ public class Pam implements UserSource {
private Map<String, String> map = null;
private PamScriptCaller pamScriptCaller = null;
+ /* Caches for groups, user-existence and password validation */
+
+ private ICacheAccess<String, HashSet<String>> groupsCache = Cache.getCache("PAM_UnixUserGroups");
+ private ICacheAccess<String, Boolean> userExistsCache = Cache.getCache("PAM_UnixUserExists");
+ private ICacheAccess<String, Boolean> passwordValidCache = Cache.getCache("PAM_Authentication");
+
@Override
public void setMap(final Map<String, String> map) {
this.map = map;
this.pamScriptCaller = null;
}
- public Map<String, String> getMap() {
+ /**
+ * Return the current configuration of this user source.
+ *
+ * @return configuration.
+ */
+ private Map<String, String> getMap() {
return this.map;
}
+ /** @see {@link UserSource#resolveRolesForUsername(String)} */
@Override
public Set<String> resolveRolesForUsername(final String username) {
final Set<String> resulting_roles = new HashSet<String>();
@@ -138,7 +173,40 @@ public class Pam implements UserSource {
return resulting_roles;
}
- private static Set<String> getGroups(final String username) {
+ /**
+ * Get the UNIX groups of the user.
+ *
+ * <p>First, try to get them from the cache. Only ask the back-end if necessary and cache the
+ * results.
+ *
+ * @param username
+ * @return A user's UNIX groups.
+ */
+ private Set<String> getGroups(final String username) {
+ Set<String> cached = groupsCache.get(username);
+ if (cached != null) {
+ return cached;
+ }
+
+ Set<String> uncached = getGroupsNoCache(username);
+ if (uncached instanceof HashSet) {
+ groupsCache.put(username, (HashSet<String>) uncached);
+ } else {
+ groupsCache.put(username, new HashSet<String>(uncached));
+ }
+ return uncached;
+ }
+
+ /**
+ * Get the UNIX groups of the user directly from the back-end.
+ *
+ * <p>If the user does not exist, an empty set is returned.
+ *
+ * @param username
+ * @return A user's UNIX groups or an empty set.
+ */
+ private Set<String> getGroupsNoCache(final String username) {
+ logger.trace("Retrieving UnixGroups", username);
if (UnixUser.exists(username)) {
try {
return new UnixUser(username).getGroups();
@@ -146,7 +214,7 @@ public class Pam implements UserSource {
throw new AuthorizationException(e);
}
}
- return null;
+ return new HashSet<String>();
}
@Override
@@ -154,11 +222,38 @@ public class Pam implements UserSource {
return "PAM";
}
+ /**
+ * Check if that user is known by the host's PAM.
+ *
+ * <p>Try the cache first. Only ask PAM directly if necessary and cache the results.
+ *
+ * @see {@link UserSource#isUserExisting(String)}.
+ * @return true iff the user is known.
+ */
@Override
public boolean isUserExisting(final String username) {
+ Boolean cached = userExistsCache.get(username);
+ if (cached != null) {
+ return cached;
+ }
+
+ boolean uncached = isUserExistingNoCache(username);
+ userExistsCache.put(username, uncached);
+ return uncached;
+ }
+
+ /**
+ * Check if that user is known by the host's PAM (without caching).
+ *
+ * @param username
+ * @return true iff the user is known.
+ */
+ private boolean isUserExistingNoCache(final String username) {
+ logger.trace("Check UnixUser.exists", username);
return username != null && UnixUser.exists(username) && isIncorporated(username);
}
+ /** @see {@link UserSource#isValid(String, String)}. */
@Override
public boolean isValid(final String username, final String password) {
if (isUserExisting(username)) {
@@ -174,8 +269,40 @@ public class Pam implements UserSource {
return this.pamScriptCaller;
}
+ /**
+ * Check the validity of the password for that user by asking the pam script caller.
+ *
+ * <p>Try the cache first, only call the pam script if necessary and cache the results.
+ *
+ * @param caller
+ * @param username
+ * @param password
+ * @return true iff the password is correct.
+ */
private boolean isValid(
final PamScriptCaller caller, final String username, final String password) {
+ String key = "<" + password + "::" + username + ">";
+ Boolean cached = passwordValidCache.get(key);
+ if (cached != null) {
+ return cached;
+ }
+
+ boolean uncached = isValidNoCache(caller, username, password);
+ passwordValidCache.put(key, uncached);
+ return uncached;
+ }
+
+ /**
+ * Check the validity of the password for that user by asking the pam script caller.
+ *
+ * @param caller
+ * @param username
+ * @param password
+ * @return true iff the password is correct.
+ */
+ private boolean isValidNoCache(
+ final PamScriptCaller caller, final String username, final String password) {
+ logger.trace("Check Password", username);
return caller.isValid(username, password);
}
@@ -278,10 +405,15 @@ public class Pam implements UserSource {
ret = n;
} else if (ret != n) {
// conflict -> ignore, go for pam-wide setting
+ ret = null;
break;
}
}
}
+
+ if (ret != null) {
+ return ret;
+ }
// by pam-wide setting
if (this.map.containsKey(KEY_DEFAULT_USER_STATUS)) {
return UserStatus.valueOf(this.map.get(KEY_DEFAULT_USER_STATUS).toUpperCase());
diff --git a/src/main/java/caosdb/server/accessControl/UserSource.java b/src/main/java/caosdb/server/accessControl/UserSource.java
index 23ce7c45ce6cb9982ae5c7fac05a3a41037a5afe..0ece8d5014227916feb1c50b986aaf4d9a9bf91b 100644
--- a/src/main/java/caosdb/server/accessControl/UserSource.java
+++ b/src/main/java/caosdb/server/accessControl/UserSource.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -25,19 +27,84 @@ package caosdb.server.accessControl;
import java.util.Map;
import java.util.Set;
+/**
+ * UserSources are sources for users - i.e. they authenticate users and contain basic information
+ * about users.
+ *
+ * <p>UserSources let you
+ * <li>check if a user exists - {@link #isUserExisting(String)}
+ * <li>authenticate a user via a password - {@link #isValid(String, String)}
+ * <li>get the default {@link UserStatus} - {@link #getDefaultUserStatus(String)}
+ * <li>get the default email address - {@link #getDefaultUserEmail(String)}
+ * <li>retrieve a users roles - {@link #resolveRolesForUsername(String)} The default email and
+ * default {@link UserStatus} might be overridden by other settings in CaosDB - that's why they
+ * are called "default".
+ *
+ * <p>Also, the user's roles might be overridden by the internal user source {@link
+ * InternalUserSource}.
+ *
+ * <p>A UserSource is configured via {@link #setMap(Map)}.
+ *
+ * @author Timm Fitschen (t.fitschen@indiscale.com)
+ */
public interface UserSource {
+ /**
+ * Every UserSource has a unique name, e.g. PAM, CaosDB (which is default name of the internal
+ * user source {@link InternalUserSource}).
+ *
+ * @return name
+ */
public String getName();
+ /**
+ * Check if a user exists.
+ *
+ * @param username
+ * @return true iff this user source knows a user with that name
+ */
public boolean isUserExisting(String username);
+ /**
+ * Return all roles that a user is associated with.
+ *
+ * @param username
+ * @return a user's roles
+ */
public Set<String> resolveRolesForUsername(final String username);
+ /**
+ * Configure this user source. The needed parameters are to be defined and documented by the
+ * implementations.
+ *
+ * @param map the configuration
+ */
public void setMap(Map<String, String> map);
+ /**
+ * Return the {@link UserStatus} of that user.
+ *
+ * @param username
+ * @return The user status of that user
+ */
public UserStatus getDefaultUserStatus(String username);
+ /**
+ * Return the email address of that user, or null if none is available as per this user source.
+ *
+ * <p>This method does not check if a user exists. So it will return null for unknown users.
+ *
+ * @param username
+ * @return The email address or null
+ */
public String getDefaultUserEmail(String username);
+ /**
+ * Check if the user can be authenticated by the given password.
+ *
+ * @param username
+ * @param password
+ * @return true iff the password was correct.
+ */
public boolean isValid(String username, String password);
}
diff --git a/src/main/java/caosdb/server/caching/Cache.java b/src/main/java/caosdb/server/caching/Cache.java
new file mode 100644
index 0000000000000000000000000000000000000000..338b1d853fd0610be780362a0242193fa46eb320
--- /dev/null
+++ b/src/main/java/caosdb/server/caching/Cache.java
@@ -0,0 +1,50 @@
+/*
+ * ** 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)
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ *
+ * ** end header
+ */
+package caosdb.server.caching;
+
+import java.io.Serializable;
+import org.apache.commons.jcs.access.behavior.ICacheAccess;
+
+/**
+ * Caching Helper Class used for all caches in the CaosDB Server.
+ *
+ * <p>The actual work is delegated to an instance of {@link JCSCacheHelper}. However, the delegate
+ * {@link #DELEGATE} can be be overridden for testing purposes with {@link #setDelegate(Cache)}.
