diff --git a/openbis_knime.feature/.project b/openbis_knime.feature/.project
deleted file mode 100644
index bd91633c3b933612c510cb314f20dca91737cfe2..0000000000000000000000000000000000000000
--- a/openbis_knime.feature/.project
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>openbis_knime.feature</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.pde.FeatureBuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.pde.FeatureNature</nature>
- </natures>
-</projectDescription>
diff --git a/openbis_knime.feature/build.properties b/openbis_knime.feature/build.properties
deleted file mode 100644
index 64f93a9f0b7328eb563aa5ad6cec7f828020e124..0000000000000000000000000000000000000000
--- a/openbis_knime.feature/build.properties
+++ /dev/null
@@ -1 +0,0 @@
-bin.includes = feature.xml
diff --git a/openbis_knime.feature/feature.xml b/openbis_knime.feature/feature.xml
deleted file mode 100644
index 07144c3ad968320fe5ef20398fe1b2545840304b..0000000000000000000000000000000000000000
--- a/openbis_knime.feature/feature.xml
+++ /dev/null
@@ -1,45 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<feature
- id="ch.systemsx.cisd.openbis.knime.feature"
- label="openBIS Knime Nodes"
- version="13.6.2.qualifier"
- provider-name="ID Scientific IT Services ETH Zürich">
-
- <description url="https://wiki-bsse.ethz.ch/display/openBISDoc1304/openBIS+KNIME+Nodes">
- KNIME Nodes to access openBIS
- </description>
-
- <copyright>
- Copyright 2013-2014 ETH Zuerich, CISD
- </copyright>
-
- <license url="http://www.apache.org/licenses/LICENSE-2.0">
- Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express
-or implied.
-See the License for the specific language governing permissions
-and limitations under the License.
- </license>
-
- <requires>
- <import plugin="org.eclipse.core.runtime"/>
- <import plugin="org.knime.workbench.core"/>
- <import plugin="org.knime.workbench.repository"/>
- <import plugin="org.knime.base"/>
- <import plugin="org.knime.core.data.uritype"/>
- </requires>
-
- <plugin
- id="ch.systemsx.cisd.openbis.knime"
- download-size="0"
- install-size="0"
- version="0.0.0"/>
-
-</feature>
diff --git a/openbis_knime.update-site/site.xml b/openbis_knime.update-site/site.xml
deleted file mode 100644
index c43fed55e393fd914e97e35393c7f06ca13cc57f..0000000000000000000000000000000000000000
--- a/openbis_knime.update-site/site.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<site>
- <category-def name="openBIS KNIME Nodes" label="openBIS KNIME Nodes">
- <description>
- Nodes for integreting openBIS into a KNIME workflow.
- </description>
- </category-def>
-</site>
diff --git a/openbis_knime/.classpath b/openbis_knime/.classpath
deleted file mode 100644
index 871772584a61fc4721dc524b1decf877a5535072..0000000000000000000000000000000000000000
--- a/openbis_knime/.classpath
+++ /dev/null
@@ -1,45 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" path="source/java"/>
- <classpathentry kind="src" path="sourceTest/java"/>
- <classpathentry kind="src" path="sourceEclipse/java"/>
- <classpathentry exported="true" kind="lib" path="lib/dss_client-S224.0-r35783.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/openBIS-query-API-S224.0-r35783.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/aopalliance-1.0.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/aspectjweaver-1.8.4.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/commons-codec-1.3.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/commons-io-1.4.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/commons-lang-2.4.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/commons-logging-1.2.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/httpclient-4.3.6.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/httpcore-4.3.3.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/log4j-1.2.15.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/spring-aop-4.1.4.RELEASE.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/spring-beans-4.1.4.RELEASE.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/spring-context-4.1.4.RELEASE.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/spring-core-4.1.4.RELEASE.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/spring-expression-4.1.4.RELEASE.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/spring-webmvc-4.1.4.RELEASE.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/spring-web-4.1.4.RELEASE.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/marathon-spring-util-1.2.5.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/sis-base-14.12.0.jar"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
- <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
- <classpathentry kind="lib" path="/libraries/commons-logging/commons-logging.jar" sourcepath="/libraries/commons-logging/src.zip"/>
- <classpathentry kind="lib" path="/libraries/commons-lang/commons-lang.jar" sourcepath="/libraries/commons-lang/src.zip"/>
- <classpathentry kind="lib" path="/libraries/commons-io/commons-io.jar" sourcepath="/libraries/commons-io/src.zip"/>
- <classpathentry kind="lib" path="/libraries/log4j/log4j.jar" sourcepath="/libraries/log4j/src.zip"/>
- <classpathentry kind="lib" path="/libraries/knime/knime-core-util.jar"/>
- <classpathentry kind="lib" path="/libraries/knime/knime-base.jar"/>
- <classpathentry kind="lib" path="/libraries/knime/knime-core.jar"/>
- <classpathentry kind="lib" path="/libraries/knime/knime-core-data-uritype.jar"/>
- <classpathentry kind="lib" path="/libraries/testng/testng-jdk15.jar" sourcepath="/libraries/testng/src.zip"/>
- <classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-core.jar"/>
- <classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-library.jar"/>
- <classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/>
- <classpathentry kind="lib" path="/libraries/sis-base/sis-base.jar" sourcepath="/libraries/sis-base/sis-base-src.zip"/>
- <classpathentry kind="lib" path="/libraries/openbis-apis/dss/dss_client.jar"/>
- <classpathentry kind="lib" path="/libraries/openbis-apis/query/openbis-query-api.jar" sourcepath="/libraries/openbis-apis/query/src.zip"/>
- <classpathentry kind="lib" path="/libraries/activation/activation.jar"/>
- <classpathentry kind="output" path="targets/classes"/>
-</classpath>
diff --git a/openbis_knime/.gitignore b/openbis_knime/.gitignore
deleted file mode 100644
index 9bb9bd28649c26afb3ac9dcdfc59738701ab4dbb..0000000000000000000000000000000000000000
--- a/openbis_knime/.gitignore
+++ /dev/null
@@ -1,6 +0,0 @@
-/targets
-/.settings
-/test-output
-/.idea/
-*.iml
-*.eml
\ No newline at end of file
diff --git a/openbis_knime/.project b/openbis_knime/.project
deleted file mode 100644
index 35a88dba01f7267159259327ead4c965deda9be9..0000000000000000000000000000000000000000
--- a/openbis_knime/.project
+++ /dev/null
@@ -1,29 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>openbis_knime</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.springsource.ide.eclipse.gradle.core.nature</nature>
- <nature>org.eclipse.jdt.core.javanature</nature>
- </natures>
- <filteredResources>
- <filter>
- <id>1332321366607</id>
- <name></name>
- <type>26</type>
- <matcher>
- <id>org.eclipse.ui.ide.multiFilter</id>
- <arguments>1.0-name-matches-true-false-.git</arguments>
- </matcher>
- </filter>
- </filteredResources>
-</projectDescription>
diff --git a/openbis_knime/META-INF/MANIFEST.MF b/openbis_knime/META-INF/MANIFEST.MF
deleted file mode 100644
index 135c740cc5451c045987b09a4a04731c5bde6f91..0000000000000000000000000000000000000000
--- a/openbis_knime/META-INF/MANIFEST.MF
+++ /dev/null
@@ -1,40 +0,0 @@
-Manifest-Version: 1.0
-Bundle-ManifestVersion: 2
-Bundle-Name: openBIS KNIME Nodes
-Bundle-SymbolicName: ch.systemsx.cisd.openbis.knime;singleton:=true
-Bundle-Version: 13.6.2.qualifier
-Bundle-Vendor: ID Scientific IT Services ETH Zürich
-Require-Bundle: org.knime.workbench.core,
- org.knime.base,
- org.knime.core.data.uritype,
- org.apache.commons.codec,
- org.apache.commons.httpclient,
- org.apache.commons.lang,
- org.apache.commons.io,
- org.apache.commons.logging,
- org.apache.log4j
-Bundle-RequiredExecutionEnvironment: JavaSE-1.6
-Bundle-ActivationPolicy: lazy
-Export-Package: ch.systemsx.cisd.openbis.knime.file,
- ch.systemsx.cisd.openbis.knime.query
-Bundle-ClassPath: lib/dss_client-S224.0-r35783.jar,
- lib/openBIS-query-API-S224.0-r35783.jar,
- openbis-knime.jar,
- lib/sis-base-14.12.0.jar,
- lib/aspectjweaver-1.8.4.jar,
- lib/commons-codec-1.3.jar,
- lib/commons-io-1.4.jar,
- lib/commons-lang-2.4.jar,
- lib/commons-logging-1.2.jar,
- lib/httpclient-4.3.6.jar,
- lib/httpcore-4.3.3.jar,
- lib/log4j-1.2.15.jar,
- lib/spring-aop-4.1.4.RELEASE.jar,
- lib/spring-beans-4.1.4.RELEASE.jar,
- lib/spring-context-4.1.4.RELEASE.jar,
- lib/spring-core-4.1.4.RELEASE.jar,
- lib/spring-expression-4.1.4.RELEASE.jar,
- lib/spring-web-4.1.4.RELEASE.jar,
- lib/spring-webmvc-4.1.4.RELEASE.jar,
- lib/marathon-spring-util-1.2.5.jar,
- lib/aopalliance-1.0.jar
diff --git a/openbis_knime/build.gradle b/openbis_knime/build.gradle
deleted file mode 100644
index 1f0cce8aeaf84bcdc505869274e3f229d81a16db..0000000000000000000000000000000000000000
--- a/openbis_knime/build.gradle
+++ /dev/null
@@ -1,29 +0,0 @@
-apply from: '../gradle/javaproject.gradle'
-
-dependencies {
- api 'cisd:cisd-base:r31435',
- 'apache:log4j:1.2.15',
- 'knime:knime:2.7.2',
- 'openbis:dss:13.04.2',
- 'openbis:query:13.04.2',
- 'rinn:restrictions:1.0.2',
- 'javax.activation:activation:1.1.1'
-
- testImplementation 'testng:testng:6.8-CISD',
- 'hamcrest:hamcrest-integration:1.3',
- 'hamcrest:hamcrest-library:1.3'
-
- testImplementation ('jmock:jmock:2.5.1') {
- exclude group: 'hamcrest', module: 'hamcrest-core'
- }
-}
-
-jar {
- baseName = 'openbis-knime-server'
- from ('targets/dist') {
- include 'BUILD*INFO'
- }
- exclude 'ch/systemsx/cisd/openbis/knime/query'
- exclude 'ch/systemsx/cisd/openbis/knime/common'
- exclude 'ch/systemsx/cisd/openbis/knime/file'
-}
diff --git a/openbis_knime/build.properties b/openbis_knime/build.properties
deleted file mode 100644
index f803f8c964ca799f59d8b07e0314cdff86622bcd..0000000000000000000000000000000000000000
--- a/openbis_knime/build.properties
+++ /dev/null
@@ -1,29 +0,0 @@
-output.. = targets/classes/
-bin.includes = META-INF/,\
- plugin.xml,\
- icons/,\
- openbis-knime.jar,\
- lib/marathon-spring-util-1.2.5.jar,\
- lib/sis-base-14.12.0.jar,\
- lib/spring-web-4.1.4.RELEASE.jar,\
- lib/aspectjweaver-1.8.4.jar,\
- lib/commons-codec-1.3.jar,\
- lib/commons-io-1.4.jar,\
- lib/commons-lang-2.4.jar,\
- lib/commons-logging-1.2.jar,\
- lib/httpclient-4.3.6.jar,\
- lib/httpcore-4.3.3.jar,\
- lib/log4j-1.2.15.jar,\
- lib/spring-aop-4.1.4.RELEASE.jar,\
- lib/spring-beans-4.1.4.RELEASE.jar,\
- lib/spring-context-4.1.4.RELEASE.jar,\
- lib/spring-core-4.1.4.RELEASE.jar,\
- lib/spring-expression-4.1.4.RELEASE.jar,\
- lib/spring-webmvc-4.1.4.RELEASE.jar,\
- lib/aopalliance-1.0.jar,\
- lib/openBIS-query-API-S224.0-r35783.jar,\
- lib/dss_client-S224.0-r35783.jar
-source.openbis-knime.jar = source/java/,\
- sourceEclipse/java/
-src.includes = source/java/,\
- sourceEclipse/java/
diff --git a/openbis_knime/build/build.xml b/openbis_knime/build/build.xml
deleted file mode 100644
index 29ec1e15752182e6f1d81bf19f82f89cc38b6501..0000000000000000000000000000000000000000
--- a/openbis_knime/build/build.xml
+++ /dev/null
@@ -1,60 +0,0 @@
-<project name="openbis_knime" default="ci" basedir="..">
- <import file="../../build_resources/ant/build-common.xml" />
- <project-classpath name="ecp" classes="${classes}" />
- <property name="mainfolder" value="openbis_knime"/>
- <property name="original.dist" value="../${ant.project.name}/dist" />
- <loadproperties srcfile="META-INF/MANIFEST.MF">
- <filterchain>
- <tokenfilter>
- <replacestring from=".qualifier" to=""/>
- </tokenfilter>
- </filterchain>
- </loadproperties>
- <property name="version" value="${Bundle-Version}"/>
- <property name="jar.file" value="${dist}/openbis-knime-server-${version}.jar"/>
-
- <!--
- // Cleans distribution directory.
- -->
- <target name="clean" description="Cleans distribution directory.">
- <delete dir="${dist}" failonerror="true" />
- <mkdir dir="${dist}" />
- </target>
-
- <!--
- // Runs tests.
- -->
- <target name="run-tests">
- <antcall target="build-common.run-tests">
- <param name="test.suite" value="tests.xml" />
- </antcall>
- </target>
-
- <!--
- // Creates build information.
- -->
- <target name="build-info" description="Creates build information.">
- <build-info revision="revision.number" version="version.number" clean="clean.flag" />
- <echo file="${build.info.file}">${version}:${revision.number}:${clean.flag}</echo>
- </target>
-
- <!--
- // Creates server JAR file.
- -->
- <target name="server-jar" depends="compile, build-info" description="Creates project jar file.">
- <delete file="${jar.file}" />
- <recursive-jar destfile="${jar.file}">
- <fileset dir="${classes}">
- <include name="**/server/*.class" />
- <include name="${build.info.filename}" />
- </fileset>
- </recursive-jar>
- </target>
-
- <!--
- // Task for continuous integration server.
- -->
- <target name="ci" depends="build-common.ci, check-dependencies, server-jar"
- description="Task for continuous integration server." />
-
-</project>
\ No newline at end of file
diff --git a/openbis_knime/developer-readme.txt b/openbis_knime/developer-readme.txt
deleted file mode 100644
index 783bfc23f1653863b08938f7232cffc3fb35ddf3..0000000000000000000000000000000000000000
--- a/openbis_knime/developer-readme.txt
+++ /dev/null
@@ -1,49 +0,0 @@
-This short text explain how to do development, build and deployment of openBIS KNIME nodes.
-Here some important remarks because this is not a project like the other ones:
-* Build has to be done manually as described below.
-* The gradle build script creates only openbis-knime-server.jar which has helper classes for DSS aggregation plugins.
-* The 3th party libraries for the actual plugin are in the lib folder.
-
-Prerequisites for developing
-============================
-
-1. There are three Eclipse projects which belong together:
- openbis_knime, openbis_knime.feature and openbis_knime.update-site
- All three have to be checked out (they won't compile properly until KNIME plug-in is installed).
-2. In addition the KNIME Node Development Tools plug-in has to be installed.
- The update site is http://www.knime.org/update/3.1/
-
-Developing and Testing
-======================
-
-Just develop as normal.
-
-For unit testing do not run a test class directly but execute the eclipse launch configuration
-'openbis knime all tests'. The reason for this is that the normal default class path doesn't work.
-
-For manual integration test with KNIME do the following:
-1. Open site.xml in project openbis_knime.update-site.
-2. Click on category 'openBIS KNIME Nodes'.
-3. Click on 'Add Feature...' and choose in the pop-up dialog the feature
- ch.systemsx.cisd.openbis.knime
-4. Click on the 'Build' button. This creates/update artifacts.jar, content.jar,
- features/ and plugins/ folder of project openbis_knime.update-site
-5. Install/update openBIS KNIME Nodes of the KNIME application from the local update site
- file:/<absolut path to your Eclipse workspace>/openbis_knime.update-site
- Be sure that update site http://update.knime.org/community-contributions/3.1/ is defined for
- the KNIME application.
-
-Build and deploy a new version
-==============================
-
-1. Open plugin.xml and change the version on the overview tab. For example from
- 13.04.02.qualifier -> 13.04.03.qualifier
-2. Does the same for feature.xml in project openbis_knime.feature.
-3. Open site.xml in project openbis_knime.update-site.
-4. Click on category 'openBIS KNIME Nodes'.
-5. Click on 'Add Feature...' and choose in the pop-up dialog the feature
- ch.systemsx.cisd.openbis.knime
-6. Click on the 'Build' button. This creates/update artifacts.jar, content.jar,
- features/ and plugins/ folder of project openbis_knime.update-site
-7. Copy these two JARs and folders to openbis@lascar:/links/groups/sis/doc/openbis/knime-update-site
-
diff --git a/openbis_knime/dist/icons/openbis.png b/openbis_knime/dist/icons/openbis.png
deleted file mode 100644
index a5b30672e374063ad0b36c4469a028e9e61090d7..0000000000000000000000000000000000000000
Binary files a/openbis_knime/dist/icons/openbis.png and /dev/null differ
diff --git a/openbis_knime/etc/log.xml b/openbis_knime/etc/log.xml
deleted file mode 100644
index c437339ded6a0516430f8b148c172fccb4ec73f3..0000000000000000000000000000000000000000
--- a/openbis_knime/etc/log.xml
+++ /dev/null
@@ -1,62 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" ?>
-<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
-
-<!--
- // This configuration file is suitable for testing purposes.
--->
-<log4j:configuration debug="true" xmlns:log4j='http://jakarta.apache.org/log4j/'>
-
- <appender name="STDOUT" class="org.apache.log4j.ConsoleAppender">
- <layout class="org.apache.log4j.PatternLayout">
- <!--
- // %d: outputs the date of the logging event.
- // %-5p: priority (i.e. level) of the logging event should be left justified to
- // a width of five characters.
- // %t: outputs the name of the thread that generated the logging event.
- // %c: outputs the category of the logging event.
- // %m: outputs the application supplied message associated with the logging event.
- // %n: outputs the platform dependent line separator character or characters.
- // %X: outputs the MDC (mapped diagnostic context) associated with the thread that generated the logging event.
- -->
- <param name="ConversionPattern"
- value="%d %-5p [%t]%X{sessionInfo} %c - %m%n" />
- </layout>
- </appender>
-
- <!--
- // Defined but not used right now.
- -->
- <appender name="NULL" class="org.apache.log4j.varia.NullAppender" />
-
- <!--
- // Enable full wire (header and content) + context logging
- // For more information look at http://jakarta.apache.org/commons/httpclient/logging.html.
- // We do not need to set a level value here as loggers inherit their level from the root logger.
- -->
-
- <!--
- // Do not use log level debug otherwise plain passwords are readable.
- -->
- <logger name="httpclient.wire">
- <level value="ERROR" />
- </logger>
-
- <!--
- // Uncomment this for debugging value binding in Hibernate
- <category name="org.hibernate.type">
- <priority value="TRACE"/>
- </category>
- -->
-
- <!--
- <logger name="org.apache.commons.httpclient">
- <level value="DEBUG" />
- </logger>
- -->
-
- <root>
- <priority value="info" />
- <appender-ref ref="STDOUT" />
- </root>
-
-</log4j:configuration>
diff --git a/openbis_knime/gradle/wrapper/gradle-wrapper.jar b/openbis_knime/gradle/wrapper/gradle-wrapper.jar
deleted file mode 100644
index 5c2d1cf016b3885f6930543d57b744ea8c220a1a..0000000000000000000000000000000000000000
Binary files a/openbis_knime/gradle/wrapper/gradle-wrapper.jar and /dev/null differ
diff --git a/openbis_knime/gradle/wrapper/gradle-wrapper.properties b/openbis_knime/gradle/wrapper/gradle-wrapper.properties
deleted file mode 100644
index 7745c4ec463c7bb1c4ff6a5e58db239890345152..0000000000000000000000000000000000000000
--- a/openbis_knime/gradle/wrapper/gradle-wrapper.properties
+++ /dev/null
@@ -1,5 +0,0 @@
-distributionBase=GRADLE_USER_HOME
-distributionPath=wrapper/dists
-distributionUrl=https\://sissource.ethz.ch/openbis/openbis-public/openbis-ivy/-/raw/main/gradle/distribution/7.4/gradle-7.4-bin.zip
-zipStoreBase=GRADLE_USER_HOME
-zipStorePath=wrapper/dists
diff --git a/openbis_knime/gradlew b/openbis_knime/gradlew
deleted file mode 100755
index 83f2acfdc319a24e8766cca78f32474ad7a22dd6..0000000000000000000000000000000000000000
--- a/openbis_knime/gradlew
+++ /dev/null
@@ -1,188 +0,0 @@
-#!/usr/bin/env sh
-
-#
-# Copyright 2015 the original author or authors.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# https://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-##############################################################################
-##
-## Gradle start up script for UN*X
-##
-##############################################################################
-
-# Attempt to set APP_HOME
-# Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
- ls=`ls -ld "$PRG"`
- link=`expr "$ls" : '.*-> \(.*\)$'`
- if expr "$link" : '/.*' > /dev/null; then
- PRG="$link"
- else
- PRG=`dirname "$PRG"`"/$link"
- fi
-done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
-
-APP_NAME="Gradle"
-APP_BASE_NAME=`basename "$0"`
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
-
-# Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
-
-warn () {
- echo "$*"
-}
-
-die () {
- echo
- echo "$*"
- echo
- exit 1
-}
-
-# OS specific support (must be 'true' or 'false').
-cygwin=false
-msys=false
-darwin=false
-nonstop=false
-case "`uname`" in
- CYGWIN* )
- cygwin=true
- ;;
- Darwin* )
- darwin=true
- ;;
- MINGW* )
- msys=true
- ;;
- NONSTOP* )
- nonstop=true
- ;;
-esac
-
-CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
-
-# Determine the Java command to use to start the JVM.
-if [ -n "$JAVA_HOME" ] ; then
- if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
- # IBM's JDK on AIX uses strange locations for the executables
- JAVACMD="$JAVA_HOME/jre/sh/java"
- else
- JAVACMD="$JAVA_HOME/bin/java"
- fi
- if [ ! -x "$JAVACMD" ] ; then
- die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
-
-Please set the JAVA_HOME variable in your environment to match the
-location of your Java installation."
- fi
-else
- JAVACMD="java"
- which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-
-Please set the JAVA_HOME variable in your environment to match the
-location of your Java installation."
-fi
-
-# Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
- MAX_FD_LIMIT=`ulimit -H -n`
- if [ $? -eq 0 ] ; then
- if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
- MAX_FD="$MAX_FD_LIMIT"
- fi
- ulimit -n $MAX_FD
- if [ $? -ne 0 ] ; then
- warn "Could not set maximum file descriptor limit: $MAX_FD"
- fi
- else
- warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
- fi
-fi
-
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
- GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-fi
-
-# For Cygwin or MSYS, switch paths to Windows format before running java
-if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
- APP_HOME=`cygpath --path --mixed "$APP_HOME"`
- CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
- JAVACMD=`cygpath --unix "$JAVACMD"`
-
- # We build the pattern for arguments to be converted via cygpath
- ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
- SEP=""
- for dir in $ROOTDIRSRAW ; do
- ROOTDIRS="$ROOTDIRS$SEP$dir"
- SEP="|"
- done
- OURCYGPATTERN="(^($ROOTDIRS))"
- # Add a user-defined pattern to the cygpath arguments
- if [ "$GRADLE_CYGPATTERN" != "" ] ; then
- OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
- fi
- # Now convert the arguments - kludge to limit ourselves to /bin/sh
- i=0
- for arg in "$@" ; do
- CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
- CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
-
- if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
- eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
- else
- eval `echo args$i`="\"$arg\""
- fi
- i=$((i+1))
- done
- case $i in
- (0) set -- ;;
- (1) set -- "$args0" ;;
- (2) set -- "$args0" "$args1" ;;
- (3) set -- "$args0" "$args1" "$args2" ;;
- (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
- (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
- (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
- (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
- (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
- (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
- esac
-fi
-
-# Escape application args
-save () {
- for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
- echo " "
-}
-APP_ARGS=$(save "$@")
-
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
-
-# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
-if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
- cd "$(dirname "$0")"
-fi
-
-exec "$JAVACMD" "$@"
diff --git a/openbis_knime/gradlew.bat b/openbis_knime/gradlew.bat
deleted file mode 100644
index 24467a141f791695fc1009c78d913b2c849d1412..0000000000000000000000000000000000000000
--- a/openbis_knime/gradlew.bat
+++ /dev/null
@@ -1,100 +0,0 @@
-@rem
-@rem Copyright 2015 the original author or authors.
-@rem
-@rem Licensed under the Apache License, Version 2.0 (the "License");
-@rem you may not use this file except in compliance with the License.
-@rem You may obtain a copy of the License at
-@rem
-@rem https://www.apache.org/licenses/LICENSE-2.0
-@rem
-@rem Unless required by applicable law or agreed to in writing, software
-@rem distributed under the License is distributed on an "AS IS" BASIS,
-@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-@rem See the License for the specific language governing permissions and
-@rem limitations under the License.
-@rem
-
-@if "%DEBUG%" == "" @echo off
-@rem ##########################################################################
-@rem
-@rem Gradle startup script for Windows
-@rem
-@rem ##########################################################################
-
-@rem Set local scope for the variables with windows NT shell
-if "%OS%"=="Windows_NT" setlocal
-
-set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
-set APP_BASE_NAME=%~n0
-set APP_HOME=%DIRNAME%
-
-@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
-
-@rem Find java.exe
-if defined JAVA_HOME goto findJavaFromJavaHome
-
-set JAVA_EXE=java.exe
-%JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto init
-
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:findJavaFromJavaHome
-set JAVA_HOME=%JAVA_HOME:"=%
-set JAVA_EXE=%JAVA_HOME%/bin/java.exe
-
-if exist "%JAVA_EXE%" goto init
-
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:init
-@rem Get command-line arguments, handling Windows variants
-
-if not "%OS%" == "Windows_NT" goto win9xME_args
-
-:win9xME_args
-@rem Slurp the command line arguments.
-set CMD_LINE_ARGS=
-set _SKIP=2
-
-:win9xME_args_slurp
-if "x%~1" == "x" goto execute
-
-set CMD_LINE_ARGS=%*
-
-:execute
-@rem Setup the command line
-
-set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
-
-@rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
-
-:end
-@rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
-
-:fail
-rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
-rem the _cmd.exe /c_ return code!
-if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
-
-:mainEnd
-if "%OS%"=="Windows_NT" endlocal
-
-:omega
diff --git a/openbis_knime/icons/openBIS_logo.png b/openbis_knime/icons/openBIS_logo.png
deleted file mode 100644
index ce6b826a93b0bcf08f86a8ee8db8995de3bc96e8..0000000000000000000000000000000000000000
Binary files a/openbis_knime/icons/openBIS_logo.png and /dev/null differ
diff --git a/openbis_knime/icons/openbis.png b/openbis_knime/icons/openbis.png
deleted file mode 100644
index a5b30672e374063ad0b36c4469a028e9e61090d7..0000000000000000000000000000000000000000
Binary files a/openbis_knime/icons/openbis.png and /dev/null differ
diff --git a/openbis_knime/lib/aopalliance-1.0.jar b/openbis_knime/lib/aopalliance-1.0.jar
deleted file mode 100644
index 578b1a0c359ef88a84461bdb91d9d0041afd54de..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/aopalliance-1.0.jar and /dev/null differ
diff --git a/openbis_knime/lib/aspectjweaver-1.8.4.jar b/openbis_knime/lib/aspectjweaver-1.8.4.jar
deleted file mode 100644
index 4458ba45c367b09f840968b35d00ac0bd7658545..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/aspectjweaver-1.8.4.jar and /dev/null differ
diff --git a/openbis_knime/lib/commons-codec-1.3.jar b/openbis_knime/lib/commons-codec-1.3.jar
deleted file mode 100644
index 957b6752af9a60c1bb2a4f65db0e90e5ce00f521..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/commons-codec-1.3.jar and /dev/null differ
diff --git a/openbis_knime/lib/commons-io-1.4.jar b/openbis_knime/lib/commons-io-1.4.jar
deleted file mode 100644
index 133dc6cb35f5ca2c5920fd0933a557c2def88680..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/commons-io-1.4.jar and /dev/null differ
diff --git a/openbis_knime/lib/commons-lang-2.4.jar b/openbis_knime/lib/commons-lang-2.4.jar
deleted file mode 100644
index 532939ecab6b77ccb77af3635c55ff9752b70ab7..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/commons-lang-2.4.jar and /dev/null differ
diff --git a/openbis_knime/lib/commons-logging-1.2.jar b/openbis_knime/lib/commons-logging-1.2.jar
deleted file mode 100644
index 93a3b9f6db406c84e270e19b9a5e70f2e27ca513..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/commons-logging-1.2.jar and /dev/null differ
diff --git a/openbis_knime/lib/dss_client-S224.0-r35783.jar b/openbis_knime/lib/dss_client-S224.0-r35783.jar
deleted file mode 100644
index 63c1d7c403f157b697f9dac444f00beab99e0864..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/dss_client-S224.0-r35783.jar and /dev/null differ
diff --git a/openbis_knime/lib/httpclient-4.3.6.jar b/openbis_knime/lib/httpclient-4.3.6.jar
deleted file mode 100644
index 00e98110dfb60487ab8a4368c035bfac54ef8f8f..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/httpclient-4.3.6.jar and /dev/null differ
diff --git a/openbis_knime/lib/httpcore-4.3.3.jar b/openbis_knime/lib/httpcore-4.3.3.jar
deleted file mode 100644
index a8747b0cf91cd89d4b2785e86fcfb057e7260154..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/httpcore-4.3.3.jar and /dev/null differ
diff --git a/openbis_knime/lib/log4j-1.2.15.jar b/openbis_knime/lib/log4j-1.2.15.jar
deleted file mode 100644
index c930a6ab4d4b73c1a6feb9e929091205664bb340..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/log4j-1.2.15.jar and /dev/null differ
diff --git a/openbis_knime/lib/marathon-spring-util-1.2.5.jar b/openbis_knime/lib/marathon-spring-util-1.2.5.jar
deleted file mode 100644
index 8ad63485b88f3e8bc66346216c4ecd3c29cbee60..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/marathon-spring-util-1.2.5.jar and /dev/null differ
diff --git a/openbis_knime/lib/openBIS-query-API-S224.0-r35783.jar b/openbis_knime/lib/openBIS-query-API-S224.0-r35783.jar
deleted file mode 100644
index ee29b7c840b4a7558e5c0c87dcc52db8dce1ccaa..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/openBIS-query-API-S224.0-r35783.jar and /dev/null differ
diff --git a/openbis_knime/lib/sis-base-14.12.0.jar b/openbis_knime/lib/sis-base-14.12.0.jar
deleted file mode 100644
index ddcf2b97d0ed674650ac6dba7c8317aea59976a4..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/sis-base-14.12.0.jar and /dev/null differ
diff --git a/openbis_knime/lib/spring-aop-4.1.4.RELEASE.jar b/openbis_knime/lib/spring-aop-4.1.4.RELEASE.jar
deleted file mode 100644
index 43d00d201e9d1471194834370f362a09579e2866..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/spring-aop-4.1.4.RELEASE.jar and /dev/null differ
diff --git a/openbis_knime/lib/spring-beans-4.1.4.RELEASE.jar b/openbis_knime/lib/spring-beans-4.1.4.RELEASE.jar
deleted file mode 100644
index aa5b9d434904466d68f59daf97132b940aea5429..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/spring-beans-4.1.4.RELEASE.jar and /dev/null differ
diff --git a/openbis_knime/lib/spring-context-4.1.4.RELEASE.jar b/openbis_knime/lib/spring-context-4.1.4.RELEASE.jar
deleted file mode 100644
index 654720805d16c41b8ef958d8630ce7e12ea77621..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/spring-context-4.1.4.RELEASE.jar and /dev/null differ
diff --git a/openbis_knime/lib/spring-core-4.1.4.RELEASE.jar b/openbis_knime/lib/spring-core-4.1.4.RELEASE.jar
deleted file mode 100644
index e4867cb0c9eb99a2c57487bb60d775cabc829b96..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/spring-core-4.1.4.RELEASE.jar and /dev/null differ
diff --git a/openbis_knime/lib/spring-expression-4.1.4.RELEASE.jar b/openbis_knime/lib/spring-expression-4.1.4.RELEASE.jar
deleted file mode 100644
index c7896e945d342ba16a0c9f395448a6652e4f93be..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/spring-expression-4.1.4.RELEASE.jar and /dev/null differ
diff --git a/openbis_knime/lib/spring-web-4.1.4.RELEASE.jar b/openbis_knime/lib/spring-web-4.1.4.RELEASE.jar
deleted file mode 100644
index 38baa28c15ff43daf8c19d5d92af126677b95334..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/spring-web-4.1.4.RELEASE.jar and /dev/null differ
diff --git a/openbis_knime/lib/spring-webmvc-4.1.4.RELEASE.jar b/openbis_knime/lib/spring-webmvc-4.1.4.RELEASE.jar
deleted file mode 100644
index 0215e7ba64313d234c27ef083bc6755a398bd3c9..0000000000000000000000000000000000000000
Binary files a/openbis_knime/lib/spring-webmvc-4.1.4.RELEASE.jar and /dev/null differ
diff --git a/openbis_knime/plugin.xml b/openbis_knime/plugin.xml
deleted file mode 100644
index 8af28de2a56f89d5ad03d5d6a9d722b80d63f31b..0000000000000000000000000000000000000000
--- a/openbis_knime/plugin.xml
+++ /dev/null
@@ -1,45 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<?eclipse version="3.0"?>
-
-<plugin>
- <extension point="org.knime.workbench.repository.nodes">
- <node category-path="/community/openbis" factory-class="ch.systemsx.cisd.openbis.knime.query.QueryNodeFactory"
- id="ch.systemsx.cisd.openbis.knime.query.QueryNodeFactory"/>
- <node category-path="/community/openbis" factory-class="ch.systemsx.cisd.openbis.knime.query.ReportNodeFactory"
- id="ch.systemsx.cisd.openbis.knime.query.ReportNodeFactory"/>
- <node category-path="/community/openbis" factory-class="ch.systemsx.cisd.openbis.knime.query.AggregatedDataTableImportNodeFactory"
- id="ch.systemsx.cisd.openbis.knime.query.AggregatedDataTableImportNodeFactory"/>
- <node category-path="/community/openbis" factory-class="ch.systemsx.cisd.openbis.knime.file.DataSetFileImportNodeFactory"
- id="ch.systemsx.cisd.openbis.knime.file.DataSetImportNodeFactory"/>
- <node category-path="/community/openbis" factory-class="ch.systemsx.cisd.openbis.knime.file.DataSetRegistrationNodeFactory"
- id="ch.systemsx.cisd.openbis.knime.file.DataSetRegistrationNodeFactory"/>
- <node category-path="/community/openbis" factory-class="ch.systemsx.cisd.openbis.knime.file.DataSetRegistrationViaFlowNodeFactory"
- id="ch.systemsx.cisd.openbis.knime.file.DataSetRegistrationNode2Factory"/>
- <node category-path="/community/openbis" factory-class="ch.systemsx.cisd.openbis.knime.file.AggregatedDataFileImportNodeFactory"
- id="ch.systemsx.cisd.openbis.knime.file.AggregatedDataFileImportNodeFactory"/>
- </extension>
-
- <extension point="org.knime.workbench.repository.categories">
- <category
- description="Nodes for accessing openBIS"
- icon="icons/openbis.png"
- level-id="openbis"
- name="openBIS"
- path="/community/"/>
- </extension>
-
- <extension point="org.knime.product.splashExtension">
- <splashExtension icon="icons/openBIS_logo.png" id="openBIS" tooltip="openBIS Nodes for KNIME"/>
- </extension>
- <extension
- point="org.eclipse.ui.preferencePages">
- <page
- category="org.knime.workbench.ui.preferences"
- class="ch.systemsx.cisd.openbis.knime.common.OpenBisPreferencePage"
- id="openbis"
- name="openBIS">
- </page>
- </extension>
-</plugin>
-
-
diff --git a/openbis_knime/resource/dependency-structure.ddf b/openbis_knime/resource/dependency-structure.ddf
deleted file mode 100644
index cf920f2f3a829bfe5a9dfce2bc05f87862cfaac2..0000000000000000000000000000000000000000
--- a/openbis_knime/resource/dependency-structure.ddf
+++ /dev/null
@@ -1,17 +0,0 @@
-#show allResults
-
-{project} = ch.systemsx.cisd.openbis.knime
-
-[server] = ${project}.server.*
-[common] = ${project}.common.*
-[file] = ${project}.file.*
-[query] = ${project}.query.*
-
-check sets [server] [common] [file] [query]
-
-layer layer-server = [server]
-layer layer-common = [common]
-layer layer-nodes = [file] [query]
-
-check layeringOf layer-server layer-common layer-nodes
-
diff --git a/openbis_knime/resource/eclipse/TestAggregatedDataImportNodeDialog.launch b/openbis_knime/resource/eclipse/TestAggregatedDataImportNodeDialog.launch
deleted file mode 100644
index 09d8daeaced60aca5bae8b78bc95cc93d2ffaad3..0000000000000000000000000000000000000000
--- a/openbis_knime/resource/eclipse/TestAggregatedDataImportNodeDialog.launch
+++ /dev/null
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/TestAggregatedDataImportNodeDialog.java"/>
-</listAttribute>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="1"/>
-</listAttribute>
-<listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry containerPath="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6" javaProject="openbis_knime" path="1" type="4"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry path="3" projectName="openbis_knime" type="1"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/libraries/commons-io/commons-io.jar" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/libraries/commons-lang/commons-lang.jar" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/libraries/commons-logging/commons-logging.jar" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/libraries/cisd-base/cisd-base.jar" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/libraries/openbis-apis/dss/dss_client.jar" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/libraries/openbis-apis/query/openbis-query-api.jar" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/libraries/log4j/log4j.jar" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/libraries/knime/knime-base.jar" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/libraries/knime/knime-core-data-uritype.jar" path="3" type="2"/> "/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <runtimeClasspathEntry internalArchive="/libraries/knime/knime-core-util.jar" path="3" type="2"/> "/>
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diff --git a/openbis_knime/resource/eclipse/TestAggregatedDataTableImportNodeDialog.launch b/openbis_knime/resource/eclipse/TestAggregatedDataTableImportNodeDialog.launch
deleted file mode 100644
index 6a90b2d0cfcf50cffe9a28ee9777cc2eaa3a9caa..0000000000000000000000000000000000000000
--- a/openbis_knime/resource/eclipse/TestAggregatedDataTableImportNodeDialog.launch
+++ /dev/null
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diff --git a/openbis_knime/resource/eclipse/TestDataSetFileImportNodeDialog.launch b/openbis_knime/resource/eclipse/TestDataSetFileImportNodeDialog.launch
deleted file mode 100644
index 7f83f0c60a2661bff1d93bf58dd88890dff2fdb4..0000000000000000000000000000000000000000
--- a/openbis_knime/resource/eclipse/TestDataSetFileImportNodeDialog.launch
+++ /dev/null
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diff --git a/openbis_knime/resource/eclipse/TestDataSetRegistrationNodeDialog.launch b/openbis_knime/resource/eclipse/TestDataSetRegistrationNodeDialog.launch
deleted file mode 100644
index 9161c10848300d610632e7a1f6ae36d8878bfce0..0000000000000000000000000000000000000000
--- a/openbis_knime/resource/eclipse/TestDataSetRegistrationNodeDialog.launch
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deleted file mode 100644
index e3ce0bd8ddef51fc0499ffbcdd174868ce1dab83..0000000000000000000000000000000000000000
--- a/openbis_knime/resource/eclipse/TestReportNodeDialog.launch
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deleted file mode 100644
index 4fb8d87b73375b5a04711b5178f5e31e568bb1ff..0000000000000000000000000000000000000000
--- a/openbis_knime/resource/eclipse/openbis knime all tests.launch
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-<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.testng.remote.RemoteTestNG"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="openbis_knime"/>
-<mapAttribute key="org.testng.eclipse.ALL_CLASS_METHODS"/>
-<listAttribute key="org.testng.eclipse.CLASS_TEST_LIST"/>
-<booleanAttribute key="org.testng.eclipse.DEBUG" value="false"/>
-<listAttribute key="org.testng.eclipse.GROUP_LIST"/>
-<listAttribute key="org.testng.eclipse.GROUP_LIST_CLASS"/>
-<stringAttribute key="org.testng.eclipse.LOG_LEVEL" value="2"/>
-<listAttribute key="org.testng.eclipse.PACKAGE_TEST_LIST"/>
-<stringAttribute key="org.testng.eclipse.PROTOCOL" value="object"/>
-<listAttribute key="org.testng.eclipse.SUITE_TEST_LIST">
-<listEntry value="/Users/felmer/dev/eclipse-workspace/openbis_knime/sourceTest/java/tests.xml"/>
-</listAttribute>
-<intAttribute key="org.testng.eclipse.TYPE" value="3"/>
-<booleanAttribute key="org.testng.eclipse.VERBOSE" value="false"/>
-</launchConfiguration>
diff --git a/openbis_knime/settings.gradle b/openbis_knime/settings.gradle
deleted file mode 100644
index 8062ac25691000178f94b7d9fc1091ef3700f632..0000000000000000000000000000000000000000
--- a/openbis_knime/settings.gradle
+++ /dev/null
@@ -1 +0,0 @@
-// Don't delete it eventough it is empty!
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/AbstractOpenBisNodeModel.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/AbstractOpenBisNodeModel.java
deleted file mode 100644
index 391e8b3c21e3050c99ac11a502d5c70dde932c71..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/AbstractOpenBisNodeModel.java
+++ /dev/null
@@ -1,156 +0,0 @@
-/*
- * Copyright 2012 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.io.File;
-import java.io.IOException;
-
-import org.apache.commons.lang.StringUtils;
-import org.knime.core.node.CanceledExecutionException;
-import org.knime.core.node.ExecutionMonitor;
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeLogger;
-import org.knime.core.node.NodeModel;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-import org.knime.core.node.port.PortType;
-import org.knime.core.node.workflow.ICredentials;
-
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.FacadeFactory;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-
-/**
- * Abstract super class of start nodes getting some data from openBIS.
