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From: <yo...@us...> - 2009-11-04 14:50:38
|
Revision: 239
http://treebase.svn.sourceforge.net/treebase/?rev=239&view=rev
Author: youjun
Date: 2009-11-04 14:50:28 +0000 (Wed, 04 Nov 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/.classpath
trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.jdt.core.prefs
trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.component
trunk/oai-pmh_data_provider/data_provider_web/pom.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/applicationContext.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/web.xml
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/index.jsp
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web.war
trunk/oai-pmh_data_provider/data_provider_web/target/war/work/webapp-cache.xml
Added Paths:
-----------
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/command/Identify.java
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/identify.properties
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/vmFiles/Identify.vm
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/vmFiles/ListSet.vm
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/applicationContext.xml
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/treebase-core-1.0-SNAPSHOT.jar
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/top-security.xml
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/top-servlet.xml
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error-403.jsp
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error-404.jsp
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error-500.jsp
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error.jsp
trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/uncaughtException.jsp
Modified: trunk/oai-pmh_data_provider/data_provider_web/.classpath
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/.classpath 2009-11-04 14:18:58 UTC (rev 238)
+++ trunk/oai-pmh_data_provider/data_provider_web/.classpath 2009-11-04 14:50:28 UTC (rev 239)
@@ -12,5 +12,6 @@
</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="lib" path="/treebase/treebase-core/target/treebase-core-1.0-SNAPSHOT.jar"/>
<classpathentry kind="output" path="target/classes"/>
</classpath>
Modified: trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.jdt.core.prefs
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.jdt.core.prefs 2009-11-04 14:18:58 UTC (rev 238)
+++ trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.jdt.core.prefs 2009-11-04 14:50:28 UTC (rev 239)
@@ -1,7 +1,12 @@
-#Tue Oct 13 10:33:14 EDT 2009
+#Mon Nov 02 11:24:22 EST 2009
eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=1.5
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.source=1.5
Modified: trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.component
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.component 2009-11-04 14:18:58 UTC (rev 238)
+++ trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.component 2009-11-04 14:50:28 UTC (rev 239)
@@ -4,7 +4,7 @@
<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="/" source-path="/src/main/webapp"/>
- <dependent-module deploy-path="/WEB-INF/lib" handle="module:/resource/treebase-core/treebase-core">
+ <dependent-module deploy-path="/WEB-INF/lib" handle="module:/resource/treebase/treebase">
<dependency-type>uses</dependency-type>
</dependent-module>
<property name="context-root" value="data_provider_web"/>
Modified: trunk/oai-pmh_data_provider/data_provider_web/pom.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/pom.xml 2009-11-04 14:18:58 UTC (rev 238)
+++ trunk/oai-pmh_data_provider/data_provider_web/pom.xml 2009-11-04 14:50:28 UTC (rev 239)
@@ -256,6 +256,7 @@
<artifactId>treebase-core</artifactId>
<version>1.0-SNAPSHOT</version>
</dependency>
+
<!-- used by Spring framework -->
<!--Older ersion not needed-->
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/command/Identify.java
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/command/Identify.java (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/command/Identify.java 2009-11-04 14:50:28 UTC (rev 239)
@@ -0,0 +1,73 @@
+package org.treebase.oai.web.command;
+
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.GregorianCalendar;
+import java.util.SimpleTimeZone;
+import java.util.TimeZone;
+
+
+public class Identify {
+
+ private String baseRUL;
+ private String repositoryName;
+ private String protocolVersion;
+ private String adminEmail;
+ private String earliestDatestamp;
+ private String deletedRecord;
+ private String granularity;
+ private String granularityPattern;
+
+ public String getBaseRUL() {
+ return baseRUL;
+ }
+ public void setBaseRUL(String baseRUL) {
+ this.baseRUL = baseRUL;
+ }
+ public String getRepositoryName() {
+ return repositoryName;
+ }
+ public void setRepositoryName(String repositoryName) {
+ this.repositoryName = repositoryName;
+ }
+ public String getProtocolVersion() {
+ return protocolVersion;
+ }
+ public void setProtocolVersion(String protocolVersion) {
+ this.protocolVersion = protocolVersion;
+ }
+ public String getAdminEmail() {
+ return adminEmail;
+ }
+ public void setAdminEmail(String adminEmail) {
+ this.adminEmail = adminEmail;
+ }
+ public String getEarliestDatestamp() {
+ return earliestDatestamp;
+ }
+ public void setEarliestDatestamp(String earliestDatestamp) {
+ this.earliestDatestamp = earliestDatestamp;
+ }
+ public String getDeletedRecord() {
+ return deletedRecord;
+ }
+ public void setDeletedRecord(String deletedRecord) {
+ this.deletedRecord = deletedRecord;
+ }
+ public String getGranularity() {
+ return granularity;
+ }
+ public void setGranularity(String granularity) {
+ this.granularity = granularity;
+ }
+
+ public String getResponseDate(Date date){
+ SimpleDateFormat format = new SimpleDateFormat(granularityPattern);
+ Calendar cal = Calendar.getInstance(new SimpleTimeZone(0, "GMT"));
+ format.setCalendar(cal);
+ return format.format(date);
+
+ }
+
+}
Modified: trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java 2009-11-04 14:18:58 UTC (rev 238)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java 2009-11-04 14:50:28 UTC (rev 239)
@@ -10,20 +10,48 @@
import org.springframework.validation.BindException;
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.AbstractCommandController;
+import org.treebase.oai.web.command.Identify;
import org.treebase.oai.web.command.OAIPMHCommand;
import org.cipres.treebase.domain.study.SubmissionService;
import org.cipres.treebase.domain.study.StudyService;
public class OAIPMHController extends AbstractCommandController{
-
+
private SubmissionService submissionService;
private StudyService studyService;
+ private Identify identify;
public OAIPMHController(){
setCommandClass(OAIPMHCommand.class);
- setCommandName("params");
+ setCommandName("requestParams");
}
+ public SubmissionService getSubmissionService() {
+ return submissionService;
+ }
+
+ public void setSubmissionService(SubmissionService submissionService) {
+ this.submissionService = submissionService;
+ }
+
+ public StudyService getStudyService() {
+ return studyService;
+ }
+
+ public void setStudyService(StudyService studyService) {
+ this.studyService = studyService;
+ }
+
+ public Identify getIdentify() {
+ return identify;
+ }
+
+ public void setIdentify(Identify identify) {
+ this.identify = identify;
+ }
+
+
+
@Override
protected ModelAndView handle(HttpServletRequest request,
HttpServletResponse response, Object command, BindException errors)
@@ -33,56 +61,59 @@
OAIPMHCommand params = (OAIPMHCommand) command;
Map model=errors.getModel();
- model.put("params", params);
+ model.put("requestParams", params);
+ model.put("identify", this.identify);
+ String responsDate;
+
Method method=null;
try{
- method=this.getClass().getMethod(params.getVerb(), new Class[]{HttpServletRequest.class, HttpServletResponse.class, Map.class});
+ method=this.getClass().getMethod(params.getVerb(), new Class[]{HttpServletRequest.class, HttpServletResponse.class, OAIPMHCommand.class, Map.class});
}catch(NoSuchMethodException e){
return new ModelAndView("badVerb.vm",model);
}
- return (ModelAndView) method.invoke(this, request, response, model);
+ return (ModelAndView) method.invoke(this, request, response, params, model);
}
- ModelAndView ListRecoed(HttpServletRequest request, HttpServletResponse response, Map model){
+ ModelAndView ListRecoed(HttpServletRequest request, HttpServletResponse response, OAIPMHCommand params, Map model){
- return (new ModelAndView(metadataPrefix+"_ListRecoed.vm",model));
+ return (new ModelAndView(params.getMetadataPrefix()+"_ListRecoed.vm",model));
}
-
-
+
- ModelAndView ListIdentifiers(HttpServletRequest request, HttpServletResponse response, Map model){
- metadataPrefix
- return (new ModelAndView(metadataPrefix+"_ListIdentifiers.vm",model));
+ ModelAndView ListIdentifiers(HttpServletRequest request, HttpServletResponse response, OAIPMHCommand params, Map model){
+
+ return (new ModelAndView(params.getMetadataPrefix()+"_ListIdentifiers.vm",model));
}
- ModelAndView GetRecord(HttpServletRequest request, HttpServletResponse response, Map model){
- metadataPrefix
- return (new ModelAndView(metadataPrefix+"_GetRecord.vm",model));
+ ModelAndView GetRecord(HttpServletRequest request, HttpServletResponse response, OAIPMHCommand params, Map model){
+
+ return (new ModelAndView(params.getMetadataPrefix()+"_GetRecord.vm",model));
}
- ModelAndView Identify(HttpServletRequest request, HttpServletResponse response, Map model){
+ ModelAndView Identify(HttpServletRequest request, HttpServletResponse response, OAIPMHCommand params, Map model){
return (new ModelAndView("Identify.vm",model));
}
- ModelAndView ListSet(HttpServletRequest request, HttpServletResponse response, Map model){
+ ModelAndView ListSet(HttpServletRequest request, HttpServletResponse response, OAIPMHCommand params, Map model){
return (new ModelAndView("ListSet.vm",model));
}
- ModelAndView ListMetadataFormats(HttpServletRequest request, HttpServletResponse response, Map model){
+ ModelAndView ListMetadataFormats(HttpServletRequest request, HttpServletResponse response, OAIPMHCommand params, Map model){
return (new ModelAndView("ListMetadataFormats.vm",model));
}
+
}
Modified: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/applicationContext.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/applicationContext.xml 2009-11-04 14:18:58 UTC (rev 238)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/applicationContext.xml 2009-11-04 14:50:28 UTC (rev 239)
@@ -9,6 +9,28 @@
http://www.directwebremoting.org/schema/spring-dwr
http://www.directwebremoting.org/schema/spring-dwr-2.0.xsd">
+ <bean id="top.propertyConfigurer"
+ class="org.springframework.beans.factory.config.PropertyPlaceholderConfigurer">
+ <property name="ignoreUnresolvablePlaceholders" value="true" />
+ <property name="locations">
+ <list>
+ <value>/WEB-INF/identify.properties</value>
+ </list>
+ </property>
+ </bean>
+
+ <bean id="top.identify" class="org.treebase.oai.web.command.Identify">
+ <property name="baseRUL" value="${identify.baseRUL}" />
+ <property name="repositoryName" value="${identify.repositoryName}" />
+ <property name="protocolVersion" value="${identify.protocolVersion}" />
+ <property name="adminEmail" value="${identify.adminEmail}" />
+ <property name="earliestDatestamp" value="${identify.earliestDatestamp}" />
+ <property name="deletedRecord" value="${identify.deletedRecord}" />
+ <property name="granularity" value="${identify.granularity}" />
+ <property name="granularityPattern" value="${identify.granularityPattern}" />
+
+ </bean>
+
<!-- ========================================================== -->
<!-- LIST OF DWR beans/methods -->
<!-- ========================================================== -->
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/identify.properties
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/identify.properties (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/identify.properties 2009-11-04 14:50:28 UTC (rev 239)
@@ -0,0 +1,8 @@
+identify.baseRUL=www.***/top.edu
+identify.repositoryName=org.treebase.oai
+identify.protocolVersion=2.0
+ide...@ya...
+identify.earliestDatestamp=1995-11-04T00:00:00Z
+identify.deletedRecord=transient
+identify.granularity=YYYY-MM-DDThh:mm:ssZ
+identify.granularityPattern=yyyy-MM-dd'T'hh:mm:ss'Z'
\ No newline at end of file
Modified: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml 2009-11-04 14:18:58 UTC (rev 238)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml 2009-11-04 14:50:28 UTC (rev 239)
@@ -25,6 +25,7 @@
<bean id="OAIPMHController" class="org.treebase.oai.web.controller.OAIPMHController">
<property name="submissionService"><ref bean="submissionService"></ref></property>
<property name="studyService"><ref bean="studyphyloTreeService"></ref></property>
+ <property name="identify"><ref bean="top.identify"></ref></property>
</bean>
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/vmFiles/Identify.vm
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/vmFiles/Identify.vm (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/vmFiles/Identify.vm 2009-11-04 14:50:28 UTC (rev 239)
@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<OAI-PMH xmlns="http://www.openarchives.org/OAI/2.0/"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/
+ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd">
+ <responseDate>${now()}</responseDate>
+ <request verb="Identify">${identify.baseRUL}</request>
+ <Identify>
+ <repositoryName>${identify.repositoryName}</repositoryName>
+ <baseURL>${identify.baseRUL}</baseURL>
+ <protocolVersion>${identify.protocolVersion}</protocolVersion>
+ <adminEmail>${identify.adminEmail}</adminEmail>
+ <earliestDatestamp>${identify.earliestDatestamp}</earliestDatestamp>
+ <deletedRecord>${identify.deletedRecord}</deletedRecord>
+ <granularity>${identify.granularity}</granularity>
+
+ <description>
+ <oai-identifier
+ xmlns="http://www.openarchives.org/OAI/2.0/oai-identifier"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation=
+ "http://www.openarchives.org/OAI/2.0/oai-identifier
+ http://www.openarchives.org/OAI/2.0/oai-identifier.xsd">
+ <scheme>oai</scheme>
+ <repositoryIdentifier>${identify.repositoryIdentifier}</repositoryIdentifier>
+ <delimiter>:</delimiter>
+ <sampleIdentifier>${identify.sampleIdentifier}</sampleIdentifier>
+ </oai-identifier>
+ </description>
+
+ </Identify>
+</OAI-PMH>
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/vmFiles/ListSet.vm
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/vmFiles/ListSet.vm (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/vmFiles/ListSet.vm 2009-11-04 14:50:28 UTC (rev 239)
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<OAI-PMH xmlns="http://www.openarchives.org/OAI/2.0/"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/
+ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd">
+ <responseDate>${identify.responseDate}</responseDate>
+ <request verb="ListSets">
+ ${identify.baseURL}</request>
+ <error code="noSetHierarchy">This repository does not
+ support sets</error>
+</OAI-PMH>
Added: trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/applicationContext.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/applicationContext.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/applicationContext.xml 2009-11-04 14:50:28 UTC (rev 239)
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<beans default-autowire="no"
+ xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:dwr="http://www.directwebremoting.org/schema/spring-dwr"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-2.0.xsd
+ http://www.directwebremoting.org/schema/spring-dwr
+ http://www.directwebremoting.org/schema/spring-dwr-2.0.xsd">
+
+ <!-- ========================================================== -->
+ <!-- LIST OF DWR beans/methods -->
+ <!-- ========================================================== -->
+
+
+
+ <!-- bean id="remoteAjaxProgressListener" class="org.cipres.treebase.web.controllers.AjaxProgressListener">
+ <dwr:remote javascript="RemoteAjaxProgressListener">
+ <dwr:include method="getStatus"/>
+ </dwr:remote>
+ </bean -->
+ <!-- dwr:configuration>
+ <dwr:convert type="bean" class="org.cipres.treebase.web.model.UploadInfoBean"/>
+ </dwr:configuration -->
+
+
+
+</beans>
Added: trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/treebase-core-1.0-SNAPSHOT.jar
===================================================================
(Binary files differ)
Property changes on: trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/lib/treebase-core-1.0-SNAPSHOT.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/top-security.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/top-security.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/top-security.xml 2009-11-04 14:50:28 UTC (rev 239)
@@ -0,0 +1,109 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN"
+ "http://www.springframework.org/dtd/spring-beans.dtd">
+
+<beans default-autowire="no">
+
+ <!-- ======================== FILTER CHAIN ======================= -->
+ <!-- if you wish to use channel security, add "channelProcessingFilter,"
+ in front of "httpSessionContextIntegrationFilter" in the list below -->
+ <bean id="filterChainProxy" class="org.acegisecurity.util.FilterChainProxy">
+ <property name="filterInvocationDefinitionSource">
+ <value>
+ CONVERT_URL_TO_LOWERCASE_BEFORE_COMPARISON
+ PATTERN_TYPE_APACHE_ANT
+ /**=httpSessionContextIntegrationFilter,authenticationProcessingFilter,requestMethodsFilter,exceptionTranslationFilter,filterInvocationInterceptor
+ </value>
+ </property>
+ </bean>
+
+ <!-- ======================== AUTHENTICATION MANAGER AND ITS DEPENDENTS ======================= -->
+ <bean id="authenticationManager" class="org.acegisecurity.providers.ProviderManager">
+ <property name="providers">
+ <list>
+ <ref local="daoAuthenticationProvider"/>
+ </list>
+ </property>
+ </bean>
+
+ <bean id="daoAuthenticationProvider" class="org.acegisecurity.providers.dao.DaoAuthenticationProvider">
+ <property name="userDetailsService"><ref bean ="userService"/></property>
+ <!-- encrypt password instead of storing in clear text in DB -->
+ <!-- property name="passwordEncoder" ref="passwordEncoder"/ -->
+ <!-- the next 2 lines are for debugging purpose -->
+ <!-- property name="userDetailsService" ref="jdbcDaoImpl"/ -->
+ <!-- property name="userDetailsService" ref="myUserServices"/ -->
+ </bean>
+ <!-- bean id="passwordEncoder" class="org.acegisecurity.providers.encoding.ShaPasswordEncoder"/ -->
+
+ <!-- bean id="myUserServices" class="org.cipres.treebase.web.controllers.UserDAOImpl"/ -->
+ <!-- use JDBC for authentication: only for debugging -->
+ <!-- bean id="jdbcDaoImpl" class="org.acegisecurity.userdetails.jdbc.JdbcDaoImpl">
+ <property name="dataSource"><ref bean="securityDataSource"/></property>
+ <property name="usersByUsernameQuery">
+ <value>SELECT username, password, 'true' as enabled FROM user WHERE username=?</value>
+ </property>
+ <property name="authoritiesByUsernameQuery">
+ <value>SELECT 'lcchan' as username, 'user' as rolename FROM user WHERE username=? </value>
+ </property>
+ </bean -->
+ <!-- =========================== HTTP REQUEST SECURITY ======================================== -->
+ <!-- Filter to propagate the established Authentication object through all requests -->
+ <bean id="httpSessionContextIntegrationFilter" class="org.acegisecurity.context.HttpSessionContextIntegrationFilter"/>
+
+ <!-- Filter to handle FORM authentication -->
+ <bean id="authenticationProcessingFilter" class="org.acegisecurity.ui.webapp.AuthenticationProcessingFilter">
+ <property name="authenticationManager" ref="authenticationManager"/>
+ <property name="authenticationFailureUrl" value="/login.jsp?error=true"/>
+ <property name="defaultTargetUrl" value="/user/processUser.html"/>
+ <property name="filterProcessesUrl" value="/j_security_check"/>
+ <property name="alwaysUseDefaultTargetUrl" value="true"/>
+ </bean>
+
+ <!-- Filter to link defintions of secured resources with the appropriate access control mechanism -->
+ <bean id="exceptionTranslationFilter" class="org.acegisecurity.ui.ExceptionTranslationFilter">
+ <property name="authenticationEntryPoint" ref="authenticationProcessingFilterEntryPoint"/>
+ </bean>
+
+ <bean id="requestMethodsFilter" class="org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter"/>
+
+ <!-- ======================== FILTER SECURITY INTERCEPTOR ======================= -->
+ <!-- Note the order that entries are placed against the objectDefinitionSource is critical.
