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[Treebase-guts] SF.net SVN: treebase:[975] trunk/treebase-web/src/main
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From: <hs...@us...> - 2011-10-28 14:08:37
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Revision: 975
http://treebase.svn.sourceforge.net/treebase/?rev=975&view=rev
Author: hshyket
Date: 2011-10-28 14:08:26 +0000 (Fri, 28 Oct 2011)
Log Message:
-----------
Updating functionality to allow download of all trees through the tree search page and also via the API query calls for Nexus and NeXML
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsListControls.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java 2011-10-27 16:58:16 UTC (rev 974)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java 2011-10-28 14:08:26 UTC (rev 975)
@@ -3,6 +3,8 @@
package org.cipres.treebase.web.controllers;
+import java.io.File;
+import java.io.FileWriter;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
@@ -12,6 +14,7 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.Properties;
import java.util.Set;
import javax.servlet.ServletException;
@@ -23,16 +26,31 @@
import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.TreebaseIDString.MalformedTreebaseIDString;
import org.cipres.treebase.domain.TBPersistable;
+import org.cipres.treebase.domain.nexus.NexusDataSet;
+import org.cipres.treebase.domain.nexus.NexusService;
+import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter;
import org.cipres.treebase.domain.search.SearchResults;
import org.cipres.treebase.domain.search.SearchResultsFrozen;
import org.cipres.treebase.domain.search.SearchResultsType;
import org.cipres.treebase.domain.search.SearchService;
import org.cipres.treebase.domain.search.StudySearchResults;
+import org.cipres.treebase.domain.search.TaxonSearchResults;
+import org.cipres.treebase.domain.search.TreeSearchResults;
+import org.cipres.treebase.domain.taxon.Taxon;
+import org.cipres.treebase.domain.taxon.TaxonLabel;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
import org.cipres.treebase.domain.taxon.TaxonLabelService;
+import org.cipres.treebase.domain.taxon.TaxonLabelSet;
+import org.cipres.treebase.domain.taxon.TaxonVariant;
+import org.cipres.treebase.domain.tree.PhyloTree;
+import org.cipres.treebase.domain.tree.TreeBlock;
import org.cipres.treebase.service.AbstractService;
import org.cipres.treebase.web.Constants;
import org.cipres.treebase.web.model.SearchCommand;
import org.cipres.treebase.web.util.SearchMessageSetter;
+import org.cipres.treebase.web.util.WebUtil;
+import org.nexml.model.Document;
+import org.nexml.model.DocumentFactory;
import org.springframework.validation.BindException;
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.view.RedirectView;
@@ -55,6 +73,12 @@
protected String formView;
private TaxonLabelService mTaxonLabelService;
+ protected static final int FORMAT_NEXUS = 1;
+ protected static final int FORMAT_NEXML = 2;
+ private static String mNexmlContentType = "application/xml; charset=UTF-8";
+ protected String mFormatParameter = "format";
+ private TaxonLabelHome mTaxonLabelHome;
+
protected abstract ModelAndView handleQueryRequest(HttpServletRequest request,HttpServletResponse response,BindException errors,String query) throws CQLParseException, IOException, InstantiationException, ParseException;
/**
@@ -122,7 +146,11 @@
onSubmitDiscardResults(request, response, command, errors);
} else if ( action.equals("refineSearch") ){
onSubmitRefineSearch(request,response,command,errors);
- } else {
+ } else if ( action.equals("downloadAllTrees") ) {
+ downloadAllTrees(request, response, errors);
+ return null;
+ }
+ else {
throw new Error("Unknown action '" + action + "'");
}
} else {
@@ -140,6 +168,116 @@
return selectResultsView(request);
}
+ protected void downloadAllTrees(HttpServletRequest request,
+ HttpServletResponse response, BindException errors) {
+ // TODO Auto-generated method stub
+
+ try {
+ java.util.Date date= new java.util.Date();
+
+ TreeSearchResults treeResults = searchResults(request).convertToTrees();
+
+ String fileName = "TB" + date.getTime();
+ StringBuilder builder = new StringBuilder();
+
+ if ( getFormat(request) == FORMAT_NEXML ) {
+ Document doc = DocumentFactory.safeCreateDocument();
+ NexmlDocumentWriter ndw = new NexmlDocumentWriter(null,getTaxonLabelHome(), doc);
+ ndw.fromTreeBaseToXml(treeResults);
+ builder.append(doc.getXmlString());
+ }
+ else {
+ Set<PhyloTree> trees = treeResults.getResults();
+ TreeBlock treeBlock = new TreeBlock();
+ TaxonLabelSet taxonLabelSet = new TaxonLabelSet();
+
+ for (PhyloTree pTree : trees) {
+ for (TaxonLabel pTaxLabel : pTree.getTreeBlock().getTaxonLabelList()) {
+ if (! taxonLabelSet.getTaxonLabelsReadOnly().contains(pTaxLabel)) {
+ taxonLabelSet.addPhyloTaxonLabel(pTaxLabel);
+ }
+ }
+ treeBlock.addPhyloTree(pTree);
