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[Treebase-guts] SF.net SVN: treebase:[249] trunk
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From: <rv...@us...> - 2009-11-04 17:04:42
|
Revision: 249
http://treebase.svn.sourceforge.net/treebase/?rev=249&view=rev
Author: rvos
Date: 2009-11-04 17:04:34 +0000 (Wed, 04 Nov 2009)
Log Message:
-----------
Cleaned up maven pom.xml files
Modified Paths:
--------------
trunk/pom.xml
trunk/treebase-core/pom.xml
trunk/treebase-web/pom.xml
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2009-11-04 16:54:08 UTC (rev 248)
+++ trunk/pom.xml 2009-11-04 17:04:34 UTC (rev 249)
@@ -7,81 +7,69 @@
<artifactId>treebase</artifactId>
<packaging>pom</packaging>
<version>1.0-SNAPSHOT</version>
- <url>http://www.phylo.org/treebase/index.php</url>
+ <url>https://sourceforge.net/projects/treebase/</url>
<issueManagement>
- <system>FogBugz</system>
- <url>https://www.ngbw.org/ngbugz</url>
+ <system>SourceForge</system>
+ <url>https://sourceforge.net/tracker/?group_id=248804</url>
</issueManagement>
<inceptionYear>2005</inceptionYear>
<scm>
- <connection>scm:svn:http://nladr-cvs.sdsc.edu/svn/CIPRES/treebase/trunk</connection>
- <developerConnection>scm:svn:http://nladr-cvs.sdsc.edu/svn/CIPRES/treebase/trunk</developerConnection>
- <url>http://nladr-cvs.sdsc.edu/svn/cipresdev/trunk</url>
+ <connection>scm:svn:https://treebase.svn.sourceforge.net/svnroot/treebase/trunk</connection>
+ <developerConnection>scm:svn:https://treebase.svn.sourceforge.net/svnroot/treebase/trunk</developerConnection>
+ <url>http://treebase.svn.sourceforge.net/viewvc/treebase/trunk</url>
</scm>
- <!-- mailingLists>
+ <mailingLists>
+
<mailingList>
- <name>cipres-dev</name>
- <subscribe>https://lists.sdsc.edu/mailman/listinfo.cgi/cipres</subscribe>
- <unsubscribe>https://lists.sdsc.edu/mailman/listinfo.cgi/cipres</unsubscribe>
- <archive>https://lists.sdsc.edu/mailman/listinfo.cgi/cipres</archive>
+ <name>treebase-devel</name>
+ <subscribe>https://lists.sourceforge.net/lists/listinfo/treebase-devel</subscribe>
+ <unsubscribe>https://lists.sourceforge.net/lists/listinfo/treebase-devel</unsubscribe>
+ <archive>https://sourceforge.net/mailarchive/forum.php?forum_name=treebase-devel</archive>
</mailingList>
- </mailingLists -->
+
+ <mailingList>
+ <name>treebase-guts</name>
+ <subscribe>https://lists.sourceforge.net/lists/listinfo/treebase-guts</subscribe>
+ <unsubscribe>https://lists.sourceforge.net/lists/listinfo/treebase-guts</unsubscribe>
+ <archive>https://sourceforge.net/mailarchive/forum.php?forum_name=treebase-guts</archive>
+ </mailingList>
+
+ <mailingList>
+ <name>treebase-users</name>
+ <subscribe>https://lists.sourceforge.net/lists/listinfo/treebase-users</subscribe>
+ <unsubscribe>https://lists.sourceforge.net/lists/listinfo/treebase-users</unsubscribe>
+ <archive>https://sourceforge.net/mailarchive/forum.php?forum_name=treebase-users</archive>
+ </mailingList>
+
+ </mailingLists>
<developers>
- <developer>
- <id>lcchan</id>
- <name>Lucie Chan</name>
- <email>lc...@sd...</email>
- <organization>SDSC</organization>
- <organizationUrl>http://www.sdsc.edu</organizationUrl>
- <roles>
- <role>developer</role>
- </roles>
- <timezone>-7</timezone>
- </developer>
- <developer>
- <id>jin</id>
- <name>Jin Ruan</name>
- <email>jr...@sd...</email>
- <organization>SDSC</organization>
- <roles>
- <role>developer</role>
- </roles>
- </developer>
- <developer>
- <id>madhu</id>
- <name>Madhusudan</name>
- <email>ma...@sd...</email>
- <organization>SDSC</organization>
- <roles>
- <role>developer</role>
- </roles>
- </developer>
- <developer>
- <id>mjd</id>
- <name>Mark Jason Dominus</name>
- <email>mj...@ge...</email>
- <organization>Penn Genome Frontiers Institute</organization>
- <organizationUrl>http://www.genomics.upenn.edu</organizationUrl>
- <roles>
- <role>developer</role>
- </roles>
- <timezone>-5</timezone>
- </developer>
+
<developer>
- <id>rvosa</id>
- <name>Rutger Vos</name>
- <email>rut...@gm...</email>
- <organization>University of British Columbia</organization>
- <organizationUrl>http://www.ubc.ca</organizationUrl>
- <timezone>-7</timezone>
- <roles>
- <role>developer</role>
- </roles>
+
+ <id>rvosa</id>
+
+ <name>Rutger Vos</name>
+
+ <email>rut...@gm...</email>
+
+ <organization>University of Reading</organization>
+
+ <organizationUrl>http://www.reading.ac.uk</organizationUrl>
+
+ <timezone>0</timezone>
+
+ <roles>
+
+ <role>developer</role>
+
+ </roles>
+
</developer>
+
</developers>
<licenses>
<license>
- <name>UCSD</name>
+ <name>BSD</name>
<url>LICENSE.txt</url>
<distribution>manual</distribution>
<comments/>
@@ -123,51 +111,15 @@
<reporting>
<plugins>
+
<plugin>
<artifactId>maven-surefire-report-plugin</artifactId>
</plugin>
+
<plugin>
<artifactId>maven-clover-plugin</artifactId>
</plugin>
- <!-- plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-jxr-plugin</artifactId>
- </plugin -->
- <!-- plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-javadoc-plugin</artifactId>
- <configuration>
- <links>
