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From: <hl...@us...> - 2010-03-17 14:39:44
|
Revision: 617
http://treebase.svn.sourceforge.net/treebase/?rev=617&view=rev
Author: hlapp
Date: 2010-03-17 14:39:38 +0000 (Wed, 17 Mar 2010)
Log Message:
-----------
Move to standard INSTALL name and removed hints to cruft.
Added Paths:
-----------
trunk/treebase-web/INSTALL.txt
Removed Paths:
-------------
trunk/treebase-web/read.txt
Copied: trunk/treebase-web/INSTALL.txt (from rev 614, trunk/treebase-web/read.txt)
===================================================================
--- trunk/treebase-web/INSTALL.txt (rev 0)
+++ trunk/treebase-web/INSTALL.txt 2010-03-17 14:39:38 UTC (rev 617)
@@ -0,0 +1,6 @@
+For information on configuring, building, and deploying TreeBASE
+consult the TreeBASE wiki:
+
+http://sourceforge.net/apps/mediawiki/treebase/
+
+Of particular relevance are sections 'Building' and 'Deploying'.
Deleted: trunk/treebase-web/read.txt
===================================================================
--- trunk/treebase-web/read.txt 2010-03-17 14:35:21 UTC (rev 616)
+++ trunk/treebase-web/read.txt 2010-03-17 14:39:38 UTC (rev 617)
@@ -1,5 +0,0 @@
-The information contained in this file was no longer up-to-date
-and no longer being maintained. For information on configuring,
-building and deploying TreeBASE, consult the wiki:
-
-http://sourceforge.net/apps/mediawiki/treebase/
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2010-03-31 18:46:36
|
Revision: 663
http://treebase.svn.sourceforge.net/treebase/?rev=663&view=rev
Author: youjun
Date: 2010-03-31 18:46:29 +0000 (Wed, 31 Mar 2010)
Log Message:
-----------
bring in urlrewrite tool, re-direct "view tree" to phylowidget.org
Modified Paths:
--------------
trunk/treebase-web/pom.xml
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/WEB-INF/urlrewrite.xml
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2010-03-31 14:49:01 UTC (rev 662)
+++ trunk/treebase-web/pom.xml 2010-03-31 18:46:29 UTC (rev 663)
@@ -77,6 +77,10 @@
<name>NeXML Remote Repository</name>
<url>http://nexml-dev.nescent.org/.m2/repository/</url>
</repository>
+ <repository>
+ <id>org.tuckey.urlrewritefilter</id>
+ <url>http://repository.jboss.org/maven2/org/tuckey/urlrewritefilter/</url>
+ </repository>
</repositories>
@@ -316,6 +320,11 @@
<version>1.0</version>
</dependency>
+ <dependency>
+ <groupId>org.tuckey</groupId>
+ <artifactId>urlrewritefilter</artifactId>
+ <version>3.0.4</version>
+ </dependency>
</dependencies>
</project>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp 2010-03-31 14:49:01 UTC (rev 662)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp 2010-03-31 18:46:29 UTC (rev 663)
@@ -19,11 +19,11 @@
export="false">
<display:column sortable="false" title="ID">
- <c:url var="treeURL" value="tree.html">
- <c:param name="id" value="${study.id}" />
- <c:param name="treeid" value="${tree.id}" />
- </c:url>
- <a href="javascript:popupWithSizes('${treeURL}',1000,900,'1')">Tr${tree.id}</a>
+ <c:url var="url" value="/tree_for_phylowidget/">
+ <!--c:param name="treeid" value="${tree.id}" /-->
+ <!--c:param name="id" value="${tree.study.id}" /-->
+ </c:url>
+ <a href="http://www.phylowidget.org/full/?tree='http://<%=request.getServerName()%>:<%=request.getServerPort()%>${url}TB2:Tr${tree.id}'" target="myplwidget">Tr${tree.id}</a>
</display:column>
<display:column
@@ -119,11 +119,11 @@
sortable="false"
class="iconColumn"
headerClass="iconColumn">
- <c:url var="treeURL" value="tree.html">
- <c:param name="id" value="${study.id}" />
- <c:param name="treeid" value="${tree.id}" />
- </c:url>
- <a href="javascript:popupWithSizes('${treeURL}',1000,900,'1')">
+ <c:url var="url" value="/tree_for_phylowidget/">
+ <!--c:param name="treeid" value="${tree.id}" /-->
+ <!--c:param name="id" value="${tree.study.id}" /-->
+ </c:url>
+ <a href="http://www.phylowidget.org/full/?tree='http://<%=request.getServerName()%>:<%=request.getServerPort()%>${url}TB2:Tr${tree.id}'" target="myplwidget">
<img
class="iconButton"
src="<fmt:message key="icons.list"/>"
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp 2010-03-31 14:49:01 UTC (rev 662)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeList.jsp 2010-03-31 18:46:29 UTC (rev 663)
@@ -14,12 +14,12 @@
export = "false">
<display:column title="" sortable="true" class="checkBoxColumn">
- <c:url var="url" value="study/tree.html">
- <c:param name="treeid" value="${tree.id}" />
- <c:param name="id" value="${tree.study.id}" />
+ <c:url var="url" value="/tree_for_phylowidget/">
+ <!--c:param name="treeid" value="${tree.id}" /-->
+ <!--c:param name="id" value="${tree.study.id}" /-->
</c:url>
<input type="checkbox" id="s-${tree.id }" name="selection" value="${tree.id }" />
- <a href="${url}" target="myplwidget">Tr${tree.id}</a>
+ <a href="http://www.phylowidget.org/full/?tree='http://<%=request.getServerName()%>:<%=request.getServerPort()%>${url}TB2:Tr${tree.id}'" target="myplwidget">Tr${tree.id}</a>
</display:column>
@@ -81,11 +81,11 @@
sortable="false"
class="iconColumn"
headerClass="iconColumn">
- <c:url var="url" value="study/tree.html">
- <c:param name="treeid" value="${tree.id}" />
- <c:param name="id" value="${tree.study.id}" />
+ <c:url var="url" value="/tree_for_phylowidget/">
+ <!--c:param name="treeid" value="${tree.id}" /-->
+ <!--c:param name="id" value="${tree.study.id}" /-->
</c:url>
- <a href="${url}" target="myplwidget">
+ <a href="http://www.phylowidget.org/full/?tree='http://<%=request.getServerName()%>:<%=request.getServerPort()%>${url}TB2:Tr${tree.id}'" target="myplwidget">
<img
class="iconButton"
src="<fmt:message key="icons.list"/>"
Added: trunk/treebase-web/src/main/webapp/WEB-INF/urlrewrite.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/urlrewrite.xml (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/urlrewrite.xml 2010-03-31 18:46:29 UTC (rev 663)
@@ -0,0 +1,97 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE urlrewrite PUBLIC "-//tuckey.org//DTD UrlRewrite 3.2//EN"
+ "http://tuckey.org/res/dtds/urlrewrite3.2.dtd">
+
+<!--
+
+ Configuration file for UrlRewriteFilter
+ http://tuckey.org/urlrewrite/
+
+-->
+<urlrewrite>
+
+ <rule>
+ <note>
+ The rule means that requests to /test/status/ will be redirected to /rewrite-status
+ the url will be rewritten.