+ The FilterSecurityInterceptor will work from the top of the list down to the FIRST pattern
+ that matches the request URL. Accordingly, you should place MOST SPECIFIC (ie a/b/c/d.*)
+ expressions first, with LEAST SPECIFIC (ie a/.*) expressions last -->
+ <bean id="filterInvocationInterceptor" class="org.acegisecurity.intercept.web.FilterSecurityInterceptor">
+ <property name="authenticationManager"><ref local ="authenticationManager"/></property>
+ <property name="accessDecisionManager"><ref local ="accessDecisionManager"/></property>
+ <property name="objectDefinitionSource">
+ <value>
+ CONVERT_URL_TO_LOWERCASE_BEFORE_COMPARISON
+ PATTERN_TYPE_APACHE_ANT
+ /submit.html=User,Admin, Associate Editor
+ /user/*=User,Admin, Associate Editor
+ /admin/*=Admin, Associate Editor
+ </value>
+ </property>
+ </bean>
+
+ <!-- ======================== ACCESSDECISION MANAGER AND ITS DEPENDENTS ======================= -->
+ <bean id="accessDecisionManager" class="org.acegisecurity.vote.AffirmativeBased">
+ <property name="allowIfAllAbstainDecisions" value="false"/>
+ <property name="decisionVoters">
+ <list>
+ <ref local ="roleVoter"/>
+ </list>
+ </property>
+ </bean>
+
+ <bean id="roleVoter" class="org.acegisecurity.vote.RoleVoter">
+ <property name="rolePrefix" value=""/>
+ </bean>
+
+ <!-- ======================== AUTHENTICATION ENTRY POINT ======================= -->
+ <bean id="authenticationProcessingFilterEntryPoint" class="org.acegisecurity.ui.webapp.AuthenticationProcessingFilterEntryPoint">
+ <property name="loginFormUrl"><value>/login.jsp</value></property>
+ <property name="forceHttps"><value>false</value></property>
+ </bean>
+
+</beans>
Added: trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/top-servlet.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/top-servlet.xml (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/top-servlet.xml 2009-11-04 14:50:28 UTC (rev 239)
@@ -0,0 +1,85 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<beans xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:dwr="http://www.directwebremoting.org/schema/spring-dwr"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-2.0.xsd
+ http://www.directwebremoting.org/schema/spring-dwr
+ http://www.directwebremoting.org/schema/spring-dwr-2.0.xsd">
+
+ <!-- ========================================================== -->
+ <!-- velocity configure -->
+ <!-- ========================================================== -->
+
+ <bean id="velocityConfigurer" class="org.springframework.web.servlet.view.velocity.VelocityConfigurer">
+ <property name="resourceLoaderPath">
+ <value>WEB-INF/vmFiles/</value>
+ </property>
+ </bean>
+
+ <!-- ========================================================== -->
+ <!-- LIST OF CONTROLLERS FOR VERBS AND FORMATS -->
+ <!-- ========================================================== -->
+
+ <!--bean id="appletInteractionController" class="org.cipres.treebase.web.controllers.AppletInteractionController">
+ <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
+ </bean-->
+
+
+ <!-- ========================================================== -->
+ <!-- LIST OF VALIDATORS FOR CONTROLLER -->
+ <!-- ========================================================== -->
+
+
+ <!-- ========================================================== -->
+ <!-- MESSAGE SOURCE DEFINITION -->
+ <!-- ========================================================== -->
+ <!--bean id="messageSource" class="org.springframework.context.support.ResourceBundleMessageSource">
+ <property name="basename"><value>ApplicationResources</value></property>
+ </bean-->
+
+ <!-- ========================================================== -->
+ <!-- Spring View Resolvers for Templates -->
+ <!-- ========================================================== -->
+ <bean id="viewResolver" class="org.springframework.web.servlet.view.velocity.VelocityViewResolver">
+ <property name="suffix">
+ <value>.vm</value>
+ </property>
+ <property name="exposeRequestAttributes">
+ <value>true</value>
+ </property>
+ <property name="exposeSessionAttributes">
+ <value>true</value>
+ </property>
+ </bean>
+
+ <!-- ========================================================== -->
+ <!-- URL MAPPING -->
+ <!-- ========================================================== -->
+ <bean id="urlMapping" class="org.springframework.web.servlet.handler.SimpleUrlHandlerMapping">
+
+ <property name="alwaysUseFullPath" value="true"/>
+ <property name="mappings">
+ <props>
+ <!--prop key="/oai-pmh verbs/metadata formats/paramaters</prop-->
+ </props>
+ </property>
+ </bean>
+ <!-- ==================================================================================================== -->
+ <!-- Exception Mappings -->
+ <!-- This bean resolves specific types of exception to corresponding error views -->
+ <!-- The default behavior of DispatcherServlet is to propagate all exceptions to the servlet container -->
+ <!-- This will happen here with all other types of exception -->
+ <!-- ==================================================================================================== -->
+ <!--bean id="exceptionResolver" class="org.springframework.web.servlet.handler.SimpleMappingExceptionResolver">
+ <property name="exceptionMappings">
+ <props>
+ <prop key="org.springframework.dao.DataAccessException">/errors/dataAccessFailure</prop>
+ <prop key="org.springframework.transaction.TransactionException">/errors/dataAccessFailure</prop>
+ <prop key="org.cipres.treebase.web.exceptions.EmptyStudyException">/errors/studyAccessFailure</prop>
+ </props>
+ </property>
+ </bean-->
+
+</beans>
Modified: trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/web.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/web.xml 2009-11-04 14:18:58 UTC (rev 238)
+++ trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/WEB-INF/web.xml 2009-11-04 14:50:28 UTC (rev 239)
@@ -1,7 +1,78 @@
-<!DOCTYPE web-app PUBLIC
- "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN"
- "http://java.sun.com/dtd/web-app_2_3.dtd" >
+<?xml version="1.0" encoding="UTF-8"?>
+<web-app id="WebApp_ID" version="2.4" xmlns="http://java.sun.com/xml/ns/j2ee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd">
+
+ <display-name>Treebase OAI-PMH Provider</display-name>
+
+ <context-param>
+ <param-name>contextConfigLocation</param-name>
+ <param-value>
+ classpath*:applicationContext-dao.xml,
+ classpath*:applicationContext-service.xml,
+ /WEB-INF/applicationContext.xml,
+ <!-- top is short for Treebase OAI-PMH Provider -->
+ <!-- /WEB-INF/top-security.xml,-->
+ <!-- /WEB-INF/top-validation.xml-->
+ <!-- validation will be done on server side -->
+ <!-- errors will be return as oai-pmh exception with vm -->
+ </param-value>
+ </context-param>
-<web-app>
- <display-name>Archetype Created Web Application</display-name>
+ <!-- ========================================================== -->
+ <!-- define the listener, one of the 3 ways to start spring -->
+ <!-- ========================================================== -->
+ <!-- listener initial the spring container while webapp start -->
+ <listener>
+ <listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
+ </listener>
+ <!-- extends customize and replaces ContextLoaderListener -->
+ <!-- listener>
+ <listener-class>org.cipres.treebase.web.listeners.StartupListener</listener-class>
+ </listener -->
+
+
+ <!-- ========================================================== -->
+ <!-- Name of our servlet processed by Spring's front controller -->
+ <!-- DispatcherServlet -->
+ <!-- ========================================================== -->
+ <servlet>
+ <servlet-name>TOPServlet</servlet-name>
+ <servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
+ <load-on-startup>1</load-on-startup>
+ </servlet>
+
+
+ <!-- ========================================================== -->
+ <!-- Processed by CXFServlet -->
+ <!-- ========================================================== -->
+ <!--servlet>
+ <servlet-name>CXFServlet</servlet-name>
+ <servlet-class>
+ org.apache.cxf.transport.servlet.CXFServlet
+ </servlet-class>
+ </servlet-->
+
+
+
+ <!-- ========================================================== -->
+ <!-- url pattern that will be processed by DispatcherServlet -->
+ <!-- ========================================================== -->
+ <servlet-mapping>
+ <servlet-name>TOPServlet</servlet-name>
+ <url-pattern>/top/*</url-pattern>
+ </servlet-mapping>
+
+ <!-- ========================================================== -->
+ <!-- url pattern that will be processed by CXFServlet -->
+ <!-- ========================================================== -->
+ <!--servlet-mapping>
+ <servlet-name>CXFServlet</servlet-name>
+ <url-pattern>/services/*</url-pattern>
+ </servlet-mapping-->
+
+
+ <!-- ========================================================== -->
+ <!-- Error Pages -->
+ <!-- ========================================================== -->
+ <!-- or errors will return as oai-pmh exception based on .vm files -->
+
</web-app>
Added: trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error-403.jsp
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error-403.jsp (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error-403.jsp 2009-11-04 14:50:28 UTC (rev 239)
@@ -0,0 +1,14 @@
+<%@ include file="/common/taglibs.jsp"%>
+
+<page:applyDecorator name="default">
+
+<title><fmt:message key="403.title"/></title>
+<content tag="heading"><fmt:message key="403.title"/></content>
+
+<p>
+ <fmt:message key="403.message">
+ <fmt:param><c:url value="/"/></fmt:param>
+ </fmt:message>
+</p>
+
+</page:applyDecorator>
Added: trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error-404.jsp
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error-404.jsp (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error-404.jsp 2009-11-04 14:50:28 UTC (rev 239)
@@ -0,0 +1,13 @@
+<%@ include file="/common/taglibs.jsp"%>
+
+<page:applyDecorator name="default">
+
+<title><fmt:message key="404.title"/></title>
+<content tag="heading"><fmt:message key="404.title"/></content>
+
+<p>
+ <fmt:message key="404.message">
+ <fmt:param><c:url value="/home.html"/></fmt:param>
+ </fmt:message>
+</p>
+</page:applyDecorator>
Added: trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error-500.jsp
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error-500.jsp (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error-500.jsp 2009-11-04 14:50:28 UTC (rev 239)
@@ -0,0 +1,28 @@
+<%@ page language="java" isErrorPage="true" %>
+<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c" %>
+<%@ taglib uri="http://java.sun.com/jstl/fmt" prefix="fmt" %>
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+
+<html>
+<head>
+ <title><fmt:message key="errorPage.title"/></title>
+ <link rel="stylesheet" type="text/css" media="all" href="<c:url value="/styles/treebase.css"/>" />
+</head>
+
+<body>
+<div id="screen">
+ <div id="content">
+ <h1><fmt:message key="errorPage.heading"/></h1>
+ <%@ include file="/common/messages.jsp" %>
+ <% if (exception != null) { %>
+ <pre><% exception.printStackTrace(new java.io.PrintWriter(out)); %></pre>
+ <% } else if ((Exception)request.getAttribute("javax.servlet.error.exception") != null) { %>
+ <pre><% ((Exception)request.getAttribute("javax.servlet.error.exception"))
+ .printStackTrace(new java.io.PrintWriter(out)); %></pre>
+ <% } %>
+ </div>
+</div>
+</body>
+</html>
Added: trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error.jsp
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error.jsp (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/error.jsp 2009-11-04 14:50:28 UTC (rev 239)
@@ -0,0 +1,28 @@
+<%@ page language="java" isErrorPage="true" %>
+<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c" %>
+<%@ taglib uri="http://java.sun.com/jstl/fmt" prefix="fmt" %>
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+
+<html>
+<head>
+ <title><fmt:message key="errorPage.title"/></title>
+ <link rel="stylesheet" type="text/css" media="all" href="<c:url value="/styles/default.css"/>" />
+</head>
+
+<body>
+<div id="screen">
+ <div id="content">
+ <h1><fmt:message key="errorPage.heading"/></h1>
+ <!-- %@ include file="/common/messages.jsp" % -->
+ <% if (exception != null) { %>
+ <pre><% exception.printStackTrace(new java.io.PrintWriter(out)); %></pre>
+ <% } else if ((Exception)request.getAttribute("javax.servlet.error.exception") != null) { %>
+ <pre><% ((Exception)request.getAttribute("javax.servlet.error.exception"))
+ .printStackTrace(new java.io.PrintWriter(out)); %></pre>
+ <% } %>
+ </div>
+</div>
+</body>
+</html>
Modified: trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/index.jsp
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/index.jsp 2009-11-04 14:18:58 UTC (rev 238)
+++ trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/index.jsp 2009-11-04 14:50:28 UTC (rev 239)
@@ -1,5 +1,3 @@
-<html>
-<body>
-<h2>Hello World!</h2>
-</body>
-</html>
+<%@ include file="/common/taglibs.jsp" %>
+
+<c:redirect url="/home.html"/>
\ No newline at end of file
Added: trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/uncaughtException.jsp
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/uncaughtException.jsp (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web/uncaughtException.jsp 2009-11-04 14:50:28 UTC (rev 239)
@@ -0,0 +1,46 @@
+<%@ include file="/common/taglibs.jsp" %>
+
+<title>Java Uncaught Exception</title>
+<content tag="heading">Uncaught Exception Encountered</content>
+
+<p>
+
+<%
+try {
+ // The Servlet spec guarantees this attribute will be available
+ Throwable exception = (Throwable) request.getAttribute("javax.servlet.error.exception");
+
+ if (exception != null) {
+ if (exception instanceof ServletException) {
+ // It's a ServletException: we should extract the root cause
+ ServletException sex = (ServletException) exception;
+ Throwable rootCause = sex.getRootCause();
+ if (rootCause == null)
+ rootCause = sex;
+ out.println("** Root cause is: "+ rootCause.getMessage());
+ rootCause.printStackTrace(new java.io.PrintWriter(out));
+ }
+ else {
+ // It's not a ServletException, so we'll just show it
+ exception.printStackTrace(new java.io.PrintWriter(out));
+ }
+ }
+ else {
+ out.println("No error information available");
+ }
+
+ // Display cookies
+ out.println("\nCookies:\n");
+ Cookie[] cookies = request.getCookies();
+ if (cookies != null) {
+ for (int i = 0; i < cookies.length; i++) {
+ out.println(cookies[i].getName() + "=[" + cookies[i].getValue() + "]");
+ }
+ }
+
+} catch (Exception ex) {
+ ex.printStackTrace(new java.io.PrintWriter(out));
+}
+%>
+<p>
+
Modified: trunk/oai-pmh_data_provider/data_provider_web/target/data_provider_web.war
===================================================================
(Binary files differ)
Modified: trunk/oai-pmh_data_provider/data_provider_web/target/war/work/webapp-cache.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/target/war/work/webapp-cache.xml 2009-11-04 14:18:58 UTC (rev 238)
+++ trunk/oai-pmh_data_provider/data_provider_web/target/war/work/webapp-cache.xml 2009-11-04 14:50:28 UTC (rev 239)
@@ -4,8 +4,16 @@
<string>currentBuild</string>
<path-set>
<pathsSet class="linked-hash-set">
+ <string>error-403.jsp</string>
+ <string>error-404.jsp</string>
+ <string>error-500.jsp</string>
+ <string>error.jsp</string>
<string>index.jsp</string>
<string>META-INF/MANIFEST.MF</string>
+ <string>uncaughtException.jsp</string>
+ <string>WEB-INF/applicationContext.xml</string>
+ <string>WEB-INF/top-security.xml</string>
+ <string>WEB-INF/top-servlet.xml</string>
<string>WEB-INF/web.xml</string>
<string>WEB-INF/lib/spring-2.0.7.jar</string>
<string>WEB-INF/lib/commons-logging-1.1.jar</string>
@@ -13,79 +21,20 @@
<string>WEB-INF/lib/logkit-1.0.1.jar</string>
<string>WEB-INF/lib/avalon-framework-4.1.3.jar</string>
<string>WEB-INF/lib/servlet-api-2.4.jar</string>
- <string>WEB-INF/lib/data_provider_core-0.0.1-SNAPSHOT.jar</string>
- <string>WEB-INF/lib/postgresql-8.3-603.jdbc3.jar</string>
- <string>WEB-INF/lib/acegi-security-1.0.1.jar</string>
- <string>WEB-INF/lib/commons-codec-1.3.jar</string>
- <string>WEB-INF/lib/oro-2.0.8.jar</string>
- <string>WEB-INF/lib/commons-collections-3.1.jar</string>
- <string>WEB-INF/lib/c3p0-0.9.1.2.jar</string>
- <string>WEB-INF/lib/hibernate-annotations-3.3.1.GA.jar</string>
- <string>WEB-INF/lib/hibernate-3.2.6.ga.jar</string>
- <string>WEB-INF/lib/ehcache-1.2.3.jar</string>
- <string>WEB-INF/lib/jta-1.0.1B.jar</string>
- <string>WEB-INF/lib/dom4j-1.6.1.jar</string>
- <string>WEB-INF/lib/antlr-2.7.6.jar</string>
- <string>WEB-INF/lib/hibernate-commons-annotations-3.0.0.ga.jar</string>
- <string>WEB-INF/lib/ejb3-persistence-1.0.1.GA.jar</string>
- <string>WEB-INF/lib/cglib-nodep-2.1_3.jar</string>
- <string>WEB-INF/lib/commons-lang-2.3.jar</string>
- <string>WEB-INF/lib/db2jcc-2.6.80.jar</string>
- <string>WEB-INF/lib/db2jcc_license_cu-2.6.80.jar</string>
- <string>WEB-INF/lib/jdbc-stdext-2.0.jar</string>
- <string>WEB-INF/lib/jdom-1.1.jar</string>
- <string>WEB-INF/lib/cxf-rt-frontend-jaxws-2.1.1.jar</string>
- <string>WEB-INF/lib/geronimo-jaxws_2.1_spec-1.0.jar</string>
- <string>WEB-INF/lib/geronimo-activation_1.1_spec-1.0.2.jar</string>
- <string>WEB-INF/lib/cxf-api-2.1.1.jar</string>
- <string>WEB-INF/lib/cxf-common-utilities-2.1.1.jar</string>
- <string>WEB-INF/lib/spring-core-2.0.8.jar</string>
- <string>WEB-INF/lib/spring-beans-2.0.8.jar</string>
- <string>WEB-INF/lib/spring-context-2.0.8.jar</string>
- <string>WEB-INF/lib/aopalliance-1.0.jar</string>
- <string>WEB-INF/lib/geronimo-annotation_1.0_spec-1.1.1.jar</string>
- <string>WEB-INF/lib/jaxb-api-2.1.jar</string>
- <string>WEB-INF/lib/geronimo-stax-api_1.0_spec-1.0.1.jar</string>
- <string>WEB-INF/lib/wsdl4j-1.6.1.jar</string>
- <string>WEB-INF/lib/xml-resolver-1.2.jar</string>
- <string>WEB-INF/lib/XmlSchema-1.4.2.jar</string>
- <string>WEB-INF/lib/wstx-asl-3.2.4.jar</string>
- <string>WEB-INF/lib/neethi-2.0.4.jar</string>
- <string>WEB-INF/lib/cxf-common-schemas-2.1.1.jar</string>
- <string>WEB-INF/lib/cxf-rt-core-2.1.1.jar</string>
- <string>WEB-INF/lib/jaxb-impl-2.1.6.jar</string>
- <string>WEB-INF/lib/geronimo-javamail_1.4_spec-1.3.jar</string>
- <string>WEB-INF/lib/FastInfoset-1.2.2.jar</string>
- <string>WEB-INF/lib/cxf-rt-bindings-soap-2.1.1.jar</string>
- <string>WEB-INF/lib/cxf-tools-common-2.1.1.jar</string>
- <string>WEB-INF/lib/velocity-1.4.jar</string>
- <string>WEB-INF/lib/velocity-dep-1.4.jar</string>
- <string>WEB-INF/lib/jaxb-xjc-2.1.6.jar</string>
- <string>WEB-INF/lib/saaj-api-1.3.jar</string>
- <string>WEB-INF/lib/geronimo-ws-metadata_2.0_spec-1.1.2.jar</string>
- <string>WEB-INF/lib/cxf-rt-databinding-jaxb-2.1.1.jar</string>
- <string>WEB-INF/lib/cxf-rt-bindings-xml-2.1.1.jar</string>
- <string>WEB-INF/lib/cxf-rt-frontend-simple-2.1.1.jar</string>
- <string>WEB-INF/lib/cxf-rt-ws-addr-2.1.1.jar</string>
- <string>WEB-INF/lib/saaj-impl-1.3.jar</string>
- <string>WEB-INF/lib/cxf-rt-transports-http-2.1.1.jar</string>
- <string>WEB-INF/lib/spring-web-2.0.8.jar</string>
- <string>WEB-INF/lib/cxf-rt-transports-http-jetty-2.1.1.jar</string>
- <string>WEB-INF/lib/jetty-6.1.9.jar</string>
- <string>WEB-INF/lib/jetty-util-6.1.9.jar</string>
- <string>WEB-INF/lib/geronimo-servlet_2.5_spec-1.2.jar</string>
- <string>WEB-INF/lib/xml-apis-1.0.b2.jar</string>
<string>WEB-INF/lib/jstl-1.1.2.jar</string>
<string>WEB-INF/lib/mail-1.4.jar</string>
<string>WEB-INF/lib/activation-1.1.jar</string>
<string>WEB-INF/lib/xalan-2.7.0.jar</string>
+ <string>WEB-INF/lib/xml-apis-1.0.b2.jar</string>
<string>WEB-INF/lib/commons-beanutils-1.7.0.jar</string>
<string>WEB-INF/lib/commons-validator-1.1.4.jar</string>
+ <string>WEB-INF/lib/commons-lang-2.3.jar</string>
<string>WEB-INF/lib/standard-1.1.2.jar</string>
<string>WEB-INF/lib/string-1.1.0.jar</string>
<string>WEB-INF/lib/struts-1.2.9.jar</string>
<string>WEB-INF/lib/sitemesh-2.3.jar</string>
<string>WEB-INF/lib/displaytag-1.1.1.jar</string>
+ <string>WEB-INF/lib/commons-collections-3.1.jar</string>
<string>WEB-INF/lib/itext-1.3.jar</string>
<string>WEB-INF/lib/jcl104-over-slf4j-1.4.2.jar</string>
<string>WEB-INF/lib/slf4j-log4j12-1.4.2.jar</string>
@@ -93,12 +42,17 @@
<string>WEB-INF/lib/struts-menu-2.3.jar</string>
<string>WEB-INF/lib/commons-digester-1.5.jar</string>
<string>WEB-INF/lib/hsqldb-1.7.1.jar</string>
+ <string>WEB-INF/lib/acegi-security-1.0.1.jar</string>
+ <string>WEB-INF/lib/commons-codec-1.3.jar</string>
+ <string>WEB-INF/lib/oro-2.0.8.jar</string>
<string>WEB-INF/lib/springmodules-validator-0.1.jar</string>
<string>WEB-INF/lib/commons-fileupload-1.2.jar</string>
<string>WEB-INF/lib/commons-io-1.3.jar</string>
<string>WEB-INF/lib/dwr-2.0.rc2.jar</string>
<string>WEB-INF/lib/jmock-1.0.1.jar</string>
+ <string>WEB-INF/lib/saaj-api-1.3.jar</string>
<string>WEB-INF/lib/cql-java-1.0.jar</string>
+ <string>WEB-INF/lib/treebase-core-1.0-SNAPSHOT.jar</string>
</pathsSet>
</path-set>
</entry>
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From: <rv...@us...> - 2009-11-04 14:19:05
|
Revision: 238
http://treebase.svn.sourceforge.net/treebase/?rev=238&view=rev
Author: rvos
Date: 2009-11-04 14:18:58 +0000 (Wed, 04 Nov 2009)
Log Message:
-----------
Changed TOMCAT_URL to point to NESCent dev server in publish script
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 2009-11-04 10:51:31 UTC (rev 237)
+++ trunk/treebase-core/src/main/perl/misc/publish 2009-11-04 14:18:58 UTC (rev 238)
@@ -25,7 +25,7 @@
update_sources=false
fi
-TOMCAT_URL=http://8ball.sdsc.edu:6666/treebase-web/
+TOMCAT_URL=http://treebasedb-dev.nescent.org:6666/treebase-web/
VERSIONFILE=${TREEBASE_HOME}/treebase-core/src/main/java/org/cipres/treebase/Version.java
# Rebuild the application WAR file, if requested
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|
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From: <rv...@us...> - 2009-11-04 10:51:38
|
Revision: 237
http://treebase.svn.sourceforge.net/treebase/?rev=237&view=rev
Author: rvos
Date: 2009-11-04 10:51:31 +0000 (Wed, 04 Nov 2009)
Log Message:
-----------
Commented out potentially spurious jsp includes
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/images/tiles/header.jsp
trunk/treebase-web/src/main/webapp/images/tiles/treebaseLayout.jsp
Modified: trunk/treebase-web/src/main/webapp/images/tiles/header.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/images/tiles/header.jsp 2009-11-04 00:19:56 UTC (rev 236)
+++ trunk/treebase-web/src/main/webapp/images/tiles/header.jsp 2009-11-04 10:51:31 UTC (rev 237)
@@ -1,5 +1,11 @@
+<%--
+This threw an error in the new eclipse, but the file never
+existed in the first place. Perhaps we didn't validate as
+stringently before? Let's see how this works if we just
+leave it out.