+ *
+ * @author Timm Fitschen (t.fitschen@indiscale.com)
+ */
+public class Cache {
+
+ /** The default cache helper delegate. */
+ private static CacheHelper DELEGATE = new JCSCacheHelper();
+
+ public static void setDelegate(CacheHelper delegate) {
+ DELEGATE = delegate;
+ }
+
+ public static final <K, V extends Serializable> ICacheAccess<K, V> getCache(String region) {
+ return DELEGATE.getCache(region);
+ }
+}
diff --git a/src/main/java/caosdb/server/caching/CacheHelper.java b/src/main/java/caosdb/server/caching/CacheHelper.java
new file mode 100644
index 0000000000000000000000000000000000000000..32c854400310959a7834fe32a6f90de9e1b584d1
--- /dev/null
+++ b/src/main/java/caosdb/server/caching/CacheHelper.java
@@ -0,0 +1,31 @@
+/*
+ * ** header v3.0
+ * This file is a part of the CaosDB Project.
+ *
+ * Copyright (C) 2019 IndiScale GmbH
+ * Copyright (C) 2019 Timm Fitschen (t.fitschen@indiscale.com)
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ *
+ * ** end header
+ */
+package caosdb.server.caching;
+
+import java.io.Serializable;
+import org.apache.commons.jcs.access.behavior.ICacheAccess;
+
+public interface CacheHelper {
+
+ public <K, V extends Serializable> ICacheAccess<K, V> getCache(String region);
+}
diff --git a/src/main/java/caosdb/server/caching/JCSCacheHelper.java b/src/main/java/caosdb/server/caching/JCSCacheHelper.java
new file mode 100644
index 0000000000000000000000000000000000000000..dab2b77ceaab3d0caaf49d798a4819ca890b5e82
--- /dev/null
+++ b/src/main/java/caosdb/server/caching/JCSCacheHelper.java
@@ -0,0 +1,91 @@
+/*
+ * ** 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)
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ *
+ * ** end header
+ */
+package caosdb.server.caching;
+
+import caosdb.server.CaosDBServer;
+import caosdb.server.ServerProperties;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.Serializable;
+import java.util.Properties;
+import org.apache.commons.jcs.JCS;
+import org.apache.commons.jcs.access.behavior.ICacheAccess;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+/**
+ * A CacheHelper implementation which is configured statically via the {@link
+ * ServerProperties#KEY_CACHE_CONF_LOC} properties file.
+ *
+ * @author Timm Fitschen (t.fitschen@indiscale.com)
+ */
+public class JCSCacheHelper implements CacheHelper {
+
+ protected static Logger logger = LogManager.getLogger(JCSCacheHelper.class);
+
+ // A No-Operation configuration for JCS
+ private static Properties getNOPCachingProperties() {
+ Properties ret = new Properties();
+ ret.setProperty(
+ "jcs.default.cacheattributes", "org.apache.commons.jcs.engine.CompositeCacheAttributes");
+ ret.setProperty("jcs.default.cacheattributes.MaxObjects", "0");
+ return ret;
+ }
+
+ // configure JCS
+ static {
+ Properties config = null;
+ try {
+ Properties p = new Properties();
+ final InputStream is =
+ new FileInputStream(CaosDBServer.getServerProperty(ServerProperties.KEY_CACHE_CONF_LOC));
+ p.load(is);
+ is.close();
+ config = p;
+ } catch (final FileNotFoundException e) {
+ logger.error(e);
+ config = getNOPCachingProperties();
+ } catch (final IOException e) {
+ logger.error(e);
+ config = getNOPCachingProperties();
+ }
+ logger.info("Configuring JCS Caching with {}", config);
+ JCS.setConfigProperties(config);
+ }
+
+ @Override
+ public <K, V extends Serializable> ICacheAccess<K, V> getCache(final String name) {
+ final ICacheAccess<K, V> cache = JCS.getInstance(name);
+ logger.info(
+ "Caching configuration for {}:\n+----{}\n+----{}",
+ name,
+ cache.getCacheAttributes(),
+ cache.getDefaultElementAttributes());
+
+ return cache;
+ }
+}
diff --git a/src/main/java/caosdb/server/database/BackendTransaction.java b/src/main/java/caosdb/server/database/BackendTransaction.java
index 1d5d5c2e68274e664c392a24a901aa4bcd65623b..4899996e6c4df2b18837259112ac7e90c534b793 100644
--- a/src/main/java/caosdb/server/database/BackendTransaction.java
+++ b/src/main/java/caosdb/server/database/BackendTransaction.java
@@ -210,7 +210,7 @@ public abstract class BackendTransaction implements Undoable {
return t;
}
- private static <K extends BackendTransactionImpl, L extends K> void setImpl(
+ public static <K extends BackendTransactionImpl, L extends K> void setImpl(
final Class<K> k, final Class<L> l) {
impl.put(k, l);
}
diff --git a/src/main/java/caosdb/server/database/CacheableBackendTransaction.java b/src/main/java/caosdb/server/database/CacheableBackendTransaction.java
index 390a177fe899f89330aeb3d0959aab5bf1d52cbc..fc4c9659d9a8ea80393bebad945bd6badf9580c4 100644
--- a/src/main/java/caosdb/server/database/CacheableBackendTransaction.java
+++ b/src/main/java/caosdb/server/database/CacheableBackendTransaction.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -24,14 +26,19 @@ package caosdb.server.database;
import caosdb.server.database.exceptions.TransactionException;
import java.io.Serializable;
-import org.apache.commons.jcs.access.CacheAccess;
+import org.apache.commons.jcs.access.behavior.ICacheAccess;
public abstract class CacheableBackendTransaction<K, V extends Serializable>
extends BackendTransaction {
- public abstract V executeNoCache() throws TransactionException;
-
private Boolean cached = null;
+ private ICacheAccess<K, V> cache;
+
+ public CacheableBackendTransaction(ICacheAccess<K, V> cache) {
+ this.cache = cache;
+ }
+
+ public abstract V executeNoCache() throws TransactionException;
@Override
public final void execute() throws TransactionException {
@@ -67,8 +74,8 @@ public abstract class CacheableBackendTransaction<K, V extends Serializable>
protected abstract K getKey();
- protected CacheAccess<K, V> getCache() {
- return null;
+ protected final ICacheAccess<K, V> getCache() {
+ return cache;
}
private final boolean cacheIsEnabled() {
diff --git a/src/main/java/caosdb/server/database/backend/transaction/DeleteSparseEntity.java b/src/main/java/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
index 4bd6e5b9706fe743be6c924c3e1f86cb6ff83371..39deb1416c743f838bfc1b96c29fd845dbcef742 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -41,6 +43,9 @@ public class DeleteSparseEntity extends BackendTransaction {
@Override
protected void execute() {
RetrieveSparseEntity.removeCached(this.entity.getId());
+ if (entity.hasFileProperties()) {
+ GetFileRecordByPath.removeCached(this.entity.getFileProperties().getPath());
+ }
final DeleteSparseEntityImpl ret = getImplementation(DeleteSparseEntityImpl.class);
diff --git a/src/main/java/caosdb/server/database/backend/transaction/GetFileRecordByPath.java b/src/main/java/caosdb/server/database/backend/transaction/GetFileRecordByPath.java
index 195f16db5341fdcd204debbaad0217635d1fd222..8e0afcbdc50985f1fa1a939940c05f8429562c90 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/GetFileRecordByPath.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/GetFileRecordByPath.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -22,20 +24,31 @@
*/
package caosdb.server.database.backend.transaction;
+import caosdb.server.caching.Cache;
import caosdb.server.database.CacheableBackendTransaction;
import caosdb.server.database.backend.interfaces.GetFileRecordByPathImpl;
import caosdb.server.database.exceptions.TransactionException;
import caosdb.server.database.proto.SparseEntity;
+import org.apache.commons.jcs.access.behavior.ICacheAccess;
public class GetFileRecordByPath extends CacheableBackendTransaction<String, SparseEntity> {
+ private static final ICacheAccess<String, SparseEntity> cache =
+ Cache.getCache("BACKEND_SparseFileRecordsByPath");
private final String path;
private SparseEntity entity;
public GetFileRecordByPath(final String path) {
+ super(cache);
this.path = path;
}
+ public static void removeCached(final String path) {
+ if (path != null && cache != null) {
+ cache.remove(path);
+ }
+ }
+
@Override
protected String getKey() {
return this.path;
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java
index 5d1545d29b9bab295c9f335fe4eb083f12f748b2..5c1b0178f51496f83a4fac6a4ce3b2447abdccd5 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveParents.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -22,26 +24,21 @@
*/
package caosdb.server.database.backend.transaction;
-import caosdb.server.CaosDBServer;
-import caosdb.server.ServerProperties;
+import caosdb.server.caching.Cache;
import caosdb.server.database.CacheableBackendTransaction;
import caosdb.server.database.DatabaseUtils;
import caosdb.server.database.backend.interfaces.RetrieveParentsImpl;
import caosdb.server.database.exceptions.TransactionException;
-import caosdb.server.database.misc.Cache;
import caosdb.server.database.proto.VerySparseEntity;
import caosdb.server.entity.EntityInterface;
import java.util.ArrayList;
-import org.apache.commons.jcs.access.CacheAccess;
+import org.apache.commons.jcs.access.behavior.ICacheAccess;
public class RetrieveParents
extends CacheableBackendTransaction<Integer, ArrayList<VerySparseEntity>> {
- private static final CacheAccess<Integer, ArrayList<VerySparseEntity>> cache =
- Cache.getCache(
- "ParentsCache",
- Integer.valueOf(
- CaosDBServer.getServerProperty(ServerProperties.KEY_SPARSE_ENTITY_CACHE_CAPACITY)));
+ private static final ICacheAccess<Integer, ArrayList<VerySparseEntity>> cache =
+ Cache.getCache("BACKEND_EntityParents");
/**
* To be called by DeleteEntityProperties on execution.