- *
- * @author Franz-Josef Elmer
- */
-public abstract class AbstractOpenBisNodeModel extends NodeModel
-{
- public static final String URL_KEY = "url";
-
- public static final String CREDENTIALS_KEY = "credentials";
-
- public static final String USER_KEY = "user";
-
- public static final String PASSWORD_KEY = "password";
-
- protected NodeLogger logger;
-
- protected String url;
-
- protected String userID;
-
- protected String password;
-
- private String credentialsName;
-
- protected AbstractOpenBisNodeModel()
- {
- super(0, 1);
- logger = NodeLogger.getLogger(getClass());
- }
-
- protected AbstractOpenBisNodeModel(PortType[] inPortTypes, PortType[] outPortTypes)
- {
- super(inPortTypes, outPortTypes);
- logger = NodeLogger.getLogger(getClass());
- }
-
- protected abstract void loadAdditionalValidatedSettingsFrom(NodeSettingsRO settings)
- throws InvalidSettingsException;
-
- protected abstract void saveAdditionalSettingsTo(NodeSettingsWO settings);
-
- @Override
- protected void loadValidatedSettingsFrom(NodeSettingsRO settings) throws InvalidSettingsException
- {
- url = settings.getString(URL_KEY);
- credentialsName = settings.getString(CREDENTIALS_KEY, "");
- if (StringUtils.isNotBlank(credentialsName))
- {
- ICredentials credentials = getCredentials(credentialsName);
- if (credentials == null)
- {
- throw new InvalidSettingsException("Unknown credentials '" + credentialsName + "'.");
- }
- userID = credentials.getLogin();
- password = credentials.getPassword();
- } else
- {
- userID = settings.getString(USER_KEY);
- password = Util.getDecryptedPassword(settings);
- }
- loadAdditionalValidatedSettingsFrom(settings);
- }
-
- protected ICredentials getCredentials(String name)
- {
- return getCredentialsProvider().get(name);
- }
-
- @Override
- protected void saveSettingsTo(NodeSettingsWO settings)
- {
- settings.addString(URL_KEY, url);
- settings.addString(CREDENTIALS_KEY, credentialsName);
- if (StringUtils.isBlank(credentialsName))
- {
- settings.addString(USER_KEY, userID);
- settings.addString(PASSWORD_KEY,
- password == null ? null : Util.getEncryptedPassword(password.toCharArray()));
- }
- saveAdditionalSettingsTo(settings);
- }
-
- @Override
- protected void validateSettings(NodeSettingsRO settings) throws InvalidSettingsException
- {
- }
-
- @Override
- protected void reset()
- {
- }
-
- @Override
- protected void saveInternals(File arg0, ExecutionMonitor arg1) throws IOException,
- CanceledExecutionException
- {
- }
-
- @Override
- protected void loadInternals(File arg0, ExecutionMonitor arg1) throws IOException,
- CanceledExecutionException
- {
- }
-
- protected IQueryApiFacade createQueryFacade()
- {
- return FacadeFactory.create(url, userID, password);
- }
-
- protected String getStringFlowVariable(String variableName)
- {
- return peekFlowVariableString(variableName);
- }
-
- protected void addFlowVariable(String name, String value)
- {
- pushFlowVariableString(name, value);
- }
-
-}
\ No newline at end of file
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/AbstractOpenBisNodeTableModel.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/AbstractOpenBisNodeTableModel.java
deleted file mode 100644
index f2ec503f57f4f0a8c262619cdcae4a310ed5ad7a..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/AbstractOpenBisNodeTableModel.java
+++ /dev/null
@@ -1,101 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.io.Serializable;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.knime.core.data.DataCell;
-import org.knime.core.data.DataTableSpec;
-import org.knime.core.data.DataType;
-import org.knime.core.data.def.DefaultRow;
-import org.knime.core.node.BufferedDataContainer;
-import org.knime.core.node.BufferedDataTable;
-import org.knime.core.node.ExecutionContext;
-import org.knime.core.node.InvalidSettingsException;
-
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableColumn;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel;
-
-/**
- * Abstract super class of node models based on {@link QueryTableModel} objects returned by {@link IQueryApiFacade}.
- *
- * @author Franz-Josef Elmer
- */
-public abstract class AbstractOpenBisNodeTableModel extends AbstractOpenBisNodeModel
-{
- protected abstract QueryTableModel getData(IQueryApiFacade facade);
-
- @Override
- protected BufferedDataTable[] execute(BufferedDataTable[] inData, ExecutionContext exec)
- throws Exception
- {
- IQueryApiFacade facade = createQueryFacade();
- try
- {
- QueryTableModel result = getData(facade);
- List<QueryTableColumn> columns = result.getColumns();
- String[] columnTitles = new String[columns.size()];
- DataType[] dataTypes = new DataType[columns.size()];
- ColumnType[] columnTypes = new ColumnType[columns.size()];
- Map<String, Integer> columnNames = new HashMap<String, Integer>();
- for (int i = 0, n = columns.size(); i < n; i++)
- {
- QueryTableColumn column = columns.get(i);
- String title = column.getTitle();
- Integer count = columnNames.get(title);
- if (count == null)
- {
- count = 0;
- }
- count++;
- columnNames.put(title, count);
- columnTitles[i] = count == 1 ? title : title + "[" + count + "]";
- columnTypes[i] = Util.getColumnType(column.getDataType());
- dataTypes[i] = columnTypes[i].getDataType();
- }
- DataTableSpec dataTableSpec = new DataTableSpec(columnTitles, dataTypes);
- BufferedDataContainer container = exec.createDataContainer(dataTableSpec);
- List<Serializable[]> rows = result.getRows();
- for (int i = 0, n = rows.size(); i < n; i++)
- {
- Serializable[] row = rows.get(i);
- DataCell[] cells = new DataCell[row.length];
- for (int c = 0; c < row.length; c++)
- {
- cells[c] = columnTypes[c].createCell(row[c]);
- }
- container.addRowToTable(new DefaultRow(Integer.toString(i), cells));
- }
- container.close();
- return new BufferedDataTable[] { container.getTable() };
- } finally
- {
- facade.logout();
- }
- }
-
- @Override
- protected DataTableSpec[] configure(final DataTableSpec[] inSpecs)
- throws InvalidSettingsException
- {
- return new DataTableSpec[1];
- }
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ActionExecutor.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ActionExecutor.java
deleted file mode 100644
index 7a8aa3417625f0936db552e8a974b67c14844800..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ActionExecutor.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ActionExecutor
-{
- public <T> void executeAsync(final ILoadingBuildingAction<T> loadingBuildingAction,
- final IAsyncNodeAction action)
- {
- execute(new Runnable()
- {
- @Override
- public void run()
- {
- try
- {
- final T data = loadingBuildingAction.load();
- action.execute(new Runnable()
- {
- @Override
- public void run()
- {
- loadingBuildingAction.build(data);
- }
- });
- } catch (Throwable ex)
- {
- action.handleException(ex);
- }
- }
- });
- }
-
- protected void execute(Runnable runnable)
- {
- new Thread(runnable).start();
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/AggregatedDataImportDescription.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/AggregatedDataImportDescription.java
deleted file mode 100644
index dc55fc2c2e977d06a7824e7d367fc37a9a58774e..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/AggregatedDataImportDescription.java
+++ /dev/null
@@ -1,114 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.io.Serializable;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription;
-
-/**
- * Wrapper of {@link AggregationServiceDescription}.
- *
- * @author Franz-Josef Elmer
- */
-public class AggregatedDataImportDescription implements Serializable
-{
- public static final String PREFIX = "knime-";
-
- public static final String FILE_PREFIX = PREFIX + "file-";
-
- public static final String AGGREGATION_DESCRIPTION_KEY = "aggregation-description";
-
- private static final long serialVersionUID = 1L;
-
- /**
- * Adds specified description to descriptions list if its service key starts with 'knime-'.
- */
- public static void addDescriptionIfDataTable(
- List<AggregatedDataImportDescription> descriptions,
- AggregationServiceDescription description)
- {
- addDescription(descriptions, description, PREFIX);
- }
-
- /**
- * Adds specified description to descriptions list if its service key starts with 'knime-file-'.
- */
- public static void addDescriptionIfDataFile(List<AggregatedDataImportDescription> descriptions,
- AggregationServiceDescription description)
- {
- addDescription(descriptions, description, FILE_PREFIX);
- }
-
- private static void addDescription(List<AggregatedDataImportDescription> descriptions,
- AggregationServiceDescription description, String keyPrefix)
- {
- String serviceKey = description.getServiceKey();
- if (serviceKey.startsWith(keyPrefix))
- {
- descriptions.add(new AggregatedDataImportDescription(description, keyPrefix));
- }
- }
-
- private final AggregationServiceDescription aggregationServiceDescription;
-
- private final String name;
-
- private final String dataStoreCode;
-
- private boolean showFullDescription;
-
- private AggregatedDataImportDescription(
- AggregationServiceDescription aggregationServiceDescription, String keyPrefix)
- {
- this.aggregationServiceDescription = aggregationServiceDescription;
- name = aggregationServiceDescription.getServiceKey().substring(keyPrefix.length());
- dataStoreCode = aggregationServiceDescription.getDataStoreCode();
- }
-
- public AggregationServiceDescription getAggregationServiceDescription()
- {
- return aggregationServiceDescription;
- }
-
- public boolean isShowFullDescription()
- {
- return showFullDescription;
- }
-
- public void setShowFullDescription(boolean showFullDescription)
- {
- this.showFullDescription = showFullDescription;
- }
-
- /**
- * Returns the service key with the prefix used for filtering.
- */
- @Override
- public String toString()
- {
- if (isShowFullDescription())
- {
- return name + " (" + dataStoreCode + ")";
- } else
- {
- return name;
- }
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ChooserTreeModel.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ChooserTreeModel.java
deleted file mode 100644
index 9a3e3c2ecf61a2bee237d7aad7679b98bc3bd2d3..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ChooserTreeModel.java
+++ /dev/null
@@ -1,678 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.EnumSet;
-import java.util.List;
-import java.util.Map.Entry;
-import java.util.TreeMap;
-
-import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.DefaultTreeModel;
-import javax.swing.tree.TreePath;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.SearchOperator;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria;
-
-/**
- * The tree model for {@link EntityChooser}.
- *
- * @author Franz-Josef Elmer
- */
-public class ChooserTreeModel extends DefaultTreeModel
-{
- static final String LOADING_TEXT = "Loading data...";
-
- private static final long serialVersionUID = 1L;
-
- private static final class RootNode implements IChooserTreeNode<String>
- {
- static final RootNode ROOT = new RootNode();
-
- @Override
- public ChooserTreeNodeType getNodeType()
- {
- return ChooserTreeNodeType.ROOT;
- }
-
- @Override
- public String getNodeObject()
- {
- return "root";
- }
-
- @Override
- public String toString()
- {
- return getNodeObject();
- }
- }
-
- private static final class SpaceNode implements IChooserTreeNode<String>
- {
- private final String spaceCode;
-
- SpaceNode(String spaceCode)
- {
- this.spaceCode = spaceCode;
- }
-
- @Override
- public ChooserTreeNodeType getNodeType()
- {
- return ChooserTreeNodeType.SPACE;
- }
-
- @Override
- public String getNodeObject()
- {
- return spaceCode;
- }
-
- @Override
- public String toString()
- {
- return getNodeObject();
- }
- }
-
- private static final class ProjectNode implements IChooserTreeNode<Project>
- {
- private final Project project;
-
- ProjectNode(Project project)
- {
- this.project = project;
- }
-
- @Override
- public ChooserTreeNodeType getNodeType()
- {
- return ChooserTreeNodeType.PROJECT;
- }
-
- @Override
- public Project getNodeObject()
- {
- return project;
- }
-
- @Override
- public String toString()
- {
- return project.getCode();
- }
- }
-
- private static final class ExperimentNode implements IChooserTreeNode<Experiment>
- {
- private final Experiment experiment;
-
- ExperimentNode(Experiment experiment)
- {
- this.experiment = experiment;
- }
-
- @Override
- public ChooserTreeNodeType getNodeType()
- {
- return ChooserTreeNodeType.EXPERIMENT;
- }
-
- @Override
- public Experiment getNodeObject()
- {
- return experiment;
- }
-
- @Override
- public String toString()
- {
- return experiment.getCode();
- }
- }
-
- private static final class SampleNode implements IChooserTreeNode<Sample>
- {
- private final Sample sample;
-
- SampleNode(Sample sample)
- {
- this.sample = sample;
- }
-
- @Override
- public ChooserTreeNodeType getNodeType()
- {
- return ChooserTreeNodeType.SAMPLE;
- }
-
- @Override
- public Sample getNodeObject()
- {
- return sample;
- }
-
- @Override
- public String toString()
- {
- return sample.getIdentifier();
- }
- }
-
- private static final class DataSetNode implements IChooserTreeNode<DataSet>
- {
- private final DataSet dataSet;
-
- DataSetNode(DataSet dataSet)
- {
- this.dataSet = dataSet;
- }
-
- @Override
- public ChooserTreeNodeType getNodeType()
- {
- return ChooserTreeNodeType.DATA_SET;
- }
-
- @Override
- public DataSet getNodeObject()
- {
- return dataSet;
- }
-
- @Override
- public String toString()
- {
- return dataSet.getCode();
- }
- }
-
- private static final class SamplesAndProjects
- {
- private final List<Sample> samples;
-
- private final List<Project> projects;
-
- SamplesAndProjects(List<Sample> samples, List<Project> projects)
- {
- this.samples = samples;
- this.projects = projects;
- }
-
- public List<Sample> getSamples()
- {
- return samples;
- }
-
- public List<Project> getProjects()
- {
- return projects;
- }
- }
-
- private static final class SamplesAndDataSets
- {
- private final List<Sample> samples;
-
- private final List<DataSet> dataSets;
-
- SamplesAndDataSets(List<Sample> samples, List<DataSet> dataSets)
- {
- this.samples = samples;
- this.dataSets = dataSets;
- }
-
- public List<Sample> getSamples()
- {
- return samples;
- }
-
- public List<DataSet> getDataSets()
- {
- return dataSets;
- }
- }
-
- private static final Comparator<Project> PROJECT_COMPARATOR = new Comparator<Project>()
- {
- @Override
- public int compare(Project p1, Project p2)
- {
- return p1.getIdentifier().compareTo(p2.getIdentifier());
- }
- };
-
- private static final Comparator<Experiment> EXPERIMENT_COMPARATOR =
- new Comparator<Experiment>()
- {
- @Override
- public int compare(Experiment e1, Experiment e2)
- {
- return e1.getCode().compareTo(e2.getCode());
- }
- };
-
- private static final Comparator<Sample> SAMPLE_COMPARATOR = new Comparator<Sample>()
- {
- @Override
- public int compare(Sample s1, Sample s2)
- {
- return s1.getIdentifier().compareTo(s2.getIdentifier());
- }
- };
-
- private static final Comparator<DataSet> DATA_SET_COMPARATOR = new Comparator<DataSet>()
- {
- @Override
- public int compare(DataSet ds1, DataSet ds2)
- {
- return ds1.getCode().compareTo(ds2.getCode());
- }
- };
-
- private final IGeneralInformationService service;
-
- private final DataSetOwnerType entityType;
-
- private final boolean ownerEntity;
-
- private final String sessionToken;
-
- private List<SampleType> sampleTypes;
-
- private TreeMap<String, List<Project>> spaceToProjectsMap;
-
- ChooserTreeModel(DataSetOwnerType entityType, boolean ownerEntity, String sessionToken,
- IGeneralInformationService service)
- {
- super(new DefaultMutableTreeNode());
- this.entityType = entityType;
- this.ownerEntity = ownerEntity;
- this.sessionToken = sessionToken;
- this.service = service;
- addTopLevelNodes();
- sampleTypes = service.listSampleTypes(sessionToken);
- }
-
- private void addTopLevelNodes()
- {
- DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) getRoot();
- rootNode.setUserObject(RootNode.ROOT);
- spaceToProjectsMap = new TreeMap<String, List<Project>>();
- List<Project> projects = service.listProjects(sessionToken);
- Collections.sort(projects, PROJECT_COMPARATOR);
- for (Project project : projects)
- {
- List<Project> list = spaceToProjectsMap.get(project.getSpaceCode());
- if (list == null)
- {
- list = new ArrayList<Project>();
- spaceToProjectsMap.put(project.getSpaceCode(), list);
- }
- list.add(project);
- }
- for (Entry<String, List<Project>> entry : spaceToProjectsMap.entrySet())
- {
- String spaceCode = entry.getKey();
- DefaultMutableTreeNode spaceNode = new DefaultMutableTreeNode(new SpaceNode(spaceCode));
- rootNode.add(spaceNode);
- spaceNode.add(createLoadingNode());
- }
- }
-
- public boolean isSelectable(TreePath path)
- {
- DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent();
- Object userObject = node.getUserObject();
- if (userObject instanceof IChooserTreeNode == false)
- {
- return false;
- }
- IChooserTreeNode<?> treeNode = (IChooserTreeNode<?>) userObject;
- ChooserTreeNodeType nodeType = treeNode.getNodeType();
- switch (entityType)
- {
- case EXPERIMENT:
- return nodeType == ChooserTreeNodeType.EXPERIMENT;
- case SAMPLE:
- return nodeType == ChooserTreeNodeType.SAMPLE;
- case DATA_SET:
- return nodeType == ChooserTreeNodeType.DATA_SET;
- }
- return false;
- }
-
- public void collapsNode(TreePath path)
- {
- DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent();
- Object userObject = node.getUserObject();
- if (userObject instanceof IChooserTreeNode)
- {
- IChooserTreeNode<?> treeNode = (IChooserTreeNode<?>) userObject;
- if (EnumSet.of(ChooserTreeNodeType.PROJECT, ChooserTreeNodeType.EXPERIMENT,
- ChooserTreeNodeType.SAMPLE).contains(treeNode.getNodeType()))
- {
- node.removeAllChildren();
- node.add(createLoadingNode());
- nodeStructureChanged(node);
- }
- }
- }
-
- public void expandNode(TreePath path, IAsyncNodeAction action)
- {
- DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent();
- Object userObject = node.getUserObject();
- String space = tryGetWrappedObject(String.class, userObject);
- if (space != null)
- {
- expandSpaceNode(node, space, action);
- return;
- }
- Project project = tryGetWrappedObject(Project.class, userObject);
- if (project != null)
- {
- expandProjectNode(node, project, action);
- return;
- }
- Experiment experiment = tryGetWrappedObject(Experiment.class, userObject);
- if (experiment != null)
- {
- expandExperimentNode(node, experiment, action);
- return;
- }
- Sample sample = tryGetWrappedObject(Sample.class, userObject);
- if (sample != null)
- {
- expandSampleNode(node, sample, action);
- }
- }
-
- private void expandSpaceNode(final DefaultMutableTreeNode node, final String space, IAsyncNodeAction action)
- {
- executeAsync(new ILoadingBuildingAction<SamplesAndProjects>()
- {
- @Override
- public SamplesAndProjects load()
- {
- List<Sample> samples = new ArrayList<Sample>();
- if (isSampleTypeButNotOwner())
- {
- gatherListableSamples(samples, space, null);
- Collections.sort(samples, SAMPLE_COMPARATOR);
- }
- List<Project> projects = spaceToProjectsMap.get(space);
- if (projects == null)
- {
- projects = Collections.emptyList();
- }
- return new SamplesAndProjects(samples, projects);
- }
-
- @Override
- public void build(SamplesAndProjects data)
- {
- node.removeAllChildren();
- List<Sample> samples = data.getSamples();
- for (Sample sample : samples)
- {
- DefaultMutableTreeNode childNode = new DefaultMutableTreeNode(new SampleNode(sample));
- node.add(childNode);
- childNode.add(createLoadingNode());
- }
- for (Project project : data.getProjects())
- {
- DefaultMutableTreeNode projectNode =
- new DefaultMutableTreeNode(new ProjectNode(project));
- node.add(projectNode);
- projectNode.add(createLoadingNode());
- }
- nodeStructureChanged(node);
- }
- }, action);
- }
-
- private void expandProjectNode(final DefaultMutableTreeNode node, final Project project,
- IAsyncNodeAction action)
- {
- executeAsync(new ILoadingBuildingAction<List<Experiment>>()
- {
- @Override
- public List<Experiment> load()
- {
- List<Experiment> experiments =
- service.listExperiments(sessionToken, Arrays.asList(project), null);
- Collections.sort(experiments, EXPERIMENT_COMPARATOR);
- return experiments;
- }
-
- @Override
- public void build(List<Experiment> data)
- {
- node.removeAllChildren();
- for (Experiment experiment : data)
- {
- DefaultMutableTreeNode childNode =
- new DefaultMutableTreeNode(new ExperimentNode(experiment));
- node.add(childNode);
- if (entityType != DataSetOwnerType.EXPERIMENT)
- {
- childNode.add(createLoadingNode());
- }
- }
- ChooserTreeModel.this.nodeStructureChanged(node);
- }
- }, action);
- }
-
- private void expandExperimentNode(final DefaultMutableTreeNode node, final Experiment experiment,
- IAsyncNodeAction action)
- {
- final String experimentPermId = experiment.getPermId();
- executeAsync(new ILoadingBuildingAction<SamplesAndDataSets>()
- {
- @Override
- public SamplesAndDataSets load()
- {
- List<Sample> samples = new ArrayList<Sample>();
- gatherListableSamples(samples, null, experimentPermId);
- Collections.sort(samples, SAMPLE_COMPARATOR);
- List<DataSet> dataSets = new ArrayList<DataSet>();
- if (entityType == DataSetOwnerType.DATA_SET)
- {
- SearchCriteria searchCriteria = new SearchCriteria();
- SearchCriteria experimentCriteria = new SearchCriteria();
- experimentCriteria.addMatchClause(MatchClause.createAttributeMatch(
- MatchClauseAttribute.PERM_ID, experimentPermId));
- searchCriteria.addSubCriteria(SearchSubCriteria
- .createExperimentCriteria(experimentCriteria));
- dataSets = service.searchForDataSets(sessionToken, searchCriteria);
- Collections.sort(dataSets, DATA_SET_COMPARATOR);
- }
- return new SamplesAndDataSets(samples, dataSets);
- }
-
- @Override
- public void build(SamplesAndDataSets data)
- {
- addSampleAndDataSetNodes(node, data);
- }
- }, action);
- }
-
- private void gatherListableSamples(List<Sample> samples, String spaceOrNull, String experimentPermIdOrNull)
- {
- for (SampleType sampleType : sampleTypes)
- {
- if (sampleType.isListable())
- {
- SearchCriteria searchCriteria = new SearchCriteria();
- searchCriteria.setOperator(SearchOperator.MATCH_ALL_CLAUSES);
- searchCriteria.addMatchClause(MatchClause.createAttributeMatch(
- MatchClauseAttribute.TYPE,
- sampleType.getCode()));
- if (spaceOrNull != null)
- {
- searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.SPACE, spaceOrNull));
- }
- if (experimentPermIdOrNull != null)
- {
- SearchCriteria experimentCriteria = new SearchCriteria();
- experimentCriteria.addMatchClause(MatchClause.createAttributeMatch(
- MatchClauseAttribute.PERM_ID, experimentPermIdOrNull));
- searchCriteria.addSubCriteria(SearchSubCriteria
- .createExperimentCriteria(experimentCriteria));
- }
- samples.addAll(service.searchForSamples(sessionToken, searchCriteria,
- null));
- }
- }
- }
-
- private void expandSampleNode(final DefaultMutableTreeNode node, final Sample sample,
- IAsyncNodeAction action)
- {
- final String samplePermId = sample.getPermId();
- executeAsync(new ILoadingBuildingAction<SamplesAndDataSets>()
- {
- @Override
- public SamplesAndDataSets load()
- {
- List<Sample> samples = new ArrayList<Sample>();
- SearchCriteria sampleCriteria = new SearchCriteria();
- sampleCriteria.addMatchClause(MatchClause.createAttributeMatch(
- MatchClauseAttribute.PERM_ID, samplePermId));
- List<Sample> sampleWithChildren =
- service.searchForSamples(sessionToken, sampleCriteria,
- EnumSet.of(SampleFetchOption.CHILDREN));
- if (sampleWithChildren.isEmpty() == false)
- {
- addFilteredSamples(samples, sampleWithChildren.get(0).getChildren());
- }
- SearchCriteria searchCriteria = new SearchCriteria();
- searchCriteria.addSubCriteria(SearchSubCriteria
- .createSampleContainerCriteria(sampleCriteria));
- addFilteredSamples(samples,
- service.searchForSamples(sessionToken, searchCriteria, null));
- Collections.sort(samples, SAMPLE_COMPARATOR);
- List<DataSet> dataSets = new ArrayList<DataSet>();
- if (entityType == DataSetOwnerType.DATA_SET)
- {
- searchCriteria = new SearchCriteria();
- sampleCriteria = new SearchCriteria();
- sampleCriteria.addMatchClause(MatchClause.createAttributeMatch(
- MatchClauseAttribute.PERM_ID, samplePermId));
- searchCriteria.addSubCriteria(SearchSubCriteria
- .createSampleCriteria(sampleCriteria));
- dataSets = service.searchForDataSets(sessionToken, searchCriteria);
- Collections.sort(dataSets, DATA_SET_COMPARATOR);
- }
- return new SamplesAndDataSets(samples, dataSets);
- }
-
- @Override
- public void build(SamplesAndDataSets data)
- {
- addSampleAndDataSetNodes(node, data);
- }
- }, action);
- }
-
- private void addFilteredSamples(List<Sample> samples, List<Sample> samplesToAdd)
- {
- boolean isNotSample = entityType != DataSetOwnerType.SAMPLE;
- for (Sample sample : samplesToAdd)
- {
- if (isSampleTypeButNotOwner() || isNotSample || sample.getExperimentIdentifierOrNull() != null)
- {
- samples.add(sample);
- }
- }
- }
-
- private boolean isSampleTypeButNotOwner()
- {
- return ownerEntity == false && entityType == DataSetOwnerType.SAMPLE;
- }
-
- private void addSampleAndDataSetNodes(DefaultMutableTreeNode node, SamplesAndDataSets data)
- {
- node.removeAllChildren();
- for (DataSet dataSet : data.getDataSets())
- {
- node.add(new DefaultMutableTreeNode(new DataSetNode(dataSet)));
- }
- for (Sample sample : data.getSamples())
- {
- DefaultMutableTreeNode childNode = new DefaultMutableTreeNode(new SampleNode(sample));
- node.add(childNode);
- childNode.add(createLoadingNode());
- }
- nodeStructureChanged(node);
- }
-
- @SuppressWarnings("unchecked")
- private <T> T tryGetWrappedObject(Class<T> clazz, Object nodeObject)
- {
- if (nodeObject instanceof IChooserTreeNode == false)
- {
- return null;
- }
- Object treeNode = ((IChooserTreeNode<?>) nodeObject).getNodeObject();
- return clazz.isInstance(treeNode) ? (T) treeNode : null;
- }
-
- private DefaultMutableTreeNode createLoadingNode()
- {
- return new DefaultMutableTreeNode(LOADING_TEXT);
- }
-
- private <T> void executeAsync(final ILoadingBuildingAction<T> loadingBuildingAction,
- final IAsyncNodeAction action)
- {
- new ActionExecutor()
- {
- @Override
- protected void execute(Runnable runnable)
- {
- ChooserTreeModel.this.execute(runnable);
- }
- }.executeAsync(loadingBuildingAction, action);
- }
-
- void execute(Runnable runnable)
- {
- new Thread(runnable).start();
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ChooserTreeNodeType.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ChooserTreeNodeType.java
deleted file mode 100644
index af712ee54578076b3e0dd84e83494c7b08bc1a3b..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ChooserTreeNodeType.java
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-/**
- * Enum of different types of nodes in {@link ChooserTreeModel}
- *
- * @author Franz-Josef Elmer
- */
-public enum ChooserTreeNodeType
-{
- ROOT(""), SPACE(""), PROJECT("P"), EXPERIMENT("E"), SAMPLE("S"), DATA_SET("DS");
-
- private final String label;
-
- private ChooserTreeNodeType(String label)
- {
- this.label = label;
- }
-
- public String getLabel()
- {
- return label;
- }
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ColumnType.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ColumnType.java
deleted file mode 100644
index 3d5dcb4bee0b6f6ef04dd388e0933325d6128317..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ColumnType.java
+++ /dev/null
@@ -1,76 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.io.Serializable;
-
-import org.knime.core.data.DataCell;
-import org.knime.core.data.DataType;
-import org.knime.core.data.def.DoubleCell;
-import org.knime.core.data.def.LongCell;
-import org.knime.core.data.def.StringCell;
-
-enum ColumnType
-{
- DOUBLE(DoubleCell.TYPE)
- {
- @Override
- public DataCell createCell(Serializable valueOrNull)
- {
- if (valueOrNull instanceof Double)
- {
- return new DoubleCell((Double) valueOrNull);
- }
- return DataType.getMissingCell();
- }
- },
- LONG(LongCell.TYPE)
- {
- @Override
- public DataCell createCell(Serializable valueOrNull)
- {
- if (valueOrNull instanceof Long)
- {
- return new LongCell((Long) valueOrNull);
- }
- return DataType.getMissingCell();
- }
- },
- STRING(StringCell.TYPE)
- {
-
- @Override
- public DataCell createCell(Serializable valueOrNull)
- {
- return new StringCell(valueOrNull == null ? "" : valueOrNull.toString());
- }
- };
-
- private final DataType dataType;
-
- private ColumnType(DataType dataType)
- {
- this.dataType = dataType;
- }
-
- public DataType getDataType()
- {
- return dataType;
- }
-
- public abstract DataCell createCell(Serializable valueOrNull);
-}
\ No newline at end of file
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/DefaultAsyncNodeAction.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/DefaultAsyncNodeAction.java
deleted file mode 100644
index 89070746d21f248c44a6ea823ca2a2dafe957bd4..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/DefaultAsyncNodeAction.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.awt.EventQueue;
-import java.awt.Window;
-
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.SwingUtilities;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DefaultAsyncNodeAction implements IAsyncNodeAction
-{
- private final IOpenBisNode node;
-
- public DefaultAsyncNodeAction(IOpenBisNode node)
- {
- this.node = node;
- }
-
- @Override
- public void execute(Runnable runnable)
- {
- EventQueue.invokeLater(runnable);
- }
-
- @Override
- public void handleException(Throwable throwable)
- {
- node.logError(throwable);
- JPanel panel = node.getPanel();
- Window windowAncestor = SwingUtilities.getWindowAncestor(panel);
- if (windowAncestor != null && windowAncestor.isVisible())
- {
- JOptionPane.showMessageDialog(panel, throwable.toString());
- }
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/EntityChooser.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/EntityChooser.java
deleted file mode 100644
index ed14dfdec52a31edf0a118781bfce3e4a677a610..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/EntityChooser.java
+++ /dev/null
@@ -1,256 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Graphics;
-import java.awt.Window;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-
-import javax.swing.Icon;
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JTree;
-import javax.swing.SwingUtilities;
-import javax.swing.event.TreeExpansionEvent;
-import javax.swing.event.TreeExpansionListener;
-import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.TreeCellRenderer;
-import javax.swing.tree.TreePath;
-
-import org.apache.commons.lang.StringUtils;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
-
-/**
- * Helper class showing a dialog for choosing a data set owner.
- *
- * @author Franz-Josef Elmer
- */
-public class EntityChooser
-{
- private static final class DecoratingTreeCellRenderer implements TreeCellRenderer
- {
- private static final class DecoratedIcon implements Icon
- {
- private final Icon icon;
-
- private final String text;
-
- DecoratedIcon(Icon icon, ChooserTreeNodeType type)
- {
- this.icon = icon;
- this.text = type.getLabel();
- }
-
- @Override
- public int getIconHeight()
- {
- return icon.getIconHeight();
- }
-
- @Override
- public int getIconWidth()
- {
- return icon.getIconWidth();
- }
-
- @Override
- public void paintIcon(Component c, Graphics g, int x, int y)
- {
- icon.paintIcon(c, g, x, y);
- Color color = g.getColor();
- Font font = g.getFont();
- g.setColor(Color.BLACK);
- g.setFont(new Font("SansSerif", Font.BOLD, 10));
- FontMetrics fontMetrics = g.getFontMetrics();
- int stringWidth = fontMetrics.stringWidth(text);
- g.drawString(text, x + getIconWidth() - stringWidth, y + getIconHeight());
- g.setColor(color);
- g.setFont(font);
- }
- }
-
- private final TreeCellRenderer cellRenderer;
-
- private DecoratingTreeCellRenderer(TreeCellRenderer cellRenderer)
- {
- this.cellRenderer = cellRenderer;
- }
-
- @Override
- public Component getTreeCellRendererComponent(JTree t, Object value,
- boolean selected, boolean expanded,
- boolean leaf, int row, boolean hasFocus)
- {
- Component component =
- cellRenderer.getTreeCellRendererComponent(t, value, selected, expanded, leaf,
- row, hasFocus);
- Object userObject = ((DefaultMutableTreeNode) value).getUserObject();
- if (component instanceof JLabel && userObject instanceof IChooserTreeNode)
- {
- JLabel label = (JLabel) component;
- Icon icon = label.getIcon();
- ChooserTreeNodeType nodeType = ((IChooserTreeNode<?>) userObject).getNodeType();
- label.setIcon(new DecoratedIcon(icon, nodeType));
- }
- return component;
- }
- }
-
- private final DataSetOwnerType entityType;
-
- private final boolean ownerEntity;
-
- private final IGeneralInformationService service;
-
- private final Component component;
-
- private final String sessionToken;
-
- private final IAsyncNodeAction asyncNodeAction;
-
- private String entityIdentifier;
-
- public EntityChooser(Component component, DataSetOwnerType entityType, boolean ownerEntity, String sessionToken,
- IGeneralInformationService service, IAsyncNodeAction asyncNodeAction)
- {
- this.component = component;
- this.entityType = entityType;
- this.ownerEntity = ownerEntity;
- this.sessionToken = sessionToken;
- this.service = service;
- this.asyncNodeAction = asyncNodeAction;
- }
-
- public String getOwnerOrNull()
- {
- final JTree tree = new JTree();
- final ChooserTreeModel chooserTreeModel = new ChooserTreeModel(entityType, ownerEntity, sessionToken, service);
- tree.setModel(chooserTreeModel);
- tree.setRootVisible(false);
- tree.setEditable(false);
- tree.setShowsRootHandles(true);
- tree.setCellRenderer(new DecoratingTreeCellRenderer(tree.getCellRenderer()));
- tree.addTreeExpansionListener(createTreeExpansionListener(tree, chooserTreeModel));
- JPanel treePanel = new JPanel(new BorderLayout());
- treePanel.add(new JScrollPane(tree), BorderLayout.CENTER);
- final JOptionPane optionPane = new JOptionPane(treePanel, JOptionPane.PLAIN_MESSAGE, JOptionPane.OK_CANCEL_OPTION);
- optionPane.setSize(800, 800);
- tree.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent e)
- {
- if (e.getClickCount() > 1)
- {
- TreePath closestPathForLocation =
- tree.getClosestPathForLocation(e.getX(), e.getY());
- if (chooserTreeModel.isSelectable(closestPathForLocation))
- {
- Window window = SwingUtilities.getWindowAncestor(tree);
- if (window != null)
- {
- optionPane.setValue(JOptionPane.OK_OPTION);
- window.setVisible(false);
- }
- }
- }
- }
- });
- String title = StringUtils.capitalize(entityType.toString().toLowerCase()) + " Chooser";
- final JDialog dialog = optionPane.createDialog(component, title);
- dialog.setResizable(true);
- optionPane.addPropertyChangeListener(new PropertyChangeListener()
- {
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- if (evt.getSource() == optionPane
- && JOptionPane.VALUE_PROPERTY.equals(evt.getPropertyName())
- && new Integer(JOptionPane.OK_OPTION).equals(evt.getNewValue()))
- {
- TreePath selectionPath = tree.getSelectionPath();
- if (selectionPath != null && chooserTreeModel.isSelectable(selectionPath) == false)
- {
- dialog.setVisible(true);
- }
- }
- }
- });
- dialog.setVisible(true);
- Object value = optionPane.getValue();
- if (new Integer(JOptionPane.OK_OPTION).equals(value))
- {
- setEntityIdentifier(tree);
- }
- return entityIdentifier;
- }
-
- private TreeExpansionListener createTreeExpansionListener(final JTree tree,
- final ChooserTreeModel chooserTreeModel)
- {
- return new TreeExpansionListener()
- {
- @Override
- public void treeExpanded(TreeExpansionEvent event)
- {
- chooserTreeModel.expandNode(event.getPath(), asyncNodeAction);
- }
-
- @Override
- public void treeCollapsed(TreeExpansionEvent event)
- {
- chooserTreeModel.collapsNode(event.getPath());
- }
- };
- }
-
- private void setEntityIdentifier(JTree tree)
- {
- TreePath selectionPath = tree.getSelectionPath();
- if (selectionPath == null)
- {
- return;
- }
- Object selectedItem =
- ((DefaultMutableTreeNode) selectionPath.getLastPathComponent()).getUserObject();
- if (selectedItem instanceof IChooserTreeNode == false)
- {
- return;
- }
- entityIdentifier = selectedItem.toString();
- Object nodeObject = ((IChooserTreeNode<?>) selectedItem).getNodeObject();
- if (nodeObject instanceof Experiment)
- {
- entityIdentifier = ((Experiment) nodeObject).getIdentifier();
- }
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/EntityField.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/EntityField.java
deleted file mode 100644
index 66355619affbdd1ff88af9d4cd3c3a2bcc1f08c9..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/EntityField.java
+++ /dev/null
@@ -1,102 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.awt.BorderLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-
-import javax.swing.JButton;
-import javax.swing.JComponent;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-
-/**
- * One-line text field for an identifier for an entity of type Experiment, Sample or Data Set. An additional button allows to use
- * {@link EntityChooser}.
- *
- * @author Franz-Josef Elmer
- */
-class EntityField implements IField
-{
- private final DataSetOwnerType ownerType;
-
- private final IQueryApiFacadeProvider facadeProvider;
-
- private final JPanel textFieldWithButton;
-
- private final JTextField ownerField;
-
- private final IAsyncNodeAction asyncNodeAction;
-
- EntityField(DataSetOwnerType entityType, IQueryApiFacadeProvider facadeProvider, IAsyncNodeAction asyncNodeAction)
- {
- this.ownerType = entityType;
- this.facadeProvider = facadeProvider;
- this.asyncNodeAction = asyncNodeAction;
- textFieldWithButton = new JPanel(new BorderLayout());
- ownerField = new JTextField(20);
- textFieldWithButton.add(ownerField, BorderLayout.CENTER);
- JButton button = new JButton("...");
- button.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- chooseOwner();
- }
- });
- textFieldWithButton.add(button, BorderLayout.EAST);
- }
-
- @Override
- public JComponent getComponent()
- {
- return textFieldWithButton;
- }
-
- @Override
- public String getValue()
- {
- return ownerField.getText();
- }
-
- @Override
- public void setValue(String value)
- {
- ownerField.setText(value);
- }
-
- private void chooseOwner()
- {
- IQueryApiFacade facade = facadeProvider.getQueryFacade();
- String sessionToken = facade.getSessionToken();
- IGeneralInformationService service = facade.getGeneralInformationService();
- String ownerOrNull =
- new EntityChooser(ownerField, ownerType, false, sessionToken, service, asyncNodeAction).getOwnerOrNull();
- if (ownerOrNull != null)
- {
- ownerField.setText(ownerOrNull);
- }
-
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/FieldDescription.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/FieldDescription.java
deleted file mode 100644
index 6d5444cb86cb2b287270930f9519526dc3ce7119..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/FieldDescription.java
+++ /dev/null
@@ -1,64 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import org.apache.commons.lang.StringUtils;
-
-import ch.systemsx.cisd.openbis.knime.server.FieldType;
-
-/**
- * Description necessary to create a {@link IField}.
- *
- * @author Franz-Josef Elmer
- */
-public class FieldDescription
-{
- private final String name;
-
- private final FieldType fieldType;
-
- private final String fieldParameters;
-
- public FieldDescription(String name, FieldType fieldType, String fieldParameters)
- {
- this.name = name;
- this.fieldType = fieldType;
- this.fieldParameters = fieldParameters;
- }
-
- public String getName()
- {
- return name;
- }
-
- public FieldType getFieldType()
- {
- return fieldType;
- }
-
- public String getFieldParameters()
- {
- return fieldParameters;
- }
-
- @Override
- public String toString()
- {
- return name + ":" + fieldType + (StringUtils.isBlank(fieldParameters) ? "" : "[" + fieldParameters + "]");
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/GUIUtil.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/GUIUtil.java
deleted file mode 100644
index d9ab81c367b8c2121552e215e6621a265cb59b8d..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/GUIUtil.java
+++ /dev/null
@@ -1,171 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Cursor;
-import java.awt.Dimension;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.JComponent;
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JTable;
-import javax.swing.JTextField;
-import javax.swing.ListSelectionModel;
-import javax.swing.RowFilter;
-import javax.swing.event.DocumentEvent;
-import javax.swing.event.DocumentListener;
-import javax.swing.table.JTableHeader;
-import javax.swing.table.TableCellRenderer;
-import javax.swing.table.TableColumnModel;
-import javax.swing.table.TableModel;
-import javax.swing.table.TableRowSorter;
-
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
-
-/**
- * GUI utility functions.