- <link>http://java.sun.com/j2se/1.4.2/docs/api</link>
- <link>http://plexus.codehaus.org/ref/1.0-alpha-9/apidocs</link>
- </links>
- <aggregate>true</aggregate>
- </configuration>
- </plugin -->
- <!-- plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-pmd-plugin</artifactId>
- <configuration>
- <targetjdk>1.5</targetjdk>
- <rulesets>
- <ruleset>/rulesets/basic.xml</ruleset>
- <ruleset>/rulesets/imports.xml</ruleset>
- <ruleset>/rulesets/unusedcode.xml</ruleset>
- <ruleset>/rulesets/finalizers.xml</ruleset>
- </rulesets>
- <format>xml</format>
- <linkXref>true</linkXref>
- <sourceEncoding>utf-8</sourceEncoding>
- <minimumTokens>100</minimumTokens>
- </configuration>
- </plugin -->
- <!-- plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-checkstyle-plugin</artifactId>
- <configuration>
- <configLocation>config/maven_checks.xml</configLocation>
- </configuration>
- </plugin -->
+
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>taglist-maven-plugin</artifactId>
@@ -180,56 +132,63 @@
</tags>
</configuration>
</plugin>
+
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>cobertura-maven-plugin</artifactId>
</plugin>
+
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
</plugin>
+
</plugins>
</reporting>
<dependencyManagement>
<dependencies>
- <dependency>
- <groupId>org.cipres.treebase</groupId>
- <artifactId>treebase-core</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.cipres.treebase</groupId>
- <artifactId>treebase-web</artifactId>
- <version>${project.version}</version>
- </dependency>
+
+ <dependency>
+ <groupId>org.cipres.treebase</groupId>
+ <artifactId>treebase-core</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.cipres.treebase</groupId>
+ <artifactId>treebase-web</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+
</dependencies>
</dependencyManagement>
<organization>
- <name>SDSC</name>
- <url>http://biology.sdsc.edu</url>
+ <name>NESCent</name>
+ <url>http://www.nescent.org</url>
</organization>
+
<!-- order of repositories used to compile the project -->
<repositories>
+
<repository>
- <id>m2.remote.repos</id>
- <name>Maven 2 Remote Repository</name>
- <url>http://8ball.sdsc.edu:9999/maven2</url>
- </repository>
- <repository>
<id>maven2</id>
<name>Default Maven2 Repository</name>
<url>http://repo1.maven.org/maven2</url>
</repository>
+
<repository>
<id>repository.jboss.org</id>
<name>JBoss Maven Repository</name>
<url>http://repository.jboss.org/maven2</url>
<layout>default</layout>
</repository>
+
</repositories>
+
<!-- make sure java 1.5 is used for annotations support -->
<build>
<plugins>
+
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
@@ -238,16 +197,16 @@
<target>1.5</target>
</configuration>
</plugin>
+
</plugins>
</build>
<distributionManagement>
<site>
<id>website</id>
- <!-- url>file:///var/www/html/sites/treebase</url -->
<url>file:///var/www/html/sites/treebase</url>
</site>
</distributionManagement>
-<profiles>
+ <profiles>
<profile>
<id>ciProfile</id>
<activation>
@@ -258,6 +217,7 @@
</activation>
<build>
<plugins>
+
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-pmd-plugin</artifactId>
@@ -269,6 +229,7 @@
</execution>
</executions>
</plugin>
+
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>cobertura-maven-plugin</artifactId>
@@ -279,20 +240,24 @@
</check>
</configuration>
<executions>
+
<execution>
<id>clean</id>
<goals>
<goal>clean</goal>
</goals>
</execution>
+
<execution>
<id>check</id>
<goals>
<goal>check</goal>
</goals>
</execution>
+
</executions>
</plugin>
+
</plugins>
</build>
</profile>
Modified: trunk/treebase-core/pom.xml
===================================================================
--- trunk/treebase-core/pom.xml 2009-11-04 16:54:08 UTC (rev 248)
+++ trunk/treebase-core/pom.xml 2009-11-04 17:04:34 UTC (rev 249)
@@ -1,323 +1,222 @@
-<project>
- <modelVersion>4.0.0</modelVersion>
- <groupId>org.cipres.treebase</groupId>
- <artifactId>treebase-core</artifactId>
- <packaging>jar</packaging>
- <version>1.0-SNAPSHOT</version>
- <name>Cipres-treebase-core</name>
- <url>http://www.phylo.org</url>
- <parent>
- <groupId>org.cipres.treebase</groupId>
- <artifactId>treebase</artifactId>
- <version>1.0-SNAPSHOT</version>
- </parent>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"> <modelVersion>4.0.0</modelVersion>
+ <groupId>org.cipres.treebase</groupId>
+ <artifactId>treebase-core</artifactId>
+ <packaging>jar</packaging>
+ <version>1.0-SNAPSHOT</version>
+ <name>treebase-core</name>
+ <url>https://sourceforge.net/projects/treebase/</url>
+ <parent>
+ <groupId>org.cipres.treebase</groupId>
+ <artifactId>treebase</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ </parent>
- <build>
- <defaultGoal>install</defaultGoal>
+ <build>
+ <defaultGoal>install</defaultGoal>
+ </build>
- <!-- the following doesn't work due to a bug in maven-install-plugin
- in the latest maven 2.0.4: Cannot override read-only parameter
- You'll need to install the following 2 cipres-dev jar files
- from the command line so treebase-core can compile.
