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From: <yo...@us...> - 2009-10-12 23:12:26
|
Revision: 192
http://treebase.svn.sourceforge.net/treebase/?rev=192&view=rev
Author: youjun
Date: 2009-10-12 23:12:11 +0000 (Mon, 12 Oct 2009)
Log Message:
-----------
oai_pmh data_provider
Added Paths:
-----------
trunk/data_provider/
trunk/data_provider/.classpath
trunk/data_provider/.project
trunk/data_provider/.settings/
trunk/data_provider/.settings/org.eclipse.jdt.core.prefs
trunk/data_provider/.settings/org.maven.ide.eclipse.prefs
trunk/data_provider/data_provider_core/
trunk/data_provider/data_provider_core/.classpath
trunk/data_provider/data_provider_core/.project
trunk/data_provider/data_provider_core/.settings/
trunk/data_provider/data_provider_core/.settings/org.eclipse.jdt.core.prefs
trunk/data_provider/data_provider_core/.settings/org.eclipse.wst.common.component
trunk/data_provider/data_provider_core/.settings/org.eclipse.wst.common.project.facet.core.xml
trunk/data_provider/data_provider_core/.settings/org.maven.ide.eclipse.prefs
trunk/data_provider/data_provider_core/pom.xml
trunk/data_provider/data_provider_core/src/
trunk/data_provider/data_provider_core/src/main/
trunk/data_provider/data_provider_core/src/main/java/
trunk/data_provider/data_provider_core/src/main/java/META-INF/
trunk/data_provider/data_provider_core/src/main/java/META-INF/MANIFEST.MF
trunk/data_provider/data_provider_core/src/main/java/org/
trunk/data_provider/data_provider_core/src/main/java/org/treebase/
trunk/data_provider/data_provider_core/src/main/java/org/treebase/oai/
trunk/data_provider/data_provider_core/src/main/java/org/treebase/oai/App.java
trunk/data_provider/data_provider_core/src/main/resources/
trunk/data_provider/data_provider_core/src/test/
trunk/data_provider/data_provider_core/src/test/java/
trunk/data_provider/data_provider_core/src/test/java/org/
trunk/data_provider/data_provider_core/src/test/java/org/treebase/
trunk/data_provider/data_provider_core/src/test/java/org/treebase/oai/
trunk/data_provider/data_provider_core/src/test/java/org/treebase/oai/AppTest.java
trunk/data_provider/data_provider_core/src/test/resources/
trunk/data_provider/data_provider_core/target/
trunk/data_provider/data_provider_core/target/classes/
trunk/data_provider/data_provider_core/target/classes/META-INF/
trunk/data_provider/data_provider_core/target/classes/META-INF/MANIFEST.MF
trunk/data_provider/data_provider_core/target/classes/org/
trunk/data_provider/data_provider_core/target/classes/org/treebase/
trunk/data_provider/data_provider_core/target/classes/org/treebase/oai/
trunk/data_provider/data_provider_core/target/classes/org/treebase/oai/App.class
trunk/data_provider/data_provider_core/target/test-classes/
trunk/data_provider/data_provider_core/target/test-classes/org/
trunk/data_provider/data_provider_core/target/test-classes/org/treebase/
trunk/data_provider/data_provider_core/target/test-classes/org/treebase/oai/
trunk/data_provider/data_provider_core/target/test-classes/org/treebase/oai/AppTest.class
trunk/data_provider/data_provider_web/
trunk/data_provider/data_provider_web/.classpath
trunk/data_provider/data_provider_web/.project
trunk/data_provider/data_provider_web/.settings/
trunk/data_provider/data_provider_web/.settings/.jsdtscope
trunk/data_provider/data_provider_web/.settings/org.eclipse.jdt.core.prefs
trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.component
trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.project.facet.core.xml
trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.jsdt.ui.superType.container
trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.jsdt.ui.superType.name
trunk/data_provider/data_provider_web/.settings/org.maven.ide.eclipse.prefs
trunk/data_provider/data_provider_web/pom.xml
trunk/data_provider/data_provider_web/src/
trunk/data_provider/data_provider_web/src/main/
trunk/data_provider/data_provider_web/src/main/java/
trunk/data_provider/data_provider_web/src/main/resources/
trunk/data_provider/data_provider_web/src/main/webapp/
trunk/data_provider/data_provider_web/src/main/webapp/META-INF/
trunk/data_provider/data_provider_web/src/main/webapp/META-INF/MANIFEST.MF
trunk/data_provider/data_provider_web/src/main/webapp/WEB-INF/
trunk/data_provider/data_provider_web/src/main/webapp/WEB-INF/lib/
trunk/data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml
trunk/data_provider/data_provider_web/src/main/webapp/index.jsp
trunk/data_provider/data_provider_web/src/test/
trunk/data_provider/data_provider_web/src/test/java/
trunk/data_provider/data_provider_web/src/test/resources/
trunk/data_provider/data_provider_web/target/
trunk/data_provider/data_provider_web/target/classes/
trunk/data_provider/data_provider_web/target/test-classes/
trunk/data_provider/pom.xml
trunk/data_provider/target/
trunk/data_provider/target/classes/
trunk/data_provider/target/classes/org/
trunk/data_provider/target/classes/org/treebase/
trunk/data_provider/target/classes/org/treebase/oai/
trunk/data_provider/target/classes/org/treebase/oai/data_provider/
trunk/data_provider/target/classes/org/treebase/oai/data_provider/App.class
trunk/data_provider/target/test-classes/
trunk/data_provider/target/test-classes/org/
trunk/data_provider/target/test-classes/org/treebase/
trunk/data_provider/target/test-classes/org/treebase/oai/
trunk/data_provider/target/test-classes/org/treebase/oai/data_provider/
trunk/data_provider/target/test-classes/org/treebase/oai/data_provider/AppTest.class
Added: trunk/data_provider/.classpath
===================================================================
--- trunk/data_provider/.classpath (rev 0)
+++ trunk/data_provider/.classpath 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <classpathentry kind="con" path="org.maven.ide.eclipse.MAVEN2_CLASSPATH_CONTAINER"/>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
Added: trunk/data_provider/.project
===================================================================
--- trunk/data_provider/.project (rev 0)
+++ trunk/data_provider/.project 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>data_provider</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.maven.ide.eclipse.maven2Builder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ <nature>org.maven.ide.eclipse.maven2Nature</nature>
+ </natures>
+</projectDescription>
Added: trunk/data_provider/.settings/org.eclipse.jdt.core.prefs
===================================================================
--- trunk/data_provider/.settings/org.eclipse.jdt.core.prefs (rev 0)
+++ trunk/data_provider/.settings/org.eclipse.jdt.core.prefs 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,5 @@
+#Mon Oct 12 12:48:37 EDT 2009
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.2
+org.eclipse.jdt.core.compiler.compliance=1.4
+org.eclipse.jdt.core.compiler.source=1.3
Added: trunk/data_provider/.settings/org.maven.ide.eclipse.prefs
===================================================================
--- trunk/data_provider/.settings/org.maven.ide.eclipse.prefs (rev 0)
+++ trunk/data_provider/.settings/org.maven.ide.eclipse.prefs 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,9 @@
+#Mon Oct 12 12:48:36 EDT 2009
+activeProfiles=
+eclipse.preferences.version=1
+fullBuildGoals=process-test-resources
+includeModules=false