- *
- * @author Franz-Josef Elmer
- */
-public class GUIUtil
-{
- public static List<DataSet> getSelectedDataSets(Component parentComponent, Cursor oldCursor,
- List<DataSet> dataSets, boolean singleSelection)
- {
- JTable table = new JTable(createTableModel(dataSets));
- table.setPreferredScrollableViewportSize(new Dimension(900, 500));
- JTableHeader tableHeader = table.getTableHeader();
- final TableColumnModel columnModel = tableHeader.getColumnModel();
- final TableCellRenderer renderer = tableHeader.getDefaultRenderer();
- tableHeader.setDefaultRenderer(new TableCellRenderer()
- {
- @Override
- public Component getTableCellRendererComponent(JTable t, Object value, boolean isSelected,
- boolean hasFocus, int row, int column)
- {
- Component component = renderer.getTableCellRendererComponent(t, value, isSelected, hasFocus, row, column);
- if (component instanceof JComponent)
- {
- String title = columnModel.getColumn(column).getHeaderValue().toString();
- ((JComponent) component).setToolTipText(title);
- }
- return component;
- }
- });
- TableRowSorter<TableModel> sorter = new TableRowSorter<TableModel>(table.getModel());
- table.setRowSorter(sorter);
- ListSelectionModel selectionModel = table.getSelectionModel();
- if (singleSelection)
- {
- selectionModel.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
- } else
- {
- selectionModel.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
- }
- JScrollPane scrollPane = new JScrollPane(table);
- JPanel panel = new JPanel(new BorderLayout());
- panel.add(new JLabel("Choose a data set:"), BorderLayout.NORTH);
- panel.add(scrollPane, BorderLayout.CENTER);
- JPanel filterPanel = new JPanel(new BorderLayout());
- filterPanel.add(new JLabel("Filter:"), BorderLayout.WEST);
- JTextField filterField = createFilterField(sorter);
- filterPanel.add(filterField, BorderLayout.CENTER);
- panel.add(filterPanel, BorderLayout.SOUTH);
- JOptionPane optionPane = new JOptionPane(panel, JOptionPane.PLAIN_MESSAGE, JOptionPane.OK_CANCEL_OPTION);
- parentComponent.setCursor(oldCursor);
- JDialog dialog = optionPane.createDialog(parentComponent, "Data Sets");
- dialog.setResizable(true);
- dialog.setVisible(true);
- List<DataSet> result = new ArrayList<DataSet>();
- Object value = optionPane.getValue();
- if (new Integer(JOptionPane.OK_OPTION).equals(value))
- {
- int[] selectedRows = table.getSelectedRows();
- for (int rowIndex : selectedRows)
- {
- result.add(dataSets.get(sorter.convertRowIndexToModel(rowIndex)));
- }
- }
- return result;
- }
-
- private static TableModel createTableModel(final List<DataSet> dataSets)
- {
- TableModelBuilder builder = new TableModelBuilder();
- for (DataSet dataSet : dataSets)
- {
- builder.add(dataSet);
- }
- return builder.getTableModel();
- }
-
- private static JTextField createFilterField(final TableRowSorter<TableModel> sorter)
- {
- final JTextField filterField = new JTextField();
- filterField.getDocument().addDocumentListener(new DocumentListener()
- {
- @Override
- public void changedUpdate(DocumentEvent e)
- {
- newFilter();
- }
-
- @Override
- public void insertUpdate(DocumentEvent e)
- {
- newFilter();
- }
-
- @Override
- public void removeUpdate(DocumentEvent e)
- {
- newFilter();
- }
-
- private void newFilter()
- {
- final String text = filterField.getText().toLowerCase();
- RowFilter<TableModel, Object> rf = new RowFilter<TableModel, Object>()
- {
- @Override
- public boolean include(
- Entry<? extends TableModel, ? extends Object> entry)
- {
- for (int i = 0, n = entry.getValueCount(); i < n; i++)
- {
- if (entry.getStringValue(i).toLowerCase().indexOf(text) >= 0)
- {
- return true;
- }
- }
- return false;
- }
- };
- sorter.setRowFilter(rf);
- }
- });
- return filterField;
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IAsyncNodeAction.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IAsyncNodeAction.java
deleted file mode 100644
index 545960183966b4bb3dae1298469966cb7f8c1369..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IAsyncNodeAction.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-/**
- * Action performed asynchronously.
- *
- * @author Franz-Josef Elmer
- */
-public interface IAsyncNodeAction
-{
- public void execute(Runnable runnable);
-
- public void handleException(Throwable throwable);
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IChooserTreeNode.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IChooserTreeNode.java
deleted file mode 100644
index aebf8963b04bda828a9fb03521bd20de35738076..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IChooserTreeNode.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-/**
- * Common interface of all nodes in a {@link ChooserTreeModel}.
- *
- * @author Franz-Josef Elmer
- */
-public interface IChooserTreeNode<T>
-{
- public ChooserTreeNodeType getNodeType();
-
- public T getNodeObject();
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IField.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IField.java
deleted file mode 100644
index 6994d526560c25376bdceafb1e00c49a2e65373f..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IField.java
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import javax.swing.JComponent;
-
-/**
- * Abstraction a GUI field with a String value. It is represented by a {@link JComponent}.
- *
- * @author Franz-Josef Elmer
- */
-public interface IField
-{
- public JComponent getComponent();
-
- public String getValue();
-
- public void setValue(String value);
-}
\ No newline at end of file
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ILoadingBuildingAction.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ILoadingBuildingAction.java
deleted file mode 100644
index fab5406dd5e098e761177d01a62e54eaa28fbc39..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ILoadingBuildingAction.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-/**
- * Two step action (done in different threads): an expensive load action and a fast build action.
- *
- * @author Franz-Josef Elmer
- */
-public interface ILoadingBuildingAction<T>
-{
- public T load();
-
- public void build(T data);
-}
\ No newline at end of file
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IOpenBisNode.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IOpenBisNode.java
deleted file mode 100644
index 1fa05d1944bbabf70256a907de617f73ef496f5b..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IOpenBisNode.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import javax.swing.JPanel;
-
-/**
- * Interface all openBIS nodes have to implement.
- *
- * @author Franz-Josef Elmer
- */
-public interface IOpenBisNode
-{
- public void logError(Throwable throwable);
-
- public JPanel getPanel();
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IOpenbisServiceFacadeFactory.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IOpenbisServiceFacadeFactory.java
deleted file mode 100644
index 1d68193d8de15ce6d534a89582cd416c00e5a3ad..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IOpenbisServiceFacadeFactory.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
-
-/**
- * Factory of a {@link IOpenbisServiceFacade}.
- *
- * @author Franz-Josef Elmer
- */
-public interface IOpenbisServiceFacadeFactory
-{
- public IOpenbisServiceFacade createFacade(String url, String userID, String password);
-
- public IOpenbisServiceFacade createFacade(String url, String sessionToken);
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IQueryApiFacadeProvider.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IQueryApiFacadeProvider.java
deleted file mode 100644
index c1fed990c15558c8d638537e464753be5506352b..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IQueryApiFacadeProvider.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-
-/**
- * Provider of an {@link IQueryApiFacade}.
- *
- * @author Franz-Josef Elmer
- */
-public interface IQueryApiFacadeProvider
-{
- public IQueryApiFacade getQueryFacade();
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IQueryFacadeAction.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IQueryFacadeAction.java
deleted file mode 100644
index 0a5e0840167294c882881885b7ef241b45eadc86..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/IQueryFacadeAction.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-
-/**
- * An action which uses {@link IQueryApiFacade}.
- *
- * @author Franz-Josef Elmer
- */
-public interface IQueryFacadeAction
-{
- public void execute(IQueryApiFacade queryFacade);
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/OpenbisServiceFacadeFactory.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/OpenbisServiceFacadeFactory.java
deleted file mode 100644
index dede6fa8de06d42c24cc345b17f672aca2feecd2..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/OpenbisServiceFacadeFactory.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
-
-/**
- * Standard implementation for {@link IOpenbisServiceFacadeFactory}.
- *
- * @author Franz-Josef Elmer
- */
-public class OpenbisServiceFacadeFactory implements IOpenbisServiceFacadeFactory
-{
- private static final int TIME_OUT = 10000;
-
- @Override
- public IOpenbisServiceFacade createFacade(String url, String userID, String password)
- {
- IOpenbisServiceFacade facade =
- ch.systemsx.cisd.openbis.dss.client.api.v1.OpenbisServiceFacadeFactory.tryCreate(
- userID, password, url, TIME_OUT);
- return check(facade, url);
- }
-
- @Override
- public IOpenbisServiceFacade createFacade(String url, String sessionToken)
- {
- IOpenbisServiceFacade facade =
- ch.systemsx.cisd.openbis.dss.client.api.v1.OpenbisServiceFacadeFactory.tryCreate(sessionToken, url, TIME_OUT);
- return check(facade, url);
- }
-
- private IOpenbisServiceFacade check(IOpenbisServiceFacade facade, String url)
- {
- if (facade == null)
- {
- throw new IllegalArgumentException("Couldn't connect to openBIS at " + url);
- }
- return facade;
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ParameterBindings.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ParameterBindings.java
deleted file mode 100644
index b89c0fe80c7c206df3a00c05ed37d962a7f08b00..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/ParameterBindings.java
+++ /dev/null
@@ -1,97 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.Map.Entry;
-
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-
-/**
- * Helper class for handling parameter bindings.
- *
- * @author Franz-Josef Elmer
- */
-public class ParameterBindings
-{
- public static final String PARAMETER_KEYS_KEY = "query-parameter-keys";
-
- public static final String PARAMETER_VALUES_KEY = "query-parameter-values";
-
- private Map<String, String> bindings = new LinkedHashMap<String, String>();
-
- public void removeAllBindings()
- {
- bindings.clear();
- }
-
- public void bind(String parameter, String value)
- {
- bindings.put(parameter, value);
- }
-
- public Map<String, String> getBindings()
- {
- return bindings;
- }
-
- public String tryToGetBinding(String parameter)
- {
- return bindings.get(parameter);
- }
-
- public void loadValidatedSettingsFrom(NodeSettingsRO settings)
- {
- String[] parameterKeys;
- String[] parameterValues;
- try
- {
- parameterKeys = settings.getStringArray(PARAMETER_KEYS_KEY);
- parameterValues = settings.getStringArray(PARAMETER_VALUES_KEY);
- } catch (InvalidSettingsException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- bindings.clear();
- for (int i = 0, n = Math.min(parameterKeys.length, parameterValues.length); i < n; i++)
- {
- bindings.put(parameterKeys[i], parameterValues[i]);
- }
- }
-
- public void saveSettingsTo(NodeSettingsWO settings)
- {
- List<String> parameterKeys = new ArrayList<String>(bindings.size());
- List<String> parameterValues = new ArrayList<String>(bindings.size());
- Set<Entry<String, String>> entrySet = bindings.entrySet();
- for (Entry<String, String> entry : entrySet)
- {
- parameterKeys.add(entry.getKey());
- parameterValues.add(entry.getValue());
- }
- settings.addStringArray(PARAMETER_KEYS_KEY, parameterKeys.toArray(new String[0]));
- settings.addStringArray(PARAMETER_VALUES_KEY, parameterValues.toArray(new String[0]));
- }
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/TableModelBuilder.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/TableModelBuilder.java
deleted file mode 100644
index f8ef1ed24be1e1be1ec6b0b2c4bd34cb71754166..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/TableModelBuilder.java
+++ /dev/null
@@ -1,209 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import javax.swing.table.AbstractTableModel;
-import javax.swing.table.TableModel;
-
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
-
-/**
- * Builder for a {@link DataSet} based {@link TableModel}.
- *
- * @author Franz-Josef Elmer
- */
-public class TableModelBuilder
-{
- private static final class Column
- {
- private final String name;
-
- private final List<String> values = new ArrayList<String>();
-
- Column(String name)
- {
- this.name = name;
- }
-
- String getName()
- {
- return name;
- }
-
- int getSize()
- {
- return values.size();
- }
-
- String getValue(int rowIndex)
- {
- return rowIndex < getSize() ? values.get(rowIndex) : "";
- }
-
- void addValueAt(int rowIndex, String value)
- {
- while (values.size() < rowIndex)
- {
- values.add("");
- }
- values.add(value == null ? "" : value);
- }
-
- boolean isEmpty()
- {
- for (String value : values)
- {
- if (value.length() > 0)
- {
- return false;
- }
- }
- return true;
- }
-
- boolean hasOnlyOneDistinctValue()
- {
- String distinctValue = null;
- for (String value : values)
- {
- if (distinctValue == null)
- {
- distinctValue = value;
- } else if (distinctValue.equals(value) == false)
- {
- return false;
- }
- }
- return true;
- }
- }
-
- private static final class DataSetTableModel extends AbstractTableModel
- {
- private static final long serialVersionUID = 1L;
-
- private final List<Column> columns;
-
- private DataSetTableModel(List<Column> columns)
- {
- this.columns = columns;
- }
-
- @Override
- public boolean isCellEditable(int row, int column)
- {
- return false;
- }
-
- @Override
- public int getRowCount()
- {
- int rowCount = 0;
- for (Column column : columns)
- {
- rowCount = Math.max(rowCount, column.getSize());
- }
- return rowCount;
- }
-
- @Override
- public int getColumnCount()
- {
- return columns.size();
- }
-
- @Override
- public String getColumnName(int columnIndex)
- {
- return columns.get(columnIndex).getName();
- }
-
- @Override
- public Object getValueAt(int rowIndex, int columnIndex)
- {
- return columns.get(columnIndex).getValue(rowIndex);
- }
- }
-
- private final Column codeColumn = new Column("Code");
-
- private final Column typeColumn = new Column("Type");
-
- private final Column experimentColumn = new Column("Experiment");
-
- private final Column sampleColumn = new Column("Sample");
-
- private final Map<String, Column> propertyColumns = new HashMap<String, Column>();
-
- private int numberOfAddedDataSets;
-
- public TableModel getTableModel()
- {
- final List<Column> columns = new ArrayList<Column>(propertyColumns.values());
- Collections.sort(columns, new Comparator<Column>()
- {
- @Override
- public int compare(Column c1, Column c2)
- {
- return c1.getName().compareTo(c2.getName());
- }
- });
- columns.add(0, experimentColumn);
- if (sampleColumn.isEmpty() == false)
- {
- columns.add(0, sampleColumn);
- }
- if (typeColumn.hasOnlyOneDistinctValue() == false)
- {
- columns.add(0, typeColumn);
- }
- columns.add(0, codeColumn);
- return new DataSetTableModel(columns);
- }
-
- public void add(DataSet dataSet)
- {
- codeColumn.addValueAt(numberOfAddedDataSets, dataSet.getCode());
- typeColumn.addValueAt(numberOfAddedDataSets, dataSet.getDataSetTypeCode());
- experimentColumn.addValueAt(numberOfAddedDataSets, dataSet.getExperimentIdentifier());
- sampleColumn.addValueAt(numberOfAddedDataSets, dataSet.getSampleIdentifierOrNull());
- HashMap<String, String> properties = dataSet.getProperties();
- Set<java.util.Map.Entry<String, String>> entrySet = properties.entrySet();
- for (Entry<String, String> entry : entrySet)
- {
- String key = entry.getKey();
- Column column = propertyColumns.get(key);
- if (column == null)
- {
- column = new Column(key);
- propertyColumns.put(key, column);
- }
- column.addValueAt(numberOfAddedDataSets, entry.getValue());
- }
- numberOfAddedDataSets++;
- }
-
-}
\ No newline at end of file
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/TextField.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/TextField.java
deleted file mode 100644
index 4acceb6f96798b5ea3509b7cdc496b6dffa89e94..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/TextField.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import javax.swing.JComponent;
-import javax.swing.JTextField;
-
-/**
- * One line text field.
- *
- * @author Franz-Josef Elmer
- */
-class TextField implements IField
-{
- private JTextField textField;
-
- TextField()
- {
- textField = new JTextField(20);
- }
-
- @Override
- public JComponent getComponent()
- {
- return textField;
- }
-
- @Override
- public String getValue()
- {
- return textField.getText();
- }
-
- @Override
- public void setValue(String value)
- {
- textField.setText(value);
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/Util.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/Util.java
deleted file mode 100644
index dfe58318372a958532cc51b8366eb0cbde2c69cd..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/Util.java
+++ /dev/null
@@ -1,310 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import static ch.systemsx.cisd.openbis.knime.common.AbstractOpenBisNodeModel.PASSWORD_KEY;
-
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import org.apache.commons.lang.StringUtils;
-import org.knime.core.node.NodeLogger;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.util.KnimeEncryption;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.openbis.knime.server.Constants;
-import ch.systemsx.cisd.openbis.knime.server.FieldType;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableColumn;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableColumnDataType;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel;
-
-/**
- * Utility methods.
- *
- * @author Franz-Josef Elmer
- */
-public class Util
-{
- public static final String VARIABLE_PREFIX = "openbis.";
-
- private static final String[] EXPECTED_COLUMNS = { Constants.PARAMETER_DESCRIPTION_NAME_COLUMN,
- Constants.PARAMETER_DESCRIPTION_TYPE_COLUMN };
-
- public static <D extends Serializable> byte[] serializeDescription(D descriptionOrNull)
- {
- if (descriptionOrNull == null)
- {
- return null;
- }
- ByteArrayOutputStream baos = new ByteArrayOutputStream();
- try
- {
- new ObjectOutputStream(baos).writeObject(descriptionOrNull);
- return baos.toByteArray();
- } catch (IOException ex)
- {
- return null;
- }
- }
-
- @SuppressWarnings("unchecked")
- public static <D extends Serializable> D deserializeDescription(byte[] serializeDescriptionOrNull)
- {
- if (serializeDescriptionOrNull == null)
- {
- return null;
- }
- ByteArrayInputStream bais = new ByteArrayInputStream(serializeDescriptionOrNull);
- try
- {
- return (D) new ObjectInputStream(bais).readObject();
- } catch (Exception ex)
- {
- return null;
- }
- }
-
- public static List<FieldDescription> getFieldDescriptions(IQueryApiFacade facade,
- AggregatedDataImportDescription description, NodeLogger logger)
- {
- List<FieldDescription> fieldDescriptions = new ArrayList<FieldDescription>();
- Map<String, Object> serviceParameters = new HashMap<String, Object>();
- serviceParameters.put(Constants.REQUEST_KEY, Constants.GET_PARAMETER_DESCRIPTIONS_REQUEST);
- QueryTableModel report =
- createReportFromAggregationService(facade, description, serviceParameters);
- List<QueryTableColumn> columns = report.getColumns();
- if (columns.size() != EXPECTED_COLUMNS.length)
- {
- throw createException(description, columns.size() + " columns instead of " + EXPECTED_COLUMNS.length);
- }
- for (int i = 0; i < EXPECTED_COLUMNS.length; i++)
- {
- String expectedColumn = EXPECTED_COLUMNS[i];
- String column = columns.get(i).getTitle();
- if (expectedColumn.equals(column) == false)
- {
- throw createException(description, (i + 1) + ". column is '" + column
- + "' instead of '" + expectedColumn + "'.");
- }
- }
- List<Serializable[]> rows = report.getRows();
- for (Serializable[] row : rows)
- {
- if (row == null || row.length == 0 || row[0] == null)
- {
- throw createException(description, "Empty row.");
- }
- String name = String.valueOf(row[0]);
- if (StringUtils.isBlank(name))
- {
- throw createException(description, "Unspecified parameter name.");
- }
- FieldType fieldType = FieldType.VARCHAR;
- String fieldParameters = "";
- if (row.length > 1)
- {
- Serializable parameter = row[1];
- if (parameter != null)
- {
- String type = String.valueOf(parameter);
- int indexOfSeparator = type.indexOf(':');
- if (indexOfSeparator >= 0)
- {
- fieldParameters = type.substring(indexOfSeparator + 1);
- type = type.substring(0, indexOfSeparator);
- }
- try
- {
- fieldType = FieldType.valueOf(type.trim().toUpperCase());
- } catch (IllegalArgumentException ex)
- {
- logger.warn("Unknown field type '" + type + "' using " + fieldType + " instead.");
- }
- }
- }
- fieldDescriptions.add(new FieldDescription(name, fieldType, fieldParameters));
- }
- return fieldDescriptions;
- }
-
- private static RuntimeException createException(AggregatedDataImportDescription description, String msg)
- {
- String service = description.getAggregationServiceDescription().getServiceKey();
- return new IllegalArgumentException("Invalid response of aggregation service '" + service + "' when invoked with parameter "
- + Constants.REQUEST_KEY + " = " + Constants.GET_PARAMETER_DESCRIPTIONS_REQUEST + ":\n" + msg);
- }
-
- public static ColumnType getColumnType(QueryTableColumnDataType dataType)
- {
- switch (dataType)
- {
- case DOUBLE:
- return ColumnType.DOUBLE;
- case LONG:
- return ColumnType.LONG;
- default:
- return ColumnType.STRING;
- }
- }
-
- public static String getDecryptedPassword(NodeSettingsRO settings)
- {
- try
- {
- String encryptedPassword = settings.getString(PASSWORD_KEY, "");
- return StringUtils.isBlank(encryptedPassword) ? "" : KnimeEncryption.decrypt(encryptedPassword);
- } catch (Exception ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- }
-
- public static String getEncryptedPassword(char[] bytes)
- {
- try
- {
- return KnimeEncryption.encrypt(bytes);
- } catch (Exception ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- }
-
- public static QueryTableModel createReportFromAggregationService(IQueryApiFacade facade,
- ParameterBindings parameterBindings, AggregatedDataImportDescription description)
- {
- Map<String, Object> serviceParameters = new HashMap<String, Object>();
- for (Entry<String, String> entry : parameterBindings.getBindings().entrySet())
- {
- serviceParameters.put(entry.getKey(), entry.getValue());
- }
- return createReportFromAggregationService(facade, description, serviceParameters);
- }
-
- public static QueryTableModel createReportFromAggregationService(IQueryApiFacade facade,
- AggregatedDataImportDescription description, Map<String, Object> serviceParameters)
- {
- QueryTableModel result = facade.createReportFromAggregationService(
- description.getAggregationServiceDescription(), serviceParameters);
- assertNoError(result, description);
- return result;
- }
-
- private static void assertNoError(QueryTableModel result, AggregatedDataImportDescription description)
- {
- List<QueryTableColumn> columns = result.getColumns();
- if (columns.size() != 5 || columns.get(0).getTitle().equals(Constants.EXCEPTION_COLUMN) == false)
- {
- return;
- }
- ExceptionReplicate rootException = null;
- ExceptionReplicate previousException = null;
- ExceptionReplicate currentExecption = null;
- List<Serializable[]> rows = result.getRows();
- List<StackTraceElement> stackTrace = new ArrayList<StackTraceElement>();
- for (Serializable[] row : rows)
- {
- Serializable exception = row[0];
- if ("".equals(exception) == false)
- {
- currentExecption = new ExceptionReplicate(String.valueOf(row[0]));
- if (previousException != null)
- {
- previousException.setStackTrace(stackTrace.toArray(new StackTraceElement[0]));
- previousException.setCause(currentExecption);
- stackTrace.clear();
- } else
- {
- rootException = currentExecption;
- }
- previousException = currentExecption;
- } else if (currentExecption != null)
- {
- int lineNumber;
- try
- {
- lineNumber = Integer.parseInt(String.valueOf(row[4]));
- } catch (NumberFormatException ex)
- {
- lineNumber = 0;
- }
- StackTraceElement stackTraceElement = new StackTraceElement(String.valueOf(row[1]),
- String.valueOf(row[2]), String.valueOf(row[3]),
- lineNumber);
- stackTrace.add(stackTraceElement);
- }
- }
- if (currentExecption != null && stackTrace.isEmpty() == false)
- {
- currentExecption.setStackTrace(stackTrace.toArray(new StackTraceElement[0]));
- }
- if (rootException != null)
- {
- throw new RuntimeException(rootException);
- }
- }
-
- private static final class ExceptionReplicate extends RuntimeException
- {
- private static final long serialVersionUID = 1L;
-
- private static String extractMessage(String toStringText)
- {
- int indexOfColon = toStringText.indexOf(":");
- return indexOfColon < 0 ? "" : toStringText.substring(indexOfColon + 1).trim();
- }
-
- private final String toStringText;
-
- private ExceptionReplicate cause;
-
- ExceptionReplicate(String toStringText)
- {
- super(extractMessage(toStringText));
- this.toStringText = toStringText;
- }
-
- public void setCause(ExceptionReplicate cause)
- {
- this.cause = cause;
- }
-
- @Override
- public Throwable getCause()
- {
- return cause;
- }
-
- @Override
- public String toString()
- {
- return toStringText;
- }
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/VocabularyField.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/VocabularyField.java
deleted file mode 100644
index 26cd1d9fd3ba4264a36a9c212c490146a8860727..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/VocabularyField.java
+++ /dev/null
@@ -1,69 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.JComboBox;
-import javax.swing.JComponent;
-
-import org.apache.commons.lang.StringUtils;
-
-/**
- * Combo box with a list of String terms.
- *
- * @author Franz-Josef Elmer
- */
-class VocabularyField implements IField
-{
- private JComboBox comboBox;
-
- public VocabularyField(String fieldParameters)
- {
- String[] splittedParameters = fieldParameters.split(",");
- List<String> terms = new ArrayList<String>();
- for (String term : splittedParameters)
- {
- if (StringUtils.isNotBlank(term))
- {
- terms.add(term.trim());
- }
- }
- comboBox = new JComboBox(terms.toArray());
- comboBox.setEditable(false);
- }
-
- @Override
- public JComponent getComponent()
- {
- return comboBox;
- }
-
- @Override
- public String getValue()
- {
- return (String) comboBox.getSelectedItem();
- }
-
- @Override
- public void setValue(String value)
- {
- comboBox.setSelectedItem(value);
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/openbis.png b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/openbis.png
deleted file mode 100644
index a5b30672e374063ad0b36c4469a028e9e61090d7..0000000000000000000000000000000000000000
Binary files a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/common/openbis.png and /dev/null differ
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeFactory.xml b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeFactory.xml
deleted file mode 100644
index 91e12e4538ad5ecfe997a626b380d623d9efa3e8..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeFactory.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
-<knimeNode icon="../common/openbis.png" type="Source">
- <name>openBIS Aggregated Data File Importer</name>
-
- <shortDescription>Imports a data file from special openBIS aggregation services.</shortDescription>
-
- <fullDescription>
- <intro>This data source node invokes a special openBIS aggregation services which creates from some input
- parameters a file which is delivered to the node at execution time.
- <p>
- For more details see <a href="https://wiki-bsse.ethz.ch/display/openBISDoc1304/openBIS+KNIME+Nodes">openBIS KNIME Nodes</a>.
- </p>
- </intro>
- </fullDescription>
-
- <ports>
- <outPort index="0" name="Result Set">URI of the imported data file.</outPort>
- </ports>
-</knimeNode>
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeModel.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeModel.java
deleted file mode 100644
index 177c92a42e8f72016487e6abfea9589235c0e8ea..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeModel.java
+++ /dev/null
@@ -1,174 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.net.URL;
-import java.net.URLEncoder;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.activation.MimetypesFileTypeMap;
-
-import org.apache.commons.io.IOUtils;
-import org.knime.core.data.uri.URIContent;
-import org.knime.core.data.uri.URIPortObject;
-import org.knime.core.data.uri.URIPortObjectSpec;
-import org.knime.core.node.ExecutionContext;
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-import org.knime.core.node.port.PortObject;
-import org.knime.core.node.port.PortObjectSpec;
-import org.knime.core.node.port.PortType;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStore;
-import ch.systemsx.cisd.openbis.knime.common.AbstractOpenBisNodeModel;
-import ch.systemsx.cisd.openbis.knime.common.AggregatedDataImportDescription;
-import ch.systemsx.cisd.openbis.knime.common.ParameterBindings;
-import ch.systemsx.cisd.openbis.knime.common.Util;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel;
-
-/**
- * Model which requests a data file created by an aggregation service.
- *
- * @author Franz-Josef Elmer
- */
-public class AggregatedDataFileImportNodeModel extends AbstractOpenBisNodeModel
-{
- static final String FILE_PATH_FLOW_VARIABLE = "absolute-file-path";
-
- private AggregatedDataImportDescription description;
-
- private ParameterBindings parameterBindings = new ParameterBindings();
-
- public AggregatedDataFileImportNodeModel()
- {
- super(new PortType[] {}, new PortType[] { new PortType(URIPortObject.class) });
- }
-
- @Override
- protected void loadAdditionalValidatedSettingsFrom(NodeSettingsRO settings)
- throws InvalidSettingsException
- {
- description = Util.deserializeDescription(
- settings.getByteArray(AggregatedDataImportDescription.AGGREGATION_DESCRIPTION_KEY));
- parameterBindings.loadValidatedSettingsFrom(settings);
- }
-
- @Override
- protected void saveAdditionalSettingsTo(NodeSettingsWO settings)
- {
- settings.addByteArray(AggregatedDataImportDescription.AGGREGATION_DESCRIPTION_KEY,
- Util.serializeDescription(description));
- parameterBindings.saveSettingsTo(settings);
- }
-
- @Override
- protected PortObjectSpec[] configure(PortObjectSpec[] inSpecs) throws InvalidSettingsException
- {
- return new PortObjectSpec[] { new URIPortObjectSpec(createType("")) };
- }
-
- @Override
- protected PortObject[] execute(PortObject[] inObjects, ExecutionContext exec) throws Exception
- {
- IQueryApiFacade facade = createQueryFacade();
- try
- {
- QueryTableModel report =
- Util.createReportFromAggregationService(facade, parameterBindings, description);
- String fileName = (String) report.getRows().get(0)[0];
- String downloadUrl = getDataStore(facade).getDownloadUrl();
- File systemTempDir = getSystemTempDir();
- File file = download(facade.getSessionToken(), systemTempDir, fileName, downloadUrl);
- addFlowVariable(FILE_PATH_FLOW_VARIABLE, file.getAbsolutePath());
- String type = createType(fileName);
- logger.info("Content MIME type: " + type);
- return new PortObject[]
- { new URIPortObject(new URIPortObjectSpec(type), Arrays.asList(new URIContent(file
- .toURI(), type))) };
- } finally
- {
- facade.logout();
- }
- }
-
- protected File getSystemTempDir()
- {
- return new File(System.getProperty("java.io.tmpdir"));
- }
-
- private File download(String sessionToken, File systemTempDir, String fileName, String baseURL)
- {
- File tempDir = new File(systemTempDir, "knime-openbis-" + sessionToken);
- tempDir.mkdirs();
- tempDir.deleteOnExit();
- File file = new File(tempDir, fileName);
- file.deleteOnExit();
- InputStream in = null;
- OutputStream out = null;
- try
- {
- in = new URL(baseURL + "/session_workspace_file_download?sessionID=" + sessionToken
- + "&filePath=" + URLEncoder.encode(fileName, "UTF-8")).openStream();
- file.getParentFile().mkdirs();
- out = new FileOutputStream(file);
- byte[] buffer = new byte[1024];
- int size = 0;
- while ((size = in.read(buffer)) != -1)
- {
- out.write(buffer, 0, size);
- }
- return file;
- } catch (Exception ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- IOUtils.closeQuietly(in);
- IOUtils.closeQuietly(out);
- }
- }
-
- private DataStore getDataStore(IQueryApiFacade facade)
- {
- String dataStoreCode = description.getAggregationServiceDescription().getDataStoreCode();
- String sessionToken = facade.getSessionToken();
- IGeneralInformationService service = facade.getGeneralInformationService();
- List<DataStore> dataStores = service.listDataStores(sessionToken);
- for (DataStore dataStore : dataStores)
- {
- if (dataStore.getCode().equals(dataStoreCode))
- {
- return dataStore;
- }
- }
- throw new IllegalArgumentException("Unknown data store: " + dataStoreCode);
- }
-
- private String createType(String fileName)
- {
- return MimetypesFileTypeMap.getDefaultFileTypeMap().getContentType(fileName);
- }
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeFactory.xml b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeFactory.xml
deleted file mode 100644
index 04a998a96824997f649663b5c8a840015fe72892..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeFactory.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
-<knimeNode icon="../common/openbis.png" type="Source">
- <name>openBIS Data Set File Importer</name>
-
- <shortDescription>Imports a file from a selected data set of an openBIS instance.</shortDescription>
-
- <fullDescription>
- <intro>A selected file of a data set is imported and stored locally.
- An URI pointing to this file is provided so that other nodes can access its content.
- <p>
- For more details see <a href="https://wiki-bsse.ethz.ch/display/openBISDoc1304/openBIS+KNIME+Nodes">openBIS KNIME Nodes</a>.
- </p>
- </intro>
- </fullDescription>
-
- <ports>
- <outPort index="0" name="Result Set">URI of the imported file.</outPort>
- </ports>
-</knimeNode>
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeModel.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeModel.java
deleted file mode 100644
index c0eda096976816be2328c39e91caecce035fced9..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeModel.java
+++ /dev/null
@@ -1,180 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.util.Arrays;
-
-import javax.activation.MimetypesFileTypeMap;
-
-import org.knime.core.data.uri.URIContent;
-import org.knime.core.data.uri.URIPortObject;
-import org.knime.core.data.uri.URIPortObjectSpec;
-import org.knime.core.node.ExecutionContext;
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-import org.knime.core.node.port.PortObject;
-import org.knime.core.node.port.PortObjectSpec;
-import org.knime.core.node.port.PortType;
-
-import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
-import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
-import ch.systemsx.cisd.openbis.knime.common.AbstractOpenBisNodeModel;
-import ch.systemsx.cisd.openbis.knime.common.IOpenbisServiceFacadeFactory;
-import ch.systemsx.cisd.openbis.knime.common.Util;
-
-/**
- * Node model for importing a file/folder from Data Store Server.
- *
- * @author Franz-Josef Elmer
- */
-public class DataSetFileImportNodeModel extends AbstractOpenBisNodeModel
-{
- static final String DATA_SET_CODE_KEY = "data-set-code";
-
- static final String FILE_PATH_KEY = "file-path";
-
- static final String DOWNLOADS_PATH_KEY = "downloads-path";
-
- static final String ABSOLUTE_FILE_PATH_KEY = "absolute-file-path";
-
- static final String REUSE_FILE = "reuse-file";
-
- private final IOpenbisServiceFacadeFactory serviceFacadeFactory;
-
- private String dataSetCode = "";
-
- private String filePath = "";
-
- private String dowloadsPath = "";
-
- private boolean reuseFile;
-
- public DataSetFileImportNodeModel(IOpenbisServiceFacadeFactory serviceFacadeFactory)
- {
- super(new PortType[] {}, new PortType[]
- { new PortType(URIPortObject.class) });
- this.serviceFacadeFactory = serviceFacadeFactory;
- }
-
- @Override
- protected void loadAdditionalValidatedSettingsFrom(NodeSettingsRO settings)
- throws InvalidSettingsException
- {
- dataSetCode = settings.getString(DATA_SET_CODE_KEY);
- filePath = settings.getString(FILE_PATH_KEY);
- dowloadsPath = settings.getString(DOWNLOADS_PATH_KEY);
- reuseFile = settings.getBoolean(REUSE_FILE, false);
- }
-
- @Override
- protected void saveAdditionalSettingsTo(NodeSettingsWO settings)
- {
- settings.addString(DATA_SET_CODE_KEY, dataSetCode);
- settings.addString(FILE_PATH_KEY, filePath);
- settings.addString(DOWNLOADS_PATH_KEY, dowloadsPath);
- settings.addString(ABSOLUTE_FILE_PATH_KEY, dowloadsPath + "/" + dataSetCode + "/" + filePath);
- settings.addBoolean(REUSE_FILE, reuseFile);
- }
-
- @Override
- protected PortObjectSpec[] configure(PortObjectSpec[] inSpecs) throws InvalidSettingsException
- {
- String type = createType();
- return new PortObjectSpec[]
- { new URIPortObjectSpec(type) };
- }
-
- @Override
- protected PortObject[] execute(PortObject[] inObjects, ExecutionContext exec) throws Exception
- {
- File file = new File(dowloadsPath, dataSetCode + "/" + filePath);
- if (reuseFile == false || file.exists() == false)
- {
- downloadTo(file);
- }
- String type = createType();
- logger.info("Content MIME type: " + type);
- return new PortObject[]
- { new URIPortObject(new URIPortObjectSpec(type), Arrays.asList(new URIContent(file.toURI(), type))) };
- }
-
- private void downloadTo(File file) throws Exception
- {
- InputStream in = null;
- OutputStream out = null;
- IOpenbisServiceFacade facade = null;
- try
- {
- facade = serviceFacadeFactory.createFacade(url, userID, password);
- DataSet dataSet = facade.getDataSet(dataSetCode);
- if (dataSet == null)
- {
- throw new IllegalArgumentException("Unknown data set '" + dataSetCode + "'.");
- }
- pushDataSetMetaDataToVariables(dataSet);
- in = dataSet.getFile(filePath);
- file.getParentFile().mkdirs();
- out = new FileOutputStream(file);
- byte[] buffer = new byte[1024];
- int size = 0;
- while ((size = in.read(buffer)) != -1)
- {
- out.write(buffer, 0, size);
- }
- } finally
- {
- if (out != null)
- {
- out.close();
- }
- if (in != null)
- {
- in.close();
- }
- if (facade != null)
- {
- facade.logout();
- }
- }
- }
-
- private void pushDataSetMetaDataToVariables(DataSet dataSet)
- {
- addFlowVariable(Util.VARIABLE_PREFIX + DataSetOwnerType.DATA_SET.name(),
- dataSet.getCode());
- addFlowVariable(Util.VARIABLE_PREFIX + DataSetOwnerType.EXPERIMENT.name(),
- dataSet.getExperimentIdentifier());
- String sampleIdentifierOrNull = dataSet.getSampleIdentifierOrNull();
- if (sampleIdentifierOrNull != null)
- {
- addFlowVariable(Util.VARIABLE_PREFIX + DataSetOwnerType.SAMPLE.name(),
- sampleIdentifierOrNull);
- }
- }
-
- private String createType()
- {
- return MimetypesFileTypeMap.getDefaultFileTypeMap().getContentType(filePath);
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeFactory.xml b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeFactory.xml
deleted file mode 100644
index 6bc5adca2603b278d1b003384d645d5790f8f2d4..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeFactory.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
-<knimeNode icon="../common/openbis.png" type="Source">
- <name>openBIS Data Set Registration (URI Port)</name>
-
- <shortDescription>Registers a file as a data set on an openBIS instance.</shortDescription>
-
- <fullDescription>
- <intro>The URI input port specifies the location of the file to be registered.
- The owner of the freshly registered data set is specified by a variable.
- <p>
- For more details see <a href="https://wiki-bsse.ethz.ch/display/openBISDoc1304/openBIS+KNIME+Nodes">openBIS KNIME Nodes</a>.
- </p>
- </intro>
- </fullDescription>
-
- <ports>
- <inPort index="0" name="Result Set">URI of the file to be registered.</inPort>
- </ports>
-</knimeNode>
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeModel.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeModel.java
deleted file mode 100644
index 810122efe2095597098a9d546afbea8481a42219..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeModel.java
+++ /dev/null
@@ -1,299 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.NoSuchElementException;
-import java.util.Set;
-
-import org.apache.commons.lang.StringUtils;
-import org.knime.core.data.uri.URIContent;
-import org.knime.core.data.uri.URIPortObject;
-import org.knime.core.node.ExecutionContext;
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeModel;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-import org.knime.core.node.port.PortObject;
-import org.knime.core.node.port.PortObjectSpec;
-import org.knime.core.node.port.PortType;
-import org.knime.core.node.port.flowvariable.FlowVariablePortObject;
-import org.knime.core.node.workflow.FlowVariable;
-
-import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
-import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
-import ch.systemsx.cisd.openbis.knime.common.AbstractOpenBisNodeModel;
-import ch.systemsx.cisd.openbis.knime.common.IOpenbisServiceFacadeFactory;
-import ch.systemsx.cisd.openbis.knime.common.Util;
-
-/**
- * {@link NodeModel} for registration of a file as a new data set. The file path is expected as an {@link URIPortObject}.
