[MOBY-guts] biomoby commit
Martin Senger
senger at dev.open-bio.org
Sun Mar 2 12:45:27 UTC 2008
senger
Sun Mar 2 07:45:27 EST 2008
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv32345/xmls
Modified Files:
dashboardBuild.xml install.xml junit.xml mosesBuild.xml
project.pom samplesBuild.xml servletsBuild.xml
Log Message:
Too Many Changes - see docs/ChangeLog
moby-live/Java/xmls dashboardBuild.xml,1.4,1.5 install.xml,1.1,1.2 junit.xml,1.2,1.3 mosesBuild.xml,1.4,1.5 project.pom,1.5,1.6 samplesBuild.xml,1.4,1.5 servletsBuild.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml 2008/02/22 00:54:30 1.4
+++ /home/repository/moby/moby-live/Java/xmls/dashboardBuild.xml 2008/03/02 12:45:27 1.5
@@ -42,8 +42,12 @@
<not><isset property="log4j.configuration.valid"/></not>
</condition>
- <java classname="org.biomoby.service.dashboard.Dashboard" taskname="Dashboard"
- classpathref="dashboard.build.classpath" fork="true" failonerror="true">
+ <java
+ classname="org.biomoby.service.dashboard.Dashboard"
+ taskname="Dashboard"
+ classpathref="dashboard.build.classpath"
+ fork="true"
+ failonerror="true">
<jvmarg value="-Xms32m"/>
<jvmarg value="-Xmx256m"/>
<arg value="${dashboard.arg.1}"/>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/install.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/xmls/install.xml 2008/02/14 06:13:37 1.1
+++ /home/repository/moby/moby-live/Java/xmls/install.xml 2008/03/02 12:45:27 1.2
@@ -9,15 +9,18 @@
<!-- ====================================================== -->
<target name="install"
- description="Install and build jMoby">
+ description="Install and build jMoby"
+ depends="pre-compile,compile,post-compile"/>
+
+<target name="pre-compile">
<echo taskname="welcome">
------------------------------------------
-Welcome to the jMoby world. |
-Project documentation is available from: |
-http://biomoby.org/ |
+| Welcome to the jMoby world. |
+| Project documentation is available at: |
+| http://biomoby.org/ |
------------------------------------------
</echo>
- <echo/>
+
<echo taskname="version">
${ant.version}
Java: ${java.version}
@@ -32,25 +35,103 @@
<available file="${lib.dir}/alltools2.jar" property="old.jar.present"/>
<antcall target="libcheck"/>
- <echo/>
- <echo taskname="build">
-The jMoby is going to build itself. It will need to fetch a lot of
-libraries from the Internet (using the Maven technology for resolving
-project dependencies). Just be patient, please...
+ <!-- Give name of the local cache -->
-Thanks for any comments and suggestions.
+ <touch file="build.properties"/>
+ <input taskname="Give Cache Name"
+ addproperty="registry.cache.dir"
+ defaultvalue="${project.home}/myCache">
+During the installation, jMoby is going to fetch data
+from the BioMoby central registry and store them in a
+local file system to allow much faster access to it.
+
+In order to do it, it needs to know a directory where
+you wish to store the local cache. For now, you can
+type it here - but for future the best is to add this
+line to your build.properties file:
+
+ registry.cache.dir = /full/name/of/cache/directory
+
+Default value (just pres ENTER to accept it) is:
+ </input>
+ <echo taskname="Give Cache Name">
+Local cache: ${registry.cache.dir}
+ </echo>
+
+ <echo file="build.properties" append="true">
+registry.cache.dir = ${registry.cache.dir}
+</echo>
+
+ <!-- build itself -->
+
+ <echo taskname="build">
+The jMoby is going to build itself. It will need to
+fetch a lot of libraries from the Internet (using the
+Maven technology for resolving project dependencies).
+Just be patient, please...