<%@ include file="/WEB-INF/jsp/include.jsp" %>
-
+ --%>
+
<tiles:importAttribute/>
<table bgcolor="lightblue" cellspacing="2" cellpadding="2" border="0" width="100%">
Modified: trunk/treebase-web/src/main/webapp/images/tiles/treebaseLayout.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/images/tiles/treebaseLayout.jsp 2009-11-04 00:19:56 UTC (rev 236)
+++ trunk/treebase-web/src/main/webapp/images/tiles/treebaseLayout.jsp 2009-11-04 10:51:31 UTC (rev 237)
@@ -1,4 +1,10 @@
+<%--
+This threw an error in the new eclipse, but the file never
+existed in the first place. Perhaps we didn't validate as
+stringently before? Let's see how this works if we just
+leave it out.
<%@ include file="/WEB-INF/jsp/include.jsp" %>
+ --%>
<html>
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|
|
From: <mjd...@us...> - 2009-11-04 00:20:55
|
Revision: 236
http://treebase.svn.sourceforge.net/treebase/?rev=236&view=rev
Author: mjdominus
Date: 2009-11-04 00:19:56 +0000 (Wed, 04 Nov 2009)
Log Message:
-----------
Added special case handling for STUDY_NEXUSFILE lob fields
Modified Paths:
--------------
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
Modified: trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-11-02 23:05:22 UTC (rev 235)
+++ trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-11-04 00:19:56 UTC (rev 236)
@@ -1,5 +1,7 @@
package CIPRES::TreeBase::RecDumper;
use Carp 'croak';
+use File::Temp qw(tempfile);
+use strict;
# XXX LOB fields should be removed from fieldlist and handled separately
sub new {
@@ -49,29 +51,26 @@
and croak("rec: too many items (expected $self->{X})");
@_ < @{$self->{F}}
and croak("rec: too few items (expected $self->{X})");
-
- @_ = $self->quote_data(@_);
my @values;
if ( $self->{'N'} ne 'STUDY_NEXUSFILE' ) {
- @values = @_;
+ @values = $self->quote_data(@_);
}
else {
+ my ( %record, $dir, $path );
+ eval {
my @fields = @{$self->{F}};
- my ( $dir, $path ) = ( $self->{'D'} );
- for my $i ( 0 .. $#fields ) {
- if ( uc $fields[$i] eq 'ID' ) {
- $path = "$dir/".$_[$i];
- }
- if ( uc $fields[$i] ne 'NEXUS' ) {
- push @values, $_[$i];
- }
- else {
- open my $nexfh, '>', $path or croak $!;
- print $nexfh $_[$i];
- close $nexfh;
- push @values, "lo_import('$path')";
- }
- }
+ %record = map { $fields[$_] => $_[$_] } ( 0 .. $#fields );
+# $dir = $self->{'D'} . '/' . $record{STUDY_ID};
+# mkdir $dir if not -d $dir;
+# $path = $dir . '/' . $record{FILENAME};
+ my ( $fh, $filename ) = tempfile( DIR => $self->{'D'} );
+ @values = ( $self->quote_data($record{STUDY_ID}), "lo_import('$filename')", $self->quote_data($record{FILENAME}) );
+# open my $nexfh, '>', $path or croak $!;
+ print $fh substr( $record{NEXUS}, 1, length($record{NEXUS}) - 2 );
+ close $fh;
+ system('gzip','-9',$filename);
+ };
+ warn 'dir: ', $dir, ' path: ', $path, ' file: ', $record{FILENAME}, ' id: ', $record{STUDY_ID}, ' msg: ', $@ if $@;
}
my $values = join ", ", @values;
my $insert = $self->{'PREFIX'} . $values . $self->{'SUFFIX'};
@@ -81,6 +80,7 @@
# Format metadata into a create statement and return (or write) the result
sub dump_create {
+ my $self = shift;
my $create = qq{CREATE TABLE "$self->{'N'}";\n};
return print {$self->{'OUT'}} $create if $self->{'OUT'};
return $create;
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|
|
From: <rv...@us...> - 2009-11-02 23:05:30
|
Revision: 235
http://treebase.svn.sourceforge.net/treebase/?rev=235&view=rev
Author: rvos
Date: 2009-11-02 23:05:22 +0000 (Mon, 02 Nov 2009)
Log Message:
-----------
Added special case for STUDY_NEXUSFILE table dumper
Modified Paths:
--------------
trunk/treebase-core/src/main/perl/dump/sqldump
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
Modified: trunk/treebase-core/src/main/perl/dump/sqldump
===================================================================
--- trunk/treebase-core/src/main/perl/dump/sqldump 2009-11-02 16:08:27 UTC (rev 234)
+++ trunk/treebase-core/src/main/perl/dump/sqldump 2009-11-02 23:05:22 UTC (rev 235)
@@ -18,6 +18,7 @@
my $nrecs; # max number of recs per table
my $where = ""; # WHERE clause to select dumped records
my $maxlen = 5 * 1024 * 1024; # Maximum field length: 5 MB by default
+my $dir = 'STUDY_NEXUSFILE'; # Location to write dumped nexus files
# get command line options, see Getopt::Long
GetOptions(
@@ -28,6 +29,7 @@
'user=s' => \$ENV{'TREEBASE_DB_USER'},
'pass=s' => \$ENV{'TREEBASE_DB_PASS'},
'dsn=s' => \$ENV{'TREEBASE_DB_DSN'},
+ 'dir=s' => \$dir,
'table=s' => \@tables,
'zip' => \$zip,
'maxlen=i' => \$maxlen,
@@ -83,7 +85,8 @@
my $dumper = CIPRES::TreeBase::RecDumper->new(
'FIELDS' => \@names,
'TYPES' => \@types,
- 'TABLE' => $table
+ 'TABLE' => $table,
+ 'DIR' => $dir,
) or die "Couldn't instantiate CIPRES::TreeBase::RecDumper";
# give dumper the output handle to write to, i.e. either STDOUT,
Modified: trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-11-02 16:08:27 UTC (rev 234)
+++ trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm 2009-11-02 23:05:22 UTC (rev 235)
@@ -8,12 +8,15 @@
my $fn = $arg{'FIELDS'} or croak("$class->new: FIELDS required");
my $ct = $arg{'TYPES'} or croak("$class->new: TYPES required");
my $tn = uc $arg{'TABLE'} or croak("$class->new: TABLE required");
- my $X = my @fieldnames = map uc, @$fn;
+ my $X = my @fieldnames = map uc, @$fn;
+ my $dir = $arg{'DIR'};
+ mkdir $dir if not -d $dir;
my $self = {
'F' => \@fieldnames,
'X' => $X,
'N' => $tn,
- 'T' => $ct
+ 'T' => $ct,
+ 'D' => $dir,
};
bless $self => $class;
$self->_initialize();
@@ -48,8 +51,29 @@
and croak("rec: too few items (expected $self->{X})");
@_ = $self->quote_data(@_);
-
- my $values = join ", ", @_;
+ my @values;
+ if ( $self->{'N'} ne 'STUDY_NEXUSFILE' ) {
+ @values = @_;
+ }
+ else {
+ my @fields = @{$self->{F}};
+ my ( $dir, $path ) = ( $self->{'D'} );
+ for my $i ( 0 .. $#fields ) {
+ if ( uc $fields[$i] eq 'ID' ) {
+ $path = "$dir/".$_[$i];
+ }
+ if ( uc $fields[$i] ne 'NEXUS' ) {
+ push @values, $_[$i];
+ }
+ else {
+ open my $nexfh, '>', $path or croak $!;
+ print $nexfh $_[$i];
+ close $nexfh;
+ push @values, "lo_import('$path')";
+ }
+ }
+ }
+ my $values = join ", ", @values;
my $insert = $self->{'PREFIX'} . $values . $self->{'SUFFIX'};
return print {$self->{'OUT'}} $insert if $self->{'OUT'};
return $insert;
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|
|
From: <rv...@us...> - 2009-11-02 16:08:33
|
Revision: 234
http://treebase.svn.sourceforge.net/treebase/?rev=234&view=rev
Author: rvos
Date: 2009-11-02 16:08:27 +0000 (Mon, 02 Nov 2009)
Log Message:
-----------
Added postgres driver to classpath
Modified Paths:
--------------
trunk/treebase-web/.classpath
Modified: trunk/treebase-web/.classpath
===================================================================
--- trunk/treebase-web/.classpath 2009-11-02 16:07:21 UTC (rev 233)
+++ trunk/treebase-web/.classpath 2009-11-02 16:08:27 UTC (rev 234)
@@ -107,5 +107,6 @@
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="con" path="org.eclipse.jst.server.core.container/org.eclipse.jst.server.tomcat.runtimeTarget/Apache Tomcat v5.5"/>
<classpathentry kind="var" path="M2_REPO/zing/z3950/org/cql-java/1.0/cql-java-1.0.jar"/>
+ <classpathentry kind="var" path="M2_REPO/postgresql/postgresql/8.3-603.jdbc3/postgresql-8.3-603.jdbc3.jar"/>
<classpathentry kind="output" path="target/classes"/>
</classpath>
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|
|
From: <rv...@us...> - 2009-11-02 16:07:29
|
Revision: 233
http://treebase.svn.sourceforge.net/treebase/?rev=233&view=rev
Author: rvos
Date: 2009-11-02 16:07:21 +0000 (Mon, 02 Nov 2009)
Log Message:
-----------
Added postgres driver to classpath
Modified Paths:
--------------
trunk/treebase-core/.classpath
Modified: trunk/treebase-core/.classpath
===================================================================
--- trunk/treebase-core/.classpath 2009-11-02 16:04:37 UTC (rev 232)
+++ trunk/treebase-core/.classpath 2009-11-02 16:07:21 UTC (rev 233)
@@ -79,5 +79,6 @@
<classpathentry kind="var" path="M2_REPO/xml-resolver/xml-resolver/1.2/xml-resolver-1.2.jar"/>
<classpathentry kind="var" path="M2_REPO/org/apache/ws/commons/schema/XmlSchema/1.4.2/XmlSchema-1.4.2.jar"/>
<classpathentry kind="var" path="M2_REPO/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.jar"/>
+ <classpathentry kind="var" path="M2_REPO/postgresql/postgresql/8.3-603.jdbc3/postgresql-8.3-603.jdbc3.jar"/>
<classpathentry kind="output" path="target/classes"/>
</classpath>
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|
From: <rv...@us...> - 2009-11-02 16:04:49
|
Revision: 232
http://treebase.svn.sourceforge.net/treebase/?rev=232&view=rev
Author: rvos
Date: 2009-11-02 16:04:37 +0000 (Mon, 02 Nov 2009)
Log Message:
-----------
Downgraded postgres driver from jdbc4 to jdbc3, for older javas. Added DB2 drivers to pom.xml
Modified Paths:
--------------
trunk/treebase-core/pom.xml
Modified: trunk/treebase-core/pom.xml
===================================================================
--- trunk/treebase-core/pom.xml 2009-11-02 13:38:44 UTC (rev 231)
+++ trunk/treebase-core/pom.xml 2009-11-02 16:04:37 UTC (rev 232)
@@ -182,7 +182,7 @@
<dependency>
<groupId>postgresql</groupId>
<artifactId>postgresql</artifactId>
- <version>8.3-603.jdbc4</version>
+ <version>8.3-603.jdbc3</version>
</dependency>
<dependency>
@@ -257,6 +257,22 @@
<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>
<!--dependency>
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|
From: <rv...@us...> - 2009-11-02 13:38:55
|
Revision: 231
http://treebase.svn.sourceforge.net/treebase/?rev=231&view=rev
Author: rvos
Date: 2009-11-02 13:38:44 +0000 (Mon, 02 Nov 2009)
Log Message:
-----------
Setting svn:ignore
Property Changed:
----------------
trunk/treebase-web/src/main/resources/
Property changes on: trunk/treebase-web/src/main/resources
___________________________________________________________________
Added: svn:ignore
+ jdbc.properties
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From: <yo...@us...> - 2009-11-02 00:19:11
|
Revision: 230
http://treebase.svn.sourceforge.net/treebase/?rev=230&view=rev
Author: youjun
Date: 2009-11-02 00:15:50 +0000 (Mon, 02 Nov 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml
trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/oai/web/controller/OAIPMHController.class
Modified: trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java 2009-11-01 22:31:20 UTC (rev 229)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java 2009-11-02 00:15:50 UTC (rev 230)
@@ -11,11 +11,17 @@
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.AbstractCommandController;
import org.treebase.oai.web.command.OAIPMHCommand;
+import org.cipres.treebase.domain.study.SubmissionService;
+import org.cipres.treebase.domain.study.StudyService;
public class OAIPMHController extends AbstractCommandController{
-
- public OAIPMHController(){
+
+ private SubmissionService submissionService;
+ private StudyService studyService;
+
+ public OAIPMHController(){
setCommandClass(OAIPMHCommand.class);
+ setCommandName("params");
}
@Override
@@ -26,7 +32,7 @@
OAIPMHCommand params = (OAIPMHCommand) command;
- Map model=new HashMap();
+ Map model=errors.getModel();
model.put("params", params);
Method method=null;
@@ -43,38 +49,40 @@
}
ModelAndView ListRecoed(HttpServletRequest request, HttpServletResponse response, Map model){
+
+ return (new ModelAndView(metadataPrefix+"_ListRecoed.vm",model));
- return null;
-
}
- ModelAndView ListMetadataFormats(HttpServletRequest request, HttpServletResponse response, Map model){
- return null;
-
- }
ModelAndView ListIdentifiers(HttpServletRequest request, HttpServletResponse response, Map model){
+ metadataPrefix
+ return (new ModelAndView(metadataPrefix+"_ListIdentifiers.vm",model));
- return null;
-
}
ModelAndView GetRecord(HttpServletRequest request, HttpServletResponse response, Map model){
+ metadataPrefix
+ return (new ModelAndView(metadataPrefix+"_GetRecord.vm",model));
- return null;
-
}
ModelAndView Identify(HttpServletRequest request, HttpServletResponse response, Map model){
- return null;
+ return (new ModelAndView("Identify.vm",model));
}
ModelAndView ListSet(HttpServletRequest request, HttpServletResponse response, Map model){
- return null;
+ return (new ModelAndView("ListSet.vm",model));
}
+
+ ModelAndView ListMetadataFormats(HttpServletRequest request, HttpServletResponse response, Map model){
+
+ return (new ModelAndView("ListMetadataFormats.vm",model));
+
+ }
}
Modified: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml 2009-11-01 22:31:20 UTC (rev 229)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-servlet.xml 2009-11-02 00:15:50 UTC (rev 230)
@@ -19,12 +19,13 @@
</bean>
<!-- ========================================================== -->
- <!-- LIST OF CONTROLLERS FOR VERBS AND FORMATS -->
+ <!-- LIST OF CONTROLLERS FOR OAI-PMH -->
<!-- ========================================================== -->
- <!--bean id="appletInteractionController" class="org.cipres.treebase.web.controllers.AppletInteractionController">
- <property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
- </bean-->
+ <bean id="OAIPMHController" class="org.treebase.oai.web.controller.OAIPMHController">
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
+ <property name="studyService"><ref bean="studyphyloTreeService"></ref></property>
+ </bean>
<!-- ========================================================== -->
@@ -62,7 +63,7 @@
<property name="alwaysUseFullPath" value="true"/>
<property name="mappings">
<props>
- <!--prop key="/oai-pmh verbs/metadata formats/paramaters</prop-->
+ <prop key="/top/**">OAIPMHController</prop>
</props>
</property>
</bean>
Modified: trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/oai/web/controller/OAIPMHController.class
===================================================================
(Binary files differ)
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From: <rv...@us...> - 2009-11-01 22:31:37
|
Revision: 229
http://treebase.svn.sourceforge.net/treebase/?rev=229&view=rev
Author: rvos
Date: 2009-11-01 22:31:20 +0000 (Sun, 01 Nov 2009)
Log Message:
-----------
reverting deletion of perl subtree. this folder structure contains scripts and supporting libraries for loading database dumps, checking for database consistency, running generic java classes and sql statements etc. this code is almost entirely due to mjdominus (who has left the project).