- Refer to read.txt for more information. I leave the code
- here in case maven fixes its bug in a future realease -->
+ <repositories>
-<!--
- <plugins>
+ <repository>
+ <id>repository.jboss.org</id>
+ <name>JBoss Maven Repository</name>
+ <url>http://repository.jboss.org/maven2</url>
+ <layout>default</layout>
+ </repository>
- <plugin>
- <artifactId>maven-install-plugin</artifactId>
- <executions>
+ <repository>
+ <id>maven2</id>
+ <name>Default Maven2 Repository</name>
+ <url>http://repo1.maven.org/maven2</url>
+ </repository>
- <execution>
- <id>copy-cipres-framework-jar</id>
- <phase>install</phase>
- <configuration>
- <file>${env.CIPRES_ROOT}/lib/cipres/cipres_framework.jar</file>
- <groupId>org.cipres</groupId>
- <artifactId>framework</artifactId>
- <version>1.0.1</version>
- <packaging>jar</packaging>
- </configuration>
- <goals><goal>install</goal></goals>
- </execution>
+ <repository>
+ <id>m2.remote.repos</id>
+ <name>Maven 2 Remote Repository</name>
+ <url>http://treebase.sourceforge.net/maven2/</url>
+ </repository>
- <execution>
- <id>copy-cipres-cipresapp-jar</id>
- <phase>compile</phase>
- <configuration>
- <file>${env.CIPRES_ROOT}/lib/cipres/cipres_cipresapp.jar</file>
- <groupId>org.cipres</groupId>
- <artifactId>cipresapp</artifactId>
- <version>1.0.1</version>
- <packaging>jar</packaging>
- </configuration>
- <goals><goal>install</goal></goals>
- </execution>
- </executions>
- </plugin>
- </plugins>
--->
- </build>
+ <repository>
+ <id>m2.nexml.repos</id>
+ <name>NeXML Remote Repository</name>
+ <url>http://nexml-dev.nescent.org/.m2/repository/</url>
+ </repository>
-<!-- already defined in parent pom.xml -->
- <repositories>
- <repository>
- <id>m2.nexml.repos</id>
- <name>NeXML Remote Repository</name>
- <url>http://nexml-dev.nescent.org/.m2/repository/</url>
- </repository>
- <repository>
- <id>m2.remote.repos</id>
- <name>Maven 2 Remote Repository</name>
- <url>http://treebase.sourceforge.net/maven2/</url>
- </repository>
- <repository>
- <id>maven2</id>
- <name>Default Maven2 Repository</name>
- <url>http://repo1.maven.org/maven2</url>
- </repository>
- <repository>
- <id>repository.jboss.org</id>
- <name>JBoss Maven Repository</name>
- <url>http://repository.jboss.org/maven2</url>
- <layout>default</layout>
- </repository>
-
- </repositories>
-
+ </repositories>
+ <dependencies>
- <dependencies>
- <dependency>
- <groupId>org.acegisecurity</groupId>
- <artifactId>acegi-security</artifactId>
- <version>1.0.1</version>
- <exclusions>
- <!-- Maven thinks 2.0 is newer than 2.1-->
- <exclusion>
- <groupId>commons-lang</groupId>
- <artifactId>commons-lang</artifactId>
- </exclusion>
- <!-- exclude older versions of Spring -->
- <exclusion>
- <groupId>org.springframework</groupId>
- <artifactId>spring-remoting</artifactId>
- </exclusion>
- <exclusion>
- <groupId>org.springframework</groupId>
- <artifactId>spring-jdbc</artifactId>
- </exclusion>
- <exclusion>
- <groupId>org.springframework</groupId>
- <artifactId>spring-support</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
+ <dependency>
+ <groupId>org.acegisecurity</groupId>
+ <artifactId>acegi-security</artifactId>
+ <version>1.0.1</version>
+ <exclusions>
+ <!-- Maven thinks 2.0 is newer than 2.1-->
+ <exclusion>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ </exclusion>
+ <!-- exclude older versions of Spring -->
+ <exclusion>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-remoting</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-jdbc</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-support</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
- <dependency>
- <groupId>c3p0</groupId>
- <artifactId>c3p0</artifactId>
- <version>0.9.1.2</version>
- </dependency>
-
- <dependency>
- <groupId>org.nexml.model</groupId>
- <artifactId>nexml</artifactId>
- <version>1.5-SNAPSHOT</version>
- </dependency>
+ <dependency>
+ <groupId>c3p0</groupId>
+ <artifactId>c3p0</artifactId>
+ <version>0.9.1.2</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.nexml.model</groupId>
+ <artifactId>nexml</artifactId>
+ <version>1.5-SNAPSHOT</version>
+ </dependency>
- <dependency>
- <groupId>org.hibernate</groupId>
- <artifactId>hibernate-annotations</artifactId>
- <version>3.3.1.GA</version>
- <exclusions>
- <exclusion>
- <groupId>asm</groupId>
- <artifactId>asm</artifactId>
- </exclusion>
- <exclusion>
- <groupId>asm</groupId>
- <artifactId>asm-attrs</artifactId>
- </exclusion>
- <exclusion>
- <groupId>cglib</groupId>
- <artifactId>cglib</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
-
- <dependency>
- <groupId>cglib</groupId>
- <artifactId>cglib-nodep</artifactId>
