From 00106ca3066baccfc08ff25bc7e593e399bb5f1c Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Fri, 27 Feb 2009 10:37:39 +0000
Subject: [PATCH] LMS-766 Create new openBIS distribution that installs 'out of
the box'
SVN: 10035
---
openbis/build/build.xml | 562 +++++++++---------
openbis/dist/etc/log.xml | 2 +-
openbis/dist/server/install.sh | 162 +++--
openbis/dist/server/jetty.xml | 60 --
openbis/dist/server/passwd.sh | 2 +-
openbis/dist/server/server.keystore | Bin 0 -> 2006 bytes
openbis/dist/server/server.xml | 373 ++++++++++++
openbis/dist/server/service.properties | 44 ++
openbis/dist/server/shutdown.sh | 16 -
openbis/dist/server/startup.sh | 20 -
openbis/etc/log_system_test.xml | 2 +-
openbis/resource/server/web.xml | 2 +-
.../client/application/GenericConstants.java | 2 +-
.../server/CommonClientServiceServlet.java | 2 +-
.../web/server/FileExportServiceServlet.java | 2 +-
.../web/server/UploadServiceServlet.java | 4 +-
.../generic/server/ETLServiceServer.java | 2 +-
.../ExperimentAttachmentDownloadServlet.java | 2 +-
.../server/GenericClientServiceServlet.java | 4 +-
.../server/ScreeningClientServiceServlet.java | 2 +-
openbis_all/source/bash/sprint_install.sh | 9 -
21 files changed, 771 insertions(+), 503 deletions(-)
delete mode 100644 openbis/dist/server/jetty.xml
create mode 100644 openbis/dist/server/server.keystore
create mode 100644 openbis/dist/server/server.xml
create mode 100644 openbis/dist/server/service.properties
delete mode 100755 openbis/dist/server/shutdown.sh
delete mode 100755 openbis/dist/server/startup.sh
diff --git a/openbis/build/build.xml b/openbis/build/build.xml
index b94a1eadb89..9d9c7ce7ffa 100644
--- a/openbis/build/build.xml
+++ b/openbis/build/build.xml
@@ -1,348 +1,332 @@
<project name="openbis" basedir="..">
- <import file="../../server-common/build/build-common.xml" />
- <project-classpath name="ecp" classes="${classes}" />
+ <import file="../../server-common/build/build-common.xml" />
+ <project-classpath name="ecp" classes="${classes}" />
- <property name="mainfolder" value="openbis" />
+ <property name="mainfolder" value="openbis" />
- <property name="gwt.lib" value="${lib}/gwt1.5" />
- <property name="gwt.dev.lib" value="${gwt.lib}/mac/gwt-dev-mac.jar" />
- <property name="gwt.user.lib" value="${gwt.lib}/gwt-user.jar" />
- <property name="gwt.tomcat.web-inf"
+ <property name="gwt.lib" value="${lib}/gwt1.5" />
+ <property name="gwt.dev.lib" value="${gwt.lib}/mac/gwt-dev-mac.jar" />
+ <property name="gwt.user.lib" value="${gwt.lib}/gwt-user.jar" />
+ <property name="gwt.tomcat.web-inf"
value="../${ant.project.name}/tomcat/webapps/ROOT/WEB-INF" />
- <property name="application.server.resource"
+ <property name="original.server.dist" value="${original.dist}/server" />
+ <property name="server.folder.name" value="openBIS-server" />
+ <property name="server.dist" value="${dist}/${server.folder.name}" />
+ <property name="server.jar.file.name" value="openBIS.jar" />
+ <property name="server.jar.file" value="${server.dist}/${server.jar.file.name}" />
+ <property name="server.webapp.file" value="${server.dist}/openBIS.war" />
+ <property name="server.service" value="${server.dist}/service" />
+ <property name="server.service.lib" value="${server.service}/lib" />
+ <property name="application.server.resource"
value="../${ant.project.name}/${server-resource}" />
- <property name="webapp.dist" value="${dist}/webapp" />
- <property name="webapp.dist.web-inf" value="${webapp.dist}/WEB-INF" />
+ <property name="webapp.dist" value="${dist}/webapp" />
+ <property name="webapp.dist.web-inf" value="${webapp.dist}/WEB-INF" />
- <property name="jar.file.name" value="${ant.project.name}.jar" />
- <property name="jar.file" value="${dist}/${jar.file.name}" />
+ <property name="jar.file.name" value="${ant.project.name}.jar" />
+ <property name="jar.file" value="${dist}/${jar.file.name}" />
- <property name="webapp.file.name" value="generic${ant.project.name}.war" />
- <property name="webapp.file" value="${dist}/${webapp.file.name}" />
+ <property name="webapp.file.name" value="${ant.project.name}.war" />
+ <property name="webapp.file" value="${server.dist}/${webapp.file.name}" />
- <!--
+ <!--
// Cleans distribution directory.
-->
- <target name="clean" description="Cleans distribution directory.">
- <delete dir="${dist}" failonerror="true" />
- <mkdir dir="${dist}" />
- </target>
+ <target name="clean" description="Cleans distribution directory.">
+ <delete dir="${dist}" failonerror="true" />
+ <mkdir dir="${dist}" />
+ </target>
- <!--
+ <!--
// Runs tests.
-->
- <target name="run-tests">
- <antcall target="build-common.run-tests">
- <param name="test.suite" value="tests.xml" />
- </antcall>
- </target>
+ <target name="run-tests">
+ <antcall target="build-common.run-tests">
+ <param name="test.suite" value="tests.xml" />
+ </antcall>
+ </target>
- <!--
+ <!--
// Runs system tests (only on Linux)
-->
- <target name="run-system-tests" depends="prepare-gwt, compile-tests">
- <delete dir="${output.test}" />
- <mkdir dir="${output.test}" />
- <junit dir="." fork="true" forkmode="once" maxmemory="512m" showoutput="true" failureproperty="tests-failed">
- <classpath>
- <pathelement location="${sources}" />
- <pathelement location="${sources.test}" />
- <pathelement path="${ecp}" />
- <pathelement location="${gwt.lib}/linux/gwt-dev-linux.jar" />
- </classpath>
- <jvmarg value="-ea" />
- <sysproperty key="authentication-service" value="file-authentication-service" />
- <sysproperty key="log4j.configuration" value="etc/log.xml" />
- <sysproperty key="database.create-from-scratch" value="true" />
- <sysproperty key="hibernate.search.index-base" value="sourceTest/lucene/indices" />
- <sysproperty key="hibernate.search.index-mode" value="NO_INDEX" />
- <sysproperty key="database.kind" value="system_test" />
- <sysproperty key="script-folder" value="sourceTest" />
- <sysproperty key="mass-upload-folder" value="sourceTest/sql/postgresql" />
- <formatter type="xml" />
- <test name="ch.systemsx.cisd.openbis.generic.SystemTestSuite" todir="${output.test}" />
- </junit>
- <fail>
- <condition><isset property="tests-failed"/></condition>
- </fail>
+ <target name="run-system-tests" depends="prepare-gwt, compile-tests">
+ <delete dir="${output.test}" />
+ <mkdir dir="${output.test}" />
+ <junit dir="." fork="true" forkmode="once" maxmemory="512m" showoutput="true" failureproperty="tests-failed">
+ <classpath>
+ <pathelement location="${sources}" />
+ <pathelement location="${sources.test}" />
+ <pathelement path="${ecp}" />
+ <pathelement location="${gwt.lib}/linux/gwt-dev-linux.jar" />
+ </classpath>
+ <jvmarg value="-ea" />
+ <sysproperty key="authentication-service" value="file-authentication-service" />
+ <sysproperty key="log4j.configuration" value="etc/log.xml" />
+ <sysproperty key="database.create-from-scratch" value="true" />
+ <sysproperty key="hibernate.search.index-base" value="sourceTest/lucene/indices" />
+ <sysproperty key="hibernate.search.index-mode" value="NO_INDEX" />
+ <sysproperty key="database.kind" value="system_test" />
+ <sysproperty key="script-folder" value="sourceTest" />
+ <sysproperty key="mass-upload-folder" value="sourceTest/sql/postgresql" />
+ <formatter type="xml" />
+ <test name="ch.systemsx.cisd.openbis.generic.SystemTestSuite" todir="${output.test}" />
+ </junit>
+ <fail>
+ <condition>
+ <isset property="tests-failed"/>
+ </condition>
+ </fail>
- </target>
+ </target>
- <!--
+ <!--
// Makes a distribution file.