+resolveWorkspaceProjects=true
+resourceFilterGoals=process-resources resources\:testResources
+skipCompilerPlugin=true
+version=1
Added: trunk/data_provider/data_provider_core/.classpath
===================================================================
--- trunk/data_provider/data_provider_core/.classpath (rev 0)
+++ trunk/data_provider/data_provider_core/.classpath 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" output="target/classes" path="src/main/java"/>
+ <classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
+ <classpathentry kind="src" path="src/main/resources"/>
+ <classpathentry kind="src" path="src/test/resources"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <classpathentry kind="con" path="org.maven.ide.eclipse.MAVEN2_CLASSPATH_CONTAINER"/>
+ <classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.module.container"/>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
Added: trunk/data_provider/data_provider_core/.project
===================================================================
--- trunk/data_provider/data_provider_core/.project (rev 0)
+++ trunk/data_provider/data_provider_core/.project 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>data_provider_core</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.wst.common.project.facet.core.builder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.maven.ide.eclipse.maven2Builder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.wst.validation.validationbuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
+ <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ <nature>org.maven.ide.eclipse.maven2Nature</nature>
+ <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
+ </natures>
+</projectDescription>
Added: trunk/data_provider/data_provider_core/.settings/org.eclipse.jdt.core.prefs
===================================================================
--- trunk/data_provider/data_provider_core/.settings/org.eclipse.jdt.core.prefs (rev 0)
+++ trunk/data_provider/data_provider_core/.settings/org.eclipse.jdt.core.prefs 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,7 @@
+#Mon Oct 12 16:25:16 EDT 2009
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.2
+org.eclipse.jdt.core.compiler.compliance=1.4
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=warning
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=warning
+org.eclipse.jdt.core.compiler.source=1.3
Added: trunk/data_provider/data_provider_core/.settings/org.eclipse.wst.common.component
===================================================================
--- trunk/data_provider/data_provider_core/.settings/org.eclipse.wst.common.component (rev 0)
+++ trunk/data_provider/data_provider_core/.settings/org.eclipse.wst.common.component 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project-modules id="moduleCoreId" project-version="1.5.0">
+ <wb-module deploy-name="data_provider_core">
+ <wb-resource deploy-path="/" source-path="/src/main/java"/>
+ <wb-resource deploy-path="/" source-path="/src/main/resource"/>
+ <wb-resource deploy-path="/" source-path="/src/test/resources"/>
+ <wb-resource deploy-path="/" source-path="/src/main/resources"/>
+ </wb-module>
+</project-modules>
Added: trunk/data_provider/data_provider_core/.settings/org.eclipse.wst.common.project.facet.core.xml
===================================================================
--- trunk/data_provider/data_provider_core/.settings/org.eclipse.wst.common.project.facet.core.xml (rev 0)
+++ trunk/data_provider/data_provider_core/.settings/org.eclipse.wst.common.project.facet.core.xml 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<faceted-project>
+ <installed facet="jst.java" version="1.4"/>
+ <installed facet="jst.utility" version="1.0"/>
+</faceted-project>
Added: trunk/data_provider/data_provider_core/.settings/org.maven.ide.eclipse.prefs
===================================================================
--- trunk/data_provider/data_provider_core/.settings/org.maven.ide.eclipse.prefs (rev 0)
+++ trunk/data_provider/data_provider_core/.settings/org.maven.ide.eclipse.prefs 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,9 @@
+#Mon Oct 12 12:55:06 EDT 2009
+activeProfiles=
+eclipse.preferences.version=1
+fullBuildGoals=process-test-resources
+includeModules=false
+resolveWorkspaceProjects=true
+resourceFilterGoals=process-resources resources\:testResources
+skipCompilerPlugin=true
+version=1
Added: trunk/data_provider/data_provider_core/pom.xml
===================================================================
--- trunk/data_provider/data_provider_core/pom.xml (rev 0)
+++ trunk/data_provider/data_provider_core/pom.xml 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,164 @@
+<?xml version="1.0" encoding="UTF-8"?><project>
+ <parent>
+ <artifactId>data_provider</artifactId>
+ <groupId>org.treebase.oai</groupId>
+ <version>0.0.1-SNAPSHOT</version>
+ </parent>
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.treebase.oai</groupId>
+ <artifactId>data_provider_core</artifactId>
+ <packaging>jar</packaging>
+ <name>data_provider_core</name>
+ <version>0.0.1-SNAPSHOT</version>
+ <url>http://maven.apache.org</url>
+
+ <build>
+ <defaultGoal>install</defaultGoal>
+ </build>
+
+ <dependencies>
+
+ <dependency>
+ <groupId>postgresql</groupId>
+ <artifactId>postgresql</artifactId>
+ <version>8.3-603.jdbc3</version>
+ </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.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>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ <version>2.1</version>
+ </dependency>
+
+ <dependency>
+ <groupId>ibm</groupId>
+ <artifactId>db2jcc</artifactId>
+ <version>2.6.80</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>dom4j</groupId>
+ <artifactId>dom4j</artifactId>
+ <version>1.6.1</version>
+ </dependency>
+
+ </dependencies>
+
+</project>
\ No newline at end of file
Added: trunk/data_provider/data_provider_core/src/main/java/META-INF/MANIFEST.MF
===================================================================
--- trunk/data_provider/data_provider_core/src/main/java/META-INF/MANIFEST.MF (rev 0)
+++ trunk/data_provider/data_provider_core/src/main/java/META-INF/MANIFEST.MF 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+Class-Path:
+
Added: trunk/data_provider/data_provider_core/src/main/java/org/treebase/oai/App.java
===================================================================
--- trunk/data_provider/data_provider_core/src/main/java/org/treebase/oai/App.java (rev 0)
+++ trunk/data_provider/data_provider_core/src/main/java/org/treebase/oai/App.java 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,13 @@
+package org.treebase.oai;
+
+/**
+ * Hello world!
+ *
+ */
+public class App
+{
+ public static void main( String[] args )
+ {
+ System.out.println( "Hello World!" );
+ }
+}
Added: trunk/data_provider/data_provider_core/src/test/java/org/treebase/oai/AppTest.java
===================================================================
--- trunk/data_provider/data_provider_core/src/test/java/org/treebase/oai/AppTest.java (rev 0)
+++ trunk/data_provider/data_provider_core/src/test/java/org/treebase/oai/AppTest.java 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,38 @@
+package org.treebase.oai;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+/**
+ * Unit test for simple App.