+ </note>
+ <from>/tree_for_phylowidget/(.*)</from>
+ <to>/phylows/tree/$1?format=nexus</to>
+ </rule>
+
+ <!--
+ <outbound-rule>
+ <note>
+ The outbound-rule specifies that when response.encodeURL is called (if you are using JSTL c:url)
+ the url /rewrite-status will be rewritten to /test/status/.
+
+ The above rule and this outbound-rule means that end users should never see the
+ url /rewrite-status only /test/status/ both in thier location bar and in hyperlinks
+ in your pages.
+ </note>
+ <from>/rewrite-status</from>
+ <to>/test/status/</to>
+ </outbound-rule>
+ -->
+
+ <!--
+
+ INSTALLATION
+
+ in your web.xml add...
+
+ <filter>
+ <filter-name>UrlRewriteFilter</filter-name>
+ <filter-class>org.tuckey.web.filters.urlrewrite.UrlRewriteFilter</filter-class>
+ <init-param>
+ <param-name>logLevel</param-name>
+ <param-value>WARN</param-value>
+ </init-param>
+ </filter>
+ <filter-mapping>
+ <filter-name>UrlRewriteFilter</filter-name>
+ <url-pattern>/*</url-pattern>
+ </filter-mapping>
+
+ EXAMPLES
+
+ Redirect one url
+ <rule>
+ <from>/some/old/page.html</from>
+ <to type="redirect">/very/new/page.html</to>
+ </rule>
+
+ Redirect a directory
+ <rule>
+ <from>/some/olddir/(.*)</from>
+ <to type="redirect">/very/newdir/$1</to>
+ </rule>
+
+ Clean a url
+ <rule>
+ <from>/products/([0-9]+)</from>
+ <to>/products/index.jsp?product_id=$1</to>
+ </rule>
+ eg, /products/1234 will be passed on to /products/index.jsp?product_id=1234 without the user noticing.
+
+ Browser detection
+ <rule>
+ <condition name="user-agent">Mozilla/[1-4]</condition>
+ <from>/some/page.html</from>
+ <to>/some/page-for-old-browsers.html</to>
+ </rule>
+ eg, will pass the request for /some/page.html on to /some/page-for-old-browsers.html only for older
+ browsers whose user agent srtings match Mozilla/1, Mozilla/2, Mozilla/3 or Mozilla/4.
+
+ Centralised browser detection
+ <rule>
+ <condition name="user-agent">Mozilla/[1-4]</condition>
+ <set type="request" name="browser">moz</set>
+ </rule>
+ eg, all requests will be checked against the condition and if matched
+ request.setAttribute("browser", "moz") will be called.
+
+ -->
+
+</urlrewrite>
+
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2010-03-31 14:49:01 UTC (rev 662)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2010-03-31 18:46:29 UTC (rev 663)
@@ -85,8 +85,12 @@
<filter-class>org.displaytag.filter.ResponseOverrideFilter</filter-class>
</filter>
-
-
+ <filter>
+ <filter-name>UrlRewriteFilter</filter-name>
+ <filter-class>org.tuckey.web.filters.urlrewrite.UrlRewriteFilter</filter-class>
+ </filter>
+
+
<!-- ========================================================== -->
<!-- Mappings for Filters defined aboved -->
@@ -114,8 +118,13 @@
<filter-name>ResponseOverrideFilter</filter-name>
<url-pattern>*.html</url-pattern>
</filter-mapping>
+
+ <filter-mapping>
+ <filter-name>UrlRewriteFilter</filter-name>
+ <url-pattern>/*</url-pattern>
+ </filter-mapping>
-
+
<!-- ========================================================== -->
<!-- define the listener -->
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2010-04-03 14:52:27
|
Revision: 672
http://treebase.svn.sourceforge.net/treebase/?rev=672&view=rev
Author: youjun
Date: 2010-04-03 14:52:13 +0000 (Sat, 03 Apr 2010)
Log Message:
-----------
import oai-pmh-provider
Modified Paths:
--------------
trunk/treebase-web/pom.xml
Added Paths:
-----------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/OAIPMHController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/Identify.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/OAIPMHCommand.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/IdentifyUtil.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/validators/OAIPMHValidator.java
trunk/treebase-web/src/main/webapp/WEB-INF/identify.properties
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2010-04-03 14:08:25 UTC (rev 671)
+++ trunk/treebase-web/pom.xml 2010-04-03 14:52:13 UTC (rev 672)
@@ -326,5 +326,20 @@
<version>3.0.4</version>
</dependency>
+ <dependency>
+ <groupId>velocity-tools</groupId>
+ <artifactId>velocity-tools</artifactId>
+ <version>1.1</version>
+ </dependency>
+ <dependency>
+ <groupId>velocity-tools</groupId>
+ <artifactId>velocity-tools-generic</artifactId>
+ <version>1.1</version>
+ </dependency>
+ <dependency>
+ <groupId>velocity-tools</groupId>
+ <artifactId>velocity-tools-view</artifactId>
+ <version>1.1</version>
+ </dependency>
</dependencies>
</project>
Added: 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 (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/OAIPMHController.java 2010-04-03 14:52:13 UTC (rev 672)
@@ -0,0 +1,275 @@
+package org.treebase.oai.web.controller;
+
+import java.lang.reflect.Method;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+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.Identify;
+import org.treebase.oai.web.command.OAIPMHCommand;
+import org.treebase.oai.web.util.IdentifyUtil;
+import org.cipres.treebase.domain.admin.Person;
+import org.cipres.treebase.domain.study.ArticleCitation;
+import org.cipres.treebase.domain.study.BookCitation;
+import org.cipres.treebase.domain.study.Citation;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.study.Submission;
+import org.cipres.treebase.domain.study.SubmissionService;
+import org.cipres.treebase.domain.study.StudyService;
+/**
+ * OAIPMHController.java
+ *
+ * Created on Nov. 1, 2009
+ *
+ * @author Youjun Guo
+ *
+ */
+public class OAIPMHController extends AbstractCommandController{