-->
- <target name="dist" description="Makes a distribution file." depends="clean, war">
- <property name="dist.file.name"
- value="${ant.project.name}-${version.number}-r${revision.number}.zip" />
- <property name="jetty.path" value="${lib}/jetty" />
- <property name="zipped.dir" value="${dist}/${ant.project.name}" />
+ <target name="dist" description="Makes a distribution file." depends="clean, war">
+ <copy file="${lib}/tomcat5/apache-tomcat.zip" todir="${server.dist}" />
+ <loadfile property="tomcat.version" srcFile="${lib}/tomcat5/version.txt">
+ <filterchain>
+ <striplinebreaks />
+ </filterchain>
+ </loadfile>
+ <echo file="${server.dist}/tomcat-version.txt">${tomcat.version}</echo>
+ <copy file="${original.server.dist}/server.xml" todir="${server.dist}" />
+ <copy file="${original.server.dist}/service.properties" todir="${server.dist}" />
+ <copy file="${original.server.dist}/server.keystore" todir="${server.dist}" />
+ <copy file="${original.server.dist}/passwd.sh" todir="${server.dist}" />
+ <property name="server.dist.file" value="${server.dist}-${version.number}-r${revision.number}.zip" />
+ <zip basedir="${dist}" destfile="${server.dist.file}" excludes="*.zip">
+ <zipfileset file="${original.server.dist}/install.sh" filemode="777" prefix="${server.folder.name}" />
+ </zip>
+ <delete dir="${server.dist}" />
+ </target>
- <mkdir dir="${zipped.dir}" />
- <move file="${webapp.file}" todir="${zipped.dir}" />
-
- <copy file="${jetty.path}/jetty.zip" todir="${zipped.dir}" />
- <copy file="${jetty.path}/version.txt" tofile="${zipped.dir}/jetty-version.txt">
- <filterchain>
- <striplinebreaks />
- </filterchain>
- </copy>
- <!--
- // Although there is already one 'service.properties' and 'log.xml' in the war, we need one here that
- // can be configured by the administrator. The idea is to replace the one in the war with it in the
- // 'install.sh' script.
- -->
- <copy todir="${zipped.dir}">
- <fileset dir="${original.dist}/etc">
- <include name="*" />
- </fileset>
- </copy>
- <!-- Copy all files but '*.sh'. -->
- <copy todir="${zipped.dir}">
- <fileset dir="${original.dist.server}">
- <exclude name="*.sh" />
- </fileset>
- </copy>
-
- <zip basedir="${dist}" destfile="${dist}/${dist.file.name}">
- <zipfileset file="${original.dist.server}/*.sh"
- filemode="755"
- prefix="${ant.project.name}" />
- </zip>
-
- <!-- Does some cleaning. -->
- <delete failonerror="true" includeemptydirs="true">
- <fileset dir="${dist}">
- <exclude name="${dist.file.name}" />
- </fileset>
- </delete>
- </target>
-
- <!--
+ <!--
// Task for continuous integration server.
-->
- <target name="ci"
+ <target name="ci"
depends="build-common.ci, check-dependencies, dist"
description="Task for continuous integration server." />
- <!--
+ <!--
// Nightly build task for continuous integration server.
-->
- <target name="nightly-build"
+ <target name="nightly-build"
depends="build-common.ci, run-system-tests, dist"
description="Nightly build task for continuous integration server." />
- <!--
+ <!--
// Compiles the javascript using GWT compiler.
-->
- <target name="compile-javascript" depends="prepare-web-client" description="Compiles the javascript using GWT compiler.">
- <property name="application.gwt.path" value="ch.systemsx.cisd.openbis.OpenBIS" />
- <delete dir="${webapp.dist}" />
- <java classpath="${ecp}:${gwt.dev.lib}:${gwt.user.lib}:${sources}"
+ <target name="compile-javascript" depends="prepare-web-client" description="Compiles the javascript using GWT compiler.">
+ <property name="application.gwt.path" value="ch.systemsx.cisd.openbis.OpenBIS" />
+ <delete dir="${webapp.dist}" />
+ <java classpath="${ecp}:${gwt.dev.lib}:${gwt.user.lib}:${sources}"
classname="com.google.gwt.dev.GWTCompiler"
fork="true">
- <jvmarg value="-Xmx512M" />
- <arg value="-out" />
- <arg value="${webapp.dist}" />
- <arg value="${application.gwt.path}" />
- </java>
- <move todir="${webapp.dist}">
- <fileset dir="${webapp.dist}/${application.gwt.path}" />
- </move>
- </target>
+ <jvmarg value="-Xmx512M" />
+ <arg value="-out" />
+ <arg value="${webapp.dist}" />
+ <arg value="${application.gwt.path}" />
+ </java>
+ <move todir="${webapp.dist}">
+ <fileset dir="${webapp.dist}/${application.gwt.path}" />
+ </move>
+ </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.number}:${revision.number}:${clean.flag}</echo>
- </target>
+ <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.number}:${revision.number}:${clean.flag}</echo>
+ </target>
- <!--
+ <!--
// Override 'prepare-gwt' target by writing out 'OpenBIS.gwt.xml' and updating 'ClientPluginProvider.java'.
-->
- <target name="prepare-gwt"
+ <target name="prepare-gwt"
description="Override 'prepare-gwt' by writing out 'OpenBIS.gwt.xml' and updating 'ClientPluginProvider.java'.">
- <antcall target="prepare-web-client" />
- <antcall target="server-common-common.prepare-gwt" />
- </target>
+ <antcall target="prepare-web-client" />
+ <antcall target="server-common-common.prepare-gwt" />
+ </target>
- <!--
+ <!--
// Updates 'ClientPluginProvider.java' and 'OpenBIS.gwt.xml' with requested plugins.
-->
- <target name="prepare-web-client" depends="compile"
+ <target name="prepare-web-client" depends="compile"
description="Updates 'ClientPluginProvider.java' and 'OpenBIS.gwt.xml' with requested plugins.">
- <java classname="ch.systemsx.cisd.openbis.generic.shared.util.WebClientFilesUpdater"
+ <java classname="ch.systemsx.cisd.openbis.generic.shared.util.WebClientFilesUpdater"
classpath="${ecp}:${sources}"
fork="true"
failonerror="true">
- <arg value="${sources}" />
- </java>
- </target>
+ <arg value="${sources}" />
+ </java>
+ </target>
- <!--
+ <!--
// Creates JAR file.
-->
- <target name="jar" depends="compile, build-info" description="Creates project jar file.">
- <delete file="${jar.file}" />
- <recursive-jar destfile="${jar.file}">
- <fileset dir="${classes}">
- <include name="**/*.class" />
- <!-- Exclude 'service.properties' and 'log.xml' file. -->
- <exclude name="service.properties" />
- <exclude name="log.xml" />
- <include name="**/*.properties" />
- <include name="${build.info.filename}" />
- </fileset>
- </recursive-jar>
- </target>
+ <target name="jar" depends="compile, build-info" description="Creates project jar file.">
+ <delete file="${jar.file}" />
+ <recursive-jar destfile="${jar.file}">
+ <fileset dir="${classes}">
+ <include name="**/*.class" />
+ <!-- Exclude 'service.properties' and 'log.xml' file. -->
+ <exclude name="service.properties" />
+ <exclude name="log.xml" />
+ <include name="**/*.properties" />
+ <include name="${build.info.filename}" />
+ </fileset>
+ </recursive-jar>
+ </target>
- <!--
+ <!--
// Creates WAR file.