+ */
+public class AppTest
+ extends TestCase
+{
+ /**
+ * Create the test case
+ *
+ * @param testName name of the test case
+ */
+ public AppTest( String testName )
+ {
+ super( testName );
+ }
+
+ /**
+ * @return the suite of tests being tested
+ */
+ public static Test suite()
+ {
+ return new TestSuite( AppTest.class );
+ }
+
+ /**
+ * Rigourous Test :-)
+ */
+ public void testApp()
+ {
+ assertTrue( true );
+ }
+}
Added: trunk/data_provider/data_provider_core/target/classes/META-INF/MANIFEST.MF
===================================================================
--- trunk/data_provider/data_provider_core/target/classes/META-INF/MANIFEST.MF (rev 0)
+++ trunk/data_provider/data_provider_core/target/classes/META-INF/MANIFEST.MF 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+Class-Path:
+
Added: trunk/data_provider/data_provider_core/target/classes/org/treebase/oai/App.class
===================================================================
(Binary files differ)
Property changes on: trunk/data_provider/data_provider_core/target/classes/org/treebase/oai/App.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/data_provider/data_provider_core/target/test-classes/org/treebase/oai/AppTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/data_provider/data_provider_core/target/test-classes/org/treebase/oai/AppTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/data_provider/data_provider_web/.classpath
===================================================================
--- trunk/data_provider/data_provider_web/.classpath (rev 0)
+++ trunk/data_provider/data_provider_web/.classpath 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
+ <classpathentry kind="src" path="src/main/java"/>
+ <classpathentry kind="src" path="src/test/java"/>
+ <classpathentry kind="src" path="src/test/resources"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <classpathentry kind="con" path="org.maven.ide.eclipse.MAVEN2_CLASSPATH_CONTAINER">
+ <attributes>
+ <attribute name="org.eclipse.jst.component.dependency" value="/WEB-INF/lib"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.web.container"/>
+ <classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.module.container"/>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
Added: trunk/data_provider/data_provider_web/.project
===================================================================
--- trunk/data_provider/data_provider_web/.project (rev 0)
+++ trunk/data_provider/data_provider_web/.project 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,42 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>data_provider_web</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.wst.jsdt.core.javascriptValidator</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.wst.common.project.facet.core.builder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.wst.validation.validationbuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.maven.ide.eclipse.maven2Builder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
+ <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ <nature>org.maven.ide.eclipse.maven2Nature</nature>
+ <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
+ <nature>org.eclipse.wst.jsdt.core.jsNature</nature>
+ </natures>
+</projectDescription>
Added: trunk/data_provider/data_provider_web/.settings/.jsdtscope
===================================================================
--- trunk/data_provider/data_provider_web/.settings/.jsdtscope (rev 0)
+++ trunk/data_provider/data_provider_web/.settings/.jsdtscope 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.JRE_CONTAINER"/>
+ <classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.WebProject">
+ <attributes>
+ <attribute name="hide" value="true"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.baseBrowserLibrary"/>
+ <classpathentry kind="output" path=""/>
+</classpath>
Added: trunk/data_provider/data_provider_web/.settings/org.eclipse.jdt.core.prefs
===================================================================
--- trunk/data_provider/data_provider_web/.settings/org.eclipse.jdt.core.prefs (rev 0)
+++ trunk/data_provider/data_provider_web/.settings/org.eclipse.jdt.core.prefs 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,7 @@
+#Mon Oct 12 12:59:49 EDT 2009
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.2
+org.eclipse.jdt.core.compiler.compliance=1.4
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=warning
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=warning
+org.eclipse.jdt.core.compiler.source=1.3
Added: trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.component
===================================================================
--- trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.component (rev 0)
+++ trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.component 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project-modules id="moduleCoreId" project-version="1.5.0">
+ <wb-module deploy-name="data_provider_web">
+ <wb-resource deploy-path="/" source-path="/src/main/webapp"/>
+ <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/resources"/>
+ <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
+ <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/test/java"/>
+ <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/test/resources"/>
+ <dependent-module deploy-path="/WEB-INF/lib" handle="module:/resource/data_provider_core/data_provider_core">
+ <dependency-type>uses</dependency-type>
+ </dependent-module>
+ <property name="context-root" value="data_provider_web"/>
+ <property name="java-output-path"/>
+ </wb-module>
+</project-modules>
Added: trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.project.facet.core.xml
===================================================================
--- trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.project.facet.core.xml (rev 0)
+++ trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.common.project.facet.core.xml 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<faceted-project>
+ <installed facet="jst.java" version="1.4"/>
+ <installed facet="jst.web" version="2.3"/>
+</faceted-project>
Added: trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.jsdt.ui.superType.container
===================================================================
--- trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.jsdt.ui.superType.container (rev 0)
+++ trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.jsdt.ui.superType.container 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1 @@
+org.eclipse.wst.jsdt.launching.baseBrowserLibrary
\ No newline at end of file
Added: trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.jsdt.ui.superType.name
===================================================================
--- trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.jsdt.ui.superType.name (rev 0)
+++ trunk/data_provider/data_provider_web/.settings/org.eclipse.wst.jsdt.ui.superType.name 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1 @@
+Window
\ No newline at end of file
Added: trunk/data_provider/data_provider_web/.settings/org.maven.ide.eclipse.prefs
===================================================================
--- trunk/data_provider/data_provider_web/.settings/org.maven.ide.eclipse.prefs (rev 0)
+++ trunk/data_provider/data_provider_web/.settings/org.maven.ide.eclipse.prefs 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,9 @@
+#Mon Oct 12 12:59:49 EDT 2009
+activeProfiles=
+eclipse.preferences.version=1
+fullBuildGoals=process-test-resources
+includeModules=false
+resolveWorkspaceProjects=true
+resourceFilterGoals=process-resources resources\:testResources
+skipCompilerPlugin=true
+version=1
Added: trunk/data_provider/data_provider_web/pom.xml
===================================================================
--- trunk/data_provider/data_provider_web/pom.xml (rev 0)
+++ trunk/data_provider/data_provider_web/pom.xml 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,299 @@
+<?xml version="1.0" encoding="UTF-8"?><project>
+ <parent>
+ <artifactId>data_provider</artifactId>
+ <groupId>org.treebase.oai</groupId>
+ <version>0.0.1-SNAPSHOT</version>
+ </parent>
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.treebase.oai</groupId>
+ <artifactId>data_provider_web</artifactId>
+ <packaging>war</packaging>
+ <name>data_provider_web Maven Webapp</name>
+ <version>0.0.1-SNAPSHOT</version>
+ <url>http://maven.apache.org</url>
+ <build>
+ <defaultGoal>install</defaultGoal>
+ <resources>
+ <resource>
+ <directory>src/main/resources</directory>
+ </resource>
+ </resources>
+ <finalName>data_provider_web</finalName>
+ <plugins>
+
+ <!-- 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>
+
+ <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>
+
+ <dependency>
+ <groupId>org.treebase.oai</groupId>
+ <artifactId>data_provider_core</artifactId>
+ <version>0.0.1-SNAPSHOT</version>
+ </dependency>
+
+ <dependency>
+ <groupId>javax.servlet</groupId>
+ <artifactId>jstl</artifactId>
+ <version>1.1.2</version>
+ </dependency>
+ <dependency>
+ <groupId>javax.mail</groupId>
+ <artifactId>mail</artifactId>
+ <version>1.4</version>
+ </dependency>
+ <dependency>
+ <groupId>xalan</groupId>
+ <artifactId>xalan</artifactId>
+ <version>2.7.0</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>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ <version>1.1</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ <version>2.3</version>