</echo>
<input taskname=" Attention ">Press Return key to continue...</input>
+ <antcall target="clean"/>
+
+</target>
+
+
- <echo/>
- <antcall target="compile"/>
+
+<target name="post-compile">
+ <antcall target="dashboard-config"/>
+
+
+ <!-- fill local cache -->
+
+ <echo taskname="Local cache">
+The jMoby is going to create local cache. Depending
+on the network speed, it may take several minutes
+(usually it should be done within about a minute).
+
+[You can check the progress in the jMoby.log file.]
+ </echo>
+
+ <java
+ taskname="Local cache"
+ classname="CacheRegistryClient"
+ fork="no"
+ failonerror="true">
+ <classpath refid="build.classpath"/>
+ <classpath refid="dependency.classpath"/>
+ <sysproperty key="log4j.configuration" value="file:${log4j.configuration}"/>
+ <arg value="-cachedir"/>
+ <arg file="${registry.cache.dir}"/>
+ <arg value="-v"/>
+ <arg value="-fill"/>
+ </java>
+
+
+ <!-- footnote message -->
<echo taskname="Success">
Installation completed.
+
+Thanks for any comments and suggestions
+(moby-l at biomoby.org or moby-dev at biomoby.org)
</echo>
+
+ <!-- start Dashboard -->
+
+ <input taskname=" Attention ">Press Return key to start Dashboard...</input>
+ <!--
+(or press Ctrl-C and start Dashboard later
+ by typing 'ant dashboard')
+</input>
+-->
+ <antcall target="dashboard"/>
+
</target>
+<!-- ====================================================== -->
+<!-- -->
+<!-- ====================================================== -->
<target name="check-ant-version">
<fail
taskname="check"
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/junit.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/xmls/junit.xml 2008/02/28 05:21:48 1.2
+++ /home/repository/moby/moby-live/Java/xmls/junit.xml 2008/03/02 12:45:27 1.3
@@ -90,7 +90,10 @@
<jvmarg value="-Dlog4j.configuration=file:${log4j.configuration}"/>
<formatter type="plain"/>
<batchtest todir="${test.report.dir}">
- <fileset dir="${build.test}" includes="**/*Test.*" />
+ <fileset dir="${build.test}">
+ <include name="**/MobyParserTest.*"/>
+ </fileset>
+ <!-- <fileset dir="${build.test}" includes="**/*Test.*" /> -->
</batchtest>
</junit>
@@ -103,16 +106,25 @@
<target name="compile-tests" if="junit.is.present" depends="compile,junit-present">
<!-- compilation options -->
- <property name="compile.test.debug" value="${compile.debugtrue}" />
- <property name="compile.test.verbose" value="${compile.verbosefalse}" />
- <property name="compile.test.deprecation" value="${compile.deprecationfalse}" />
- <property name="compile.test.optimize" value="${compile.optimizefalse}" />
- <property name="compile.test.warnings" value="${compile.warningsfalse}" />
+ <property name="compile.test.debug" value="${compile.debug}" />
+ <property name="compile.test.verbose" value="${compile.verbose}" />
+ <property name="compile.test.deprecation" value="${compile.deprecation}" />
+ <property name="compile.test.optimize" value="${compile.optimize}" />
+ <property name="compile.test.warnings" value="${compile.warnings}" />
<condition property="xlint.test.param" value="-Xlint:unchecked" else="-Xlint:none">
<istrue value="${compile.test.warnings}"/>
</condition>
+ <path id="tests.classpath">
+ <pathelement location="${build.classes}"/>
+ <pathelement path="${classes.datatypes}"/>
+ <pathelement path="${classes.skeletons}"/>
+ <fileset dir="${lib.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ </path>
+
<javac
srcdir="${src.test}"
destdir="${build.test}"
@@ -122,7 +134,7 @@
deprecation="${compile.test.deprecation}"
optimize="${compile.test.optimize}"
excludes="${project.excludes}">
- <classpath refid="build.classpath"/>
+ <classpath refid="tests.classpath"/>