+ }
+
+ treeBlock.setTaxonLabelSet(taxonLabelSet);
+ taxonLabelSet.setTitle("TB" + date.getTime());
+
+
+ builder.append("#NEXUS\n\n");
+
+ taxonLabelSet.buildNexusBlockTaxa(builder, true, false);
+
+ treeBlock.generateAFileDynamically(builder);
+ fileName += ".nex";
+ }
+
+ String downloadDirName = request.getSession().getServletContext().getRealPath(
+ TreebaseUtil.FILESEP + "NexusFileDownload")
+ + TreebaseUtil.FILESEP + request.getRemoteUser();
+
+
+ File file = new File(downloadDirName + TreebaseUtil.FILESEP + fileName);
+ FileWriter out = new FileWriter(file);
+ out.write(builder.toString());
+ out.close();
+
+ if ( getFormat(request) == FORMAT_NEXML ) {
+ WebUtil.downloadFile(response, downloadDirName, fileName, mNexmlContentType);
+ }
+ else {
+ WebUtil.downloadFile(response, downloadDirName, fileName);
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ }
+
+ /**
+ *
+ * @param request
+ * @return
+ */
+ protected int getFormat (HttpServletRequest request) {
+ String requestedFormat = request.getParameter(mFormatParameter);
+ if ( null != requestedFormat ) {
+ if ( requestedFormat.equalsIgnoreCase("nexml") ) {
+ return FORMAT_NEXML;
+ }
+ else {
+ return FORMAT_NEXUS; // default
+ }
+ }
+ else {
+ return FORMAT_NEXUS; // default
+ }
+ }
+
+ protected Properties getDefaultProperties(HttpServletRequest request) {
+ Properties properties = new Properties();
+
+ properties.setProperty("nexml.uri.base", TreebaseUtil.getPurlBase());
+ return properties;
+ }
+
+ /**
+ *
+ * @return
+ */
+ public TaxonLabelHome getTaxonLabelHome() {
+ return mTaxonLabelHome;
+ }
+
+ /**
+ *
+ * @param nexmlService
+ */
+ public void setTaxonLabelHome(TaxonLabelHome taxonLabelHome) {
+ mTaxonLabelHome = taxonLabelHome;
+ }
+
protected ModelAndView searchResultsAsRDF (SearchResults<?> searchResults,HttpServletRequest request,CQLNode root, String schema, String original) throws UnsupportedEncodingException {
//${baseURL}
//${phyloWSPath}
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 2011-10-27 16:58:16 UTC (rev 974)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java 2011-10-28 14:08:26 UTC (rev 975)
@@ -409,7 +409,10 @@
Set<Taxon> queryResults = doCQLQuery(root, new HashSet<Taxon>(),request);
TaxonSearchResults tsr = new TaxonSearchResults(queryResults);
saveSearchResults(request, tsr);
- if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
+ if ( TreebaseUtil.isEmpty(request.getParameter("format")) ||
+ (! request.getParameter("format").equals("rss1") &&
+ ! request.getParameter("format").equals("nexus") &&
+ ! request.getParameter("format").equals("nexml")) ) {
return samePage(request);
}
else {
@@ -428,7 +431,16 @@
}
}
this.saveSearchResults(request, res);
- return this.searchResultsAsRDF(res, request, root,schema,"taxon");
+
+ if (schema.equals("tree") &&
+ ( request.getParameter("format").equals("nexus") ||
+ request.getParameter("format").equals("nexml") )) {
+ super.downloadAllTrees(request, response, errors);
+ return null;
+ }
+ else {
+ return this.searchResultsAsRDF(res, request, root,schema,"taxon");
+ }
}
}
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsListControls.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsListControls.jsp 2011-10-27 16:58:16 UTC (rev 974)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsListControls.jsp 2011-10-28 14:08:26 UTC (rev 975)
@@ -24,5 +24,8 @@
<input style="align: right;" type="submit" id="discardResults" value="Discard All Results" onclick="confirmDiscard()"/>
<a href="#" class="openHelp" onclick="openHelp('s+res+discard-these-results+btn')"><img class="iconButton" src="<fmt:message key="icons.help"/>" /></a>
-
+ <c:if test="${resultSet.resultType == 'TREE'}">
+ <input style="align: right;" type="submit" id="downloadAllTrees" value="Download All Trees" onclick="doAction('downloadAllTrees')"/>
+ <a href="#" class="openHelp" onclick="openHelp('s+res+download-all-treess+btn')"><img class="iconButton" src="<fmt:message key="icons.help"/>" /></a>
+ </c:if>
</c:if>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2011-10-27 16:58:16 UTC (rev 974)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2011-10-28 14:08:26 UTC (rev 975)
@@ -749,7 +749,8 @@
<property name="commandName"><value>search</value></property>
<property name="commandClass"><value>org.cipres.treebase.web.model.SearchCommand</value></property>
<property name="taxonLabelService"><ref bean="taxonLabelService"></ref></property>
- <property name="searchService"><ref bean="searchService"></ref></property>
+ <property name="searchService"><ref bean="searchService"></ref></property>
+ <property name="taxonLabelHome"><ref bean="taxonLabelHome"></ref></property>
</bean>
<!-- bean id="mainSearchController" parent="searchController" class="org.cipres.treebase.web.controllers.MainSearchController">
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