- <version>2.1_3</version>
- </dependency>
+ <dependency>
+ <groupId>org.hibernate</groupId>
+ <artifactId>hibernate-annotations</artifactId>
+ <version>3.3.1.GA</version>
+ <exclusions>
+ <exclusion>
+ <groupId>asm</groupId>
+ <artifactId>asm</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>asm</groupId>
+ <artifactId>asm-attrs</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>cglib</groupId>
+ <artifactId>cglib</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
- <!--dependency> // defined in hibernate
- <groupId>javax.security</groupId>
- <artifactId>jacc</artifactId>
- <version>1.0</version>
- </dependency-->
-
- <!-- dependency>
- <groupId>javax.persistence</groupId>
- <artifactId>ejb</artifactId>
- <version>3.0-public-draft-20060327</version>
- </dependency-->
-
- <dependency>
- <groupId>commons-lang</groupId>
- <artifactId>commons-lang</artifactId>
- <version>2.1</version>
- </dependency>
+ <dependency>
+ <groupId>cglib</groupId>
+ <artifactId>cglib-nodep</artifactId>
+ <version>2.1_3</version>
+ </dependency>
-<!--
-we no longer use db2
- <dependency>
- <groupId>ibm</groupId>
- <artifactId>db2jcc</artifactId>
- <version>2.6.80</version>
- </dependency>
--->
- <dependency>
- <groupId>postgresql</groupId>
- <artifactId>postgresql</artifactId>
- <version>8.3-603.jdbc3</version>
- </dependency>
+ <dependency>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ <version>2.1</version>
+ </dependency>
+
+ <dependency>
+ <groupId>postgresql</groupId>
+ <artifactId>postgresql</artifactId>
+ <version>8.3-603.jdbc3</version>
+ </dependency>
+
+ <dependency>
+ <groupId>mesquite</groupId>
+ <artifactId>mesquite</artifactId>
+ <version>2.01.tb</version>
+ </dependency>
- <dependency>
- <groupId>mesquite</groupId>
- <artifactId>mesquite</artifactId>
- <version>2.01.tb</version>
- </dependency>
+ <dependency>
+ <groupId>org.cipres</groupId>
+ <artifactId>framework</artifactId>
+ <version>1.0.1</version>
+ <scope>compile</scope>
+ </dependency>
- <dependency>
- <groupId>org.cipres</groupId>
- <artifactId>framework</artifactId>
- <version>1.0.1</version>
- <scope>compile</scope>
- </dependency>
-
- <dependency>
- <groupId>jdom</groupId>
- <artifactId>jdom</artifactId>
- <version>1.1</version>
- </dependency>
-
- <dependency>
- <groupId>org.apache.cxf</groupId>
- <artifactId>cxf-rt-frontend-jaxws</artifactId>
- <version>2.1.1</version>
- <exclusions>
- <exclusion>
- <groupId>asm</groupId>
- <artifactId>asm</artifactId>
- </exclusion>
-
- <exclusion>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-jdk14</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
-
- <dependency>
- <groupId>org.apache.cxf</groupId>
- <artifactId>cxf-rt-transports-http</artifactId>
- <version>2.1.1</version>
- <exclusions>
- <exclusion>
- <groupId>asm</groupId>
- <artifactId>asm</artifactId>
- </exclusion>
-
- <exclusion>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-jdk14</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
-
- <dependency>
- <groupId>org.apache.cxf</groupId>
- <artifactId>cxf-rt-transports-http-jetty</artifactId>
- <version>2.1.1</version>
- <exclusions>
- <exclusion>
- <groupId>asm</groupId>
- <artifactId>asm</artifactId>
- </exclusion>
- <exclusion>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-jdk14</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
- <dependency>
- <groupId>dom4j</groupId>
- <artifactId>dom4j</artifactId>
- <version>1.6.1</version>
- </dependency>
+ <dependency>
+ <groupId>jdom</groupId>
+ <artifactId>jdom</artifactId>
+ <version>1.1</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.cxf</groupId>
+ <artifactId>cxf-rt-frontend-jaxws</artifactId>
+ <version>2.1.1</version>
+ <exclusions>
+ <exclusion>
+ <groupId>asm</groupId>
+ <artifactId>asm</artifactId>
+ </exclusion>
+
+ <exclusion>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-jdk14</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.cxf</groupId>
+ <artifactId>cxf-rt-transports-http</artifactId>
+ <version>2.1.1</version>
+ <exclusions>
+ <exclusion>
+ <groupId>asm</groupId>
+ <artifactId>asm</artifactId>
+ </exclusion>
+
+ <exclusion>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-jdk14</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.cxf</groupId>
+ <artifactId>cxf-rt-transports-http-jetty</artifactId>
+ <version>2.1.1</version>
+ <exclusions>
+ <exclusion>
+ <groupId>asm</groupId>
+ <artifactId>asm</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-jdk14</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
- <dependency>
- <groupId>javax.sql</groupId>
- <artifactId>jdbc-stdext</artifactId>
- <version>2.0</version>
