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[Treebase-guts] SF.net SVN: treebase:[678] trunk/treebase-web/src/main
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From: <yo...@us...> - 2010-04-06 20:37:53
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Revision: 678
http://treebase.svn.sourceforge.net/treebase/?rev=678&view=rev
Author: youjun
Date: 2010-04-06 20:37:41 +0000 (Tue, 06 Apr 2010)
Log Message:
-----------
modify oai-pmh-data-provider code to fit in treebase
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/OAIPMHController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/IdentifyUtil.java
trunk/treebase-web/src/main/webapp/WEB-INF/identify.properties
trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/
trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/GetRecord.vm
trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/Identify.vm
trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/ListMetadataFormats.vm
trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/ListRecords.vm
trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/ListSets.vm
trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/error.vm
trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/head.vm
trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/oai_dc_ListIdentifiers.vm
trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/oai_dc_record.vm
Removed Paths:
-------------
trunk/treebase-web/src/main/webapp/WEB-INF/mvFiles/
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/OAIPMHController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/OAIPMHController.java 2010-04-06 01:55:28 UTC (rev 677)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/OAIPMHController.java 2010-04-06 20:37:41 UTC (rev 678)
@@ -24,6 +24,7 @@
import org.cipres.treebase.domain.study.Submission;
import org.cipres.treebase.domain.study.SubmissionService;
import org.cipres.treebase.domain.study.StudyService;
+
/**
* OAIPMHController.java
*
@@ -231,16 +232,16 @@
List<Person> authors=citation.getAuthors();
- map.put("title", citation.getTitle());
+ map.put("title", IdentifyUtil.escape4XML(citation.getTitle()));
map.put("creator", authors);
- map.put("subject", citation.getKeywords());
+ map.put("subject", IdentifyUtil.escape4XML(citation.getKeywords()));
if(study.getName()!=null&study.getNotes()!=null)
- map.put("description", study.getName()+" "+study.getNotes());
+ map.put("description", IdentifyUtil.escape4XML(study.getName()+" "+study.getNotes()));
else if(study.getNotes()==null)
- map.put("description",study.getName());
+ map.put("description",IdentifyUtil.escape4XML(study.getName()));
else
- map.put("description",study.getNotes());
- map.put("publisher", publisher);
+ map.put("description",IdentifyUtil.escape4XML(study.getNotes()));
+ map.put("publisher", IdentifyUtil.escape4XML(publisher));
map.put("date", "published on "+citation.getPublishYear());
map.put("identifier", "TreeBASE.org/study/TB2:s"+study.getId());
map.put("datestamp", study.getReleaseDate());
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/IdentifyUtil.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/IdentifyUtil.java 2010-04-06 01:55:28 UTC (rev 677)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/IdentifyUtil.java 2010-04-06 20:37:41 UTC (rev 678)
@@ -1,7 +1,9 @@
package org.cipres.treebase.web.util;
+import java.text.CharacterIterator;
import java.text.ParseException;
import java.text.SimpleDateFormat;
+import java.text.StringCharacterIterator;
import java.util.Calendar;
import java.util.Date;
import java.util.GregorianCalendar;
@@ -48,4 +50,35 @@
cal.setTimeInMillis(utcMiliseconds);
return new Date(utcMiliseconds + cal.get(Calendar.ZONE_OFFSET) + cal.get(Calendar.DST_OFFSET));
}
+
+ public static String escape4XML(String aText){
+ final StringBuilder result = new StringBuilder();
+ final StringCharacterIterator iterator = new StringCharacterIterator(aText);
+ char character = iterator.current();
+ while (character != CharacterIterator.DONE ){
+ if (character == '<') {
+ result.append("<");
+ }
+ else if (character == '>') {
+ result.append(">");
+ }
+ else if (character == '\"') {
+ result.append(""");
+ }
+ else if (character == '\'') {
+ result.append("'");
+ }
+ else if (character == '&') {
+ result.append("&");
+ }
+ else {
+ //the char is not a special one
+ //add it to the result as is
+ result.append(character);
+ }
+ character = iterator.next();
+ }
+ return result.toString();
+ }
+
}
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/identify.properties
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/identify.properties 2010-04-06 01:55:28 UTC (rev 677)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/identify.properties 2010-04-06 20:37:41 UTC (rev 678)
@@ -1,4 +1,4 @@
-identify.baseURL=www.***.***:port/top
+identify.baseURL=www.treebase.org/treebase-web/top/oai
identify.repositoryName=TreeBASE repository
identify.protocolVersion=2.0
identify.adminEmail=you...@ya...