+ </dependency>
+ <dependency>
+ <groupId>taglibs</groupId>
+ <artifactId>standard</artifactId>
+ <version>1.1.2</version>
+ </dependency>
+ <dependency>
+ <groupId>taglibs</groupId>
+ <artifactId>string</artifactId>
+ <version>1.1.0</version>
+ </dependency>
+ <dependency>
+ <groupId>struts</groupId>
+ <artifactId>struts</artifactId>
+ <version>1.2.9</version>
+ </dependency>
+ <dependency>
+ <groupId>opensymphony</groupId>
+ <artifactId>sitemesh</artifactId>
+ <version>2.3</version>
+ </dependency>
+ <dependency>
+ <groupId>displaytag</groupId>
+ <artifactId>displaytag</artifactId>
+ <version>1.1.1</version>
+ </dependency>
+ <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>
+ <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>
+ <dependency>
+ <groupId>javax.servlet</groupId>
+ <artifactId>servlet-api</artifactId>
+ <version>2.4</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-->
+
+ <!-- used by Spring framework -->
+
+ <!-- Jin 05/12/08: do we need xalan? 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>
+ -->
+
+ <!--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-->
+
+
+ </dependencies>
+ <dependencyManagement>
+ <dependencies>
+ </dependencies>
+ </dependencyManagement>
+
+</project>
\ No newline at end of file
Added: trunk/data_provider/data_provider_web/src/main/webapp/META-INF/MANIFEST.MF
===================================================================
--- trunk/data_provider/data_provider_web/src/main/webapp/META-INF/MANIFEST.MF (rev 0)
+++ trunk/data_provider/data_provider_web/src/main/webapp/META-INF/MANIFEST.MF 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+Class-Path:
+
Added: trunk/data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml (rev 0)
+++ trunk/data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,7 @@
+<!DOCTYPE web-app PUBLIC
+ "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN"
+ "http://java.sun.com/dtd/web-app_2_3.dtd" >
+
+<web-app>
+ <display-name>Archetype Created Web Application</display-name>
+</web-app>
Added: trunk/data_provider/data_provider_web/src/main/webapp/index.jsp
===================================================================
--- trunk/data_provider/data_provider_web/src/main/webapp/index.jsp (rev 0)
+++ trunk/data_provider/data_provider_web/src/main/webapp/index.jsp 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,5 @@
+<html>
+<body>
+<h2>Hello World!</h2>
+</body>
+</html>
Added: trunk/data_provider/pom.xml
===================================================================
--- trunk/data_provider/pom.xml (rev 0)
+++ trunk/data_provider/pom.xml 2009-10-12 23:12:11 UTC (rev 192)
@@ -0,0 +1,271 @@
+<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.treebase.oai</groupId>
+ <artifactId>data_provider</artifactId>
+ <packaging>pom</packaging>
+ <version>0.0.1-SNAPSHOT</version>
+ <name>data_provider</name>
+ <url>http://maven.apache.org</url>
+ <!-- issueManagement>
+ <system>FogBugz</system>
+ <url>https://www.xxx.org/bugz</url>
+ </issueManagement-->
+ <!-- inceptionYear></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>
+ </scm-->
+ <!-- mailingLists>
+ <mailingList>
+ <name>treebase-dev</name>
+ <subscribe></subscribe>
+ <unsubscribe></unsubscribe>
+ <archive></archive>
+ </mailingList>
+ </mailingLists -->
+ <developers>
+ <developer>
+ <id>youjun</id>
+ <name>Youjun Guo</name>
+ <email>you...@ya...</email>
+ <organization>Peabody.Yale</organization>
+ <organizationUrl>http://www.yale.edu</organizationUrl>
+ <roles>
+ <role>developer</role>
+ </roles>
+ <timezone>-7</timezone>
+ </developer>
+ </developers>
+ <licenses>
+ <license>
+ <name></name>
+ <url></url>
+ <distribution></distribution>
+ <comments/>
+ </license>
+ </licenses>
+ <modules>
+ <module>data_provider_core</module>
+ <module>data_provider_web</module>
+ </modules>
+<pluginRepositories>
+ </pluginRepositories>
+ <dependencies>
+
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring</artifactId>
+ <version>2.0.7</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-mock</artifactId>
+ <version>2.0.7</version>
+ <scope>test</scope>
+ </dependency>
+
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>3.8.1</version>
+ <scope>test</scope>
+ </dependency>
+
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ <version>1.2.13</version>
+ </dependency>
+
+ </dependencies>
+
+ <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>
+ <configuration>
+ <tags>
+ <tag>TODO</tag>
+ <tag>@todo</tag>
+ <tag>FIXME</tag>
+ <tag>XXX</tag>
+ </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.treebase.oai</groupId>
+ <artifactId>data_provider_core</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.treebase.oai</groupId>
+ <artifactId>data_provider_web</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+ </dependencyManagement>
+
+ <organization>
+ <name></name>
+ <url></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://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>
+ <repository>
+ <id>postgresql</id>
+ <url>http://jdbc.postgresql.org</url>
+ </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>
+ <configuration>
+ <source>1.5</source>
+ <target>1.5</target>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <distributionManagement>
+ <site>
+ <id>website</id>
+ <url></url>
+ </site>
+ </distributionManagement>
+
+ <profiles>
+
+ <!--profile>
+ <id>xxx</id>
+ <activation>
+ <property>
+ <name>enablexxxprofile</name>
+ <value>true</value>
+ </property>
+ </activation>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-pmd-plugin</artifactId>
+ <executions>
+ <execution>
+ <goals>
+ <goal>check</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>cobertura-maven-plugin</artifactId>
+ <configuration>
+ <check>
+ <totalLineRate>80</totalLineRate>
+ <totalBranchRate>100</totalBranchRate>
+ </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-->
+
+ </profiles>
+</project>
Added: trunk/data_provider/target/classes/org/treebase/oai/data_provider/App.class
===================================================================
(Binary files differ)
Property changes on: trunk/data_provider/target/classes/org/treebase/oai/data_provider/App.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/data_provider/target/test-classes/org/treebase/oai/data_provider/AppTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/data_provider/target/test-classes/org/treebase/oai/data_provider/AppTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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From: <sfr...@us...> - 2009-10-02 19:52:39
|
Revision: 191
http://treebase.svn.sourceforge.net/treebase/?rev=191&view=rev
Author: sfrgpiel
Date: 2009-10-02 19:52:32 +0000 (Fri, 02 Oct 2009)
Log Message:
-----------
Added folder for S2493
Added Paths:
-----------
trunk/treebase-curation/S2493/
trunk/treebase-curation/S2493/127-tax cpDNA A
trunk/treebase-curation/S2493/127-tax cpDNA B
trunk/treebase-curation/S2493/127-taxon, combined cpDNA
trunk/treebase-curation/S2493/50-tax cpDNA-nrDNA A
trunk/treebase-curation/S2493/50-tax cpDNA-nrDNA B
trunk/treebase-curation/S2493/50-taxon, combined cpDNA:nrDNA
trunk/treebase-curation/S2493/Appendix 1.doc
trunk/treebase-curation/S2493/Readme
Added: trunk/treebase-curation/S2493/127-tax cpDNA A
===================================================================
--- trunk/treebase-curation/S2493/127-tax cpDNA A (rev 0)
+++ trunk/treebase-curation/S2493/127-tax cpDNA A 2009-10-02 19:52:32 UTC (rev 191)
@@ -0,0 +1,294 @@
@@ Diff output truncated at 100000 characters. @@
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From: <rsc...@us...> - 2009-10-02 13:13:54
|
Revision: 190
http://treebase.svn.sourceforge.net/treebase/?rev=190&view=rev
Author: rscherle
Date: 2009-10-02 13:13:38 +0000 (Fri, 02 Oct 2009)
Log Message:
-----------
updated citations from curation work
Modified Paths:
--------------
trunk/treebase-curation/studyCitations.enl
Modified: trunk/treebase-curation/studyCitations.enl
===================================================================
(Binary files differ)
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From: <rsc...@us...> - 2009-10-02 13:12:24
|
Revision: 189
http://treebase.svn.sourceforge.net/treebase/?rev=189&view=rev
Author: rscherle
Date: 2009-10-02 13:12:17 +0000 (Fri, 02 Oct 2009)
Log Message:
-----------
initial Endnote citations (from TreeBASE January 2009)
Added Paths:
-----------
trunk/treebase-curation/
trunk/treebase-curation/studyCitations.enl
Added: trunk/treebase-curation/studyCitations.enl
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-curation/studyCitations.enl
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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From: SourceForge.net <no...@so...> - 2009-09-30 17:51:35
|
Bugs item #2870903, was opened at 2009-09-30 13:51 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2870903&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 9 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Cannot get Matrix Row List to work Initial Comment: Requesting a Matrix Row List, e.g.: http://8ball.sdsc.edu:6666/treebase-web/user/matrixRowList.html?id=1495 generates an uncaught exception. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2870903&group_id=248804 |
|
From: <rv...@us...> - 2009-09-26 08:25:51
|
Revision: 188