- </dependency>
- <dependency>
- <groupId>ibm</groupId>
- <artifactId>db2jcc_license_cu</artifactId>
- <version>2.6.80</version>
- </dependency>
- <dependency>
- <groupId>ibm</groupId>
- <artifactId>db2jcc</artifactId>
- <version>2.6.80</version>
- </dependency>
-
- <!--dependency>
- <groupId>asm</groupId>
- <artifactId>asm-all</artifactId>
- <version>2.2.3</version>
- </dependency-->
-
- <!--dependency>
- <groupId>org.codehaus.xfire</groupId>
- <artifactId>xfire-spring</artifactId>
- <version>1.2.6</version>
- </dependency-->
-
- <!--dependency>
- <groupId>org.codehaus.xfire</groupId>
- <artifactId>xfire-jaxws</artifactId>
- <version>1.2.6</version>
- <This exclusions was inserted on April 23, 2008 Madhu>
- <Just to make sure that there is no XML parsing problem when was war file is created with maven>
- <exclusions>
- <exclusion>
- <groupId>com.sun.xml.bind</groupId>
- <artifactId>jaxb-xjc</artifactId>
- </exclusion>
- <exclusion>
- <groupId>xml-apis</groupId>
- <artifactId>xml-apis</artifactId>
- </exclusion>
- <exclusion>
- <groupId>xerces</groupId>
- <artifactId>xercesImpl</artifactId>
- </exclusion>
- </exclusions>
- </dependency-->
-
- <!-- dependency>
- <stax should be refered by xfire-core, but it does not work for some reason >
- <groupId>stax</groupId>
- <artifactId>stax</artifactId>
- <version>1.2.0</version>
- </dependency-->
-
-
-
- </dependencies>
+ <dependency>
+ <groupId>dom4j</groupId>
+ <artifactId>dom4j</artifactId>
+ <version>1.6.1</version>
+ </dependency>
+
+ <dependency>
+ <groupId>javax.sql</groupId>
+ <artifactId>jdbc-stdext</artifactId>
+ <version>2.0</version>
+ </dependency>
+
+ <dependency>
+ <groupId>ibm</groupId>
+ <artifactId>db2jcc_license_cu</artifactId>
+ <version>2.6.80</version>
+ </dependency>
+
+ <dependency>
+ <groupId>ibm</groupId>
+ <artifactId>db2jcc</artifactId>
+ <version>2.6.80</version>
+ </dependency>
+ </dependencies>
+
</project>
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2009-11-04 16:54:08 UTC (rev 248)
+++ trunk/treebase-web/pom.xml 2009-11-04 17:04:34 UTC (rev 249)
@@ -1,396 +1,312 @@
-<?xml version="1.0"?><project>
- <parent>
- <artifactId>treebase</artifactId>
- <groupId>org.cipres.treebase</groupId>
- <version>1.0-SNAPSHOT</version>
- </parent>
- <modelVersion>4.0.0</modelVersion>
- <groupId>org.cipres.treebase</groupId>
- <artifactId>treebase-web</artifactId>
- <packaging>war</packaging>
- <name>Cipres-treebase-web</name>
- <version>1.0-SNAPSHOT</version>
- <url>http://maven.apache.org</url>
- <build>
- <defaultGoal>install</defaultGoal>
- <resources>
- <resource>
- <directory>src/main/resources</directory>
- </resource>
- </resources>
- <finalName>treebase-web</finalName>
- <plugins>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <parent>
+ <artifactId>treebase</artifactId>
+ <groupId>org.cipres.treebase</groupId>
+ <version>1.0-SNAPSHOT</version>
+ </parent>
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.cipres.treebase</groupId>
+ <artifactId>treebase-web</artifactId>
+ <packaging>war</packaging>
+ <name>treebase-web</name>
+ <version>1.0-SNAPSHOT</version>
+ <url>http://maven.apache.org</url>
+ <build>
+ <defaultGoal>install</defaultGoal>
+ <resources>
+ <resource>
+ <directory>src/main/resources</directory>
+ </resource>
+ </resources>
+ <finalName>treebase-web</finalName>
+ <plugins>
- <!-- Ant Task plugin-->
- <plugin>
- <artifactId>maven-antrun-plugin</artifactId>
- <executions>
+ <!-- Ant Task plugin-->
+ <plugin>
+ <artifactId>maven-antrun-plugin</artifactId>
+ <executions>
+ <!-- make sure jdbc.properties is copied since it's not checked in -->
+ <execution>
+ <id>copy-jdbc-properties</id>
+ <phase>install</phase>
+ <configuration>
+ <tasks>
+ <copy todir="${basedir}/src/main/resources" failonerror="true"
+ verbose="true" overwrite="true">
+ <fileset dir="${env.JDBC_HOME}">
+ <include name="jdbc.properties" />
+ </fileset>
+ </copy>
+ </tasks>
+ </configuration>
+ <goals>
+ <goal>run</goal>
+ </goals>
+ </execution>
+
+ </executions>
+ </plugin>
+
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>tomcat-maven-plugin</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ </plugin>
+
+ </plugins>
+ </build>
+ <!-- already defined in parent pom.xml -->
+ <repositories>
+
+ <repository>
+ <id>maven2</id>
+ <name>Default Maven2 Repository</name>
+ <url>http://repo1.maven.org/maven2</url>
+ </repository>
+
+ <repository>
+ <id>m2.remote.repos</id>
+ <name>Maven 2 Remote Repository</name>
+ <url>http://treebase.sourceforge.net/maven2/</url>
+ </repository>
+
+ <repository>
+ <id>m2.nexml.repos</id>
+ <name>NeXML Remote Repository</name>