<classpath refid="dependency.classpath"/>
<compilerarg value="${xlint.test.param}"/>
</javac>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml 2008/02/28 05:21:49 1.4
+++ /home/repository/moby/moby-live/Java/xmls/mosesBuild.xml 2008/03/02 12:45:27 1.5
@@ -21,6 +21,7 @@
generate-datatypes generate-services
clean-datatypes clean-services
+ compile-datatypes compile-services
jar-datatypes jar-services
moses-datatypes moses-services
@@ -107,6 +108,10 @@
</or>
</condition>
+ <condition property="xlint.param" value="-Xlint:unchecked" else="-Xlint:none">
+ <istrue value="${compile.warnings}"/>
+ </condition>
+
</target>
<!-- ================================================================== -->
@@ -125,6 +130,7 @@
<property name="moses.filter.dt" value=""""/>
<property name="dot.location" value=""""/>
+ <property name="registry.cache.dir" value=""/>
<java classname="MosesGenerators" taskname="Data Types"
classpathref="moses.build.classpath" fork="true" failonerror="true">
@@ -189,9 +195,6 @@
<delete includeemptydirs="true" quiet="true">
<fileset dir="${src.skeletons}" includes="**/*"/>
</delete>
- <delete includeemptydirs="true">
- <fileset dir="${classes.skeletons}" includes="**/*"/>
- </delete>
</target>
<target name="generate-services" depends="moses-init,service-check"
@@ -200,6 +203,7 @@
<property name="moses.service" value=""""/>
<property name="moses.authority" value=""""/>
<property name="dot.location" value=""""/>
+ <property name="registry.cache.dir" value=""/>
<java classname="MosesGenerators" taskname="Service(s)"
classpathref="moses.build.classpath" fork="true" failonerror="true">
@@ -267,21 +271,36 @@
<!-- ================================================================== -->
<!-- Moses generally: Compile generated datatypes and skeletons -->
<!-- ================================================================== -->
-<target name="moses-compile" depends="moses-init,compile"
- description="Compile all generated sources.">
- <javac srcdir="${src.datatypes}"
+<target name="moses-compile" depends="compile-datatypes,compile-services"
+ description="Compile all generated sources."/>
+
+<target name="compile-datatypes" depends="moses-init,compile">
+ <javac
+ srcdir="${src.datatypes}"
destdir="${classes.datatypes}"
- debug="true"
+ verbose="${compile.verbose}"
+ debug="${compile.debug}"
debuglevel="lines,vars,source"
+ deprecation="${compile.deprecation}"
+ optimize="${compile.optimize}"
excludes="${project.excludes}">
<classpath refid="moses.build.classpath"/>
+ <compilerarg value="${xlint.param}"/>
</javac>
- <javac srcdir="${src.skeletons}"
- debug="true"
- debuglevel="lines,vars,source"
+</target>
+
+<target name="compile-services" depends="moses-init,compile">
+ <javac
+ srcdir="${src.skeletons}"
destdir="${classes.skeletons}"
+ verbose="${compile.verbose}"
+ debug="${compile.debug}"
+ debuglevel="lines,vars,source"
+ deprecation="${compile.deprecation}"
+ optimize="${compile.optimize}"
excludes="${project.excludes}">
<classpath refid="moses.build.classpath"/>
+ <compilerarg value="${xlint.param}"/>
</javac>
</target>
@@ -349,3 +368,14 @@
<target name="moses-jars" depends="jar-datatypes,jar-services"
description="Create jar files with generated data types and skeletons.">
</target>
+
+<!-- ================================================================== -->
+<!-- Moses generally: do it all -->
+<!-- ================================================================== -->
+<target name="moses"
+ depends="compile,moses-clean,clean-services,generate-datatypes,compile-datatypes,generate-services,compile-services,moses-jars"
+ description="Clean/enerate/compile/pack data types and skeletons.">
+</target>
+