+
+ private SubmissionService submissionService;
+ private StudyService studyService;
+ private Identify identify;
+
+ public OAIPMHController(){
+ setCommandClass(OAIPMHCommand.class);
+ 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)
+ throws Exception {
+ // TODO Auto-generated method stub
+
+ OAIPMHCommand params = (OAIPMHCommand) command;
+
+ Map model=errors.getModel();
+ model.put("requestParams", params);
+ model.put("identify", this.identify);
+
+ if(errors.getErrorCount()>0){
+ if(errors.hasFieldErrors("metadataPrefix")){
+ model.put("error_code", "cannotDisseminateFormat");
+ model.put("error", "bad metadataPrefix");
+ return new ModelAndView("error",model);
+ }
+ if(errors.hasFieldErrors("verb")){
+ model.put("error_code", "badVerb");
+ model.put("error", "no verb was found");
+ return new ModelAndView("error",model);
+ }
+ if(errors.hasFieldErrors("identifier")){
+ model.put("error_code", "idDoesNotExist");
+ model.put("error", "no id was found");
+ return new ModelAndView("error",model);
+ }
+ }
+
+ Method method=null;
+ try{
+ method=this.getClass().getMethod(params.getVerb(), new Class[]{OAIPMHCommand.class, Map.class});
+ }catch(NoSuchMethodException nsme){
+ model.put("error_code", "badVerb");
+ model.put("error", "invalid verb");
+ return new ModelAndView("error",model);
+ }catch(NullPointerException e){
+ model.put("error_code", "badVerb");
+ model.put("error", "missing verb");
+ return (new ModelAndView("error",model));
+ }
+
+ return (ModelAndView) method.invoke(this, params, model);
+
+ }
+
+ public ModelAndView ListRecords(OAIPMHCommand params, Map model){
+
+ List<Submission> list=null;
+ try {
+ list = (List)submissionService.findSubmissionByCreateDateRange(IdentifyUtil.parseGranularity(identify.getGranularityPattern(),params.getModifiedFrom()),
+ IdentifyUtil.parseGranularity(identify.getGranularityPattern(),params.getModifiedUntil()));
+ } catch (ParseException e) {
+ model.put("error_code", "badArgument");
+ model.put("error", "invalid from or until format");
+ return (new ModelAndView("error",model));
+ }
+ model.put("recordList", getRecordList(list));
+ return (new ModelAndView("ListRecords",model));
+
+ }
+
+
+ public ModelAndView ListIdentifiers( OAIPMHCommand params, Map model){
+
+ List<Submission> list=null;
+ try {
+ list = (List)submissionService.findSubmissionByCreateDateRange(IdentifyUtil.parseGranularity(identify.getGranularityPattern(),params.getModifiedFrom()),
+ IdentifyUtil.parseGranularity(identify.getGranularityPattern(), params.getModifiedUntil()));
+ } catch (ParseException e) {
+ model.put("error_code", "badArgument");
+ model.put("error", "invalid from or until format");
+ return (new ModelAndView("error",model));
+ }
+ model.put("recordList", getRecordList(list));
+ return (new ModelAndView(params.getMetadataPrefix()+"_ListIdentifiers",model));
+
+ }
+
+ public ModelAndView GetRecord( OAIPMHCommand params, Map model){
+
+ Submission submission = null;
+
+ try{
+ long id = IdentifyUtil.parseID(params);
+ submission = studyService.findByID(id).getSubmission();
+ }catch(NumberFormatException nfe){
+ model.put("error_code", "badArgument");
+ model.put("error", "invalid id format");
+ return (new ModelAndView("error",model));
+
+ }
+ catch (NullPointerException e){
+
+ model.put("error_code", "idDoesNotExist");
+ model.put("error", "invalid id");
+ return (new ModelAndView("error",model));
+
+ }
+ model.put("record", getRecordMap(submission));
+ return (new ModelAndView("GetRecord",model));
+
+ }
+
+ public ModelAndView Identify(OAIPMHCommand params, Map model){
+
+
+ return (new ModelAndView("Identify",model));
+
+ }
+
+ public ModelAndView ListSets(OAIPMHCommand params, Map model){
+ model.put("error_code", "noSetHierarchy");
+ model.put("error", "This repository does not support sets");
+ return (new ModelAndView("error",model));
+
+ }
+
+ public ModelAndView ListMetadataFormats(OAIPMHCommand params, Map model){
+
+ Submission submission = null;
+
+ try{
+ long id = IdentifyUtil.parseID(params);
+ submission = studyService.findByID(id).getSubmission();
+ }catch(NumberFormatException nfe){
+ model.put("error_code", "badArgument");
+ model.put("error", "invalid id format");
+ return (new ModelAndView("error",model));
+
+ }
+ catch (NullPointerException e){
+ //id is optional for ListMetadataFormats
+ //return (new ModelAndView("error",model));
+ }
+
+
+ return (new ModelAndView("ListMetadataFormats",model));
+
+ }
+
+
+ private Map getRecordMap(Submission submission){
+
+ Map map= new HashMap();
+
+ Study study=submission.getStudy();
+ Citation citation=study.getCitation();
+ String publisher=null;
+ if(!study.isPublished())return null;
+
+ //System.out.println("ctype: "+citation.getCitationType());
+ try{
+ if(citation.getCitationType().toUpperCase().contains("BOOK"))
+ publisher=((BookCitation)citation).getPublisher();
+ else publisher=((ArticleCitation)citation).getJournal();
+
+
+ List<Person> authors=citation.getAuthors();
+
+
+ map.put("title", citation.getTitle());
+ map.put("creator", authors);
+ map.put("subject", citation.getKeywords());
+ if(study.getName()!=null&study.getNotes()!=null)
+ map.put("description", study.getName()+" "+study.getNotes());
+ else if(study.getNotes()==null)
+ map.put("description",study.getName());
+ else
+ map.put("description",study.getNotes());
+ map.put("publisher", publisher);
+ map.put("date", "published on "+citation.getPublishYear());