+ <url>http://nexml-dev.nescent.org/.m2/repository/</url>
+ </repository>
+
+ </repositories>
+
+ <pluginRepositories>
+ <pluginRepository>
+ <id>Maven Snapshots</id>
+ <url>http://snapshots.maven.codehaus.org/maven2</url>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ </pluginRepository>
+ </pluginRepositories>
+
+ <dependencies>
- <!-- make sure jdbc.properties is copied since it's not checked in -->
- <execution>
- <id>copy-jdbc-properties</id>
- <phase>install</phase>
- <configuration>
- <tasks>
- <copy todir="${basedir}/src/main/resources"
- failonerror="true" verbose="true" overwrite="true">
- <fileset dir="${env.JDBC_HOME}">
- <include name="jdbc.properties"/>
- </fileset>
- </copy>
- </tasks>
- </configuration>
- <goals><goal>run</goal></goals>
- </execution>
+ <dependency>
+ <groupId>org.nexml.model</groupId>
+ <artifactId>nexml</artifactId>
+ <version>1.5-SNAPSHOT</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.cipres.treebase</groupId>
+ <artifactId>treebase-core</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ </dependency>
- <!--
- <execution>
- <id>copy-cipres-dev-resources</id>
- <phase>install</phase>
- <configuration>
- <tasks>
- <copy todir="${basedir}/src/main/resources"
- failonerror="true" verbose="true" overwrite="true">
- <fileset dir="${env.CIPRES_ROOT}/resources">
- <include name="cipres_registry.xml"/>
- <include name="cipres_config.properties"/>
- </fileset>
- </copy>
- </tasks>
- </configuration>
- <goals><goal>run</goal></goals>
- </execution>
+ <dependency>
+ <groupId>javax.servlet</groupId>
+ <artifactId>servlet-api</artifactId>
+ <version>2.4</version>
+ </dependency>
- <execution>
- <id>copy-cipres-jar</id>
- <phase>install</phase>
- <configuration>
- <tasks>
- <copy todir="${project.build.directory}/treebase-web/WEB-INF/lib">
- <copy todir="${basedir}/src/main/webapp/WEB-INF/lib">
- failonerror="true" verbose="true" overwrite="true">
- <fileset dir="${env.CIPRES_ROOT}/lib/cipres">
- <include name="cipres_cipresapp.jar"/>
- <include name="cipres_framework.jar"/>
- <include name="classpath.jar"/>
- </fileset>
- <fileset dir="${env.CIPRES_ROOT}/lib/activation/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/axis/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/castor/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/commons-discovery/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/commons-logging/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/forester/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/jacorb/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/javahelp/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/jbcl/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/jcommon/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/jep/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/jfreechart/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/junit/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/log4j/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/pal/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/uddi4j/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/wsdl4j/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/xerces/jars" includes="*.jar"/>
- <fileset dir="${env.CIPRES_ROOT}/lib/xml-apis/jars" includes="*.jar"/>
- </copy>
- </tasks>
- </configuration>
- <goals><goal>run</goal></goals>
- </execution>
- -->
-
- </executions>
- </plugin>
+ <dependency>
+ <groupId>javax.servlet</groupId>
+ <artifactId>jstl</artifactId>
+ <version>1.1.2</version>
+ </dependency>
- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>tomcat-maven-plugin</artifactId>
- <version>1.0-SNAPSHOT</version>
- </plugin>
-
- </plugins>
- </build>
- <!-- already defined in parent pom.xml -->
- <repositories>
- <repository>
- <id>m2.nexml.repos</id>
- <name>NeXML Remote Repository</name>
- <url>http://nexml-dev.nescent.org/.m2/repository/</url>
- </repository>
- <repository>
- <id>m2.remote.repos</id>
- <name>Maven 2 Remote Repository</name>
- <url>http://treebase.sourceforge.net/maven2/</url>
- </repository>
- <repository>
- <id>maven2</id>
- <name>Default Maven2 Repository</name>
- <url>http://repo1.maven.org/maven2</url>
- </repository>
- </repositories>
+ <!-- used by Spring framework -->
+ <dependency>
+ <groupId>javax.mail</groupId>
+ <artifactId>mail</artifactId>
+ <version>1.4</version>
+ </dependency>
- <pluginRepositories>
- <pluginRepository>
- <id>Maven Snapshots</id>
- <url>http://snapshots.maven.codehaus.org/maven2</url>
- <snapshots><enabled>true</enabled></snapshots>
- <releases><enabled>false</enabled></releases>
- </pluginRepository>
- </pluginRepositories>