http://treebase.svn.sourceforge.net/treebase/?rev=188&view=rev
Author: rvos
Date: 2009-09-26 08:25:44 +0000 (Sat, 26 Sep 2009)
Log Message:
-----------
Updated JDBC driver dependency configuration
Modified Paths:
--------------
trunk/treebase-core/pom.xml
Modified: trunk/treebase-core/pom.xml
===================================================================
--- trunk/treebase-core/pom.xml 2009-09-26 04:41:53 UTC (rev 187)
+++ trunk/treebase-core/pom.xml 2009-09-26 08:25:44 UTC (rev 188)
@@ -171,11 +171,19 @@
<version>2.1</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.jdbc4</version>
+ </dependency>
<dependency>
<groupId>mesquite</groupId>
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From: <rv...@us...> - 2009-09-26 04:42:01
|
Revision: 187
http://treebase.svn.sourceforge.net/treebase/?rev=187&view=rev
Author: rvos
Date: 2009-09-26 04:41:53 +0000 (Sat, 26 Sep 2009)
Log Message:
-----------
Debugging perly login methods
Modified Paths:
--------------
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/DBIUtil.pm
Modified: trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/DBIUtil.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/DBIUtil.pm 2009-09-26 04:04:53 UTC (rev 186)
+++ trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/DBIUtil.pm 2009-09-26 04:41:53 UTC (rev 187)
@@ -16,7 +16,6 @@
my $user = $opts{user} || $login_info_class->user;
my $pass = $opts{pass} || $login_info_class->pass;
my $dsn = $opts{dsn} ? sprintf $opts{dsn}, $user, $pass : $login_info_class->dsn($user, $pass);
-
my $h = DBI->connect($dsn);
$h->{private_cipres_treebase_dbiutil_username} = $user if $h;
return $h;
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From: <rv...@us...> - 2009-09-26 04:05:08
|
Revision: 186
http://treebase.svn.sourceforge.net/treebase/?rev=186&view=rev
Author: rvos
Date: 2009-09-26 04:04:53 +0000 (Sat, 26 Sep 2009)
Log Message:
-----------
Made publish scrip more portable w.r.t. source location, using TREEBASE_HOME env var
Modified Paths:
--------------
trunk/treebase-core/src/main/perl/misc/publish
Modified: trunk/treebase-core/src/main/perl/misc/publish
===================================================================
--- trunk/treebase-core/src/main/perl/misc/publish 2009-09-12 17:38:56 UTC (rev 185)
+++ trunk/treebase-core/src/main/perl/misc/publish 2009-09-26 04:04:53 UTC (rev 186)
@@ -26,11 +26,11 @@
fi
TOMCAT_URL=http://8ball.sdsc.edu:6666/treebase-web/
-VERSIONFILE=treebase-core/src/main/java/org/cipres/treebase/Version.java
+VERSIONFILE=${TREEBASE_HOME}/treebase-core/src/main/java/org/cipres/treebase/Version.java
# Rebuild the application WAR file, if requested
if $update_sources; then
- cd $HOME/treebase/trunk || die "cd treebase/trunk";
+ cd $TREEBASE_HOME || die "cd $TREEBASE_HOME";
rm -f $VERSIONFILE
svn update || die
# mvn clean || die
@@ -43,7 +43,7 @@
perl -i -lpe 'BEGIN { while ($ARGV[0] =~ /=/) {my($k,$v) = split /=/, shift(), 2; $prop{$k} = $v } } s/##(\w+)##/$prop{$1}/g' "VCSID=$svnrevision" "VCSDATESTRING=$svndatestring" $VERSIONFILE
- touch treebase-web/src/main/webapp/common/footer.jsp
+ touch ${TREEBASE_HOME}/treebase-web/src/main/webapp/common/footer.jsp
mvn install -Dmaven.test.skip=true
fi
@@ -58,7 +58,7 @@
# and move the new warfile into place
if $update_sources; then
cd $WEBAPPS && rm -rf $TARGET_DIR && rm -f treebase-web.war
- if cp -v warLocation/treebase-web.war . ; then
+ if cp -v ${TREEBASE_HOME}/treebase-web/target/treebase-web.war . ; then
:
else
die "Installation failed: no WAR file"
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From: SourceForge.net <no...@so...> - 2009-09-19 16:20:52
|
Bugs item #2862220, was opened at 2009-09-19 11:20 Message generated for change (Tracker Item Submitted) made by rscherle You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2862220&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 3 Private: No Submitted By: Ryan Scherle (rscherle) Assigned to: Nobody/Anonymous (nobody) Summary: license files Initial Comment: The source contains many symbolic links named LICENSE.txt. The actual LICENSE.txt file referenced by the links is no longer present. Should there be a LICENSE.txt file, or should the links be removed? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2862220&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2009-09-19 14:00:32
|
Bugs item #2861595, was opened at 2009-09-18 14:01 Message generated for change (Comment added) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2861595&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 5 Private: No Submitted By: Ryan Scherle (rscherle) Assigned to: Nobody/Anonymous (nobody) Summary: matrices cannot be viewed Initial Comment: When I click on the ID for a matrix, or any of the download icons, I receive an error from Hibernate. ---------------------------------------------------------------------- >Comment By: William Piel (sfrgpiel) Date: 2009-09-19 10:00 Message: This seems to be related to PhyloWS. If you try to download a matrix from the search tabs, it works. e.g: http://8ball.sdsc.edu:6666/treebase-web/search/downloadAMatrix.html?id=1282&matrixid=2855 But if you try to download the very same matrix after tunneling through the study, the method used is not with PhyloWS, and the result throws and uncaught exception: http://8ball.sdsc.edu:6666/treebase-web/phylows/matrix/TB2:M2855?format=nexus ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2861595&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2009-09-18 18:01:46
|
Bugs item #2861595, was opened at 2009-09-18 13:01 Message generated for change (Tracker Item Submitted) made by rscherle You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2861595&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 5 Private: No Submitted By: Ryan Scherle (rscherle) Assigned to: Nobody/Anonymous (nobody) Summary: matrices cannot be viewed Initial Comment: When I click on the ID for a matrix, or any of the download icons, I receive an error from Hibernate. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2861595&group_id=248804 |
|
From: <rv...@us...> - 2009-09-12 17:39:03
|
Revision: 185
http://treebase.svn.sourceforge.net/treebase/?rev=185&view=rev
Author: rvos
Date: 2009-09-12 17:38:56 +0000 (Sat, 12 Sep 2009)
Log Message:
-----------
The maven2 pom.xml files now point to the new repository at http://treebase.sourceforge.net/maven2/
Modified Paths:
--------------
trunk/treebase-core/pom.xml
trunk/treebase-web/pom.xml
Modified: trunk/treebase-core/pom.xml
===================================================================
--- trunk/treebase-core/pom.xml 2009-08-14 17:58:49 UTC (rev 184)
+++ trunk/treebase-core/pom.xml 2009-09-12 17:38:56 UTC (rev 185)
@@ -70,7 +70,7 @@
<repository>
<id>m2.remote.repos</id>
<name>Maven 2 Remote Repository</name>
- <url>http://8ball.sdsc.edu:9999/maven2</url>
+ <url>http://treebase.sourceforge.net/maven2/</url>
</repository>
<repository>
<id>maven2</id>
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2009-08-14 17:58:49 UTC (rev 184)
+++ trunk/treebase-web/pom.xml 2009-09-12 17:38:56 UTC (rev 185)
@@ -121,7 +121,7 @@
<repository>
<id>m2.remote.repos</id>
<name>Maven 2 Remote Repository</name>
- <url>http://8ball.sdsc.edu:9999/maven2</url>
+ <url>http://treebase.sourceforge.net/maven2/</url>
</repository>
<repository>
<id>maven2</id>
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From: SourceForge.net <no...@so...> - 2009-09-11 13:16:09
|
Bugs item #2856832, was opened at 2009-09-11 08:16 Message generated for change (Tracker Item Submitted) made by rscherle You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2856832&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Ryan Scherle (rscherle) Assigned to: Nobody/Anonymous (nobody) Summary: Session status error report Initial Comment: This morning, when I tried to go to the search page, I received an error message. I'm guessing this was caused because my session is timed out and/or I have a different IP address than yesterday. Regardless, the stack trace that is displayed is not helpful for end-users (see attached screen shot). It should be replaced with a real error message. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2856832&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2009-09-10 16:59:33
|
Bugs item #2856183, was opened at 2009-09-10 11:59 Message generated for change (Tracker Item Submitted) made by rscherle You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2856183&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Ryan Scherle (rscherle) Assigned to: Nobody/Anonymous (nobody) Summary: long legacy IDs are not searchable Initial Comment: Legacy study IDs that are more complex cannot be found via searches. For example, S2x4x96c13c48c42 cannot be found, even though it is listed as a legacy ID on the page for S200. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2856183&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2009-09-08 23:07:57
|
Bugs item #2854768, was opened at 2009-09-08 19:07 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854768&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Editors and Administrators Cannot Edit Ready Submissions Initial Comment: When an Associate Editor or Administrator is examining a submission with the status of "Ready", the submission should be editable to the Associate Editor or Administrator but not to the User. Currently, it is editable by nobody, except that an Associate Editor or Administrator can toggle it to "Published" status. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854768&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2009-09-08 23:06:50