@@ -54,14 +51,10 @@ public class RetrieveParents
}
}
- @Override
- protected CacheAccess<Integer, ArrayList<VerySparseEntity>> getCache() {
- return cache;
- }
-
private final EntityInterface entity;
public RetrieveParents(final EntityInterface entity) {
+ super(cache);
this.entity = entity;
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrievePermissionRules.java b/src/main/java/caosdb/server/database/backend/transaction/RetrievePermissionRules.java
index c0daecbc46ac90630eac83d0c7334d7da148d429..7e9925777c21a6d041759cfdade7682b85458566 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrievePermissionRules.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrievePermissionRules.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -22,28 +24,24 @@
*/
package caosdb.server.database.backend.transaction;
-import caosdb.server.CaosDBServer;
-import caosdb.server.ServerProperties;
+import caosdb.server.caching.Cache;
import caosdb.server.database.CacheableBackendTransaction;
import caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
import caosdb.server.database.exceptions.TransactionException;
-import caosdb.server.database.misc.Cache;
import caosdb.server.permissions.PermissionRule;
import java.util.HashSet;
-import org.apache.commons.jcs.access.CacheAccess;
+import org.apache.commons.jcs.access.behavior.ICacheAccess;
public class RetrievePermissionRules
extends CacheableBackendTransaction<String, HashSet<PermissionRule>> {
- private static final CacheAccess<String, HashSet<PermissionRule>> cache =
- Cache.getCache(
- "PermissionRulesCache",
- Integer.valueOf(
- CaosDBServer.getServerProperty(ServerProperties.KEY_GROUP_CACHE_CAPACITY)));
+ private static final ICacheAccess<String, HashSet<PermissionRule>> cache =
+ Cache.getCache("BACKEND_PermissionRules");
private HashSet<PermissionRule> rules;
private final String role;
public RetrievePermissionRules(final String role) {
+ super(cache);
this.role = role;
}
@@ -51,11 +49,6 @@ public class RetrievePermissionRules
cache.remove(role);
}
- @Override
- protected CacheAccess<String, HashSet<PermissionRule>> getCache() {
- return cache;
- }
-
@Override
public HashSet<PermissionRule> executeNoCache() throws TransactionException {
final RetrievePermissionRulesImpl t = getImplementation(RetrievePermissionRulesImpl.class);
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveProperties.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveProperties.java
index b75d91acba76a4d97b16395701afe42ff05c5fac..650cae3676ed2b6b50f86c76a5ce92b195290fc3 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveProperties.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveProperties.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -22,29 +24,24 @@
*/
package caosdb.server.database.backend.transaction;
-import caosdb.server.CaosDBServer;
-import caosdb.server.ServerProperties;
+import caosdb.server.caching.Cache;
import caosdb.server.database.CacheableBackendTransaction;
import caosdb.server.database.DatabaseUtils;
import caosdb.server.database.backend.interfaces.RetrievePropertiesImpl;
import caosdb.server.database.exceptions.TransactionException;
-import caosdb.server.database.misc.Cache;
import caosdb.server.database.proto.ProtoProperty;
import caosdb.server.entity.EntityInterface;
import caosdb.server.entity.Role;
import caosdb.server.entity.wrapper.Property;
import java.util.ArrayList;
-import org.apache.commons.jcs.access.CacheAccess;
+import org.apache.commons.jcs.access.behavior.ICacheAccess;
public class RetrieveProperties
extends CacheableBackendTransaction<Integer, ArrayList<ProtoProperty>> {
private final EntityInterface entity;
- private static final CacheAccess<Integer, ArrayList<ProtoProperty>> cache =
- Cache.getCache(
- "PropertiesCache",
- Integer.valueOf(
- CaosDBServer.getServerProperty(ServerProperties.KEY_PROPERTIES_CACHE_CAPACITY)));
+ private static final ICacheAccess<Integer, ArrayList<ProtoProperty>> cache =
+ Cache.getCache("BACKEND_EntityProperties");
/**
* To be called by DeleteEntityProperties on execution.
@@ -57,12 +54,8 @@ public class RetrieveProperties
}
}
- @Override
- protected CacheAccess<Integer, ArrayList<ProtoProperty>> getCache() {
- return cache;
- }
-
public RetrieveProperties(final EntityInterface entity) {
+ super(cache);
this.entity = entity;
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveRole.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveRole.java
index e45879964ef8bafad0106238073ff8c9d87e2287..5bb6150a8640f45997a4a3432ad4ac27196cd15c 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveRole.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveRole.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -22,36 +24,26 @@
*/
package caosdb.server.database.backend.transaction;
-import caosdb.server.CaosDBServer;
-import caosdb.server.ServerProperties;
import caosdb.server.accessControl.Role;
+import caosdb.server.caching.Cache;
import caosdb.server.database.CacheableBackendTransaction;
import caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
import caosdb.server.database.exceptions.TransactionException;
-import caosdb.server.database.misc.Cache;
-import org.apache.commons.jcs.access.CacheAccess;
+import org.apache.commons.jcs.access.behavior.ICacheAccess;
public class RetrieveRole extends CacheableBackendTransaction<String, Role> {
- private static final CacheAccess<String, Role> cache =
- Cache.getCache(
- "RolesCache",
- Integer.valueOf(
- CaosDBServer.getServerProperty(ServerProperties.KEY_GROUP_CACHE_CAPACITY)));
+ private static final ICacheAccess<String, Role> cache = Cache.getCache("BACKEND_UserRoles");
private final String role_name;
private Role role;
- @Override
- protected CacheAccess<String, Role> getCache() {
- return cache;
- }
-
public Role getRole() {
return this.role;
}
public RetrieveRole(final String role) {
+ super(cache);
this.role_name = role;
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
index df9f58671184fb70fca99ca7707f9270f75c87a1..a91b5021f1fa722a8e8831234fc8ebc2032ba115 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -22,30 +24,25 @@
*/
package caosdb.server.database.backend.transaction;
-import caosdb.server.CaosDBServer;
-import caosdb.server.ServerProperties;
+import caosdb.server.caching.Cache;
import caosdb.server.database.CacheableBackendTransaction;
import caosdb.server.database.DatabaseUtils;
import caosdb.server.database.backend.interfaces.RetrieveSparseEntityImpl;
import caosdb.server.database.exceptions.TransactionException;
-import caosdb.server.database.misc.Cache;
import caosdb.server.database.proto.SparseEntity;
import caosdb.server.entity.Entity;
import caosdb.server.entity.EntityInterface;
import caosdb.server.utils.EntityStatus;
-import org.apache.commons.jcs.access.CacheAccess;
+import org.apache.commons.jcs.access.behavior.ICacheAccess;
public class RetrieveSparseEntity extends CacheableBackendTransaction<Integer, SparseEntity> {
private final EntityInterface entity;
- private static final CacheAccess<Integer, SparseEntity> cache =
- Cache.getCache(
- "SparseEntityCache",
- Integer.valueOf(
- CaosDBServer.getServerProperty(ServerProperties.KEY_SPARSE_ENTITY_CACHE_CAPACITY)));
+ private static final ICacheAccess<Integer, SparseEntity> cache =
+ Cache.getCache("BACKEND_SparseEntities");
/**
- * To be called by UpdateSparseEntity and DeleteEntity on execution.
+ * To be called by {@link UpdateSparseEntity} and {@link DeleteEntity} on execution.