+ <!-- Jin 05/12/08: do we need xalan? dependency-->
+ <dependency>
+ <groupId>xalan</groupId>
+ <artifactId>xalan</artifactId>
+ <version>2.7.0</version>
+ </dependency>
- <dependencies>
-
- <dependency>
- <groupId>org.nexml.model</groupId>
- <artifactId>nexml</artifactId>
- <version>1.5-SNAPSHOT</version>
- </dependency>
-
- <dependency>
- <groupId>org.cipres.treebase</groupId>
- <artifactId>treebase-core</artifactId>
- <version>1.0-SNAPSHOT</version>
- </dependency>
+ <dependency>
+ <groupId>commons-beanutils</groupId>
+ <artifactId>commons-beanutils</artifactId>
+ <version>1.7.0</version>
+ </dependency>
- <dependency>
- <groupId>javax.servlet</groupId>
- <artifactId>servlet-api</artifactId>
- <version>2.4</version>
- </dependency>
+ <dependency>
+ <groupId>commons-validator</groupId>
+ <artifactId>commons-validator</artifactId>
+ <version>1.1.4</version>
+ </dependency>
- <dependency>
- <groupId>javax.servlet</groupId>
- <artifactId>jstl</artifactId>
- <version>1.1.2</version>
- </dependency>
+ <dependency>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ <version>1.1</version>
+ </dependency>
- <!-- used by Spring framework -->
- <!--Older ersion not needed-->
- <!-- Commented on April 23, 2008 Madhu-->
- <!--dependency>
- <groupId>javax.activation</groupId>
- <artifactId>activation</artifactId>
- <version>1.1</version>
- </dependency-->
+ <dependency>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ <version>2.3</version>
+ </dependency>
- <!-- used by Spring framework -->
- <dependency>
- <groupId>javax.mail</groupId>
- <artifactId>mail</artifactId>
- <version>1.4</version>
- </dependency>
-
- <!-- Jin 05/12/08: do we need xalan? dependency-->
- <dependency>
- <groupId>xalan</groupId>
- <artifactId>xalan</artifactId>
- <version>2.7.0</version>
- </dependency>
+ <dependency>
+ <groupId>taglibs</groupId>
+ <artifactId>standard</artifactId>
+ <version>1.1.2</version>
+ </dependency>
- <dependency>
- <groupId>commons-beanutils</groupId>
- <artifactId>commons-beanutils</artifactId>
- <version>1.7.0</version>
- </dependency>
-
-
- <dependency>
- <groupId>commons-validator</groupId>
- <artifactId>commons-validator</artifactId>
- <version>1.1.4</version>
- </dependency>
+ <dependency>
+ <groupId>taglibs</groupId>
+ <artifactId>string</artifactId>
+ <version>1.1.0</version>
+ </dependency>
- <dependency>
- <groupId>commons-logging</groupId>
- <artifactId>commons-logging</artifactId>
- <version>1.1</version>
- </dependency>
+ <dependency>
+ <groupId>struts</groupId>
+ <artifactId>struts</artifactId>
+ <version>1.2.9</version>
+ </dependency>
- <dependency>
- <groupId>commons-lang</groupId>
- <artifactId>commons-lang</artifactId>
- <version>2.3</version>
- </dependency>
+ <dependency>
+ <groupId>opensymphony</groupId>
+ <artifactId>sitemesh</artifactId>
+ <version>2.3</version>
+ </dependency>
- <dependency>
- <groupId>taglibs</groupId>
- <artifactId>standard</artifactId>
- <version>1.1.2</version>
- </dependency>
+ <dependency>
+ <groupId>displaytag</groupId>
+ <artifactId>displaytag</artifactId>
+ <version>1.1.1</version>
+ </dependency>
- <dependency>
- <groupId>taglibs</groupId>
- <artifactId>string</artifactId>
- <version>1.1.0</version>
- </dependency>
+ <dependency>
+ <groupId>struts-menu</groupId>
+ <artifactId>struts-menu</artifactId>
+ <version>2.3</version>
- <dependency>
- <groupId>struts</groupId>
- <artifactId>struts</artifactId>
- <version>1.2.9</version>
- </dependency>
+ <exclusions>
+ <!-- Older versions are not needed -->
+ <exclusion>
+ <groupId>taglibs</groupId>
+ <artifactId>string</artifactId>
+ </exclusion>
- <dependency>
- <groupId>opensymphony</groupId>
- <artifactId>sitemesh</artifactId>
- <version>2.3</version>
- </dependency>
+ <exclusion>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ </exclusion>
- <dependency>
- <groupId>displaytag</groupId>
- <artifactId>displaytag</artifactId>
- <version>1.1.1</version>
- </dependency>
+ <exclusion>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ </exclusion>
- <dependency>
- <groupId>struts-menu</groupId>
- <artifactId>struts-menu</artifactId>
- <version>2.3</version>
-
- <exclusions>
- <!-- Older versions are not needed -->
- <exclusion>
- <groupId>taglibs</groupId>
- <artifactId>string</artifactId>
- </exclusion>
-
-
- <exclusion>
- <groupId>commons-lang</groupId>
- <artifactId>commons-lang</artifactId>
- </exclusion>
-
- <exclusion>
- <groupId>commons-logging</groupId>
- <artifactId>commons-logging</artifactId>
- </exclusion>
-
- <exclusion>
- <groupId>javax.servlet</groupId>
- <artifactId>servlet-api</artifactId>
- </exclusion>
-
- <exclusion>
