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[Treebase-guts] SF.net SVN: treebase:[1087] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers
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From: <rv...@us...> - 2012-02-23 15:25:12
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Revision: 1087
http://treebase.svn.sourceforge.net/treebase/?rev=1087&view=rev
Author: rvos
Date: 2012-02-23 15:25:03 +0000 (Thu, 23 Feb 2012)
Log Message:
-----------
Removing code dealing with old-style search forms
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java 2012-02-22 19:24:32 UTC (rev 1086)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java 2012-02-23 15:25:03 UTC (rev 1087)
@@ -62,60 +62,9 @@
HttpServletResponse response,
Object command,
BindException errors) throws Exception {
-
LOGGER.info("in matrixSearchController.onSubmit");
-
clearMessages(request);
- String formName = request.getParameter("formName");
- String query = request.getParameter("query");
-
- LOGGER.info("formName is '" + formName + "'");
-
- if ( ! TreebaseUtil.isEmpty(query) ) {
- return this.handleQueryRequest(request, response, errors, query);
- }
-
- if (formName.equals("matrixSimple")) {
- String buttonName = request.getParameter("searchButton");
- Set<Matrix> matches = new HashSet<Matrix>();
- String searchTerm = convertStars(request.getParameter("searchTerm"));
- SearchMessageSetter mSetter = new RequestMessageSetter(request);
- MatrixSearchResults oldRes;
- {
- SearchResults<?> sr = searchResults(request);
- if (sr != null) {
- oldRes = (MatrixSearchResults) sr.convertToMatrices();
- } else {
- oldRes = new MatrixSearchResults (); // TODO: Convert existing search results to new type
- }
- }
- if (buttonName.equals("matrixID")) {
- matches.addAll(doSearch(request, response, SearchType.byID, errors,searchTerm));
- } else if (buttonName.equals("matrixTitle")) {
- matches.addAll(doSearch(request, response, SearchType.byTitle, errors,searchTerm));
- } else if (buttonName.equals("matrixType")) {
- matches.addAll(doSearch(request, response, SearchType.byType, errors,searchTerm));
- } else if (buttonName.equals("matrixNTAX")) {
- matches.addAll(doSearch(request, response, SearchType.byNTAX, errors,searchTerm));
- } else if (buttonName.equals("matrixNCHAR")) {
- matches.addAll(doSearch(request, response, SearchType.byNCHAR, errors,searchTerm));
- } else {
- throw new Error("Unknown search button name '" + buttonName + "'");
- }
- if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
- SearchResults<Matrix> newRes = intersectSearchResults(oldRes,
- new MatrixSearchResults(matches), mSetter, "No matching matrices found");
- saveSearchResults(request, newRes);
- return new ModelAndView("search/matrixSearch", Constants.RESULT_SET, newRes);
- }
- else {
- return this.searchResultsAsRDF(new MatrixSearchResults(matches), request, null, "matrix", "matrix");
- }
- }
-
- else {
- return super.onSubmit(request, response, command, errors);
- }
+ return handleQueryRequest(request, response, errors, request.getParameter("query"));
}
protected Set<Matrix> doCQLQuery(
@@ -161,7 +110,7 @@
} else if ( index.startsWith("tb.ntax") ) {
results.addAll(doSearch(request, response, SearchType.byNTAX, errors, term.getTerm()));
} else if ( index.startsWith("tb.nchar") ) {
- results.addAll(doSearch(request, response, SearchType.byNTAX, errors, term.getTerm()));
+ results.addAll(doSearch(request, response, SearchType.byNCHAR, errors, term.getTerm()));
} else {
// issue warnings
addMessage(request, "Unsupported index: " + index);
@@ -246,7 +195,6 @@
@Override
protected ModelAndView handleQueryRequest(HttpServletRequest request,HttpServletResponse response,BindException errors, String query) throws CQLParseException, IOException, InstantiationException {
- //String query = request.getParameter("query");
CQLParser parser = new CQLParser();
CQLNode root = parser.parse(query);
root = normalizeParseTree(root);
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java 2012-02-22 19:24:32 UTC (rev 1086)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java 2012-02-23 15:25:03 UTC (rev 1087)