+ map.put("identifier", "TreeBASE.org/study/TB2:s"+study.getId());
+ map.put("datestamp", study.getReleaseDate());
+
+ }catch(NullPointerException e){
+ //study 253 citation= null, data should be fixed
+ System.err.println("study "+study.getId()+
+ " citation= "+e.getMessage());
+ return null;
+ }
+
+ //map.put("type", "text");
+ //map.put("language", "en");
+
+ //map.put("issued", citation.getPublishYear());
+ //map.put("abstract", citation.getAbstract());
+
+
+ return map;
+ }
+
+ private List getRecordList(List<Submission> sList)
+ {
+ List recordList=new ArrayList<Map>();
+
+ for(int i =0; i< sList.size(); i++){
+ Map map=getRecordMap(sList.get(i));
+ if(map!=null)recordList.add(map);
+ }
+ return recordList;
+ }
+}
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/Identify.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/Identify.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/Identify.java 2010-04-03 14:52:13 UTC (rev 672)
@@ -0,0 +1,125 @@
+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;
+/**
+ *
+ * @author youjun
+ * class hold identify data about the service
+ */
+
+public class Identify {
+
+
+ private String baseURL;
+ private String repositoryName;
+ private String protocolVersion;
+ private String adminEmail;
+ private String earliestDatestamp;
+ private String deletedRecord;
+ private String granularity;
+ private String granularityPattern;
+ private String repositoryIdentifier;
+ private String sampleIdentifier;
+ private String dryadPerfix;
+ private String identifierDelimiter;
+ private String dublinPerfix;
+
+
+ public String getGranularityPattern() {
+ return granularityPattern;
+ }
+ public void setGranularityPattern(String granularityPattern) {
+ this.granularityPattern = granularityPattern;
+ }
+
+
+ public String getIdentifierDelimiter() {
+ return identifierDelimiter;
+ }
+ public void setIdentifierDelimiter(String identifierDelimiter) {
+ this.identifierDelimiter = identifierDelimiter;
+ }
+ public String getDublinPerfix() {
+ return dublinPerfix;
+ }
+ public void setDublinPerfix(String dublinPerfix) {
+ this.dublinPerfix = dublinPerfix;
+ }
+ public String getDryadPerfix() {
+ return dryadPerfix;
+ }
+ public void setDryadPerfix(String dryadPerfix) {
+ this.dryadPerfix = dryadPerfix;
+ }
+
+ public String getRepositoryIdentifier() {
+ return repositoryIdentifier;
+ }
+ public void setRepositoryIdentifier(String repositoryIdentifier) {
+ this.repositoryIdentifier = repositoryIdentifier;
+ }
+ public String getSampleIdentifier() {
+ return sampleIdentifier;
+ }
+ public void setSampleIdentifier(String sampleIdentifier) {
+ this.sampleIdentifier = sampleIdentifier;
+ }
+
+ public String getBaseURL() {
+ return baseURL;
+ }
+ public void setBaseURL(String baseRUL) {
+ this.baseURL = 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;
+ }
+
+ // return a current date object in UTC
+ public String getResponseDate(){
+ SimpleDateFormat format = new SimpleDateFormat(granularityPattern);
+ Calendar cal = Calendar.getInstance(new SimpleTimeZone(0, "GMT"));
+ format.setCalendar(cal);
+ return format.format(new Date());
+
+ }
+
+}
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/OAIPMHCommand.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/OAIPMHCommand.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/model/OAIPMHCommand.java 2010-04-03 14:52:13 UTC (rev 672)
@@ -0,0 +1,74 @@
+package org.treebase.oai.web.command;
+/**
+ *
+ * @author youjun
+ * class transfer page/query input data to controller
+ */
+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 getModifiedFrom() {
+ if(from!=null&&from.trim()!="")return from;
+ return "1995-11-04T00:00:00Z";
+ }
+
+ public String getFrom() {
+ return from;
+ }
+
+ public void setFrom(String from) {
+ this.from = from;
+ }
+ public String getModifiedUntil() {
+ if(until != null && until.trim()!="") return until;
+ return "";
+ }
+
+ 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/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 (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/IdentifyUtil.java 2010-04-03 14:52:13 UTC (rev 672)
@@ -0,0 +1,51 @@
+package org.treebase.oai.web.util;
+
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.GregorianCalendar;
+import java.util.TimeZone;
+
+import org.treebase.oai.web.command.Identify;
+import org.treebase.oai.web.command.OAIPMHCommand;
+/*
+ *
+ * @author youjun
+ *
+ */
+public class IdentifyUtil {
+
+ // return a studyID by parsing params.identifier
+
+ public static long parseID(OAIPMHCommand params)
+ {
+ String [] ids = params.getIdentifier().split("[/:.]");
+
+ return Long.parseLong(ids[ids.length-1].replaceAll("[a-zA-Z]",""));
+ }
+
+
+ // convert a time String to date object based on granularity
+
+ public static Date parseGranularity(String granularity, String time ) throws ParseException
+ {
+ if(time=="")return new Date();
+ SimpleDateFormat sdf = new SimpleDateFormat(granularity);
+ Date utcDate = sdf.parse(time);
+ return utcToLocal(utcDate);
+
+
+ }
+
+ //convert a date object from utc to local
+
+ protected static Date utcToLocal(Date utcDate)
+ {
+ long utcMiliseconds = utcDate.getTime();
+
+ Calendar cal = new GregorianCalendar();
+ cal.setTimeInMillis(utcMiliseconds);
+ return new Date(utcMiliseconds + cal.get(Calendar.ZONE_OFFSET) + cal.get(Calendar.DST_OFFSET));
+ }
+}
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/validators/OAIPMHValidator.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/validators/OAIPMHValidator.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/validators/OAIPMHValidator.java 2010-04-03 14:52:13 UTC (rev 672)