-->
- <target name="war" depends="jar, compile-javascript" description="Creates project war file.">
- <mkdir dir="${webapp.dist.web-inf}" />
- <copy todir="${webapp.dist.web-inf}">
- <fileset dir="${application.server.resource}">
- <include name="spring-servlet.xml" />
- </fileset>
- <fileset dir="../server-common/${server-resource}">
- <include name="web-common.xml" />
- </fileset>
- </copy>
- <!-- Create an empty 'gwt.xml' file. -->
- <echo file="${webapp.dist.web-inf}/gwt.xml" message="" />
- <war warfile="${webapp.file}" webxml="${application.server.resource}/web.xml">
- <fileset dir="${webapp.dist}" />
- <classes dir="source">
- <include name="**/*.sql" />
- </classes>
- <!-- Add 'applicationContext.xml' and related files. -->
- <classes dir="../server-common/${sources}">
- <include name="**/*.xml" />
- </classes>
- <classes dir="${sources}">
- <include name="**/*.xml" />
- </classes>
- <classes dir="${original.dist}">
- <include name="etc/log.xml" />
- </classes>
- <lib dir="${dist}">
- <include name="${jar.file.name}" />
- </lib>
- <lib dir="${lib}/commons-lang">
- <include name="commons-lang.jar" />
- </lib>
- <lib dir="${lib}/commons-logging">
- <include name="*.jar" />
- </lib>
- <lib dir="${lib}/commons-io">
- <include name="commons-io.jar" />
- </lib>
- <lib dir="${lib}/jline">
- <include name="jline.jar" />
- </lib>
- <lib dir="${lib}/commons-codec">
- <include name="commons-codec.jar" />
- </lib>
- <lib dir="${lib}/commons-httpclient">
- <include name="commons-httpclient.jar" />
- </lib>
- <lib dir="${lib}/log4j">
- <include name="log4j.jar" />
- </lib>
- <lib dir="${lib}/spring">
- <include name="spring.jar" />
- </lib>
- <lib dir="${lib}/spring/webmvc">
- <include name="spring-webmvc.jar" />
- </lib>
- <lib dir="${lib}/activation">
- <include name="activation.jar" />
- </lib>
- <lib dir="${lib}/mail">
- <include name="mail.jar" />
- </lib>
- <lib dir="${gwt.lib}">
- <include name="gwt-servlet.jar" />
- </lib>
- <lib dir="${lib}/commons-fileupload">
- <include name="*.jar" />
- </lib>
- <!-- Database -->
- <lib dir="${lib}/postgresql">
- <include name="postgresql.jar" />
- </lib>
- <lib dir="${lib}/commons-dbcp">
- <include name="commons-dbcp.jar" />
- </lib>
- <lib dir="${lib}/commons-pool">
- <include name="commons-pool.jar" />
- </lib>
- <!-- Hibernate -->
- <lib dir="${lib}/antlr">
- <include name="antlr.jar" />
- </lib>
- <lib dir="${lib}/commons-collections">
- <include name="commons-collections.jar" />
- </lib>
- <lib dir="${lib}/dom4j">
- <include name="dom4j.jar" />
- </lib>
- <lib dir="${lib}/hibernate">
- <include name="hibernate3.jar" />
- </lib>
- <lib dir="${lib}/hibernate/jta">
- <include name="jta.jar" />
- </lib>
- <lib dir="${lib}/ehcache">
- <include name="ehcache.jar" />
- </lib>
- <lib dir="${lib}/cglib">
- <include name="asm.jar" />
- <include name="asm-attrs.jar" />
- <include name="cglib.jar" />
- </lib>
- <lib dir="${lib}/hibernate-annotations">
- <include name="*.jar" />
- </lib>
- <lib dir="${lib}/hibernate-validator">
- <include name="*.jar" />
- </lib>
- <lib dir="${lib}/javassist">
- <include name="*.jar" />
- </lib>
- <lib dir="${lib}/slf4j">
- <include name="*.jar" />
- <exclude name="src.jar" />
- </lib>
- <lib dir="${lib}/slf4j/log4j12">
- <include name="*.jar" />
- <exclude name="src.jar" />
- </lib>
- <!-- Beanlib -->
- <lib dir="${lib}/beanlib">
- <include name="beanlib.jar" />
- </lib>
- <lib dir="${lib}/beanlib-hibernate">
- <include name="beanlib-hibernate.jar" />
- </lib>
- <!-- Hibernate Search -->
- <lib dir="${lib}/hibernate-search">
- <include name="*.jar" />
- </lib>
- <lib dir="${lib}/lucene">
- <include name="*.jar" />
- </lib>
- <lib dir="${lib}/lucene-highlighter">
- <include name="lucene-highlighter.jar" />
- </lib>
- </war>
- <!-- Does some cleaning. -->
- <delete file="${jar.file}" failonerror="true" />
- <delete dir="${webapp.dist}" failonerror="true" />
- </target>
+ <target name="war" depends="jar, compile-javascript" description="Creates project war file.">
+ <mkdir dir="${webapp.dist.web-inf}" />
+ <copy todir="${webapp.dist.web-inf}">
+ <fileset dir="${application.server.resource}">
+ <include name="spring-servlet.xml" />
+ </fileset>
+ <fileset dir="../server-common/${server-resource}">
+ <include name="web-common.xml" />
+ </fileset>
+ </copy>
+ <!-- Create an empty 'gwt.xml' file. -->
+ <echo file="${webapp.dist.web-inf}/gwt.xml" message="" />
+ <mkdir dir="${server.dist}" />
+ <war warfile="${webapp.file}" webxml="${application.server.resource}/web.xml">
+ <fileset dir="${webapp.dist}" />
+ <classes dir="source">
+ <include name="**/*.sql" />
+ </classes>
+ <!-- Add 'applicationContext.xml' and related files. -->
+ <classes dir="../server-common/${sources}">
+ <include name="**/*.xml" />
+ </classes>
+ <classes dir="${sources}">
+ <include name="**/*.xml" />
+ </classes>
+ <classes dir="${original.dist}">
+ <include name="etc/log.xml" />
+ </classes>
+ <lib dir="${dist}">
+ <include name="${jar.file.name}" />
+ </lib>
+ <lib dir="${lib}/commons-lang">
+ <include name="commons-lang.jar" />
+ </lib>
+ <lib dir="${lib}/commons-logging">
+ <include name="*.jar" />
+ </lib>
+ <lib dir="${lib}/commons-io">
+ <include name="commons-io.jar" />
+ </lib>
+ <lib dir="${lib}/jline">
+ <include name="jline.jar" />
+ </lib>
+ <lib dir="${lib}/commons-codec">
+ <include name="commons-codec.jar" />
+ </lib>
+ <lib dir="${lib}/commons-httpclient">
+ <include name="commons-httpclient.jar" />
+ </lib>
+ <lib dir="${lib}/log4j">
+ <include name="log4j.jar" />
+ </lib>
+ <lib dir="${lib}/spring">
+ <include name="spring.jar" />
+ </lib>
+ <lib dir="${lib}/spring/webmvc">
+ <include name="spring-webmvc.jar" />
+ </lib>
+ <lib dir="${lib}/activation">
+ <include name="activation.jar" />
+ </lib>
+ <lib dir="${lib}/mail">
+ <include name="mail.jar" />
+ </lib>
+ <lib dir="${gwt.lib}">
+ <include name="gwt-servlet.jar" />
+ </lib>
+ <lib dir="${lib}/commons-fileupload">
+ <include name="*.jar" />
+ </lib>
+ <!-- Database -->
+ <lib dir="${lib}/postgresql">
+ <include name="postgresql.jar" />
+ </lib>
+ <lib dir="${lib}/commons-dbcp">
+ <include name="commons-dbcp.jar" />
+ </lib>
+ <lib dir="${lib}/commons-pool">
+ <include name="commons-pool.jar" />
+ </lib>
+ <!-- Hibernate -->
+ <lib dir="${lib}/antlr">
+ <include name="antlr.jar" />
+ </lib>
+ <lib dir="${lib}/commons-collections">
+ <include name="commons-collections.jar" />
+ </lib>
+ <lib dir="${lib}/dom4j">
+ <include name="dom4j.jar" />
+ </lib>
+ <lib dir="${lib}/hibernate">
+ <include name="hibernate3.jar" />
+ </lib>
+ <lib dir="${lib}/hibernate/jta">
+ <include name="jta.jar" />
+ </lib>
+ <lib dir="${lib}/ehcache">
+ <include name="ehcache.jar" />
+ </lib>
+ <lib dir="${lib}/cglib">
+ <include name="asm.jar" />
+ <include name="asm-attrs.jar" />
+ <include name="cglib.jar" />
+ </lib>
+ <lib dir="${lib}/hibernate-annotations">
+ <include name="*.jar" />
+ </lib>
+ <lib dir="${lib}/hibernate-validator">
+ <include name="*.jar" />
+ </lib>
+ <lib dir="${lib}/javassist">
+ <include name="*.jar" />
+ </lib>
+ <lib dir="${lib}/slf4j">
+ <include name="*.jar" />
+ <exclude name="src.jar" />
+ </lib>
+ <lib dir="${lib}/slf4j/log4j12">
+ <include name="*.jar" />
+ <exclude name="src.jar" />
+ </lib>
+ <!-- Beanlib -->
+ <lib dir="${lib}/beanlib">
+ <include name="beanlib.jar" />
+ </lib>
+ <lib dir="${lib}/beanlib-hibernate">
+ <include name="beanlib-hibernate.jar" />
+ </lib>
+ <!-- Hibernate Search -->
+ <lib dir="${lib}/hibernate-search">
+ <include name="*.jar" />
+ </lib>
+ <lib dir="${lib}/lucene">
+ <include name="*.jar" />
+ </lib>
+ <lib dir="${lib}/lucene-highlighter">
+ <include name="lucene-highlighter.jar" />
+ </lib>
+ </war>
+ <!-- Does some cleaning. -->
+ <delete file="${jar.file}" failonerror="true" />
+ <delete dir="${webapp.dist}" failonerror="true" />
+ </target>
</project>
\ No newline at end of file
diff --git a/openbis/dist/etc/log.xml b/openbis/dist/etc/log.xml
index d8b951be20a..15d96894f89 100644
--- a/openbis/dist/etc/log.xml
+++ b/openbis/dist/etc/log.xml
@@ -5,7 +5,7 @@
<appender name="DEFAULT" class="org.apache.log4j.DailyRollingFileAppender">
- <param name="File" value="logs/genericopenbis_log.txt" />
+ <param name="File" value="logs/openbis_log.txt" />
<param name="DatePattern" value="'.'yyyy-MM-dd" />
<layout class="org.apache.log4j.PatternLayout">
diff --git a/openbis/dist/server/install.sh b/openbis/dist/server/install.sh
index 48b115305b7..9681eff5d05 100755
--- a/openbis/dist/server/install.sh
+++ b/openbis/dist/server/install.sh
@@ -1,123 +1,95 @@
#! /bin/bash
-APPLICATION_NAME=genericopenbis
-usage() {
- echo "Usage: $0 [--port <port number>] <server folder> [<service properties file> <log configuration file>]"
- exit 1
-}
-
-# Checks whether the number of arguments is smaller than one.