@@ -101,69 +101,9 @@
HttpServletResponse response,
Object command,
BindException errors) throws Exception {
-
LOGGER.info("in StudySearchController.onSubmit");
-
clearMessages(request);
- String formName = request.getParameter("formName");
- String query = request.getParameter("query");
-
- LOGGER.info("formName is '" + formName + "'");
-
- if ( ! TreebaseUtil.isEmpty(query) && ! query.equals("")) {
- LOGGER.info("query is '" + query + "'");
- return this.handleQueryRequest(request, response, errors, query);
- }
-
- if (formName.equals("searchKeyword")) {
- SearchType searchType;
- String buttonName = request.getParameter("searchButton");
- String searchTerm = convertStars(request.getParameter("searchTerm"));
- StudySearchResults oldRes;
- {
- SearchResults<?> sr = searchResults(request);
- if (sr != null) {
- oldRes = (StudySearchResults) sr.convertToStudies();
- } else {
- oldRes = new StudySearchResults (); // TODO: Convert existing search results to new type
- }
- }
- if (buttonName.equals("authorKeyword")) {
- searchType = SearchType.byAuthorName;
- } else if (buttonName.equals("studyID")) {
- searchType = SearchType.byID;
- } else if (buttonName.equals("legacyStudyID")) {
- searchType = SearchType.byLegacyID;
- } else if (buttonName.equals("titleKeyword")) {
- searchType = SearchType.byTitle;
- } else if (buttonName.equals("textKeyword")) {
- searchType = SearchType.byKeyword;
- } else if (buttonName.equals("citationKeyword")) {
- searchType = SearchType.inCitation;
- } else if (buttonName.equals("abstractKeyword")) {
- searchType = SearchType.inAbstract;
- } else if (buttonName.equals("doiKeyword")) {
- searchType = SearchType.byDOI;
- }
- else {
- throw new Error("Unknown search button name '" + buttonName + "'");
- }
- // XXX we now never do an exact match with terms provided through the web app. We can change
- // this, e.g. by adding a check box whose value is the boolean argument of doSearch()
- Collection<Study> matches = doSearch(request, response, searchType, errors,searchTerm,false,null);
- if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
- SearchResults<Study> newRes = intersectSearchResults(oldRes, new StudySearchResults(matches),
- new RequestMessageSetter(request), "No matching studies found");
- saveSearchResults(request, newRes);
- return new ModelAndView("search/studySearch", Constants.RESULT_SET, newRes);
- }
- else {
- return this.searchResultsAsRDF(new StudySearchResults(matches), request, null,"study","study");
- }
- }
- else {
- return super.onSubmit(request, response, command, errors);
- }
+ return handleQueryRequest(request, response, errors, request.getParameter("query"));
}
protected Set<Study> doCQLQuery(
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 2012-02-22 19:24:32 UTC (rev 1086)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java 2012-02-23 15:25:03 UTC (rev 1087)
@@ -51,48 +51,7 @@
HttpServletResponse response, Object searchCommand, BindException errors)
throws Exception {
clearMessages(request);
- String formName = request.getParameter("formName");
- String query = request.getParameter("query");
- if ( ! TreebaseUtil.isEmpty(query) ) {
- return this.handleQueryRequest(request, response, errors, query);
- }
- if (formName.equals("searchByTaxonLabel")) {
- SearchCommand newSearchCommand = (SearchCommand)searchCommand;
- String searchOn = request.getParameter("searchOn");
- String searchTerm = convertStars(request.getParameter("searchTerm"));
- String[] searchTerms = searchTerm.split("\\r\\n");
- Collection<Taxon> taxa = new HashSet<Taxon>();
- for ( int i = 0; i < searchTerms.length; i++ ) {
- if ( searchOn.equals("TextSearch") ) {
- taxa.addAll(doTaxonSearch(request, newSearchCommand, searchTerms[i], SearchIndex.LABEL, null));
- }
- else if ( searchOn.equals("Identifiers") ) {
- String objectIdentifier = request.getParameter("objectIdentifier");
- if ( objectIdentifier.equals("TreeBASE") ) {
- taxa.addAll(doTaxonSearch(request,newSearchCommand,searchTerms[i],SearchIndex.ID,NamingAuthority.TREEBASE));
- }
- else if ( objectIdentifier.equals("NCBI") ) {