@@ -0,0 +1,40 @@
+package org.treebase.oai.web.validator;
+
+import org.springframework.validation.Errors;
+import org.springframework.validation.ValidationUtils;
+import org.springframework.validation.Validator;
+import org.treebase.oai.web.command.OAIPMHCommand;
+
+public class OAIPMHValidator implements Validator {
+
+ public boolean supports(Class pClass) {
+ return OAIPMHCommand.class.equals(pClass);
+ }
+
+ public void validate(Object pValidatable, Errors pError) {
+ // ValidationUtils.rejectIfEmpty(e, "name", "name.empty");
+ OAIPMHCommand command = (OAIPMHCommand) pValidatable;
+
+ String verb = command.getVerb();
+ String fPrefix = command.getMetadataPrefix();
+
+ ValidationUtils.rejectIfEmptyOrWhitespace(pError, "verb", "empyt verb");
+
+
+ if(verb!=null && verb.equals("GetRecord"))
+ ValidationUtils.rejectIfEmptyOrWhitespace(pError, "identifier", "empyt id");
+
+ // check format prefix
+ if(verb!=null){
+ if(verb.equals("GetRecord")||verb.equals("ListIdentifiers")||verb.equals("ListRecords")){
+
+ ValidationUtils.rejectIfEmptyOrWhitespace(pError, "metadataPrefix", "cannotDisseminateFormat");
+
+ if(fPrefix!=null)
+ if(!(fPrefix.equals("oai_dc")||fPrefix.equals("dryad")))
+ pError.rejectValue("metadataPrefix","cannotDisseminateFormat");
+ }
+ }
+ }
+
+}
Added: trunk/treebase-web/src/main/webapp/WEB-INF/identify.properties
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/identify.properties (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/identify.properties 2010-04-03 14:52:13 UTC (rev 672)
@@ -0,0 +1,13 @@
+identify.baseURL=www.***.***:port/top
+identify.repositoryName=TreeBASE repository
+identify.protocolVersion=2.0
+identify.adminEmail=you...@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'
+identify.sampleIdentifier=TreeBASE.org/study/TB2:s6705
+identify.repositoryIdentifier=TreeBASE.org
+identify.identifierDelimiter=:
+identify.dublinPerfix=oai_dc
+identify.dryadPerfix=dryad
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <yo...@us...> - 2010-07-13 16:38:10
|
Revision: 731
http://treebase.svn.sourceforge.net/treebase/?rev=731&view=rev
Author: youjun
Date: 2010-07-13 16:38:00 +0000 (Tue, 13 Jul 2010)
Log Message:
-----------
Modified Paths:
--------------
trunk/treebase-web/pom.xml
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Added Paths:
-----------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/UnTarTool.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/webservices/DryadImportor.java
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2010-07-07 19:32:38 UTC (rev 730)
+++ trunk/treebase-web/pom.xml 2010-07-13 16:38:00 UTC (rev 731)
@@ -21,6 +21,9 @@
</resource>
</resources>
<finalName>treebase-web</finalName>
+
+
+
<plugins>
<!-- Ant Task plugin-->
@@ -80,26 +83,20 @@
<repository>
<id>org.tuckey.urlrewritefilter</id>
<url>http://repository.jboss.org/maven2/org/tuckey/urlrewritefilter/</url>
- </repository>
-
+ </repository>
+ <repository>
+ <id>java.net</id>
+ <url>http://download.java.net/maven/2</url>
+ </repository>
+
+
</repositories>
+
- <pluginRepositories>
- <pluginRepository>
- <id>Maven Snapshots</id>
- <url>http://snapshots.maven.codehaus.org/maven2</url>
- <snapshots>
- <enabled>true</enabled>
- </snapshots>
- <releases>
- <enabled>false</enabled>
- </releases>
- </pluginRepository>
- </pluginRepositories>
- <dependencies>
-
-
+
+
+ <dependencies>
<dependency>
<groupId>org.nexml.model</groupId>
@@ -341,5 +338,36 @@
<artifactId>velocity-tools-view</artifactId>
<version>1.1</version>
</dependency>
- </dependencies>
+
+<dependency>
+<groupId>com.sun.jersey</groupId>
+<artifactId>jersey-client</artifactId>
+<version>1.1.5</version>
+</dependency>
+
+<dependency>
+<groupId>com.sun.jersey</groupId>
+<artifactId>jersey-server</artifactId>
+<version>1.1.5</version>
+</dependency>
+
+<dependency>
+<groupId>com.sun.jersey.contribs</groupId>
+<artifactId>jersey-multipart</artifactId>
+<version>1.1.5</version>
+</dependency>
+
+<dependency>
+<groupId>com.sun.jersey</groupId>
+<artifactId>jersey-bundle</artifactId>
+<version>1.1.5</version>
+</dependency>
+
+<dependency>
+<groupId>javax.ws.rs</groupId>
+<artifactId>jsr311-api</artifactId>
+<version>1.0</version>
+</dependency>
+</dependencies>
+
</project>
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/UnTarTool.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/UnTarTool.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/UnTarTool.java 2010-07-13 16:38:00 UTC (rev 731)
@@ -0,0 +1,69 @@
+package org.cipres.treebase.web.util;
+
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.zip.GZIPInputStream;
+
+import org.apache.tools.tar.TarEntry;
+import org.apache.tools.tar.TarInputStream;
+
+public class UnTarTool
+{
+
+ public static void unTarGz(File file,File outDir) throws IOException{
+
+ TarInputStream tarIn = null;
+
+ try{
+
+ tarIn = new TarInputStream(new GZIPInputStream(
+ new BufferedInputStream(new FileInputStream(file))),
+ 1024);
+
+ TarEntry entry = null;
+ //tarIn.getNextEntry();
+ //File outputDir = new File(outDir, "myBag");
+ //outputDir.mkdirs();
+ while( (entry = tarIn.getNextEntry()) != null ){
+ File f = new File(outDir,entry.getName());
+ if(entry.isDirectory()){
+ f.mkdirs();
+ }else{
+ f.getParentFile().mkdirs();
+ f.createNewFile();
+ OutputStream out = null;
+ try{
+ out = new FileOutputStream(f);
+ int length = 0;
+ byte[] b = new byte[1024];