*
* @param id
*/
@@ -55,17 +52,13 @@ public class RetrieveSparseEntity extends CacheableBackendTransaction<Integer, S
}
}
- @Override
- protected CacheAccess<Integer, SparseEntity> getCache() {
- return cache;
- }
-
public RetrieveSparseEntity(final EntityInterface entity) {
+ super(cache);
this.entity = entity;
}
public RetrieveSparseEntity(final int id) {
- this.entity = new Entity(id);
+ this(new Entity(id));
}
@Override
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveTransactionHistory.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveTransactionHistory.java
index cb9cdd9e993b9399f2bec5c9bff7316e0754b9ed..72bc1e5b1ec3a3509cc5cbba23e38b908d4e969f 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveTransactionHistory.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveTransactionHistory.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -23,17 +25,15 @@
package caosdb.server.database.backend.transaction;
import caosdb.datetime.UTCDateTime;
-import caosdb.server.database.CacheableBackendTransaction;
+import caosdb.server.database.BackendTransaction;
import caosdb.server.database.backend.interfaces.RetrieveTransactionHistoryImpl;
import caosdb.server.database.exceptions.TransactionException;
import caosdb.server.database.proto.ProtoTransactionLogMessage;
import caosdb.server.entity.EntityInterface;
import caosdb.server.utils.TransactionLogMessage;
import java.util.ArrayList;
-import org.apache.commons.jcs.access.CacheAccess;
-public class RetrieveTransactionHistory
- extends CacheableBackendTransaction<Integer, ArrayList<ProtoTransactionLogMessage>> {
+public class RetrieveTransactionHistory extends BackendTransaction {
private final EntityInterface entity;
@@ -42,25 +42,13 @@ public class RetrieveTransactionHistory
}
@Override
- protected Integer getKey() {
- return this.entity.getId();
- }
-
- @Override
- protected CacheAccess<Integer, ArrayList<ProtoTransactionLogMessage>> getCache() {
- return null;
- }
-
- @Override
- public ArrayList<ProtoTransactionLogMessage> executeNoCache() throws TransactionException {
+ protected void execute() {
final RetrieveTransactionHistoryImpl t =
getImplementation(RetrieveTransactionHistoryImpl.class);
- return t.execute(getKey());
+ process(t.execute(entity.getId()));
}
- @Override
- protected void process(final ArrayList<ProtoTransactionLogMessage> l)
- throws TransactionException {
+ private void process(final ArrayList<ProtoTransactionLogMessage> l) throws TransactionException {
for (final ProtoTransactionLogMessage t : l) {
final UTCDateTime dateTime = UTCDateTime.UTCSeconds(t.seconds, t.nanos);
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RetrieveUser.java b/src/main/java/caosdb/server/database/backend/transaction/RetrieveUser.java
index 7492df38adfcfd24d18f1a263be5070a8916c9c8..9f27152030f5c953ee7bd4ecfff8c83d3cbc8a73 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RetrieveUser.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RetrieveUser.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -22,43 +24,29 @@
*/
package caosdb.server.database.backend.transaction;
-import caosdb.server.CaosDBServer;
-import caosdb.server.ServerProperties;
import caosdb.server.accessControl.Principal;
+import caosdb.server.caching.Cache;
import caosdb.server.database.CacheableBackendTransaction;
import caosdb.server.database.backend.interfaces.RetrieveUserImpl;
import caosdb.server.database.exceptions.TransactionException;
-import caosdb.server.database.misc.Cache;
import caosdb.server.database.proto.ProtoUser;
-import org.apache.commons.jcs.access.CacheAccess;
+import org.apache.commons.jcs.access.behavior.ICacheAccess;
public class RetrieveUser extends CacheableBackendTransaction<Principal, ProtoUser> {
private ProtoUser user;
- private static final CacheAccess<Principal, ProtoUser> cache =
- Cache.getCache(
- "UserAccountCache",
- Integer.valueOf(
- CaosDBServer.getServerProperty(ServerProperties.KEY_USER_ACCOUNT_CACHE_CAPACITY)));
+ private static final ICacheAccess<Principal, ProtoUser> cache = Cache.getCache("BACKEND_Users");
private final Principal principal;
- /**
- * To be called by DeleteSparseEntity, SetPassword, and UpdateSparseEntity on execution.
- *
- * @param u
- */
+ /** To be called by DeleteSparseEntity, SetPassword, and UpdateSparseEntity on execution. */
public static void removeCached(final Principal principal) {
if (principal != null && cache != null) {
cache.remove(principal);
}
}
- @Override
- protected CacheAccess<Principal, ProtoUser> getCache() {
- return cache;
- }
-
public RetrieveUser(final Principal principal) {
+ super(cache);
this.principal = principal;
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/RuleLoader.java b/src/main/java/caosdb/server/database/backend/transaction/RuleLoader.java
index 1a8698ac1d698946e7a3e239c03e386bc200e2b6..303029b42179a697c939767e2caf4d490a803a69 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/RuleLoader.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/RuleLoader.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -22,22 +24,22 @@
*/
package caosdb.server.database.backend.transaction;
-import caosdb.server.CaosDBServer;
-import caosdb.server.ServerProperties;
+import caosdb.server.caching.Cache;
import caosdb.server.database.CacheableBackendTransaction;
import caosdb.server.database.backend.interfaces.RuleLoaderImpl;
import caosdb.server.database.exceptions.TransactionException;
-import caosdb.server.database.misc.Cache;
import caosdb.server.database.proto.Rule;
import caosdb.server.entity.EntityInterface;
import caosdb.server.entity.container.TransactionContainer;
import caosdb.server.jobs.Job;
import caosdb.server.transaction.Transaction;
import java.util.ArrayList;
-import org.apache.commons.jcs.access.CacheAccess;
+import org.apache.commons.jcs.access.behavior.ICacheAccess;
public class RuleLoader extends CacheableBackendTransaction<String, ArrayList<Rule>> {
+ private static final ICacheAccess<String, ArrayList<Rule>> cache =
+ Cache.getCache("BACKEND_JobRules");
private final Transaction<? extends TransactionContainer> transaction;
private final EntityInterface e;
private final Integer entity;
@@ -49,6 +51,7 @@ public class RuleLoader extends CacheableBackendTransaction<String, ArrayList<Ru
final Integer entity,
final EntityInterface e,
final Transaction<? extends TransactionContainer> transaction) {
+ super(cache);
this.domain = domain;
this.entity = entity;
this.e = e;
@@ -66,17 +69,6 @@ public class RuleLoader extends CacheableBackendTransaction<String, ArrayList<Ru
+ ">";
}
- @Override
- protected CacheAccess<String, ArrayList<Rule>> getCache() {
- return rulesCache;
- }
-
- private static CacheAccess<String, ArrayList<Rule>> rulesCache =
- Cache.getCache(
- "RulesCache",
- Integer.valueOf(
- CaosDBServer.getServerProperty(ServerProperties.KEY_RULES_CACHE_CAPACITY)));
-
public ArrayList<Job> getJobs() {
return this.jobs;
}
diff --git a/src/main/java/caosdb/server/database/backend/transaction/UpdateSparseEntity.java b/src/main/java/caosdb/server/database/backend/transaction/UpdateSparseEntity.java
index 57d22ef226e83caf7e3b37b48b53c1025afaa93f..c6a1c7683409e0c875484e14553e4aeac2757a71 100644
--- a/src/main/java/caosdb/server/database/backend/transaction/UpdateSparseEntity.java
+++ b/src/main/java/caosdb/server/database/backend/transaction/UpdateSparseEntity.java
@@ -4,6 +4,8 @@
*
* 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)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -39,6 +41,9 @@ public class UpdateSparseEntity extends BackendTransaction {
@Override
public void execute() throws TransactionException {
RetrieveSparseEntity.removeCached(this.entity.getId());
+ if (entity.hasFileProperties()) {
+ GetFileRecordByPath.removeCached(this.entity.getFileProperties().getPath());
+ }
final UpdateSparseEntityImpl t = getImplementation(UpdateSparseEntityImpl.class);
diff --git a/src/main/java/caosdb/server/database/misc/Cache.java b/src/main/java/caosdb/server/database/misc/Cache.java
deleted file mode 100644
index 7f364d4ab3e2ddc2d3e5e0638be4fe5dfa252ccd..0000000000000000000000000000000000000000
--- a/src/main/java/caosdb/server/database/misc/Cache.java
+++ /dev/null
@@ -1,78 +0,0 @@
-/*
- * ** header v3.0
- * This file is a part of the CaosDB Project.
- *
- * Copyright (C) 2018 Research Group Biomedical Physics,
- * Max-Planck-Institute for Dynamics and Self-Organization Göttingen
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as
- * published by the Free Software Foundation, either version 3 of the
- * License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program. If not, see <https://www.gnu.org/licenses/>.