Added Paths:
-----------
trunk/treebase-core/src/main/perl/
trunk/treebase-core/src/main/perl/bin/
trunk/treebase-core/src/main/perl/bin/check
trunk/treebase-core/src/main/perl/bin/digester
trunk/treebase-core/src/main/perl/bin/dosql
trunk/treebase-core/src/main/perl/bin/findby
trunk/treebase-core/src/main/perl/bin/gc
trunk/treebase-core/src/main/perl/bin/publish
trunk/treebase-core/src/main/perl/bin/sel
trunk/treebase-core/src/main/perl/bin/show
trunk/treebase-core/src/main/perl/bin/sqldump
trunk/treebase-core/src/main/perl/bin/tbo
trunk/treebase-core/src/main/perl/bin/td
trunk/treebase-core/src/main/perl/bin/undump
trunk/treebase-core/src/main/perl/check/
trunk/treebase-core/src/main/perl/check/check
trunk/treebase-core/src/main/perl/check/digester
trunk/treebase-core/src/main/perl/check/gc
trunk/treebase-core/src/main/perl/dump/
trunk/treebase-core/src/main/perl/dump/dosql
trunk/treebase-core/src/main/perl/dump/findby
trunk/treebase-core/src/main/perl/dump/iq
trunk/treebase-core/src/main/perl/dump/loadspeed
trunk/treebase-core/src/main/perl/dump/sel
trunk/treebase-core/src/main/perl/dump/show
trunk/treebase-core/src/main/perl/dump/showanalyses
trunk/treebase-core/src/main/perl/dump/showmatrices
trunk/treebase-core/src/main/perl/dump/showmatrix
trunk/treebase-core/src/main/perl/dump/showtree
trunk/treebase-core/src/main/perl/dump/showtrees
trunk/treebase-core/src/main/perl/dump/sqldump
trunk/treebase-core/src/main/perl/dump/tbo
trunk/treebase-core/src/main/perl/dump/td
trunk/treebase-core/src/main/perl/jrun
trunk/treebase-core/src/main/perl/lib/
trunk/treebase-core/src/main/perl/lib/CIPRES/
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/DBILogin.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/DBIUtil.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/TreeBaseObjects.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/VeryBadORM.pm
trunk/treebase-core/src/main/perl/misc/
trunk/treebase-core/src/main/perl/misc/build_and_deploy_treebase.sh
trunk/treebase-core/src/main/perl/misc/fix-sequence
trunk/treebase-core/src/main/perl/misc/kill-jrun
trunk/treebase-core/src/main/perl/misc/publish
trunk/treebase-core/src/main/perl/misc/upload-manager
Removed Paths:
-------------
trunk/treebase-core/src/main/perl/bin/
trunk/treebase-core/src/main/perl/bin/check
trunk/treebase-core/src/main/perl/bin/digester
trunk/treebase-core/src/main/perl/bin/dosql
trunk/treebase-core/src/main/perl/bin/findby
trunk/treebase-core/src/main/perl/bin/gc
trunk/treebase-core/src/main/perl/bin/publish
trunk/treebase-core/src/main/perl/bin/sel
trunk/treebase-core/src/main/perl/bin/show
trunk/treebase-core/src/main/perl/bin/sqldump
trunk/treebase-core/src/main/perl/bin/tbo
trunk/treebase-core/src/main/perl/bin/td
trunk/treebase-core/src/main/perl/bin/undump
trunk/treebase-core/src/main/perl/check/
trunk/treebase-core/src/main/perl/check/check
trunk/treebase-core/src/main/perl/check/digester
trunk/treebase-core/src/main/perl/check/gc
trunk/treebase-core/src/main/perl/dump/
trunk/treebase-core/src/main/perl/dump/dosql
trunk/treebase-core/src/main/perl/dump/findby
trunk/treebase-core/src/main/perl/dump/iq
trunk/treebase-core/src/main/perl/dump/loadspeed
trunk/treebase-core/src/main/perl/dump/sel
trunk/treebase-core/src/main/perl/dump/show
trunk/treebase-core/src/main/perl/dump/showanalyses
trunk/treebase-core/src/main/perl/dump/showmatrices
trunk/treebase-core/src/main/perl/dump/showmatrix
trunk/treebase-core/src/main/perl/dump/showtree
trunk/treebase-core/src/main/perl/dump/showtrees
trunk/treebase-core/src/main/perl/dump/sqldump
trunk/treebase-core/src/main/perl/dump/tbo
trunk/treebase-core/src/main/perl/dump/td
trunk/treebase-core/src/main/perl/jrun
trunk/treebase-core/src/main/perl/lib/
trunk/treebase-core/src/main/perl/lib/CIPRES/
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/DBILogin.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/DBIUtil.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/RecDumper.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/TreeBaseObjects.pm
trunk/treebase-core/src/main/perl/lib/CIPRES/TreeBase/VeryBadORM.pm
trunk/treebase-core/src/main/perl/misc/
trunk/treebase-core/src/main/perl/misc/build_and_deploy_treebase.sh
trunk/treebase-core/src/main/perl/misc/fix-sequence
trunk/treebase-core/src/main/perl/misc/kill-jrun
trunk/treebase-core/src/main/perl/misc/publish
trunk/treebase-core/src/main/perl/misc/upload-manager
Deleted: trunk/treebase-core/src/main/perl/bin/check
===================================================================
--- trunk/treebase-core/src/main/perl/bin/check 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/check 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../check/check
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/check (from rev 212, trunk/treebase-core/src/main/perl/bin/check)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/check (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/check 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../check/check
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/digester
===================================================================
--- trunk/treebase-core/src/main/perl/bin/digester 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/digester 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../check/digester
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/digester (from rev 212, trunk/treebase-core/src/main/perl/bin/digester)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/digester (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/digester 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../check/digester
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/dosql
===================================================================
--- trunk/treebase-core/src/main/perl/bin/dosql 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/dosql 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../dump/dosql
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/dosql (from rev 212, trunk/treebase-core/src/main/perl/bin/dosql)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/dosql (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/dosql 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../dump/dosql
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/findby
===================================================================
--- trunk/treebase-core/src/main/perl/bin/findby 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/findby 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../dump/findby
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/findby (from rev 212, trunk/treebase-core/src/main/perl/bin/findby)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/findby (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/findby 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../dump/findby
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/gc
===================================================================
--- trunk/treebase-core/src/main/perl/bin/gc 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/gc 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../check/gc
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/gc (from rev 212, trunk/treebase-core/src/main/perl/bin/gc)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/gc (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/gc 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../check/gc
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/publish
===================================================================
--- trunk/treebase-core/src/main/perl/bin/publish 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/publish 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../misc/publish
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/publish (from rev 212, trunk/treebase-core/src/main/perl/bin/publish)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/publish (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/publish 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../misc/publish
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/sel
===================================================================
--- trunk/treebase-core/src/main/perl/bin/sel 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/sel 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../dump/sel
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/sel (from rev 212, trunk/treebase-core/src/main/perl/bin/sel)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/sel (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/sel 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../dump/sel
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/show
===================================================================
--- trunk/treebase-core/src/main/perl/bin/show 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/show 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../dump/show
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/show (from rev 212, trunk/treebase-core/src/main/perl/bin/show)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/show (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/show 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../dump/show
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/sqldump
===================================================================
--- trunk/treebase-core/src/main/perl/bin/sqldump 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/sqldump 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../dump/sqldump
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/sqldump (from rev 212, trunk/treebase-core/src/main/perl/bin/sqldump)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/sqldump (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/sqldump 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../dump/sqldump
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/tbo
===================================================================
--- trunk/treebase-core/src/main/perl/bin/tbo 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/tbo 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../dump/tbo
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/tbo (from rev 212, trunk/treebase-core/src/main/perl/bin/tbo)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/tbo (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/tbo 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../dump/tbo
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/td
===================================================================
--- trunk/treebase-core/src/main/perl/bin/td 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/td 2009-11-01 22:31:20 UTC (rev 229)
@@ -1 +0,0 @@
-link ../dump/td
\ No newline at end of file
Copied: trunk/treebase-core/src/main/perl/bin/td (from rev 212, trunk/treebase-core/src/main/perl/bin/td)
===================================================================
--- trunk/treebase-core/src/main/perl/bin/td (rev 0)
+++ trunk/treebase-core/src/main/perl/bin/td 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1 @@
+link ../dump/td
\ No newline at end of file
Deleted: trunk/treebase-core/src/main/perl/bin/undump
===================================================================
--- trunk/treebase-core/src/main/perl/bin/undump 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/bin/undump 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,92 +0,0 @@
-#!/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;
-}
Copied: trunk/treebase-core/src/main/perl/bin/undump (from rev 212, 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 2009-11-01 22:31:20 UTC (rev 229)
@@ -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;
+}
Deleted: trunk/treebase-core/src/main/perl/check/check
===================================================================
--- trunk/treebase-core/src/main/perl/check/check 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/check/check 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,186 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use CIPRES::TreeBase::DBIUtil;
-use CIPRES::TreeBase::TreeBaseObjects;
-use Getopt::Std;
-our $indent = 0;
-
-my $TERMINAL;
-if (-t STDOUT) {
- $| = 1;
- $TERMINAL = 1;
-}
-
-my %opt;
-getopts('chasd:p:RC:X', \%opt) or usage();
-if ($opt{X}) { list_known_classes(); }
-if ($opt{h}) { usage(); }
-if ($opt{R}) {
- if ($opt{d}) { die "-R and -d are incompatible\n"; }
- $opt{d} = 0;
-}
-if ($opt{c}) {
- if ($opt{C}) { die "-c and -C are inconsistent\n"; }
- $opt{C} = ""; # set, but no classes
-}
-
-my %prune = map { $_ => 1 } split /,\s*/, $opt{p};
-my $all_consistency_checks = ! defined $opt{C};
-my %consistency_check = map { $_ => 1 } split /,\s*/, $opt{C};
-
-if ($opt{s}) {
- # prune out "small" classes
- $prune{$_} = 1 for qw(MatrixRow PhyloTreeNode TaxonLabel MatrixKind TreeType);
-}
-
-my $type = shift or usage();
-my $id = shift or usage();
-$id =~ s/^#//;
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-CIPRES::TreeBase::TreeBaseObjects->set_db_connection($dbh);
-$dbh->{ShowErrorStatement} = 1;
-use Carp 'croak';
-sub full_str {
- my $self = shift;
- $self->reify;
- my @keys = sort(grep !/[^A-Z]/, keys %$self);
- my @components = map "$_ => $self->{$_}", @keys;
- return join ", ", @components;
-}
-
-sub attr_check {
- my ($obj, $attr_name, $attr, $warnings) = @_;
-# warn "checking to see that this object has $attr_name = $attr->{$attr_name}\n";
-
- # If $attr is just a scalar, fake up an attr hash with one attribute
- unless (ref $attr) {
- $attr = { $attr_name => $attr };
- }
-
- unless ($warnings || $attr->{warnings}) {
- croak "No warning target variable specified";
- }
-
- return 1 unless exists $attr->{$attr_name};
- if (not defined $obj->$attr_name) {
- # attribute is missing from the object
-
- # ... okay, if it is specifically required to be missing
- return 1 if ! defined $attr->{$attr_name};
-
- # otherwise, record an error
- push @$warnings,
- "Object ". $obj->CIPRES::TreeBase::VeryBadORM::to_str.
- " should have $attr_name = $attr->{$attr_name}, ".
- " but it is missing.";
- return;
- }
-
- return 1 if $obj->$attr_name->id == $attr->{$attr_name};
- push @$warnings,
- "Object ". $obj->CIPRES::TreeBase::VeryBadORM::to_str.
- " should have $attr_name = $attr->{$attr_name}, ".
- " but instead has " . $obj->$attr_name->id;
- return;
-}
-
-my $OK = 1;
-my @warnings;
-$type->new($id)->dump(action => \&prt, seen => {},
- prune => \%prune,
- show_all => $opt{a},
- warnings => \@warnings,
- attr_check => \&attr_check,
- defined($opt{d}) ? (maxdepth => $opt{d}) : (),
- );
-
-for my $w (@warnings) {
- print STDERR "*** $w\n";
-}
-if (! $OK) {
- warn "Inconsistencies detected\n";
- exit 1;
-} else {
- exit 0;
-}
-
-
-sub prt {
- my ($self, %attr) = @_;
- my $seen = $attr{seen}{$self->class}{$self->id}++;
- my $str = $attr{show_all} ? full_str($self) : $self->to_str;
- my $indent = " " x $attr{depth};
- my $consistent;
-
- my ($class, $id) = ($self->class, $self->id);
-
- if (! $seen) {
- my $z;
- if ($TERMINAL) {
- $z = "(Checking consistency of $class $id.)";
- print $z, "\r";
- }
-
- {
- my $do_check = $all_consistency_checks || $consistency_check{$class};
- $consistent = $do_check ? $self->consistent(%attr) : 1;
- }
-
- $OK &&= $consistent;
- if ($TERMINAL) {
- print " " x length($z), "\r";
- }
- }
-
- unless ($class->is_nested) {
- if (exists $attr{$class} &&
- $attr{$class} != $id) {
- push @{$attr{warnings}}, "** Expected $class $attr{$class}, found $id insead\n";
- }
- }
-
- my $mark = $seen ? "|-" : $consistent ? "| " : "|*";
- return 0 if $attr{prune}{$self->class};
- print "| " x $attr{depth}, "$mark$str\n";
-
- return !$seen;
-}
-
-sub list_known_classes {
- my $kch = CIPRES::TreeBase::VeryBadORM->known_class_hash();
- for my $k (sort values %$kch) {
- print "$k\n";
- }
- exit 0;
-}
-
-sub usage {
- print STDERR qq<Usage: $0 [-X] [-acsR] [-d n] [-pClass1,Class2,...] [-CClasses...] Class IDnumber
-
-Recursively print the contents of the specified object of the
-specified class. For example, "$0 Study 1234" prints out study #1234
-and all of its trees, matrices, analyses, etc., and their contents.
-
-Use "$0 -X" for a list of known classes.
-
-Options:
- -a: show *all* attributes of every object (default: pretty-print objects)
- -s: do not recurse into "small" objects (Currently: MatrixRow,
- PhyloTreeNode, TaxonLabel)
- -R: do not recurse at all, printing only the top object
- -c: Skip all consistency checking
-
- -d n: recurse only n levels deep
-
- -pClasses... : 'prune': do not display or recurse into objects of these
- classes.
- -CClasses... : Perform consistency checking of these classes only
->;
- exit 1;
-}
-
-
-1;
Copied: trunk/treebase-core/src/main/perl/check/check (from rev 212, trunk/treebase-core/src/main/perl/check/check)
===================================================================
--- trunk/treebase-core/src/main/perl/check/check (rev 0)
+++ trunk/treebase-core/src/main/perl/check/check 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,186 @@
+#!/usr/bin/perl
+
+use strict;
+use CIPRES::TreeBase::DBIUtil;
+use CIPRES::TreeBase::TreeBaseObjects;
+use Getopt::Std;
+our $indent = 0;
+
+my $TERMINAL;
+if (-t STDOUT) {
+ $| = 1;
+ $TERMINAL = 1;
+}
+
+my %opt;
+getopts('chasd:p:RC:X', \%opt) or usage();
+if ($opt{X}) { list_known_classes(); }
+if ($opt{h}) { usage(); }
+if ($opt{R}) {
+ if ($opt{d}) { die "-R and -d are incompatible\n"; }
+ $opt{d} = 0;
+}
+if ($opt{c}) {
+ if ($opt{C}) { die "-c and -C are inconsistent\n"; }
+ $opt{C} = ""; # set, but no classes
+}
+
+my %prune = map { $_ => 1 } split /,\s*/, $opt{p};
+my $all_consistency_checks = ! defined $opt{C};
+my %consistency_check = map { $_ => 1 } split /,\s*/, $opt{C};
+
+if ($opt{s}) {
+ # prune out "small" classes
+ $prune{$_} = 1 for qw(MatrixRow PhyloTreeNode TaxonLabel MatrixKind TreeType);
+}
+
+my $type = shift or usage();
+my $id = shift or usage();
+$id =~ s/^#//;
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+CIPRES::TreeBase::TreeBaseObjects->set_db_connection($dbh);
+$dbh->{ShowErrorStatement} = 1;
+use Carp 'croak';
+sub full_str {
+ my $self = shift;
+ $self->reify;
+ my @keys = sort(grep !/[^A-Z]/, keys %$self);
+ my @components = map "$_ => $self->{$_}", @keys;
+ return join ", ", @components;
+}
+
+sub attr_check {
+ my ($obj, $attr_name, $attr, $warnings) = @_;
+# warn "checking to see that this object has $attr_name = $attr->{$attr_name}\n";
+
+ # If $attr is just a scalar, fake up an attr hash with one attribute
+ unless (ref $attr) {
+ $attr = { $attr_name => $attr };
+ }
+
+ unless ($warnings || $attr->{warnings}) {
+ croak "No warning target variable specified";
+ }
+
+ return 1 unless exists $attr->{$attr_name};
+ if (not defined $obj->$attr_name) {
+ # attribute is missing from the object
+
+ # ... okay, if it is specifically required to be missing
+ return 1 if ! defined $attr->{$attr_name};
+
+ # otherwise, record an error
+ push @$warnings,
+ "Object ". $obj->CIPRES::TreeBase::VeryBadORM::to_str.
+ " should have $attr_name = $attr->{$attr_name}, ".
+ " but it is missing.";
+ return;
+ }
+
+ return 1 if $obj->$attr_name->id == $attr->{$attr_name};
+ push @$warnings,
+ "Object ". $obj->CIPRES::TreeBase::VeryBadORM::to_str.
+ " should have $attr_name = $attr->{$attr_name}, ".
+ " but instead has " . $obj->$attr_name->id;
+ return;
+}
+
+my $OK = 1;
+my @warnings;
+$type->new($id)->dump(action => \&prt, seen => {},
+ prune => \%prune,
+ show_all => $opt{a},
+ warnings => \@warnings,
+ attr_check => \&attr_check,
+ defined($opt{d}) ? (maxdepth => $opt{d}) : (),
+ );
+
+for my $w (@warnings) {
+ print STDERR "*** $w\n";
+}
+if (! $OK) {
+ warn "Inconsistencies detected\n";
+ exit 1;
+} else {
+ exit 0;
+}
+
+
+sub prt {
+ my ($self, %attr) = @_;
+ my $seen = $attr{seen}{$self->class}{$self->id}++;
+ my $str = $attr{show_all} ? full_str($self) : $self->to_str;
+ my $indent = " " x $attr{depth};
+ my $consistent;
+
+ my ($class, $id) = ($self->class, $self->id);
+
+ if (! $seen) {
+ my $z;
+ if ($TERMINAL) {
+ $z = "(Checking consistency of $class $id.)";
+ print $z, "\r";
+ }
+
+ {
+ my $do_check = $all_consistency_checks || $consistency_check{$class};
+ $consistent = $do_check ? $self->consistent(%attr) : 1;
+ }
+
+ $OK &&= $consistent;
+ if ($TERMINAL) {
+ print " " x length($z), "\r";
+ }
+ }
+
+ unless ($class->is_nested) {
+ if (exists $attr{$class} &&
+ $attr{$class} != $id) {
+ push @{$attr{warnings}}, "** Expected $class $attr{$class}, found $id insead\n";
+ }
+ }
+
+ my $mark = $seen ? "|-" : $consistent ? "| " : "|*";
+ return 0 if $attr{prune}{$self->class};
+ print "| " x $attr{depth}, "$mark$str\n";
+
+ return !$seen;
+}
+
+sub list_known_classes {
+ my $kch = CIPRES::TreeBase::VeryBadORM->known_class_hash();
+ for my $k (sort values %$kch) {
+ print "$k\n";
+ }
+ exit 0;
+}
+
+sub usage {
+ print STDERR qq<Usage: $0 [-X] [-acsR] [-d n] [-pClass1,Class2,...] [-CClasses...] Class IDnumber
+
+Recursively print the contents of the specified object of the
+specified class. For example, "$0 Study 1234" prints out study #1234
+and all of its trees, matrices, analyses, etc., and their contents.
+
+Use "$0 -X" for a list of known classes.
+
+Options:
+ -a: show *all* attributes of every object (default: pretty-print objects)
+ -s: do not recurse into "small" objects (Currently: MatrixRow,
+ PhyloTreeNode, TaxonLabel)
+ -R: do not recurse at all, printing only the top object
+ -c: Skip all consistency checking
+
+ -d n: recurse only n levels deep
+
+ -pClasses... : 'prune': do not display or recurse into objects of these
+ classes.