+ while((length = tarIn.read(b)) != -1){
+ out.write(b, 0, length);
+ }
+
+ }catch(IOException ex){
+ throw ex;
+ }finally{
+ if(out!=null)
+ out.close();
+ }
+ }
+ }
+ }catch(IOException ex){
+ throw ex;
+ } finally{
+ try{
+ if(tarIn != null){
+ tarIn.close();
+ }
+ }catch(IOException ex){
+ throw ex;
+ }
+ }
+
+ }
+
+}
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/webservices/DryadImportor.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/webservices/DryadImportor.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/webservices/DryadImportor.java 2010-07-13 16:38:00 UTC (rev 731)
@@ -0,0 +1,104 @@
+package org.cipres.treebase.web.webservices;
+
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+
+import com.sun.jersey.multipart.*;
+import javax.servlet.http.HttpServletRequest;
+import javax.ws.rs.Consumes;
+//import javax.ws.rs.POST;
+import javax.ws.rs.PUT;
+import javax.ws.rs.Path;
+import javax.ws.rs.core.Context;
+
+import org.cipres.treebase.TreebaseUtil;
+import org.cipres.treebase.web.util.UnTarTool;
+
+
+
+@Path("/dryadImport")
+
+public class DryadImportor {
+
+ @Context
+ HttpServletRequest httpRequest;
+
+ @PUT
+ //@POST
+ //@GET
+
+ @Consumes("multipart/mixed")
+
+public String processMultiparts(MultiPart multiPart) {
+
+ String ip = httpRequest.getRemoteAddr();
+ if(!AllowIP.isAllowIP(ip))return "not authorized";
+
+ BodyPartEntity bpe = (BodyPartEntity) multiPart.getBodyParts().get(0).getEntity();
+ File unzipFold;
+ String systemTime;
+
+ do{
+ systemTime = "" + System.currentTimeMillis();
+ String uploadDir = httpRequest.getSession().getServletContext()
+ .getRealPath(TreebaseUtil.FILESEP + "DryadFileUpload")
+ + TreebaseUtil.FILESEP + systemTime;
+ unzipFold = new File(uploadDir);
+ }while(unzipFold.exists());
+
+
+ File zipfile = new File(unzipFold,"data.tar.gz");
+
+ try {
+ unzipFold.mkdirs();
+ zipfile.createNewFile();
+ InputStream in = bpe.getInputStream();
+ OutputStream out=new FileOutputStream(zipfile);
+
+ byte[] buf = new byte[1024];
+ int len;
+ while ((len = in.read(buf)) > 0){
+ out.write(buf, 0, len);
+ }
+ in.close();
+ out.close();
+ UnTarTool.unTarGz(zipfile,unzipFold);
+
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ StringWriter sw = new StringWriter();
+ e.printStackTrace(new PrintWriter(sw));
+ return sw.getBuffer().toString();
+ }
+ String[] baseURL=httpRequest.getRequestURL().toString().split("handshaking");
+ String importURL= baseURL[0] + "login.jsp?importKey=" + systemTime;
+
+ return importURL;
+
+ }
+
+}
+
+class AllowIP{
+ private static final String dryad1 = "152.1.24.8";
+ private static final String dryad2 = "152.3.105.16";
+ private static final String yale1 = "130.132.27.141";
+ private static final String yale2 = "130.132.27.212";
+
+ static boolean isAllowIP(String ip){
+
+ if (ip.compareTo(dryad1)==0) return true;
+ if (ip.compareTo(dryad2)==0) return true;
+ if (ip.compareTo(yale1)==0)return true;
+ if (ip.compareTo(yale2)==0)return true;
+
+ return false;
+ }
+
+}
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2010-07-07 19:32:38 UTC (rev 730)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2010-07-13 16:38:00 UTC (rev 731)
@@ -120,13 +120,67 @@
<!-- ========================================================== -->
<filter-mapping>
<filter-name>securityFilter</filter-name>
- <url-pattern>/*</url-pattern>
+ <url-pattern>/*</url-pattern>
</filter-mapping>
- <filter-mapping>
+
+ <filter-mapping>
<filter-name>sitemesh</filter-name>
- <url-pattern>/*</url-pattern>
+ <url-pattern>*.html</url-pattern>
<dispatcher>REQUEST</dispatcher>
<dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>sitemesh</filter-name>
+ <url-pattern>*.jsp</url-pattern>
+ <dispatcher>REQUEST</dispatcher>
+ <dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>sitemesh</filter-name>
+ <url-pattern>*.htm</url-pattern>
+ <dispatcher>REQUEST</dispatcher>
+ <dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>sitemesh</filter-name>
+ <url-pattern>*.rdf</url-pattern>
+ <dispatcher>REQUEST</dispatcher>
+ <dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>sitemesh</filter-name>
+ <url-pattern>/</url-pattern>
+ <dispatcher>REQUEST</dispatcher>
+ <dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+ <filter-mapping>
+ <filter-name>sitemesh</filter-name>
+ <url-pattern>/phylows/*</url-pattern>
+ <dispatcher>REQUEST</dispatcher>
+ <dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>sitemesh</filter-name>
+ <url-pattern>/top/*</url-pattern>
+ <dispatcher>REQUEST</dispatcher>
+ <dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>sitemesh</filter-name>
+ <url-pattern>/services/*</url-pattern>
+ <dispatcher>REQUEST</dispatcher>
+ <dispatcher>FORWARD</dispatcher>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>hibernateFilter</filter-name>
+ <url-pattern>*.html</url-pattern>
</filter-mapping>
<filter-mapping>
<filter-name>hibernateFilter</filter-name>
@@ -197,8 +251,22 @@
</servlet-class>
</servlet>
-
+ <!-- ========================================================== -->
+ <!-- Processed by Jersey -->
+ <!-- ========================================================== -->
+ <servlet>
+ <servlet-name>HandshakingServlet</servlet-name>
+ <servlet-class>
+ com.sun.jersey.spi.container.servlet.ServletContainer
+ </servlet-class>
+ <init-param>
+ <param-name>com.sun.jersey.config.property.packages</param-name>
+ <param-value>org.cipres.treebase.web.webservices</param-value>
+ </init-param>
+ <load-on-startup>1</load-on-startup>