- *
- * ** end header
- */
-package caosdb.server.database.misc;
-
-import caosdb.server.CaosDBServer;
-import caosdb.server.ServerProperties;
-import caosdb.server.terminal.StatLabel;
-import caosdb.server.terminal.StatsPanel;
-import caosdb.server.utils.AbstractObservable;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.Serializable;
-import java.util.Properties;
-import org.apache.commons.jcs.JCS;
-import org.apache.commons.jcs.access.CacheAccess;
-
-public class Cache {
-
- static {
- final Properties p = new Properties();
- try {
- final InputStream is =
- new FileInputStream(CaosDBServer.getServerProperty(ServerProperties.KEY_CACHE_CONF_LOC));
- p.load(is);
- is.close();
- } catch (final FileNotFoundException e) {
- e.printStackTrace();
- } catch (final IOException e) {
- e.printStackTrace();
- }
- JCS.setConfigProperties(p);
- }
-
- public static <K, V extends Serializable> CacheAccess<K, V> getCache(
- final String name, final int capacity) {
- if (capacity > 0) {
- final CacheAccess<K, V> cache = JCS.getInstance(name);
- cache.getCacheAttributes().setMaxObjects(capacity);
- StatsPanel.addStat(
- name,
- new AbstractObservable() {
- @Override
- public String toString() {
- return cache.getStats();
- };
- });
- StatsPanel.addStat(
- name,
- new StatLabel(
- "Configuration", cache.getCacheAttributes().toString().replaceAll(",", "\n")));
-
- return cache;
- }
- return null;
- }
-}
diff --git a/src/main/java/caosdb/server/datatype/GenericValue.java b/src/main/java/caosdb/server/datatype/GenericValue.java
index d6140ff75a80908e0cf82880aeee336a6f21cb87..8e8f1dd41e49305ddba2090b1f897a35a3765f93 100644
--- a/src/main/java/caosdb/server/datatype/GenericValue.java
+++ b/src/main/java/caosdb/server/datatype/GenericValue.java
@@ -44,7 +44,11 @@ public class GenericValue implements SingleValue {
throw new NullPointerException();
}
this.value = d;
- this.table = Table.double_data;
+ if (d.isNaN()) {
+ this.table = Table.text_data;
+ } else {
+ this.table = Table.double_data;
+ }
}
public GenericValue(final String s) {
diff --git a/src/main/java/caosdb/server/jobs/core/InsertFilesInDir.java b/src/main/java/caosdb/server/jobs/core/InsertFilesInDir.java
index 773ac27525e0b28a1a10f23f1a2ee9cfd9fbf799..9dbc2a68b684b7a5757a00c816f81f3716e55dc9 100644
--- a/src/main/java/caosdb/server/jobs/core/InsertFilesInDir.java
+++ b/src/main/java/caosdb/server/jobs/core/InsertFilesInDir.java
@@ -22,6 +22,7 @@
*/
package caosdb.server.jobs.core;
+import caosdb.server.CaosDBException;
import caosdb.server.CaosDBServer;
import caosdb.server.FileSystem;
import caosdb.server.ServerProperties;
@@ -153,7 +154,7 @@ public class InsertFilesInDir extends FlagJob {
try {
final Undoable delete = FileUtils.delete(InsertFilesInDir.this.tmp, true);
delete.cleanUp();
- } catch (final IOException e) {
+ } catch (final IOException | CaosDBException | InterruptedException e) {
e.printStackTrace();
}
}
@@ -163,7 +164,7 @@ public class InsertFilesInDir extends FlagJob {
try {
final Undoable delete = FileUtils.delete(InsertFilesInDir.this.tmp, true);
delete.cleanUp();
- } catch (final IOException e) {
+ } catch (final IOException | CaosDBException | InterruptedException e) {
e.printStackTrace();
}
}
diff --git a/src/main/java/caosdb/server/query/Query.java b/src/main/java/caosdb/server/query/Query.java
index c9bff5a5f11aa5775582c613d80062419f9adb4c..d3e0e927d14d0b2021f056ad52f10df548c5734c 100644
--- a/src/main/java/caosdb/server/query/Query.java
+++ b/src/main/java/caosdb/server/query/Query.java
@@ -415,6 +415,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
}
public void parse() throws ParsingException {
+ final long t1 = System.currentTimeMillis();
CQLLexer lexer;
lexer = new CQLLexer(CharStreams.fromString(this.query));
final CommonTokenStream tokens = new CommonTokenStream(lexer);
@@ -434,6 +435,8 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
this.type = cq.t;
this.filter = cq.filter;
this.selections = cq.s;
+ final long t2 = System.currentTimeMillis();
+ addBenchmark("parse (" + this.query + ")", t2 - t1);
}
private String executeStrategy() throws QueryException {
diff --git a/src/main/java/caosdb/server/resource/AbstractCaosDBServerResource.java b/src/main/java/caosdb/server/resource/AbstractCaosDBServerResource.java
index c88bbd75a34aea81198b2c9d48702ca6f66a41e0..948b4eab2fda1c906f4acf2802c0d83184b875bc 100644
--- a/src/main/java/caosdb/server/resource/AbstractCaosDBServerResource.java
+++ b/src/main/java/caosdb/server/resource/AbstractCaosDBServerResource.java
@@ -101,7 +101,8 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
}
public Subject getUser() {
- return SecurityUtils.getSubject();
+ Subject ret = SecurityUtils.getSubject();
+ return ret;
}
/**
@@ -331,6 +332,7 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
this.xslScript = s;
}
+ /** Wrap an element for an "OK" response. */
protected JdomRepresentation ok(Element root) {
return ok(new Document(root));
}
diff --git a/src/main/java/caosdb/server/resource/InfoResource.java b/src/main/java/caosdb/server/resource/InfoResource.java
index 96459212a804d2451c2b978bd858bba954640bca..c2342cc46f7e62fd6a398218b39e804ab9f1767d 100644
--- a/src/main/java/caosdb/server/resource/InfoResource.java
+++ b/src/main/java/caosdb/server/resource/InfoResource.java
@@ -30,10 +30,15 @@ import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.restlet.representation.Representation;
-import org.restlet.resource.Options;
+/** This class represents the information retrieved by /Info requests (only GET) to CaosDB. */
public class InfoResource extends AbstractCaosDBServerResource {
+ /**
+ * The response to the HTTP GET request is generated here.
+ *
+ * @return The response code for OK and the resulting info XML document.
+ */
@Override
protected Representation httpGetInChildClass() throws Exception {
final Document doc = new Document();
@@ -45,14 +50,10 @@ public class InfoResource extends AbstractCaosDBServerResource {
return ok(doc);
}
+ /** There is no POST request specified for the /Info resource. */
@Override
protected Representation httpPostInChildClass(final Representation entity)
throws ConnectionException, JDOMException {
return null;
}
-
- @Options
- public static Representation describeResource() {
- return null;
- }
}
diff --git a/src/main/java/caosdb/server/resource/ScriptingResource.java b/src/main/java/caosdb/server/resource/ScriptingResource.java
index 81a84ab631d9cd2206fd163b5c64eaac4c967286..57ada4aa7b4ed2a588e7de6e50c85de1b7fb6670 100644
--- a/src/main/java/caosdb/server/resource/ScriptingResource.java
+++ b/src/main/java/caosdb/server/resource/ScriptingResource.java
@@ -27,6 +27,7 @@ package caosdb.server.resource;
import caosdb.server.FileSystem;
import caosdb.server.accessControl.Principal;
import caosdb.server.accessControl.SessionToken;
+import caosdb.server.accessControl.UserSources;
import caosdb.server.entity.FileProperties;
import caosdb.server.entity.Message;
import caosdb.server.scripting.CallerSerializer;
@@ -82,6 +83,9 @@ public class ScriptingResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpPostInChildClass(Representation entity) throws Exception {
+ if (isAnonymous()) {
+ return error(ServerMessages.AUTHORIZATION_ERROR, Status.CLIENT_ERROR_FORBIDDEN);
+ }
MediaType mediaType = entity.getMediaType();
try {
if (mediaType.equals(MediaType.MULTIPART_FORM_DATA, true)) {
@@ -202,6 +206,11 @@ public class ScriptingResource extends AbstractCaosDBServerResource {
return SessionToken.generate((Principal) getUser().getPrincipal(), null);
}
+ boolean isAnonymous() {
+ boolean ret = getUser().hasRole(UserSources.ANONYMOUS_ROLE);
+ return ret;
+ }
+
public int callScript(
List<String> commandLine, Integer timeoutMs, List<FileProperties> files, Object authToken)
throws Message {
diff --git a/src/main/java/caosdb/server/resource/transaction/EntityResource.java b/src/main/java/caosdb/server/resource/transaction/EntityResource.java
index 0e78c46a1f20fd870aca972f5c272c38c78438d0..f55c2b7ae0cb736305086ae131c3a3eeac1ba0ab 100644
--- a/src/main/java/caosdb/server/resource/transaction/EntityResource.java
+++ b/src/main/java/caosdb/server/resource/transaction/EntityResource.java
@@ -99,6 +99,7 @@ public class EntityResource extends AbstractCaosDBServerResource {
throws ConnectionException, IOException, SQLException, CaosDBException,
NoSuchAlgorithmException, Exception {
+ final long t1 = System.currentTimeMillis();
if (!this.get) {
getResponse().setStatus(Status.CLIENT_ERROR_METHOD_NOT_ALLOWED);
return null;
@@ -112,6 +113,10 @@ public class EntityResource extends AbstractCaosDBServerResource {
final Retrieve retrieve = new Retrieve(entityContainer);
retrieve.execute();
+ final long t2 = System.currentTimeMillis();
+ entityContainer
+ .getTransactionBenchmark()
+ .addBenchmark(getClass().getSimpleName() + ".httpGetInChildClass", t2 - t1);
final Element rootElem = generateRootElement();
entityContainer.addToElement(rootElem);
doc.setRootElement(rootElem);
diff --git a/src/main/java/caosdb/server/scripting/ServerSideScriptingCaller.java b/src/main/java/caosdb/server/scripting/ServerSideScriptingCaller.java
index 7af6ba1ca5ac15868f991e6a2a8c7e85b2847bd7..6fa5d1a479df47c20d9d3a5d3a7134e1c0898ad1 100644
--- a/src/main/java/caosdb/server/scripting/ServerSideScriptingCaller.java
+++ b/src/main/java/caosdb/server/scripting/ServerSideScriptingCaller.java
@@ -25,7 +25,9 @@
package caosdb.server.scripting;
import caosdb.server.CaosDBException;
+import caosdb.server.CaosDBServer;
import caosdb.server.FileSystem;
+import caosdb.server.ServerProperties;
import caosdb.server.entity.FileProperties;
import caosdb.server.entity.Message;
import caosdb.server.utils.ServerMessages;
@@ -54,6 +56,7 @@ public class ServerSideScriptingCaller {
private ScriptingUtils utils;
private List<FileProperties> files;
private File workingDir;
+ private File tmpHome;
private File sharedDir;
private Object authToken;
private Map<String, String> env;
@@ -110,6 +113,7 @@ public class ServerSideScriptingCaller {
this.authToken = authToken;
this.env = env;
this.workingDir = workingDir;
+ this.tmpHome = (new File(getTmpWorkingDir(), "temphome")).getAbsoluteFile();
this.stdOutFile = utils.getStdOutFile(workingDir);
this.stdErrFile = utils.getStdErrFile(workingDir);
}
@@ -122,6 +126,7 @@ public class ServerSideScriptingCaller {
createWorkingDir();
putFilesInWorkingDir(files);
createSharedDir();
+ createTmpHomeDir();
updateEnvironment();
} catch (final Exception e) {
e.printStackTrace();
@@ -171,17 +176,41 @@ public class ServerSideScriptingCaller {
}
// create working dir
- getTmpWorkingDir().mkdirs();
+ if (!getTmpWorkingDir().mkdirs()) {
+ throw new Exception("Creating the temporary working dir failed.");
+ }
}
- /** Creates a temporary directory for shareing by the script and sets `sharedDir` accordingly. */
+ /**
+ * Create a writable "home like" directory, needed for some Python libs, e.g. caosdb-pylib.