-# We at least need the server folder.
-check_arguments() {
- if [ $# -lt 1 ]; then
- usage
- fi
-}
-
-check_arguments $@
-JETTY_PORT=8443
-if [ $1 == "--port" ]; then
- shift
- check_arguments $@
- JETTY_PORT=$1
+nostartup=0
+if [[ "$1" = '-n' || "$1" = '--nostartup' ]]; then
+ nostartup=1
shift
fi
-check_arguments $@
-# Installation folder: where the distribution zip file has been unzipped (and where this script resides)
+if [ $# -lt 1 ]; then
+ echo "Usage: $0 [--nostartup] <server folder> [<service properties file>]"
+ echo " --nostartup: do not start up tomcat automatically"
+ exit 1
+fi
+
installation_folder="`dirname $0`"
if [ ${installation_folder#/} == ${installation_folder} ]; then
installation_folder="`pwd`/${installation_folder}"
fi
-# Where the server will be installed.
server_folder=$1
+shift
if [ ${server_folder#/} == ${server_folder} ]; then
server_folder="`pwd`/${server_folder}"
fi
-properties_file="$installation_folder/service.properties"
-logconf_file="$installation_folder/log.xml"
-if [ $# -gt 1 ]; then
- if [ $# -lt 3 ]; then
- usage
+properties_file="${installation_folder}/service.properties"
+# Check whether given properties file exists and is a regular file.
+if [ $1 ]; then
+ if [ ! -f $1 ]; then
+ echo "Given properties file '$1' does not exist!"
+ exit 1
fi
- properties_file="$2"
- # Specify properties file path as absolute
+ properties_file="$1"
if [ "${properties_file#/}" == "${properties_file}" ]; then
properties_file="`pwd`/${properties_file}"
fi
- logconf_file="$3"
- # Specify log configuration file path as absolute
- if [ "logconf_file#/}" == "logconf_file}" ]; then
- logconf_file="`pwd`/logconf_file}"
- fi
-fi
-# Check whether given properties file exists and is a regular file.
-if [ ! -f $properties_file ]; then
- echo Given properties file \'$properties_file\' does not exist!
- exit 1
fi
-# Check whether given log configuration file exists and is a regular file.
-if [ ! -f $logconf_file ]; then
- echo Given log configuration file \'$logconf_file\' does not exist!
- exit 1
-fi
-
-rel_jetty_folder="jetty-`cat $installation_folder/jetty-version.txt`"
-jetty_folder="${server_folder}/${rel_jetty_folder}"
+rel_tomcat_folder="apache-tomcat-`cat \"${installation_folder}/tomcat-version.txt\"`"
+tomcat_folder="${server_folder}/${rel_tomcat_folder}"
+rel_openbis_web_folder=webapps/openbis
+openbis_web_folder="${tomcat_folder}/${rel_openbis_web_folder}"
+rel_openbis_web_inf=${rel_openbis_web_folder}/WEB-INF
+openbis_web_inf="${tomcat_folder}/${rel_openbis_web_inf}"
+startup_script_path="${tomcat_folder}/bin/startup.sh"
# Creates server folder.
-mkdir -p "$server_folder"
+mkdir -p "${server_folder}"
-# Checks whether a jetty folder already exists.
-if [ -d $jetty_folder ]; then
- echo "There exists already a Jetty folder."
- echo "Please shutdown and remove this Jetty installation"
+# Checks whether a tomcat folder already exists.
+if [ -d "${tomcat_folder}" ]; then
+ echo "There exists already a Tomcat folder."
+ echo "Please shutdown and remove this Tomcat installation"
echo "or choose another server folder."
exit 1
fi
-echo Unzipping Jetty...
-# Files are unzipped in $rel_jetty_folder
-unzip -q "$installation_folder/jetty.zip" -d "$server_folder"
-cp -p "$installation_folder"/jetty.xml "$jetty_folder"/etc
-
-echo Preparing and installing web archive...
-war_classes=WEB-INF/classes
-mkdir -p "$war_classes"/etc
-# Replace 'service.properties' and 'log.xml' files in war
-cp -p "$properties_file" "$war_classes/service.properties"
-cp -p "$logconf_file" "$war_classes/etc/log.xml"
-zip -u "$installation_folder"/$APPLICATION_NAME.war "$war_classes"/service.properties "$war_classes"/etc/log.xml
-cp -p "$installation_folder"/$APPLICATION_NAME.war "$jetty_folder"/webapps
-rm -rf WEB-INF
-
-# Create symlinks for easier access.
-cd "$server_folder"
-ln -s "${rel_jetty_folder}" jetty
-
-JETTY_BIN_DIR="$jetty_folder"/bin
-cp -p "$installation_folder"/startup.sh "$JETTY_BIN_DIR"
-cp -p "$installation_folder"/shutdown.sh "$JETTY_BIN_DIR"
-cp -p "$installation_folder"/passwd.sh "$JETTY_BIN_DIR"
-
-# Create a file called 'jetty.properties'.
-JETTY_PROPERTIES="$JETTY_BIN_DIR"/jetty.properties
-echo "JETTY_PORT=$JETTY_PORT" > "$JETTY_PROPERTIES"
-echo "JETTY_STOP_PORT=8079" >> "$JETTY_PROPERTIES"
-echo "JETTY_STOP_KEY=secret" >> "$JETTY_PROPERTIES"
-# Here goes the path of the JVM in case you need to set it hard
-echo "JVM=\"java\"" >> "$JETTY_PROPERTIES"
-# The default memory of the JVM at start up.
-echo "VM_STARTUP_MEM=\"256M\"" >> "$JETTY_PROPERTIES"
-# The maximum memory for the JVM
-echo "VM_MAX_MEM=\"786M\"" >> "$JETTY_PROPERTIES"
-
-# Create a 'work' directory in jetty folder. Web applications will be unpacked there.
-mkdir -p "$jetty_folder"/work
-
-cd "$jetty_folder"
-echo Starting Jetty...