+ </servlet>
+
<!-- ========================================================== -->
<!-- url pattern that will be processed by DispatcherServlet -->
<!-- ========================================================== -->
@@ -239,6 +307,14 @@
<servlet-mapping>
<servlet-name>CXFServlet</servlet-name>
<url-pattern>/services/*</url-pattern>
+ </servlet-mapping>
+
+ <!-- ========================================================== -->
+ <!-- url pattern that will be processed by CXFServlet -->
+ <!-- ========================================================== -->
+ <servlet-mapping>
+ <servlet-name>HandshakingServlet</servlet-name>
+ <url-pattern>/handshaking/*</url-pattern>
</servlet-mapping>
<!-- ========================================================== -->
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <hs...@us...> - 2011-11-17 21:46:00
|
Revision: 982
http://treebase.svn.sourceforge.net/treebase/?rev=982&view=rev
Author: hshyket
Date: 2011-11-17 21:45:53 +0000 (Thu, 17 Nov 2011)
Log Message:
-----------
Updating the error message for when no study is found (and also handling no Taxa found). Adding JavaMelody monitoring system
Modified Paths:
--------------
trunk/treebase-web/pom.xml
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java
trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Added Paths:
-----------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/exceptions/NoStudySpecifiedError.java
trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/itemNotFound.jsp
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2011-11-16 17:08:00 UTC (rev 981)
+++ trunk/treebase-web/pom.xml 2011-11-17 21:45:53 UTC (rev 982)
@@ -393,6 +393,33 @@
<version>1.0</version>
</dependency>
+<!-- javamelody-core -->
+ <dependency>
+ <groupId>net.bull.javamelody</groupId>
+ <artifactId>javamelody-core</artifactId>
+ <version>1.32.1</version>
+ </dependency>
+ <!-- itext, option to add PDF export -->
+ <dependency>
+ <groupId>com.lowagie</groupId>
+ <artifactId>itext</artifactId>
+ <version>2.1.7</version>
+ <exclusions>
+ <exclusion>
+ <artifactId>bcmail-jdk14</artifactId>
+ <groupId>bouncycastle</groupId>
+ </exclusion>
+ <exclusion>
+ <artifactId>bcprov-jdk14</artifactId>
+ <groupId>bouncycastle</groupId>
+ </exclusion>
+ <exclusion>
+ <artifactId>bctsp-jdk14</artifactId>
+ <groupId>bouncycastle</groupId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+
</dependencies>
</project>
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java 2011-11-16 17:08:00 UTC (rev 981)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java 2011-11-17 21:45:53 UTC (rev 982)
@@ -50,6 +50,7 @@
import org.cipres.treebase.web.util.AnalyzedDataComparator;
import org.cipres.treebase.web.util.ControllerUtil;
+import org.cipres.treebase.web.exceptions.NoStudySpecifiedError;
import org.springframework.validation.BindException;
import org.springframework.web.servlet.ModelAndView;
@@ -71,7 +72,6 @@
String defaultPage = null;
private static final Logger LOGGER = Logger.getLogger(SearchSummaryController.class);
- class NoStudySpecifiedError extends Error { }
class UnknownStudyError extends Error { }
class RestrictedStudyError extends Error { }
@@ -90,7 +90,7 @@
theStudy = null;
{
Long studyID = getIDParam(param, "id");
- if (studyID == null) { throw new NoStudySpecifiedError(); }
+ if (studyID == null) { throw new NoStudySpecifiedError("No study was found"); }
theStudy = getStudyService().findByID(studyID);
if (theStudy == null) { throw new UnknownStudyError(); }
LOGGER.debug("formBackingObject found study " + theStudy);
@@ -268,7 +268,17 @@
*/
private Long getIDParam(Map<String, String []> params, String paramName) {
String [] IDParam = params.get(paramName);
- return IDParam.length == 0 ? null : Long.parseLong(IDParam[0]);
+ if (IDParam == null || IDParam.length == 0) {
+ return null;
+ }
+ else {
+ try {
+ return Long.parseLong(IDParam[0]);
+ }
+ catch(Exception e) {
+ return null;
+ }
+ }
}
@Override
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java 2011-11-16 17:08:00 UTC (rev 981)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java 2011-11-17 21:45:53 UTC (rev 982)
@@ -239,7 +239,7 @@
switch(namingAuthority) {
case TREEBASE :
LOGGER.debug("Going to search for TreeBASE IDs");
- if ( ! index.endsWith(".tb1") ) {
+ if (null != index && ! index.endsWith(".tb1") ) {
TreebaseIDString idstr;
try {
idstr = new TreebaseIDString(identifier, Taxon.class, true);
@@ -261,7 +261,7 @@
addMessage(request, "Ignoring malformed TreeBASE1 ID string '" + identifier + "', because: " + e.getMessage());
LOGGER.error("Couldn't parse legacy ID: "+e.getMessage());
}
- if ( null != tb1LegacyId && index.matches(".*taxonVariant.*") ) {
+ if ( null != tb1LegacyId && null != index && index.matches(".*taxonVariant.*") ) {
TaxonVariant tv = getTaxonHome().findVariantByTB1LegacyId(tb1LegacyId);
LOGGER.debug("Found taxon variant: " + tv.getId());
if ( null != tv.getTaxon() ) {
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/exceptions/NoStudySpecifiedError.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/exceptions/NoStudySpecifiedError.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/exceptions/NoStudySpecifiedError.java 2011-11-17 21:45:53 UTC (rev 982)
@@ -0,0 +1,19 @@
+
+package org.cipres.treebase.web.exceptions;
+
+/**
+ * EmptySubmissionException.java
+ *
+ * Created on Jun 7, 2006
+ * @author lcchan
+ *
+ */
+public class NoStudySpecifiedError extends RuntimeException {
+
+ /**
+ * Constructor.