+ *
+ * <p>The temporary working directory must exist when this method is called.
+ */
+ void createTmpHomeDir() throws Exception, IOException {
+ if (!getTmpWorkingDir().exists()) {
+ throw new Exception(
+ "The temp working dir ("
+ + getTmpWorkingDir().toString()
+ + ") must exist before the home dir can be created.");
+ }
+ if (getTmpHomeDir().exists()) {
+ throw new Exception("The home directory must be non-existing when the caller is invoked.");
+ }
+ File srcDir =
+ new File(
+ CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_HOME_DIR));
+ FileUtils.copyDirectory(srcDir, this.tmpHome);
+ }
+
+ /** Creates a temporary directory for sharing by the script and sets `sharedDir` accordingly. */
void createSharedDir() throws Exception {
sharedDir = new File(FileSystem.assertDir(null));
}
/** Sets environment variables for the script, according to the current state of the caller. */
- void updateEnvironment() {
+ void updateEnvironment() throws Exception {
env.put("SHARED_DIR", sharedDir.toString());
+ env.put("HOME", tmpHome.toString());
}
void cleanup() {
@@ -263,6 +292,10 @@ public class ServerSideScriptingCaller {
return this.workingDir;
}
+ File getTmpHomeDir() {
+ return this.tmpHome;
+ }
+
File getSharedDir() {
return this.sharedDir;
}
diff --git a/src/main/java/caosdb/server/utils/FileUtils.java b/src/main/java/caosdb/server/utils/FileUtils.java
index 7441e73c1223f39d31ce4017618572486dfd8a64..824646caab6983863acd7d35a276a1213b393235 100644
--- a/src/main/java/caosdb/server/utils/FileUtils.java
+++ b/src/main/java/caosdb/server/utils/FileUtils.java
@@ -303,17 +303,34 @@ public class FileUtils {
return java.nio.file.Files.isDirectory(file.toPath(), LinkOption.NOFOLLOW_LINKS);
}
- private static void moveReplace(File file, File target) throws IOException {
+ private static void moveReplace(File file, File target)
+ throws IOException, CaosDBException, InterruptedException {
if (exists(target)) {
org.apache.commons.io.FileUtils.forceDelete(target);
}
if (isDir(file)) {
org.apache.commons.io.FileUtils.moveDirectory(file, target);
+ } else if (isSymlink(file)) {
+ moveSymlink(file, target);
} else {
org.apache.commons.io.FileUtils.moveFile(file, target);
}
}
+ /**
+ * @param oldlink
+ * @param newlink
+ * @throws IOException
+ * @throws InterruptedException
+ * @throws CaosDBException
+ */
+ private static void moveSymlink(File oldlink, File newlink)
+ throws IOException, CaosDBException, InterruptedException {
+ File target = oldlink.toPath().toRealPath().toFile();
+ createSymlink(newlink, target);
+ callPosixUnlink(oldlink);
+ }
+
public static Undoable rename(final File file, final File target) throws Message, IOException {
final File backup;
if (target.getAbsoluteFile().equals(file.getAbsoluteFile())) {
@@ -325,16 +342,16 @@ public class FileUtils {
public void cleanUp() {}
};
}
- if (exists(target)) {
- // in case this is a update transaction, the old version of the file
- // must be stored somewhere until the transaction is done.
- final File tmp = getTmpFile(target.getName());
- moveReplace(target, tmp);
- backup = tmp;
- } else {
- backup = null;
- }
try {
+ if (exists(target)) {
+ // in case this is a update transaction, the old version of the file
+ // must be stored somewhere until the transaction is done.
+ final File tmp = getTmpFile(target.getName());
+ moveReplace(target, tmp);
+ backup = tmp;
+ } else {
+ backup = null;
+ }
moveReplace(file, target);
return new UndoHandler() {
@@ -383,7 +400,8 @@ public class FileUtils {
org.apache.commons.io.FileUtils.forceDelete(file);
}
- public static Undoable delete(final File file) throws IOException {
+ public static Undoable delete(final File file)
+ throws IOException, CaosDBException, InterruptedException {
return delete(file, false);
}
@@ -397,8 +415,11 @@ public class FileUtils {
* @param recursive
* @return
* @throws IOException
+ * @throws InterruptedException
+ * @throws CaosDBException
*/
- public static Undoable delete(final File file, final boolean recursive) throws IOException {
+ public static Undoable delete(final File file, final boolean recursive)
+ throws IOException, CaosDBException, InterruptedException {
if (file.exists() && file.isFile()) {
// delete file
final File backup = getTmpFile(file.getName());
@@ -496,18 +517,22 @@ public class FileUtils {
return isSymbolicLink(file.toPath());
}
- public static Undoable unlink(final File file)
- throws IOException, InterruptedException, CaosDBException {
- final String target = file.getCanonicalPath();
+ private static void callPosixUnlink(File file) throws IOException, InterruptedException {
final Process cmd = Runtime.getRuntime().exec("unlink " + file.getAbsolutePath());
if (cmd.waitFor() != 0) {
throw new CaosDBException("could not unlink " + file.getAbsolutePath());
}
+ }
+
+ public static Undoable unlink(final File file) throws IOException, InterruptedException {
+ callPosixUnlink(file);
+
+ final String path = file.getCanonicalPath();
return new Undoable() {
@Override
public void undo() {
try {
- Runtime.getRuntime().exec("ln -s " + target + " " + file.getAbsolutePath());
+ Runtime.getRuntime().exec("ln -s " + path + " " + file.getAbsolutePath());
} catch (final IOException e) {
e.printStackTrace();
}
diff --git a/src/main/java/caosdb/server/utils/Info.java b/src/main/java/caosdb/server/utils/Info.java
index bba346716624f3802aac449b86b2191c7cbcee10..445374a105fbe8fbff1bc95a90fcceba197b09f4 100644
--- a/src/main/java/caosdb/server/utils/Info.java
+++ b/src/main/java/caosdb/server/utils/Info.java
@@ -95,6 +95,18 @@ public class Info extends AbstractObservable implements Observer, TransactionInt
return recordTypesCount;
}
+ /**
+ * Utility function that takes an array of file objects and returns a linked list containing XML
+ * representations of all files within each contained directory. All files in the array that are
+ * directories are recursively traversed. This function is used for files within the drop off box
+ * only.
+ *
+ * @param files An array of file objects.
+ * @return A linked list containing XML elements. The path attribute of these elements is set to
+ * the absolute path of the filenames where the path to the drop off box is removed at the
+ * beginning.
+ * @fixme Should check if the files are inside the DropOffBox path.