-./bin/startup.sh
\ No newline at end of file
+unzip -q "${installation_folder}/apache-tomcat.zip" -d "$server_folder"
+cp -p "${installation_folder}"/*.keystore "${tomcat_folder}"
+cp -p "${installation_folder}/server.xml" "${tomcat_folder}/conf"
+cp -p "${installation_folder}/passwd.sh" "${tomcat_folder}/bin"
+chmod 755 "${tomcat_folder}/bin/passwd.sh"
+STARTUP_TMP=`mktemp startup.sh.XXXXXX`
+sed -e "33i\\
+CATALINA_OPTS=\"-Xmx512M -Ddatabase.create-from-scratch=false -Ddatabase.script-single-step-mode=false\"\\
+export CATALINA_OPTS\\
+\\
+if [ \${PRGDIR#/} == \${PRGDIR} ]; then\\
+ PRGDIR=\"\`pwd\`/\${PRGDIR}\"\\
+fi\\
+cd \"\${PRGDIR}/..\"\\
+" -e "s/\/bin\/sh/\/bin\/bash/" "${startup_script_path}" "${startup_script_path}" > ${STARTUP_TMP}
+mv ${STARTUP_TMP} "${startup_script_path}"
+chmod 744 "${tomcat_folder}"/bin/*.sh
+
+unzip -q "${installation_folder}/openBIS.war" -d "${openbis_web_folder}"
+mkdir "${openbis_web_inf}/conf"
+
+# Copy configuration files
+
+cp -p "${properties_file}" "${openbis_web_inf}/classes/service.properties"
+echo Given properties file \'${properties_file}\' copied to \'${openbis_web_inf}/classes/service.properties\'
+
+# Create symlinks for easier access
+
+cd "${server_folder}"
+ln -s "${rel_tomcat_folder}" apache-tomcat
+cd "${tomcat_folder}"
+mkdir etc
+ln -s "../${rel_openbis_web_inf}"/classes/service.properties etc/
+
+if [ "$nostartup" -eq 0 ]; then
+ echo Starting tomcat...
+ bin/startup.sh
+fi
\ No newline at end of file
diff --git a/openbis/dist/server/jetty.xml b/openbis/dist/server/jetty.xml
deleted file mode 100644
index f9d6ccb9b2e..00000000000
--- a/openbis/dist/server/jetty.xml
+++ /dev/null
@@ -1,60 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE Configure PUBLIC "-//Mort Bay Consulting//DTD Configure//EN" "http://jetty.mortbay.org/configure.dtd">
-
-<Configure id="Server" class="org.mortbay.jetty.Server">
-
- <!--
- // Java5 bounded threadpool with job queue.
- // Can be found in library 'jetty-java5-threadpool.jar'.
- -->
- <Set name="threadPool">
- <New class="org.mortbay.thread.concurrent.ThreadPool">
- <Set name="corePoolSize">250</Set>
- <Set name="maximumPoolSize">250</Set>
- </New>
- </Set>
-
- <Call name="addConnector">
- <Arg>
- <!--
- // Java5 bounded threadpool with job queue.
- // Can be found in library 'jetty-java5-threadpool.jar'.
- -->
- <New class="org.mortbay.jetty.security.SslSelectChannelConnector">
- <Set name="Port">
- <SystemProperty name="jetty.port" default="8443" />
- </Set>
- <Set name="maxIdleTime">30000</Set>
- <Set name="Acceptors">2</Set>
- <Set name="AcceptQueueSize">100</Set>
- <Set name="Keystore">
- <SystemProperty name="jetty.home" default="." />/etc/keystore
- </Set>
- <Set name="Password">OBF:1vny1zlo1x8e1vnw1vn61x8g1zlu1vn4</Set>
- <Set name="KeyPassword">OBF:1u2u1wml1z7s1z7a1wnl1u2g</Set>
- </New>
- </Arg>
- </Call>
-
- <Set name="handler">
- <New class="org.mortbay.jetty.webapp.WebAppContext">
- <Set name="contextPath">/genericopenbis</Set>
- <Set name="war">
- <SystemProperty name="jetty.home" default="." />/webapps/genericopenbis.war
- </Set>
- <Set name="tempDirectory">
- <SystemProperty name="jetty.home" default="." />/work/genericopenbis
- </Set>
- </New>
- </Set>
-
- <!-- =========================================================== -->
- <!-- extra options -->
- <!-- =========================================================== -->
-
- <Set name="stopAtShutdown">true</Set>
- <Set name="sendServerVersion">true</Set>
- <Set name="sendDateHeader">true</Set>
- <Set name="gracefulShutdown">1000</Set>
-
-</Configure>
diff --git a/openbis/dist/server/passwd.sh b/openbis/dist/server/passwd.sh
index e6563e34219..0bd18f25c71 100755
--- a/openbis/dist/server/passwd.sh
+++ b/openbis/dist/server/passwd.sh
@@ -31,7 +31,7 @@ if [ ! -x "$JAVA_BIN" ]; then
fi
-LIB=work/$APPLICATION_NAME/webapp/WEB-INF/lib
+LIB=webapps/$APPLICATION_NAME/WEB-INF/lib
$JAVA_HOME/bin/java \
-cp $LIB/commons-lang.jar:$LIB/commons-io.jar:$LIB/commons-codec.jar:$LIB/jline.jar:$LIB/log4j.jar:$LIB/$APPLICATION_NAME.jar \
ch.systemsx.cisd.authentication.file.PasswordEditorCommand "$@"
diff --git a/openbis/dist/server/server.keystore b/openbis/dist/server/server.keystore
new file mode 100644
index 0000000000000000000000000000000000000000..3982a68319e9e1fed5ace51f72682d79e448eaa2
GIT binary patch
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diff --git a/openbis/dist/server/server.xml b/openbis/dist/server/server.xml
new file mode 100644
index 00000000000..baf7beebebb
--- /dev/null
+++ b/openbis/dist/server/server.xml
@@ -0,0 +1,373 @@
+<!-- Example Server Configuration File -->
+<!-- Note that component elements are nested corresponding to their
+ parent-child relationships with each other -->
+
+<!-- A "Server" is a singleton element that represents the entire JVM,
+ which may contain one or more "Service" instances. The Server
+ listens for a shutdown command on the indicated port.
+
+ Note: A "Server" is not itself a "Container", so you may not
+ define subcomponents such as "Valves" or "Loggers" at this level.
+ -->
+
+<Server port="8005" shutdown="SHUTDOWN">
+
+ <!-- Comment these entries out to disable JMX MBeans support used for the
+ administration web application -->
+ <Listener className="org.apache.catalina.core.AprLifecycleListener" />
+ <Listener className="org.apache.catalina.mbeans.ServerLifecycleListener" />
+ <Listener className="org.apache.catalina.mbeans.GlobalResourcesLifecycleListener" />
+ <Listener className="org.apache.catalina.storeconfig.StoreConfigLifecycleListener"/>
+
+ <!-- Global JNDI resources -->
+ <GlobalNamingResources>
+
+ <!-- Test entry for demonstration purposes -->
+ <Environment name="simpleValue" type="java.lang.Integer" value="30"/>
+
+ <!-- Editable user database that can also be used by
+ UserDatabaseRealm to authenticate users -->
+ <Resource name="UserDatabase" auth="Container"
+ type="org.apache.catalina.UserDatabase"
+ description="User database that can be updated and saved"
+ factory="org.apache.catalina.users.MemoryUserDatabaseFactory"
+ pathname="conf/tomcat-users.xml" />
+
+ </GlobalNamingResources>
+
+ <!-- A "Service" is a collection of one or more "Connectors" that share
+ a single "Container" (and therefore the web applications visible
+ within that Container). Normally, that Container is an "Engine",
+ but this is not required.
+
+ Note: A "Service" is not itself a "Container", so you may not
+ define subcomponents such as "Valves" or "Loggers" at this level.
+ -->
+
+ <!-- Define the Tomcat Stand-Alone Service -->
+ <Service name="Catalina">
+
+ <!-- A "Connector" represents an endpoint by which requests are received
+ and responses are returned. Each Connector passes requests on to the
+ associated "Container" (normally an Engine) for processing.
+
+ By default, a non-SSL HTTP/1.1 Connector is established on port 8080.