- *
- * @author Franz-Josef Elmer
- */
-public class DataSetRegistrationNodeModel extends AbstractOpenBisNodeModel
-{
- static final String DATA_SET_TYPE_KEY = "data-set-type";
-
- static final String OWNER_TYPE_KEY = "owner-type";
-
- static final String OWNER_KEY = "owner";
-
- static final String FILE_VARIABLE_KEY = "file-variable";
-
- static final String PROPERTY_TYPE_CODES_KEY = "property-type-codes";
-
- static final String PROPERTY_VALUES_KEY = "property-values";
-
- private final IOpenbisServiceFacadeFactory serviceFacadeFactory;
-
- private DataSetOwnerType ownerType;
-
- private String owner;
-
- private String fileVariable;
-
- private Map<String, String> properties;
-
- private DataSetType dataSetType;
-
- public DataSetRegistrationNodeModel(IOpenbisServiceFacadeFactory serviceFacadeFactory)
- {
- this(URIPortObject.class, serviceFacadeFactory);
- }
-
- protected DataSetRegistrationNodeModel(Class<? extends PortObject> portObjectClass,
- IOpenbisServiceFacadeFactory serviceFacadeFactory)
- {
- super(new PortType[] { new PortType(portObjectClass) }, new PortType[] {});
- this.serviceFacadeFactory = serviceFacadeFactory;
- }
-
- @Override
- protected PortObjectSpec[] configure(PortObjectSpec[] inSpecs) throws InvalidSettingsException
- {
- return new PortObjectSpec[] {};
- }
-
- @Override
- protected void loadAdditionalValidatedSettingsFrom(NodeSettingsRO settings)
- throws InvalidSettingsException
- {
- byte[] bytes = settings.getByteArray(DATA_SET_TYPE_KEY, null);
- dataSetType = (DataSetType) Util.deserializeDescription(bytes);
- ownerType = DataSetOwnerType.valueOf(settings.getString(OWNER_TYPE_KEY));
- owner = settings.getString(OWNER_KEY);
- fileVariable = settings.getString(FILE_VARIABLE_KEY, null);
- properties = getProperties(settings);
- }
-
- static Map<String, String> getProperties(NodeSettingsRO settings)
- throws InvalidSettingsException
- {
- String[] propertyTypeCodes = settings.getStringArray(PROPERTY_TYPE_CODES_KEY, new String[0]);
- String[] propertyValues = settings.getStringArray(PROPERTY_VALUES_KEY, new String[0]);
- if (propertyTypeCodes.length != propertyValues.length)
- {
- throw new InvalidSettingsException("Corrupted properties: " + propertyTypeCodes.length
- + " property type codes but " + propertyValues.length + " values.");
- }
- Map<String, String> props = new HashMap<String, String>();
- for (int i = 0; i < propertyTypeCodes.length; i++)
- {
- String propertyValue = propertyValues[i];
- if (StringUtils.isNotBlank(propertyValue))
- {
- props.put(propertyTypeCodes[i], propertyValue);
- }
- }
- return props;
- }
-
- @Override
- protected void saveAdditionalSettingsTo(NodeSettingsWO settings)
- {
- if (fileVariable != null)
- {
- settings.addString(FILE_VARIABLE_KEY, fileVariable);
- }
- if (dataSetType != null)
- {
- settings.addByteArray(DATA_SET_TYPE_KEY, Util.serializeDescription(dataSetType));
- }
- settings.addString(OWNER_TYPE_KEY, (ownerType == null ? DataSetOwnerType.EXPERIMENT
- : ownerType).name());
- settings.addString(OWNER_KEY, owner);
- if (properties != null)
- {
- List<String> propertyTypeCodes = new ArrayList<String>(properties.size());
- List<String> propertyValues = new ArrayList<String>(properties.size());
- Set<Entry<String, String>> entrySet = properties.entrySet();
- for (Entry<String, String> entry : entrySet)
- {
- String value = entry.getValue();
- if (StringUtils.isNotBlank(value))
- {
- propertyTypeCodes.add(entry.getKey());
- propertyValues.add(value);
- }
- }
- settings.addStringArray(PROPERTY_TYPE_CODES_KEY, propertyTypeCodes.toArray(new String[0]));
- settings.addStringArray(PROPERTY_VALUES_KEY, propertyValues.toArray(new String[0]));
- }
- }
-
- @Override
- protected PortObject[] execute(PortObject[] inObjects, ExecutionContext exec) throws Exception
- {
- File file = getFirstFile(inObjects);
- logger.info("data set file: " + file);
- NewDataSetDTOBuilder builder = new NewDataSetDTOBuilder();
- builder.setDataSetOwnerType(ownerType);
- if (owner != null && owner.trim().length() > 0)
- {
- builder.setDataSetOwnerIdentifier(owner.trim());
- } else
- {
- String variableName = Util.VARIABLE_PREFIX + ownerType.name();
- try
- {
- builder.setDataSetOwnerIdentifier(getStringFlowVariable(variableName));
- } catch (NoSuchElementException ex)
- {
- throw new IllegalArgumentException("Owner " + ownerType.toString().toLowerCase()
- + " hasn't been specified. Also flow variable '"
- + variableName + "' is undefined.");
- }
- }
- builder.setFile(file);
- NewDataSetMetadataDTO dataSetMetadata = builder.getDataSetMetadata();
- dataSetMetadata.setDataSetTypeOrNull(dataSetType.getCode());
- dataSetMetadata.setProperties(properties);
- NewDataSetDTO dataSetDTO = builder.asNewDataSetDTO();
-
- IOpenbisServiceFacade facade = null;
- try
- {
- facade = serviceFacadeFactory.createFacade(url, userID, password);
- checkOwner(dataSetDTO, facade);
- facade.putDataSet(dataSetDTO, file);
- return new PortObject[] {};
- } finally
- {
- if (facade != null)
- {
- facade.logout();
- }
- }
- }
-
- private void checkOwner(NewDataSetDTO dataSetDTO, IOpenbisServiceFacade facade)
- {
- String identifier = dataSetDTO.getDataSetOwner().getIdentifier();
- DataSetOwnerType type = dataSetDTO.getDataSetOwner().getType();
- try
- {
- switch (type)
- {
- case EXPERIMENT:
- List<Experiment> experiments = facade.getExperiments(Collections.singletonList(identifier));
- if (experiments.isEmpty())
- {
- throw new IllegalArgumentException("Unknown experiment.");
- }
- break;
- case SAMPLE:
- List<Sample> samples = facade.getSamples(Collections.singletonList(identifier));
- if (samples.isEmpty())
- {
- throw new IllegalArgumentException("Unknown sample.");
- } else if (samples.get(0).getExperimentIdentifierOrNull() == null)
- {
- throw new IllegalArgumentException("Not directly linked to an experiment.");
- }
- break;
- case DATA_SET:
- DataSet dataSet = facade.getDataSet(identifier);
- if (dataSet == null)
- {
- throw new IllegalArgumentException("Unknown data set.");
- }
- }
- } catch (Exception ex)
- {
- throw new IllegalArgumentException("Error for data set owner of type " + type.toString().toLowerCase() + " '"
- + identifier + "': " + ex.getMessage(), ex);
- }
- }
-
- private File getFirstFile(PortObject[] inObjects)
- {
- if (inObjects.length != 1)
- {
- throw new IllegalArgumentException("Expecting exactly one port instead of " + inObjects.length + ".");
- }
- PortObject portObject = inObjects[0];
- File file;
- if (portObject instanceof URIPortObject)
- {
- List<URIContent> uriContents = ((URIPortObject) portObject).getURIContents();
- if (uriContents.isEmpty())
- {
- throw new IllegalArgumentException("Expecting at least on URI in input port.");
- }
- if (uriContents.size() > 1)
- {
- logger.warn(uriContents.size() + " URIs instead of only one: " + uriContents);
- }
- file = new File(uriContents.get(0).getURI());
- } else if (portObject instanceof FlowVariablePortObject)
- {
- if (StringUtils.isBlank(fileVariable))
- {
- throw new IllegalArgumentException("Unspecified file variable.");
- }
- file = new File(getStringFlowVariable(fileVariable));
- } else
- {
- throw new IllegalArgumentException("Invalid port: " + portObject.getClass().getName() + ".");
- }
- if (file.exists() == false)
- {
- throw new IllegalArgumentException("File does not exist: " + file);
- }
- return file;
- }
-
- protected Map<String, FlowVariable> getFlowVariables()
- {
- return getAvailableFlowVariables();
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationViaFlowNodeFactory.xml b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationViaFlowNodeFactory.xml
deleted file mode 100644
index 1f7e38543401be35e184fadce2df9ce01ab1cc80..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationViaFlowNodeFactory.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
-<knimeNode icon="../common/openbis.png" type="Source">
- <name>openBIS Data Set Registration (Flow Variable Port)</name>
-
- <shortDescription>Registers a file as a data set on an openBIS instance.</shortDescription>
-
- <fullDescription>
- <intro>A flow variable specifies the location of the file to be registered.
- The owner of the freshly registered data set is specified by a variable.
- <p>
- For more details see <a href="https://wiki-bsse.ethz.ch/display/openBISDoc1304/openBIS+KNIME+Nodes">openBIS KNIME Nodes</a>.
- </p>
- </intro>
- </fullDescription>
-
- <ports>
- <inPort index="0" name="Result Set">Flow variables.</inPort>
- </ports>
-</knimeNode>
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationViaFlowNodeModel.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationViaFlowNodeModel.java
deleted file mode 100644
index 92fe00bc5da38870a6dc997b5b978d26b35ad839..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationViaFlowNodeModel.java
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import org.knime.core.node.NodeModel;
-import org.knime.core.node.port.flowvariable.FlowVariablePortObject;
-
-import ch.systemsx.cisd.openbis.knime.common.IOpenbisServiceFacadeFactory;
-
-/**
- * {@link NodeModel} for registration of a file as a new data set. The file path is expected as a flow variable.
- *
- * @author Franz-Josef Elmer
- */
-public class DataSetRegistrationViaFlowNodeModel extends DataSetRegistrationNodeModel
-{
-
- protected DataSetRegistrationViaFlowNodeModel(IOpenbisServiceFacadeFactory serviceFacadeFactory)
- {
- super(FlowVariablePortObject.class, serviceFacadeFactory);
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/FileChooser.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/FileChooser.java
deleted file mode 100644
index 6bc59ae8efc08b7d0f9efbde39d3a2ea6e9cd4ec..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/file/FileChooser.java
+++ /dev/null
@@ -1,239 +0,0 @@
-/*
- * Copyright 2012 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.Window;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Comparator;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JTree;
-import javax.swing.SwingUtilities;
-import javax.swing.tree.DefaultTreeModel;
-import javax.swing.tree.TreeNode;
-import javax.swing.tree.TreePath;
-import javax.swing.tree.TreeSelectionModel;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
-
-/**
- * Chooser for files in a data set.
- *
- * @author Franz-Josef Elmer
- */
-public class FileChooser extends JPanel
-{
- private static final class FileNode implements TreeNode
- {
- private final FileInfoDssDTO fileInfo;
-
- private final String fileName;
-
- private final List<FileNode> children;
-
- private FileNode parent;
-
- FileNode(FileInfoDssDTO fileInfo)
- {
- this.fileInfo = fileInfo;
- children = fileInfo.isDirectory() ? new ArrayList<FileNode>() : null;
- fileName = extractFileName(fileInfo);
- }
-
- @Override
- public boolean getAllowsChildren()
- {
- return fileInfo.isDirectory();
- }
-
- @Override
- public boolean isLeaf()
- {
- return fileInfo.isDirectory() == false;
- }
-
- @Override
- public Enumeration<FileNode> children()
- {
- return new Enumeration<FileNode>()
- {
- Iterator<FileNode> iterator = children.iterator();
-
- @Override
- public boolean hasMoreElements()
- {
- return iterator.hasNext();
- }
-
- @Override
- public FileNode nextElement()
- {
- return iterator.next();
- }
- };
- }
-
- @Override
- public TreeNode getChildAt(int index)
- {
- return children.get(index);
- }
-
- @Override
- public int getChildCount()
- {
- return children == null ? 0 : children.size();
- }
-
- @Override
- public int getIndex(TreeNode node)
- {
- return children.indexOf(node);
- }
-
- @Override
- public TreeNode getParent()
- {
- return parent;
- }
-
- void addChild(FileNode fileNode)
- {
- if (isLeaf() == false)
- {
- children.add(fileNode);
- fileNode.parent = this;
- }
- }
-
- FileInfoDssDTO getFileInfo()
- {
- return fileInfo;
- }
-
- @Override
- public String toString()
- {
- return fileName;
- }
- }
-
- private static final long serialVersionUID = 1L;
-
- private static String extractParentFileName(FileInfoDssDTO fileInfo)
- {
- String path = fileInfo.getPathInDataSet();
- int lastIndexOfPathSeparator = path.lastIndexOf('/');
- return lastIndexOfPathSeparator < 0 ? null : path.substring(0, lastIndexOfPathSeparator);
- }
-
- private static String extractFileName(FileInfoDssDTO fileInfo)
- {
- String path = fileInfo.getPathInDataSet();
- int lastIndexOfPathSeparator = path.lastIndexOf('/');
- return lastIndexOfPathSeparator < 0 ? path : path.substring(lastIndexOfPathSeparator + 1);
- }
-
- private JTree tree;
-
- FileChooser(String dataSetCode, FileInfoDssDTO[] fileInfos)
- {
- super(new BorderLayout());
- add(new JLabel("Choose a single file:"), BorderLayout.NORTH);
- tree = new JTree(new DefaultTreeModel(createTree(dataSetCode, fileInfos), true));
- tree.getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION);
- tree.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent e)
- {
- if (e.getClickCount() < 2)
- {
- return;
- }
- TreePath path = tree.getClosestPathForLocation(e.getX(), e.getY());
- if (path == null)
- {
- return;
- }
- FileInfoDssDTO fileInfo = ((FileNode) path.getLastPathComponent()).getFileInfo();
- if (fileInfo.isDirectory())
- {
- return;
- }
- Window window = SwingUtilities.getWindowAncestor(tree);
- if (window == null)
- {
- return;
- }
- JOptionPane op = (JOptionPane) SwingUtilities.getAncestorOfClass(JOptionPane.class, tree);
- if (op != null)
- {
- op.setValue(JOptionPane.OK_OPTION);
- }
- window.setVisible(false);
- }
- });
- add(new JScrollPane(tree), BorderLayout.CENTER);
- setPreferredSize(new Dimension(500, 700));
- }
-
- private FileNode createTree(String dataSetCode, FileInfoDssDTO[] fileInfos)
- {
- Arrays.sort(fileInfos, new Comparator<FileInfoDssDTO>()
- {
- @Override
- public int compare(FileInfoDssDTO i1, FileInfoDssDTO i2)
- {
- return i1.getPathInDataSet().compareTo(i2.getPathInDataSet());
- }
- });
- FileNode root = new FileNode(new FileInfoDssDTO(dataSetCode, null, true, -1));
- Map<String, FileNode> directories = new HashMap<String, FileChooser.FileNode>();
- for (FileInfoDssDTO fileInfo : fileInfos)
- {
- String parentFileName = extractParentFileName(fileInfo);
- FileNode fileNode = new FileNode(fileInfo);
- (parentFileName == null ? root : directories.get(parentFileName)).addChild(fileNode);
- if (fileInfo.isDirectory())
- {
- directories.put(fileInfo.getPathInDataSet(), fileNode);
- }
- }
- return root;
- }
-
- FileInfoDssDTO getSelectedFileInfoOrNull()
- {
- TreePath selectionPath = tree.getSelectionPath();
- return selectionPath == null ? null : ((FileNode) selectionPath.getLastPathComponent())
- .getFileInfo();
- }
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/AggregatedDataTableImportNodeFactory.xml b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/AggregatedDataTableImportNodeFactory.xml
deleted file mode 100644
index cfa0dc75186fc50d2b1b7b397dd69b54c4258232..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/AggregatedDataTableImportNodeFactory.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
-<knimeNode icon="../common/openbis.png" type="Source">
- <name>openBIS Aggregation Service Report Reader</name>
-
- <shortDescription>Provides the result table form an invocation of a special openBIS aggregation services.</shortDescription>
-
- <fullDescription>
- <intro>This node invokes a special openBIS aggregation services which creates from some input
- parameters a table.
- <p>
- For more details see <a href="https://wiki-bsse.ethz.ch/display/openBISDoc1304/openBIS+KNIME+Nodes">openBIS KNIME Nodes</a>.
- </p>
- </intro>
- </fullDescription>
-
- <ports>
- <outPort index="0" name="Result Set">Table</outPort>
- </ports>
-</knimeNode>
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/AggregatedDataTableImportNodeModel.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/AggregatedDataTableImportNodeModel.java
deleted file mode 100644
index 427f85f95851b2f13976979072e1f719b6d5809d..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/AggregatedDataTableImportNodeModel.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.query;
-
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-
-import ch.systemsx.cisd.openbis.knime.common.AbstractOpenBisNodeTableModel;
-import ch.systemsx.cisd.openbis.knime.common.AggregatedDataImportDescription;
-import ch.systemsx.cisd.openbis.knime.common.ParameterBindings;
-import ch.systemsx.cisd.openbis.knime.common.Util;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class AggregatedDataTableImportNodeModel extends AbstractOpenBisNodeTableModel
-{
- private AggregatedDataImportDescription description;
-
- private ParameterBindings parameterBindings = new ParameterBindings();
-
- @Override
- protected void loadAdditionalValidatedSettingsFrom(NodeSettingsRO settings)
- throws InvalidSettingsException
- {
- description = Util.deserializeDescription(
- settings.getByteArray(AggregatedDataImportDescription.AGGREGATION_DESCRIPTION_KEY));
- parameterBindings.loadValidatedSettingsFrom(settings);
- }
-
- @Override
- protected void saveAdditionalSettingsTo(NodeSettingsWO settings)
- {
- settings.addByteArray(AggregatedDataImportDescription.AGGREGATION_DESCRIPTION_KEY,
- Util.serializeDescription(description));
- parameterBindings.saveSettingsTo(settings);
- }
-
- @Override
- protected QueryTableModel getData(IQueryApiFacade facade)
- {
- return Util.createReportFromAggregationService(facade, parameterBindings, description);
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeFactory.xml b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeFactory.xml
deleted file mode 100644
index 4d9509b1e364798d1890b4f6bea8159d249ef32a..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeFactory.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
-<knimeNode icon="../common/openbis.png" type="Source">
- <name>openBIS Query Reader</name>
-
- <shortDescription>Provides the result table form an invocation of a parameterized SQL Query on an openBIS instance.</shortDescription>
-
- <fullDescription>
- <intro>This data source node invokes a parameterized SQL query on an openBIS Application Server.
- <p>
- For more details see <a href="https://wiki-bsse.ethz.ch/display/openBISDoc1304/openBIS+KNIME+Nodes">openBIS KNIME Nodes</a>.
- </p>
- </intro>
- </fullDescription>
-
- <ports>
- <outPort index="0" name="Result Set">Table with a result set</outPort>
- </ports>
-</knimeNode>
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeModel.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeModel.java
deleted file mode 100644
index e9c196519c01eac3625ddcf734ca3da8180d8f38..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeModel.java
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.query;
-
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-
-import ch.systemsx.cisd.openbis.knime.common.AbstractOpenBisNodeTableModel;
-import ch.systemsx.cisd.openbis.knime.common.ParameterBindings;
-import ch.systemsx.cisd.openbis.knime.common.Util;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel;
-
-/**
- * Node model for SQL parameterized queries.
- *
- * @author Franz-Josef Elmer
- */
-public class QueryNodeModel extends AbstractOpenBisNodeTableModel
-{
- static final String QUERY_DESCRIPTION_KEY = "query-description";
-
- private QueryDescription queryDescription;
-
- private ParameterBindings parameterBindings = new ParameterBindings();
-
- @Override
- protected void loadAdditionalValidatedSettingsFrom(NodeSettingsRO settings)
- throws InvalidSettingsException
- {
- queryDescription =
- Util.deserializeDescription(settings.getByteArray(QUERY_DESCRIPTION_KEY));
- parameterBindings.loadValidatedSettingsFrom(settings);
- }
-
- @Override
- protected void saveAdditionalSettingsTo(NodeSettingsWO settings)
- {
- settings.addByteArray(QUERY_DESCRIPTION_KEY, Util
- .serializeDescription(queryDescription));
- parameterBindings.saveSettingsTo(settings);
- }
-
- @Override
- protected QueryTableModel getData(IQueryApiFacade facade)
- {
- return facade.executeQuery(queryDescription.getId(), parameterBindings.getBindings());
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/ReportNodeFactory.xml b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/ReportNodeFactory.xml
deleted file mode 100644
index 74d9825e908980dcf2d4dc805e43d42d845d3d3f..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/ReportNodeFactory.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
-<knimeNode icon="../common/openbis.png" type="Source">
- <name>openBIS Report Reader</name>
-
- <shortDescription>Provides the result table form an invocation of an openBIS reporting plugin.</shortDescription>
-
- <fullDescription>
- <intro>This data source node invokes a reporting plugin on an openBIS Application Server.
- <p>
- For more details see <a href="https://wiki-bsse.ethz.ch/display/openBISDoc1304/openBIS+KNIME+Nodes">openBIS KNIME Nodes</a>.
- </p>
- </intro>
- </fullDescription>
-
- <ports>
- <outPort index="0" name="Result Set">Table</outPort>
- </ports>
-</knimeNode>
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/ReportNodeModel.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/ReportNodeModel.java
deleted file mode 100644
index 37e12b6772d66801a995c3a85595189388ed18f3..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/ReportNodeModel.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.query;
-
-import java.util.Arrays;
-
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-
-import ch.systemsx.cisd.openbis.knime.common.AbstractOpenBisNodeTableModel;
-import ch.systemsx.cisd.openbis.knime.common.Util;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.ReportDescription;
-
-/**
- * Node model for report reader node.
- *
- * @author Franz-Josef Elmer
- */
-public class ReportNodeModel extends AbstractOpenBisNodeTableModel
-{
- static final String REPORT_DESCRIPTION_KEY = "report-description";
-
- static final String DATA_SET_CODES_KEY = "data-set-codes";
-
- private ReportDescription reportDescription;
-
- private String[] dataSetCodes;
-
- @Override
- protected void loadAdditionalValidatedSettingsFrom(NodeSettingsRO settings)
- throws InvalidSettingsException
- {
- reportDescription =
- Util.deserializeDescription(settings.getByteArray(REPORT_DESCRIPTION_KEY));
- dataSetCodes = settings.getStringArray(DATA_SET_CODES_KEY);
- }
-
- @Override
- protected void saveAdditionalSettingsTo(NodeSettingsWO settings)
- {
- settings.addByteArray(REPORT_DESCRIPTION_KEY, Util.serializeDescription(reportDescription));
- settings.addStringArray(DATA_SET_CODES_KEY, dataSetCodes);
- }
-
- @Override
- protected QueryTableModel getData(IQueryApiFacade facade)
- {
- return facade.createReportFromDataSets(reportDescription.getKey(), Arrays.asList(dataSetCodes));
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/AggregationCommand.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/AggregationCommand.java
deleted file mode 100644
index fc4ff4a9714e20d0445332b31504fb8851630e98..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/AggregationCommand.java
+++ /dev/null
@@ -1,102 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.server;
-
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.ITableModel;
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.ISimpleTableModelBuilderAdaptor;
-
-/**
- * Super class of all aggregation commands.
- *
- * @author Franz-Josef Elmer
- */
-public class AggregationCommand
-{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- AggregationCommand.class);
-
- public final void handleRequest(Map<String, Object> parameters,
- ISimpleTableModelBuilderAdaptor tableBuilder)
- {
- try
- {
- Object requestKey = parameters.get(Constants.REQUEST_KEY);
- if (Constants.GET_PARAMETER_DESCRIPTIONS_REQUEST.equals(requestKey))
- {
- defineParameters(new ParameterDescriptionsBuilder(tableBuilder));
- } else
- {
- aggregate(parameters, tableBuilder);
- }
- } catch (Throwable ex)
- {
- operationLog.error("", ex);
- ITableModel tableModel = tableBuilder.getTableModel();
- if (tableModel instanceof TableModel)
- {
- // Put complete stack trace into the table if we can clear it
- TableModel tm = (TableModel) tableModel;
- tm.getHeader().clear();
- tm.getRows().clear();
- tableBuilder.addHeader(Constants.EXCEPTION_COLUMN);
- tableBuilder.addHeader(Constants.STACK_TRACE_CLASS_COLUMN);
- tableBuilder.addHeader(Constants.STACK_TRACE_METHOD_NAME_COLUMN);
- tableBuilder.addHeader(Constants.STACK_TRACE_FILE_NAME_COLUMN);
- tableBuilder.addHeader(Constants.STACK_TRACE_LINE_NUMBER_COLUMN);
- for (Throwable throwable = ex; throwable != null; throwable = throwable.getCause())
- {
- tableBuilder.addFullRow(throwable.toString(), "", "", "", "");
- StackTraceElement[] stackTraceElements = throwable.getStackTrace();
- for (StackTraceElement stackTraceElement : stackTraceElements)
- {
- tableBuilder.addFullRow("", stackTraceElement.getClassName(),
- stackTraceElement.getMethodName(),
- stackTraceElement.getFileName(),
- Integer.toString(stackTraceElement.getLineNumber()));
- }
- }
- } else
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- }
- }
-
- /**
- * Defines parameters and their type by using specified {@link ParameterDescriptionsBuilder}. Should be overwritten by subclasses.
- */
- protected void defineParameters(ParameterDescriptionsBuilder parameters)
- {
- }
-
- /**
- * Aggregates data in tabular form based on specified parameter values. Should be overwritten by subclasses.
- */
- protected void aggregate(Map<String, Object> parameters,
- ISimpleTableModelBuilderAdaptor tableBuilder)
- {
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/AggregationFileCommand.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/AggregationFileCommand.java
deleted file mode 100644
index 03ec47e446b6696054e4ef019e11650a21b9af6b..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/AggregationFileCommand.java
+++ /dev/null
@@ -1,49 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.server;
-
-import java.util.Map;
-
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.ISimpleTableModelBuilderAdaptor;
-
-/**
- * Aggregation command which creates a file in session workspace and returns the file name.
- *
- * @author Franz-Josef Elmer
- */
-public class AggregationFileCommand extends AggregationCommand
-{
-
- @Override
- protected void aggregate(Map<String, Object> parameters,
- ISimpleTableModelBuilderAdaptor tableBuilder)
- {
- String fileName = createFile(parameters);
- tableBuilder.addHeader(Constants.FILE_NAME_COLUMN);
- tableBuilder.addRow().setCell(Constants.FILE_NAME_COLUMN, fileName);
- }
-
- /**
- * Creates a file by aggregating data based on specified parameters. Should be overridden by subclasses.
- *
- * @return the file name.
- */
- protected String createFile(Map<String, Object> parameters)
- {
- return null;
- }
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/Constants.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/Constants.java
deleted file mode 100644
index d9b8841d5d6b9e9036d06998d7066ac29eece169..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/Constants.java
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.server;
-
-/**
- * Basic constants.
- *
- * @author Franz-Josef Elmer
- */
-public class Constants
-{
- public static final String REQUEST_KEY = "_REQUEST_";
-
- public static final String GET_PARAMETER_DESCRIPTIONS_REQUEST = "getParameterDescriptions";
-
- public static final String EXCEPTION_COLUMN = "_EXCEPTION_";
-
- public static final String STACK_TRACE_CLASS_COLUMN = "_STACK_TRACE_CLASS_";
-
- public static final String STACK_TRACE_METHOD_NAME_COLUMN = "_STACK_TRACE_METHOD_NAME_";
-
- public static final String STACK_TRACE_FILE_NAME_COLUMN = "_STACK_TRACE_FILE_NAME_";
-
- public static final String STACK_TRACE_LINE_NUMBER_COLUMN = "_STACK_TRACE_LINE_NUMBER_";
-
- public static final String PARAMETER_DESCRIPTION_NAME_COLUMN = "name";
-
- public static final String PARAMETER_DESCRIPTION_TYPE_COLUMN = "type";
-
- public static final String FILE_NAME_COLUMN = "filename";
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/FieldType.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/FieldType.java
deleted file mode 100644
index ad03d7cc2ed9fa783cf218eec91e68c54234c55b..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/FieldType.java
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.server;
-
-/**
- * Enumeration of parameter field types.
- *
- * @author Franz-Josef Elmer
- */
-public enum FieldType
-{
- VARCHAR, VOCABULARY, EXPERIMENT, SAMPLE, DATA_SET;
-}
\ No newline at end of file
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/ParameterDescriptionBuilder.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/ParameterDescriptionBuilder.java
deleted file mode 100644
index 6fe4ef12210eced905bfa64f69e5529b71d3a835..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/ParameterDescriptionBuilder.java
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.server;
-
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.IRowBuilderAdaptor;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ParameterDescriptionBuilder
-{
- private final IRowBuilderAdaptor row;
-
- ParameterDescriptionBuilder(IRowBuilderAdaptor row)
- {
- this.row = row;
- }
-
- public void text()
- {
- row.setCell(Constants.PARAMETER_DESCRIPTION_TYPE_COLUMN, FieldType.VARCHAR.toString());
- }
-
- public void experiment()
- {
- row.setCell(Constants.PARAMETER_DESCRIPTION_TYPE_COLUMN, FieldType.EXPERIMENT.toString());
- }
-
- public void sample()
- {
- row.setCell(Constants.PARAMETER_DESCRIPTION_TYPE_COLUMN, FieldType.SAMPLE.toString());
- }
-
- public void dataSet()
- {
- row.setCell(Constants.PARAMETER_DESCRIPTION_TYPE_COLUMN, FieldType.DATA_SET.toString());
- }
-
- public VocabularyBuilder vocabulary(String... terms)
- {
- VocabularyBuilder vocabularyBuilder = new VocabularyBuilder(row);
- for (String term : terms)
- {
- vocabularyBuilder.term(term);
- }
- return vocabularyBuilder;
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/ParameterDescriptionsBuilder.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/ParameterDescriptionsBuilder.java
deleted file mode 100644
index ea92c96e814bdd7aa119e415b862dbbb680e694c..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/ParameterDescriptionsBuilder.java
+++ /dev/null
@@ -1,53 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.server;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.IRowBuilderAdaptor;
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.ISimpleTableModelBuilderAdaptor;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ParameterDescriptionsBuilder
-{
- private final ISimpleTableModelBuilderAdaptor tableBuilder;
-
- private final Set<String> names = new HashSet<String>();
-
- ParameterDescriptionsBuilder(ISimpleTableModelBuilderAdaptor tableBuilder)
- {
- this.tableBuilder = tableBuilder;
- tableBuilder.addHeader(Constants.PARAMETER_DESCRIPTION_NAME_COLUMN);
- tableBuilder.addHeader(Constants.PARAMETER_DESCRIPTION_TYPE_COLUMN);
- }
-
- public ParameterDescriptionBuilder parameter(String name)
- {
- if (names.contains(name))
- {
- throw new IllegalArgumentException("There is already a parameter with name '" + name + "'.");
- }
- names.add(name);
- IRowBuilderAdaptor row = tableBuilder.addRow();
- row.setCell(Constants.PARAMETER_DESCRIPTION_NAME_COLUMN, name);
- return new ParameterDescriptionBuilder(row);
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/VocabularyBuilder.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/VocabularyBuilder.java
deleted file mode 100644
index 228881ee18ad0c9f3aa1f50d067a723cbdba2af2..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/server/VocabularyBuilder.java
+++ /dev/null
@@ -1,57 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.server;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.IRowBuilderAdaptor;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class VocabularyBuilder
-{
- private final IRowBuilderAdaptor row;
-
- private final Set<String> terms = new HashSet<String>();
-
- private final StringBuilder termsBuilder = new StringBuilder();
-
- VocabularyBuilder(IRowBuilderAdaptor row)
- {
- this.row = row;
- row.setCell(Constants.PARAMETER_DESCRIPTION_TYPE_COLUMN, FieldType.VOCABULARY.toString());
- }
-
- public VocabularyBuilder term(String term)
- {
- if (terms.contains(term))
- {
- throw new IllegalArgumentException("There is already a term '" + term + "' defined.");
- }
- if (termsBuilder.length() > 0)
- {
- termsBuilder.append(", ");
- }
- termsBuilder.append(term);
- row.setCell(Constants.PARAMETER_DESCRIPTION_TYPE_COLUMN,
- FieldType.VOCABULARY + ":" + termsBuilder);
- return this;
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractAggregatedDataImportNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractAggregatedDataImportNodeDialog.java
deleted file mode 100644
index cf8781ced3b6345273d8c5b5a1e6d9cf23ac6278..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractAggregatedDataImportNodeDialog.java
+++ /dev/null
@@ -1,98 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription;
-
-/**
- * Abstract super class of nodes dialogs for importing data from an aggregation service.
- *
- * @author Franz-Josef Elmer
- */
-public abstract class AbstractAggregatedDataImportNodeDialog
- extends AbstractParameterDescriptionBasedNodeDialog<AggregatedDataImportDescription>
-{
- protected AbstractAggregatedDataImportNodeDialog(String tabTitle)
- {
- super(tabTitle);
- }
-
- @Override
- protected List<FieldDescription> getFieldDescriptions(
- AggregatedDataImportDescription description)
- {
- return Util.getFieldDescriptions(createFacade(), description, logger);
- }
-
- @Override
- protected List<AggregatedDataImportDescription> getSortedDescriptions(IQueryApiFacade facade)
- {
- List<AggregationServiceDescription> services = facade.listAggregationServices();
- Collections.sort(services, new Comparator<AggregationServiceDescription>()
- {
- @Override
- public int compare(AggregationServiceDescription d1,
- AggregationServiceDescription d2)
- {
- return d1.getServiceKey().compareTo(d2.getServiceKey());
- }
- });
- List<AggregatedDataImportDescription> descriptions =
- new ArrayList<AggregatedDataImportDescription>();
- Set<String> dssCodes = new HashSet<String>();
-
- for (AggregationServiceDescription aggregationServiceDescription : services)
- {
- addDescription(descriptions, aggregationServiceDescription);
- dssCodes.add(aggregationServiceDescription.getDataStoreCode());
- }
-
- if (dssCodes.size() > 1)
- {
- for (AggregatedDataImportDescription description : descriptions)
- {
- description.setShowFullDescription(true);
- }
- }
-
- return descriptions;
- }
-
- protected abstract void addDescription(List<AggregatedDataImportDescription> descriptions,
- AggregationServiceDescription aggregationServiceDescription);
-
- @Override
- protected String getDescriptionKey()
- {
- return AggregatedDataImportDescription.AGGREGATION_DESCRIPTION_KEY;
- }
-
- @Override
- protected String getParametersSectionLabel()
- {
- return "Service Parameters";
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractDescriptionBasedNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractDescriptionBasedNodeDialog.java
deleted file mode 100644
index 18d4ad796919f3006e7870663140291648295fa7..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractDescriptionBasedNodeDialog.java
+++ /dev/null
@@ -1,126 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.awt.event.FocusAdapter;
-import java.awt.event.FocusEvent;
-import java.io.Serializable;
-import java.util.List;
-
-import javax.swing.JComboBox;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-import org.knime.core.node.NotConfigurableException;
-import org.knime.core.node.port.PortObjectSpec;
-
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-
-/**
- * @author Franz-Josef Elmer
- */
-public abstract class AbstractDescriptionBasedNodeDialog<D extends Serializable> extends AbstractOpenBisNodeDialog
-{
- private JComboBox descriptionComboBox;
-
- private FocusAdapter focusListener;
-
- protected AbstractDescriptionBasedNodeDialog(String tabTitle)
- {
- super(tabTitle);
- }
-
- @Override
- protected void defineQueryForm(JPanel queryPanel)
- {
- descriptionComboBox = new JComboBox();
- focusListener = new FocusAdapter()
- {
- @Override
- public void focusGained(FocusEvent e)
- {
- JOptionPane.showMessageDialog(descriptionComboBox,
- "Please, reconnect to openBIS to get all available " + getDescriptionKey() + ".");
- descriptionComboBox.removeFocusListener(focusListener);
- }
- };
- descriptionComboBox.addFocusListener(focusListener);
- defineQueryForm(queryPanel, descriptionComboBox);
- }
-
- @Override
- protected void updateQueryForm(IQueryApiFacade queryFacade)
- {
- List<D> descriptions = getSortedDescriptions(queryFacade);
- D selectedQueryDescription = getSelectedDescriptionOrNull();
- descriptionComboBox.removeFocusListener(focusListener);
- descriptionComboBox.removeAllItems();
- for (D description : descriptions)
- {
- descriptionComboBox.addItem(description);
- if (description.equals(selectedQueryDescription))
- {
- descriptionComboBox.setSelectedItem(description);
- }
- }
- }
-
- @SuppressWarnings("unchecked")
- protected D getSelectedDescriptionOrNull()
- {
- Object selectedItem = descriptionComboBox.getSelectedItem();
- return selectedItem == null ? null : (D) selectedItem;
- }
-
- @Override
- protected final void loadAdditionalSettingsFrom(NodeSettingsRO settings, PortObjectSpec[] specs)
- throws NotConfigurableException
- {
- byte[] bytes = settings.getByteArray(getDescriptionKey(), null);
- D descriptionOrNull = Util.deserializeDescription(bytes);
- if (descriptionOrNull != null && descriptionComboBox.getItemCount() == 0)
- {
- descriptionComboBox.addItem(descriptionOrNull);
- descriptionComboBox.setSelectedIndex(0);
- }
- loadMoreSettingsFrom(settings, specs);
- }
-
- @Override
- protected final void saveAdditionalSettingsTo(NodeSettingsWO settings)
- throws InvalidSettingsException
- {
- byte[] bytes = Util.serializeDescription(getSelectedDescriptionOrNull());
- settings.addByteArray(getDescriptionKey(), bytes);
- saveMoreSettingsTo(settings);
- }
-
- protected abstract void defineQueryForm(JPanel queryPanel, JComboBox comboBoxWithDescriptions);
-
- protected abstract List<D> getSortedDescriptions(IQueryApiFacade facade);
-
- protected abstract String getDescriptionKey();
-
- protected abstract void loadMoreSettingsFrom(NodeSettingsRO settings, PortObjectSpec[] specs)
- throws NotConfigurableException;
-
- protected abstract void saveMoreSettingsTo(NodeSettingsWO settings)
- throws InvalidSettingsException;
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractOpenBisNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractOpenBisNodeDialog.java
deleted file mode 100644
index 1d2709e6d9e9009ff08acafe0179818ed0fd9959..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractOpenBisNodeDialog.java
+++ /dev/null
@@ -1,471 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import static ch.systemsx.cisd.openbis.knime.common.AbstractOpenBisNodeModel.CREDENTIALS_KEY;
-import static ch.systemsx.cisd.openbis.knime.common.AbstractOpenBisNodeModel.PASSWORD_KEY;
-import static ch.systemsx.cisd.openbis.knime.common.AbstractOpenBisNodeModel.URL_KEY;
-import static ch.systemsx.cisd.openbis.knime.common.AbstractOpenBisNodeModel.USER_KEY;
-
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Container;
-import java.awt.Cursor;
-import java.awt.Dimension;
-import java.awt.EventQueue;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.Insets;
-import java.awt.Window;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Map;
-
-import javax.swing.BorderFactory;
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JComponent;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JPasswordField;
-import javax.swing.JScrollPane;
-import javax.swing.JTextField;
-import javax.swing.SwingUtilities;
-
-import org.apache.commons.lang.StringUtils;
-import org.eclipse.jface.preference.IPreferenceStore;
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeLogger;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-import org.knime.core.node.NotConfigurableException;
-import org.knime.core.node.port.PortObjectSpec;
-import org.knime.core.node.workflow.Credentials;
-import org.knime.core.node.workflow.ICredentials;
-import org.knime.workbench.core.KNIMECorePlugin;
-
-import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.FacadeFactory;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-
-/**
- * Abstract super class of all openBIS KNIME nodes.