+ -CClasses... : Perform consistency checking of these classes only
+>;
+ exit 1;
+}
+
+
+1;
Deleted: trunk/treebase-core/src/main/perl/check/digester
===================================================================
--- trunk/treebase-core/src/main/perl/check/digester 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/check/digester 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,49 +0,0 @@
-#!/usr/bin/perl
-#
-# Digest reports that come out of the checker:
-# grep out all the lines that begin with '***'
-# pass them through this program
-# This program will sort each different kind of message into a separate file
-# To have the files placed in some other directory, use the -d option
-# 20090327 MJD
-#
-
-use Getopt::Std;
-my %opt = (d => ".");
-getopts('d:', \%opt) or die;
--d($opt{d}) || mkdir($opt{d}) || die "$opt{d}: $!";
-
-while (<>) {
- chomp;
- my $k = $_;
- $k =~ s/\d+/#/g;
- $k =~ s/#(\s*#)+/##/g;
- $k =~ s/^S#:\s+//;
- push @{$msg{$k}}, $_;
-}
-
-for my $k (keys %msg) {
- my $f = abbr($k);
- open my($fh), ">", "$opt{d}/$f" or die "$opt{d}/$f: $!";
- print $fh $_, "\n" for @{$msg{$k}};
- close $fh;
-}
-
-my $q;
-BEGIN { $q = 1 };
-my %seen;
-
-sub abbr {
- my $s = shift;
- $s =~ tr/A-Z /a-z_/;
- $s =~ tr/A-Za-z_//cd;
- $s =~ tr/_/_/s;
- $s =~ s/^_//;
-
- substr($s, 30) = "" if length($s) > 30;
- if ($seen{$s}) {
- $s .= $q++;
- }
- return $s;
-}
-
Copied: trunk/treebase-core/src/main/perl/check/digester (from rev 212, trunk/treebase-core/src/main/perl/check/digester)
===================================================================
--- trunk/treebase-core/src/main/perl/check/digester (rev 0)
+++ trunk/treebase-core/src/main/perl/check/digester 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,49 @@
+#!/usr/bin/perl
+#
+# Digest reports that come out of the checker:
+# grep out all the lines that begin with '***'
+# pass them through this program
+# This program will sort each different kind of message into a separate file
+# To have the files placed in some other directory, use the -d option
+# 20090327 MJD
+#
+
+use Getopt::Std;
+my %opt = (d => ".");
+getopts('d:', \%opt) or die;
+-d($opt{d}) || mkdir($opt{d}) || die "$opt{d}: $!";
+
+while (<>) {
+ chomp;
+ my $k = $_;
+ $k =~ s/\d+/#/g;
+ $k =~ s/#(\s*#)+/##/g;
+ $k =~ s/^S#:\s+//;
+ push @{$msg{$k}}, $_;
+}
+
+for my $k (keys %msg) {
+ my $f = abbr($k);
+ open my($fh), ">", "$opt{d}/$f" or die "$opt{d}/$f: $!";
+ print $fh $_, "\n" for @{$msg{$k}};
+ close $fh;
+}
+
+my $q;
+BEGIN { $q = 1 };
+my %seen;
+
+sub abbr {
+ my $s = shift;
+ $s =~ tr/A-Z /a-z_/;
+ $s =~ tr/A-Za-z_//cd;
+ $s =~ tr/_/_/s;
+ $s =~ s/^_//;
+
+ substr($s, 30) = "" if length($s) > 30;
+ if ($seen{$s}) {
+ $s .= $q++;
+ }
+ return $s;
+}
+
Deleted: trunk/treebase-core/src/main/perl/check/gc
===================================================================
--- trunk/treebase-core/src/main/perl/check/gc 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/check/gc 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,90 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use CIPRES::TreeBase::DBIUtil;
-use CIPRES::TreeBase::TreeBaseObjects;
-use Getopt::Std;
-use Carp 'croak';
-
-# $seen{$class}{$id} is 0 if the object was in the DB but unreferenced
-# 1 if the object was in the DB and referenced
-my %SEEN = ();
-my $count = 0;
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-CIPRES::TreeBase::TreeBaseObjects->set_db_connection($dbh);
-
-my @CLASSES = qw(Analysis AnalysisStep AnalyzedData
- Matrix MatrixRow
- PhyloTree PhyloTreeNode
- Study
- TaxonLabel
- );
-
-
-for my $class (@CLASSES) {
- for my $id (get_all_ids($class)) {
- $SEEN{$class}{$id} = 0;
- }
- warn "Database contains ", scalar(keys %{$SEEN{$class}}), " $class items\n";
-}
-
-for my $study (map {Study->new($_)} keys %{$SEEN{Study}}) {
- next if $SEEN{Study}{$study->id}++;
- my $N = $study->analyzed_data;
- my $PREFIX = "S" . $study->id;
- print STDERR $PREFIX;
- my $C = 0;
-
- for my $analysis ($study->analyses) {
- next if $SEEN{Analysis}{$analysis->id}++;
- for my $astep ($analysis->analysissteps) {
- next if $SEEN{AnalysisStep}{$astep->id}++;
- for my $adata ($astep->analyzeddata) {
- next if $SEEN{AnalyzedData}{$adata->id}++;
- $C++;
- print STDERR " $C/$N\r$PREFIX";
- if (my $matrix = $adata->matrix) {
- next if $SEEN{Matrix}{$matrix->id}++;
- for my $row ($matrix->rows) {
- next if $SEEN{MatrixRow}{$row->id}++;
- $SEEN{TaxonLabel}{$row->taxonlabel->id} = 1 if $row->taxonlabel
- }
- } elsif (my $tree = $adata->phylotree) {
- for my $node ($tree->nodes) {
- next if $SEEN{PhyloTreeNode}{$node->id}++;
- $SEEN{TaxonLabel}{$node->taxonlabel->id} = 1 if $node->taxonlabel
- }
- }
- }
- }
- }
- print STDERR "\n";
-}
-
-for my $class (sort keys %SEEN) {
- my $classHash = $SEEN{$class};
- for my $id (sort {$a <=> $b} keys %$classHash) {
- if ($classHash->{$id} == 0) {
- print "* $class $id\n";
- }
- }
-}
-
-
-sub get_all_ids {
- my $class = shift;
- my $table = $class->table or croak "Unknown object class '$class'";
- my $id_attr = $class->id_attr or croak "Unknown object class '$class'";
- my $sql = "select $id_attr from $table";
- my $ids = $dbh->selectcol_arrayref($sql);
- return wantarray ? @$ids : $ids;
-}
-
-sub get_all {
- my $class = shift;
- my @ids = sort {$a<=>$b} get_all_ids($class);
- my @objs = map { $class->new($_) } @ids;
- return wantarray ? @objs : \@objs;
-}
Copied: trunk/treebase-core/src/main/perl/check/gc (from rev 212, trunk/treebase-core/src/main/perl/check/gc)
===================================================================
--- trunk/treebase-core/src/main/perl/check/gc (rev 0)
+++ trunk/treebase-core/src/main/perl/check/gc 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,90 @@
+#!/usr/bin/perl
+
+use strict;
+use CIPRES::TreeBase::DBIUtil;
+use CIPRES::TreeBase::TreeBaseObjects;
+use Getopt::Std;
+use Carp 'croak';
+
+# $seen{$class}{$id} is 0 if the object was in the DB but unreferenced
+# 1 if the object was in the DB and referenced
+my %SEEN = ();
+my $count = 0;
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+CIPRES::TreeBase::TreeBaseObjects->set_db_connection($dbh);
+
+my @CLASSES = qw(Analysis AnalysisStep AnalyzedData
+ Matrix MatrixRow
+ PhyloTree PhyloTreeNode
+ Study
+ TaxonLabel
+ );
+
+
+for my $class (@CLASSES) {
+ for my $id (get_all_ids($class)) {
+ $SEEN{$class}{$id} = 0;
+ }
+ warn "Database contains ", scalar(keys %{$SEEN{$class}}), " $class items\n";
+}
+
+for my $study (map {Study->new($_)} keys %{$SEEN{Study}}) {
+ next if $SEEN{Study}{$study->id}++;
+ my $N = $study->analyzed_data;
+ my $PREFIX = "S" . $study->id;
+ print STDERR $PREFIX;
+ my $C = 0;
+
+ for my $analysis ($study->analyses) {
+ next if $SEEN{Analysis}{$analysis->id}++;
+ for my $astep ($analysis->analysissteps) {
+ next if $SEEN{AnalysisStep}{$astep->id}++;
+ for my $adata ($astep->analyzeddata) {
+ next if $SEEN{AnalyzedData}{$adata->id}++;
+ $C++;
+ print STDERR " $C/$N\r$PREFIX";
+ if (my $matrix = $adata->matrix) {
+ next if $SEEN{Matrix}{$matrix->id}++;
+ for my $row ($matrix->rows) {
+ next if $SEEN{MatrixRow}{$row->id}++;
+ $SEEN{TaxonLabel}{$row->taxonlabel->id} = 1 if $row->taxonlabel
+ }
+ } elsif (my $tree = $adata->phylotree) {
+ for my $node ($tree->nodes) {
+ next if $SEEN{PhyloTreeNode}{$node->id}++;
+ $SEEN{TaxonLabel}{$node->taxonlabel->id} = 1 if $node->taxonlabel
+ }
+ }
+ }
+ }
+ }
+ print STDERR "\n";
+}
+
+for my $class (sort keys %SEEN) {
+ my $classHash = $SEEN{$class};
+ for my $id (sort {$a <=> $b} keys %$classHash) {
+ if ($classHash->{$id} == 0) {
+ print "* $class $id\n";
+ }
+ }
+}
+
+
+sub get_all_ids {
+ my $class = shift;
+ my $table = $class->table or croak "Unknown object class '$class'";
+ my $id_attr = $class->id_attr or croak "Unknown object class '$class'";
+ my $sql = "select $id_attr from $table";
+ my $ids = $dbh->selectcol_arrayref($sql);
+ return wantarray ? @$ids : $ids;
+}
+
+sub get_all {
+ my $class = shift;
+ my @ids = sort {$a<=>$b} get_all_ids($class);
+ my @objs = map { $class->new($_) } @ids;
+ return wantarray ? @objs : \@objs;
+}
Deleted: trunk/treebase-core/src/main/perl/dump/dosql
===================================================================
--- trunk/treebase-core/src/main/perl/dump/dosql 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/dump/dosql 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,25 +0,0 @@
-#!/usr/bin/perl
-
-use CIPRES::TreeBase::DBIUtil;
-use Getopt::Std;
-
-getopts('s') or die "Usage: $0 SQL statement on command line";
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-
-if ($opt_s) {
- my @statements = split /;[ \t]*\r?\n/, join "", <ARGV>;
- for my $Q (@statements) {
- next unless $Q =~ /\S/;
- print "$Q\n";
- $dbh->do($Q)
- or die "Couldn't prepare statement:\n\t$Q\n\t" . $dbh->errstr;
- }
-} else {
- my $Q = join " ", @ARGV;
- $dbh->do($Q)
- or die "Couldn't prepare statement: " . $dbh->errstr;
-}
-
-$dbh->disconnect;
Copied: trunk/treebase-core/src/main/perl/dump/dosql (from rev 212, trunk/treebase-core/src/main/perl/dump/dosql)
===================================================================
--- trunk/treebase-core/src/main/perl/dump/dosql (rev 0)
+++ trunk/treebase-core/src/main/perl/dump/dosql 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,25 @@
+#!/usr/bin/perl
+
+use CIPRES::TreeBase::DBIUtil;
+use Getopt::Std;
+
+getopts('s') or die "Usage: $0 SQL statement on command line";
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+
+if ($opt_s) {
+ my @statements = split /;[ \t]*\r?\n/, join "", <ARGV>;
+ for my $Q (@statements) {
+ next unless $Q =~ /\S/;
+ print "$Q\n";
+ $dbh->do($Q)
+ or die "Couldn't prepare statement:\n\t$Q\n\t" . $dbh->errstr;
+ }
+} else {
+ my $Q = join " ", @ARGV;
+ $dbh->do($Q)
+ or die "Couldn't prepare statement: " . $dbh->errstr;
+}
+
+$dbh->disconnect;
Deleted: trunk/treebase-core/src/main/perl/dump/findby
===================================================================
--- trunk/treebase-core/src/main/perl/dump/findby 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/dump/findby 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,31 +0,0 @@
-#!/usr/bin/perl
-# -*- cperl -*-
-
-use CIPRES::TreeBase::DBIUtil;
-use Getopt::Std;
-
-my %opt = ();
-getopts('', \%opt) or usage();
-my ($class, $attr, $val) = @ARGV;
-defined($class) && defined($attr) && defined($val) or usage();
-
-my $query = "select $class\_id from $class where $attr = ?";
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-my $sth = $dbh->prepare($query)
- or die "Couldn't prepare statement: " . $dbh->errstr;
-my $rc = $sth->execute($val)
- or die "Couldn't execute statement: " . $dbh->errstr;
-my $row;
-while (my ($id) = $sth->fetchrow_array) {
- print "$id\n";
-}
-
-$dbh->disconnect;
-
-sub usage {
- print "$0 [-n nullsymbol] table id#\n";
- exit 1;
-}
-
Copied: trunk/treebase-core/src/main/perl/dump/findby (from rev 212, trunk/treebase-core/src/main/perl/dump/findby)
===================================================================
--- trunk/treebase-core/src/main/perl/dump/findby (rev 0)
+++ trunk/treebase-core/src/main/perl/dump/findby 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,31 @@
+#!/usr/bin/perl
+# -*- cperl -*-
+
+use CIPRES::TreeBase::DBIUtil;
+use Getopt::Std;
+
+my %opt = ();
+getopts('', \%opt) or usage();
+my ($class, $attr, $val) = @ARGV;
+defined($class) && defined($attr) && defined($val) or usage();
+
+my $query = "select $class\_id from $class where $attr = ?";
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+my $sth = $dbh->prepare($query)
+ or die "Couldn't prepare statement: " . $dbh->errstr;
+my $rc = $sth->execute($val)
+ or die "Couldn't execute statement: " . $dbh->errstr;
+my $row;
+while (my ($id) = $sth->fetchrow_array) {
+ print "$id\n";
+}
+
+$dbh->disconnect;
+
+sub usage {
+ print "$0 [-n nullsymbol] table id#\n";
+ exit 1;
+}
+
Deleted: trunk/treebase-core/src/main/perl/dump/iq
===================================================================
--- trunk/treebase-core/src/main/perl/dump/iq 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/dump/iq 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,140 +0,0 @@
-#!/usr/bin/perl
-# -*- cperl -*-
-
-use CIPRES::TreeBase::DBIUtil;
-use Getopt::Std;
-use Text::ParseWords;
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-$dbh->{RaiseError} = undef;
-$dbh->{PrintError} = 'on';
-
-my %opt = (e => $ENV{IQEDITOR} || $ENV{VISUAL} || $ENV{EDITOR} || "vi",
- m => 20,
- n => "--",
- );
-getopts('e:m:n:', \%opt) or usage();
-
-my $query = "";
-my $sth;
-my $editor = $opt{e};
-my $maxrows = $opt{m};
-my @rows;
-
-while (1) {
-# print $query, "\n" if $query;
- print "> ";
- my $r = <>;
- trim($r);
- last if $r eq "";
-
- if ($r eq "e") {
- $query = edit($query);
- print "$query\n";
- $sth = maybe_run_query($query);
- } elsif (my ($pat, $rep, $g) = ($r =~ m{s/(.*)/(.*)/(g?)})) {
- if ($g) {
- $query =~ s/$pat/$rep/g;
- } else {
- $query =~ s/$pat/$rep/;
- }
- $sth = maybe_run_query($query);
- } elsif ($r =~ s/^x\s*//) {
- (my $q = $query) =~ tr/\n/ /;
- compile_query($query) unless defined $sth;
- run_query($sth, shellwords($r));
- } elsif ($r eq "p") {
- print_aoh(\@rows, $opt_n);
- } elsif ($r =~ s/^w\s*//) {
- if (open my($f), ">", $r) {
- my $ofh = select $f;
- print_aoh(\@rows, $opt_n);
- select $ofh;
- } else {
- warn "Couldn't open '$r' for writing: $!\n";
- }
- } else {
- $query = $r;
- $sth = maybe_run_query($query);
- }
-}
-
-exit;
-
-################################################################
-
-sub compile_query {
- my $query = shift;
- $query =~ tr/\n/ /;
- my $_sth;
- eval {
- $_sth = $dbh->prepare($query);
- };
- if ($_sth) {
- $sth = $_sth;
- } else {
- warn $dbh->errstr . "\n";
- }
- return defined($_sth);
-}
-
-sub maybe_run_query {
- eval {
- my $query = shift;
- compile_query($query) or return;
-
- return unless $sth->{NUM_OF_PARAMS} == 0;
-
-
- run_query($sth);
- return $sth;
- };
-}
-
-sub run_query {
- my $sth = shift;
- return unless defined $sth;
- my @params = @_;
- my @_rows;
-
- warn "Executing...\n";
- $sth->execute(@params) or return;
- while (my $row = $sth->fetchrow_hashref) {
- push @_rows, {%$row};
- }
-
-
- $sth->finish;
- if (@_rows == 0) {
- print "Empty result.\n";
- return;
- } elsif (@_rows <= $maxrows) {
- print_aoh(\@rows, $opt_n);
- } else {
- print "result: " . @_rows . " rows; use 'p' to display\n";
- }
- @rows = @_rows;
-}
-
-sub edit {
- my $tmp = "/tmp/iq.$$";
- my $data = shift;
- $data .= "\n" unless $data =~ /\n\z/;
- open my($f), ">", $tmp or die "Couldn't write temp file '$tmp': $!";
- print $f $data;
- close $f;
- if (system($editor, $tmp) == 0) {
- open my($f), "<", $tmp or die "Couldn't read modified temp file '$tmp': $!";
- $data = join "", <$f>;
- } else {
- warn "Editor failed; ignoring changes\n";
- }
- unlink $tmp;
- return $data;
-}
-
-sub trim {
- $_[0] =~ s/^\s+//;
- $_[0] =~ s/\s+$//;
-}
Copied: trunk/treebase-core/src/main/perl/dump/iq (from rev 212, trunk/treebase-core/src/main/perl/dump/iq)
===================================================================
--- trunk/treebase-core/src/main/perl/dump/iq (rev 0)
+++ trunk/treebase-core/src/main/perl/dump/iq 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,140 @@
+#!/usr/bin/perl
+# -*- cperl -*-
+
+use CIPRES::TreeBase::DBIUtil;
+use Getopt::Std;
+use Text::ParseWords;
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+$dbh->{RaiseError} = undef;
+$dbh->{PrintError} = 'on';
+
+my %opt = (e => $ENV{IQEDITOR} || $ENV{VISUAL} || $ENV{EDITOR} || "vi",
+ m => 20,
+ n => "--",
+ );
+getopts('e:m:n:', \%opt) or usage();
+
+my $query = "";
+my $sth;
+my $editor = $opt{e};
+my $maxrows = $opt{m};
+my @rows;
+
+while (1) {
+# print $query, "\n" if $query;
+ print "> ";
+ my $r = <>;
+ trim($r);
+ last if $r eq "";
+
+ if ($r eq "e") {
+ $query = edit($query);
+ print "$query\n";
+ $sth = maybe_run_query($query);
+ } elsif (my ($pat, $rep, $g) = ($r =~ m{s/(.*)/(.*)/(g?)})) {
+ if ($g) {
+ $query =~ s/$pat/$rep/g;
+ } else {
+ $query =~ s/$pat/$rep/;
+ }
+ $sth = maybe_run_query($query);
+ } elsif ($r =~ s/^x\s*//) {
+ (my $q = $query) =~ tr/\n/ /;
+ compile_query($query) unless defined $sth;
+ run_query($sth, shellwords($r));
+ } elsif ($r eq "p") {
+ print_aoh(\@rows, $opt_n);
+ } elsif ($r =~ s/^w\s*//) {
+ if (open my($f), ">", $r) {
+ my $ofh = select $f;
+ print_aoh(\@rows, $opt_n);
+ select $ofh;
+ } else {
+ warn "Couldn't open '$r' for writing: $!\n";
+ }
+ } else {
+ $query = $r;
+ $sth = maybe_run_query($query);
+ }
+}
+
+exit;
+
+################################################################
+
+sub compile_query {
+ my $query = shift;
+ $query =~ tr/\n/ /;
+ my $_sth;
+ eval {
+ $_sth = $dbh->prepare($query);
+ };
+ if ($_sth) {
+ $sth = $_sth;
+ } else {
+ warn $dbh->errstr . "\n";
+ }
+ return defined($_sth);
+}
+
+sub maybe_run_query {
+ eval {
+ my $query = shift;
+ compile_query($query) or return;
+
+ return unless $sth->{NUM_OF_PARAMS} == 0;
+
+
+ run_query($sth);
+ return $sth;
+ };
+}
+
+sub run_query {
+ my $sth = shift;
+ return unless defined $sth;
+ my @params = @_;
+ my @_rows;
+
+ warn "Executing...\n";
+ $sth->execute(@params) or return;
+ while (my $row = $sth->fetchrow_hashref) {
+ push @_rows, {%$row};
+ }
+
+
+ $sth->finish;
+ if (@_rows == 0) {
+ print "Empty result.\n";
+ return;
+ } elsif (@_rows <= $maxrows) {
+ print_aoh(\@rows, $opt_n);
+ } else {
+ print "result: " . @_rows . " rows; use 'p' to display\n";
+ }
+ @rows = @_rows;
+}
+
+sub edit {
+ my $tmp = "/tmp/iq.$$";
+ my $data = shift;
+ $data .= "\n" unless $data =~ /\n\z/;
+ open my($f), ">", $tmp or die "Couldn't write temp file '$tmp': $!";
+ print $f $data;
+ close $f;
+ if (system($editor, $tmp) == 0) {
+ open my($f), "<", $tmp or die "Couldn't read modified temp file '$tmp': $!";
+ $data = join "", <$f>;
+ } else {
+ warn "Editor failed; ignoring changes\n";
+ }
+ unlink $tmp;
+ return $data;
+}
+
+sub trim {
+ $_[0] =~ s/^\s+//;
+ $_[0] =~ s/\s+$//;
+}
Deleted: trunk/treebase-core/src/main/perl/dump/loadspeed
===================================================================
--- trunk/treebase-core/src/main/perl/dump/loadspeed 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/dump/loadspeed 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,39 +0,0 @@
-#!/usr/bin/perl
-# -*- cperl -*-
-
-use CIPRES::TreeBase::DBIUtil;
-use Getopt::Std;
-
-my %opt = (z => 30);
-getopts('sz:', \%opt) or usage();
-
-@ARGV || usage();
-my $table = shift;
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-my $sth = $dbh->prepare("select count(*) from $table")
- or die "Couldn't prepare statement: " . $dbh->errstr;
-my $rc = $sth->execute()
- or die "Couldn't execute statement: " . $dbh->errstr;
-my ($before) = $sth->fetchrow_array;
-$sth->finish;
-#1 while $sth->fetch;
-warn "$before rows\n" unless $opt{s};
-sleep $opt{z};
-my $rc = $sth->execute()
- or die "Couldn't execute statement: " . $dbh->errstr;
-my ($after) = $sth->fetchrow_array;
-$sth->finish;
-warn "$after rows\n" unless $opt{s};
-my $rate = ($after-$before)*60/$opt{z};
-printf (($opt{s} ? "%.2f\n" : "%.2f records per minute\n"), $rate);
-
-$dbh->disconnect;
-exit;
-
-sub usage {
- print "$0 [-s] [-z time-delay] table-name\n";
- print " -s : short output format\n";
- exit 1;
-}
Copied: trunk/treebase-core/src/main/perl/dump/loadspeed (from rev 212, trunk/treebase-core/src/main/perl/dump/loadspeed)
===================================================================
--- trunk/treebase-core/src/main/perl/dump/loadspeed (rev 0)
+++ trunk/treebase-core/src/main/perl/dump/loadspeed 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,39 @@
+#!/usr/bin/perl
+# -*- cperl -*-
+
+use CIPRES::TreeBase::DBIUtil;
+use Getopt::Std;
+
+my %opt = (z => 30);
+getopts('sz:', \%opt) or usage();
+
+@ARGV || usage();
+my $table = shift;
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+my $sth = $dbh->prepare("select count(*) from $table")
+ or die "Couldn't prepare statement: " . $dbh->errstr;
+my $rc = $sth->execute()
+ or die "Couldn't execute statement: " . $dbh->errstr;
+my ($before) = $sth->fetchrow_array;
+$sth->finish;
+#1 while $sth->fetch;
+warn "$before rows\n" unless $opt{s};
+sleep $opt{z};
+my $rc = $sth->execute()
+ or die "Couldn't execute statement: " . $dbh->errstr;
+my ($after) = $sth->fetchrow_array;
+$sth->finish;
+warn "$after rows\n" unless $opt{s};
+my $rate = ($after-$before)*60/$opt{z};
+printf (($opt{s} ? "%.2f\n" : "%.2f records per minute\n"), $rate);
+
+$dbh->disconnect;