+ You can also enable an SSL HTTP/1.1 Connector on port 8443 by
+ following the instructions below and uncommenting the second Connector
+ entry. SSL support requires the following steps (see the SSL Config
+ HOWTO in the Tomcat 5 documentation bundle for more detailed
+ instructions):
+ * If your JDK version 1.3 or prior, download and install JSSE 1.0.2 or
+ later, and put the JAR files into "$JAVA_HOME/jre/lib/ext".
+ * Execute:
+ %JAVA_HOME%\bin\keytool -genkey -alias tomcat -keyalg RSA (Windows)
+ $JAVA_HOME/bin/keytool -genkey -alias tomcat -keyalg RSA (Unix)
+ with a password value of "changeit" for both the certificate and
+ the keystore itself.
+
+ By default, DNS lookups are enabled when a web application calls
+ request.getRemoteHost(). This can have an adverse impact on
+ performance, so you can disable it by setting the
+ "enableLookups" attribute to "false". When DNS lookups are disabled,
+ request.getRemoteHost() will return the String version of the
+ IP address of the remote client.
+ -->
+
+ <!-- Define a non-SSL HTTP/1.1 Connector on port 8080 -->
+ <Connector port="8080" maxHttpHeaderSize="8192"
+ maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
+ enableLookups="false" redirectPort="8443" acceptCount="100"
+ connectionTimeout="0" disableUploadTimeout="true" />
+ <!-- Note : To disable connection timeouts, set connectionTimeout value
+ to 0 -->
+
+ <!-- Note : To use gzip compression you could set the following properties :
+
+ compression="on"
+ compressionMinSize="2048"
+ noCompressionUserAgents="gozilla, traviata"
+ compressableMimeType="text/html,text/xml"
+ -->
+
+ <!-- Define a SSL HTTP/1.1 Connector on port 8443 -->
+ <Connector port="8443" maxHttpHeaderSize="8192"
+ maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
+ keystoreFile="server.keystore"
+ enableLookups="false" disableUploadTimeout="true"
+ acceptCount="100" scheme="https" secure="true"
+ clientAuth="false" sslProtocol="TLS" />
+
+ <!-- Define an AJP 1.3 Connector on port 8009 -->
+ <Connector port="8009"
+ enableLookups="false" redirectPort="8443" protocol="AJP/1.3" />
+
+ <!-- Define a Proxied HTTP/1.1 Connector on port 8082 -->
+ <!-- See proxy documentation for more information about using this. -->
+ <!--
+ <Connector port="8082"
+ maxThreads="150" minSpareThreads="25" maxSpareThreads="75"
+ enableLookups="false" acceptCount="100" connectionTimeout="20000"
+ proxyPort="80" disableUploadTimeout="true" />
+ -->
+
+ <!-- An Engine represents the entry point (within Catalina) that processes
+ every request. The Engine implementation for Tomcat stand alone
+ analyzes the HTTP headers included with the request, and passes them
+ on to the appropriate Host (virtual host). -->
+
+ <!-- You should set jvmRoute to support load-balancing via AJP ie :
+ <Engine name="Standalone" defaultHost="localhost" jvmRoute="jvm1">
+ -->
+
+ <!-- Define the top level container in our container hierarchy -->
+ <Engine name="Catalina" defaultHost="localhost">
+
+ <!-- The request dumper valve dumps useful debugging information about
+ the request headers and cookies that were received, and the response
+ headers and cookies that were sent, for all requests received by
+ this instance of Tomcat. If you care only about requests to a
+ particular virtual host, or a particular application, nest this
+ element inside the corresponding <Host> or <Context> entry instead.
+
+ For a similar mechanism that is portable to all Servlet 2.4
+ containers, check out the "RequestDumperFilter" Filter in the
+ example application (the source for this filter may be found in
+ "$CATALINA_HOME/webapps/examples/WEB-INF/classes/filters").
+
+ Note that this Valve uses the platform's default character encoding.
+ This may cause problems for developers in another encoding, e.g.
+ UTF-8. Use the RequestDumperFilter instead.
+
+ Also note that enabling this Valve will write a ton of stuff to your
+ logs. They are likely to grow quite large. This extensive log writing
+ will definitely slow down your server.
+
+ Request dumping is disabled by default. Uncomment the following
+ element to enable it. -->
+ <!--
+ <Valve className="org.apache.catalina.valves.RequestDumperValve"/>
+ -->
+
+ <!-- Because this Realm is here, an instance will be shared globally -->
+
+ <!-- This Realm uses the UserDatabase configured in the global JNDI
+ resources under the key "UserDatabase". Any edits
+ that are performed against this UserDatabase are immediately
+ available for use by the Realm. -->
+ <Realm className="org.apache.catalina.realm.UserDatabaseRealm"
+ resourceName="UserDatabase"/>
+
+ <!-- Comment out the old realm but leave here for now in case we
+ need to go back quickly -->
+ <!--
+ <Realm className="org.apache.catalina.realm.MemoryRealm" />
+ -->
+
+ <!-- Replace the above Realm with one of the following to get a Realm
+ stored in a database and accessed via JDBC -->
+
+ <!--
+ <Realm className="org.apache.catalina.realm.JDBCRealm"
+ driverName="org.gjt.mm.mysql.Driver"
+ connectionURL="jdbc:mysql://localhost/authority"
+ connectionName="test" connectionPassword="test"
+ userTable="users" userNameCol="user_name" userCredCol="user_pass"
+ userRoleTable="user_roles" roleNameCol="role_name" />
+ -->
+
+ <!--
+ <Realm className="org.apache.catalina.realm.JDBCRealm"
+ driverName="oracle.jdbc.driver.OracleDriver"
+ connectionURL="jdbc:oracle:thin:@ntserver:1521:ORCL"
+ connectionName="scott" connectionPassword="tiger"
+ userTable="users" userNameCol="user_name" userCredCol="user_pass"
+ userRoleTable="user_roles" roleNameCol="role_name" />
+ -->
+
+ <!--
+ <Realm className="org.apache.catalina.realm.JDBCRealm"
+ driverName="sun.jdbc.odbc.JdbcOdbcDriver"
+ connectionURL="jdbc:odbc:CATALINA"
+ userTable="users" userNameCol="user_name" userCredCol="user_pass"
+ userRoleTable="user_roles" roleNameCol="role_name" />
+ -->
+
+ <!-- Define the default virtual host
+ Note: XML Schema validation will not work with Xerces 2.2.
+ -->
+ <Host name="localhost" appBase="webapps"
+ unpackWARs="true" autoDeploy="true"
+ xmlValidation="false" xmlNamespaceAware="false">
+
+ <!-- Defines a cluster for this node,
+ By defining this element, means that every manager will be changed.
+ So when running a cluster, only make sure that you have webapps in there
+ that need to be clustered and remove the other ones.
+ A cluster has the following parameters:
+
+ className = the fully qualified name of the cluster class
+
+ clusterName = a descriptive name for your cluster, can be anything
+
+ mcastAddr = the multicast address, has to be the same for all the nodes
+
+ mcastPort = the multicast port, has to be the same for all the nodes
+
+ mcastBindAddress = bind the multicast socket to a specific address
+
+ mcastTTL = the multicast TTL if you want to limit your broadcast
+
+ mcastSoTimeout = the multicast readtimeout
+
+ mcastFrequency = the number of milliseconds in between sending a "I'm alive" heartbeat
+
+ mcastDropTime = the number a milliseconds before a node is considered "dead" if no heartbeat is received
+
+ tcpThreadCount = the number of threads to handle incoming replication requests, optimal would be the same amount of threads as nodes
+
+ tcpListenAddress = the listen address (bind address) for TCP cluster request on this host,
+ in case of multiple ethernet cards.
+ auto means that address becomes
+ InetAddress.getLocalHost().getHostAddress()
+
+ tcpListenPort = the tcp listen port
+
+ tcpSelectorTimeout = the timeout (ms) for the Selector.select() method in case the OS
+ has a wakup bug in java.nio. Set to 0 for no timeout
+
+ printToScreen = true means that managers will also print to std.out
+
+ expireSessionsOnShutdown = true means that
+
+ useDirtyFlag = true means that we only replicate a session after setAttribute,removeAttribute has been called.
+ false means to replicate the session after each request.