- *
- * @author Franz-Josef Elmer
- */
-public abstract class AbstractOpenBisNodeDialog extends NodeDialogPane implements IOpenBisNode
-{
- private static final class Key
- {
- private final String url;
-
- private final String userID;
-
- private final String password;
-
- Key(String url, String userID, String password)
- {
- this.url = url;
- this.userID = userID;
- this.password = password;
- }
-
- @Override
- public boolean equals(Object obj)
- {
- if (obj == this)
- {
- return true;
- }
- if (obj instanceof Key == false)
- {
- return false;
- }
- Key key = (Key) obj;
- return String.valueOf(key.url).equals(String.valueOf(url))
- && String.valueOf(key.userID).equals(String.valueOf(userID))
- && String.valueOf(key.password).equals(String.valueOf(password));
- }
-
- @Override
- public int hashCode()
- {
- int result = String.valueOf(url).hashCode();
- result = 37 * result + String.valueOf(userID).hashCode();
- result = 37 * result + String.valueOf(password).hashCode();
- return result;
- }
- }
-
- private Map<Key, IQueryApiFacade> facades = new HashMap<Key, IQueryApiFacade>();
-
- protected NodeLogger logger;
-
- private JComboBox urlField;
-
- private JComboBox credentialsField;
-
- private JTextField userField;
-
- private JPasswordField passwordField;
-
- private final IOpenbisServiceFacadeFactory serviceFacadeFactory;
-
- protected AbstractOpenBisNodeDialog(String tabTitle)
- {
- this(tabTitle, new OpenbisServiceFacadeFactory());
- }
-
- protected AbstractOpenBisNodeDialog(String tabTitle, IOpenbisServiceFacadeFactory serviceFacadeFactory)
- {
- this.serviceFacadeFactory = serviceFacadeFactory;
- logger = NodeLogger.getLogger(getClass());
- addTab(tabTitle, createTab());
- }
-
- private Component createTab()
- {
- JPanel panel = new JPanel(new BorderLayout());
- JPanel connectionPanel = new JPanel(new GridBagLayout());
- connectionPanel.setBorder(BorderFactory.createTitledBorder("Connection Parameters"));
- urlField = addField(connectionPanel, "openBIS URL", new JComboBox());
- urlField.setToolTipText("Additional URLs can be defined on the KNIME openBIS preference page.");
- credentialsField = addField(connectionPanel, "Credentials", new JComboBox());
- credentialsField.addItemListener(new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent event)
- {
- boolean enable = "".equals(event.getItem());
- enableField(userField, enable);
- enableField(passwordField, enable);
- }
- });
- credentialsField.setToolTipText("<html>Additional credentials can be defined by the menu item 'Workflow Credentials...'<br>"
- + "of the context menu of workflow in the KNIME Explorer.<br><br>"
- + "For security reasons it is not recommended to use the fields 'User' and 'Password'<br>"
- + "because the password is only encrypted if the KNIME Master Key has been defined.");
- userField = addField(connectionPanel, "User", new JTextField(20));
- passwordField = addField(connectionPanel, "Password", new JPasswordField(20));
- JButton button = new JButton("connect");
- button.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- connectServer();
- }
- });
- connectionPanel.add(button, createLast());
- panel.add(connectionPanel, BorderLayout.NORTH);
- JPanel queryPanel = new JPanel(new BorderLayout());
- defineQueryForm(queryPanel);
- panel.add(queryPanel, BorderLayout.CENTER);
-
- JScrollPane scrollPane = new JScrollPane(panel);
- scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
- scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
- scrollPane.setPreferredSize(new Dimension(600, 450));
-
- return scrollPane;
- }
-
- @Override
- public void logError(Throwable throwable)
- {
- logger.error(throwable.toString(), throwable);
- }
-
- @Override
- protected final void loadSettingsFrom(NodeSettingsRO settings, PortObjectSpec[] specs)
- throws NotConfigurableException
- {
- String[] urls = getUrls();
- urlField.removeAllItems();
- for (String url : urls)
- {
- urlField.addItem(url);
- }
- urlField.setSelectedItem(settings.getString(URL_KEY, ""));
- credentialsField.removeAllItems();
- credentialsField.addItem("");
- Collection<String> credentialsNames = getAllCredentialsNames();
- for (String credentialsName : credentialsNames)
- {
- credentialsField.addItem(credentialsName);
- }
- String credential = settings.getString(CREDENTIALS_KEY, "");
- credentialsField.setSelectedItem(credential);
- userField.setText(settings.getString(USER_KEY, ""));
- passwordField.setText(Util.getDecryptedPassword(settings));
- loadAdditionalSettingsFrom(settings, specs);
- }
-
- protected Collection<String> getAllCredentialsNames()
- {
- return getCredentialsNames();
- }
-
- protected String[] getUrls()
- {
- IPreferenceStore preferenceStore = KNIMECorePlugin.getDefault().getPreferenceStore();
- return preferenceStore.getString(OpenBisPreferencePage.OPENBIS_URLS_KEY).split("\n");
- }
-
- @Override
- protected final void saveSettingsTo(NodeSettingsWO settings) throws InvalidSettingsException
- {
- settings.addString(URL_KEY, getUrl());
- Object selectedCredentials = credentialsField.getSelectedItem();
- String credentialsName = selectedCredentials == null ? "" : selectedCredentials.toString();
- settings.addString(CREDENTIALS_KEY, credentialsName);
- if (StringUtils.isBlank(credentialsName))
- {
- settings.addString(USER_KEY, userField.getText().trim());
- settings.addString(PASSWORD_KEY, Util.getEncryptedPassword(passwordField.getPassword()));
- }
- saveAdditionalSettingsTo(settings);
- }
-
- protected void showException(Throwable throwable)
- {
- logger.error(throwable.toString(), throwable);
- final String message = createMessage(throwable);
- final JPanel panel = getPanel();
- Window windowAncestor = SwingUtilities.getWindowAncestor(panel);
- if (windowAncestor != null && windowAncestor.isVisible())
- {
- EventQueue.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- JOptionPane.showMessageDialog(panel, message, "Error", JOptionPane.ERROR_MESSAGE);
- }
- });
- }
- }
-
- private String createMessage(Throwable throwable)
- {
- String message = throwable.toString();
- String[] lines = message.split("\n");
- int maxNumberOfLines = 10;
- if (lines.length < maxNumberOfLines)
- {
- return message;
- }
- StringBuilder builder = new StringBuilder();
- for (int i = 0; i < maxNumberOfLines; i++)
- {
- builder.append(lines[i]).append('\n');
- }
- builder.append("...\n\nSee KNIME log for the complete error message.");
- return builder.toString();
- }
-
- protected abstract void defineQueryForm(JPanel queryPanel);
-
- protected abstract void updateQueryForm(IQueryApiFacade queryFacade);
-
- protected abstract void loadAdditionalSettingsFrom(NodeSettingsRO settings,
- PortObjectSpec[] specs) throws NotConfigurableException;
-
- protected abstract void saveAdditionalSettingsTo(NodeSettingsWO settings)
- throws InvalidSettingsException;
-
- private void connectServer()
- {
- performAction(new IQueryFacadeAction()
- {
- @Override
- public void execute(IQueryApiFacade queryFacade)
- {
- updateQueryForm(queryFacade);
- }
- });
- }
-
- @Override
- public void onCancel()
- {
- logoutAndRemoveAllFacades();
- }
-
- @Override
- public void onClose()
- {
- logoutAndRemoveAllFacades();
- }
-
- private void logoutAndRemoveAllFacades()
- {
- for (IQueryApiFacade facade : facades.values())
- {
- facade.logout();
- }
- facades.clear();
- }
-
- protected void performAction(final IQueryFacadeAction action)
- {
- performAction(new ILoadingBuildingAction<IQueryApiFacade>()
- {
- @Override
- public IQueryApiFacade load()
- {
- return createFacade();
- }
-
- @Override
- public void build(IQueryApiFacade facade)
- {
- action.execute(facade);
- }
- });
- }
-
- protected <T> void performAction(ILoadingBuildingAction<T> loadingBuildingAction)
- {
- new ActionExecutor().executeAsync(loadingBuildingAction,
- new DefaultAsyncNodeAction(AbstractOpenBisNodeDialog.this));
- }
-
- protected IQueryApiFacade createFacade()
- {
- try
- {
- String url = getUrl();
- ICredentials credentials = getCredentials();
- String userID = credentials.getLogin();
- String password = credentials.getPassword();
- Key key = new Key(url, userID, password);
- IQueryApiFacade facade = facades.get(key);
- if (facade == null)
- {
- JPanel panel = getPanel();
- Cursor cursor = panel.getCursor();
- try
- {
- panel.setCursor(new Cursor(Cursor.WAIT_CURSOR));
- facade = FacadeFactory.create(url, userID, password);
- } finally
- {
- panel.setCursor(cursor);
- }
- facades.put(key, facade);
- }
- return facade;
- } catch (RuntimeException ex)
- {
- showException(ex);
- throw ex;
- }
- }
-
- protected IOpenbisServiceFacade createOpenbisFacade(String sessionToken)
- {
- try
- {
- return serviceFacadeFactory.createFacade(getUrl(), sessionToken);
- } catch (RuntimeException ex)
- {
- showException(ex);
- throw ex;
- }
- }
-
- protected String getUrl()
- {
- Object selectedItem = urlField.getSelectedItem();
- if (selectedItem == null)
- {
- throw new IllegalArgumentException("Missing URL.");
- }
- return selectedItem.toString();
- }
-
- protected ICredentials getCredentials()
- {
- Object selectedItem = credentialsField.getSelectedItem();
- if (selectedItem == null || selectedItem.toString().trim().length() == 0)
- {
- String user = userField.getText();
- if (StringUtils.isBlank(user))
- {
- throw new IllegalArgumentException("Unspecified credentials or missing user.");
- }
- char[] password = passwordField.getPassword();
- if (password == null || password.length == 0)
- {
- throw new IllegalArgumentException("Unspecified credentials or missing password.");
- }
- return new Credentials("_", user, new String(password));
- }
- return getCredentialsProvider().get(selectedItem.toString());
- }
-
- protected <T extends JComponent> T addField(Container panel, String label, T field)
- {
- return addField(panel, label, field, false);
- }
-
- protected <T extends JComponent> T addField(Container panel, String label, T field,
- boolean mandatory)
- {
- panel.add(new JLabel(label + (mandatory ? ":*" : ":")), createFirst());
- panel.add(field, createLast());
- return field;
- }
-
- protected GridBagConstraints createLast()
- {
- GridBagConstraints last = createFirst();
- last.gridwidth = GridBagConstraints.REMAINDER;
- return last;
- }
-
- protected GridBagConstraints createFirst()
- {
- GridBagConstraints constraints = new GridBagConstraints();
- constraints.anchor = GridBagConstraints.WEST;
- constraints.fill = GridBagConstraints.HORIZONTAL;
- constraints.insets = new Insets(2, 3, 2, 3);
- return constraints;
- }
-
- protected void enableField(JComponent field, boolean enable)
- {
- field.setEnabled(enable);
- Component[] components = field.getParent().getComponents();
- for (int i = 1; i < components.length; i++)
- {
- if (components[i] == field)
- {
- components[i - 1].setEnabled(enable);
- break;
- }
- }
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractParameterDescriptionBasedNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractParameterDescriptionBasedNodeDialog.java
deleted file mode 100644
index ead153b9c7285daf05775b9bcb2d0ea9b2b6b429..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractParameterDescriptionBasedNodeDialog.java
+++ /dev/null
@@ -1,194 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.awt.BorderLayout;
-import java.awt.FlowLayout;
-import java.awt.GridBagLayout;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.io.Serializable;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import javax.swing.BorderFactory;
-import javax.swing.JComboBox;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-import org.knime.core.node.NotConfigurableException;
-import org.knime.core.node.port.PortObjectSpec;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
-import ch.systemsx.cisd.openbis.knime.server.FieldType;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-
-/**
- * Abstract super class of node dialogs with a description and a set of parameters different for each description.
- *
- * @author Franz-Josef Elmer
- */
-public abstract class AbstractParameterDescriptionBasedNodeDialog<D extends Serializable>
- extends AbstractDescriptionBasedNodeDialog<D>
-{
- private ParameterBindings parameterBindings = new ParameterBindings();
-
- private Map<String, IField> parameterFields = new HashMap<String, IField>();
-
- private JPanel parametersPanel;
-
- protected AbstractParameterDescriptionBasedNodeDialog(String tabTitle)
- {
- super(tabTitle);
- }
-
- protected abstract List<FieldDescription> getFieldDescriptions(D description);
-
- protected abstract String getDescriptionComboBoxLabel();
-
- protected String getParametersSectionLabel()
- {
- return getDescriptionComboBoxLabel() + " Parameters";
- }
-
- @Override
- protected void defineQueryForm(JPanel queryPanel, JComboBox comboBoxWithDescriptions)
- {
- comboBoxWithDescriptions.addItemListener(new ItemListener()
- {
- @SuppressWarnings("unchecked")
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- if (e.getStateChange() == ItemEvent.SELECTED)
- {
- try
- {
- updateParametersPanel((D) e.getItem());
- } catch (Throwable ex)
- {
- showException(ex);
- }
- }
- }
- });
- JPanel querySelectionPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
- querySelectionPanel.add(new JLabel(getDescriptionComboBoxLabel() + ":"));
- querySelectionPanel.add(comboBoxWithDescriptions);
- queryPanel.add(querySelectionPanel, BorderLayout.NORTH);
- parametersPanel = new JPanel(new GridBagLayout());
- JPanel northPanel = new JPanel(new BorderLayout());
- JPanel northWestPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
- northWestPanel.setBorder(BorderFactory.createTitledBorder(getParametersSectionLabel()));
- northWestPanel.add(parametersPanel);
- northPanel.add(northWestPanel, BorderLayout.NORTH);
- queryPanel.add(northPanel, BorderLayout.CENTER);
- }
-
- private void updateParametersPanel(final D description)
- {
- new ActionExecutor().executeAsync(new ILoadingBuildingAction<List<FieldDescription>>()
- {
- @Override
- public List<FieldDescription> load()
- {
- return getFieldDescriptions(description);
- }
-
- @Override
- public void build(List<FieldDescription> fieldDescriptions)
- {
- parametersPanel.removeAll();
- parameterFields.clear();
- parametersPanel.getParent().setVisible(fieldDescriptions.isEmpty() == false);
- for (FieldDescription fieldDescription : fieldDescriptions)
- {
- String name = fieldDescription.getName();
- IField field = parameterFields.get(name);
- if (field == null)
- {
- String fieldParameters = fieldDescription.getFieldParameters();
- FieldType fieldType = fieldDescription.getFieldType();
- field = createField(fieldType, fieldParameters);
- parameterFields.put(name, field);
- }
- String value = parameterBindings.tryToGetBinding(name);
- if (value != null)
- {
- field.setValue(value);
- }
- addField(parametersPanel, name, field.getComponent());
- }
- parametersPanel.invalidate();
- parametersPanel.getParent().getParent().validate();
- }
- }, new DefaultAsyncNodeAction(this));
- }
-
- private IField createField(FieldType fieldType, String fieldParameters)
- {
- IQueryApiFacadeProvider facadeProvider = new IQueryApiFacadeProvider()
- {
- @Override
- public IQueryApiFacade getQueryFacade()
- {
- return createFacade();
- }
- };
- IAsyncNodeAction asyncNodeAction = new DefaultAsyncNodeAction(this);
- switch (fieldType)
- {
- case VOCABULARY:
- return new VocabularyField(fieldParameters);
- case EXPERIMENT:
- return new EntityField(DataSetOwnerType.EXPERIMENT, facadeProvider, asyncNodeAction);
- case SAMPLE:
- return new EntityField(DataSetOwnerType.SAMPLE, facadeProvider, asyncNodeAction);
- case DATA_SET:
- return new EntityField(DataSetOwnerType.DATA_SET, facadeProvider, asyncNodeAction);
- default:
- return new TextField();
- }
- }
-
- @Override
- protected void loadMoreSettingsFrom(NodeSettingsRO settings, PortObjectSpec[] specs)
- throws NotConfigurableException
- {
- parameterBindings.loadValidatedSettingsFrom(settings);
-
- }
-
- @Override
- protected void saveMoreSettingsTo(NodeSettingsWO settings) throws InvalidSettingsException
- {
- parameterBindings.removeAllBindings();
- Set<Entry<String, IField>> entrySet = parameterFields.entrySet();
- for (Entry<String, IField> entry : entrySet)
- {
- parameterBindings.bind(entry.getKey(), entry.getValue().getValue());
- }
- parameterBindings.saveSettingsTo(settings);
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractTestNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractTestNodeDialog.java
deleted file mode 100644
index f652810ab70a5e37193742d1eb87294fc5574b09..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/AbstractTestNodeDialog.java
+++ /dev/null
@@ -1,149 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.awt.BorderLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-
-import javax.swing.JButton;
-import javax.swing.JFrame;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeSettings;
-import org.knime.core.node.NotConfigurableException;
-
-import ch.systemsx.cisd.common.logging.LogInitializer;
-import ch.systemsx.cisd.openbis.knime.common.AbstractOpenBisNodeModel;
-import ch.systemsx.cisd.openbis.knime.common.Util;
-
-/**
- * @author Franz-Josef Elmer
- */
-public abstract class AbstractTestNodeDialog
-{
- public static NodeSettings createSettings()
- {
- NodeSettings settings = new NodeSettings("");
- settings.addString(AbstractOpenBisNodeModel.URL_KEY, "http://localhost:8888");
- settings.addString(AbstractOpenBisNodeModel.USER_KEY, "test");
- settings.addString(AbstractOpenBisNodeModel.PASSWORD_KEY,
- Util.getEncryptedPassword("a".toCharArray()));
- return settings;
- }
-
- public static void createAndShow(AbstractTestNodeDialog factory)
- {
- LogInitializer.init();
- JFrame frame = new JFrame("test");
- JPanel panel = new JPanel(new BorderLayout());
- frame.getContentPane().add(panel);
- final NodeManager nodeManager = new NodeManager(panel, factory);
- nodeManager.createNode();
- JPanel buttonPanel = new JPanel();
- JButton saveButton = new JButton("Save");
- saveButton.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- nodeManager.saveSettings();
- }
- });
- buttonPanel.add(saveButton);
- JButton readButton = new JButton("Read");
- readButton.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- nodeManager.createNode();
- }
- });
- buttonPanel.add(readButton);
- panel.add(buttonPanel, BorderLayout.SOUTH);
- frame.pack();
- frame.setVisible(true);
- }
-
- public abstract NodeDialogPane create() throws NotConfigurableException;
-
- private static final class NodeManager
- {
- private final JPanel panel;
-
- private final AbstractTestNodeDialog nodeDialogFactory;
-
- private NodeDialogPane nodeDialog;
-
- private byte[] settings;
-
- NodeManager(JPanel panel, AbstractTestNodeDialog nodeDialogFactory)
- {
- this.panel = panel;
- this.nodeDialogFactory = nodeDialogFactory;
- }
-
- void createNode()
- {
- try
- {
- if (nodeDialog != null)
- {
- panel.remove(nodeDialog.getPanel());
- }
- nodeDialog = nodeDialogFactory.create();
- if (settings != null)
- {
- nodeDialog.loadSettingsFrom(new ByteArrayInputStream(settings));
- }
- panel.add(nodeDialog.getPanel(), BorderLayout.CENTER);
- panel.invalidate();
- panel.getParent().validate();
- } catch (Exception ex)
- {
- showMessage(ex);
- }
- }
-
- void saveSettings()
- {
- try
- {
- ByteArrayOutputStream out = new ByteArrayOutputStream();
- nodeDialog.saveSettingsTo(out);
- System.out.println(out.toString());
- settings = out.toByteArray();
- } catch (Exception ex)
- {
- showMessage(ex);
- }
- }
-
- private void showMessage(Exception ex)
- {
- ex.printStackTrace();
- JPanel component = nodeDialog == null ? null : nodeDialog.getPanel();
- JOptionPane.showMessageDialog(component, ex.toString());
- }
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/OpenBisPreferencePage.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/OpenBisPreferencePage.java
deleted file mode 100644
index 8c3c8e73f04eed0a5af80d0325da60810736b32b..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/common/OpenBisPreferencePage.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import org.eclipse.jface.dialogs.InputDialog;
-import org.eclipse.jface.preference.FieldEditorPreferencePage;
-import org.eclipse.jface.preference.ListEditor;
-import org.eclipse.swt.widgets.Display;
-import org.eclipse.swt.widgets.Shell;
-import org.eclipse.ui.IWorkbench;
-import org.eclipse.ui.IWorkbenchPreferencePage;
-import org.knime.workbench.core.KNIMECorePlugin;
-
-/**
- * Preference page for openBIS KNIME nodes.
- *
- * @author Franz-Josef Elmer
- */
-public class OpenBisPreferencePage extends FieldEditorPreferencePage implements IWorkbenchPreferencePage
-{
- public static final String OPENBIS_URLS_KEY = "openbis_urls";
-
- public OpenBisPreferencePage()
- {
- super("openBIS", null, GRID);
- }
-
- @Override
- public void init(IWorkbench workbench)
- {
- setPreferenceStore(KNIMECorePlugin.getDefault().getPreferenceStore());
- }
-
- @Override
- protected void createFieldEditors()
- {
- final Shell shell = Display.getDefault().getActiveShell();
- addField(new ListEditor(OPENBIS_URLS_KEY, "List of openBIS URLs which can be used to configure nodes:", getFieldEditorParent())
- {
- @Override
- protected String[] parseString(String stringList)
- {
- return stringList.split("\n");
- }
-
- @Override
- protected String getNewInputObject()
- {
- InputDialog inputDialog = new InputDialog(shell, "openBIS URL",
- "Enter the base URL of an openBIS application server", "", null);
- inputDialog.setBlockOnOpen(true);
- return inputDialog.open() == InputDialog.OK ? inputDialog.getValue() : null;
- }
-
- @Override
- protected String createList(String[] items)
- {
- StringBuilder builder = new StringBuilder();
- for (String item : items)
- {
- if (builder.length() > 0)
- {
- builder.append('\n');
- }
- builder.append(item);
- }
- return builder.toString();
- }
- });
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeDialog.java
deleted file mode 100644
index b91331c6f33e35a7a2d965e7a7a5e10ebdaf2b25..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeDialog.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.knime.common.AbstractAggregatedDataImportNodeDialog;
-import ch.systemsx.cisd.openbis.knime.common.AggregatedDataImportDescription;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription;
-
-/**
- * Node dialog for get a data file created by an aggregation service.
- *
- * @author Franz-Josef Elmer
- */
-class AggregatedDataFileImportNodeDialog extends AbstractAggregatedDataImportNodeDialog
-{
- AggregatedDataFileImportNodeDialog()
- {
- super("Aggregated Data File Importing Settings");
- }
-
- @Override
- protected void addDescription(List<AggregatedDataImportDescription> descriptions,
- AggregationServiceDescription aggregationServiceDescription)
- {
- AggregatedDataImportDescription.addDescriptionIfDataFile(descriptions,
- aggregationServiceDescription);
- }
-
- @Override
- protected String getDescriptionComboBoxLabel()
- {
- return "Data File Importing Service";
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeFactory.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeFactory.java
deleted file mode 100644
index 40334fab5e1d4e7912acae820dfdbff22aa8aeaa..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeFactory.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeFactory;
-import org.knime.core.node.NodeView;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class AggregatedDataFileImportNodeFactory extends NodeFactory<AggregatedDataFileImportNodeModel>
-{
- @Override
- public AggregatedDataFileImportNodeModel createNodeModel()
- {
- return new AggregatedDataFileImportNodeModel();
- }
-
- @Override
- protected NodeDialogPane createNodeDialogPane()
- {
- return new AggregatedDataFileImportNodeDialog();
- }
-
- @Override
- protected int getNrNodeViews()
- {
- return 0;
- }
-
- @Override
- public NodeView<AggregatedDataFileImportNodeModel> createNodeView(int viewIndex,
- AggregatedDataFileImportNodeModel nodeModel)
- {
- return null;
- }
-
- @Override
- protected boolean hasDialog()
- {
- return true;
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeDialog.java
deleted file mode 100644
index e01cdc1a63a4653c37b35c4c939acc24bb7491f0..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeDialog.java
+++ /dev/null
@@ -1,271 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import java.awt.BorderLayout;
-import java.awt.GridBagLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.File;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.List;
-
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JFileChooser;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-import javax.swing.text.JTextComponent;
-
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-import org.knime.core.node.NotConfigurableException;
-import org.knime.core.node.port.PortObjectSpec;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
-import ch.systemsx.cisd.openbis.knime.common.AbstractDescriptionBasedNodeDialog;
-import ch.systemsx.cisd.openbis.knime.common.DefaultAsyncNodeAction;
-import ch.systemsx.cisd.openbis.knime.common.EntityChooser;
-import ch.systemsx.cisd.openbis.knime.common.ILoadingBuildingAction;
-import ch.systemsx.cisd.openbis.knime.common.IQueryFacadeAction;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.ReportDescription;
-
-/**
- * Node for downloading a file of an openBIS data set.
- *
- * @author Franz-Josef Elmer
- */
-public class DataSetFileImportNodeDialog extends AbstractDescriptionBasedNodeDialog<ReportDescription>
-{
- private static boolean isBlank(String text)
- {
- return text == null || text.trim().length() == 0;
- }
-
- private JTextComponent dataSetCodeField;
-
- private JTextComponent filePathField;
-
- private JTextComponent downloadsPathField;
-
- private JCheckBox reuseCheckBox;
-
- DataSetFileImportNodeDialog()
- {
- super("Data Set File Importer Settings");
- }
-
- @Override
- protected void defineQueryForm(JPanel queryPanel, JComboBox reportComboBox)
- {
- JPanel panel = new JPanel(new GridBagLayout());
- dataSetCodeField = createTextFieldWithButton("Data Set Code", new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- performAction(new IQueryFacadeAction()
- {
- @Override
- public void execute(IQueryApiFacade queryFacade)
- {
- chooseDataSet(queryFacade);
- }
- });
- }
- }, panel);
- filePathField = createTextFieldWithButton("File", new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- chooseDataSetFile();
- }
- }, panel);
- downloadsPathField =
- createTextFieldWithButton("Location of Downloads", new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- chooseTempFolder();
- }
- }, panel);
- reuseCheckBox = new JCheckBox();
- addField(panel, "Reuse already downloaded file", reuseCheckBox);
- JPanel northPanel = new JPanel(new BorderLayout());
- northPanel.add(panel, BorderLayout.NORTH);
- queryPanel.add(northPanel, BorderLayout.CENTER);
- }
-
- private JTextComponent createTextFieldWithButton(String label, ActionListener actionListener,
- JPanel panel)
- {
- JPanel textFieldWithButton = new JPanel(new BorderLayout());
- JTextField field = new JTextField(20);
- textFieldWithButton.add(field, BorderLayout.CENTER);
- JButton button = new JButton("...");
- button.addActionListener(actionListener);
- textFieldWithButton.add(button, BorderLayout.EAST);
- addField(panel, label, textFieldWithButton);
- return field;
- }
-
- @Override
- protected List<ReportDescription> getSortedDescriptions(IQueryApiFacade facade)
- {
- List<ReportDescription> descriptions = facade.listTableReportDescriptions();
- Collections.sort(descriptions, new Comparator<ReportDescription>()
- {
- @Override
- public int compare(ReportDescription o1, ReportDescription o2)
- {
- return o1.getLabel().compareTo(o2.getLabel());
- }
- });
- return descriptions;
- }
-
- @Override
- protected String getDescriptionKey()
- {
- return "";
- }
-
- @Override
- protected void loadMoreSettingsFrom(NodeSettingsRO settings, PortObjectSpec[] specs)
- throws NotConfigurableException
- {
- dataSetCodeField.setText(settings.getString(DataSetFileImportNodeModel.DATA_SET_CODE_KEY,
- ""));
- filePathField.setText(settings.getString(DataSetFileImportNodeModel.FILE_PATH_KEY, ""));
- downloadsPathField.setText(settings.getString(
- DataSetFileImportNodeModel.DOWNLOADS_PATH_KEY, ""));
- reuseCheckBox.setSelected(settings.getBoolean(DataSetFileImportNodeModel.REUSE_FILE, true));
- }
-
- @Override
- protected void saveMoreSettingsTo(NodeSettingsWO settings) throws InvalidSettingsException
- {
- String dataSetCode = dataSetCodeField.getText();
- if (isBlank(dataSetCode))
- {
- throw new InvalidSettingsException("Data set code hasn't been specified.");
- }
- settings.addString(DataSetFileImportNodeModel.DATA_SET_CODE_KEY, dataSetCode);
- String filePath = filePathField.getText();
- if (isBlank(filePath))
- {
- throw new InvalidSettingsException("Data set file path hasn't been specified.");
- }
- settings.addString(DataSetFileImportNodeModel.FILE_PATH_KEY, filePath);
- String downloadsPath = downloadsPathField.getText();
- if (isBlank(downloadsPath))
- {
- throw new InvalidSettingsException("Location of downloads hasn't been specified.");
- }
- settings.addString(DataSetFileImportNodeModel.DOWNLOADS_PATH_KEY, downloadsPath);
- settings.addString(DataSetFileImportNodeModel.ABSOLUTE_FILE_PATH_KEY,
- downloadsPath + "/" + dataSetCode + "/" + filePath);
- settings.addBoolean(DataSetFileImportNodeModel.REUSE_FILE, reuseCheckBox.isSelected());
- }
-
- private void chooseDataSet(IQueryApiFacade facade)
- {
- try
- {
- String ownerOrNull = new EntityChooser(getPanel(), DataSetOwnerType.DATA_SET, true,
- facade.getSessionToken(), facade.getGeneralInformationService(),
- new DefaultAsyncNodeAction(this)).getOwnerOrNull();
- if (ownerOrNull != null)
- {
- dataSetCodeField.setText(ownerOrNull);
- filePathField.setText("");
- }
- } catch (Exception ex)
- {
- showException(ex);
- }
- }
-
- private void chooseDataSetFile()
- {
- final String dataSetCode = dataSetCodeField.getText();
- if (isBlank(dataSetCode))
- {
- return;
- }
-
- performAction(new ILoadingBuildingAction<FileInfoDssDTO[]>()
- {
- @Override
- public FileInfoDssDTO[] load()
- {
- IOpenbisServiceFacade openbisFacade = createOpenbisFacade(createFacade().getSessionToken());
- ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet dataSet =
- openbisFacade.getDataSet(dataSetCode);
- if (dataSet == null)
- {
- throw new UserFailureException("Unknown data set: " + dataSetCode);
- }
- return dataSet.listFiles("", true);
- }
-
- @Override
- public void build(FileInfoDssDTO[] files)
- {
- FileChooser fileChooser = new FileChooser(dataSetCode, files);
- int result = JOptionPane.showOptionDialog(getPanel(), fileChooser, "Data Set File Chooser",
- JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null, null, null);
- FileInfoDssDTO fileInfo = fileChooser.getSelectedFileInfoOrNull();
- if (fileInfo != null && fileInfo.getPathInListing() != null
- && fileInfo.isDirectory() == false && result == JOptionPane.OK_OPTION)
- {
- filePathField.setText(fileInfo.getPathInDataSet());
- }
- }
- });
- }
-
- private void chooseTempFolder()
- {
- JFileChooser chooser = new JFileChooser();
- String path = downloadsPathField.getText();
- if (isBlank(path) == false)
- {
- chooser.setSelectedFile(new File(path));
- }
- chooser.setDialogType(JFileChooser.OPEN_DIALOG);
- chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
- chooser.setMultiSelectionEnabled(false);
- chooser.showDialog(getPanel(), "Select");
- File selectedFile = chooser.getSelectedFile();
- if (selectedFile != null)
- {
- downloadsPathField.setText(selectedFile.getPath());
- }
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeFactory.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeFactory.java
deleted file mode 100644
index b14ca0d7241f3db5020e0bfe2c399388a1f1f0dd..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeFactory.java
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeFactory;
-import org.knime.core.node.NodeView;
-
-import ch.systemsx.cisd.openbis.knime.common.IOpenbisServiceFacadeFactory;
-import ch.systemsx.cisd.openbis.knime.common.OpenbisServiceFacadeFactory;
-
-/**
- * Factory for {@link DataSetFileImportNodeDialog} and {@link DataSetFileImportNodeModel}.
- *
- * @author Franz-Josef Elmer
- */
-public class DataSetFileImportNodeFactory extends NodeFactory<DataSetFileImportNodeModel>
-{
- private final IOpenbisServiceFacadeFactory factory = new OpenbisServiceFacadeFactory();
-
- @Override
- protected NodeDialogPane createNodeDialogPane()
- {
- return new DataSetFileImportNodeDialog();
- }
-
- @Override
- public DataSetFileImportNodeModel createNodeModel()
- {
- return new DataSetFileImportNodeModel(factory);
- }
-
- @Override
- public NodeView<DataSetFileImportNodeModel> createNodeView(int viewIndex,
- DataSetFileImportNodeModel model)
- {
- return null;
- }
-
- @Override
- protected int getNrNodeViews()
- {
- return 0;
- }
-
- @Override
- protected boolean hasDialog()
- {
- return true;
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeDialog.java
deleted file mode 100644
index f3ac427caf95bbfeda46cb93ac9e7d3bc4cb0e92..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeDialog.java
+++ /dev/null
@@ -1,580 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Container;
-import java.awt.GridBagLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JComponent;
-import javax.swing.JPanel;
-import javax.swing.JSeparator;
-import javax.swing.JTextField;
-import javax.swing.JViewport;
-import javax.swing.text.JTextComponent;
-
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-import org.knime.core.node.NotConfigurableException;
-import org.knime.core.node.port.PortObjectSpec;
-import org.knime.core.node.util.FlowVariableListCellRenderer;
-import org.knime.core.node.workflow.FlowVariable;
-import org.knime.core.node.workflow.FlowVariable.Type;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType.VocabularyTerm;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.util.SimplePropertyValidator;
-import ch.systemsx.cisd.openbis.knime.common.AbstractOpenBisNodeDialog;
-import ch.systemsx.cisd.openbis.knime.common.DefaultAsyncNodeAction;
-import ch.systemsx.cisd.openbis.knime.common.EntityChooser;
-import ch.systemsx.cisd.openbis.knime.common.IOpenbisServiceFacadeFactory;
-import ch.systemsx.cisd.openbis.knime.common.IQueryFacadeAction;
-import ch.systemsx.cisd.openbis.knime.common.Util;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DataSetRegistrationNodeDialog extends AbstractOpenBisNodeDialog
-{
- private static final class ValidationHandler
- {
- private final StringBuilder builder = new StringBuilder();
-
- private final SimplePropertyValidator validator;
-
- ValidationHandler(SimplePropertyValidator validator)
- {
- this.validator = validator;
- }
-
- String getErrorMessage()
- {
- return builder.toString();
- }
-
- void validate(PropertyType propertyType, String value)
- {
- if (value == null || value.trim().length() == 0)
- {
- if (propertyType.isMandatory())
- {
- addErrorMessage(propertyType, "Missing mandatory value");
- }
- } else
- {
- DataTypeCode dataType = propertyType.getDataType();
- if (validator.canValidate(dataType))
- {
- try
- {
- validator.validatePropertyValue(dataType, value);
- } catch (UserFailureException ex)
- {
- addErrorMessage(propertyType, ex.getMessage());
- }
- }
- }
- }
-
- private void addErrorMessage(PropertyType propertyType, String message)
- {
- builder.append("Invalid property '").append(propertyType.getLabel());
- builder.append("': ").append(message).append(".\n");
- }
- }
-
- private static final class DataSetTypeAdapter
- {
- private final DataSetType dataSetType;
-
- DataSetTypeAdapter(DataSetType dataSetType)
- {
- this.dataSetType = dataSetType;
- }
-
- public DataSetType getDataSetType()
- {
- return dataSetType;
- }
-
- @Override
- public String toString()
- {
- return dataSetType.getCode();
- }
- }
-
- private static final class TermAdapter
- {
- private final VocabularyTerm vocabularyTerm;
-
- TermAdapter(VocabularyTerm vocabularyTerm)
- {
- this.vocabularyTerm = vocabularyTerm;
- }
-
- public VocabularyTerm getVocabularyTerm()
- {
- return vocabularyTerm;
- }
-
- @Override
- public String toString()
- {
- return getVocabularyTerm().getLabel();
- }
- }
-
- private static enum FieldFactory
- {
- VOCABULARY_FIELD_FACTORY()
- {
- @Override
- boolean canCreate(PropertyType propertyType)
- {
- return propertyType instanceof ControlledVocabularyPropertyType;
- }
-
- @Override
- JComponent create(PropertyType propertyType, String valueOrNull)
- {
- List<VocabularyTerm> terms =
- ((ControlledVocabularyPropertyType) propertyType).getTerms();
- JComboBox comboBox = new JComboBox();
- for (VocabularyTerm vocabularyTerm : terms)
- {
- TermAdapter termAdapter = new TermAdapter(vocabularyTerm);
- comboBox.addItem(termAdapter);
- if (vocabularyTerm.getCode().equals(valueOrNull))
- {
- comboBox.setSelectedItem(termAdapter);
- }
- }
- return comboBox;
- }
- },
- CHECK_BOX_FIELD_FACTORY()
- {
- @Override
- boolean canCreate(PropertyType propertyType)
- {
- return propertyType.getDataType() == DataTypeCode.BOOLEAN;
- }
-
- @Override
- JComponent create(PropertyType propertyType, String valueOrNull)
- {
- JCheckBox checkBox = new JCheckBox();
- checkBox.setSelected(Boolean.parseBoolean(valueOrNull));
- return checkBox;
- }
- },
- FIELD_FACTORY()
- {
- @Override
- boolean canCreate(PropertyType propertyType)
- {
- return true;
- }
-
- @Override
- JComponent create(PropertyType propertyType, String valueOrNull)
- {
- JTextField textField = new JTextField(10);
- if (valueOrNull != null)
- {
- textField.setText(valueOrNull);
- }
- return textField;
- }
- },
- ;
-
- abstract boolean canCreate(PropertyType propertyType);
-
- abstract JComponent create(PropertyType propertyType, String valueOrNull);
- }
-
- private JComboBox ownerTypeComboBox;
-
- private JTextField ownerField;
-
- private JComboBox fileVariableComboBox;
-
- private JComboBox dataSetTypeComboBox;
-
- private Map<String, JComponent> propertyFieldRepository = new HashMap<String, JComponent>();
-
- private Map<String, JComponent> propertyFields = new HashMap<String, JComponent>();
-
- private JComponent propertiesLabel;
-
- protected DataSetRegistrationNodeDialog(IOpenbisServiceFacadeFactory serviceFacadeFactory)
- {
- super("Data Set Registration Settings", serviceFacadeFactory);
- }
-
- @Override
- protected void defineQueryForm(JPanel queryPanel)
- {
- JPanel fields = new JPanel(new GridBagLayout());
- ownerTypeComboBox = new JComboBox(DataSetOwnerType.values());
- ownerTypeComboBox.addItemListener(new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent event)
- {
- setOwnerToolTip();
- ownerField.setText("");
- }
- });
- addField(fields, "Owner type", ownerTypeComboBox)
- .setToolTipText("The type of entity the new data set will directly be linked to.");
- ownerField = new JTextField(20);
- setOwnerToolTip();
- JPanel textFieldWithButton = new JPanel(new BorderLayout());
- textFieldWithButton.add(ownerField, BorderLayout.CENTER);
- JButton button = new JButton("...");
- button.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- performAction(new IQueryFacadeAction()
- {
- @Override
- public void execute(IQueryApiFacade queryFacade)
- {
- chooseOwner(queryFacade);
- }
- });
- }
- });
- textFieldWithButton.add(button, BorderLayout.EAST);
- addField(fields, "Owner", textFieldWithButton)
- .setToolTipText("Owner is the experiment/sample/data set the new data set will directly be linked to.");
- dataSetTypeComboBox = new JComboBox();
- addField(fields, "Data Set Type", dataSetTypeComboBox);
- if (withFileVariable())
- {
- fileVariableComboBox = new JComboBox();
- fileVariableComboBox.setRenderer(new FlowVariableListCellRenderer());
- addField(fields, "File Variable", fileVariableComboBox)
- .setToolTipText("The flow variable storing the location of the file to be registered.");
- }
- propertiesLabel = new JSeparator();
- fields.add(propertiesLabel, createLast());
- queryPanel.add(fields, BorderLayout.NORTH);
- }
-
- protected boolean withFileVariable()
- {
- return false;
- }
-
- private void setOwnerToolTip()
- {
- DataSetOwnerType ownerType = getSelectedOwnerType();
- String ownerTypeName = null;
- switch (ownerType)
- {
- case EXPERIMENT:
- ownerTypeName = "an experiment";
- break;
- case SAMPLE:
- ownerTypeName = "a sample";
- break;
- case DATA_SET:
- ownerTypeName = "a data set";
- break;
- }
- ownerField.setToolTipText("Choose " + ownerTypeName + " or keep it empty if flow variable "
- + Util.VARIABLE_PREFIX + ownerType.name() + " should be used.");
- }
-
- private DataSetOwnerType getSelectedOwnerType()
- {
- return (DataSetOwnerType) ownerTypeComboBox.getSelectedItem();
- }
-
- private void chooseOwner(IQueryApiFacade facade)
- {
- DataSetOwnerType ownerType = getSelectedOwnerType();
- String sessionToken = facade.getSessionToken();
- IGeneralInformationService service = facade.getGeneralInformationService();
- String ownerOrNull = new EntityChooser(ownerField, ownerType, true, sessionToken, service,
- new DefaultAsyncNodeAction(this)).getOwnerOrNull();
- if (ownerOrNull != null)
- {
- ownerField.setText(ownerOrNull);
- }
- }
-
- @Override
- protected void updateQueryForm(IQueryApiFacade queryFacade)
- {
- DataSetTypeAdapter dataSetTypeAdapter = null;
- Object selectedItem = dataSetTypeComboBox.getSelectedItem();
- if (selectedItem instanceof DataSetTypeAdapter)
- {
- dataSetTypeAdapter = (DataSetTypeAdapter) selectedItem;
- }
- dataSetTypeComboBox.removeAllItems();
- String sessionToken = queryFacade.getSessionToken();
- List<DataSetType> dataSetTypes = createOpenbisFacade(sessionToken).listDataSetTypes();
- for (DataSetType dataSetType : dataSetTypes)
- {
- dataSetTypeComboBox.addItem(new DataSetTypeAdapter(dataSetType));
- }
- dataSetTypeComboBox.addItemListener(new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent event)
- {
- changeDataSetType(((DataSetTypeAdapter) event.getItem()).getDataSetType(),
- new HashMap<String, String>());
- }
- });
- if (dataSetTypes.isEmpty() == false)
- {
- int index = 0;
- if (dataSetTypeAdapter != null)
- {
- String dataSetTypeCode = dataSetTypeAdapter.getDataSetType().getCode();
- for (int i = 0, n = dataSetTypeComboBox.getItemCount(); i < n; i++)
- {
- Object item = dataSetTypeComboBox.getItemAt(i);
- if (item instanceof DataSetTypeAdapter)
- {
- DataSetTypeAdapter dAdapter = (DataSetTypeAdapter) item;
- if (dAdapter.getDataSetType().getCode().equals(dataSetTypeCode))
- {
- index = i;
- break;
- }
- }
- }
- }
- dataSetTypeComboBox.setSelectedIndex(index);
- changeDataSetType(dataSetTypes.get(index), new HashMap<String, String>());
- }
- }
-
- private void changeDataSetType(DataSetType dataSetType, Map<String, String> properties)
- {
- Container parent = propertiesLabel.getParent();
- Component[] components = parent.getComponents();
- boolean removing = false;
- for (Component component : components)
- {
- if (removing)
- {
- parent.remove(component);
- } else if (component == propertiesLabel)
- {
- removing = true;
- }
- }
- propertyFields.clear();
- List<PropertyTypeGroup> propertyTypeGroups = dataSetType.getPropertyTypeGroups();
- for (PropertyTypeGroup propertyTypeGroup : propertyTypeGroups)
- {
- List<PropertyType> propertyTypes = propertyTypeGroup.getPropertyTypes();
- for (PropertyType propertyType : propertyTypes)
- {
- String code = propertyType.getCode();
- String valueOrNull = properties.get(code);
- JComponent field = getField(propertyType, valueOrNull);
- addField(parent, propertyType.getLabel(), field, propertyType.isMandatory());
- propertyFields.put(code, field);
- }
- }
- parent.invalidate();
- while (parent != null && parent instanceof JViewport == false)
- {
- parent = parent.getParent();
- }
- parent.validate();
- }
-
- private JComponent getField(PropertyType propertyType, String valueOrNull)
- {
- JComponent field = propertyFieldRepository.get(propertyType.getCode());
- if (field == null)
- {
- FieldFactory[] values = FieldFactory.values();
- for (FieldFactory fieldFactory : values)
- {
- if (fieldFactory.canCreate(propertyType))
- {
- field = fieldFactory.create(propertyType, valueOrNull);
- field.setToolTipText(propertyType.getDescription());
- propertyFieldRepository.put(propertyType.getCode(), field);
- break;
- }
- }
- }
- return field;
- }
-
- @Override
- protected void loadAdditionalSettingsFrom(NodeSettingsRO settings, PortObjectSpec[] specs)
- throws NotConfigurableException
- {
- ownerTypeComboBox.setSelectedItem(DataSetOwnerType.valueOf(settings.getString(
- DataSetRegistrationNodeModel.OWNER_TYPE_KEY, DataSetOwnerType.EXPERIMENT.name())));
- ownerField.setText(settings.getString(DataSetRegistrationNodeModel.OWNER_KEY, ""));
- if (fileVariableComboBox != null)
- {
- fileVariableComboBox.removeAllItems();
- String fileVariable = settings.getString(DataSetRegistrationNodeModel.FILE_VARIABLE_KEY, "");
- for (FlowVariable flowVariable : getFlowVariables())
- {
- if (flowVariable.getType().equals(Type.STRING))
- {
- fileVariableComboBox.addItem(flowVariable);
- if (flowVariable.getName().equals(fileVariable))
- {
- fileVariableComboBox.setSelectedItem(flowVariable);
- }
- }
- }
- }
- byte[] bytes = settings.getByteArray(DataSetRegistrationNodeModel.DATA_SET_TYPE_KEY, null);
- DataSetType dataSetType = Util.deserializeDescription(bytes);
- if (dataSetType != null && dataSetTypeComboBox.getItemCount() == 0)
- {
- dataSetTypeComboBox.addItem(new DataSetTypeAdapter(dataSetType));
- dataSetTypeComboBox.setSelectedIndex(0);
- try
- {
- changeDataSetType(dataSetType, DataSetRegistrationNodeModel.getProperties(settings));
- } catch (InvalidSettingsException ex)
- {
- throw new NotConfigurableException("Couldn't get properties", ex);
- }
- }
- }
-
- protected Collection<FlowVariable> getFlowVariables()
- {
- return getAvailableFlowVariables().values();
- }
-
- @Override
- protected void saveAdditionalSettingsTo(NodeSettingsWO settings)
- throws InvalidSettingsException
- {
- SimplePropertyValidator propertyValidator = new SimplePropertyValidator();
- settings.addString(DataSetRegistrationNodeModel.OWNER_TYPE_KEY,
- getSelectedOwnerType().name());
- settings.addString(DataSetRegistrationNodeModel.OWNER_KEY, ownerField.getText());
- if (fileVariableComboBox != null)
- {
- Object selectedItem = fileVariableComboBox.getSelectedItem();
- if (selectedItem instanceof FlowVariable)
- {
- FlowVariable flowVariable = (FlowVariable) selectedItem;
- settings.addString(DataSetRegistrationNodeModel.FILE_VARIABLE_KEY, flowVariable.getName());
- }
- }
- DataSetTypeAdapter dataSetTypeAdapter =
- (DataSetTypeAdapter) dataSetTypeComboBox.getSelectedItem();
- if (dataSetTypeAdapter == null)
- {
- throw new InvalidSettingsException("Unspecified data set type.");
- }
- DataSetType dataSetType = dataSetTypeAdapter.getDataSetType();
- byte[] bytes = Util.serializeDescription(dataSetType);
- settings.addByteArray(DataSetRegistrationNodeModel.DATA_SET_TYPE_KEY, bytes);
- Map<String, PropertyType> propertyTypes = getPropertyTypes(dataSetType);
- List<String> propertyTypeCodes = new ArrayList<String>(propertyFields.size());
- List<String> propertyValues = new ArrayList<String>(propertyFields.size());
- ValidationHandler validationHandler = new ValidationHandler(propertyValidator);
- for (Entry<String, JComponent> entry : propertyFields.entrySet())
- {
- String propertyTypeCode = entry.getKey();
- propertyTypeCodes.add(propertyTypeCode);
- JComponent component = entry.getValue();
- String value = null;
- if (component instanceof JTextComponent)
- {
- JTextComponent textComponent = (JTextComponent) component;
- value = textComponent.getText();
- } else if (component instanceof JCheckBox)
- {
- JCheckBox checkBox = (JCheckBox) component;
- value = Boolean.toString(checkBox.isSelected());
- } else if (component instanceof JComboBox)
- {
- JComboBox comboBox = (JComboBox) component;
- value = ((TermAdapter) comboBox.getSelectedItem()).getVocabularyTerm().getCode();
- }
- PropertyType propertyType = propertyTypes.get(propertyTypeCode);
- validationHandler.validate(propertyType, value);
- propertyValues.add(value);
- }
- String errorMessage = validationHandler.getErrorMessage();
- if (errorMessage.length() > 0)
- {
- throw new InvalidSettingsException(errorMessage);
- }
- settings.addStringArray(DataSetRegistrationNodeModel.PROPERTY_TYPE_CODES_KEY,
- propertyTypeCodes.toArray(new String[0]));
- settings.addStringArray(DataSetRegistrationNodeModel.PROPERTY_VALUES_KEY,
- propertyValues.toArray(new String[0]));
- }
-
- private Map<String, PropertyType> getPropertyTypes(DataSetType dataSetType)
- {
- List<PropertyTypeGroup> propertyTypeGroups = dataSetType.getPropertyTypeGroups();
- Map<String, PropertyType> result = new HashMap<String, PropertyType>();
- for (PropertyTypeGroup propertyTypeGroup : propertyTypeGroups)
- {
- List<PropertyType> propertyTypes = propertyTypeGroup.getPropertyTypes();
- for (PropertyType propertyType : propertyTypes)
- {
- result.put(propertyType.getCode(), propertyType);
- }
- }
- return result;
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeFactory.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeFactory.java
deleted file mode 100644
index 931f22feed8a8128a78b16a0f3fb305e22879d89..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeFactory.java
+++ /dev/null
@@ -1,64 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeFactory;
-import org.knime.core.node.NodeView;
-
-import ch.systemsx.cisd.openbis.knime.common.IOpenbisServiceFacadeFactory;
-import ch.systemsx.cisd.openbis.knime.common.OpenbisServiceFacadeFactory;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DataSetRegistrationNodeFactory extends NodeFactory<DataSetRegistrationNodeModel>
-{
- private final IOpenbisServiceFacadeFactory factory = new OpenbisServiceFacadeFactory();
-
- @Override
- protected NodeDialogPane createNodeDialogPane()
- {
- return new DataSetRegistrationNodeDialog(factory);
- }
-
- @Override
- public DataSetRegistrationNodeModel createNodeModel()
- {
- return new DataSetRegistrationNodeModel(factory);
- }
-
- @Override
- protected int getNrNodeViews()
- {
- return 0;
- }
-
- @Override
- public NodeView<DataSetRegistrationNodeModel> createNodeView(int viewIndex,
- DataSetRegistrationNodeModel nodeModel)
- {
- return null;
- }
-
- @Override
- protected boolean hasDialog()
- {
- return true;
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationViaFlowNodeFactory.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationViaFlowNodeFactory.java
deleted file mode 100644
index 50d265530491fe655bc3a7d817821d9cd038983b..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationViaFlowNodeFactory.java
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeFactory;
-import org.knime.core.node.NodeView;
-
-import ch.systemsx.cisd.openbis.knime.common.IOpenbisServiceFacadeFactory;
-import ch.systemsx.cisd.openbis.knime.common.OpenbisServiceFacadeFactory;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DataSetRegistrationViaFlowNodeFactory extends NodeFactory<DataSetRegistrationViaFlowNodeModel>
-{
- private final IOpenbisServiceFacadeFactory factory = new OpenbisServiceFacadeFactory();
-
- @Override
- protected NodeDialogPane createNodeDialogPane()
- {
- return new DataSetRegistrationNodeDialog(factory)
- {
- @Override
- protected boolean withFileVariable()
- {
- return true;
- }
- };
- }
-
- @Override
- public DataSetRegistrationViaFlowNodeModel createNodeModel()
- {
- return new DataSetRegistrationViaFlowNodeModel(factory);
- }
-
- @Override
- protected int getNrNodeViews()
- {
- return 0;
- }
-
- @Override
- public NodeView<DataSetRegistrationViaFlowNodeModel> createNodeView(int viewIndex,
- DataSetRegistrationViaFlowNodeModel nodeModel)
- {
- return null;
- }
-
- @Override
- protected boolean hasDialog()
- {
- return true;
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/TestAggregatedDataImportNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/TestAggregatedDataImportNodeDialog.java
deleted file mode 100644
index c380aaeabb8e422c13cae49fe6a2b5aef0c49906..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/TestAggregatedDataImportNodeDialog.java
+++ /dev/null
@@ -1,77 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import java.util.Arrays;
-import java.util.Collection;
-
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeSettings;
-import org.knime.core.node.NotConfigurableException;
-import org.knime.core.node.port.PortObjectSpec;
-import org.knime.core.node.workflow.Credentials;
-import org.knime.core.node.workflow.ICredentials;
-
-import ch.systemsx.cisd.openbis.knime.common.AbstractTestNodeDialog;
-import ch.systemsx.cisd.openbis.knime.common.ParameterBindings;
-
-/**
- * Stand alone application for testing {@link AggregatedDataFileImportNodeDialog}.