|
Bugs item #2854767, was opened at 2009-09-08 19:06 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854767&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Associate Editors can Delete or Edit other Officers Initial Comment: "Associate Editors" should not have the power to delete or edit "Administrators" or other "Associate Editors", but currently they do. This needs correcting. Note that they do have the power to Update User Info, Merge Users, and Merge Persons so long as none of these are Associate Editors or Administrators. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854767&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2009-09-08 23:03:15
|
Bugs item #2854613, was opened at 2009-09-08 16:11 Message generated for change (Comment added) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854613&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 9 Private: No Submitted By: Ryan Scherle (rscherle) Assigned to: Nobody/Anonymous (nobody) Summary: right-hand menu missing Initial Comment: When I try to create a new submission, or edit an existing submission, the menu on the right does not appear, and I cannot complete the submission. ---------------------------------------------------------------------- >Comment By: William Piel (sfrgpiel) Date: 2009-09-08 19:03 Message: Just to be clear: this is an issue that affects Associate Editors -- I think it's okay for normal users and Administrators. Definitely needs fixing, though. ---------------------------------------------------------------------- Comment By: Ryan Scherle (rscherle) Date: 2009-09-08 16:14 Message: I tested this with several different browsers, and two different user accounts. ---------------------------------------------------------------------- Comment By: Ryan Scherle (rscherle) Date: 2009-09-08 16:13 Message: (see attached screenshot) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854613&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2009-09-08 20:14:09
|
Bugs item #2854613, was opened at 2009-09-08 15:11 Message generated for change (Comment added) made by rscherle You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854613&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 9 Private: No Submitted By: Ryan Scherle (rscherle) Assigned to: Nobody/Anonymous (nobody) Summary: right-hand menu missing Initial Comment: When I try to create a new submission, or edit an existing submission, the menu on the right does not appear, and I cannot complete the submission. ---------------------------------------------------------------------- >Comment By: Ryan Scherle (rscherle) Date: 2009-09-08 15:14 Message: I tested this with several different browsers, and two different user accounts. ---------------------------------------------------------------------- Comment By: Ryan Scherle (rscherle) Date: 2009-09-08 15:13 Message: (see attached screenshot) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854613&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2009-09-08 20:13:04
|
Bugs item #2854613, was opened at 2009-09-08 15:11 Message generated for change (Comment added) made by rscherle You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854613&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 9 Private: No Submitted By: Ryan Scherle (rscherle) Assigned to: Nobody/Anonymous (nobody) Summary: right-hand menu missing Initial Comment: When I try to create a new submission, or edit an existing submission, the menu on the right does not appear, and I cannot complete the submission. ---------------------------------------------------------------------- >Comment By: Ryan Scherle (rscherle) Date: 2009-09-08 15:13 Message: (see attached screenshot) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854613&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2009-09-08 20:12:33
|
Bugs item #2854613, was opened at 2009-09-08 15:11 Message generated for change (Settings changed) made by rscherle You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854613&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open >Priority: 9 Private: No Submitted By: Ryan Scherle (rscherle) Assigned to: Nobody/Anonymous (nobody) Summary: right-hand menu missing Initial Comment: When I try to create a new submission, or edit an existing submission, the menu on the right does not appear, and I cannot complete the submission. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854613&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2009-09-08 20:11:46
|
Bugs item #2854613, was opened at 2009-09-08 15:11 Message generated for change (Tracker Item Submitted) made by rscherle You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854613&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 5 Private: No Submitted By: Ryan Scherle (rscherle) Assigned to: Nobody/Anonymous (nobody) Summary: right-hand menu missing Initial Comment: When I try to create a new submission, or edit an existing submission, the menu on the right does not appear, and I cannot complete the submission. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2854613&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2009-08-28 20:06:39
|
Bugs item #2846456, was opened at 2009-08-28 15:28 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2846456&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: data Group: None Status: Open Priority: 6 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Mark Dominus (mjdominus) Summary: Need PhyloWS API search by date-time-stamp Initial Comment: We need to be sure that our API can search using data-time-stamps. i.e. "find all studies that were modified since Jan 23, 2010." (and separately, "find all studies that were made public after Jan 23, 2010"). This may require investigating how and where TreeBASE2 is currently tracking modification stamps. If it does not do so yet, we should probably add modification stamp fields on some key tables -- and it's probably easier to do this with a postgresql-level trigger or part of the schema. At any rate, any of the following modifications should stamped and searchable by the API: modifications to the citation, matrix metadata (including row-segment additions/subtractions), tree metadata (including re-rooting a tree), taxon labels, and mapping between taxon labels and taxon variants, and mapping between taxon variants and taxa. i.e., if a study contains a matrix for which a taxon label gets re-mapped to a different taxon variant or taxon at time/date x, then the whole study should be considered changed at time/date x. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2846456&group_id=248804 |
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From: <mjd...@us...> - 2009-08-14 17:59:48
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Revision: 184
http://treebase.svn.sourceforge.net/treebase/?rev=184&view=rev
Author: mjdominus
Date: 2009-08-14 17:58:49 +0000 (Fri, 14 Aug 2009)
Log Message:
-----------
perl utility to load dump files into psql
Added Paths:
-----------
trunk/treebase-core/src/main/perl/bin/undump
Added: trunk/treebase-core/src/main/perl/bin/undump
===================================================================
--- trunk/treebase-core/src/main/perl/bin/undump (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/undump 2009-08-14 17:58:49 UTC (rev 184)
@@ -0,0 +1,92 @@
+#!/usr/bin/perl
+# preprocess DB2 dump files for importation into pg via psql command
+#
+
+use Getopt::Std;
+my $commit_batch_size;
+my @pending; # records read but not written out
+getopts('xdn:', \%opt) or usage();
+$commit_batch_size ||= $opt{n};
+
+my $BEGIN = "BEGIN TRANSACTION;\n";
+$BEGIN .= "SET CONSTAINTS ALL DEFERRED;\n" if $opt{d};
+
+my $OK = 1;
+
+TABLE:
+for my $table (@ARGV) {
+ if (-e $table) {
+ my $FH;
+ unless (open($FH, "<", $table) ) {
+ warn "Couldn't open file '$table': $!; skipping\n";
+ $OK = 0;
+ next TABLE;
+ }
+ do_table($table, $FH);
+ } elsif (-e "$table.gz") {
+ my $fh = IO::Zlib->new;
+ unless ($fh->open("$table.gz", "rb")) {
+ warn "Couldn't open file '$table.gz': $!; skipping\n";
+ $OK = 0;
+ next TABLE;
+ }
+ do_table($table, $fh);
+ } else {
+ warn "Couldn't find dump file for table '$table'; skipping\n";
+ $OK = 0;
+ }
+}
+
+sub do_table {
+ my ($table, $fh) = @_;
+ my ($start, $length);
+ local *_;
+ local *.;
+
+ while (<$fh>) {
+ if ($. == 1) {
+ /INSERT INTO \"/ or die "unparseable";
+ $start = $+[0] - 1;
+ substr($_, $start) =~ /(.*\)) VALUES \(/ or die "unparseable";
+ $length = $+[1];
+ die unless defined($start) && defined($length);
+ }
+
+
+ substr($_, $start, $length) =~ s/"(\w+?)"/"\L$1\E"/g;
+
+ if (defined($commit_batch_size)) {
+ push @pending, $_;
+ if (@pending >= $commit_batch_size) {
+ print "BEGIN TRANSACTION;\n", @pending, "COMMIT;\n";
+ @pending = ();
+ }
+ } else {
+ print;
+ }
+ if ($opt{x}) {
+ warn "$.\n" if $. % 10_000 == 0;
+ }
+ }
+
+# possibly a final partial batch
+ if (@pending) {
+ print "BEGIN TRANSACTION;\n", @pending, "COMMIT;\n";
+ @pending = ();
+ }
+
+ close $fh;
+}
+
+################################################################
+
+sub usage {
+ print STDERR qq{Usage: $0 [-dx] [-n batchsize] TABLE...