+ false means that replication would work for the following piece of code: (only for SimpleTcpReplicationManager)
+ <%
+ HashMap map = (HashMap)session.getAttribute("map");
+ map.put("key","value");
+ %>
+ replicationMode = can be either 'pooled', 'synchronous' or 'asynchronous'.
+ * Pooled means that the replication happens using several sockets in a synchronous way. Ie, the data gets replicated, then the request return. This is the same as the 'synchronous' setting except it uses a pool of sockets, hence it is multithreaded. This is the fastest and safest configuration. To use this, also increase the nr of tcp threads that you have dealing with replication.
+ * Synchronous means that the thread that executes the request, is also the
+ thread the replicates the data to the other nodes, and will not return until all
+ nodes have received the information.
+ * Asynchronous means that there is a specific 'sender' thread for each cluster node,
+ so the request thread will queue the replication request into a "smart" queue,
+ and then return to the client.
+ The "smart" queue is a queue where when a session is added to the queue, and the same session
+ already exists in the queue from a previous request, that session will be replaced
+ in the queue instead of replicating two requests. This almost never happens, unless there is a
+ large network delay.
+ -->
+ <!--
+ When configuring for clustering, you also add in a valve to catch all the requests
+ coming in, at the end of the request, the session may or may not be replicated.
+ A session is replicated if and only if all the conditions are met:
+ 1. useDirtyFlag is true or setAttribute or removeAttribute has been called AND
+ 2. a session exists (has been created)
+ 3. the request is not trapped by the "filter" attribute
+
+ The filter attribute is to filter out requests that could not modify the session,
+ hence we don't replicate the session after the end of this request.
+ The filter is negative, ie, anything you put in the filter, you mean to filter out,
+ ie, no replication will be done on requests that match one of the filters.
+ The filter attribute is delimited by ;, so you can't escape out ; even if you wanted to.
+
+ filter=".*\.gif;.*\.js;" means that we will not replicate the session after requests with the URI
+ ending with .gif and .js are intercepted.
+
+ The deployer element can be used to deploy apps cluster wide.
+ Currently the deployment only deploys/undeploys to working members in the cluster
+ so no WARs are copied upons startup of a broken node.
+ The deployer watches a directory (watchDir) for WAR files when watchEnabled="true"
+ When a new war file is added the war gets deployed to the local instance,
+ and then deployed to the other instances in the cluster.
+ When a war file is deleted from the watchDir the war is undeployed locally
+ and cluster wide
+ -->
+
+ <!--
+ <Cluster className="org.apache.catalina.cluster.tcp.SimpleTcpCluster"
+ managerClassName="org.apache.catalina.cluster.session.DeltaManager"
+ expireSessionsOnShutdown="false"
+ useDirtyFlag="true"
+ notifyListenersOnReplication="true">
+
+ <Membership
+ className="org.apache.catalina.cluster.mcast.McastService"
+ mcastAddr="228.0.0.4"
+ mcastPort="45564"
+ mcastFrequency="500"
+ mcastDropTime="3000"/>
+
+ <Receiver
+ className="org.apache.catalina.cluster.tcp.ReplicationListener"
+ tcpListenAddress="auto"
+ tcpListenPort="4001"
+ tcpSelectorTimeout="100"
+ tcpThreadCount="6"/>
+
+ <Sender
+ className="org.apache.catalina.cluster.tcp.ReplicationTransmitter"
+ replicationMode="pooled"
+ ackTimeout="15000"
+ waitForAck="true"/>
+
+ <Valve className="org.apache.catalina.cluster.tcp.ReplicationValve"
+ filter=".*\.gif;.*\.js;.*\.jpg;.*\.png;.*\.htm;.*\.html;.*\.css;.*\.txt;"/>
+
+ <Deployer className="org.apache.catalina.cluster.deploy.FarmWarDeployer"
+ tempDir="/tmp/war-temp/"
+ deployDir="/tmp/war-deploy/"
+ watchDir="/tmp/war-listen/"
+ watchEnabled="false"/>
+
+ <ClusterListener className="org.apache.catalina.cluster.session.ClusterSessionListener"/>
+ </Cluster>
+ -->
+
+
+
+ <!-- Normally, users must authenticate themselves to each web app
+ individually. Uncomment the following entry if you would like
+ a user to be authenticated the first time they encounter a
+ resource protected by a security constraint, and then have that
+ user identity maintained across *all* web applications contained
+ in this virtual host. -->
+ <!--
+ <Valve className="org.apache.catalina.authenticator.SingleSignOn" />
+ -->
+
+ <!-- Access log processes all requests for this virtual host. By
+ default, log files are created in the "logs" directory relative to
+ $CATALINA_HOME. If you wish, you can specify a different
+ directory with the "directory" attribute. Specify either a relative
+ (to $CATALINA_HOME) or absolute path to the desired directory.
+ -->
+ <!--
+ <Valve className="org.apache.catalina.valves.AccessLogValve"
+ directory="logs" prefix="localhost_access_log." suffix=".txt"
+ pattern="common" resolveHosts="false"/>
+ -->
+
+ <!-- Access log processes all requests for this virtual host. By
+ default, log files are created in the "logs" directory relative to
+ $CATALINA_HOME. If you wish, you can specify a different
+ directory with the "directory" attribute. Specify either a relative
+ (to $CATALINA_HOME) or absolute path to the desired directory.
+ This access log implementation is optimized for maximum performance,
+ but is hardcoded to support only the "common" and "combined" patterns.
+ -->
+ <!--
+ <Valve className="org.apache.catalina.valves.FastCommonAccessLogValve"
+ directory="logs" prefix="localhost_access_log." suffix=".txt"
+ pattern="common" resolveHosts="false"/>
+ -->
+
+ </Host>
+
+ </Engine>
+
+ </Service>
+
+</Server>
diff --git a/openbis/dist/server/service.properties b/openbis/dist/server/service.properties
new file mode 100644
index 00000000000..80a94fc8d9f
--- /dev/null
+++ b/openbis/dist/server/service.properties
@@ -0,0 +1,44 @@
+# Supported: 'file-authentication-service' and 'crowd-authentication-service'
+authentication-service = file-authentication-service
+
+# The time after which an inactive session is expired by the service (in minutes).
+session-timeout = 30
+
+# Authorization
+# Supported: 'no-authorization' and 'active-authorization'
+authorization-component-factory = active-authorization
+
+script-folder = .
+
+# Supported: currently only 'postgresql' is supported
+database.engine = postgresql
+database.create-from-scratch = false
+# For debugging set this value to true.
+database.script-single-step-mode = false
+database.url-host-part =
+database.kind = demo
+database.owner =
+database.owner-password =
+database.admin-user =
+database.admin-password =
+
+crowd.service.host = crowd.systemsx.ch
+crowd.service.port = 8443
+crowd.application.name = openbis
+crowd.application.password =
+
+# The database instance local unique identifier. Used when the new database is created.
+database-instance = CISD
+
+# Base URL of the Data Store Server
+data-store-server-base-url = https://localhost:8889/dataset-download
+
+# Hibernate Search
+# The working directory.
+hibernate.search.index-base = ./indices
+# One of NO_INDEX, SKIP_IF_MARKER_FOUND, INDEX_FROM_SCRATCH.
+# If not specified, default (SKIP_IF_MARKER_FOUND) is taken.
+hibernate.search.index-mode = SKIP_IF_MARKER_FOUND
+# Defines the maximum number of elements indexed before flushing the transaction-bound queue.
+# Default is 1000.
+hibernate.search.batch-size = 1000
\ No newline at end of file
diff --git a/openbis/dist/server/shutdown.sh b/openbis/dist/server/shutdown.sh
deleted file mode 100755
index 219ab3516c0..00000000000
--- a/openbis/dist/server/shutdown.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#! /bin/bash
-
-# Load properties that become environment variables
-# NOTE: it would be possible to specify a normal java properties file after the 'start.jar'
-
-JETTY_BIN_DIR=`dirname "$0"`
-if [ ${JETTY_BIN_DIR#/} == ${JETTY_BIN_DIR} ]; then
- JETTY_BIN_DIR="`pwd`/${JETTY_BIN_DIR}"
-fi
-
-source "$JETTY_BIN_DIR"/jetty.properties
-cd "$JETTY_BIN_DIR"/..