- *
- * @author Franz-Josef Elmer
- */
-public class TestAggregatedDataImportNodeDialog extends AbstractTestNodeDialog
-{
-
- public static void main(String[] args) throws NotConfigurableException
- {
- AbstractTestNodeDialog.createAndShow(new TestAggregatedDataImportNodeDialog());
- }
-
- @Override
- public NodeDialogPane create() throws NotConfigurableException
- {
- return new AggregatedDataFileImportNodeDialog()
- {
- {
- NodeSettings settings = createSettings();
- settings.addStringArray(ParameterBindings.PARAMETER_KEYS_KEY, new String[0]);
- settings.addStringArray(ParameterBindings.PARAMETER_VALUES_KEY, new String[0]);
- loadSettingsFrom(settings, (PortObjectSpec[]) null);
- }
-
- @Override
- protected String[] getUrls()
- {
- return new String[] { "http://localhost:8888" };
- }
-
- @Override
- protected Collection<String> getAllCredentialsNames()
- {
- return Arrays.asList("test");
- }
-
- @Override
- protected ICredentials getCredentials()
- {
- return new Credentials("_", "test", "a");
- }
-
- };
- }
-}
\ No newline at end of file
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/TestDataSetFileImportNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/TestDataSetFileImportNodeDialog.java
deleted file mode 100644
index 19f4ba97f3a5a735de02c9bc829e6605fdd2b13e..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/TestDataSetFileImportNodeDialog.java
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
- * Copyright 2012 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import java.util.Arrays;
-import java.util.Collection;
-
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeSettings;
-import org.knime.core.node.NotConfigurableException;
-import org.knime.core.node.port.PortObjectSpec;
-import org.knime.core.node.workflow.Credentials;
-import org.knime.core.node.workflow.ICredentials;
-
-import ch.systemsx.cisd.openbis.knime.common.AbstractTestNodeDialog;
-import ch.systemsx.cisd.openbis.knime.common.ParameterBindings;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class TestDataSetFileImportNodeDialog extends AbstractTestNodeDialog
-{
- public static void main(String[] args)
- {
- AbstractTestNodeDialog.createAndShow(new TestDataSetFileImportNodeDialog());
- }
-
- @Override
- public NodeDialogPane create() throws NotConfigurableException
- {
- return new DataSetFileImportNodeDialog()
- {
- {
- NodeSettings settings = createSettings();
- settings.addStringArray(ParameterBindings.PARAMETER_KEYS_KEY, new String[0]);
- settings.addStringArray(ParameterBindings.PARAMETER_VALUES_KEY, new String[0]);
- loadSettingsFrom(settings, (PortObjectSpec[]) null);
- }
-
- @Override
- protected String[] getUrls()
- {
- return new String[] { "http://localhost:8888" };
- }
-
- @Override
- protected Collection<String> getAllCredentialsNames()
- {
- return Arrays.asList("test");
- }
-
- @Override
- protected ICredentials getCredentials()
- {
- return new Credentials("_", "test", "a");
- }
-
- };
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/TestDataSetRegistrationNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/TestDataSetRegistrationNodeDialog.java
deleted file mode 100644
index 858033cc10007028a1bbcbe8ab4ee1816c6044f2..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/file/TestDataSetRegistrationNodeDialog.java
+++ /dev/null
@@ -1,89 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import java.util.Arrays;
-import java.util.Collection;
-
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeSettings;
-import org.knime.core.node.NotConfigurableException;
-import org.knime.core.node.port.PortObjectSpec;
-import org.knime.core.node.workflow.Credentials;
-import org.knime.core.node.workflow.FlowVariable;
-import org.knime.core.node.workflow.ICredentials;
-
-import ch.systemsx.cisd.openbis.knime.common.AbstractTestNodeDialog;
-import ch.systemsx.cisd.openbis.knime.common.OpenbisServiceFacadeFactory;
-
-/**
- * Stand alone application for testing {@link DataSetRegistrationNodeDialog}.
- *
- * @author Franz-Josef Elmer
- */
-public class TestDataSetRegistrationNodeDialog extends AbstractTestNodeDialog
-{
-
- public static void main(String[] args) throws NotConfigurableException
- {
- AbstractTestNodeDialog.createAndShow(new TestDataSetRegistrationNodeDialog());
- }
-
- @Override
- public NodeDialogPane create() throws NotConfigurableException
- {
- return new DataSetRegistrationNodeDialog(new OpenbisServiceFacadeFactory())
- {
- {
- NodeSettings settings = createSettings();
- loadSettingsFrom(settings, (PortObjectSpec[]) null);
- }
-
- @Override
- protected String[] getUrls()
- {
- return new String[] { "http://localhost:8888" };
- }
-
- @Override
- protected Collection<String> getAllCredentialsNames()
- {
- return Arrays.asList("test");
- }
-
- @Override
- protected ICredentials getCredentials()
- {
- return new Credentials("_", "test", "a");
- }
-
- @Override
- protected boolean withFileVariable()
- {
- return true;
- }
-
- @Override
- protected Collection<FlowVariable> getFlowVariables()
- {
- return Arrays.asList(new FlowVariable("answer", 42),
- new FlowVariable("fname", "here/and/there"),
- new FlowVariable("file-name", "this/and/that"));
- }
- };
- }
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/AggregatedDataTableImportNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/AggregatedDataTableImportNodeDialog.java
deleted file mode 100644
index 4adb3ea272eb47af1769f64cefc3a58c7321049f..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/AggregatedDataTableImportNodeDialog.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.query;
-
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.knime.common.AbstractAggregatedDataImportNodeDialog;
-import ch.systemsx.cisd.openbis.knime.common.AggregatedDataImportDescription;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription;
-
-/**
- * Node dialog for get a table created by an aggregation service.
- *
- * @author Franz-Josef Elmer
- */
-class AggregatedDataTableImportNodeDialog extends AbstractAggregatedDataImportNodeDialog
-{
- AggregatedDataTableImportNodeDialog()
- {
- super("Aggregation Service Report Settings");
- }
-
- @Override
- protected void addDescription(List<AggregatedDataImportDescription> descriptions,
- AggregationServiceDescription aggregationServiceDescription)
- {
- AggregatedDataImportDescription.addDescriptionIfDataTable(descriptions,
- aggregationServiceDescription);
- }
-
- @Override
- protected String getDescriptionComboBoxLabel()
- {
- return "Aggregation Service";
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/AggregatedDataTableImportNodeFactory.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/AggregatedDataTableImportNodeFactory.java
deleted file mode 100644
index bb829e86eec43c451668cfa9fd363cf70090fa97..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/AggregatedDataTableImportNodeFactory.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.query;
-
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeFactory;
-import org.knime.core.node.NodeView;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class AggregatedDataTableImportNodeFactory extends NodeFactory<AggregatedDataTableImportNodeModel>
-{
- @Override
- public AggregatedDataTableImportNodeModel createNodeModel()
- {
- return new AggregatedDataTableImportNodeModel();
- }
-
- @Override
- protected NodeDialogPane createNodeDialogPane()
- {
- return new AggregatedDataTableImportNodeDialog();
- }
-
- @Override
- protected int getNrNodeViews()
- {
- return 0;
- }
-
- @Override
- public NodeView<AggregatedDataTableImportNodeModel> createNodeView(int viewIndex,
- AggregatedDataTableImportNodeModel nodeModel)
- {
- return null;
- }
-
- @Override
- protected boolean hasDialog()
- {
- return true;
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeDialog.java
deleted file mode 100644
index d4acf7befc7c8efc0d98348b4e2707129b5e62e9..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeDialog.java
+++ /dev/null
@@ -1,83 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.query;
-
-import static ch.systemsx.cisd.openbis.knime.query.QueryNodeModel.QUERY_DESCRIPTION_KEY;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.knime.common.AbstractParameterDescriptionBasedNodeDialog;
-import ch.systemsx.cisd.openbis.knime.common.FieldDescription;
-import ch.systemsx.cisd.openbis.knime.server.FieldType;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription;
-
-/**
- * Node dialog for an openBIS SQL query.
- *
- * @author Franz-Josef Elmer
- */
-class QueryNodeDialog extends AbstractParameterDescriptionBasedNodeDialog<QueryDescription>
-{
- QueryNodeDialog()
- {
- super("Query Settings");
- }
-
- @Override
- protected List<FieldDescription> getFieldDescriptions(QueryDescription description)
- {
- List<FieldDescription> fieldDescriptions = new ArrayList<FieldDescription>();
- List<String> parameters = description.getParameters();
- for (String parameter : parameters)
- {
- fieldDescriptions.add(new FieldDescription(parameter, FieldType.VARCHAR, ""));
- }
- return fieldDescriptions;
- }
-
- @Override
- protected List<QueryDescription> getSortedDescriptions(IQueryApiFacade facade)
- {
- List<QueryDescription> queries = facade.listQueries();
- Collections.sort(queries, new Comparator<QueryDescription>()
- {
- @Override
- public int compare(QueryDescription d1, QueryDescription d2)
- {
- return d1.getName().compareTo(d2.getName());
- }
- });
- return queries;
- }
-
- @Override
- protected String getDescriptionKey()
- {
- return QUERY_DESCRIPTION_KEY;
- }
-
- @Override
- protected String getDescriptionComboBoxLabel()
- {
- return "Query";
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeFactory.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeFactory.java
deleted file mode 100644
index f18c57bec1e290faceb94f55dcae9e7269ca28b0..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeFactory.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.query;
-
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeFactory;
-import org.knime.core.node.NodeView;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class QueryNodeFactory extends NodeFactory<QueryNodeModel>
-{
-
- @Override
- protected NodeDialogPane createNodeDialogPane()
- {
- return new QueryNodeDialog();
- }
-
- @Override
- public QueryNodeModel createNodeModel()
- {
- return new QueryNodeModel();
- }
-
- @Override
- public NodeView<QueryNodeModel> createNodeView(int viewIndex, QueryNodeModel model)
- {
- return null;
- }
-
- @Override
- protected int getNrNodeViews()
- {
- return 0;
- }
-
- @Override
- protected boolean hasDialog()
- {
- return true;
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/ReportNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/ReportNodeDialog.java
deleted file mode 100644
index 9ba530ae451bbd283e369c1154095ec53cfd5268..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/ReportNodeDialog.java
+++ /dev/null
@@ -1,230 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.query;
-
-import java.awt.BorderLayout;
-import java.awt.Cursor;
-import java.awt.GridBagLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-import javax.swing.text.JTextComponent;
-
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-import org.knime.core.node.NotConfigurableException;
-import org.knime.core.node.port.PortObjectSpec;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.SearchOperator;
-import ch.systemsx.cisd.openbis.knime.common.AbstractDescriptionBasedNodeDialog;
-import ch.systemsx.cisd.openbis.knime.common.GUIUtil;
-import ch.systemsx.cisd.openbis.knime.common.IQueryFacadeAction;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.ReportDescription;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ReportNodeDialog extends AbstractDescriptionBasedNodeDialog<ReportDescription>
-{
- private static final String DELIMITER = ", ";
-
- private JTextComponent dataSetCodeFields;
-
- ReportNodeDialog()
- {
- super("Report Settings");
- }
-
- @Override
- protected void defineQueryForm(JPanel queryPanel, JComboBox reportComboBox)
- {
- JPanel panel = new JPanel(new GridBagLayout());
- addField(panel, "Reports", reportComboBox);
- JPanel textFieldWithButton = new JPanel(new BorderLayout());
- dataSetCodeFields = new JTextField(20);
- textFieldWithButton.add(dataSetCodeFields, BorderLayout.CENTER);
- JButton button = new JButton("...");
- button.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- performAction(new IQueryFacadeAction()
- {
- @Override
- public void execute(IQueryApiFacade queryFacade)
- {
- chooseDataSet(queryFacade);
- }
- });
- }
- });
- textFieldWithButton.add(button, BorderLayout.EAST);
- addField(panel, "Data Set Codes", textFieldWithButton);
- JPanel northPanel = new JPanel(new BorderLayout());
- northPanel.add(panel, BorderLayout.NORTH);
- queryPanel.add(northPanel, BorderLayout.CENTER);
- }
-
- @Override
- protected List<ReportDescription> getSortedDescriptions(IQueryApiFacade facade)
- {
- List<ReportDescription> descriptions = facade.listTableReportDescriptions();
-
- if (descriptions != null)
- {
- Set<String> keys = new HashSet<String>();
- List<ReportDescription> uniqueDescriptions = new ArrayList<ReportDescription>();
-
- for (ReportDescription description : descriptions)
- {
- if (keys.contains(description.getKey()) == false)
- {
- uniqueDescriptions.add(description);
- keys.add(description.getKey());
- }
- }
-
- Collections.sort(uniqueDescriptions, new Comparator<ReportDescription>()
- {
- @Override
- public int compare(ReportDescription o1, ReportDescription o2)
- {
- return o1.getLabel().compareToIgnoreCase(o2.getLabel());
- }
- });
-
- return uniqueDescriptions;
- } else
- {
- return Collections.emptyList();
- }
- }
-
- @Override
- protected String getDescriptionKey()
- {
- return ReportNodeModel.REPORT_DESCRIPTION_KEY;
- }
-
- @Override
- protected void loadMoreSettingsFrom(NodeSettingsRO settings, PortObjectSpec[] specs)
- throws NotConfigurableException
- {
- String[] dataSetCodes;
- try
- {
- dataSetCodes = settings.getStringArray(ReportNodeModel.DATA_SET_CODES_KEY);
- } catch (InvalidSettingsException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- StringBuilder builder = new StringBuilder();
- for (String dataSetCode : dataSetCodes)
- {
- if (builder.length() > 0)
- {
- builder.append(DELIMITER);
- }
- builder.append(dataSetCode);
- }
- dataSetCodeFields.setText(builder.toString());
- }
-
- @Override
- protected void saveMoreSettingsTo(NodeSettingsWO settings) throws InvalidSettingsException
- {
- String dataSetCodes = dataSetCodeFields.getText();
- if (dataSetCodes == null || dataSetCodes.trim().length() == 0)
- {
- throw new InvalidSettingsException("Data set code hasn't been specified.");
- }
- settings.addStringArray(ReportNodeModel.DATA_SET_CODES_KEY, dataSetCodes.split(" *, *"));
- }
-
- private void chooseDataSet(IQueryApiFacade facade)
- {
- ReportDescription description = getSelectedDescriptionOrNull();
- if (description == null)
- {
- return;
- }
- JPanel panel = getPanel();
- Cursor cursor = panel.getCursor();
- try
- {
- panel.setCursor(new Cursor(Cursor.WAIT_CURSOR));
- List<DataSet> dataSets = loadDataSets(description, facade);
- List<DataSet> selectedDataSets = GUIUtil.getSelectedDataSets(getPanel(), cursor, dataSets, false);
- if (selectedDataSets.isEmpty())
- {
- return;
- }
- StringBuilder builder = new StringBuilder();
- for (DataSet dataSet : selectedDataSets)
- {
-
- if (builder.length() > 0)
- {
- builder.append(DELIMITER);
- }
- builder.append(dataSet.getCode());
- }
- dataSetCodeFields.setText(builder.toString());
- } finally
- {
- panel.setCursor(cursor);
- }
- }
-
- private List<DataSet> loadDataSets(ReportDescription description, IQueryApiFacade facade)
- {
- List<String> dataSetTypes = description.getDataSetTypes();
- IGeneralInformationService service = facade.getGeneralInformationService();
- List<DataSet> allDataSets = new ArrayList<DataSet>();
- for (String dataSetType : dataSetTypes)
- {
- SearchCriteria searchCriteria = new SearchCriteria();
- searchCriteria.setOperator(SearchOperator.MATCH_ANY_CLAUSES);
- MatchClause clause =
- MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE, dataSetType);
- searchCriteria.addMatchClause(clause);
- List<DataSet> dataSets = service.searchForDataSets(facade.getSessionToken(), searchCriteria);
- logger.info(dataSets.size() + " data sets of type " + dataSetType);
- allDataSets.addAll(dataSets);
- }
- return allDataSets;
- }
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/ReportNodeFactory.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/ReportNodeFactory.java
deleted file mode 100644
index b61ac6d3df170e25570b39a6231faa4a07725e8a..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/ReportNodeFactory.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.query;
-
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeFactory;
-import org.knime.core.node.NodeView;
-
-/**
- * Factory for {@link ReportNodeDialog} and {@link ReportNodeModel}.
- *
- * @author Franz-Josef Elmer
- */
-public class ReportNodeFactory extends NodeFactory<ReportNodeModel>
-{
-
- @Override
- protected NodeDialogPane createNodeDialogPane()
- {
- return new ReportNodeDialog();
- }
-
- @Override
- public ReportNodeModel createNodeModel()
- {
- return new ReportNodeModel();
- }
-
- @Override
- public NodeView<ReportNodeModel> createNodeView(int viewIndex, ReportNodeModel model)
- {
- return null;
- }
-
- @Override
- protected int getNrNodeViews()
- {
- return 0;
- }
-
- @Override
- protected boolean hasDialog()
- {
- return true;
- }
-
-}
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/TestAggregatedDataTableImportNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/TestAggregatedDataTableImportNodeDialog.java
deleted file mode 100644
index 590a6d77bcb6cc6ffed2eab33268c516115f5562..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/TestAggregatedDataTableImportNodeDialog.java
+++ /dev/null
@@ -1,77 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.query;
-
-import java.util.Arrays;
-import java.util.Collection;
-
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeSettings;
-import org.knime.core.node.NotConfigurableException;
-import org.knime.core.node.port.PortObjectSpec;
-import org.knime.core.node.workflow.Credentials;
-import org.knime.core.node.workflow.ICredentials;
-
-import ch.systemsx.cisd.openbis.knime.common.AbstractTestNodeDialog;
-import ch.systemsx.cisd.openbis.knime.common.ParameterBindings;
-
-/**
- * Stand alone application for testing {@link AggregatedDataTableImportNodeDialog}.
- *
- * @author Franz-Josef Elmer
- */
-public class TestAggregatedDataTableImportNodeDialog extends AbstractTestNodeDialog
-{
-
- public static void main(String[] args) throws NotConfigurableException
- {
- AbstractTestNodeDialog.createAndShow(new TestAggregatedDataTableImportNodeDialog());
- }
-
- @Override
- public NodeDialogPane create() throws NotConfigurableException
- {
- return new AggregatedDataTableImportNodeDialog()
- {
- {
- NodeSettings settings = createSettings();
- settings.addStringArray(ParameterBindings.PARAMETER_KEYS_KEY, new String[0]);
- settings.addStringArray(ParameterBindings.PARAMETER_VALUES_KEY, new String[0]);
- loadSettingsFrom(settings, (PortObjectSpec[]) null);
- }
-
- @Override
- protected String[] getUrls()
- {
- return new String[] { "http://localhost:8888" };
- }
-
- @Override
- protected Collection<String> getAllCredentialsNames()
- {
- return Arrays.asList("test");
- }
-
- @Override
- protected ICredentials getCredentials()
- {
- return new Credentials("_", "test", "a");
- }
-
- };
- }
-}
\ No newline at end of file
diff --git a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/TestReportNodeDialog.java b/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/TestReportNodeDialog.java
deleted file mode 100644
index 9ac04f8651c0564d42969b75ab254b74bc43bc7d..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceEclipse/java/ch/systemsx/cisd/openbis/knime/query/TestReportNodeDialog.java
+++ /dev/null
@@ -1,74 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.query;
-
-import java.util.Arrays;
-import java.util.Collection;
-
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeSettings;
-import org.knime.core.node.NotConfigurableException;
-import org.knime.core.node.port.PortObjectSpec;
-import org.knime.core.node.workflow.Credentials;
-import org.knime.core.node.workflow.ICredentials;
-
-import ch.systemsx.cisd.openbis.knime.common.AbstractTestNodeDialog;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class TestReportNodeDialog extends AbstractTestNodeDialog
-{
-
- public static void main(String[] args) throws NotConfigurableException
- {
- AbstractTestNodeDialog.createAndShow(new TestReportNodeDialog());
- }
-
- @Override
- public NodeDialogPane create() throws NotConfigurableException
- {
- return new ReportNodeDialog()
- {
- {
- NodeSettings settings = createSettings();
- settings.addStringArray(ReportNodeModel.DATA_SET_CODES_KEY, new String[0]);
- loadSettingsFrom(settings, (PortObjectSpec[]) null);
- }
-
- @Override
- protected String[] getUrls()
- {
- return new String[] { "http://localhost:8888" };
- }
-
- @Override
- protected Collection<String> getAllCredentialsNames()
- {
- return Arrays.asList("test");
- }
-
- @Override
- protected ICredentials getCredentials()
- {
- return new Credentials("_", "test", "a");
- }
- };
-
- }
-
-}
diff --git a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/common/ChooserTreeModelTest.java b/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/common/ChooserTreeModelTest.java
deleted file mode 100644
index fd06c022627a7d29c7e0a29de5cd9160a63dc1b7..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/common/ChooserTreeModelTest.java
+++ /dev/null
@@ -1,826 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import static ch.systemsx.cisd.openbis.knime.common.ChooserTreeModel.LOADING_TEXT;
-
-import java.util.Arrays;
-import java.util.EnumSet;
-import java.util.List;
-
-import javax.swing.event.TreeModelEvent;
-import javax.swing.event.TreeModelListener;
-import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.TreeNode;
-import javax.swing.tree.TreePath;
-
-import org.hamcrest.core.IsNull;
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.jmock.internal.NamedSequence;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.logging.LogInitializer;
-import ch.systemsx.cisd.common.test.RecordingMatcher;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ChooserTreeModelTest extends AssertJUnit
-{
- private static final class NonThreadChooserTreeModel extends ChooserTreeModel
- {
- private static final long serialVersionUID = 1L;
-
- NonThreadChooserTreeModel(DataSetOwnerType entityType, String sessionToken,
- IGeneralInformationService service)
- {
- this(entityType, true, sessionToken, service);
- }
-
- NonThreadChooserTreeModel(DataSetOwnerType entityType, boolean ownerEntity, String sessionToken,
- IGeneralInformationService service)
- {
- super(entityType, ownerEntity, sessionToken, service);
- }
-
- @Override
- void execute(Runnable runnable)
- {
- runnable.run();
- }
- }
-
- private static final class MockNodeAction implements IAsyncNodeAction
- {
- private boolean executed;
-
- private Throwable handledException;
-
- @Override
- public void execute(Runnable runnable)
- {
- executed = true;
- runnable.run();
- }
-
- @Override
- public void handleException(Throwable throwable)
- {
- handledException = throwable;
- }
- }
-
- private static final String SESSION_TOKEN = "s-token";
-
- private static final String LISTABLE_SAMPLE_TYPE = "ST1";
-
- private static final String NON_LISTABLE_SAMPLE_TYPE = "ST2";
-
- private static final String SPACE_1 = "SP1";
-
- private static final String SPACE_2 = "SP2";
-
- private static final String P_1 = "P1";
-
- private static final String P_2 = "P2";
-
- private static final String EXP_1 = "EXP1";
-
- private static final String EXP_2 = "EXP2";
-
- private static final String SAMPLE_1 = "S1";
-
- private static final String SAMPLE_2 = "S2";
-
- private Mockery context;
-
- private IGeneralInformationService service;
-
- private ChooserTreeModel experimentChooserModel;
-
- private ChooserTreeModel sampleChooserModel;
-
- private ChooserTreeModel dataSetChooserModel;
-
- private MockNodeAction nodeAction;
-
- private TreeModelListener treeModelListener;
-
- private RecordingMatcher<SearchCriteria> criteriaMatcher;
-
- private NamedSequence searchForSequence;
-
- @BeforeMethod
- public void beforeMethod()
- {
- LogInitializer.init();
- context = new Mockery();
- service = context.mock(IGeneralInformationService.class);
- treeModelListener = context.mock(TreeModelListener.class);
- nodeAction = new MockNodeAction();
- context.checking(new Expectations()
- {
- {
- atLeast(3).of(service).listSampleTypes(SESSION_TOKEN);
- SampleType.SampleTypeInitializer sampleTypeInitializer =
- new SampleType.SampleTypeInitializer();
- sampleTypeInitializer.setCode(LISTABLE_SAMPLE_TYPE);
- sampleTypeInitializer.setListable(true);
- SampleType listableSampleType = new SampleType(sampleTypeInitializer);
- sampleTypeInitializer.setCode(NON_LISTABLE_SAMPLE_TYPE);
- sampleTypeInitializer.setListable(false);
- SampleType nonListableSampleType = new SampleType(sampleTypeInitializer);
- will(returnValue(Arrays.asList(listableSampleType, nonListableSampleType)));
-
- atLeast(3).of(service).listProjects(SESSION_TOKEN);
- will(returnValue(Arrays.asList(new Project(SPACE_1, P_1),
- new Project(SPACE_2, P_1),
- new Project(SPACE_1, P_2))));
- }
- });
- experimentChooserModel =
- new NonThreadChooserTreeModel(DataSetOwnerType.EXPERIMENT, SESSION_TOKEN, service);
- experimentChooserModel.addTreeModelListener(treeModelListener);
- sampleChooserModel =
- new NonThreadChooserTreeModel(DataSetOwnerType.SAMPLE, SESSION_TOKEN, service);
- sampleChooserModel.addTreeModelListener(treeModelListener);
- dataSetChooserModel =
- new NonThreadChooserTreeModel(DataSetOwnerType.DATA_SET, SESSION_TOKEN, service);
- dataSetChooserModel.addTreeModelListener(treeModelListener);
- criteriaMatcher = new RecordingMatcher<SearchCriteria>();
- searchForSequence = new NamedSequence("criteria-matcher");
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testSpaces()
- {
- Object root = experimentChooserModel.getRoot();
- Object space1 = experimentChooserModel.getChild(root, 0);
- Object space2 = experimentChooserModel.getChild(root, 1);
- Object loadingNode1 = experimentChooserModel.getChild(space1, 0);
- Object loadingNode2 = experimentChooserModel.getChild(space2, 0);
-
- assertEquals(2, experimentChooserModel.getChildCount(root));
- assertEquals(SPACE_1, space1.toString());
- assertEquals(SPACE_2, space2.toString());
- assertEquals(1, experimentChooserModel.getChildCount(space1));
- assertEquals(1, experimentChooserModel.getChildCount(space2));
- assertEquals(LOADING_TEXT, loadingNode1.toString());
- assertEquals(LOADING_TEXT, loadingNode2.toString());
- assertEquals(0, experimentChooserModel.getChildCount(loadingNode1));
- assertEquals(0, experimentChooserModel.getChildCount(loadingNode2));
- assertSelectibility(false, experimentChooserModel, root);
- assertSelectibility(false, experimentChooserModel, space1);
- assertSelectibility(false, experimentChooserModel, loadingNode1);
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExpandSpaceNodeInDataSetChooserForOwner()
- {
- Object root = dataSetChooserModel.getRoot();
- Object space1 = dataSetChooserModel.getChild(root, 0);
- RecordingMatcher<TreeModelEvent> matcher = prepareTreeStructureChanged(1);
-
- dataSetChooserModel.expandNode(createPath(dataSetChooserModel, space1), nodeAction);
-
- assertEquals(null, nodeAction.handledException);
- assertEquals(true, nodeAction.executed);
- assertEquals(2, dataSetChooserModel.getChildCount(space1));
- assertEquals("P1", dataSetChooserModel.getChild(space1, 0).toString());
- assertEquals("P2", dataSetChooserModel.getChild(space1, 1).toString());
- assertEquals(createPath(dataSetChooserModel, space1).toString(),
- matcher.recordedObject().getTreePath().toString());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExpandSpaceNodeInDataSetChooserForNoOwner()
- {
- NonThreadChooserTreeModel chooser = new NonThreadChooserTreeModel(DataSetOwnerType.DATA_SET, false, SESSION_TOKEN, service);
- chooser.addTreeModelListener(treeModelListener);
- Object root = chooser.getRoot();
- Object space1 = chooser.getChild(root, 0);
- RecordingMatcher<TreeModelEvent> matcher = prepareTreeStructureChanged(1);
-
- chooser.expandNode(createPath(chooser, space1), nodeAction);
-
- assertEquals(null, nodeAction.handledException);
- assertEquals(true, nodeAction.executed);
- assertEquals(2, chooser.getChildCount(space1));
- assertEquals("P1", chooser.getChild(space1, 0).toString());
- assertEquals("P2", chooser.getChild(space1, 1).toString());
- assertEquals(createPath(chooser, space1).toString(),
- matcher.recordedObject().getTreePath().toString());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExpandSpaceNodeInSampleChooserForOwner()
- {
- Object root = sampleChooserModel.getRoot();
- Object space1 = sampleChooserModel.getChild(root, 0);
- RecordingMatcher<TreeModelEvent> matcher = prepareTreeStructureChanged(1);
-
- sampleChooserModel.expandNode(createPath(sampleChooserModel, space1), nodeAction);
-
- assertEquals(null, nodeAction.handledException);
- assertEquals(true, nodeAction.executed);
- assertEquals(2, sampleChooserModel.getChildCount(space1));
- assertEquals("P1", sampleChooserModel.getChild(space1, 0).toString());
- assertEquals("P2", sampleChooserModel.getChild(space1, 1).toString());
- assertEquals(createPath(sampleChooserModel, space1).toString(),
- matcher.recordedObject().getTreePath().toString());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExpandSpaceNodeInSampleChooserForNoOwner()
- {
- NonThreadChooserTreeModel chooser = new NonThreadChooserTreeModel(DataSetOwnerType.SAMPLE, false, SESSION_TOKEN, service);
- chooser.addTreeModelListener(treeModelListener);
- Object root = chooser.getRoot();
- Object space1 = chooser.getChild(root, 0);
- RecordingMatcher<TreeModelEvent> matcher = prepareTreeStructureChanged(1);
- Sample s2 = TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_1, SAMPLE_2);
- Sample s1 = TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_1, SAMPLE_1);
- prepareSearchForSamples(s2, s1);
-
- chooser.expandNode(createPath(chooser, space1), nodeAction);
-
- assertEquals(null, nodeAction.handledException);
- assertEquals(true, nodeAction.executed);
- assertEquals(4, chooser.getChildCount(space1));
- assertEquals("/SP1/S1", chooser.getChild(space1, 0).toString());
- assertEquals("/SP1/S2", chooser.getChild(space1, 1).toString());
- assertEquals("P1", chooser.getChild(space1, 2).toString());
- assertEquals("P2", chooser.getChild(space1, 3).toString());
- assertEquals(createPath(chooser, space1).toString(),
- matcher.recordedObject().getTreePath().toString());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testCollapseSpaceNode()
- {
- Object root = dataSetChooserModel.getRoot();
- Object space1 = dataSetChooserModel.getChild(root, 0);
- prepareTreeStructureChanged(1);
- dataSetChooserModel.expandNode(createPath(dataSetChooserModel, space1), nodeAction);
- assertEquals(null, nodeAction.handledException);
- assertEquals(2, dataSetChooserModel.getChildCount(space1));
-
- dataSetChooserModel.collapsNode(createPath(dataSetChooserModel, space1));
-
- Object project11 = dataSetChooserModel.getChild(space1, 0);
- assertEquals(P_1, project11.toString());
- assertEquals(2, dataSetChooserModel.getChildCount(space1));
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExpandProjectNodeInExperimentChooser()
- {
- Object root = experimentChooserModel.getRoot();
- Object space1 = experimentChooserModel.getChild(root, 0);
- RecordingMatcher<TreeModelEvent> matcher = prepareTreeStructureChanged(2);
- experimentChooserModel.expandNode(createPath(experimentChooserModel, space1), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object project11 = experimentChooserModel.getChild(space1, 0);
- prepareListExperiments(project11);
-
- experimentChooserModel.expandNode(createPath(experimentChooserModel, project11), nodeAction);
-
- assertEquals(null, nodeAction.handledException);
- assertEquals(true, nodeAction.executed);
- assertEquals(2, experimentChooserModel.getChildCount(project11));
- Object child1 = experimentChooserModel.getChild(project11, 0);
- assertEquals(EXP_1, child1.toString());
- assertEquals(0, experimentChooserModel.getChildCount(child1));
- assertEquals(true, experimentChooserModel.isLeaf(child1));
- Object child2 = experimentChooserModel.getChild(project11, 1);
- assertEquals(EXP_2, child2.toString());
- assertEquals(0, experimentChooserModel.getChildCount(child2));
- assertEquals(true, experimentChooserModel.isLeaf(child2));
- assertEquals(createPath(experimentChooserModel, space1).toString(),
- matcher.getRecordedObjects().get(0).getTreePath().toString());
- assertEquals(createPath(experimentChooserModel, project11).toString(),
- matcher.getRecordedObjects().get(1).getTreePath().toString());
- assertEquals(2, matcher.getRecordedObjects().size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExpandProjectNodeInSampleChooser()
- {
- Object root = sampleChooserModel.getRoot();
- Object space1 = sampleChooserModel.getChild(root, 0);
- RecordingMatcher<TreeModelEvent> matcher = prepareTreeStructureChanged(2);
- sampleChooserModel.expandNode(createPath(sampleChooserModel, space1), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object project11 = sampleChooserModel.getChild(space1, 0);
- prepareListExperiments(project11);
-
- sampleChooserModel.expandNode(createPath(sampleChooserModel, project11), nodeAction);
-
- assertEquals(null, nodeAction.handledException);
- assertEquals(true, nodeAction.executed);
- assertEquals(2, sampleChooserModel.getChildCount(project11));
- Object child1 = sampleChooserModel.getChild(project11, 0);
- assertEquals(EXP_1, child1.toString());
- assertEquals(1, sampleChooserModel.getChildCount(child1));
- assertEquals(LOADING_TEXT, sampleChooserModel.getChild(child1, 0).toString());
- assertEquals(false, sampleChooserModel.isLeaf(child1));
- Object child2 = sampleChooserModel.getChild(project11, 1);
- assertEquals(EXP_2, child2.toString());
- assertEquals(1, sampleChooserModel.getChildCount(child2));
- assertEquals(LOADING_TEXT, sampleChooserModel.getChild(child2, 0).toString());
- assertEquals(false, sampleChooserModel.isLeaf(child2));
- assertEquals(createPath(sampleChooserModel, space1).toString(),
- matcher.getRecordedObjects().get(0).getTreePath().toString());
- assertEquals(createPath(sampleChooserModel, project11).toString(),
- matcher.getRecordedObjects().get(1).getTreePath().toString());
- assertEquals(2, matcher.getRecordedObjects().size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testCollapsProjectNode()
- {
- Object root = dataSetChooserModel.getRoot();
- Object space1 = dataSetChooserModel.getChild(root, 0);
- prepareTreeStructureChanged(3);
- dataSetChooserModel.expandNode(createPath(dataSetChooserModel, space1), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object project11 = dataSetChooserModel.getChild(space1, 0);
- prepareListExperiments(project11);
- TreePath path = createPath(dataSetChooserModel, project11);
- dataSetChooserModel.expandNode(path, nodeAction);
- assertEquals(null, nodeAction.handledException);
- assertEquals(2, dataSetChooserModel.getChildCount(project11));
-
- dataSetChooserModel.collapsNode(path);
-
- assertEquals(1, dataSetChooserModel.getChildCount(project11));
- assertEquals(LOADING_TEXT, dataSetChooserModel.getChild(project11, 0).toString());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExpandExperimentNodeInSampleChooser()
- {
- Object root = sampleChooserModel.getRoot();
- Object space1 = sampleChooserModel.getChild(root, 0);
- RecordingMatcher<TreeModelEvent> eventMatcher = prepareTreeStructureChanged(3);
- sampleChooserModel.expandNode(createPath(sampleChooserModel, space1), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object project11 = sampleChooserModel.getChild(space1, 0);
- prepareListExperiments(project11);
- sampleChooserModel.expandNode(createPath(sampleChooserModel, project11), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object exp1 = sampleChooserModel.getChild(project11, 0);
- assertEquals(EXP_1, exp1.toString());
- Sample sample = TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_1, SAMPLE_1);
- prepareSearchForSamples(sample);
-
- sampleChooserModel.expandNode(createPath(sampleChooserModel, exp1), nodeAction);
-
- assertEquals(null, nodeAction.handledException);
- assertEquals(true, nodeAction.executed);
- List<TreeModelEvent> recordedObjects = eventMatcher.getRecordedObjects();
- assertEquals(createPath(sampleChooserModel, space1).toString(),
- recordedObjects.get(0).getTreePath().toString());
- assertEquals(createPath(sampleChooserModel, project11).toString(),
- recordedObjects.get(1).getTreePath().toString());
- assertEquals(createPath(sampleChooserModel, exp1).toString(),
- recordedObjects.get(2).getTreePath().toString());
- assertEquals(3, recordedObjects.size());
- assertEquals("SearchCriteria[MATCH_ALL_CLAUSES,["
- + "SearchCriteria.AttributeMatchClause[ATTRIBUTE,TYPE,ST1,EQUALS]],"
- + "[SearchSubCriteria[EXPERIMENT,SearchCriteria[MATCH_ALL_CLAUSES,"
- + "[SearchCriteria.AttributeMatchClause[ATTRIBUTE,PERM_ID,"
- + "PERM-/SP1/P1/EXP1,EQUALS]],[]]]]]", criteriaMatcher.recordedObject().toString());
- Object child = sampleChooserModel.getChild(exp1, 0);
- IChooserTreeNode<?> childNodeObject = getTreeNode(child);
- assertEquals(ChooserTreeNodeType.SAMPLE, childNodeObject.getNodeType());
- assertSame(sample, childNodeObject.getNodeObject());
- assertEquals(1, sampleChooserModel.getChildCount(exp1));
- assertEquals(LOADING_TEXT, sampleChooserModel.getChild(child, 0).toString());
- assertEquals(1, sampleChooserModel.getChildCount(child));
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExpandExperimentNodeInDataSetChooser()
- {
- Object root = dataSetChooserModel.getRoot();
- Object space1 = dataSetChooserModel.getChild(root, 0);
- RecordingMatcher<TreeModelEvent> eventMatcher = prepareTreeStructureChanged(3);
- dataSetChooserModel.expandNode(createPath(dataSetChooserModel, space1), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object project11 = dataSetChooserModel.getChild(space1, 0);
- prepareListExperiments(project11);
- dataSetChooserModel.expandNode(createPath(dataSetChooserModel, project11), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object exp1 = dataSetChooserModel.getChild(project11, 0);
- assertEquals(EXP_1, exp1.toString());
- Sample sample = TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_1, SAMPLE_1);
- prepareSearchForSamples(sample);
- DataSet dataSet = TestUtils.dataSet("DS-1");
- prepareSearchForDataSets(dataSet);
-
- dataSetChooserModel.expandNode(createPath(dataSetChooserModel, exp1), nodeAction);
-
- assertEquals(null, nodeAction.handledException);
- assertEquals(true, nodeAction.executed);