+ */
private static LinkedList<Element> getFlatList(final File[] files) {
try {
final LinkedList<Element> ret = new LinkedList<Element>();
@@ -104,7 +116,7 @@ public class Info extends AbstractObservable implements Observer, TransactionInt
} else {
final Element element = new Element("file");
final String tempPath =
- file.getAbsolutePath().substring(dropOffBox.getCanonicalPath().length() + 1);
+ file.getCanonicalPath().substring(dropOffBox.getCanonicalPath().length() + 1);
element.setAttribute("path", tempPath);
ret.add(element);
}
@@ -158,6 +170,22 @@ public class Info extends AbstractObservable implements Observer, TransactionInt
return toElement(false);
}
+ /**
+ * Generates an XML element showing the information for the /Info resource in CaosDB.
+ *
+ * @return An XML element containing:
+ * <ul>
+ * <li>The number of records
+ * <li>The number of properties
+ * <li>The number of record types
+ * <li>The number of files
+ * <li>The total file size
+ * <li>The number of temp files
+ * <li>The path of the DropOffBox
+ * <li>A tree of files in the DropOffBox
+ * </ul>
+ * TODO: The error format for missing or not readable drop off box has to be specified.
+ */
public static Element toElement(final boolean tree) throws Exception, SQLException {
dropOffBox = new File(FileSystem.getDropOffBox());
final Element info = new Element("Stats");
@@ -173,14 +201,20 @@ public class Info extends AbstractObservable implements Observer, TransactionInt
}
final Element e = new Element("dropOffBox");
if (dropOffBox.isDirectory()) {
- if (tree) {
- e.setAttribute("path", dropOffBox.getAbsolutePath());
- e.addContent(getTree(dropOffBox.listFiles()));
+ if (dropOffBox.canRead()) {
+ if (tree) {
+ e.setAttribute("path", dropOffBox.getAbsolutePath());
+ e.addContent(getTree(dropOffBox.listFiles()));
+ } else {
+ e.setAttribute("path", dropOffBox.getAbsolutePath());
+ e.addContent(getFlatList(dropOffBox.listFiles()));
+ }
} else {
- e.setAttribute("path", dropOffBox.getAbsolutePath());
- e.addContent(getFlatList(dropOffBox.listFiles()));
+ // TODO: return a message that the DropOffBox is not readable.
}
} else {
+ // TODO: This function should at least return a message that the DropOffBox is disabled or not
+ // present.
}
info.addContent(counts);
info.addContent(e);
diff --git a/src/test/java/caosdb/server/Misc.java b/src/test/java/caosdb/server/Misc.java
index e94d91513be40459910a05559a6f526bb94e9872..92e8b198bf8cd60b8407dac4e7fcd4e9ed671a25 100644
--- a/src/test/java/caosdb/server/Misc.java
+++ b/src/test/java/caosdb/server/Misc.java
@@ -43,6 +43,7 @@ import java.util.regex.Pattern;
import org.apache.commons.jcs.JCS;
import org.apache.commons.jcs.access.CacheAccess;
import org.apache.shiro.SecurityUtils;
+import org.apache.shiro.config.Ini;
import org.apache.shiro.config.IniSecurityManagerFactory;
import org.apache.shiro.mgt.SecurityManager;
import org.apache.shiro.subject.Subject;
@@ -316,7 +317,8 @@ public class Misc {
@Test
public void testShiro() {
- final Factory<SecurityManager> factory = new IniSecurityManagerFactory();
+ Ini config = CaosDBServer.getShiroConfig();
+ final Factory<SecurityManager> factory = new IniSecurityManagerFactory(config);
final SecurityManager securityManager = factory.getInstance();
diff --git a/src/test/java/caosdb/server/logging/TestLogging.java b/src/test/java/caosdb/server/logging/TestLogging.java
index 35667f35363af5165596ea1f32fa2f96963595aa..6e35d96585683d99c81a0fc2c669d4dc977bc09a 100644
--- a/src/test/java/caosdb/server/logging/TestLogging.java
+++ b/src/test/java/caosdb/server/logging/TestLogging.java
@@ -51,6 +51,8 @@ public class TestLogging {
@Test
public void testRequestTimeLogger() {
+ Assert.assertTrue(CaosDBServer.isDebugMode());
Assert.assertFalse(request_time_logger.isErrorEnabled());
+ Assert.assertFalse(request_time_logger.isTraceEnabled());
}
}
diff --git a/src/test/java/caosdb/server/resource/TestScriptingResource.java b/src/test/java/caosdb/server/resource/TestScriptingResource.java
index 3b035fe703409605c59a77df70421e7516230376..8ea1cc2e888ceacd51213ef1d1516ede498a8267 100644
--- a/src/test/java/caosdb/server/resource/TestScriptingResource.java
+++ b/src/test/java/caosdb/server/resource/TestScriptingResource.java
@@ -23,23 +23,114 @@
package caosdb.server.resource;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import caosdb.server.CaosDBServer;
+import caosdb.server.accessControl.AuthenticationUtils;
+import caosdb.server.accessControl.CredentialsValidator;
+import caosdb.server.accessControl.Principal;
+import caosdb.server.accessControl.Role;
+import caosdb.server.accessControl.SessionToken;
+import caosdb.server.database.BackendTransaction;
+import caosdb.server.database.access.Access;
+import caosdb.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
+import caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
+import caosdb.server.database.backend.interfaces.RetrieveUserImpl;
+import caosdb.server.database.exceptions.TransactionException;
+import caosdb.server.database.proto.ProtoUser;
import caosdb.server.entity.Message;
+import caosdb.server.permissions.PermissionRule;
import java.io.IOException;
import java.util.Date;
+import java.util.HashSet;
import java.util.List;
+import org.apache.shiro.SecurityUtils;
+import org.apache.shiro.config.Ini;
+import org.apache.shiro.config.IniSecurityManagerFactory;
+import org.apache.shiro.mgt.SecurityManager;
+import org.apache.shiro.subject.Subject;
+import org.apache.shiro.util.Factory;
+import org.junit.BeforeClass;
import org.junit.Test;
import org.restlet.Request;
import org.restlet.Response;
import org.restlet.data.Form;
import org.restlet.data.MediaType;
import org.restlet.data.Method;
+import org.restlet.data.Reference;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
import org.restlet.representation.StringRepresentation;
public class TestScriptingResource {
+ public static class RetrieveRole implements RetrieveRoleImpl {
+
+ public RetrieveRole(Access a) {}
+
+ @Override
+ public Role retrieve(String role) throws TransactionException {
+ Role ret = new Role();
+ ret.name = "anonymous";
+ ret.description = "bla";
+ return ret;
+ }
+ }
+
+ public static class RetrievePermissionRules implements RetrievePermissionRulesImpl {
+
+ public RetrievePermissionRules(Access a) {}
+
+ @Override
+ public HashSet<PermissionRule> retrievePermissionRule(String role) throws TransactionException {
+ return new HashSet<>();
+ }
+ }
+
+ public static class RetrieveUser implements RetrieveUserImpl {
+
+ public RetrieveUser(Access a) {}
+
+ @Override
+ public ProtoUser execute(Principal principal) throws TransactionException {
+ return new ProtoUser();
+ }
+ }
+
+ public static class RetrievePasswordValidator implements RetrievePasswordValidatorImpl {
+
+ public RetrievePasswordValidator(Access a) {}
+
+ @Override
+ public CredentialsValidator<String> execute(String name) throws TransactionException {
+ return new CredentialsValidator<String>() {
+
+ @Override
+ public boolean isValid(String credential) {
+ return true;
+ }
+ };
+ }
+ }
+
+ @BeforeClass
+ public static void setupShiro() throws IOException {
+ BackendTransaction.setImpl(RetrieveRoleImpl.class, RetrieveRole.class);
+ BackendTransaction.setImpl(RetrievePermissionRulesImpl.class, RetrievePermissionRules.class);
+ BackendTransaction.setImpl(RetrieveUserImpl.class, RetrieveUser.class);
+ BackendTransaction.setImpl(
+ RetrievePasswordValidatorImpl.class, RetrievePasswordValidator.class);
+
+ CaosDBServer.initServerProperties();
+ Ini config = CaosDBServer.getShiroConfig();
+ final Factory<SecurityManager> factory = new IniSecurityManagerFactory(config);
+
+ final SecurityManager securityManager = factory.getInstance();
+
+ SecurityUtils.setSecurityManager(securityManager);
+ }
+
ScriptingResource resource =
new ScriptingResource() {
@Override
@@ -60,6 +151,12 @@ public class TestScriptingResource {
@Test
public void testUnsupportedMediaType() {
+ Subject user = SecurityUtils.getSubject();
+ if (user.isAuthenticated()) {
+ user.logout();
+ }
+ SessionToken t = SessionToken.generate(new Principal("CaosDB", "user"), null);
+ user.login(t);