-
-$JVM -DSTOP.PORT=$JETTY_STOP_PORT \
- -DSTOP.KEY=$JETTY_STOP_KEY \
- -jar start.jar --stop
\ No newline at end of file
diff --git a/openbis/dist/server/startup.sh b/openbis/dist/server/startup.sh
deleted file mode 100755
index 31aaf37fdd1..00000000000
--- a/openbis/dist/server/startup.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-#! /bin/bash
-
-# Load properties that become environment variables
-# NOTE: it would be possible to specify a normal java properties file after the 'start.jar'
-
-JETTY_BIN_DIR=`dirname "$0"`
-if [ ${JETTY_BIN_DIR#/} == ${JETTY_BIN_DIR} ]; then
- JETTY_BIN_DIR="`pwd`/${JETTY_BIN_DIR}"
-fi
-
-source "$JETTY_BIN_DIR"/jetty.properties
-cd "$JETTY_BIN_DIR"/..
-
-$JVM -DSTOP.PORT=$JETTY_STOP_PORT \
- -DSTOP.KEY=$JETTY_STOP_KEY \
- -Djetty.port=$JETTY_PORT \
- -server \
- -Xms${VM_STARTUP_MEM} \
- -Xmx${VM_MAX_MEM} \
- -jar start.jar etc/jetty.xml >> logs/jetty.out 2>&1 &
\ No newline at end of file
diff --git a/openbis/etc/log_system_test.xml b/openbis/etc/log_system_test.xml
index def37b0bb4c..b69c992b1aa 100644
--- a/openbis/etc/log_system_test.xml
+++ b/openbis/etc/log_system_test.xml
@@ -8,7 +8,7 @@
<appender name="FILE" class="org.apache.log4j.FileAppender">
- <param name="File" value="targets/genericopenbis_log.txt" />
+ <param name="File" value="targets/openbis_log.txt" />
<param name="Append" value="false" />
<layout class="org.apache.log4j.PatternLayout">
diff --git a/openbis/resource/server/web.xml b/openbis/resource/server/web.xml
index e0db4ef9505..cf721a7bafe 100644
--- a/openbis/resource/server/web.xml
+++ b/openbis/resource/server/web.xml
@@ -19,7 +19,7 @@
<!-- Trying kind of extension (i.e., '*.do') here as 'url-pattern' does not work. -->
<servlet-mapping>
<servlet-name>spring</servlet-name>
- <url-pattern>/genericopenbis/*</url-pattern>
+ <url-pattern>/openbis/*</url-pattern>
</servlet-mapping>
<!--
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/GenericConstants.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/GenericConstants.java
index f5c1825aac6..e987688024c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/GenericConstants.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/GenericConstants.java
@@ -40,7 +40,7 @@ public final class GenericConstants
*/
public static final String ID_PREFIX = "openbis_";
- private static final String APPLICATION_NAME = "genericopenbis";
+ private static final String APPLICATION_NAME = "openbis";
public static final String COMMON_SERVER_NAME = createServicePath("common");
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceServlet.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceServlet.java
index 9131b8489b3..0c34172be24 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceServlet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceServlet.java
@@ -37,7 +37,7 @@ import ch.systemsx.cisd.openbis.generic.shared.ResourceNames;
*/
@Controller
@RequestMapping(
- { "/common", "/genericopenbis/common" })
+ { "/common", "/openbis/common" })
public final class CommonClientServiceServlet extends GWTRPCServiceExporter
{
private static final long serialVersionUID = 1L;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/FileExportServiceServlet.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/FileExportServiceServlet.java
index 2783438165f..65878c5b452 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/FileExportServiceServlet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/FileExportServiceServlet.java
@@ -32,7 +32,7 @@ import ch.systemsx.cisd.openbis.generic.shared.ResourceNames;
*/
@Controller
@RequestMapping(
- { "/export-file-downloader", "/genericopenbis/export-file-downloader" })
+ { "/export-file-downloader", "/openbis/export-file-downloader" })
public class FileExportServiceServlet extends AbstractFileDownloadServlet
{
@Resource(name = ResourceNames.COMMON_SERVICE)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/UploadServiceServlet.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/UploadServiceServlet.java
index fc0c64a8c4d..4d109f1a193 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/UploadServiceServlet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/UploadServiceServlet.java
@@ -54,14 +54,14 @@ import ch.systemsx.cisd.common.utilities.Message;
* string in case of exception.
* </p>
* <p>
- * <i>URL</i> mappings are: <code>/upload</code> and <code>/genericopenbis/upload</code>.
+ * <i>URL</i> mappings are: <code>/upload</code> and <code>/openbis/upload</code>.
* </p>
*
* @author Christian Ribeaud
*/
@Controller
@RequestMapping(
- { "/upload", "/genericopenbis/upload" })
+ { "/upload", "/openbis/upload" })
public final class UploadServiceServlet extends AbstractCommandController
{
private static final Logger operationLog =
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceServer.java
index 1619d703fb5..9d956e830c2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceServer.java
@@ -32,7 +32,7 @@ import ch.systemsx.cisd.openbis.generic.shared.ResourceNames;
*/
@Controller
@RequestMapping(
- { "/rmi-etl", "/genericopenbis/rmi-etl" })
+ { "/rmi-etl", "/openbis/rmi-etl" })
public class ETLServiceServer extends HttpInvokerServiceExporter
{
@Resource(name = ResourceNames.ETL_SERVICE)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/ExperimentAttachmentDownloadServlet.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/ExperimentAttachmentDownloadServlet.java
index 4d820657c6a..933f294866d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/ExperimentAttachmentDownloadServlet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/ExperimentAttachmentDownloadServlet.java
@@ -38,7 +38,7 @@ import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
*/
@Controller
@RequestMapping(
- { "/experiment-attachment-download", "/genericopenbis/experiment-attachment-download" })
+ { "/experiment-attachment-download", "/openbis/experiment-attachment-download" })
public class ExperimentAttachmentDownloadServlet extends AbstractFileDownloadServlet
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceServlet.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceServlet.java
index 993148e25fc..175606ff1f4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceServlet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceServlet.java
@@ -29,7 +29,7 @@ import ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames;
/**
* The {@link GWTRPCServiceExporter} for the <i>generic</i> service.
* <p>
- * <i>URL</i> mappings are: <code>/generic</code> and <code>/genericopenbis/generic</code>.
+ * <i>URL</i> mappings are: <code>/generic</code> and <code>/openbis/generic</code>.
* The encapsulated {@link ICommonClientService} service implementation is expected to be defined as
* bean with name <code>generic-service</code>.
* </p>
@@ -38,7 +38,7 @@ import ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames;
*/
@Controller
@RequestMapping(
- { "/generic", "/genericopenbis/generic" })
+ { "/generic", "/openbis/generic" })
public final class GenericClientServiceServlet extends GWTRPCServiceExporter
{
private static final long serialVersionUID = 1L;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientServiceServlet.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientServiceServlet.java
index 264b520fa56..90fbf4b761e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientServiceServlet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientServiceServlet.java
@@ -38,7 +38,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.ResourceNames;
*/
@Controller
@RequestMapping(
- { "/screening", "/genericopenbis/screening" })
+ { "/screening", "/openbis/screening" })
public final class ScreeningClientServiceServlet extends GWTRPCServiceExporter
{
private static final long serialVersionUID = 1L;
diff --git a/openbis_all/source/bash/sprint_install.sh b/openbis_all/source/bash/sprint_install.sh
index 465f9d4ee7c..e7dd285d650 100755
--- a/openbis_all/source/bash/sprint_install.sh
+++ b/openbis_all/source/bash/sprint_install.sh
@@ -43,15 +43,6 @@ chmod 700 download-service.sh
export JAVA_HOME=/usr
./download-service.sh start
-echo Installing generic openBIS...
-cd ~
-unzip openbis-S$VER*
-WAR_FILE=openbis/genericopenbis.war
-# Put the previous 'service.properties' file into the war file.
-jar -uf $WAR_FILE -C old/sprint-$PREV_VER/openBIS-server/apache-tomcat/webapps/genericopenbis WEB-INF/classes/service.properties
-# Just put the war file in the weapps directory, Tomcat will do the rest
-mv $WAR_FILE sprint/openBIS-server/apache-tomcat/webapps
-
echo Doing some cleaning...
cd
mv *.zip tmp
--
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