- List<TreeModelEvent> recordedObjects = eventMatcher.getRecordedObjects();
- assertEquals(createPath(dataSetChooserModel, space1).toString(),
- recordedObjects.get(0).getTreePath().toString());
- assertEquals(createPath(dataSetChooserModel, project11).toString(),
- recordedObjects.get(1).getTreePath().toString());
- assertEquals(createPath(dataSetChooserModel, exp1).toString(),
- recordedObjects.get(2).getTreePath().toString());
- assertEquals(3, recordedObjects.size());
- assertEquals("SearchCriteria[MATCH_ALL_CLAUSES,["
- + "SearchCriteria.AttributeMatchClause[ATTRIBUTE,TYPE,ST1,EQUALS]],"
- + "[SearchSubCriteria[EXPERIMENT,SearchCriteria[MATCH_ALL_CLAUSES,"
- + "[SearchCriteria.AttributeMatchClause[ATTRIBUTE,PERM_ID,"
- + "PERM-/SP1/P1/EXP1,EQUALS]],[]]]]]",
- criteriaMatcher.getRecordedObjects().get(0).toString());
- assertEquals("SearchCriteria[MATCH_ALL_CLAUSES,[],[SearchSubCriteria[EXPERIMENT,"
- + "SearchCriteria[MATCH_ALL_CLAUSES,[SearchCriteria.AttributeMatchClause["
- + "ATTRIBUTE,PERM_ID,PERM-/SP1/P1/EXP1,EQUALS]],[]]]]]",
- criteriaMatcher.getRecordedObjects().get(1).toString());
- assertEquals(2, criteriaMatcher.getRecordedObjects().size());
- Object dataSetChild = dataSetChooserModel.getChild(exp1, 0);
- IChooserTreeNode<?> dataSetObject = getTreeNode(dataSetChild);
- assertEquals(ChooserTreeNodeType.DATA_SET, dataSetObject.getNodeType());
- assertSame(dataSet, dataSetObject.getNodeObject());
- assertEquals(true, dataSetChooserModel.isLeaf(dataSetChild));
- Object sampleChild = dataSetChooserModel.getChild(exp1, 1);
- IChooserTreeNode<?> sampleObject = getTreeNode(sampleChild);
- assertEquals(ChooserTreeNodeType.SAMPLE, sampleObject.getNodeType());
- assertSame(sample, sampleObject.getNodeObject());
- assertEquals(2, dataSetChooserModel.getChildCount(exp1));
- assertEquals(LOADING_TEXT, dataSetChooserModel.getChild(sampleChild, 0).toString());
- assertEquals(1, dataSetChooserModel.getChildCount(sampleChild));
- context.assertIsSatisfied();
- }
-
- @Test
- public void testCollapsExperimentNode()
- {
- Object root = sampleChooserModel.getRoot();
- Object space1 = sampleChooserModel.getChild(root, 0);
- prepareTreeStructureChanged(4);
- sampleChooserModel.expandNode(createPath(sampleChooserModel, space1), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object project11 = sampleChooserModel.getChild(space1, 0);
- prepareListExperiments(project11);
- sampleChooserModel.expandNode(createPath(sampleChooserModel, project11), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object exp1 = sampleChooserModel.getChild(project11, 0);
- assertEquals(EXP_1, exp1.toString());
- prepareSearchForSamples(TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_1, SAMPLE_2),
- TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_1, SAMPLE_1));
- TreePath path = createPath(sampleChooserModel, exp1);
- sampleChooserModel.expandNode(path, nodeAction);
- assertEquals(null, nodeAction.handledException);
- assertEquals(2, sampleChooserModel.getChildCount(exp1));
-
- sampleChooserModel.collapsNode(path);
-
- assertEquals(1, sampleChooserModel.getChildCount(exp1));
- assertEquals(LOADING_TEXT, sampleChooserModel.getChild(exp1, 0).toString());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExpandSampleNodeInSampleChooser()
- {
- Object root = sampleChooserModel.getRoot();
- Object space1 = sampleChooserModel.getChild(root, 0);
- RecordingMatcher<TreeModelEvent> eventMatcher = prepareTreeStructureChanged(4);
- sampleChooserModel.expandNode(createPath(sampleChooserModel, space1), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object project11 = sampleChooserModel.getChild(space1, 0);
- prepareListExperiments(project11);
- sampleChooserModel.expandNode(createPath(sampleChooserModel, project11), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object exp1 = sampleChooserModel.getChild(project11, 0);
- prepareSearchForSamples(TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_1, SAMPLE_1));
- sampleChooserModel.expandNode(createPath(sampleChooserModel, exp1), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object sample1 = sampleChooserModel.getChild(exp1, 0);
- String experimentIdentifier = "/" + SPACE_1 + "/" + P_1 + "/" + EXP_1;
- Sample childSampleWithExperiment =
- TestUtils.sample(NON_LISTABLE_SAMPLE_TYPE, SPACE_2, "CHILD_WE", experimentIdentifier);
- Sample childSampleWithoutExperiment = TestUtils.sample(NON_LISTABLE_SAMPLE_TYPE, SPACE_2, "CHILD_WOE");
- prepareSearchForSamplesWithChildren(childSampleWithExperiment, childSampleWithoutExperiment);
- Sample containedSampleWithoutExperiment = TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_1, "CONT_WOE");
- Sample containedSampleWithExperiment =
- TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_1, "CONT_WE", experimentIdentifier);
- prepareSearchForSamples(containedSampleWithExperiment, containedSampleWithoutExperiment);
-
- sampleChooserModel.expandNode(createPath(sampleChooserModel, sample1), nodeAction);
-
- assertEquals(null, nodeAction.handledException);
- assertEquals(true, nodeAction.executed);
- List<TreeModelEvent> recordedObjects = eventMatcher.getRecordedObjects();
- assertEquals(createPath(sampleChooserModel, space1).toString(),
- recordedObjects.get(0).getTreePath().toString());
- assertEquals(createPath(sampleChooserModel, project11).toString(),
- recordedObjects.get(1).getTreePath().toString());
- assertEquals(createPath(sampleChooserModel, exp1).toString(),
- recordedObjects.get(2).getTreePath().toString());
- assertEquals(createPath(sampleChooserModel, sample1).toString(),
- recordedObjects.get(3).getTreePath().toString());
- assertEquals(4, recordedObjects.size());
- assertEquals("SearchCriteria[MATCH_ALL_CLAUSES,["
- + "SearchCriteria.AttributeMatchClause[ATTRIBUTE,TYPE,ST1,EQUALS]],"
- + "[SearchSubCriteria[EXPERIMENT,SearchCriteria[MATCH_ALL_CLAUSES,"
- + "[SearchCriteria.AttributeMatchClause[ATTRIBUTE,PERM_ID,"
- + "PERM-/SP1/P1/EXP1,EQUALS]],[]]]]]",
- criteriaMatcher.getRecordedObjects().get(0).toString());
- assertEquals("SearchCriteria[MATCH_ALL_CLAUSES,[SearchCriteria.AttributeMatchClause["
- + "ATTRIBUTE,PERM_ID,PERM-/SP1/S1,EQUALS]],[]]",
- criteriaMatcher.getRecordedObjects().get(1).toString());
- assertEquals("SearchCriteria[MATCH_ALL_CLAUSES,[],[SearchSubCriteria[SAMPLE_CONTAINER,"
- + "SearchCriteria[MATCH_ALL_CLAUSES,[SearchCriteria.AttributeMatchClause["
- + "ATTRIBUTE,PERM_ID,PERM-/SP1/S1,EQUALS]],[]]]]]",
- criteriaMatcher.getRecordedObjects().get(2).toString());
- assertEquals(3, criteriaMatcher.getRecordedObjects().size());
- Object child = sampleChooserModel.getChild(exp1, 0);
- Object child1 = sampleChooserModel.getChild(child, 0);
- IChooserTreeNode<?> sampleNode1 = getTreeNode(child1);
- assertEquals(ChooserTreeNodeType.SAMPLE, sampleNode1.getNodeType());
- assertSame(containedSampleWithExperiment, sampleNode1.getNodeObject());
- assertEquals(1, sampleChooserModel.getChildCount(child1));
- assertEquals(LOADING_TEXT, sampleChooserModel.getChild(child1, 0).toString());
- Object child2 = sampleChooserModel.getChild(child, 1);
- IChooserTreeNode<?> sampleNode2 = getTreeNode(child2);
- assertEquals(ChooserTreeNodeType.SAMPLE, sampleNode2.getNodeType());
- assertSame(childSampleWithExperiment, sampleNode2.getNodeObject());
- assertEquals(1, sampleChooserModel.getChildCount(child2));
- assertEquals(LOADING_TEXT, sampleChooserModel.getChild(child2, 0).toString());
- assertEquals(2, sampleChooserModel.getChildCount(child));
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExpandSampleNodeInDataSetChooser()
- {
- Object root = dataSetChooserModel.getRoot();
- Object space1 = dataSetChooserModel.getChild(root, 0);
- RecordingMatcher<TreeModelEvent> eventMatcher = prepareTreeStructureChanged(4);
- dataSetChooserModel.expandNode(createPath(dataSetChooserModel, space1), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object project11 = dataSetChooserModel.getChild(space1, 0);
- prepareListExperiments(project11);
- dataSetChooserModel.expandNode(createPath(dataSetChooserModel, project11), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object exp1 = dataSetChooserModel.getChild(project11, 0);
- prepareSearchForSamples(TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_1, SAMPLE_1));
- prepareSearchForDataSets();
- dataSetChooserModel.expandNode(createPath(dataSetChooserModel, exp1), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object sample1 = dataSetChooserModel.getChild(exp1, 0);
- String experimentIdentifier = "/" + SPACE_1 + "/" + P_1 + "/" + EXP_1;
- prepareSearchForSamplesWithChildren();
- Sample containedSampleWithoutExperiment = TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_1, "CONT_WOE");
- Sample containedSampleWithExperiment =
- TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_1, "CONT_WE", experimentIdentifier);
- prepareSearchForSamples(containedSampleWithExperiment, containedSampleWithoutExperiment);
- DataSet dataSet = TestUtils.dataSet("DS1");
- prepareSearchForDataSets(dataSet);
-
- dataSetChooserModel.expandNode(createPath(dataSetChooserModel, sample1), nodeAction);
-
- assertEquals(null, nodeAction.handledException);
- assertEquals(true, nodeAction.executed);
- List<TreeModelEvent> recordedObjects = eventMatcher.getRecordedObjects();
- assertEquals(createPath(dataSetChooserModel, space1).toString(),
- recordedObjects.get(0).getTreePath().toString());
- assertEquals(createPath(dataSetChooserModel, project11).toString(),
- recordedObjects.get(1).getTreePath().toString());
- assertEquals(createPath(dataSetChooserModel, exp1).toString(),
- recordedObjects.get(2).getTreePath().toString());
- assertEquals(createPath(dataSetChooserModel, sample1).toString(),
- recordedObjects.get(3).getTreePath().toString());
- assertEquals(4, recordedObjects.size());
- assertEquals("SearchCriteria[MATCH_ALL_CLAUSES,["
- + "SearchCriteria.AttributeMatchClause[ATTRIBUTE,TYPE,ST1,EQUALS]],"
- + "[SearchSubCriteria[EXPERIMENT,SearchCriteria[MATCH_ALL_CLAUSES,"
- + "[SearchCriteria.AttributeMatchClause[ATTRIBUTE,PERM_ID,"
- + "PERM-/SP1/P1/EXP1,EQUALS]],[]]]]]",
- criteriaMatcher.getRecordedObjects().get(0).toString());
- assertEquals("SearchCriteria[MATCH_ALL_CLAUSES,[],[SearchSubCriteria[EXPERIMENT,"
- + "SearchCriteria[MATCH_ALL_CLAUSES,[SearchCriteria.AttributeMatchClause["
- + "ATTRIBUTE,PERM_ID,PERM-/SP1/P1/EXP1,EQUALS]],[]]]]]",
- criteriaMatcher.getRecordedObjects().get(1).toString());
- assertEquals("SearchCriteria[MATCH_ALL_CLAUSES,[SearchCriteria.AttributeMatchClause["
- + "ATTRIBUTE,PERM_ID,PERM-/SP1/S1,EQUALS]],[]]",
- criteriaMatcher.getRecordedObjects().get(2).toString());
- assertEquals("SearchCriteria[MATCH_ALL_CLAUSES,[],[SearchSubCriteria[SAMPLE_CONTAINER,"
- + "SearchCriteria[MATCH_ALL_CLAUSES,[SearchCriteria.AttributeMatchClause["
- + "ATTRIBUTE,PERM_ID,PERM-/SP1/S1,EQUALS]],[]]]]]",
- criteriaMatcher.getRecordedObjects().get(3).toString());
- assertEquals("SearchCriteria[MATCH_ALL_CLAUSES,[],[SearchSubCriteria[SAMPLE,"
- + "SearchCriteria[MATCH_ALL_CLAUSES,[SearchCriteria.AttributeMatchClause["
- + "ATTRIBUTE,PERM_ID,PERM-/SP1/S1,EQUALS]],[]]]]]",
- criteriaMatcher.getRecordedObjects().get(4).toString());
- assertEquals(5, criteriaMatcher.getRecordedObjects().size());
- Object child = dataSetChooserModel.getChild(exp1, 0);
- Object child1 = dataSetChooserModel.getChild(child, 0);
- IChooserTreeNode<?> dataSetNode = getTreeNode(child1);
- assertEquals(ChooserTreeNodeType.DATA_SET, dataSetNode.getNodeType());
- assertSame(dataSet, dataSetNode.getNodeObject());
- assertEquals(0, dataSetChooserModel.getChildCount(child1));
- assertEquals(true, dataSetChooserModel.isLeaf(child1));
- Object child2 = dataSetChooserModel.getChild(child, 1);
- IChooserTreeNode<?> sampleNode2 = getTreeNode(child2);
- assertEquals(ChooserTreeNodeType.SAMPLE, sampleNode2.getNodeType());
- assertSame(containedSampleWithExperiment, sampleNode2.getNodeObject());
- assertEquals(1, dataSetChooserModel.getChildCount(child2));
- assertEquals(LOADING_TEXT, dataSetChooserModel.getChild(child2, 0).toString());
- Object child3 = dataSetChooserModel.getChild(child, 2);
- IChooserTreeNode<?> sampleNode3 = getTreeNode(child3);
- assertEquals(ChooserTreeNodeType.SAMPLE, sampleNode3.getNodeType());
- assertSame(containedSampleWithoutExperiment, sampleNode3.getNodeObject());
- assertEquals(1, dataSetChooserModel.getChildCount(child3));
- assertEquals(LOADING_TEXT, dataSetChooserModel.getChild(child3, 0).toString());
- assertEquals(3, dataSetChooserModel.getChildCount(child));
- context.assertIsSatisfied();
- }
-
- @Test
- public void testCollapsSampleNode()
- {
- Object root = sampleChooserModel.getRoot();
- Object space1 = sampleChooserModel.getChild(root, 0);
- prepareTreeStructureChanged(5);
- sampleChooserModel.expandNode(createPath(sampleChooserModel, space1), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object project11 = sampleChooserModel.getChild(space1, 0);
- prepareListExperiments(project11);
- sampleChooserModel.expandNode(createPath(sampleChooserModel, project11), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object exp1 = sampleChooserModel.getChild(project11, 0);
- assertEquals(EXP_1, exp1.toString());
- prepareSearchForSamples(TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_1, SAMPLE_2));
- sampleChooserModel.expandNode(createPath(sampleChooserModel, exp1), nodeAction);
- assertEquals(null, nodeAction.handledException);
- Object sample1 = sampleChooserModel.getChild(exp1, 0);
- String experimentIdentifier = "/" + SPACE_1 + "/" + P_1 + "/" + EXP_1;
- Sample s1 = TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_2, SAMPLE_1, experimentIdentifier);
- Sample s2 = TestUtils.sample(LISTABLE_SAMPLE_TYPE, SPACE_2, SAMPLE_2, experimentIdentifier);
- prepareSearchForSamplesWithChildren(s2, s1);
- prepareSearchForSamples();
- TreePath path = createPath(sampleChooserModel, sample1);
- sampleChooserModel.expandNode(path, nodeAction);
- assertEquals(null, nodeAction.handledException);
- assertEquals(2, sampleChooserModel.getChildCount(sample1));
-
- sampleChooserModel.collapsNode(path);
-
- assertEquals(1, sampleChooserModel.getChildCount(sample1));
- assertEquals(LOADING_TEXT, sampleChooserModel.getChild(sample1, 0).toString());
- context.assertIsSatisfied();
- }
-
- private void prepareSearchForSamplesWithChildren(final Sample... childSamples)
- {
- context.checking(new Expectations()
- {
- {
- one(service).searchForSamples(with(SESSION_TOKEN), with(criteriaMatcher),
- with(EnumSet.of(SampleFetchOption.CHILDREN)));
- if (childSamples.length == 0)
- {
- will(returnValue(Arrays.asList()));
- } else
- {
- will(returnValue(Arrays.asList(sampleWithChildren(childSamples))));
- }
- inSequence(searchForSequence);
- }
- });
- }
-
- private void prepareSearchForSamples(final Sample... samples)
- {
- context.checking(new Expectations()
- {
- {
- one(service).searchForSamples(with(SESSION_TOKEN), with(criteriaMatcher),
- with(new IsNull<EnumSet<SampleFetchOption>>()));
- will(returnValue(Arrays.asList(samples)));
- inSequence(searchForSequence);
- }
- });
- }
-
- private void prepareSearchForDataSets(final DataSet... dataSets)
- {
- context.checking(new Expectations()
- {
- {
- one(service).searchForDataSets(with(SESSION_TOKEN), with(criteriaMatcher));
- will(returnValue(Arrays.asList(dataSets)));
- inSequence(searchForSequence);
- }
- });
- }
-
- private void prepareListExperiments(final Object projectObject)
- {
- context.checking(new Expectations()
- {
- {
- Project project = getWrappedObject(projectObject);
- one(service).listExperiments(SESSION_TOKEN, Arrays.asList(project), null);
- will(returnValue(Arrays.asList(TestUtils.experiment(project, EXP_2),
- TestUtils.experiment(project, EXP_1))));
- }
- });
- }
-
- private RecordingMatcher<TreeModelEvent> prepareTreeStructureChanged(final int numberOfEvents)
- {
- final RecordingMatcher<TreeModelEvent> matcher = new RecordingMatcher<TreeModelEvent>();
- context.checking(new Expectations()
- {
- {
- exactly(numberOfEvents).of(treeModelListener).treeStructureChanged(
- with(matcher));
- }
- });
- return matcher;
- }
-
- private Sample sampleWithChildren(Sample... children)
- {
- SampleInitializer initializer =
- TestUtils.createSampleInitializer(LISTABLE_SAMPLE_TYPE, SPACE_1, SAMPLE_2, null);
- initializer.setRetrievedFetchOptions(EnumSet.of(SampleFetchOption.CHILDREN));
- initializer.setChildren(Arrays.asList(children));
- return new Sample(initializer);
- }
-
- private IChooserTreeNode<?> getTreeNode(Object node)
- {
- return (IChooserTreeNode<?>) ((DefaultMutableTreeNode) node).getUserObject();
- }
-
- @SuppressWarnings("unchecked")
- private <T> T getWrappedObject(Object node)
- {
- return ((IChooserTreeNode<T>) ((DefaultMutableTreeNode) node).getUserObject()).getNodeObject();
- }
-
- private void assertSelectibility(boolean expected, ChooserTreeModel model, Object node)
- {
- assertEquals(expected, model.isSelectable(createPath(model, node)));
- }
-
- private TreePath createPath(ChooserTreeModel model, Object node)
- {
- return new TreePath(model.getPathToRoot((TreeNode) node));
- }
-
-}
diff --git a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/common/TestUtils.java b/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/common/TestUtils.java
deleted file mode 100644
index 2542100494869e0b2c5c1ce5fd58bf8459aafa81..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/common/TestUtils.java
+++ /dev/null
@@ -1,93 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class TestUtils
-{
-
- public static DataSet dataSet(String code)
- {
- DataSetInitializer initializer = new DataSetInitializer();
- initializer.setDataSetTypeCode("DT");
- initializer.setCode(code);
- initializer.setRegistrationDetails(registrationDetails());
- return new DataSet(initializer);
- }
-
- public static Experiment experiment(Project project, String experimentCode)
- {
- return experiment(project.getIdentifier(), experimentCode);
- }
-
- public static Experiment experiment(String projectIdentifier, String experimentCode)
- {
- ExperimentInitializer initializer = new ExperimentInitializer();
- initializer.setCode(experimentCode);
- initializer.setExperimentTypeCode("ET");
- initializer.setIdentifier(projectIdentifier + "/" + experimentCode);
- initializer.setPermId("PERM-" + initializer.getIdentifier());
- initializer.setId((long) initializer.getIdentifier().hashCode());
- initializer.setRegistrationDetails(registrationDetails());
- return new Experiment(initializer);
- }
-
- public static SampleInitializer createSampleInitializer(String sampleTypeCode, String spaceCode,
- String sampleCode, String experimentIdentifierOrNull)
- {
- SampleInitializer initializer = new SampleInitializer();
- initializer.setSampleTypeCode(sampleTypeCode);
- initializer.setSampleTypeId(new Long(sampleTypeCode.hashCode()));
- initializer.setCode(sampleCode);
- initializer.setIdentifier("/" + spaceCode + "/" + sampleCode);
- initializer.setPermId("PERM-" + initializer.getIdentifier());
- initializer.setId((long) initializer.getIdentifier().hashCode());
- initializer.setExperimentIdentifierOrNull(experimentIdentifierOrNull);
- initializer.setRegistrationDetails(registrationDetails());
- return initializer;
- }
-
- public static Sample sample(String sampleTypeCode, String spaceCode, String sampleCode,
- String experimentIdentifierOrNull)
- {
- return new Sample(createSampleInitializer(sampleTypeCode, spaceCode, sampleCode,
- experimentIdentifierOrNull));
- }
-
- public static Sample sample(String sampleTypeCode, String spaceCode, String sampleCode)
- {
- return sample(sampleTypeCode, spaceCode, sampleCode, null);
- }
-
- private static EntityRegistrationDetails registrationDetails()
- {
- return new EntityRegistrationDetails(new EntityRegistrationDetailsInitializer());
- }
-
-}
diff --git a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/common/UtilTest.java b/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/common/UtilTest.java
deleted file mode 100644
index 163727c1285aafc3cba3a88d8ad01096d650ae5a..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/common/UtilTest.java
+++ /dev/null
@@ -1,182 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.common;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Level;
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.knime.core.node.NodeLogger;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.logging.BufferedAppender;
-import ch.systemsx.cisd.common.logging.LogInitializer;
-import ch.systemsx.cisd.openbis.generic.shared.util.IRowBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.util.SimpleTableModelBuilder;
-import ch.systemsx.cisd.openbis.knime.server.Constants;
-import ch.systemsx.cisd.openbis.knime.server.FieldType;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel;
-import ch.systemsx.cisd.openbis.plugin.query.shared.translator.QueryTableModelTranslator;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class UtilTest extends AssertJUnit
-{
- private BufferedAppender logRecorder;
-
- private Mockery context;
-
- private IQueryApiFacade facade;
-
- private NodeLogger logger;
-
- private AggregatedDataImportDescription description;
-
- @BeforeMethod
- public void beforeMethod()
- {
- LogInitializer.init();
- logRecorder = new BufferedAppender("%-5p %c - %m%n", Level.DEBUG);
- context = new Mockery();
- facade = context.mock(IQueryApiFacade.class);
- logger = NodeLogger.getLogger("test");
- AggregationServiceDescription desc = new AggregationServiceDescription();
- desc.setServiceKey(AggregatedDataImportDescription.PREFIX + "as");
- ArrayList<AggregatedDataImportDescription> descriptions = new ArrayList<AggregatedDataImportDescription>();
- AggregatedDataImportDescription.addDescriptionIfDataTable(descriptions, desc);
- description = descriptions.get(0);
- }
-
- @AfterMethod
- public void afterMethod()
- {
- logRecorder.reset();
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testGetFieldDescriptionsWithEmptyTable()
- {
- SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
- prepareCreateReport(builder);
-
- assertGetFieldDescriptionsFailed("0 columns instead of 2");
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testGetFieldDescriptionsWithOneColumn()
- {
- SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
- builder.addHeader(Constants.PARAMETER_DESCRIPTION_NAME_COLUMN);
- prepareCreateReport(builder);
-
- assertGetFieldDescriptionsFailed("1 columns instead of 2");
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testGetFieldDescriptionsWithWrongColumns()
- {
- SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
- builder.addHeader(Constants.PARAMETER_DESCRIPTION_NAME_COLUMN);
- builder.addHeader("blabla");
- prepareCreateReport(builder);
-
- assertGetFieldDescriptionsFailed("2. column is 'blabla' instead of 'type'.");
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testGetFieldDescriptionsWithUnspecifiedName()
- {
- SimpleTableModelBuilder builder = new SimpleTableModelBuilder(true);
- builder.addHeader(Constants.PARAMETER_DESCRIPTION_NAME_COLUMN);
- builder.addHeader(Constants.PARAMETER_DESCRIPTION_TYPE_COLUMN);
- builder.addRow();
- prepareCreateReport(builder);
-
- assertGetFieldDescriptionsFailed("Unspecified parameter name.");
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testGetFieldDescriptionsWithUnspecifiedType()
- {
- SimpleTableModelBuilder builder = new SimpleTableModelBuilder(true);
- builder.addHeader(Constants.PARAMETER_DESCRIPTION_NAME_COLUMN);
- builder.addHeader(Constants.PARAMETER_DESCRIPTION_TYPE_COLUMN);
- builder.addRow().setCell(Constants.PARAMETER_DESCRIPTION_NAME_COLUMN, "Description");
- IRowBuilder row = builder.addRow();
- row.setCell(Constants.PARAMETER_DESCRIPTION_NAME_COLUMN, "Greetings");
- row.setCell(Constants.PARAMETER_DESCRIPTION_TYPE_COLUMN, FieldType.VOCABULARY + ":Hi, Hello");
- prepareCreateReport(builder);
-
- List<FieldDescription> fieldDescriptions = Util.getFieldDescriptions(facade, description, logger);
-
- assertEquals("[Description:VARCHAR, Greetings:VOCABULARY[Hi, Hello]]", fieldDescriptions.toString());
- assertEquals("WARN test - Unknown field type '' using VARCHAR instead.", logRecorder.getLogContent());
- context.assertIsSatisfied();
- }
-
- private void assertGetFieldDescriptionsFailed(String expectedMessage)
- {
- try
- {
- Util.getFieldDescriptions(facade, description, logger);
- fail("IllegalArgumentException expected.");
- } catch (IllegalArgumentException ex)
- {
- String serviceKey = description.getAggregationServiceDescription().getServiceKey();
- assertEquals("Invalid response of aggregation service '" + serviceKey + "' when invoked with parameter "
- + Constants.REQUEST_KEY + " = " + Constants.GET_PARAMETER_DESCRIPTIONS_REQUEST + ":\n" +
- expectedMessage, ex.getMessage());
- }
- }
-
- private void prepareCreateReport(SimpleTableModelBuilder builder)
- {
- final QueryTableModel tableModel = new QueryTableModelTranslator(builder.getTableModel()).translate();
- context.checking(new Expectations()
- {
- {
- Map<String, Object> parameters = new HashMap<String, Object>();
- parameters.put(Constants.REQUEST_KEY, Constants.GET_PARAMETER_DESCRIPTIONS_REQUEST);
-
- one(facade).createReportFromAggregationService(description.getAggregationServiceDescription(), parameters);
- will(returnValue(tableModel));
- }
- });
- }
-
-}
diff --git a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeModelTest.java b/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeModelTest.java
deleted file mode 100644
index 3cedb80bb843138ca3170a919aa191fa65d2c77b..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/file/AggregatedDataFileImportNodeModelTest.java
+++ /dev/null
@@ -1,192 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.TreeMap;
-
-import org.apache.log4j.Level;
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.knime.core.node.NodeSettingsRO;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.logging.BufferedAppender;
-import ch.systemsx.cisd.common.logging.LogInitializer;
-import ch.systemsx.cisd.common.test.RecordingMatcher;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStore;
-import ch.systemsx.cisd.openbis.generic.shared.util.SimpleTableModelBuilder;
-import ch.systemsx.cisd.openbis.knime.common.AggregatedDataImportDescription;
-import ch.systemsx.cisd.openbis.knime.common.ParameterBindings;
-import ch.systemsx.cisd.openbis.knime.common.Util;
-import ch.systemsx.cisd.openbis.knime.server.Constants;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.AggregationServiceDescription;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel;
-import ch.systemsx.cisd.openbis.plugin.query.shared.translator.QueryTableModelTranslator;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class AggregatedDataFileImportNodeModelTest extends AbstractFileSystemTestCase
-{
- private static final String SESSION_TOKEN = "session";
-
- private static final String DATA_STORE_CODE = "DS";
-
- private static final class MockAggregatedDataFileImportNodeModel extends AggregatedDataFileImportNodeModel
- {
- private final Map<String, String> flowVariables = new TreeMap<String, String>();
-
- private final IQueryApiFacade facade;
-
- private final File sysTempDir;
-
- MockAggregatedDataFileImportNodeModel(IQueryApiFacade facade, File sysTempDir)
- {
- this.facade = facade;
- this.sysTempDir = sysTempDir;
- }
-
- @Override
- protected File getSystemTempDir()
- {
- return sysTempDir;
- }
-
- @Override
- protected IQueryApiFacade createQueryFacade()
- {
- return facade;
- }
-
- @Override
- protected void addFlowVariable(String name, String value)
- {
- flowVariables.put(name, value);
- }
-
- }
-
- private BufferedAppender logRecorder;
-
- private Mockery context;
-
- private IQueryApiFacade facade;
-
- private IGeneralInformationService service;
-
- private File tempDir;
-
- private MockAggregatedDataFileImportNodeModel model;
-
- private NodeSettingsRO nodeSettingsRO;
-
- private AggregationServiceDescription description;
-
- @BeforeMethod
- public void setUpModel() throws Exception
- {
- LogInitializer.init();
- logRecorder = new BufferedAppender("%-5p %c - %m%n", Level.DEBUG);
- context = new Mockery();
- service = context.mock(IGeneralInformationService.class);
- facade = context.mock(IQueryApiFacade.class);
- nodeSettingsRO = context.mock(NodeSettingsRO.class);
- description = new AggregationServiceDescription();
- description.setDataStoreCode(DATA_STORE_CODE);
- description.setServiceKey(AggregatedDataImportDescription.PREFIX + "as");
- ArrayList<AggregatedDataImportDescription> descriptions = new ArrayList<AggregatedDataImportDescription>();
- AggregatedDataImportDescription.addDescriptionIfDataTable(descriptions, description);
- final byte[] bytes = Util.serializeDescription(descriptions.get(0));
- context.checking(new Expectations()
- {
- {
- allowing(nodeSettingsRO).getByteArray(AggregatedDataImportDescription.AGGREGATION_DESCRIPTION_KEY);
- will(returnValue(bytes));
-
- allowing(nodeSettingsRO).getStringArray(ParameterBindings.PARAMETER_KEYS_KEY);
- allowing(nodeSettingsRO).getStringArray(ParameterBindings.PARAMETER_VALUES_KEY);
-
- allowing(facade).getSessionToken();
- will(returnValue(SESSION_TOKEN));
-
- allowing(facade).getGeneralInformationService();
- will(returnValue(service));
- }
- });
- tempDir = new File(workingDirectory, "temp");
- model = new MockAggregatedDataFileImportNodeModel(facade, tempDir);
- File reportFile = new File(workingDirectory, "session_workspace_file_download");
- FileUtilities.writeToFile(reportFile, "hello world");
- }
-
- @AfterMethod
- public void afterMethod()
- {
- logRecorder.reset();
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecute() throws Exception
- {
- final RecordingMatcher<AggregationServiceDescription> descriptionRecorder = new RecordingMatcher<AggregationServiceDescription>();
- SimpleTableModelBuilder builder = new SimpleTableModelBuilder(true);
- builder.addHeader(Constants.FILE_NAME_COLUMN);
- builder.addRow().setCell(Constants.FILE_NAME_COLUMN, "report.txt");
- final QueryTableModel tableModel = new QueryTableModelTranslator(builder.getTableModel()).translate();
- context.checking(new Expectations()
- {
- {
- one(facade).createReportFromAggregationService(with(descriptionRecorder), with(new HashMap<String, Object>()));
- will(returnValue(tableModel));
-
- one(facade).logout();
-
- one(service).listDataStores(SESSION_TOKEN);
- DataStore dataStore = new DataStore(DATA_STORE_CODE, "file://" + workingDirectory.getAbsolutePath(), "");
- will(returnValue(Arrays.asList(dataStore)));
- }
- });
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- logRecorder.resetLogContent();
-
- model.execute(null, null);
-
- assertEquals("AggregationServiceDescription [dataStoreCode=DS, serviceKey=knime-as, label=null, type=null]",
- descriptionRecorder.recordedObject().toString());
- assertEquals("hello world", FileUtilities.loadToString(new File(tempDir, "knime-openbis-session/report.txt")).trim());
- assertEquals("INFO " + MockAggregatedDataFileImportNodeModel.class.getName()
- + " - Content MIME type: text/plain", logRecorder.getLogContent());
- assertEquals(new File(tempDir, "knime-openbis-session/report.txt").getAbsolutePath(),
- model.flowVariables.get(AggregatedDataFileImportNodeModel.FILE_PATH_FLOW_VARIABLE));
- context.assertIsSatisfied();
- }
-
-}
diff --git a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeModelTest.java b/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeModelTest.java
deleted file mode 100644
index 93dc58bdbf9fa81ec59366547e1418622516dee5..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/file/DataSetFileImportNodeModelTest.java
+++ /dev/null
@@ -1,413 +0,0 @@
-/*
- * Copyright 2012 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.InputStream;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Random;
-import java.util.TreeMap;
-
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.knime.core.data.uri.URIContent;
-import org.knime.core.data.uri.URIPortObject;
-import org.knime.core.data.uri.URIPortObjectSpec;
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeSettings;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-import org.knime.core.node.port.PortObject;
-import org.knime.core.node.port.PortObjectSpec;
-import org.knime.core.node.workflow.Credentials;
-import org.knime.core.node.workflow.ICredentials;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.logging.LogInitializer;
-import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
-import ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss;
-import ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent;
-import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer;
-import ch.systemsx.cisd.openbis.knime.common.AbstractOpenBisNodeModel;
-import ch.systemsx.cisd.openbis.knime.common.IOpenbisServiceFacadeFactory;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DataSetFileImportNodeModelTest extends AbstractFileSystemTestCase
-{
- private static final String FILE_PATH = "document.txt";
-
- private static final String DATA_SET_CODE = "DS-42";
-
- private static final String MY_PASSWORD = "my-password";
-
- private static final String MY_PASSWORD2 = "my-password2";
-
- private static final String CREDENTIALS_NAME = "my-credentials";
-
- private static final String USER = "albert";
-
- private static final String USER2 = "isaac";
-
- private static final String URL = "https://open.bis";
-
- private static final class Model extends DataSetFileImportNodeModel
- {
- private final Map<String, String> flowVariables = new TreeMap<String, String>();
-
- private final Map<String, ICredentials> credentialsMap = new HashMap<String, ICredentials>();
-
- public Model(IOpenbisServiceFacadeFactory factory)
- {
- super(factory);
- }
-
- @Override
- protected void loadValidatedSettingsFrom(NodeSettingsRO settings)
- throws InvalidSettingsException
- {
- super.loadValidatedSettingsFrom(settings);
- }
-
- @Override
- protected void saveSettingsTo(NodeSettingsWO settings)
- {
- super.saveSettingsTo(settings);
- }
-
- @Override
- protected void addFlowVariable(String name, String value)
- {
- flowVariables.put(name, value);
- }
-
- void addCredentials(String name, ICredentials credentials)
- {
- credentialsMap.put(name, credentials);
- }
-
- @Override
- protected ICredentials getCredentials(String name)
- {
- return credentialsMap.get(name);
- }
-
- String getUrl()
- {
- return url;
- }
-
- String getUserId()
- {
- return userID;
- }
-
- String getPassword()
- {
- return password;
- }
- }
-
- private Mockery context;
-
- private IOpenbisServiceFacadeFactory facadeFactory;
-
- private Model model;
-
- private NodeSettingsRO nodeSettingsRO;
-
- private NodeSettingsWO nodeSettingsWO;
-
- private IOpenbisServiceFacade facade;
-
- private IDssComponent dssComponent;
-
- private IDataSetDss dataSetDss;
-
- private ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet metadata;
-
- private DataSet dataSet;
-
- @BeforeMethod
- public void beforeMethod()
- {
- LogInitializer.init();
- context = new Mockery();
- facadeFactory = context.mock(IOpenbisServiceFacadeFactory.class);
- nodeSettingsRO = context.mock(NodeSettingsRO.class);
- nodeSettingsWO = context.mock(NodeSettingsWO.class);
- dataSetDss = context.mock(IDataSetDss.class);
- facade = context.mock(IOpenbisServiceFacade.class);
- DataSetInitializer dataSetInitializer = new DataSetInitializer();
- dataSetInitializer.setCode(DATA_SET_CODE);
- dataSetInitializer.setDataSetTypeCode("MY-TYPE");
- EntityRegistrationDetailsInitializer regDetailsInit =
- new EntityRegistrationDetailsInitializer();
- dataSetInitializer.setRegistrationDetails(new EntityRegistrationDetails(regDetailsInit));
- dataSetInitializer.setExperimentIdentifier("/A/B/C");
- dataSetInitializer.setSampleIdentifierOrNull("/A/B");
- metadata = new ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet(dataSetInitializer);
- model = new Model(facadeFactory);
- model.addCredentials(CREDENTIALS_NAME, new Credentials(CREDENTIALS_NAME, USER2, MY_PASSWORD2));
- dataSet = new DataSet(facade, dssComponent, metadata, dataSetDss);
- context.checking(new Expectations()
- {
- {
- allowing(dataSetDss).getCode();
- will(returnValue(DATA_SET_CODE));
-
- allowing(facade).getDataSet(DATA_SET_CODE);
- will(returnValue(dataSet));
- }
- });
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testLoadingAndSavingSettingsWithCredentials() throws InvalidSettingsException
- {
- prepareLoadSaveStringSetting(AbstractOpenBisNodeModel.URL_KEY, URL);
- prepareLoadSaveStringSetting(AbstractOpenBisNodeModel.CREDENTIALS_KEY, CREDENTIALS_NAME, "");
- prepareLoadSaveStringSetting(DataSetFileImportNodeModel.DATA_SET_CODE_KEY, DATA_SET_CODE);
- prepareLoadSaveStringSetting(DataSetFileImportNodeModel.FILE_PATH_KEY, FILE_PATH);
- prepareLoadSaveStringSetting(DataSetFileImportNodeModel.DOWNLOADS_PATH_KEY, workingDirectory.getAbsolutePath());
- prepareSaveStringSetting(DataSetFileImportNodeModel.ABSOLUTE_FILE_PATH_KEY,
- new File(workingDirectory, DATA_SET_CODE + "/" + FILE_PATH).getAbsolutePath());
- context.checking(new Expectations()
- {
- {
- one(nodeSettingsRO).getBoolean(DataSetFileImportNodeModel.REUSE_FILE, false);
- will(returnValue(true));
-
- one(nodeSettingsWO).addBoolean(DataSetFileImportNodeModel.REUSE_FILE, true);
- }
- });
-
- model.loadValidatedSettingsFrom(nodeSettingsRO);
- model.saveSettingsTo(nodeSettingsWO);
-
- assertEquals(URL, model.getUrl());
- assertEquals(USER2, model.getUserId());
- assertEquals(MY_PASSWORD2, model.getPassword());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testLoadingAndSavingSettingsWithUserAndPassword() throws InvalidSettingsException
- {
- prepareLoadSaveStringSetting(AbstractOpenBisNodeModel.URL_KEY, URL);
- prepareLoadSaveStringSetting(AbstractOpenBisNodeModel.CREDENTIALS_KEY, "", "");
- prepareLoadSaveStringSetting(AbstractOpenBisNodeModel.USER_KEY, USER);
- prepareLoadSaveStringSetting(AbstractOpenBisNodeModel.PASSWORD_KEY, MY_PASSWORD, "");
- prepareLoadSaveStringSetting(DataSetFileImportNodeModel.DATA_SET_CODE_KEY, DATA_SET_CODE);
- prepareLoadSaveStringSetting(DataSetFileImportNodeModel.FILE_PATH_KEY, FILE_PATH);
- prepareLoadSaveStringSetting(DataSetFileImportNodeModel.DOWNLOADS_PATH_KEY, workingDirectory.getAbsolutePath());
- prepareSaveStringSetting(DataSetFileImportNodeModel.ABSOLUTE_FILE_PATH_KEY,
- new File(workingDirectory, DATA_SET_CODE + "/" + FILE_PATH).getAbsolutePath());
- context.checking(new Expectations()
- {
- {
- one(nodeSettingsRO).getBoolean(DataSetFileImportNodeModel.REUSE_FILE, false);
- will(returnValue(true));
-
- one(nodeSettingsWO).addBoolean(DataSetFileImportNodeModel.REUSE_FILE, true);
- }
- });
-
- model.loadValidatedSettingsFrom(nodeSettingsRO);
- model.saveSettingsTo(nodeSettingsWO);
-
- assertEquals(URL, model.getUrl());
- assertEquals(USER, model.getUserId());
- assertEquals(MY_PASSWORD, model.getPassword());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testConfigure() throws Exception
- {
- NodeSettings settings = createSettings();
- model.loadValidatedSettingsFrom(settings);
-
- PortObjectSpec[] portSpecs = model.configure(null);
-
- assertEquals("[text/plain]", ((URIPortObjectSpec) portSpecs[0])