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2010-04-06 01:55:28 UTC (rev 677)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2010-04-06 20:37:41 UTC (rev 678)
@@ -13,11 +13,9 @@
<!-- velocity configure -->
<!-- ========================================================== -->
- <bean id="velocityConfigurer" class="org.springframework.web.servlet.view.velocity.VelocityConfigurer">
- <property name="resourceLoaderPath">
- <value>WEB-INF/vmFiles/</value>
- </property>
- </bean>
+ <bean id="velocityConfigurer" class="org.springframework.web.servlet.view.velocity.VelocityConfigurer">
+ <property name="resourceLoaderPath" value="/WEB-INF/vmFiles/" />
+ </bean>
<!-- ========================================================== -->
<!-- LIST OF CONTROLLERS FOR WEB-TIER -->
@@ -860,14 +858,11 @@
<!-- ========================================================== -->
<!-- Spring View Resolvers for JSPs and .vm files -->
<!-- ========================================================== -->
- <!--
+
<bean id="chainableVelocityViewResolver" class="org.cipres.treebase.web.viewresolver.ChainableVelocityViewResolver">
<property name="chainableResolver">
- <bean class="org.springframework.web.servlet.view.velocity. VelocityViewResolver">
- <property name="order" value="1"></property>
- <property name="suffix">
- <value>.vm</value>
- </property>
+ <bean class="org.springframework.web.servlet.view.velocity.VelocityViewResolver">
+ <property name="suffix" value=".vm"/>
<property name="exposeRequestAttributes">
<value>true</value>
</property>
@@ -876,8 +871,7 @@
</property>
<property name="contentType" value="application/xml;charset=UTF-8" />
</bean>
- </property>
- <property name="order"><value>1</value></property>
+ </property>
<property name="views">
<list>
<value>error</value>
@@ -891,7 +885,7 @@
</property>
</bean>
- -->
+
<bean id="viewResolver" class="org.springframework.web.servlet.view.InternalResourceViewResolver">
<property name="requestContextAttribute" value="rc"/>
<property name="viewClass" value="org.springframework.web.servlet.view.JstlView"/>
Added: trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/GetRecord.vm
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/GetRecord.vm (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/GetRecord.vm 2010-04-06 20:37:41 UTC (rev 678)
@@ -0,0 +1,7 @@
+#parse("head.vm")
+<GetRecord>
+#if($!requestParams.metadataPrefix=="oai_dc")
+#parse("oai_dc_record.vm")
+#end
+</GetRecord>
+</OAI-PMH>
Added: trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/Identify.vm
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/Identify.vm (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/Identify.vm 2010-04-06 20:37:41 UTC (rev 678)
@@ -0,0 +1,25 @@
+#parse("head.vm")
+ <Identify>
+ <repositoryName>${identify.repositoryName}</repositoryName>
+ <baseURL>${identify.baseURL}</baseURL>
+ <protocolVersion>${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>${identify.repositoryIdentifier}</repositoryIdentifier>
+ <delimiter>${identify.identifierDelimiter}</delimiter>
+ <sampleIdentifier>${identify.sampleIdentifier}</sampleIdentifier>
+ </oai-identifier>
+ </description>
+ </Identify>
+</OAI-PMH>
Added: trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/ListMetadataFormats.vm
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/ListMetadataFormats.vm (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/ListMetadataFormats.vm 2010-04-06 20:37:41 UTC (rev 678)
@@ -0,0 +1,19 @@
+#parse("head.vm")
+ <ListMetadataFormats>
+ <metadataFormat>
+ <metadataPrefix>oai_dc</metadataPrefix>
+ <schema>http://www.openarchives.org/OAI/2.0/oai_dc.xsd
+ </schema>
+ <metadataNamespace>http://www.openarchives.org/OAI/2.0/oai_dc/
+ </metadataNamespace>
+ </metadataFormat>
+
+ <metadataFormat>
+ <metadataPrefix>dryad</metadataPrefix>
+ <schema>http://ils.unc.edu/mrc/dryad/version1_0/dryad_1_0.xsd</schema>
+ <metadataNamespace>http://ils.unc.edu/mrc/dryad/
+ </metadataNamespace>
+ </metadataFormat>
+
+ </ListMetadataFormats>
+</OAI-PMH>
Added: trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/ListRecords.vm
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/ListRecords.vm (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/ListRecords.vm 2010-04-06 20:37:41 UTC (rev 678)