+ -d defer constraint checking to the end of each transaction
+ -x print progress information to stderr
+ -n batchsize commit records in batches of /batchsize/
+
+ records for TABLE are read from file TABLE or from TABLE.gz
+};
+ exit 1;
+}
Property changes on: trunk/treebase-core/src/main/perl/bin/undump
___________________________________________________________________
Added: svn:executable
+ *
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From: <mjd...@us...> - 2009-07-29 19:21:33
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Revision: 182
http://treebase.svn.sourceforge.net/treebase/?rev=182&view=rev
Author: mjdominus
Date: 2009-07-29 19:01:17 +0000 (Wed, 29 Jul 2009)
Log Message:
-----------
another file that was not carried over from the old respoitory
Added Paths:
-----------
trunk/treebase-core/src/main/resources/initTreebase.sql
Added: trunk/treebase-core/src/main/resources/initTreebase.sql
===================================================================
--- trunk/treebase-core/src/main/resources/initTreebase.sql (rev 0)
+++ trunk/treebase-core/src/main/resources/initTreebase.sql 2009-07-29 19:01:17 UTC (rev 182)
@@ -0,0 +1,292 @@
+delete from citationStatus;
+insert into citationStatus(citationstatus_id, version, description) values
+(1, 1, 'In Prep'),
+(2, 1, 'In Review'),
+(3, 1, 'Accepted with Minor Changes'),
+(4, 1, 'In Press'),
+(5, 1, 'Published');
+--alter table citationstatus alter column citationstatus_id restart with 6;
+commit;
+
+delete from gapMode;
+insert into gapMode(gapMode_id, VERSION, Description) values
+(1, 1, 'Missing'),
+(2, 1, 'NewState');
+--alter table gapMode alter column gapMode_id restart with 3;
+commit;
+
+delete from itemDefinition;
+insert into itemDefinition(itemDefinition_id, VERSION, Description) values
+(1, 1, 'Min'),
+(2, 1, 'Max'),
+(3, 1, 'Median'),
+(4, 1, 'Avg'),
+(5, 1, 'Variance'),
+(6, 1, 'StdError'),
+(7, 1, 'SampleSize'),
+(8, 1, 'States');
+
+alter table itemDefinition alter column itemDefinition_id restart with 9;
+commit;
+
+delete from PolyTCount;
+insert into PolyTCount(polyTCount_id, VERSION, Description) values
+(1, 1, 'MinSteps'),
+(2, 1, 'MaxSteps');
+--alter table polyTCount alter column polyTCount_id restart with 3;
+commit;
+
+delete from stateFormat;
+insert into stateFormat(stateFormat_id, VERSION, Description) values
+(1, 1, 'Count'),
+(2, 1, 'Frequency'),
+(3, 1, 'StatePresent'),
+(4, 1, 'Individuals');
+--alter table stateformat alter column stateformat_id restart with 5;
+commit;
+
+delete from treekind;
+INSERT INTO TREEKIND(TREEKIND_ID, VERSION, DESCRIPTION) values
+(1, 1, 'Species Tree'),
+(2, 1, 'Gene Tree'),
+(3, 1, 'Language Tree'),
+(4, 1, 'Area Tree'),
+(5, 1, 'Barcode Tree'),
+(6, 1, 'Object Classification Tree');
+alter table treekind alter column treekind_id restart with 7;
+commit;
+
+delete from treetype;
+INSERT INTO TREETYPE(TREETYPE_ID, VERSION, DESCRIPTION) values
+(1, 1, 'Single'),
+(2, 1, 'Consensus'),
+(3, 1, 'SuperTree');
+alter table treetype alter column treetype_id restart with 4;
+commit;
+
+delete from treequality;
+INSERT INTO TREEQUALITY(TREEQUALITY_ID, VERSION, DESCRIPTION) values
+(1, 1, 'Unrated'),
+(2, 1, 'Preferred Tree'),
+(3, 1, 'Alternative Tree'),
+(4, 1, 'Suboptimal Tree');
+alter table treequality alter column treequality_id restart with 5;
+commit;
+
+delete from matrixkind;
+INSERT INTO MATRIXKIND(MATRIXKIND_ID, VERSION, DESCRIPTION) values
+(1, 1, 'Unspecified'),
+(2, 1, 'Allozyme'),
+(3, 1, 'Amino Acid'),
+(4, 1, 'Behavior'),
+(5, 1, 'Combination'),
+(6, 1, 'Karyotype'),
+(7, 1, 'Matrix Representation'),
+(8, 1, 'Morphological'),
+(9, 1, 'Nucleic Acid'),
+(10, 1, 'Restriction Site'),
+(11, 1, 'Secondary Chemistry');
+alter table matrixkind alter column matrixkind_id restart with 12;
+commit;
+
+-- DiscreteCharState and MatrixDataType depend on PhyloChar, so we must handle them together
+--
+-- If you update the PHYLOCHAR section, be sure to adjust
+-- org.cipres.treebase.Constants.MIN_INTERESTING_PHYLOCHAR_ID
+-- also. 20090317 MJD
+--
+-- BEGIN DiscreteCharState, MatrixDataTpe, and PhyloChar
+delete from DiscreteCharState;
+delete from MatrixDataType;
+delete from phylochar;
+insert into phylochar (TYPE, PHYLOCHAR_ID, VERSION, DESCRIPTION) values
+('D', 1, 1, 'Standard'),
+('D', 2, 1, 'DNA'),
+('D', 3, 1, 'RNA'),
+('D', 4, 1, 'Nucleotide'),
+('D', 5, 1, 'Protein');
+--('C', 6, 1, 'Continuous');
+-- 1:Standard, 2:DNA, 3:RNA, 4:Nucleotide, 5:Protein, 6:Continuous
+
+
+alter table phylochar alter column phylochar_id restart with 7;
+commit;
+
+insert into MatrixDataType (MatrixDataType_ID, Version, PhyloChar_ID, Description) values
+(1, 1, null, 'Standard'),
+(2, 1, 2, 'DNA'),
+(3, 1, 3, 'RNA'),
+(4, 1, 4, 'Nucleotide'),
+(5, 1, 5, 'Protein'),
+(6, 1, null, 'Continuous'),
+(7, 1, null, 'Distance');
+alter table MatrixDataType alter column MatrixDataType_id restart with 10;
+commit;
+
+-- DNA symbols
+insert into DiscreteCharState (DiscreteCharState_ID, Version, Description, PhyloChar_ID, StateSet_ID, AncestralState_ID) values
+(1, 1, 'A', 2, null, null),
+(2, 1, 'C', 2, null, null),
+(3, 1, 'G', 2, null, null),
+(4, 1, 'T', 2, null, null),
+(5, 1, '?', 2, null, null),
+(6, 1, 'R', 2, null, null),
+(7, 1, 'Y', 2, null, null),
+(8, 1, 'M', 2, null, null),
+(9, 1, 'K', 2, null, null),
+(10, 1, 'S', 2, null, null),
+(11, 1, 'W', 2, null, null),
+(12, 1, 'H', 2, null, null),
+(13, 1, 'B', 2, null, null),
+(14, 1, 'V', 2, null, null),
+(15, 1, 'D', 2, null, null),
+(16, 1, 'N', 2, null, null);
+commit;
+
+-- RNA symbols
+insert into DiscreteCharState (DiscreteCharState_ID, Version, Description, PhyloChar_ID, StateSet_ID, AncestralState_ID) values
+(21, 1, 'A', 3, null, null),
+(22, 1, 'C', 3, null, null),
+(23, 1, 'G', 3, null, null),