- .getFileExtensions().toString());
- assertEquals(1, portSpecs.length);
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteReuseFile() throws Exception
- {
- NodeSettings settings = createSettings();
- settings.addBoolean(DataSetFileImportNodeModel.REUSE_FILE, true);
- model.loadValidatedSettingsFrom(settings);
- File file = new File(workingDirectory, DATA_SET_CODE + "/" + FILE_PATH);
- file.getParentFile().mkdirs();
- FileUtilities.writeToFile(file, "hello world");
-
- PortObject[] portObjects = model.execute(null, null);
-
- URIPortObject uriPortObject = (URIPortObject) portObjects[0];
- assertEquals("[text/plain]", uriPortObject.getSpec().getFileExtensions().toString());
- List<URIContent> uriContents = uriPortObject.getURIContents();
- assertEquals(file.toURI().toString(), uriContents.get(0).getURI().toString());
- assertEquals(1, uriContents.size());
- assertEquals(1, portObjects.length);
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteReuseFileButFileDoesNotExist() throws Exception
- {
- NodeSettings settings = createSettings();
- settings.addBoolean(DataSetFileImportNodeModel.REUSE_FILE, true);
- model.loadValidatedSettingsFrom(settings);
- File file = new File(workingDirectory, DATA_SET_CODE + "/" + FILE_PATH);
- prepareGetDataSetFile(FILE_PATH, new ByteArrayInputStream("hello world".getBytes()));
-
- PortObject[] portObjects = model.execute(null, null);
-
- assertEquals("hello world", FileUtilities.loadToString(file).trim());
- URIPortObject uriPortObject = (URIPortObject) portObjects[0];
- assertEquals("[text/plain]", uriPortObject.getSpec().getFileExtensions().toString());
- List<URIContent> uriContents = uriPortObject.getURIContents();
- assertEquals(file.toURI().toString(), uriContents.get(0).getURI().toString());
- assertEquals(1, uriContents.size());
- assertEquals(1, portObjects.length);
- assertEquals("{openbis.DATA_SET=DS-42, openbis.EXPERIMENT=/A/B/C, openbis.SAMPLE=/A/B}",
- model.flowVariables.toString());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteDoNotReuseFile() throws Exception
- {
- NodeSettings settings = createSettings();
- settings.addBoolean(DataSetFileImportNodeModel.REUSE_FILE, false);
- model.loadValidatedSettingsFrom(settings);
- File file = new File(workingDirectory, DATA_SET_CODE + "/" + FILE_PATH);
- file.getParentFile().mkdirs();
- FileUtilities.writeToFile(file, "hello world");
- StringBuilder builder = new StringBuilder();
- Random random = new Random();
- for (int i = 0; i < 1200; i++)
- {
- builder.append(random.nextInt(5));
- }
- String exampleContent = builder.toString();
- prepareGetDataSetFile(FILE_PATH, new ByteArrayInputStream(exampleContent.getBytes()));
-
- PortObject[] portObjects = model.execute(null, null);
-
- assertEquals(exampleContent, FileUtilities.loadToString(file).trim());
- URIPortObject uriPortObject = (URIPortObject) portObjects[0];
- assertEquals("[text/plain]", uriPortObject.getSpec().getFileExtensions().toString());
- List<URIContent> uriContents = uriPortObject.getURIContents();
- assertEquals(file.toURI().toString(), uriContents.get(0).getURI().toString());
- assertEquals(1, uriContents.size());
- assertEquals(1, portObjects.length);
- context.assertIsSatisfied();
- }
-
- private NodeSettings createSettings()
- {
- NodeSettings settings = new NodeSettings("test");
- settings.addString(AbstractOpenBisNodeModel.URL_KEY, URL);
- settings.addString(AbstractOpenBisNodeModel.USER_KEY, USER);
- settings.addString(AbstractOpenBisNodeModel.PASSWORD_KEY, MY_PASSWORD);
- settings.addString(DataSetFileImportNodeModel.DATA_SET_CODE_KEY, DATA_SET_CODE);
- settings.addString(DataSetFileImportNodeModel.FILE_PATH_KEY, FILE_PATH);
- settings.addString(DataSetFileImportNodeModel.DOWNLOADS_PATH_KEY, workingDirectory.getAbsolutePath());
- return settings;
- }
-
- private void prepareGetDataSetFile(final String filePath, final InputStream inputStream)
- {
- context.checking(new Expectations()
- {
- {
- one(facadeFactory).createFacade(URL, USER, MY_PASSWORD);
- will(returnValue(facade));
-
- one(dataSetDss).getFile(filePath);
- will(returnValue(inputStream));
-
- one(facade).logout();
- }
- });
- }
-
- private void prepareLoadSaveStringSetting(final String key, final String value)
- throws InvalidSettingsException
- {
- context.checking(new Expectations()
- {
- {
- one(nodeSettingsRO).getString(key);
- will(returnValue(value));
-
- one(nodeSettingsWO).addString(key, value);
- }
- });
- }
-
- private void prepareSaveStringSetting(final String key, final String value)
- throws InvalidSettingsException
- {
- context.checking(new Expectations()
- {
- {
- one(nodeSettingsWO).addString(key, value);
- }
- });
- }
-
- private void prepareLoadSaveStringSetting(final String key, final String value,
- final String defaultValue) throws InvalidSettingsException
- {
- context.checking(new Expectations()
- {
- {
- one(nodeSettingsRO).getString(key, defaultValue);
- will(returnValue(value));
-
- one(nodeSettingsWO).addString(key, value);
- }
- });
- }
-
-}
diff --git a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeModelTest.java b/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeModelTest.java
deleted file mode 100644
index 638edb94dae27630c010bd7b91432fcb2991ab1c..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/file/DataSetRegistrationNodeModelTest.java
+++ /dev/null
@@ -1,615 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.file;
-
-import java.io.File;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.NoSuchElementException;
-
-import org.apache.log4j.Level;
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.knime.core.data.uri.URIContent;
-import org.knime.core.data.uri.URIPortObject;
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-import org.knime.core.node.port.PortObject;
-import org.knime.core.node.port.flowvariable.FlowVariablePortObject;
-import org.knime.core.node.port.image.ImagePortObject;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.logging.BufferedAppender;
-import ch.systemsx.cisd.common.logging.LogInitializer;
-import ch.systemsx.cisd.common.test.RecordingMatcher;
-import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
-import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType.DataSetTypeInitializer;
-import ch.systemsx.cisd.openbis.knime.common.IOpenbisServiceFacadeFactory;
-import ch.systemsx.cisd.openbis.knime.common.TestUtils;
-import ch.systemsx.cisd.openbis.knime.common.Util;
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class DataSetRegistrationNodeModelTest extends AbstractFileSystemTestCase
-{
- private static final class MockDataSetRegistrationNodeModel extends DataSetRegistrationNodeModel
- {
- private final IQueryApiFacade queryFacade;
-
- private final Map<String, String> flowVariables;
-
- public MockDataSetRegistrationNodeModel(IQueryApiFacade queryFacade,
- IOpenbisServiceFacadeFactory serviceFacadeFactory, Map<String, String> flowVariables)
- {
- super(serviceFacadeFactory);
- this.queryFacade = queryFacade;
- this.flowVariables = flowVariables;
- }
-
- @Override
- protected IQueryApiFacade createQueryFacade()
- {
- return queryFacade;
- }
-
- @Override
- protected String getStringFlowVariable(String variableName)
- {
- String value = flowVariables.get(variableName);
- if (value == null)
- {
- throw new NoSuchElementException(variableName);
- }
- return value;
- }
- }
-
- private BufferedAppender logRecorder;
-
- private Mockery context;
-
- private IOpenbisServiceFacadeFactory facadeFactory;
-
- private IOpenbisServiceFacade serviceFacade;
-
- private IQueryApiFacade queryFacade;
-
- private MockDataSetRegistrationNodeModel model;
-
- private NodeSettingsRO nodeSettingsRO;
-
- private NodeSettingsWO nodeSettingsWO;
-
- private File file;
-
- private Map<String, String> flowVariables;
-
- private DataSetType dataSetType;
-
- @BeforeMethod
- public void beforeMethod() throws Exception
- {
- LogInitializer.init();
- context = new Mockery();
- facadeFactory = context.mock(IOpenbisServiceFacadeFactory.class);
- serviceFacade = context.mock(IOpenbisServiceFacade.class);
- queryFacade = context.mock(IQueryApiFacade.class);
- nodeSettingsRO = context.mock(NodeSettingsRO.class);
- nodeSettingsWO = context.mock(NodeSettingsWO.class);
- DataSetTypeInitializer dataSetTypeInitializer = new DataSetTypeInitializer();
- dataSetTypeInitializer.setCode("MY_TYPE");
- dataSetType = new DataSetType(dataSetTypeInitializer);
- final byte[] bytes = Util.serializeDescription(dataSetType);
- context.checking(new Expectations()
- {
- {
- allowing(nodeSettingsRO).getByteArray(DataSetRegistrationNodeModel.DATA_SET_TYPE_KEY, null);
- will(returnValue(bytes));
-
- allowing(facadeFactory).createFacade(null, null, null);
- will(returnValue(serviceFacade));
-
- allowing(queryFacade).logout();
- allowing(serviceFacade).logout();
- }
- });
- flowVariables = new HashMap<String, String>();
- model = new MockDataSetRegistrationNodeModel(queryFacade, facadeFactory, flowVariables);
- file = new File(workingDirectory, "hello.txt");
- FileUtilities.writeToFile(file, "hello");
- logRecorder = new BufferedAppender("%-5p %c - %m%n", Level.DEBUG);
- }
-
- @AfterMethod
- public void afterMethod()
- {
- logRecorder.reset();
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testSaveAdditionalSettingsTo() throws Exception
- {
- prepareFileVariableOwnerAndType(DataSetOwnerType.SAMPLE, "/SPACE/SAMPLE1", "fname");
- preparePropertyTypeCodes("Name");
- preparePropertyValues("Albert");
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- context.checking(new Expectations()
- {
- {
- one(nodeSettingsWO).addString(DataSetRegistrationNodeModel.FILE_VARIABLE_KEY, "fname");
- one(nodeSettingsWO).addString(DataSetRegistrationNodeModel.OWNER_TYPE_KEY, DataSetOwnerType.SAMPLE.name());
- one(nodeSettingsWO).addString(DataSetRegistrationNodeModel.OWNER_KEY, "/SPACE/SAMPLE1");
- one(nodeSettingsWO).addByteArray(DataSetRegistrationNodeModel.DATA_SET_TYPE_KEY, Util.serializeDescription(dataSetType));
- one(nodeSettingsWO).addStringArray(DataSetRegistrationNodeModel.PROPERTY_TYPE_CODES_KEY, "Name");
- one(nodeSettingsWO).addStringArray(DataSetRegistrationNodeModel.PROPERTY_VALUES_KEY, "Albert");
- }
- });
-
- model.saveAdditionalSettingsTo(nodeSettingsWO);
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteWithInvalidNumberOfInputPorts() throws Exception
- {
- prepareOwnerAndType(DataSetOwnerType.SAMPLE, "/SPACE/SAMPLE1");
- preparePropertyTypeCodes();
- preparePropertyValues();
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- logRecorder.resetLogContent();
-
- try
- {
- model.execute(new PortObject[2], null);
- fail("IllegalArgumentException expected");
- } catch (IllegalArgumentException ex)
- {
- assertEquals("Expecting exactly one port instead of 2.", ex.getMessage());
- }
-
- assertEquals("", logRecorder.getLogContent());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteWithInvalidInputPortType() throws Exception
- {
- prepareOwnerAndType(DataSetOwnerType.SAMPLE, "/SPACE/SAMPLE1");
- preparePropertyTypeCodes();
- preparePropertyValues();
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- logRecorder.resetLogContent();
-
- try
- {
- model.execute(new PortObject[] { new ImagePortObject() }, null);
- fail("IllegalArgumentException expected");
- } catch (IllegalArgumentException ex)
- {
- assertEquals("Invalid port: " + ImagePortObject.class.getName() + ".", ex.getMessage());
- }
-
- assertEquals("", logRecorder.getLogContent());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteWithNoUriContent() throws Exception
- {
- prepareOwnerAndType(DataSetOwnerType.SAMPLE, "/SPACE/SAMPLE1");
- preparePropertyTypeCodes();
- preparePropertyValues();
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- logRecorder.resetLogContent();
-
- try
- {
- model.execute(new PortObject[] { new URIPortObject(Arrays.<URIContent> asList()) }, null);
- fail("IllegalArgumentException expected");
- } catch (IllegalArgumentException ex)
- {
- assertEquals("Expecting at least on URI in input port.", ex.getMessage());
- }
-
- assertEquals("", logRecorder.getLogContent());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteWithUnspecifiedFileVariable() throws Exception
- {
- prepareOwnerAndType(DataSetOwnerType.SAMPLE, "/SPACE/SAMPLE1");
- preparePropertyTypeCodes();
- preparePropertyValues();
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- logRecorder.resetLogContent();
-
- try
- {
- model.execute(new PortObject[] { FlowVariablePortObject.INSTANCE }, null);
- fail("IllegalArgumentException expected");
- } catch (IllegalArgumentException ex)
- {
- assertEquals("Unspecified file variable.", ex.getMessage());
- }
-
- assertEquals("", logRecorder.getLogContent());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteForUnknownExperimentOwner() throws Exception
- {
- prepareOwnerAndType(DataSetOwnerType.EXPERIMENT, "/SPACE/PROJECT/EXPERIMENT1");
- preparePropertyTypeCodes();
- preparePropertyValues();
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- context.checking(new Expectations()
- {
- {
- one(serviceFacade).getExperiments(Arrays.asList("/SPACE/PROJECT/EXPERIMENT1"));
- will(returnValue(Arrays.asList()));
- }
- });
-
- try
- {
- URIContent content = new URIContent(file.toURI(), "txt");
- model.execute(new PortObject[] { new URIPortObject(Arrays.asList(content)) }, null);
- } catch (IllegalArgumentException ex)
- {
- assertEquals("Error for data set owner of type experiment "
- + "'/SPACE/PROJECT/EXPERIMENT1': Unknown experiment.", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteForExperimentOwner() throws Exception
- {
- prepareOwnerAndType(DataSetOwnerType.EXPERIMENT, "/SPACE/PROJECT/EXPERIMENT1");
- preparePropertyTypeCodes("GREETINGS");
- preparePropertyValues("HI");
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- final RecordingMatcher<NewDataSetDTO> dataSetMatcher = new RecordingMatcher<NewDataSetDTO>();
- final RecordingMatcher<File> fileMatcher = new RecordingMatcher<File>();
- context.checking(new Expectations()
- {
- {
- one(serviceFacade).getExperiments(Arrays.asList("/SPACE/PROJECT/EXPERIMENT1"));
- will(returnValue(Arrays.asList(TestUtils.experiment("/SPACE/PROJECT", "EXPERIMENT1"))));
-
- one(serviceFacade).putDataSet(with(dataSetMatcher), with(fileMatcher));
- }
- });
- logRecorder.resetLogContent();
-
- URIContent content = new URIContent(file.toURI(), "txt");
- URIContent content2 = new URIContent(file.getParentFile().toURI(), "txt");
- model.execute(new PortObject[] { new URIPortObject(Arrays.asList(content, content2)) }, null);
-
- assertEquals("NewDataSetDTO[NewDataSetMetadataDTO[data set type=MY_TYPE,property GREETINGS=HI],"
- + "NewDataSetDTO.DataSetOwner[Experiment,/SPACE/PROJECT/EXPERIMENT1],"
- + "[FileInfoDssDTO[hello.txt,hello.txt,5]]]",
- dataSetMatcher.recordedObject().toString());
- assertEquals(file.getAbsolutePath(), fileMatcher.recordedObject().getAbsolutePath());
- assertEquals("WARN " + MockDataSetRegistrationNodeModel.class.getName() + " - 2 URIs instead of only one: ["
- + "URI: " + file.toURI() + "; EXT: txt, URI: " + file.getParentFile().toURI() + "; EXT: txt]\n"
- + "INFO " + MockDataSetRegistrationNodeModel.class.getName() + " - data set file: "
- + file.getAbsolutePath(), logRecorder.getLogContent());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteForUnknownSampleOwner() throws Exception
- {
- prepareOwnerAndType(DataSetOwnerType.SAMPLE, "/SPACE/SAMPLE1");
- preparePropertyTypeCodes();
- preparePropertyValues();
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- context.checking(new Expectations()
- {
- {
- one(serviceFacade).getSamples(Arrays.asList("/SPACE/SAMPLE1"));
- will(returnValue(Arrays.asList()));
- }
- });
-
- try
- {
- URIContent content = new URIContent(file.toURI(), "txt");
- model.execute(new PortObject[] { new URIPortObject(Arrays.asList(content)) }, null);
- } catch (IllegalArgumentException ex)
- {
- assertEquals("Error for data set owner of type sample "
- + "'/SPACE/SAMPLE1': Unknown sample.", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteForSampleOwnerNotLinkedToExperiment() throws Exception
- {
- prepareOwnerAndType(DataSetOwnerType.SAMPLE, "/SPACE/SAMPLE1");
- preparePropertyTypeCodes();
- preparePropertyValues();
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- context.checking(new Expectations()
- {
- {
- one(serviceFacade).getSamples(Arrays.asList("/SPACE/SAMPLE1"));
- will(returnValue(Arrays.asList(TestUtils.sample("T", "S", "S", null))));
- }
- });
-
- try
- {
- URIContent content = new URIContent(file.toURI(), "txt");
- model.execute(new PortObject[] { new URIPortObject(Arrays.asList(content)) }, null);
- } catch (IllegalArgumentException ex)
- {
- assertEquals("Error for data set owner of type sample "
- + "'/SPACE/SAMPLE1': Not directly linked to an experiment.", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteForSampleOwner() throws Exception
- {
- prepareOwnerAndType(DataSetOwnerType.SAMPLE, "/SPACE/SAMPLE1");
- preparePropertyTypeCodes();
- preparePropertyValues();
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- final RecordingMatcher<NewDataSetDTO> dataSetMatcher = new RecordingMatcher<NewDataSetDTO>();
- final RecordingMatcher<File> fileMatcher = new RecordingMatcher<File>();
- context.checking(new Expectations()
- {
- {
- one(serviceFacade).getSamples(Arrays.asList("/SPACE/SAMPLE1"));
- will(returnValue(Arrays.asList(TestUtils.sample("T", "S", "S", "/S/P/E"))));
-
- one(serviceFacade).putDataSet(with(dataSetMatcher), with(fileMatcher));
- }
- });
- logRecorder.resetLogContent();
-
- URIContent content = new URIContent(file.toURI(), "txt");
- model.execute(new PortObject[] { new URIPortObject(Arrays.asList(content)) }, null);
-
- assertEquals("NewDataSetDTO[NewDataSetMetadataDTO[data set type=MY_TYPE],"
- + "NewDataSetDTO.DataSetOwner[Sample,/SPACE/SAMPLE1],[FileInfoDssDTO[hello.txt,hello.txt,5]]]",
- dataSetMatcher.recordedObject().toString());
- assertEquals(file.getAbsolutePath(), fileMatcher.recordedObject().getAbsolutePath());
- assertEquals("INFO " + MockDataSetRegistrationNodeModel.class.getName() + " - data set file: "
- + file.getAbsolutePath(), logRecorder.getLogContent());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteForSampleOwnerForFileFromFlowVariable() throws Exception
- {
- flowVariables.put("file-name", file.getAbsolutePath());
- prepareFileVariableOwnerAndType(DataSetOwnerType.SAMPLE, "/SPACE/SAMPLE1", "file-name");
- preparePropertyTypeCodes();
- preparePropertyValues();
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- final RecordingMatcher<NewDataSetDTO> dataSetMatcher = new RecordingMatcher<NewDataSetDTO>();
- final RecordingMatcher<File> fileMatcher = new RecordingMatcher<File>();
- context.checking(new Expectations()
- {
- {
- one(serviceFacade).getSamples(Arrays.asList("/SPACE/SAMPLE1"));
- will(returnValue(Arrays.asList(TestUtils.sample("T", "S", "S", "/S/P/E"))));
-
- one(serviceFacade).putDataSet(with(dataSetMatcher), with(fileMatcher));
- }
- });
- logRecorder.resetLogContent();
-
- model.execute(new PortObject[] { FlowVariablePortObject.INSTANCE }, null);
-
- assertEquals("NewDataSetDTO[NewDataSetMetadataDTO[data set type=MY_TYPE],"
- + "NewDataSetDTO.DataSetOwner[Sample,/SPACE/SAMPLE1],[FileInfoDssDTO[hello.txt,hello.txt,5]]]",
- dataSetMatcher.recordedObject().toString());
- assertEquals(file.getAbsolutePath(), fileMatcher.recordedObject().getAbsolutePath());
- assertEquals("INFO " + MockDataSetRegistrationNodeModel.class.getName() + " - data set file: "
- + file.getAbsolutePath(), logRecorder.getLogContent());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteForUnknownDataSetOwner() throws Exception
- {
- prepareOwnerAndType(DataSetOwnerType.DATA_SET, "DS1");
- preparePropertyTypeCodes();
- preparePropertyValues();
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- context.checking(new Expectations()
- {
- {
- one(serviceFacade).getDataSet("DS1");
- }
- });
- logRecorder.resetLogContent();
-
- try
- {
- URIContent content = new URIContent(file.toURI(), "txt");
- model.execute(new PortObject[] { new URIPortObject(Arrays.asList(content)) }, null);
- } catch (IllegalArgumentException ex)
- {
- assertEquals("Error for data set owner of type data set "
- + "'DS1': Unknown data set.", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteForDataSetOwner() throws Exception
- {
- prepareOwnerAndType(DataSetOwnerType.DATA_SET, " DS1 ");
- preparePropertyTypeCodes();
- preparePropertyValues();
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- final RecordingMatcher<NewDataSetDTO> dataSetMatcher = new RecordingMatcher<NewDataSetDTO>();
- final RecordingMatcher<File> fileMatcher = new RecordingMatcher<File>();
- context.checking(new Expectations()
- {
- {
- one(serviceFacade).getDataSet("DS1");
- will(returnValue(new DataSet(serviceFacade, null, TestUtils.dataSet("DS1"), null)));
-
- one(serviceFacade).putDataSet(with(dataSetMatcher), with(fileMatcher));
- }
- });
- logRecorder.resetLogContent();
-
- URIContent content = new URIContent(file.toURI(), "txt");
- model.execute(new PortObject[] { new URIPortObject(Arrays.asList(content)) }, null);
-
- assertEquals("NewDataSetDTO[NewDataSetMetadataDTO[data set type=MY_TYPE],"
- + "NewDataSetDTO.DataSetOwner[Data Set,DS1],[FileInfoDssDTO[hello.txt,hello.txt,5]]]",
- dataSetMatcher.recordedObject().toString());
- assertEquals(file.getAbsolutePath(), fileMatcher.recordedObject().getAbsolutePath());
- assertEquals("INFO " + MockDataSetRegistrationNodeModel.class.getName() + " - data set file: "
- + file.getAbsolutePath(), logRecorder.getLogContent());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteForUnspecifiedDataSetOwner() throws Exception
- {
- prepareOwnerAndType(DataSetOwnerType.DATA_SET, "");
- preparePropertyTypeCodes();
- preparePropertyValues();
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- logRecorder.resetLogContent();
-
- try
- {
- URIContent content = new URIContent(file.toURI(), "txt");
- model.execute(new PortObject[] { new URIPortObject(Arrays.asList(content)) }, null);
- } catch (IllegalArgumentException ex)
- {
- assertEquals("Owner data set hasn't been specified. "
- + "Also flow variable 'openbis.DATA_SET' is undefined.", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testExecuteForDataSetOwnerSpecifiedByFlowVariable() throws Exception
- {
- prepareOwnerAndType(DataSetOwnerType.DATA_SET, "");
- preparePropertyTypeCodes();
- preparePropertyValues();
- model.loadAdditionalValidatedSettingsFrom(nodeSettingsRO);
- final RecordingMatcher<NewDataSetDTO> dataSetMatcher = new RecordingMatcher<NewDataSetDTO>();
- final RecordingMatcher<File> fileMatcher = new RecordingMatcher<File>();
- context.checking(new Expectations()
- {
- {
- one(serviceFacade).getDataSet("DS1");
- will(returnValue(new DataSet(serviceFacade, null, TestUtils.dataSet("DS1"), null)));
-
- one(serviceFacade).putDataSet(with(dataSetMatcher), with(fileMatcher));
- }
- });
- flowVariables.put(Util.VARIABLE_PREFIX + DataSetOwnerType.DATA_SET.name(), "DS1");
- logRecorder.resetLogContent();
-
- URIContent content = new URIContent(file.toURI(), "txt");
- model.execute(new PortObject[] { new URIPortObject(Arrays.asList(content)) }, null);
-
- assertEquals("NewDataSetDTO[NewDataSetMetadataDTO[data set type=MY_TYPE],"
- + "NewDataSetDTO.DataSetOwner[Data Set,DS1],[FileInfoDssDTO[hello.txt,hello.txt,5]]]",
- dataSetMatcher.recordedObject().toString());
- assertEquals(file.getAbsolutePath(), fileMatcher.recordedObject().getAbsolutePath());
- assertEquals("INFO " + MockDataSetRegistrationNodeModel.class.getName() + " - data set file: "
- + file.getAbsolutePath(), logRecorder.getLogContent());
- context.assertIsSatisfied();
- }
-
- private void prepareOwnerAndType(DataSetOwnerType ownerType, String owner) throws InvalidSettingsException
- {
- prepareFileVariableOwnerAndType(ownerType, owner, null);
- }
-
- private void prepareFileVariableOwnerAndType(final DataSetOwnerType ownerType, final String owner,
- final String fileVariable) throws InvalidSettingsException
- {
- context.checking(new Expectations()
- {
- {
- one(nodeSettingsRO).getString(DataSetRegistrationNodeModel.OWNER_TYPE_KEY);
- will(returnValue(ownerType == null ? null : ownerType.name()));
-
- one(nodeSettingsRO).getString(DataSetRegistrationNodeModel.OWNER_KEY);
- will(returnValue(owner));
-
- one(nodeSettingsRO).getString(DataSetRegistrationNodeModel.FILE_VARIABLE_KEY, null);
- will(returnValue(fileVariable));
- }
- });
- }
-
- private void preparePropertyTypeCodes(final String... propertyTypeCodes) throws InvalidSettingsException
- {
- context.checking(new Expectations()
- {
- {
- one(nodeSettingsRO).getStringArray(DataSetRegistrationNodeModel.PROPERTY_TYPE_CODES_KEY,
- new String[0]);
- will(returnValue(propertyTypeCodes));
- }
- });
- }
-
- private void preparePropertyValues(final String... propertyValues) throws InvalidSettingsException
- {
- context.checking(new Expectations()
- {
- {
- one(nodeSettingsRO).getStringArray(DataSetRegistrationNodeModel.PROPERTY_VALUES_KEY,
- new String[0]);
- will(returnValue(propertyValues));
- }
- });
- }
-}
diff --git a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/query/TableModelBuilderTest.java b/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/query/TableModelBuilderTest.java
deleted file mode 100644
index 6b7d4bf6de1fba425986edcb6ae1464b381b2d97..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/query/TableModelBuilderTest.java
+++ /dev/null
@@ -1,136 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.query;
-
-import javax.swing.table.TableModel;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer;
-import ch.systemsx.cisd.openbis.knime.common.TableModelBuilder;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class TableModelBuilderTest extends AssertJUnit
-{
-
- @Test
- public void testTwoDataSetOfSameTypeNoSamples()
- {
- TableModelBuilder builder = new TableModelBuilder();
- builder.add(new DataSetBuilder("1-2").type("A").experiment("/A/B/C").property("A", "abc")
- .getDataSet());
- builder.add(new DataSetBuilder("1-3").type("A").experiment("/A/B/D").property("B", "def")
- .getDataSet());
-
- TableModel tableModel = builder.getTableModel();
-
- assertEquals("Code,Experiment,A,B\n" + "1-2,/A/B/C,abc,\n" + "1-3,/A/B/D,,def\n",
- render(tableModel));
- }
-
- @Test
- public void testTwoDataSetOfDifferentTypeWithSamples()
- {
- TableModelBuilder builder = new TableModelBuilder();
- builder.add(new DataSetBuilder("1-2").type("A").experiment("/A/B/C").sample("/A/1")
- .getDataSet());
- builder.add(new DataSetBuilder("1-3").type("B").experiment("/A/B/D").getDataSet());
-
- TableModel tableModel = builder.getTableModel();
-
- assertEquals("Code,Type,Sample,Experiment\n" + "1-2,A,/A/1,/A/B/C\n" + "1-3,B,,/A/B/D\n",
- render(tableModel));
- }
-
- private String render(TableModel tableModel)
- {
- StringBuilder builder = new StringBuilder();
- int rowCount = tableModel.getRowCount();
- int columnCount = tableModel.getColumnCount();
- for (int columnIndex = 0; columnIndex < columnCount; columnIndex++)
- {
- if (columnIndex > 0)
- {
- builder.append(",");
- }
- builder.append(tableModel.getColumnName(columnIndex));
- }
- builder.append("\n");
- for (int rowIndex = 0; rowIndex < rowCount; rowIndex++)
- {
- for (int columnIndex = 0; columnIndex < columnCount; columnIndex++)
- {
- if (columnIndex > 0)
- {
- builder.append(",");
- }
- builder.append(tableModel.getValueAt(rowIndex, columnIndex));
- }
- builder.append("\n");
- }
- return builder.toString();
- }
-
- private static final class DataSetBuilder
- {
- private DataSetInitializer initializer = new DataSetInitializer();
-
- DataSetBuilder(String code)
- {
- initializer.setCode(code);
- initializer.setRegistrationDetails(new EntityRegistrationDetails(
- new EntityRegistrationDetailsInitializer()));
- }
-
- DataSet getDataSet()
- {
- return new DataSet(initializer);
- }
-
- DataSetBuilder type(String type)
- {
- initializer.setDataSetTypeCode(type);
- return this;
- }
-
- DataSetBuilder sample(String sampleIdentifier)
- {
- initializer.setSampleIdentifierOrNull(sampleIdentifier);
- return this;
- }
-
- DataSetBuilder experiment(String experimentIdentifier)
- {
- initializer.setExperimentIdentifier(experimentIdentifier);
- return this;
- }
-
- DataSetBuilder property(String key, String value)
- {
- initializer.getProperties().put(key, value);
- return this;
- }
-
- }
-
-}
diff --git a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/query/UtilTest.java b/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/query/UtilTest.java
deleted file mode 100644
index 8ca9469ef048ca035708b0857e5abfd934aa263a..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/query/UtilTest.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.query;
-
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.knime.common.Util;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class UtilTest extends AssertJUnit
-{
-
- @Test
- public void testSerializationDeserializationOfQueryDescription()
- {
- QueryDescription queryDescription = new QueryDescription();
- queryDescription.setDescription("description");
-
- byte[] serializedQueryDescription = Util.serializeDescription(queryDescription);
- QueryDescription deserializedQueryDescription = Util.deserializeDescription(serializedQueryDescription);
-
- assertEquals(queryDescription.getDescription(), deserializedQueryDescription.getDescription());
- }
-
-}
diff --git a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/server/AggregationCommandTest.java b/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/server/AggregationCommandTest.java
deleted file mode 100644
index 3a26b82d1e3495be35638e633689eb908935b9d0..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/server/AggregationCommandTest.java
+++ /dev/null
@@ -1,200 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.server;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.jmock.internal.NamedSequence;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.StringTableCell;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelColumnHeader;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.IRowBuilderAdaptor;
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.ISimpleTableModelBuilderAdaptor;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class AggregationCommandTest extends AssertJUnit
-{
- private static final class MockAggregationCommand extends AggregationCommand
- {
- private final Throwable aggregateThrowableOrNull;
-
- MockAggregationCommand(Throwable aggregateThrowableOrNull)
- {
- this.aggregateThrowableOrNull = aggregateThrowableOrNull;
- }
-
- private ParameterDescriptionsBuilder recordedParametersBuilder;
-
- private Map<String, Object> recordedParameters;
-
- private ISimpleTableModelBuilderAdaptor recordedTableBuilder;
-
- @Override
- protected void defineParameters(ParameterDescriptionsBuilder parameters)
- {
- this.recordedParametersBuilder = parameters;
- }
-
- @Override
- protected void aggregate(Map<String, Object> parameters, ISimpleTableModelBuilderAdaptor tableBuilder)
- {
- this.recordedParameters = parameters;
- this.recordedTableBuilder = tableBuilder;
- if (aggregateThrowableOrNull instanceof Error)
- {
- throw (Error) aggregateThrowableOrNull;
- }
- if (aggregateThrowableOrNull instanceof RuntimeException)
- {
- throw (RuntimeException) aggregateThrowableOrNull;
- }
- }
- }
-
- private Mockery context;
-
- private Map<String, Object> parameters;
-
- private ISimpleTableModelBuilderAdaptor tableBuilder;
-
- private IRowBuilderAdaptor rowBuilder;
-
- @BeforeMethod
- public void setUp()
- {
- context = new Mockery();
- tableBuilder = context.mock(ISimpleTableModelBuilderAdaptor.class);
- rowBuilder = context.mock(IRowBuilderAdaptor.class);
- parameters = new HashMap<String, Object>();
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testDefineParameters()
- {
- MockAggregationCommand command = new MockAggregationCommand(null);
- parameters.put(Constants.REQUEST_KEY, Constants.GET_PARAMETER_DESCRIPTIONS_REQUEST);
- context.checking(new Expectations()
- {
- {
- one(tableBuilder).addHeader(Constants.PARAMETER_DESCRIPTION_NAME_COLUMN);
- one(tableBuilder).addHeader(Constants.PARAMETER_DESCRIPTION_TYPE_COLUMN);
-
- one(tableBuilder).addRow();
- will(returnValue(rowBuilder));
-
- one(rowBuilder).setCell(Constants.PARAMETER_DESCRIPTION_NAME_COLUMN, "Name");
- }
- });
-
- command.handleRequest(parameters, tableBuilder);
- command.recordedParametersBuilder.parameter("Name");
-
- assertEquals(null, command.recordedParameters);
- assertEquals(null, command.recordedTableBuilder);
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAggregate()
- {
- MockAggregationCommand command = new MockAggregationCommand(null);
-
- command.handleRequest(parameters, tableBuilder);
-
- assertEquals(null, command.recordedParametersBuilder);
- assertSame(parameters, command.recordedParameters);
- assertSame(tableBuilder, command.recordedTableBuilder);
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAggregateFails()
- {
- final IllegalArgumentException nestedException = new IllegalArgumentException();
- final RuntimeException exception = new RuntimeException("Oohps!", nestedException);
- MockAggregationCommand command = new MockAggregationCommand(exception);
- final List<TableModelColumnHeader> headers = new ArrayList<TableModelColumnHeader>(Arrays.asList(new TableModelColumnHeader()));
- List<ISerializableComparable> row = Arrays.<ISerializableComparable> asList(new StringTableCell("hi"));
- final List<TableModelRow> rows = new ArrayList<TableModelRow>(Arrays.asList(new TableModelRow(row)));
- final NamedSequence sequence = new NamedSequence("table");
- context.checking(new Expectations()
- {
- {
- one(tableBuilder).getTableModel();
- will(returnValue(new TableModel(headers, rows)));
-
- one(tableBuilder).addHeader(Constants.EXCEPTION_COLUMN);
- inSequence(sequence);
- one(tableBuilder).addHeader(Constants.STACK_TRACE_CLASS_COLUMN);
- inSequence(sequence);
- one(tableBuilder).addHeader(Constants.STACK_TRACE_METHOD_NAME_COLUMN);
- inSequence(sequence);
- one(tableBuilder).addHeader(Constants.STACK_TRACE_FILE_NAME_COLUMN);
- inSequence(sequence);
- one(tableBuilder).addHeader(Constants.STACK_TRACE_LINE_NUMBER_COLUMN);
- inSequence(sequence);
-
- one(tableBuilder).addFullRow(exception.toString(), "", "", "", "");
- inSequence(sequence);
- for (StackTraceElement element : exception.getStackTrace())
- {
- one(tableBuilder).addFullRow("", element.getClassName(), element.getMethodName(),
- element.getFileName(), Integer.toString(element.getLineNumber()));
- inSequence(sequence);
- }
- one(tableBuilder).addFullRow(nestedException.toString(), "", "", "", "");
- inSequence(sequence);
- for (StackTraceElement element : nestedException.getStackTrace())
- {
- one(tableBuilder).addFullRow("", element.getClassName(), element.getMethodName(),
- element.getFileName(), Integer.toString(element.getLineNumber()));
- inSequence(sequence);
- }
- }
- });
-
- command.handleRequest(parameters, tableBuilder);
-
- assertEquals(0, headers.size());
- assertEquals(0, rows.size());
- context.assertIsSatisfied();
- }
-
-}
diff --git a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/server/ParameterDescriptionsBuilderTest.java b/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/server/ParameterDescriptionsBuilderTest.java
deleted file mode 100644
index 14da20e320852f859ca3185acde4c5dc2fc21867..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceTest/java/ch/systemsx/cisd/openbis/knime/server/ParameterDescriptionsBuilderTest.java
+++ /dev/null
@@ -1,161 +0,0 @@
-/*
- * Copyright 2013 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime.server;
-
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.IRowBuilderAdaptor;
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.ISimpleTableModelBuilderAdaptor;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ParameterDescriptionsBuilderTest extends AssertJUnit
-{
- private Mockery context;
-
- private ISimpleTableModelBuilderAdaptor tableBuilder;
-
- private IRowBuilderAdaptor rowBuilder;
-
- private ParameterDescriptionsBuilder builder;
-
- @BeforeMethod
- public void setUp()
- {
- context = new Mockery();
- tableBuilder = context.mock(ISimpleTableModelBuilderAdaptor.class);
- rowBuilder = context.mock(IRowBuilderAdaptor.class);
- context.checking(new Expectations()
- {
- {
- one(tableBuilder).addHeader(Constants.PARAMETER_DESCRIPTION_NAME_COLUMN);
- one(tableBuilder).addHeader(Constants.PARAMETER_DESCRIPTION_TYPE_COLUMN);
- }
- });
- builder = new ParameterDescriptionsBuilder(tableBuilder);
- }
-
- @AfterMethod
- public void afterMethod()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAddParameter()
- {
- prepareAddRow("Name");
-
- builder.parameter("Name");
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAddParameterOfTypeText()
- {
- prepareAddRow("Variable");
- prepareSetType(FieldType.VARCHAR);
-
- builder.parameter("Variable").text();
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAddParameterOfTypeExperiment()
- {
- prepareAddRow("Variable");
- prepareSetType(FieldType.EXPERIMENT);
-
- builder.parameter("Variable").experiment();
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAddParameterOfTypeSample()
- {
- prepareAddRow("Variable");
- prepareSetType(FieldType.SAMPLE);
-
- builder.parameter("Variable").sample();
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAddParameterOfTypeDataSet()
- {
- prepareAddRow("Variable");
- prepareSetType(FieldType.DATA_SET);
-
- builder.parameter("Variable").dataSet();
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAddSameParameterTwice()
- {
- prepareAddRow("Variable");
- builder.parameter("Variable");
-
- try
- {
- builder.parameter("Variable");
- fail("IllegalArgumentException expected.");
- } catch (IllegalArgumentException ex)
- {
- assertEquals("There is already a parameter with name 'Variable'.", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- private void prepareAddRow(final String parameterName)
- {
- context.checking(new Expectations()
- {
- {
- one(tableBuilder).addRow();
- will(returnValue(rowBuilder));
-
- one(rowBuilder).setCell(Constants.PARAMETER_DESCRIPTION_NAME_COLUMN, parameterName);
- }
- });
- }
-
- private void prepareSetType(final FieldType fieldType)
- {
- context.checking(new Expectations()
- {
- {
- one(rowBuilder).setCell(Constants.PARAMETER_DESCRIPTION_TYPE_COLUMN, fieldType.toString());
- }
- });
- }
-
-}
diff --git a/openbis_knime/sourceTest/java/tests.xml b/openbis_knime/sourceTest/java/tests.xml
deleted file mode 100644
index d6fcc353a921992980028fa4851192497b6d8264..0000000000000000000000000000000000000000
--- a/openbis_knime/sourceTest/java/tests.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<suite name="All" verbose="1" >
- <test name="All">
- <groups>
- <run>
- <exclude name="broken" />
- </run>
- </groups>
- <packages>
- <package name="ch.systemsx.cisd.openbis.knime.*">
- </package>
- </packages>
- </test>
-</suite>
diff --git a/openbis_knime/targets/.gitignore b/openbis_knime/targets/.gitignore
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000