- <groupId>javax.servlet</groupId>
- <artifactId>jstl</artifactId>
- </exclusion>
-
- </exclusions>
-
-
- </dependency>
+ <exclusion>
+ <groupId>javax.servlet</groupId>
+ <artifactId>servlet-api</artifactId>
+ </exclusion>
- <dependency>
- <groupId>org.acegisecurity</groupId>
- <artifactId>acegi-security</artifactId>
- <version>1.0.1</version>
- <exclusions>
- <!-- exclude older versions of Spring -->
- <exclusion>
- <groupId>org.springframework</groupId>
- <artifactId>spring-remoting</artifactId>
- </exclusion>
- <exclusion>
- <groupId>org.springframework</groupId>
- <artifactId>spring-jdbc</artifactId>
- </exclusion>
- <exclusion>
- <groupId>org.springframework</groupId>
- <artifactId>spring-support</artifactId>
- </exclusion>
- <exclusion>
- <groupId>org.springframework</groupId>
- <artifactId>spring-mock</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
+ <exclusion>
+ <groupId>javax.servlet</groupId>
+ <artifactId>jstl</artifactId>
+ </exclusion>
- <dependency>
- <groupId>springmodules</groupId>
- <artifactId>springmodules-validator</artifactId>
- <version>0.1</version>
- </dependency>
-
-
- <dependency>
- <groupId>commons-fileupload</groupId>
- <artifactId>commons-fileupload</artifactId>
- <version>1.2</version>
-
- <exclusions>
- <exclusion>
- <groupId>javax.servlet</groupId>
- <artifactId>servlet-api</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
-
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <version>1.3</version>
- </dependency>
-
-
- <dependency>
- <groupId>org.directwebremoting</groupId>
- <artifactId>dwr</artifactId>
- <version>2.0.rc2</version>
- <exclusions>
- <exclusion>
- <groupId>org.springframework</groupId>
- <artifactId>spring</artifactId>
- </exclusion>
- <exclusion>
- <groupId>org.hibernate</groupId>
- <artifactId>hibernate</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
-
- <dependency>
- <groupId>jmock</groupId>
- <artifactId>jmock</artifactId>
- <version>1.0.1</version>
- </dependency>
-
- <!-- remove 05/13/08 to avoid xml parser conflicts>
- <dependency>
- <groupId>org.springframework.ws</groupId>
- <artifactId>spring-ws-core</artifactId>
- <version>1.0.2</version>
- </dependency>
- -->
-
- <!-- remove 05/13/08 to avoid xml parser conflicts.>
- <dependency>
- <groupId>jaxen</groupId>
- <artifactId>jaxen</artifactId>
- <version>1.1</version>
- </dependency>
- -->
-
- <dependency>
- <groupId>javax.xml.soap</groupId>
- <artifactId>saaj-api</artifactId>
- <version>1.3</version>
- <scope>runtime</scope>
- </dependency>
- <dependency>
- <groupId>zing.z3950.org</groupId>
- <artifactId>cql-java</artifactId>
- <version>1.0</version>
- </dependency>
+ </exclusions>
- <!--commented on April 23, 2008 Madhu-->
- <!--dependency>
- <groupId>com.sun.xml.messaging.saaj</groupId>
- <artifactId>saaj-impl</artifactId>
- <version>1.3</version>
- <scope>runtime</scope>
- </dependency-->
-
+ </dependency>
- </dependencies>
+ <dependency>
+ <groupId>org.acegisecurity</groupId>
+ <artifactId>acegi-security</artifactId>
+ <version>1.0.1</version>
+ <exclusions>
+ <!-- exclude older versions of Spring -->
+ <exclusion>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-remoting</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-jdbc</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-support</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-mock</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+
+ <dependency>
+ <groupId>springmodules</groupId>
+ <artifactId>springmodules-validator</artifactId>
+ <version>0.1</version>
+ </dependency>
+
+ <dependency>
+ <groupId>commons-fileupload</groupId>
+ <artifactId>commons-fileupload</artifactId>
+ <version>1.2</version>
+
+ <exclusions>
+ <exclusion>
+ <groupId>javax.servlet</groupId>
+ <artifactId>servlet-api</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>1.3</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.directwebremoting</groupId>
+ <artifactId>dwr</artifactId>
+ <version>2.0.rc2</version>
+ <exclusions>
+ <exclusion>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>org.hibernate</groupId>
+ <artifactId>hibernate</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+
+ <dependency>
+ <groupId>jmock</groupId>
+ <artifactId>jmock</artifactId>
+ <version>1.0.1</version>
+ </dependency>
+
+ <dependency>
+ <groupId>javax.xml.soap</groupId>
+ <artifactId>saaj-api</artifactId>
+ <version>1.3</version>
+ <scope>runtime</scope>
+ </dependency>
+
+ <dependency>
+ <groupId>zing.z3950.org</groupId>
+ <artifactId>cql-java</artifactId>
+ <version>1.0</version>
+ </dependency>
+
+ </dependencies>
</project>
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