@@ -0,0 +1,9 @@
+#parse("head.vm")
+<ListRecords>
+#if($!requestParams.metadataPrefix=="oai_dc")
+#foreach($record in $recordList)
+#parse("oai_dc_record.vm")
+#end
+#end
+</ListRecords>
+</OAI-PMH>
Added: trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/ListSets.vm
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/ListSets.vm (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/ListSets.vm 2010-04-06 20:37:41 UTC (rev 678)
@@ -0,0 +1,3 @@
+#parse("head.vm")
+ <error code="noSetHierarchy">This repository does not support sets</error>
+</OAI-PMH>
Added: trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/error.vm
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/error.vm (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/error.vm 2010-04-06 20:37:41 UTC (rev 678)
@@ -0,0 +1,3 @@
+#parse("head.vm")
+<error code="$!error_code">$!error</error>
+</OAI-PMH>
Added: trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/head.vm
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/head.vm (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/head.vm 2010-04-06 20:37:41 UTC (rev 678)
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<OAI-PMH xmlns="http://www.openarchives.org/OAI/2.0/"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/
+ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd">
+<responseDate>${identify.getResponseDate()}</responseDate>
+<request #if($!requestParams.verb)verb="$!requestParams.verb" #end
+#if($!requestParams.identifier)identifier="$!requestParams.identifier" #end
+#if($!requestParams.metadataPrefix)metadataPrefix="$!requestParams.metadataPrefix" #end
+#if($!requestParams.from)from="$!requestParams.from" #end
+#if($!requestParams.until)until="$!requestParams.until" #end
+#if($!requestParams.resumptionToken)resumptionToken="$!requestParams.resumptionToken" #end
+#if($!requestParams.set)set="$!requestParams.set" #end>
+$!identify.BaseURL</request>
Added: trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/oai_dc_ListIdentifiers.vm
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/oai_dc_ListIdentifiers.vm (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/oai_dc_ListIdentifiers.vm 2010-04-06 20:37:41 UTC (rev 678)
@@ -0,0 +1,10 @@
+#parse("head.vm")
+<ListIdentifiers>
+#foreach ( $record in $recordList)
+<header>
+<identifier>${record.identifier}</identifier>
+<datestamp>$!record.datestamp</datestamp>
+</header>
+#end
+</ListIdentifiers>
+</OAI-PMH>
Added: trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/oai_dc_record.vm
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/oai_dc_record.vm (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/oai_dc_record.vm 2010-04-06 20:37:41 UTC (rev 678)
@@ -0,0 +1,64 @@
+<record>
+<header>
+<identifier>${record.identifier}</identifier>
+<datestamp>$!record.datestamp</datestamp>
+</header>
+<metadata>
+<oai_dc:dc
+ xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/
+ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
+#if($record.title)
+<dc:title>${record.title}</dc:title>
+#end
+#if($record.creator)
+#foreach ($person in $record.creator)
+<dc:creator>${person.lastName}, ${person.firstName}</dc:creator>
+#end
+#end
+#if($record.subject)
+<dc:subject>${record.subject}</dc:subject>
+#end
+#if($record.description)
+<dc:description>${record.description}</dc:description>
+#end
+#if($record.publisher)
+<dc:publisher>${record.publisher}</dc:publisher>
+#end
+#if($record.contributor)
+<dc:contributor>${record.contributor}</dc:contributor>
+#end
+#if($record.date)
+<dc:date>${record.date}</dc:date>
+#end
+#if($record.type)
+<dc:type>${record.type}</dc:type>
+#end
+#if($record.format)
+<dc:format>${record.format}</dc:format>
+#end
+
+#if($record.identifier)
+<dc:identifier>${record.identifier}</dc:identifier>
+#end
+
+#if($record.source)
+<dc:source>{record.source}</dc:source>
+#end
+#if($record.language)
+<dc:language>${record.language}</dc:language>
+#end
+#if($record.relation)
+<dc:relation>${record.relation}</dc:relation>
+#end
+#if($record.coverage)
+<dc:coverage>${record.coverage}</dc:coverage>
+#end
+#if($record.rights)
+<dc:rights>${record.rights}</dc:rights>
+#end
+</oai_dc:dc>
+</metadata>
+</record>
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