+exit;
+
+sub usage {
+ print "$0 [-s] [-z time-delay] table-name\n";
+ print " -s : short output format\n";
+ exit 1;
+}
Deleted: trunk/treebase-core/src/main/perl/dump/sel
===================================================================
--- trunk/treebase-core/src/main/perl/dump/sel 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/dump/sel 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,42 +0,0 @@
-#!/usr/bin/perl
-# -*- cperl -*-
-
-use CIPRES::TreeBase::DBIUtil;
-use Getopt::Std;
-
-my %opt = (n => '--');
-getopts('n:', \%opt) or usage();
-
-@ARGV || usage();
-my $query = join " ", @ARGV;
-
-$query =~ s/^/SELECT / unless $query =~ /^select\s+/i;
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-my $sth = $dbh->prepare($query)
- or die "Couldn't prepare statement: " . $dbh->errstr;
-my $rc = $sth->execute()
- or die "Couldn't execute statement: " . $dbh->errstr;
-while (my $row = $sth->fetchrow_hashref) {
- push @rows, {%$row};
-}
-
-
-$dbh->disconnect;
-if (@rows) {
- if (@rows == 1 && keys %{$rows[0]} == 1) {
- # Special case for a single selected value
- my ($value) = values %{$rows[0]};
- print "$value\n";
- } else {
- print_aoh(\@rows, $opt_n);
- }
-} else {
- print "Empty result.\n";
-}
-
-sub usage {
- print "$0 [-n nullsymbol] '....'\n";
- exit 1;
-}
Copied: trunk/treebase-core/src/main/perl/dump/sel (from rev 212, trunk/treebase-core/src/main/perl/dump/sel)
===================================================================
--- trunk/treebase-core/src/main/perl/dump/sel (rev 0)
+++ trunk/treebase-core/src/main/perl/dump/sel 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,42 @@
+#!/usr/bin/perl
+# -*- cperl -*-
+
+use CIPRES::TreeBase::DBIUtil;
+use Getopt::Std;
+
+my %opt = (n => '--');
+getopts('n:', \%opt) or usage();
+
+@ARGV || usage();
+my $query = join " ", @ARGV;
+
+$query =~ s/^/SELECT / unless $query =~ /^select\s+/i;
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+my $sth = $dbh->prepare($query)
+ or die "Couldn't prepare statement: " . $dbh->errstr;
+my $rc = $sth->execute()
+ or die "Couldn't execute statement: " . $dbh->errstr;
+while (my $row = $sth->fetchrow_hashref) {
+ push @rows, {%$row};
+}
+
+
+$dbh->disconnect;
+if (@rows) {
+ if (@rows == 1 && keys %{$rows[0]} == 1) {
+ # Special case for a single selected value
+ my ($value) = values %{$rows[0]};
+ print "$value\n";
+ } else {
+ print_aoh(\@rows, $opt_n);
+ }
+} else {
+ print "Empty result.\n";
+}
+
+sub usage {
+ print "$0 [-n nullsymbol] '....'\n";
+ exit 1;
+}
Deleted: trunk/treebase-core/src/main/perl/dump/show
===================================================================
--- trunk/treebase-core/src/main/perl/dump/show 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/dump/show 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,51 +0,0 @@
-#!/usr/bin/perl
-# -*- cperl -*-
-
-use CIPRES::TreeBase::DBIUtil;
-use Getopt::Std;
-
-my %opt = (n => $ENV{NULLSYMBOL} || '--');
-getopts('n:', \%opt) or usage();
-my ($class, $id) = @ARGV;
-defined($class) && defined($id) && $id =~ /^\d+$/ or usage();
-my $query = "select * from $class where $class\_id = ?";
-
-my $dbh = CIPRES::TreeBase::DBIUtil->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-my $sth = $dbh->prepare($query)
- or die "Couldn't prepare statement: " . $dbh->errstr;
-my $rc = $sth->execute($id)
- or die "Couldn't execute statement: " . $dbh->errstr;
-my $row;
-while (my $r = $sth->fetchrow_hashref) {
- if (defined $row) {
- die "Multiple matching rows!!\n";
- }
- $row = $r;
-}
-
-$dbh->disconnect;
-if (! defined $row) { die "show: No such object\n"; }
-
-my $c1 = max(map length(), keys %$row);
-
-for my $k (sort keys %$row) {
- if (! defined $row->{$k}) { $row->{$k} = $opt{n} }
- print fill($c1, $k), " $row->{$k}\n";
-}
-
-sub usage {
- print "$0 [-n nullsymbol] table id#\n";
- exit 1;
-}
-
-sub max {
- my $m = shift;
- $m = $m > $_ ? $m : $_ for @_;
- return $m;
-}
-
-sub fill {
- my ($n, $s) = @_;
- return length($s) > $n ? $s : $s . " " x ($n - length($s));
-}
Copied: trunk/treebase-core/src/main/perl/dump/show (from rev 212, trunk/treebase-core/src/main/perl/dump/show)
===================================================================
--- trunk/treebase-core/src/main/perl/dump/show (rev 0)
+++ trunk/treebase-core/src/main/perl/dump/show 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,51 @@
+#!/usr/bin/perl
+# -*- cperl -*-
+
+use CIPRES::TreeBase::DBIUtil;
+use Getopt::Std;
+
+my %opt = (n => $ENV{NULLSYMBOL} || '--');
+getopts('n:', \%opt) or usage();
+my ($class, $id) = @ARGV;
+defined($class) && defined($id) && $id =~ /^\d+$/ or usage();
+my $query = "select * from $class where $class\_id = ?";
+
+my $dbh = CIPRES::TreeBase::DBIUtil->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+my $sth = $dbh->prepare($query)
+ or die "Couldn't prepare statement: " . $dbh->errstr;
+my $rc = $sth->execute($id)
+ or die "Couldn't execute statement: " . $dbh->errstr;
+my $row;
+while (my $r = $sth->fetchrow_hashref) {
+ if (defined $row) {
+ die "Multiple matching rows!!\n";
+ }
+ $row = $r;
+}
+
+$dbh->disconnect;
+if (! defined $row) { die "show: No such object\n"; }
+
+my $c1 = max(map length(), keys %$row);
+
+for my $k (sort keys %$row) {
+ if (! defined $row->{$k}) { $row->{$k} = $opt{n} }
+ print fill($c1, $k), " $row->{$k}\n";
+}
+
+sub usage {
+ print "$0 [-n nullsymbol] table id#\n";
+ exit 1;
+}
+
+sub max {
+ my $m = shift;
+ $m = $m > $_ ? $m : $_ for @_;
+ return $m;
+}
+
+sub fill {
+ my ($n, $s) = @_;
+ return length($s) > $n ? $s : $s . " " x ($n - length($s));
+}
Deleted: trunk/treebase-core/src/main/perl/dump/showanalyses
===================================================================
--- trunk/treebase-core/src/main/perl/dump/showanalyses 2009-10-23 15:17:51 UTC (rev 212)
+++ trunk/treebase-core/src/main/perl/dump/showanalyses 2009-11-01 22:31:20 UTC (rev 229)
@@ -1,76 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use CIPRES::TreeBase::DBIUtil;
-use Getopt::Std;
-
-my %opt;
-getopts('', \%opt) or usage();
-
-my $study_id = shift || usage();
-
-my $dbh = CIPRES::TreeBase::Util->dbh
- or die "Couldn't connect to database: " . DBI->errstr;
-
-for my $analysis_row (query("analysis", "study_id", $study_id)) {
- my $a_id = $analysis_row->{ANALYSIS_ID};
- print " Analysis $a_id:\n";
- for my $analysisstep_row (query("analysisstep", "analysis_id", $a_id)) {
- my $as_id = $analysisstep_row->{ANALYSISSTEP_ID};
- print " Step $as_id:\n";
- for my $analyzeddata_row (query("analyzeddata", "analysisstep_id", $as_id)) {
- my $ad_id = $analyzeddata_row->{ANALYZEDDATA_ID};
- my $type = $analyzeddata_row->{TYPE};
- my $Type = {M => "matrix", T => "phyloTree"}->{$type};
- my $input = $analyzeddata_row->{INPUT} ? "input" : "output";
- my $d_id = $analyzeddata_row->{"\U$Type\E_ID"};
- my $nameField = {M => "TITLE", T => "LABEL"}->{$type};
- print " Data $ad_id ($input):\n";
-# print " ", join " ", %$analyzeddata_row;
-
- for my $row (query($Type, $Type . "_id", $d_id)) {
- my $s_id = $row->{STUDY_ID};
- my $ERR = "";
- if (! defined $s_id) {
- $ERR = "(no study!) ";
- } elsif ($s_id != $study_id) {
- $ERR = "(study s_id) ";
- }
- if ($type eq "T" && not defined $row->{TREEBLOCK_ID}) {
- $ERR .= "(no treeblock!) "
- }
-
- my $spc = $ERR ? "**" : " ";
- print " $spc \u$Type $d_id: $ERR'$row->{$nameField}'\n";
- }
- }
- }
-}
-
-$dbh->disconnect;
-
-################################################################
-
-sub usage {
- print "$0 [-tb] tree-id\n";
- print "\t-t : check taxonlabels\n";
- print "\t-b : check treeblocks\n";
- exit 1;
-}
-
-################################################################
-
-sub query {
- my ($table, $qcolumn, $qvalue) = @_;
- unless (defined $qcolumn) {
- $qcolumn = $table . "_id";
- }
- my $sth = $dbh->prepare_cached("select * from $table where $qcolumn = ?");
- $sth->execute($qvalue);
- my @rows;
- while (my $row = $sth->fetchrow_hashref()) {
- push @rows, $row;
- }
- $sth->finish;
- return @rows;
-}
Copied: trunk/treebase-core/src/main/perl/dump/showanalyses (from rev 212, trunk/treebase-core/src/main/perl/dump/showanalyses)
===================================================================
--- trunk/treebase-core/src/main/perl/dump/showanalyses (rev 0)
+++ trunk/treebase-core/src/main/perl/dump/showanalyses 2009-11-01 22:31:20 UTC (rev 229)
@@ -0,0 +1,76 @@
+#!/usr/bin/perl
+
+use strict;
+use CIPRES::TreeBase::DBIUtil;
+use Getopt::Std;
+
+my %opt;
+getopts('', \%opt) or usage();
+
+my $study_id = shift || usage();
+
+my $dbh = CIPRES::TreeBase::Util->dbh
+ or die "Couldn't connect to database: " . DBI->errstr;
+
+for my $analysis_row (query("analysis", "study_id", $study_id)) {
+ my $a_id = $analysis_row->{ANALYSIS_ID};
+ print " Analysis $a_id:\n";
+ for my $analysisstep_row (query(...
[truncated message content] |
|
From: <yo...@us...> - 2009-11-01 14:47:57
|
Revision: 228
http://treebase.svn.sourceforge.net/treebase/?rev=228&view=rev
Author: youjun
Date: 2009-11-01 14:47:47 +0000 (Sun, 01 Nov 2009)
Log Message:
-----------
Added Paths:
-----------
trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/
trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/
trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/oai/
trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/oai/web/
trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/oai/web/command/
trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/oai/web/command/OAIPMHCommand.class
trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/oai/web/controller/
trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/oai/web/controller/OAIPMHController.class
trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/oai/web/util/
trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/oai/web/validator/
Added: trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/oai/web/command/OAIPMHCommand.class
===================================================================
(Binary files differ)
Property changes on: trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/oai/web/command/OAIPMHCommand.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/oai/web/controller/OAIPMHController.class
===================================================================
(Binary files differ)
Property changes on: trunk/oai-pmh_data_provider/data_provider_web/target/classes/org/treebase/oai/web/controller/OAIPMHController.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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|
|
From: <yo...@us...> - 2009-10-31 02:35:00
|
Revision: 227
http://treebase.svn.sourceforge.net/treebase/?rev=227&view=rev
Author: youjun
Date: 2009-10-31 02:34:46 +0000 (Sat, 31 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.component
trunk/oai-pmh_data_provider/data_provider_web/.settings/org.maven.ide.eclipse.prefs
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java
Modified: trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.component
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.component 2009-10-30 20:06:11 UTC (rev 226)
+++ trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.component 2009-10-31 02:34:46 UTC (rev 227)
@@ -4,7 +4,7 @@
<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="/" source-path="/src/main/webapp"/>
- <dependent-module deploy-path="/WEB-INF/lib" handle="module:/resource/treebase/treebase">
+ <dependent-module deploy-path="/WEB-INF/lib" handle="module:/resource/treebase-core/treebase-core">
<dependency-type>uses</dependency-type>
</dependent-module>
<property name="context-root" value="data_provider_web"/>
Modified: trunk/oai-pmh_data_provider/data_provider_web/.settings/org.maven.ide.eclipse.prefs
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/.settings/org.maven.ide.eclipse.prefs 2009-10-30 20:06:11 UTC (rev 226)
+++ trunk/oai-pmh_data_provider/data_provider_web/.settings/org.maven.ide.eclipse.prefs 2009-10-31 02:34:46 UTC (rev 227)
@@ -1,8 +1,8 @@
-#Thu Oct 29 16:24:17 EDT 2009
+#Fri Oct 30 18:03:12 EDT 2009
activeProfiles=
eclipse.preferences.version=1
fullBuildGoals=process-test-resources
-includeModules=true
+includeModules=false
resolveWorkspaceProjects=true
resourceFilterGoals=process-resources resources\:testResources
skipCompilerPlugin=true
Modified: trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java 2009-10-30 20:06:11 UTC (rev 226)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java 2009-10-31 02:34:46 UTC (rev 227)
@@ -35,10 +35,46 @@
try{
method=this.getClass().getMethod(params.getVerb(), new Class[]{HttpServletRequest.class, HttpServletResponse.class, Map.class});
}catch(NoSuchMethodException e){
- return new ModelAndView("badVerb.vm",model);
+
+ return new ModelAndView("badVerb.vm",model);
}
- return (ModelAndView) method.invoke(this, request, response, model);
- }
+ return (ModelAndView) method.invoke(this, request, response, model);
+ }
+ ModelAndView ListRecoed(HttpServletRequest request, HttpServletResponse response, Map model){
+
+ return null;
+
+ }
+
+ ModelAndView ListMetadataFormats(HttpServletRequest request, HttpServletResponse response, Map model){
+
+ return null;
+
+ }
+
+ ModelAndView ListIdentifiers(HttpServletRequest request, HttpServletResponse response, Map model){
+
+ return null;
+
+ }
+
+ ModelAndView GetRecord(HttpServletRequest request, HttpServletResponse response, Map model){
+
+ return null;
+
+ }
+
+ ModelAndView Identify(HttpServletRequest request, HttpServletResponse response, Map model){
+
+ return null;
+
+ }
+
+ ModelAndView ListSet(HttpServletRequest request, HttpServletResponse response, Map model){
+
+ return null;
+
+ }
}
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|
|
From: <yo...@us...> - 2009-10-30 20:06:18
|
Revision: 226
http://treebase.svn.sourceforge.net/treebase/?rev=226&view=rev
Author: youjun
Date: 2009-10-30 20:06:11 +0000 (Fri, 30 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java
Modified: trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java 2009-10-30 16:25:42 UTC (rev 225)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java 2009-10-30 20:06:11 UTC (rev 226)
@@ -1,6 +1,8 @@
package org.treebase.oai.web.controller;
import java.lang.reflect.Method;
+import java.util.HashMap;
+import java.util.Map;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
@@ -23,14 +25,20 @@
// TODO Auto-generated method stub
OAIPMHCommand params = (OAIPMHCommand) command;
+
+ Map model=new HashMap();
+ model.put("params", params);
+
Method method=null;
+
+
try{
- method=this.getClass().getMethod(params.getVerb(), new Class[]{HttpServletRequest.class, HttpServletResponse.class, OAIPMHCommand.class});
+ method=this.getClass().getMethod(params.getVerb(), new Class[]{HttpServletRequest.class, HttpServletResponse.class, Map.class});
}catch(NoSuchMethodException e){
- return new ModelAndView("bad verb: "+ params.getVerb());
+ return new ModelAndView("badVerb.vm",model);
}
- return (ModelAndView) method.invoke(this, request, response, params);
+ return (ModelAndView) method.invoke(this, request, response, model);
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-30 16:25:57
|
Revision: 225
http://treebase.svn.sourceforge.net/treebase/?rev=225&view=rev
Author: youjun
Date: 2009-10-30 16:25:42 +0000 (Fri, 30 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java
Modified: trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java 2009-10-30 16:24:33 UTC (rev 224)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java 2009-10-30 16:25:42 UTC (rev 225)
@@ -1,20 +1,36 @@
package org.treebase.oai.web.controller;
+import java.lang.reflect.Method;
+
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.springframework.validation.BindException;
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.AbstractCommandController;
+import org.treebase.oai.web.command.OAIPMHCommand;
public class OAIPMHController extends AbstractCommandController{
+ public OAIPMHController(){
+ setCommandClass(OAIPMHCommand.class);
+ }
+
@Override
protected ModelAndView handle(HttpServletRequest request,
HttpServletResponse response, Object command, BindException errors)
throws Exception {
// TODO Auto-generated method stub
- return null;
+
+ OAIPMHCommand params = (OAIPMHCommand) command;
+ Method method=null;
+ try{
+ method=this.getClass().getMethod(params.getVerb(), new Class[]{HttpServletRequest.class, HttpServletResponse.class, OAIPMHCommand.class});
+ }catch(NoSuchMethodException e){
+ return new ModelAndView("bad verb: "+ params.getVerb());
+ }
+
+ return (ModelAndView) method.invoke(this, request, response, params);
}
}
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|
|
From: <rsc...@us...> - 2009-10-30 16:24:44
|
Revision: 224
http://treebase.svn.sourceforge.net/treebase/?rev=224&view=rev
Author: rscherle
Date: 2009-10-30 16:24:33 +0000 (Fri, 30 Oct 2009)
Log Message:
-----------
updated endnote citations
Modified Paths:
--------------
trunk/treebase-curation/studyCitations.enl
Modified: trunk/treebase-curation/studyCitations.enl
===================================================================
(Binary files differ)
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|
|
From: <yo...@us...> - 2009-10-30 15:41:50
|
Revision: 223
http://treebase.svn.sourceforge.net/treebase/?rev=223&view=rev
Author: youjun
Date: 2009-10-30 15:41:44 +0000 (Fri, 30 Oct 2009)
Log Message:
-----------
Added Paths:
-----------
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/command/
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/command/OAIPMHCommand.java
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/util/
trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/validator/
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/command/OAIPMHCommand.java
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/command/OAIPMHCommand.java (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/command/OAIPMHCommand.java 2009-10-30 15:41:44 UTC (rev 223)
@@ -0,0 +1,58 @@
+package org.treebase.oai.web.command;
+
+public class OAIPMHCommand {
+
+ private String from;
+ private String until;
+ private String resumptionToken;
+ private String identifier;
+ private String metadataPrefix;
+ private String set;
+ private String verb;
+
+ public String getVerb() {
+ return verb;
+ }
+ public void setVerb(String verb) {
+ this.verb = verb;
+ }
+ public String getFrom() {
+ return from;
+ }
+ public void setFrom(String from) {
+ this.from = from;
+ }
+ public String getUntil() {
+ return until;
+ }
+ public void setUntil(String until) {
+ this.until = until;
+ }
+ public String getResumptionToken() {
+ return resumptionToken;
+ }
+ public void setResumptionToken(String resumptionToken) {
+ this.resumptionToken = resumptionToken;
+ }
+ public String getIdentifier() {
+ return identifier;
+ }
+ public void setIdentifier(String identifier) {
+ this.identifier = identifier;
+ }
+ public String getMetadataPrefix() {
+ return metadataPrefix;
+ }
+ public void setMetadataPrefix(String metadataPrefix) {
+ this.metadataPrefix = metadataPrefix;
+ }
+ public String getSet() {
+ return set;
+ }
+ public void setSet(String set) {
+ this.set = set;
+ }
+
+
+
+}
Added: trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java (rev 0)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/java/org/treebase/oai/web/controller/OAIPMHController.java 2009-10-30 15:41:44 UTC (rev 223)
@@ -0,0 +1,20 @@
+package org.treebase.oai.web.controller;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.springframework.validation.BindException;
+import org.springframework.web.servlet.ModelAndView;
+import org.springframework.web.servlet.mvc.AbstractCommandController;
+
+public class OAIPMHController extends AbstractCommandController{
+
+ @Override
+ protected ModelAndView handle(HttpServletRequest request,
+ HttpServletResponse response, Object command, BindException errors)
+ throws Exception {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+}
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|
|
From: <yo...@us...> - 2009-10-30 13:25:37
|
Revision: 222
http://treebase.svn.sourceforge.net/treebase/?rev=222&view=rev
Author: youjun
Date: 2009-10-30 13:25:23 +0000 (Fri, 30 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_core/.classpath
trunk/oai-pmh_data_provider/data_provider_core/pom.xml
trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/hibernate.cfg.xml
trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.component
trunk/oai-pmh_data_provider/data_provider_web/.settings/org.maven.ide.eclipse.prefs