+(24, 1, 'U', 3, null, null),
+(25, 1, '?', 3, null, null),
+(26, 1, 'R', 3, null, null),
+(27, 1, 'Y', 3, null, null),
+(28, 1, 'M', 3, null, null),
+(29, 1, 'K', 3, null, null),
+(30, 1, 'S', 3, null, null),
+(31, 1, 'W', 3, null, null),
+(32, 1, 'H', 3, null, null),
+(33, 1, 'B', 3, null, null),
+(34, 1, 'V', 3, null, null),
+(35, 1, 'D', 3, null, null),
+(36, 1, 'N', 3, null, null);
+commit;
+
+-- Nucleotide symbols
+insert into DiscreteCharState (DiscreteCharState_ID, Version, Description, PhyloChar_ID, StateSet_ID, AncestralState_ID) values
+(41, 1, 'A', 4, null, null),
+(42, 1, 'C', 4, null, null),
+(43, 1, 'G', 4, null, null),
+(44, 1, 'T', 4, null, null),
+(45, 1, 'U', 4, null, null),
+(46, 1, '?', 4, null, null),
+(47, 1, 'R', 4, null, null),
+(48, 1, 'Y', 4, null, null),
+(49, 1, 'M', 4, null, null),
+(50, 1, 'K', 4, null, null),
+(51, 1, 'S', 4, null, null),
+(52, 1, 'W', 4, null, null),
+(53, 1, 'H', 4, null, null),
+(54, 1, 'B', 4, null, null),
+(55, 1, 'V', 4, null, null),
+(56, 1, 'D', 4, null, null),
+(57, 1, 'N', 4, null, null);
+commit;
+
+-- protein symbols
+insert into DiscreteCharState (DiscreteCharState_ID, Version, Description, PhyloChar_ID, StateSet_ID, AncestralState_ID) values
+(81, 1, 'A', 5, null, null),
+(82, 1, 'C', 5, null, null),
+(83, 1, 'D', 5, null, null),
+(84, 1, 'E', 5, null, null),
+(85, 1, 'F', 5, null, null),
+(86, 1, 'G', 5, null, null),
+(87, 1, 'H', 5, null, null),
+(88, 1, 'I', 5, null, null),
+(89, 1, 'K', 5, null, null),
+(90, 1, 'L', 5, null, null),
+(91, 1, 'M', 5, null, null),
+(92, 1, 'N', 5, null, null),
+(93, 1, 'P', 5, null, null),
+(94, 1, 'Q', 5, null, null),
+(95, 1, 'R', 5, null, null),
+(96, 1, 'S', 5, null, null),
+(97, 1, 'T', 5, null, null),
+(98, 1, 'V', 5, null, null),
+(99, 1, 'W', 5, null, null),
+(100, 1, 'Y', 5, null, null),
+(101, 1, '*', 5, null, null),
+(102, 1, '?', 5, null, null),
+(103, 1, 'X', 5, null, null),
+(104, 1, 'B', 5, null, null),
+(105, 1, 'Z', 5, null, null);
+
+alter table discretecharstate alter column Discretecharstate_id restart with 120;
+commit;
+
+UPDATE DISCRETECHARSTATE SET SYMBOL=DESCRIPTION
+ WHERE length(DESCRIPTION) = 1;
+commit;
+-- END DiscreteCharState, MatrixDataTpe, and PhyloChar
+
+-- Submission depends on User, which depends on Person, which depends
+-- on userRole, so we handle them together
+-- BEGIN Person, Submission, User, UserRole
+-- Add base users and people
+delete from submission;
+delete from user;
+delete from person;
+delete from userRole;
+insert into userRole(userRole_id, VERSION, AUTHORITY) values
+ (1, 1, 'Admin'),
+ (2, 1, 'User'),
+ (3, 1, 'Associate Editor');
+
+alter table userrole alter column userrole_id restart with 5;
+
+INSERT INTO PERSON(PERSON_ID, VERSION, LASTNAME, FIRSTNAME, MNAME, PHONE, EMAIL, AUTHORID)
+ VALUES
+ (0, 0, 'TESTUSER','TIMOTHY', 'T.', '', 'wil...@ya...', ''),
+ (1, 0, 'Piel', 'William', 'H.', '+1 203 716 907 3538', 'wil...@ya...', ''),
+ (2, 0, 'Dominus', 'Mark', 'Jason', '+1 215 573 5387', 'mj...@ge...', ''),
+ (3, 0, 'Tannen', 'Val', '', '', 'va...@ci...', ''),
+ (4, 0, 'Vos', 'Rutger', 'A.', '', 'rut...@gm...', '');
+ (5, 0, 'TB 1 importation suite', '', '', '', '', '');
+alter table person alter column person_id restart with 6;
+
+INSERT INTO USER(USER_ID, VERSION, USERNAME, PASSWORD, USERROLE_ID, PERSON_ID)
+ VALUES
+ (1, 0, 'piel', '*', 2, 1),
+ (2, 0, 'mjd', '*', 1, 2),
+ (3, 0, 'val', '*', 2, 3),
+ (4, 0, 'rvosa','*', 1, 4),
+ (5, 0, 'tb1importer','*', 3, 5),
+ (11, 0, 't1', '*', 1, 0),
+ (12, 0, 't2', '*', 2, 0),
+ (13, 0, 't3', '*', 3, 0);
+alter table user alter column user_id restart with 100;
+
+commit;
+-- END Person, User, UserRole
+
+
+-- Study depends on StudyStatus, so we handle them together
+-- BEGIN Study, StudyStatus, Submission
+delete from study;
+delete from studyStatus;
+insert into studyStatus(studystatus_id, version, description) values
+(1, 1, 'In Progress'),
+(2, 1, 'Ready'),
+(3, 1, 'Published');
+--alter table studystatus alter column studystatus_id restart with 4;
+commit;
+
+-- Create initial submission amd study
+INSERT INTO STUDY(STUDY_ID, VERSION, NOTES, ACCESSIONNUMBER, RELEASEDATE, NAME, CITATION_ID, STUDYSTATUS_ID, TB_STUDYID)
+ VALUES(1, 0, 'Mesquite parser test only', '1', current date, 'MesquiteTestStudy', null, 1, null);
+INSERT INTO SUBMISSION(SUBMISSION_ID, VERSION, SUBMISSIONNUMBER, CREATEDATE, STUDY_ID, USER_ID, TEST)
+ VALUES(1, 0, '1', current date, 1, 1, 1);
+
+alter table submission alter column submission_id restart with 2;
+alter table study alter column study_id restart with 2;
+commit;
+-- END Study, StudyStatus, Submission
+
+-- Add indices
+--CREATE INDEX "TREENODE_TREE_IDX"
+-- ON "PHYLOTREENODE"("PHYLOTREE_ID")
+-- CLUSTER
+-- PCTFREE 10
+-- MINPCTUSED 10;
+--commit;
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|
From: <mjd...@us...> - 2009-07-29 19:21:04
|
Revision: 183
http://treebase.svn.sourceforge.net/treebase/?rev=183&view=rev
Author: mjdominus
Date: 2009-07-29 19:03:36 +0000 (Wed, 29 Jul 2009)
Log Message:
-----------
quote name of USER table in Hibernate SQL commands
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/User.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/User.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/User.java 2009-07-29 19:01:17 UTC (rev 182)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/admin/User.java 2009-07-29 19:03:36 UTC (rev 183)
@@ -55,7 +55,7 @@
*
*/
@Entity
-@Table(name = "USER")
+@Table(name = "`user`")
@AttributeOverride(name = "id", column = @Column(name = "USER_ID"))
@Cache(usage = CacheConcurrencyStrategy.READ_WRITE, region = "adminCache")
public class User extends AbstractPersistedObject implements UserDetails {
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