+<target name="moses-test" depends="generate-datatypes,moses-compile">
+</target>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/xmls/project.pom 2008/02/28 05:21:49 1.5
+++ /home/repository/moby/moby-live/Java/xmls/project.pom 2008/03/02 12:45:27 1.6
@@ -167,6 +167,21 @@
</dependency>
<dependency>
+ <groupId>commons-configuration</groupId>
+ <artifactId>commons-configuration</artifactId>
+ <version>1.5</version>
+ <!-- we need to exclude this in order to get Java 1.5. XML parser
+ (otherwise axis will complain about the lexical-handler
+ feature not supported -->
+ <exclusions>
+ <exclusion>
+ <groupId>xerces</groupId>
+ <artifactId>xerces</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+
+ <dependency>
<groupId>castor</groupId>
<artifactId>castor</artifactId>
<version>0.9.5</version>
@@ -366,6 +381,12 @@
</dependency>
<dependency>
+ <groupId>org.apache.ant</groupId>
+ <artifactId>ant-nodeps</artifactId>
+ <version>1.7.0</version>
+ </dependency>
+
+ <dependency>
<groupId>ant-contrib</groupId>
<artifactId>ant-contrib</artifactId>
<version>1.0b2</version>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml 2008/02/22 00:54:30 1.4
+++ /home/repository/moby/moby-live/Java/xmls/samplesBuild.xml 2008/03/02 12:45:27 1.5
@@ -57,6 +57,10 @@
<pathelement location="${classes.samples}"/>
</path>
+ <condition property="xlint.param" value="-Xlint:unchecked" else="-Xlint:none">
+ <istrue value="${compile.warnings}"/>
+ </condition>
+
</target>
<!-- ================================================================== -->
@@ -64,15 +68,22 @@
<!-- ================================================================== -->
<target name="samples-compile" depends="samples-init,moses-compile"
description="Compile samples and tutorial.">
+
<copy todir="${classes.samples}/resources">
<fileset dir="${samples.resources}"/>
</copy>
- <javac srcdir="${src.samples}"
- debug="true"
- debuglevel="lines,vars,source"
+
+ <javac
+ srcdir="${src.samples}"
destdir="${classes.samples}"
+ verbose="${compile.verbose}"
+ debug="${compile.debug}"
+ debuglevel="lines,vars,source"
+ deprecation="${compile.deprecation}"
+ optimize="${compile.optimize}"
excludes="${project.excludes}">
<classpath refid="samples.build.classpath"/>
+ <compilerarg value="${xlint.param}"/>
</javac>
</target>
@@ -154,13 +165,14 @@
<antcall target="generate-services">
<param name="moses.authority" value="samples.jmoby.net"/>
</antcall>
+ <antcall target="generate-services">
+ <param name="moses.service" value="getFeatureList|TrimSequenceVector"/>
+ </antcall>
</target>
<!-- ================================================================== -->
<!-- Samples: All in one -->
<!-- ================================================================== -->
-<!-- <target name="samples" depends="samples-generate,samples-compile,samples-jar,samples-docs,deploy-services" -->
-<!-- <target name="samples" depends="samples-compile,samples-jar,deploy-services" -->
-<target name="samples" depends="samples-compile,samples-jar"
+<target name="samples" depends="moses,samples-compile,samples-jar"
description="Do (almost) everything for samples."/>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/servletsBuild.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/xmls/servletsBuild.xml 2006/04/28 00:13:41 1.1
+++ /home/repository/moby/moby-live/Java/xmls/servletsBuild.xml 2008/03/02 12:45:27 1.2
@@ -25,6 +25,9 @@
description="Create a war file with jMoby servlets.">
<mkdir dir="${build.webapps}"/>
<mkdir dir="${build.webapps}/cache"/>
+
+ <property name="registry.cache.dir" value=""/>
+
<copy file="${src.webapps}/web.xml.template"
tofile="${build.webapps}/web.xml"
overwrite="yes">
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