+ */
+ public NoStudySpecifiedError(String s) {
+ super(s);
+ }
+}
Added: trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/itemNotFound.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/itemNotFound.jsp (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/itemNotFound.jsp 2011-11-17 21:45:53 UTC (rev 982)
@@ -0,0 +1,3 @@
+<%@ include file="/common/taglibs.jsp" %>
+
+${requestScope.exception.message}
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2011-11-16 17:08:00 UTC (rev 981)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2011-11-17 21:45:53 UTC (rev 982)
@@ -1112,7 +1112,8 @@
<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>
+ <prop key="org.cipres.treebase.web.exceptions.EmptyStudyException">/errors/studyAccessFailure</prop>
+ <prop key="org.cipres.treebase.web.exceptions.NoStudySpecifiedError">/errors/itemNotFound</prop>
</props>
</property>
</bean>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-16 17:08:00 UTC (rev 981)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-17 21:45:53 UTC (rev 982)
@@ -111,7 +111,17 @@
<filter>
<filter-name>UrlRewriteFilter</filter-name>
<filter-class>org.tuckey.web.filters.urlrewrite.UrlRewriteFilter</filter-class>
- </filter>
+ </filter>
+
+ <filter>
+ <filter-name>monitoring</filter-name>
+ <filter-class>net.bull.javamelody.MonitoringFilter</filter-class>
+ <init-param>
+ <param-name>system-actions-enabled</param-name>
+ <param-value>true</param-value>
+ </init-param>
+ </filter>
+
@@ -200,6 +210,12 @@
<filter-name>UrlRewriteFilter</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
+
+ <filter-mapping>
+ <filter-name>monitoring</filter-name>
+ <url-pattern>/*</url-pattern>
+ </filter-mapping>
+
@@ -215,6 +231,9 @@
<listener>
<listener-class>net.sf.navigator.menu.MenuContextListener</listener-class>
</listener>
+ <listener>
+ <listener-class>net.bull.javamelody.SessionListener</listener-class>
+ </listener>
<!-- listener>
<listener-class>org.cipres.treebase.web.listeners.EventListener</listener-class>
</listener -->
@@ -356,6 +375,10 @@
<exception-type>java.lang.Exception</exception-type>
<location>/WEB-INF/pages/errors/uncaughtException.jsp</location>
</error-page>
+ <error-page>
+ <exception-type>java.lang.Exception</exception-type>
+ <location>/WEB-INF/pages/errors/uncaughtException.jsp</location>
+ </error-page>
<!-- Internal Server Error -->
<error-page>
<error-code>500</error-code>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <hs...@us...> - 2011-11-22 20:38:32
|
Revision: 986
http://treebase.svn.sourceforge.net/treebase/?rev=986&view=rev
Author: hshyket
Date: 2011-11-22 20:38:26 +0000 (Tue, 22 Nov 2011)
Log Message:
-----------
Adding OSCache with expiration time so that Apache can cache study downloads
Modified Paths:
--------------
trunk/treebase-web/pom.xml
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2011-11-18 22:22:51 UTC (rev 985)
+++ trunk/treebase-web/pom.xml 2011-11-22 20:38:26 UTC (rev 986)
@@ -419,6 +419,12 @@
</exclusion>
</exclusions>
</dependency>
+
+ <dependency>
+ <groupId>opensymphony</groupId>
+ <artifactId>oscache</artifactId>
+ <version>2.4.1</version>
+ </dependency>
</dependencies>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-18 22:22:51 UTC (rev 985)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-22 20:38:26 UTC (rev 986)
@@ -58,8 +58,26 @@
<listener>
<listener-class>net.bull.javamelody.SessionListener</listener-class>
</listener>
-
+
+ <filter>
+ <filter-name>CacheFilter</filter-name>
+ <filter-class>com.opensymphony.oscache.web.filter.CacheFilter</filter-class>
+ <init-param>
+ <param-name>expires</param-name>
+ <param-value>time</param-value>
+ </init-param>
+ <init-param>
+ <param-name>time</param-name>
+ <param-value>2592000</param-value> <!-- one month -->
+ </init-param>
+ </filter>
+ <filter-mapping>
+ <filter-name>CacheFilter</filter-name>
+ <url-pattern>/search/downloadAStudy.html*</url-pattern>
+ </filter-mapping>
+
+
<!-- =================================================================== -->
<!-- Declarations of JNDI Resources expected from the Tomcat container -->
<!-- =================================================================== -->
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <hs...@us...> - 2012-05-25 15:25:55
|
Revision: 1093
http://treebase.svn.sourceforge.net/treebase/?rev=1093&view=rev
Author: hshyket
Date: 2012-05-25 15:25:44 +0000 (Fri, 25 May 2012)
Log Message:
-----------
Removing Caching
Modified Paths:
--------------
trunk/treebase-web/pom.xml
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2012-04-03 14:24:26 UTC (rev 1092)
+++ trunk/treebase-web/pom.xml 2012-05-25 15:25:44 UTC (rev 1093)
@@ -419,13 +419,6 @@
</exclusion>
</exclusions>
</dependency>
-
- <dependency>
- <groupId>opensymphony</groupId>
- <artifactId>oscache</artifactId>
- <version>2.4.1</version>
- </dependency>
-
</dependencies>
</project>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2012-04-03 14:24:26 UTC (rev 1092)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2012-05-25 15:25:44 UTC (rev 1093)
@@ -58,47 +58,7 @@
<listener>
<listener-class>net.bull.javamelody.SessionListener</listener-class>
</listener>
-
- <filter>
- <filter-name>CacheFilter</filter-name>
- <filter-class>com.opensymphony.oscache.web.filter.CacheFilter</filter-class>
- <init-param>
- <param-name>expires</param-name>
- <param-value>time</param-value>
- </init-param>
- <init-param>
- <param-name>time</param-name>
- <param-value>2592000</param-value> <!-- one month -->
- </init-param>
- </filter>
- <filter-mapping>
- <filter-name>CacheFilter</filter-name>
- <url-pattern>/search/downloadAStudy.html</url-pattern>
- </filter-mapping>
-
- <filter-mapping>
- <filter-name>CacheFilter</filter-name>
- <url-pattern>/search/study/anyObjectAsRDF.rdf</url-pattern>
- </filter-mapping>
-
- <filter-mapping>
- <filter-name>CacheFilter</filter-name>
- <url-pattern>/search/downloadANexusFile.html</url-pattern>
- </filter-mapping>
-
- <filter-mapping>
- <filter-name>CacheFilter</filter-name>
- <url-pattern>/search/downloadAMatrix.html</url-pattern>
- </filter-mapping>
-
- <filter-mapping>
- <filter-name>CacheFilter</filter-name>
- <url-pattern>/search/downloadATree.html</url-pattern>
- </filter-mapping>
-
-
-
<!-- =================================================================== -->
<!-- Declarations of JNDI Resources expected from the Tomcat container -->
<!-- =================================================================== -->
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
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