trunk/oai-pmh_data_provider/data_provider_web/pom.xml
trunk/oai-pmh_data_provider/pom.xml
Modified: trunk/oai-pmh_data_provider/data_provider_core/.classpath
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_core/.classpath 2009-10-27 19:54:56 UTC (rev 221)
+++ trunk/oai-pmh_data_provider/data_provider_core/.classpath 2009-10-30 13:25:23 UTC (rev 222)
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
- <classpathentry kind="src" path="src/main/java"/>
- <classpathentry kind="src" path="src/main/resources"/>
- <classpathentry kind="src" path="src/test/java"/>
- <classpathentry kind="src" path="src/test/resources"/>
+ <classpathentry kind="src" output="target/classes" path="src/main/java"/>
+ <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
+ <classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
+ <classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5"/>
<classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.module.container"/>
<classpathentry kind="con" path="org.maven.ide.eclipse.MAVEN2_CLASSPATH_CONTAINER"/>
Modified: trunk/oai-pmh_data_provider/data_provider_core/pom.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_core/pom.xml 2009-10-27 19:54:56 UTC (rev 221)
+++ trunk/oai-pmh_data_provider/data_provider_core/pom.xml 2009-10-30 13:25:23 UTC (rev 222)
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?><project>
- <parent>
+ <!-- parent>
<artifactId>oai-pmh_data_provider</artifactId>
<groupId>org.treebase.oai</groupId>
<version>0.0.1-SNAPSHOT</version>
- </parent>
+ </parent-->
<modelVersion>4.0.0</modelVersion>
<groupId>org.treebase.oai</groupId>
<artifactId>data_provider_core</artifactId>
Modified: trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/hibernate.cfg.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/hibernate.cfg.xml 2009-10-27 19:54:56 UTC (rev 221)
+++ trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/hibernate.cfg.xml 2009-10-30 13:25:23 UTC (rev 222)
@@ -26,7 +26,7 @@
<property name="hibernate.connection.release_mode">auto</property>
<property name="hibernate.query.substitutions">true 'T', false 'F'</property>
- <!-- Mapping files -->
+ <!-- Mapping files use annotation -->
<!-- mapping package="org.cipres.treebase.domain" /-->
<mapping class="org.cipres.treebase.domain.AbstractPersistedObject" />
Modified: trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.component
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.component 2009-10-27 19:54:56 UTC (rev 221)
+++ trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.component 2009-10-30 13:25:23 UTC (rev 222)
@@ -4,7 +4,7 @@
<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="/" source-path="/src/main/webapp"/>
- <dependent-module deploy-path="/WEB-INF/lib" handle="module:/resource/data_provider_core/data_provider_core">
+ <dependent-module deploy-path="/WEB-INF/lib" handle="module:/resource/treebase/treebase">
<dependency-type>uses</dependency-type>
</dependent-module>
<property name="context-root" value="data_provider_web"/>
Modified: trunk/oai-pmh_data_provider/data_provider_web/.settings/org.maven.ide.eclipse.prefs
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/.settings/org.maven.ide.eclipse.prefs 2009-10-27 19:54:56 UTC (rev 221)
+++ trunk/oai-pmh_data_provider/data_provider_web/.settings/org.maven.ide.eclipse.prefs 2009-10-30 13:25:23 UTC (rev 222)
@@ -1,8 +1,8 @@
-#Mon Oct 12 12:59:49 EDT 2009
+#Thu Oct 29 16:24:17 EDT 2009
activeProfiles=
eclipse.preferences.version=1
fullBuildGoals=process-test-resources
-includeModules=false
+includeModules=true
resolveWorkspaceProjects=true
resourceFilterGoals=process-resources resources\:testResources
skipCompilerPlugin=true
Modified: trunk/oai-pmh_data_provider/data_provider_web/pom.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/pom.xml 2009-10-27 19:54:56 UTC (rev 221)
+++ trunk/oai-pmh_data_provider/data_provider_web/pom.xml 2009-10-30 13:25:23 UTC (rev 222)
@@ -66,11 +66,11 @@
<dependencies>
- <dependency>
+ <!-- dependency>
<groupId>org.treebase.oai</groupId>
<artifactId>data_provider_core</artifactId>
<version>0.0.1-SNAPSHOT</version>
- </dependency>
+ </dependency -->
<dependency>
<groupId>javax.servlet</groupId>
@@ -251,6 +251,11 @@
<artifactId>servlet-api</artifactId>
<version>2.4</version>
</dependency>
+ <dependency>
+ <groupId>org.cipres.treebase</groupId>
+ <artifactId>treebase-core</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ </dependency>
<!-- used by Spring framework -->
<!--Older ersion not needed-->
Modified: trunk/oai-pmh_data_provider/pom.xml
===================================================================
--- trunk/oai-pmh_data_provider/pom.xml 2009-10-27 19:54:56 UTC (rev 221)
+++ trunk/oai-pmh_data_provider/pom.xml 2009-10-30 13:25:23 UTC (rev 222)
@@ -47,7 +47,7 @@
</license>
</licenses>
<modules>
- <module>data_provider_core</module>
+ <!-- module>data_provider_core</module -->
<module>data_provider_web</module>
</modules>
<pluginRepositories>
@@ -154,11 +154,11 @@
<dependencyManagement>
<dependencies>
- <dependency>
+ <!-- dependency>
<groupId>org.treebase.oai</groupId>
<artifactId>data_provider_core</artifactId>
<version>${project.version}</version>
- </dependency>
+ </dependency -->
<dependency>
<groupId>org.treebase.oai</groupId>
<artifactId>data_provider_web</artifactId>
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|
|
From: <yo...@us...> - 2009-10-27 19:55:03
|
Revision: 221
http://treebase.svn.sourceforge.net/treebase/?rev=221&view=rev
Author: youjun
Date: 2009-10-27 19:54:56 +0000 (Tue, 27 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml
Modified: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml 2009-10-27 19:24:24 UTC (rev 220)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/web.xml 2009-10-27 19:54:56 UTC (rev 221)
@@ -10,8 +10,10 @@
classpath*:applicationContext-service.xml,
/WEB-INF/applicationContext.xml,
<!-- top is short for Treebase OAI-PMH Provider -->
- /WEB-INF/top-security.xml,
- /WEB-INF/top-validation.xml
+ <!-- /WEB-INF/top-security.xml,-->
+ <!-- /WEB-INF/top-validation.xml-->
+ <!-- validation will be done on server side -->
+ <!-- errors will be return as oai-pmh exception with vm -->
</param-value>
</context-param>
@@ -23,9 +25,9 @@
<listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
</listener>
<!-- extends customize and replaces ContextLoaderListener -->
- <!--listener>
+ <!-- listener>
<listener-class>org.cipres.treebase.web.listeners.StartupListener</listener-class>
- </listener-->
+ </listener -->
<!-- ========================================================== -->
@@ -68,25 +70,9 @@
</servlet-mapping-->
-
<!-- ========================================================== -->
- <!-- define some default pages -->
- <!-- ========================================================== -->
- <welcome-file-list>
- <welcome-file>index.jsp</welcome-file>
- </welcome-file-list>
-
- <!-- ========================================================== -->
<!-- Error Pages -->
<!-- ========================================================== -->
- <error-page>
- <exception-type>java.lang.Exception</exception-type>
- <location>/uncaughtException.jsp</location>
- </error-page>
- <!-- Internal Server Error -->
- <error-page>
- <error-code>500</error-code>
- <location>/error-500.jsp</location>
- </error-page>
+ <!-- or errors will return as oai-pmh exception based on .vm files -->
</web-app>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-27 19:24:31
|
Revision: 220
http://treebase.svn.sourceforge.net/treebase/?rev=220&view=rev
Author: youjun
Date: 2009-10-27 19:24:24 +0000 (Tue, 27 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.project.facet.core.xml
Removed Paths:
-------------
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-validation.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/validation.xml
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/validator-rules.xml
Modified: trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.project.facet.core.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.project.facet.core.xml 2009-10-27 13:33:26 UTC (rev 219)
+++ trunk/oai-pmh_data_provider/data_provider_web/.settings/org.eclipse.wst.common.project.facet.core.xml 2009-10-27 19:24:24 UTC (rev 220)
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<faceted-project>
<installed facet="jst.java" version="5.0"/>
- <installed facet="jst.web" version="2.3"/>
+ <installed facet="jst.web" version="2.4"/>
</faceted-project>
Deleted: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-validation.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-validation.xml 2009-10-27 13:33:26 UTC (rev 219)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/top-validation.xml 2009-10-27 19:24:24 UTC (rev 220)
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN"
- "http://www.springframework.org/dtd/spring-beans.dtd">
-
-<beans default-autowire="no">
- <bean id="validatorFactory" class="org.springmodules.commons.validator.DefaultValidatorFactory">
- <property name="validationConfigLocations">
- <list>
- <value>/WEB-INF/validation.xml</value>
- <value>/WEB-INF/validator-rules.xml</value>
- </list>
- </property>
- </bean>
-
- <bean id="beanValidator" class="org.springmodules.commons.validator.DefaultBeanValidator">
- <property name="validatorFactory" ref="validatorFactory"/>
- </bean>
-
-</beans>
Deleted: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/validation.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/validation.xml 2009-10-27 13:33:26 UTC (rev 219)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/validation.xml 2009-10-27 19:24:24 UTC (rev 220)
@@ -1,69 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE form-validation PUBLIC
- "-//Apache Software Foundation//DTD Commons Validator Rules Configuration 1.3.0//EN"
- "http://jakarta.apache.org/commons/dtds/validator_1_3_0.dtd">
-
-<form-validation>
- <formset>
- <form name="user">
- <field property="username" depends="required">
- <arg key="user.username"/>
- </field>
- <field property="password" depends="required">
- <arg key="user.password"/>
- </field>
- <field property="lastName" depends="required">
- <arg key="user.lastname"/>
- </field>
- <field property="firstName" depends="required">
- <arg key="user.firstname"/>
- </field>
- <field property="emailAddressString" depends="required,email">
- <arg key="user.emailaddressstring"/>
- </field>
- </form>
- <!--author and editor object have been changed to generic element person-->
- <!--form name="author">
- <field property="lastName" depends="required">
- <arg key="user.lastname"/>
- </field>
- <field property="firstName" depends="required">
- <arg key="user.firstname"/>
- </field>
- <field property="emailAddressString" depends="required,email">
- <arg key="user.emailaddressstring"/>
- </field>
- </form-->
-
- <form name="person">
- <field property="lastName" depends="required">
- <arg key="lastname"/>
- </field>
- <field property="firstName" depends="required">
- <arg key="firstname"/>
- </field>
- <field property="emailAddressString" depends="required,email">
- <arg key="emailaddressstring"/>
- </field>
- </form>
-
- <form name="password">
- <field property="username" depends="required">
- <arg key="user.username"/>
- </field>
- </form>
-
- <form name="edtTxnLbl">
- <field property="taxonLabel" depends="required,minlength">
- <arg key="taxonlabel.title"/>
- <arg key="${var:minlength}" name="minlength" resource="false"/>
- <var>
- <var-name>minlength</var-name>
- <var-value>5</var-value>
- </var>
- </field>
- </form>
-
- </formset>
-
-</form-validation>
Deleted: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/validator-rules.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/validator-rules.xml 2009-10-27 13:33:26 UTC (rev 219)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/validator-rules.xml 2009-10-27 19:24:24 UTC (rev 220)
@@ -1,1009 +0,0 @@
-<!DOCTYPE form-validation PUBLIC
- "-//Apache Software Foundation//DTD Commons Validator Rules Configuration 1.2.0//EN"
- "http://jakarta.apache.org/commons/dtds/validator_1_2_0.dtd">
-
-<form-validation>
-
- <global>
-
- <validator name="required"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateRequired"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
- msg="errors.required">
-
- <javascript><![CDATA[
- function validateRequired(form) {
- var isValid = true;
- var focusField = null;
- var i = 0;
- var fields = new Array();
- oRequired = new required();
- for (x in oRequired) {
- var field = form[oRequired[x][0]];
-
- if (field.type == 'text' ||
- field.type == 'textarea' ||
- field.type == 'file' ||
- field.type == 'select-one' ||
- field.type == 'radio' ||
- field.type == 'password') {
-
- var value = '';
- // get field's value
- if (field.type == "select-one") {
- var si = field.selectedIndex;
- if (si >= 0) {
- value = field.options[si].value;
- }
- } else {
- value = field.value;
- }
-
- if (trim(value).length == 0) {
-
- if (i == 0) {
- focusField = field;
- }
- fields[i++] = oRequired[x][1];
- isValid = false;
- }
- }
- }
- if (fields.length > 0) {
- focusField.focus();
- alert(fields.join('\n'));
- }
- return isValid;
- }
-
- // Trim whitespace from left and right sides of s.
- function trim(s) {
- return s.replace( /^\s*/, "" ).replace( /\s*$/, "" );
- }
-
- ]]>
- </javascript>
-
- </validator>
-
- <validator name="requiredif"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateRequiredIf"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors,
- org.apache.commons.validator.Validator"
-
- msg="errors.required">
- </validator>
-
- <validator name="minlength"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateMinLength"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends=""
- msg="errors.minlength">
-
- <javascript><![CDATA[
- function validateMinLength(form) {
- var isValid = true;
- var focusField = null;
- var i = 0;
- var fields = new Array();
- oMinLength = new minlength();
- for (x in oMinLength) {
- var field = form[oMinLength[x][0]];
-
- if (field.type == 'text' ||
- field.type == 'textarea') {
-
- var iMin = parseInt(oMinLength[x][2]("minlength"));
- if ((trim(field.value).length > 0) && (field.value.length < iMin)) {
- if (i == 0) {
- focusField = field;
- }
- fields[i++] = oMinLength[x][1];
- isValid = false;
- }
- }
- }
- if (fields.length > 0) {
- focusField.focus();
- alert(fields.join('\n'));
- }
- return isValid;
- }]]>
- </javascript>
-
- </validator>
-
-
- <validator name="maxlength"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateMaxLength"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends=""
- msg="errors.maxlength">
-
- <javascript><![CDATA[
- function validateMaxLength(form) {
- var isValid = true;
- var focusField = null;
- var i = 0;
- var fields = new Array();
- oMaxLength = new maxlength();
- for (x in oMaxLength) {
- var field = form[oMaxLength[x][0]];
-
- if (field.type == 'text' ||
- field.type == 'textarea') {
-
- var iMax = parseInt(oMaxLength[x][2]("maxlength"));
- if (field.value.length > iMax) {
- if (i == 0) {
- focusField = field;
- }
- fields[i++] = oMaxLength[x][1];
- isValid = false;
- }
- }
- }
- if (fields.length > 0) {
- focusField.focus();
- alert(fields.join('\n'));
- }
- return isValid;
- }]]>
- </javascript>
-
- </validator>
-
-
- <validator name="mask"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateMask"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends=""
- msg="errors.invalid">
-
- <javascript><![CDATA[
- function validateMask(form) {
- var isValid = true;
- var focusField = null;
- var i = 0;
- var fields = new Array();
- oMasked = new mask();
- for (x in oMasked) {
- var field = form[oMasked[x][0]];
-
- if ((field.type == 'text' ||
- field.type == 'textarea') &&
- (field.value.length > 0)) {
-
- if (!matchPattern(field.value, oMasked[x][2]("mask"))) {
- if (i == 0) {
- focusField = field;
- }
- fields[i++] = oMasked[x][1];
- isValid = false;
- }
- }
- }
-
- if (fields.length > 0) {
- focusField.focus();
- alert(fields.join('\n'));
- }
- return isValid;
- }
-
- function matchPattern(value, mask) {
- return mask.exec(value);
- }]]>
- </javascript>
-
- </validator>
-
-
- <validator name="byte"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateByte"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends=""
- msg="errors.byte"
- jsFunctionName="ByteValidations">
-
- <javascript><![CDATA[
- function validateByte(form) {
- var bValid = true;
- var focusField = null;
- var i = 0;
- var fields = new Array();
- oByte = new ByteValidations();
- for (x in oByte) {
- var field = form[oByte[x][0]];
-
- if (field.type == 'text' ||
- field.type == 'textarea' ||
- field.type == 'select-one' ||
- field.type == 'radio') {
-
- var value = '';
- // get field's value
- if (field.type == "select-one") {
- var si = field.selectedIndex;
- if (si >= 0) {
- value = field.options[si].value;
- }
- } else {
- value = field.value;
- }
-
- if (value.length > 0) {
- if (!isAllDigits(value)) {
- bValid = false;
- if (i == 0) {
- focusField = field;
- }
- fields[i++] = oByte[x][1];
-
- } else {
-
- var iValue = parseInt(value);
- if (isNaN(iValue) || !(iValue >= -128 && iValue <= 127)) {
- if (i == 0) {
- focusField = field;
- }
- fields[i++] = oByte[x][1];
- bValid = false;
- }
- }
- }
-
- }
- }
- if (fields.length > 0) {
- focusField.focus();
- alert(fields.join('\n'));
- }
- return bValid;
- }]]>
- </javascript>
-
- </validator>
-
-
- <validator name="short"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateShort"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends=""
- msg="errors.short"
- jsFunctionName="ShortValidations">
-
- <javascript><![CDATA[
- function validateShort(form) {
- var bValid = true;
- var focusField = null;
- var i = 0;
- var fields = new Array();
- oShort = new ShortValidations();
- for (x in oShort) {
- var field = form[oShort[x][0]];
-
- if (field.type == 'text' ||
- field.type == 'textarea' ||
- field.type == 'select-one' ||
- field.type == 'radio') {
-
- var value = '';
- // get field's value
- if (field.type == "select-one") {
- var si = field.selectedIndex;
- if (si >= 0) {
- value = field.options[si].value;
- }
- } else {
- value = field.value;
- }
-
- if (value.length > 0) {
- if (!isAllDigits(value)) {
- bValid = false;
- if (i == 0) {
- focusField = field;
- }
- fields[i++] = oShort[x][1];
-
- } else {
-
- var iValue = parseInt(value);
- if (isNaN(iValue) || !(iValue >= -32768 && iValue <= 32767)) {
- if (i == 0) {
- focusField = field;
- }
- fields[i++] = oShort[x][1];
- bValid = false;
- }
- }
- }
- }
- }
- if (fields.length > 0) {
- focusField.focus();
- alert(fields.join('\n'));
- }
- return bValid;
- }]]>
- </javascript>
-
- </validator>
-
-
- <validator name="integer"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateInteger"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends=""
- msg="errors.integer"
- jsFunctionName="IntegerValidations">
-
- <javascript><![CDATA[
- function validateInteger(form) {
- var bValid = true;
- var focusField = null;
- var i = 0;
- var fields = new Array();
- oInteger = new IntegerValidations();
- for (x in oInteger) {
- var field = form[oInteger[x][0]];
-
- if (field.type == 'text' ||
- field.type == 'textarea' ||
- field.type == 'select-one' ||
- field.type == 'radio') {
-
- var value = '';
- // get field's value
- if (field.type == "select-one") {
- var si = field.selectedIndex;
- if (si >= 0) {
- value = field.options[si].value;
- }
- } else {
- value = field.value;
- }
-
- if (value.length > 0) {
-
- if (!isAllDigits(value)) {
- bValid = false;
- if (i == 0) {
- focusField = field;
- }
- fields[i++] = oInteger[x][1];
-
- } else {
- var iValue = parseInt(value);
- if (isNaN(iValue) || !(iValue >= -2147483648 && iValue <= 2147483647)) {
- if (i == 0) {
- focusField = field;
- }
- fields[i++] = oInteger[x][1];
- bValid = false;
- }
- }
- }
- }
- }
- if (fields.length > 0) {
- focusField.focus();
- alert(fields.join('\n'));
- }
- return bValid;
- }
-
- function isAllDigits(argvalue) {
- argvalue = argvalue.toString();
- var validChars = "0123456789";
- var startFrom = 0;
- if (argvalue.substring(0, 2) == "0x") {
- validChars = "0123456789abcdefABCDEF";
- startFrom = 2;
- } else if (argvalue.charAt(0) == "0") {
- validChars = "01234567";
- startFrom = 1;
- } else if (argvalue.charAt(0) == "-") {
- startFrom = 1;
- }
-
- for (var n = startFrom; n < argvalue.length; n++) {
- if (validChars.indexOf(argvalue.substring(n, n+1)) == -1) return false;
- }
- return true;