- taxa.addAll(doTaxonSearch(request,newSearchCommand,searchTerms[i],SearchIndex.ID,NamingAuthority.NCBI));
- }
- else if ( objectIdentifier.equals("uBio") ) {
- taxa.addAll(doTaxonSearch(request,newSearchCommand,searchTerms[i],SearchIndex.ID,NamingAuthority.UBIO));
- }
- }
- }
- TaxonSearchResults tsr = new TaxonSearchResults(taxa);
- saveSearchResults(request, tsr);
- if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
- return samePage(request);
- }
- else {
- return this.searchResultsAsRDF(tsr, request, null,"taxon","taxon");
- }
-
- } else if (formName.equals("taxonResultsAction")) {
- return modifySearchResults(request, response, errors);
- } else {
- return super.onSubmit(request, response, (SearchCommand) searchCommand, errors);
- }
+ return handleQueryRequest(request, response, errors, request.getParameter("query"));
}
protected Set<Taxon> doCQLQuery(CQLNode node, Set<Taxon> results, HttpServletRequest request) {
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java 2012-02-22 19:24:32 UTC (rev 1086)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java 2012-02-23 15:25:03 UTC (rev 1087)
@@ -65,65 +65,7 @@
LOGGER.info("in TreeSearchController.onSubmit");
clearMessages(request);
- String formName = request.getParameter("formName");
- String query = request.getParameter("query");
-
- LOGGER.info("formName is '" + formName + "'");
-
- if ( ! TreebaseUtil.isEmpty(query) ) {
- return this.handleQueryRequest(request, response, errors, query);
- }
-
- if (formName.equals("treeSimple")) {
- String buttonName = request.getParameter("searchButton");
- String searchTerm = convertStars(request.getParameter("searchTerm"));
- Collection<PhyloTree> matches = null;
- TreeSearchResults oldRes;
- {
- SearchResults<?> sr = searchResults(request);
- if (sr != null) {
- oldRes = (TreeSearchResults) sr.convertToTrees();
- } else {
- oldRes = new TreeSearchResults (); // TODO: Convert existing search results to new type
- }
- }
- if (buttonName.equals("treeID")) {
- matches = doSearch(request, response, SearchType.byID, errors, searchTerm);
- } else if (buttonName.equals("treeTitle")) {
- matches = doSearch(request, response, SearchType.byTitle, errors, searchTerm);
- } else if (buttonName.equals("treeType")) {
- matches = doSearch(request, response, SearchType.byType, errors, searchTerm);
- } else if (buttonName.equals("treeKind")) {
- matches = doSearch(request, response, SearchType.byKind, errors, searchTerm);
- } else if (buttonName.equals("treeQuality")) {
- matches = doSearch(request, response, SearchType.byQuality, errors, searchTerm);
- } else if (buttonName.equals("treeNTAX")) {
- matches = doSearch(request, response, SearchType.byNTAX, errors, searchTerm);
- } else {
- throw new Error("Unknown search button name '" + buttonName + "'");
- }
-
- // XXX need to filter out orphaned matrices or matrices whose studies are unpublished
- Collection<PhyloTree> orphanedTrees = new HashSet<PhyloTree>();
- for ( PhyloTree t : matches ) {
- if (t.getStudy() == null || (t.getStudy().isPublished() == false)){
- orphanedTrees.add(t);
- }
- }
- matches.removeAll(orphanedTrees);
-
- SearchResults<PhyloTree> newRes = intersectSearchResults(oldRes, new TreeSearchResults(matches),
- new RequestMessageSetter(request), "No matching trees found");
- saveSearchResults(request, newRes);
- if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
- return new ModelAndView("search/treeSearch", Constants.RESULT_SET, newRes);
- }
- else {
- return this.searchResultsAsRDF(newRes, request, null,"tree","tree");
- }
- } else {
- return super.onSubmit(request, response, command, errors);
- }
+ return handleQueryRequest(request, response, errors, request.getParameter("query"));
}
protected Set<PhyloTree> doCQLQuery(
@@ -248,7 +190,6 @@
protected ModelAndView handleQueryRequest(HttpServletRequest request,
HttpServletResponse response, BindException errors, String query)
throws CQLParseException, IOException, InstantiationException {
- //String query = request.getParameter("query");
CQLParser parser = new CQLParser();
CQLNode root = parser.parse(query);
root = normalizeParseTree(root);
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