Representation entity = new StringRepresentation("asdf");
entity.setMediaType(MediaType.TEXT_ALL);
Request request = new Request(Method.POST, "../test", entity);
@@ -70,6 +167,23 @@ public class TestScriptingResource {
assertEquals(Status.CLIENT_ERROR_UNSUPPORTED_MEDIA_TYPE, resource.getResponse().getStatus());
}
+ @Test
+ public void testAnonymous() {
+ Subject user = SecurityUtils.getSubject();
+ user.login(AuthenticationUtils.ANONYMOUS_USER);
+ assertTrue(resource.isAnonymous());
+ Representation entity = new StringRepresentation("asdf");
+ entity.setMediaType(MediaType.TEXT_ALL);
+ Request request = new Request(Method.POST, "../test", entity);
+ request.setRootRef(new Reference("bla"));
+ request.getAttributes().put("SRID", "asdf1234");
+ request.setDate(new Date());
+ resource.init(null, request, new Response(null));
+
+ resource.handle();
+ assertEquals(Status.CLIENT_ERROR_FORBIDDEN, resource.getResponse().getStatus());
+ }
+
@Test
public void testForm2invocation() throws Message {
Form form =
diff --git a/src/test/java/caosdb/server/scripting/TestServerSideScriptingCaller.java b/src/test/java/caosdb/server/scripting/TestServerSideScriptingCaller.java
index 668d75fbc9271babc8df20a872f661d3bd0a9646..f752c29c2f99b33d30a75ff3e09c7043c92fc464 100644
--- a/src/test/java/caosdb/server/scripting/TestServerSideScriptingCaller.java
+++ b/src/test/java/caosdb/server/scripting/TestServerSideScriptingCaller.java
@@ -492,6 +492,9 @@ public class TestServerSideScriptingCaller extends CaosDBTestClass {
public void putFilesInWorkingDir(final Collection<FileProperties> files)
throws FileNotFoundException, CaosDBException {}
+ @Override
+ public void createTmpHomeDir() throws Exception {}
+
@Override
public int callScript() throws IOException {
throw new IOException();
@@ -609,4 +612,76 @@ public class TestServerSideScriptingCaller extends CaosDBTestClass {
null, -1, null, "authToken", emptyEnv, new ScriptingUtils(), this.pwd);
caller.cleanup();
}
+
+ /** Does the order of directory creation matter? */
+ @Test
+ public void testDirectoriesInWrongOrder() throws Message {
+ final String[] cmd = {testExecutable.getAbsolutePath()};
+ final ServerSideScriptingCaller caller =
+ new ServerSideScriptingCaller(
+ cmd, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
+ this.exception.expect(
+ new BaseMatcher<Exception>() {
+
+ @Override
+ public boolean matches(final Object item) {
+ return item == ServerMessages.SERVER_SIDE_SCRIPT_ERROR;
+ }
+
+ @Override
+ public void describeTo(final Description description) {
+ description.appendValue(ServerMessages.SERVER_SIDE_SCRIPT_ERROR);
+ }
+ });
+ try {
+ caller.createTmpHomeDir();
+ caller.createWorkingDir();
+ } catch (final Exception e) {
+ e.printStackTrace();
+ throw ServerMessages.SERVER_SIDE_SCRIPT_ERROR;
+ }
+ caller.cleanup();
+ }
+
+ /** Is the new home directory created correctly? */
+ @Test
+ public void testWorkingDirCreation() throws Exception {
+ final String[] cmd = {testExecutable.getAbsolutePath()};
+ final ServerSideScriptingCaller caller =
+ new ServerSideScriptingCaller(
+ cmd, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
+ caller.createWorkingDir();
+ caller.createTmpHomeDir();
+ assertTrue(caller.getTmpHomeDir().exists());
+ caller.cleanup();
+ }
+
+ /** Does copying files over to the new home directory work? */
+ @Test
+ public void testWorkingDirCopying() throws Exception {
+ final String[] cmd = {testExecutable.getAbsolutePath()};
+ final ServerSideScriptingCaller caller =
+ new ServerSideScriptingCaller(
+ cmd, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
+ caller.createWorkingDir();
+ // Create source folder in working directory
+ String scriptingHomeDir = CaosDBServer.getServerProperty("SERVER_SIDE_SCRIPTING_HOME_DIR");
+ File tempHomeDirSrc = new File(caller.getTmpWorkingDir(), "home_source");
+ CaosDBServer.setProperty("SERVER_SIDE_SCRIPTING_HOME_DIR", tempHomeDirSrc.toString());
+ tempHomeDirSrc.mkdir();
+ String testFileName = "testfile.txt";
+ String testContent = "sloikdfgu89w4t78930tvgyum9q238456t27ht2";
+ File testFile = new File(tempHomeDirSrc, testFileName);
+ // testFile.createNewFile();
+ FileUtils.write(testFile, testContent, "UTF-8");
+ // Attempt to copy the source to the new home
+ caller.createTmpHomeDir();
+ // Compare source and new home
+ File expectedFile = new File(caller.getTmpHomeDir(), testFileName);
+ assertTrue(expectedFile.exists());
+ String expectedFileContent = FileUtils.readFileToString(expectedFile, "UTF-8");
+ assertEquals(expectedFileContent, testContent);
+ caller.cleanup();
+ CaosDBServer.setProperty("SERVER_SIDE_SCRIPTING_HOME_DIR", scriptingHomeDir);
+ }
}
diff --git a/src/test/java/caosdb/server/utils/FileUtilsTest.java b/src/test/java/caosdb/server/utils/FileUtilsTest.java
index 183f5cf834783f7ad9c6e63bcdb25df1c7870822..c80f8ebb8b71785dcf8b6f5c8adaaec5e61b0332 100644
--- a/src/test/java/caosdb/server/utils/FileUtilsTest.java
+++ b/src/test/java/caosdb/server/utils/FileUtilsTest.java
@@ -69,9 +69,11 @@ public class FileUtilsTest {
public static File tmpFolderCaosDB;
@BeforeClass
- public static void setup() throws Message, IOException {
+ public static void setup() throws Message, IOException, CaosDBException, InterruptedException {
CaosDBServer.initServerProperties();
testRoot = tempFolder.newFolder("fileutils_testfolder");
+ File basePath = tempFolder.newFolder("caosdbRoot");
+ File dropOffBox = tempFolder.newFolder("dropOffBox");
someDir = testRoot.toPath().resolve("some_dir").toFile();
linkToSomeDir = testRoot.toPath().resolve("link_to_some_dir").toFile();
someFile = testRoot.toPath().resolve("some_file").toFile();
@@ -79,12 +81,15 @@ public class FileUtilsTest {
linkToSomeFile = testRoot.toPath().resolve("link_to_some_file").toFile();
tmpFolderCaosDB = tempFolder.newFolder();
+ CaosDBServer.setProperty(ServerProperties.KEY_FILE_SYSTEM_ROOT, basePath.toString());
+ CaosDBServer.setProperty(ServerProperties.KEY_DROP_OFF_BOX, dropOffBox.toString());
CaosDBServer.setProperty(ServerProperties.KEY_TMP_FILES, tmpFolderCaosDB.toString());
FileSystem.init();
- Assert.assertTrue(new File(FileSystem.getBasepath()).canWrite());
- Assert.assertTrue(new File(FileSystem.getBasepath()).canRead());
- Assert.assertTrue(new File(FileSystem.getBasepath()).canExecute());
+ basePath = new File(FileSystem.getBasepath());
+ Assert.assertTrue(basePath.canWrite());
+ Assert.assertTrue(basePath.canRead());
+ Assert.assertTrue(basePath.canExecute());
Assert.assertTrue(new File(FileSystem.getTmp()).canWrite());
Assert.assertTrue(new File(FileSystem.getTmp()).canRead());
Assert.assertTrue(new File(FileSystem.getTmp()).canExecute());
@@ -102,7 +107,7 @@ public class FileUtilsTest {
}
@AfterClass
- public static void teardown() throws IOException {
+ public static void teardown() throws IOException, CaosDBException, InterruptedException {
System.err.println("teardown");
FileUtils.delete(testRoot, true);
deleteTmp();
@@ -110,9 +115,13 @@ public class FileUtilsTest {
// assertEquals(0, new File(FileSystem.getTmp()).listFiles().length);
}
- /** @fixme Currently still fails due to https://github.com/junit-team/junit4/issues/1223 */
+ /**
+ * @throws InterruptedException
+ * @throws CaosDBException
+ * @fixme Currently still fails due to https://github.com/junit-team/junit4/issues/1223
+ */
@Before
- public void testTmpEmpty() throws IOException {
+ public void testTmpEmpty() throws IOException, CaosDBException, InterruptedException {
if (new File(FileSystem.getTmp()).exists()) {
if (0 != new File(FileSystem.getTmp()).list().length) {
System.err.println("TMP not empty, aborting test!");
@@ -128,7 +137,7 @@ public class FileUtilsTest {
}
}
- public static void deleteTmp() throws IOException {
+ public static void deleteTmp() throws IOException, CaosDBException, InterruptedException {
File tmpDir = new File(FileSystem.getTmp());
if (tmpDir.exists())
for (File f : tmpDir.listFiles()) {
@@ -138,7 +147,7 @@ public class FileUtilsTest {
}
@After
- public void callDeleteTmp() throws IOException {
+ public void callDeleteTmp() throws IOException, CaosDBException, InterruptedException {
deleteTmp();
}