- }]]>
- </javascript>
-
- </validator>
-
-
- <validator name="long"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateLong"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends=""
- msg="errors.long"/>
-
-
- <validator name="float"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateFloat"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends=""
- msg="errors.float"
- jsFunctionName="FloatValidations">
-
- <javascript><![CDATA[
- function validateFloat(form) {
- var bValid = true;
- var focusField = null;
- var i = 0;
- var fields = new Array();
- oFloat = new FloatValidations();
- for (x in oFloat) {
- var field = form[oFloat[x][0]];
-
- if (field.type == 'text' ||
- field.type == 'textarea' ||
- field.type == 'select-one' ||
- field.type == 'radio') {
-
- var value = '';
- // get field's value
- if (field.type == "select-one") {
- var si = field.selectedIndex;
- if (si >= 0) {
- value = field.options[si].value;
- }
- } else {
- value = field.value;
- }
-
- if (value.length > 0) {
- // remove '.' before checking digits
- var tempArray = value.split('.');
- var joinedString= tempArray.join('');
-
- if (!isAllDigits(joinedString)) {
- bValid = false;
- if (i == 0) {
- focusField = field;
- }
- fields[i++] = oFloat[x][1];
-
- } else {
- var iValue = parseFloat(value);
- if (isNaN(iValue)) {
- if (i == 0) {
- focusField = field;
- }
- fields[i++] = oFloat[x][1];
- bValid = false;
- }
- }
- }
- }
- }
- if (fields.length > 0) {
- focusField.focus();
- alert(fields.join('\n'));
- }
- return bValid;
- }]]>
- </javascript>
-
- </validator>
-
-
- <validator name="double"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateDouble"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends=""
- msg="errors.double"/>
-
-
- <validator name="date"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateDate"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends=""
- msg="errors.date"
- jsFunctionName="DateValidations">
-
- <javascript><![CDATA[
- function validateDate(form) {
- var bValid = true;
- var focusField = null;
- var i = 0;
- var fields = new Array();
- oDate = new DateValidations();
- for (x in oDate) {
- var value = form[oDate[x][0]].value;
- var datePattern = oDate[x][2]("datePatternStrict");
- // try loose pattern
- if (datePattern == null)
- datePattern = oDate[x][2]("datePattern");
- if ((form[oDate[x][0]].type == 'text' ||
- form[oDate[x][0]].type == 'textarea') &&
- (value.length > 0) &&
- (datePattern.length > 0)) {
- var MONTH = "MM";
- var DAY = "dd";
- var YEAR = "yyyy";
- var orderMonth = datePattern.indexOf(MONTH);
- var orderDay = datePattern.indexOf(DAY);
- var orderYear = datePattern.indexOf(YEAR);
- if ((orderDay < orderYear && orderDay > orderMonth)) {
- var iDelim1 = orderMonth + MONTH.length;
- var iDelim2 = orderDay + DAY.length;
- var delim1 = datePattern.substring(iDelim1, iDelim1 + 1);
- var delim2 = datePattern.substring(iDelim2, iDelim2 + 1);
- if (iDelim1 == orderDay && iDelim2 == orderYear) {
- dateRegexp = new RegExp("^(\\d{2})(\\d{2})(\\d{4})$");
- } else if (iDelim1 == orderDay) {
- dateRegexp = new RegExp("^(\\d{2})(\\d{2})[" + delim2 + "](\\d{4})$");
- } else if (iDelim2 == orderYear) {
- dateRegexp = new RegExp("^(\\d{2})[" + delim1 + "](\\d{2})(\\d{4})$");
- } else {
- dateRegexp = new RegExp("^(\\d{2})[" + delim1 + "](\\d{2})[" + delim2 + "](\\d{4})$");
- }
- var matched = dateRegexp.exec(value);
- if(matched != null) {
- if (!isValidDate(matched[2], matched[1], matched[3])) {
- if (i == 0) {
- focusField = form[oDate[x][0]];
- }
- fields[i++] = oDate[x][1];
- bValid = false;
- }
- } else {
- if (i == 0) {
- focusField = form[oDate[x][0]];
- }
- fields[i++] = oDate[x][1];
- bValid = false;
- }
- } else if ((orderMonth < orderYear && orderMonth > orderDay)) {
- var iDelim1 = orderDay + DAY.length;
- var iDelim2 = orderMonth + MONTH.length;
- var delim1 = datePattern.substring(iDelim1, iDelim1 + 1);
- var delim2 = datePattern.substring(iDelim2, iDelim2 + 1);
- if (iDelim1 == orderMonth && iDelim2 == orderYear) {
- dateRegexp = new RegExp("^(\\d{2})(\\d{2})(\\d{4})$");
- } else if (iDelim1 == orderMonth) {
- dateRegexp = new RegExp("^(\\d{2})(\\d{2})[" + delim2 + "](\\d{4})$");
- } else if (iDelim2 == orderYear) {
- dateRegexp = new RegExp("^(\\d{2})[" + delim1 + "](\\d{2})(\\d{4})$");
- } else {
- dateRegexp = new RegExp("^(\\d{2})[" + delim1 + "](\\d{2})[" + delim2 + "](\\d{4})$");
- }
- var matched = dateRegexp.exec(value);
- if(matched != null) {
- if (!isValidDate(matched[1], matched[2], matched[3])) {
- if (i == 0) {
- focusField = form[oDate[x][0]];
- }
- fields[i++] = oDate[x][1];
- bValid = false;
- }
- } else {
- if (i == 0) {
- focusField = form[oDate[x][0]];
- }
- fields[i++] = oDate[x][1];
- bValid = false;
- }
- } else if ((orderMonth > orderYear && orderMonth < orderDay)) {
- var iDelim1 = orderYear + YEAR.length;
- var iDelim2 = orderMonth + MONTH.length;
- var delim1 = datePattern.substring(iDelim1, iDelim1 + 1);
- var delim2 = datePattern.substring(iDelim2, iDelim2 + 1);
- if (iDelim1 == orderMonth && iDelim2 == orderDay) {
- dateRegexp = new RegExp("^(\\d{4})(\\d{2})(\\d{2})$");
- } else if (iDelim1 == orderMonth) {
- dateRegexp = new RegExp("^(\\d{4})(\\d{2})[" + delim2 + "](\\d{2})$");
- } else if (iDelim2 == orderDay) {
- dateRegexp = new RegExp("^(\\d{4})[" + delim1 + "](\\d{2})(\\d{2})$");
- } else {
- dateRegexp = new RegExp("^(\\d{4})[" + delim1 + "](\\d{2})[" + delim2 + "](\\d{2})$");
- }
- var matched = dateRegexp.exec(value);
- if(matched != null) {
- if (!isValidDate(matched[3], matched[2], matched[1])) {
- if (i == 0) {
- focusField = form[oDate[x][0]];
- }
- fields[i++] = oDate[x][1];
- bValid = false;
- }
- } else {
- if (i == 0) {
- focusField = form[oDate[x][0]];
- }
- fields[i++] = oDate[x][1];
- bValid = false;
- }
- } else {
- if (i == 0) {
- focusField = form[oDate[x][0]];
- }
- fields[i++] = oDate[x][1];
- bValid = false;
- }
- }
- }
- if (fields.length > 0) {
- focusField.focus();
- alert(fields.join('\n'));
- }
- return bValid;
- }
-
- function isValidDate(day, month, year) {
- if (month < 1 || month > 12) {
- return false;
- }
- if (day < 1 || day > 31) {
- return false;
- }
- if ((month == 4 || month == 6 || month == 9 || month == 11) &&
- (day == 31)) {
- return false;
- }
- if (month == 2) {
- var leap = (year % 4 == 0 &&
- (year % 100 != 0 || year % 400 == 0));
- if (day>29 || (day == 29 && !leap)) {
- return false;
- }
- }
- return true;
- }]]>
- </javascript>
-
- </validator>
-
-<!-- range is deprecated use intRange instead -->
- <validator name="range"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateIntRange"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends="integer"
- msg="errors.range">
-
- <javascript><![CDATA[
- function validateRange(form) {
- return validateIntRange(form);
- }]]>
- </javascript>
-
- </validator>
-
- <validator name="intRange"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateIntRange"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends="integer"
- msg="errors.range">
-
- <javascript><![CDATA[
- function validateIntRange(form) {
- var isValid = true;
- var focusField = null;
- var i = 0;
- var fields = new Array();
- oRange = new intRange();
- for (x in oRange) {
- var field = form[oRange[x][0]];
-
- if ((field.type == 'text' ||
- field.type == 'textarea') &&
- (field.value.length > 0)) {
-
- var iMin = parseInt(oRange[x][2]("min"));
- var iMax = parseInt(oRange[x][2]("max"));
- var iValue = parseInt(field.value);
- if (!(iValue >= iMin && iValue <= iMax)) {
- if (i == 0) {
- focusField = field;
- }
- fields[i++] = oRange[x][1];
- isValid = false;
- }
- }
- }
- if (fields.length > 0) {
- focusField.focus();
- alert(fields.join('\n'));
- }
- return isValid;
- }]]>
- </javascript>
-
- </validator>
-
- <validator name="floatRange"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateFloatRange"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends="float"
- msg="errors.range">
-
- <javascript><![CDATA[
- function validateFloatRange(form) {
- var isValid = true;
- var focusField = null;
- var i = 0;
- var fields = new Array();
- oRange = new floatRange();
- for (x in oRange) {
- var field = form[oRange[x][0]];
-
- if ((field.type == 'text' ||
- field.type == 'textarea') &&
- (field.value.length > 0)) {
-
- var fMin = parseFloat(oRange[x][2]("min"));
- var fMax = parseFloat(oRange[x][2]("max"));
- var fValue = parseFloat(field.value);
- if (!(fValue >= fMin && fValue <= fMax)) {
- if (i == 0) {
- focusField = field;
- }
- fields[i++] = oRange[x][1];
- isValid = false;
- }
- }
- }
- if (fields.length > 0) {
- focusField.focus();
- alert(fields.join('\n'));
- }
- return isValid;
- }]]>
- </javascript>
-
- </validator>
-
- <validator name="creditCard"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateCreditCard"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends=""
- msg="errors.creditcard">
-
- <javascript><![CDATA[
- function validateCreditCard(form) {
- var bValid = true;
- var focusField = null;
- var i = 0;
- var fields = new Array();
- oCreditCard = new creditCard();
- for (x in oCreditCard) {
- if ((form[oCreditCard[x][0]].type == 'text' ||
- form[oCreditCard[x][0]].type == 'textarea') &&
- (form[oCreditCard[x][0]].value.length > 0)) {
- if (!luhnCheck(form[oCreditCard[x][0]].value)) {
- if (i == 0) {
- focusField = form[oCreditCard[x][0]];
- }
- fields[i++] = oCreditCard[x][1];
- bValid = false;
- }
- }
- }
- if (fields.length > 0) {
- focusField.focus();
- alert(fields.join('\n'));
- }
- return bValid;
- }
-
- /**
- * Reference: http://www.ling.nwu.edu/~sburke/pub/luhn_lib.pl
- */
- function luhnCheck(cardNumber) {
- if (isLuhnNum(cardNumber)) {
- var no_digit = cardNumber.length;
- var oddoeven = no_digit & 1;
- var sum = 0;
- for (var count = 0; count < no_digit; count++) {
- var digit = parseInt(cardNumber.charAt(count));
- if (!((count & 1) ^ oddoeven)) {
- digit *= 2;
- if (digit > 9) digit -= 9;
- };
- sum += digit;
- };
- if (sum == 0) return false;
- if (sum % 10 == 0) return true;
- };
- return false;
- }
-
- function isLuhnNum(argvalue) {
- argvalue = argvalue.toString();
- if (argvalue.length == 0) {
- return false;
- }
- for (var n = 0; n < argvalue.length; n++) {
- if ((argvalue.substring(n, n+1) < "0") ||
- (argvalue.substring(n,n+1) > "9")) {
- return false;
- }
- }
- return true;
- }]]>
- </javascript>
-
- </validator>
-
-
- <validator name="email"
- classname="org.springmodules.commons.validator.FieldChecks"
- method="validateEmail"
- methodParams="java.lang.Object,
- org.apache.commons.validator.ValidatorAction,
- org.apache.commons.validator.Field,
- org.springframework.validation.Errors"
-
- depends=""
- msg="errors.email">
-
- <javascript><![CDATA[
- function validateEmail(form) {
- var bValid = true;
- var focusField = null;
- var i = 0;
- var fields = new Array();
- oEmail = new email();
- for (x in oEmail) {
- if ((form[oEmail[x][0]].type == 'text' ||
- form[oEmail[x][0]].type == 'textarea') &&
- (form[oEmail[x][0]].value.length > 0)) {
- if (!checkEmail(form[oEmail[x][0]].value)) {
- if (i == 0) {
- focusField = form[oEmail[x][0]];
- }
- fields[i++] = oEmail[x][1];
- bValid = false;
- }
- }
- }
- if (fields.length > 0) {
- focusField.focus();
- alert(fields.join('\n'));
- }
- return bValid;
- }
-
- /**
- * Reference: Sandeep V. Tamhankar (sta...@ho...),
- * http://javascript.internet.com
- */
- function checkEmail(emailStr) {
- if (emailStr.length == 0) {
- return true;
- }
- var emailPat=/^(.+)@(.+)$/;
- var specialChars="\\(\\)<>@,;:\\\\\\\"\\.\\[\\]";
- var validChars="\[^\\s" + specialChars + "\]";
- var quotedUser="(\"[^\"]*\")";
- var ipDomainPat=/^(\d{1,3})[.](\d{1,3})[.](\d{1,3})[.](\d{1,3})$/;
- var atom=validChars + '+';
- var word="(" + atom + "|" + quotedUser + ")";
- var userPat=new RegExp("^" + word + "(\\." + word + ")*$");
- var domainPat=new RegExp("^" + atom + "(\\." + atom + ")*$");
- var matchArray=emailStr.match(emailPat);
- if (matchArray == null) {
- return false;
- }
- var user=matchArray[1];
- var domain=matchArray[2];
- if (user.match(userPat) == null) {
- return false;
- }
- var IPArray = domain.match(ipDomainPat);
- if (IPArray != null) {
- for (var i = 1; i <= 4; i++) {
- if (IPArray[i] > 255) {
- return false;
- }
- }
- return true;
- }
- var domainArray=domain.match(domainPat);
- if (domainArray == null) {
- return false;
- }
- var atomPat=new RegExp(atom,"g");
- var domArr=domain.match(atomPat);
- var len=domArr.length;
- if ((domArr[domArr.length-1].length < 2) ||
- (domArr[domArr.length-1].length > 3)) {
- return false;
- }
- if (len < 2) {
- return false;
- }
- return true;
- }]]>
- </javascript>
-
- </validator>
-
- </global>
-
-</form-validation>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-27 13:33:32
|
Revision: 219
http://treebase.svn.sourceforge.net/treebase/?rev=219&view=rev
Author: youjun
Date: 2009-10-27 13:33:26 +0000 (Tue, 27 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/applicationContext.xml
Modified: trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/applicationContext.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/applicationContext.xml 2009-10-27 00:42:46 UTC (rev 218)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/main/webapp/WEB-INF/applicationContext.xml 2009-10-27 13:33:26 UTC (rev 219)
@@ -9,5 +9,21 @@
http://www.directwebremoting.org/schema/spring-dwr
http://www.directwebremoting.org/schema/spring-dwr-2.0.xsd">
+ <!-- ========================================================== -->
+ <!-- LIST OF DWR beans/methods -->
+ <!-- ========================================================== -->
+
+
+
+ <!-- bean id="remoteAjaxProgressListener" class="org.cipres.treebase.web.controllers.AjaxProgressListener">
+ <dwr:remote javascript="RemoteAjaxProgressListener">
+ <dwr:include method="getStatus"/>
+ </dwr:remote>
+ </bean -->
+ <!-- dwr:configuration>
+ <dwr:convert type="bean" class="org.cipres.treebase.web.model.UploadInfoBean"/>
+ </dwr:configuration -->
+
+
</beans>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-27 00:42:57
|
Revision: 218
http://treebase.svn.sourceforge.net/treebase/?rev=218&view=rev
Author: youjun
Date: 2009-10-27 00:42:46 +0000 (Tue, 27 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-dao.xml
Modified: trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-dao.xml
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-dao.xml 2009-10-24 15:05:09 UTC (rev 217)
+++ trunk/oai-pmh_data_provider/data_provider_core/src/main/resources/applicationContext-dao.xml 2009-10-27 00:42:46 UTC (rev 218)
@@ -9,7 +9,7 @@
http://www.directwebremoting.org/schema/spring-dwr-2.0.xsd"
default-autowire="no">
-
+ <!-- point to property files location allow ${} operator to use properties value -->
<bean id="propertyConfigurer"
class="org.springframework.beans.factory.config.PropertyPlaceholderConfigurer">
@@ -59,13 +59,14 @@
</property>
</bean>
+ <!-- needed for transaction set up -->
<bean id="transactionManager"
class="org.springframework.orm.hibernate3.HibernateTransactionManager">
<property name="sessionFactory" ref="sessionFactory" />
</bean>
<!-- A parent bean definition which is a base definition for transaction proxies.
- - The attributes can still be overridden in child bean definitions.
+ - The attributes can still be overridden in child bean definitions.
-->
<bean id="baseTransactionProxy"
class="org.springframework.transaction.interceptor.TransactionProxyFactoryBean" abstract="true">
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rsc...@us...> - 2009-10-24 15:05:20
|
Revision: 217
http://treebase.svn.sourceforge.net/treebase/?rev=217&view=rev
Author: rscherle
Date: 2009-10-24 15:05:09 +0000 (Sat, 24 Oct 2009)
Log Message:
-----------
updated citations
Modified Paths:
--------------
trunk/treebase-curation/studyCitations.enl
Modified: trunk/treebase-curation/studyCitations.enl
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2009-10-23 22:43:01
|
Revision: 216
http://treebase.svn.sourceforge.net/treebase/?rev=216&view=rev
Author: youjun
Date: 2009-10-23 22:42:33 +0000 (Fri, 23 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_core/.classpath
trunk/oai-pmh_data_provider/data_provider_core/.settings/org.eclipse.wst.common.component
Added Paths:
-----------
trunk/oai-pmh_data_provider/data_provider_core/src/main/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/Constants.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/ContextManager.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/NamespacedGUID.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/PhyloWSPath.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/RangeExpression.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/TreebaseIDString.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/TreebaseUtil.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/Version.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/Action.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/ActionParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AddMetaDataAction.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AlternationParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AnalysisSectionParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AssignmentParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AssignmentSequenceParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AuthorParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AuxData.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/AuxiliaryDataParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/CheckMatrixNChars.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/CommitStudy.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/CompleteStudyAction.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/ConcatenationParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/Filter.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/FilterParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/FilterTrivial.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/Generator.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/GenericAction.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/GenericAuxDataAction.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/HeadlineParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/HistoryParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/IOParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/InputMatrixParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/LazyList.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/MatrixParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/MultipleMatchError.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/OptionalParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/OutputTreeParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/RDParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/RDParserArgumentFailureException.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/RDParserFailure.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/RDParserResult.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/RepeatedParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/SideCondition.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/SimpleSectionParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/SingleTokenParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/SpecificHeadlineParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/StudyItemParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/StudyParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/Token.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/TokenReader.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/TokenSequenceParser.java
trunk/oai-pmh_data_provider/data_provider_core/src/main/java/org/cipres/treebase/auxdata/TreeStudyMapping.java
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From: <yo...@us...> - 2009-10-23 15:52:52
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Revision: 215
http://treebase.svn.sourceforge.net/treebase/?rev=215&view=rev
Author: youjun
Date: 2009-10-23 15:52:46 +0000 (Fri, 23 Oct 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_core/target/data_provider_core-0.0.1-SNAPSHOT.jar
Modified: trunk/oai-pmh_data_provider/data_provider_core/target/data_provider_core-0.0.1-SNAPSHOT.jar
===================================================================
(Binary files differ)
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