Changeset 20754

Timestamp:

01/03/10 14:19:02 (2 years ago)

Author:

julie

Message:

portal bug fix

Location:

trunk

Files:

• bio/tools/main/src/org/intermine/bio/logic/Mine.java (modified) (1 diff)
• bio/webapp/src/org/intermine/bio/web/logic/OrthologueConverter.java (modified) (5 diffs)
• intermine/web/main/src/org/intermine/web/struts/PortalQueryAction.java (modified) (7 diffs)

trunk/bio/tools/main/src/org/intermine/bio/logic/Mine.java

@@ -29 +29 @@
     private Set<String> organismNames = new HashSet();
 
-    // gene.organismName --> gene.orthologue.organismName --> local/remote --> gene.orthologue.datasets
+    // gene.organismName --> gene.orthologue.organismName --> local/remote
+    // --> gene.orthologue.datasets
     private Map<String, Map<String, Set[]>> orthologues = new HashMap();
 

trunk/bio/webapp/src/org/intermine/bio/web/logic/OrthologueConverter.java

@@ -38 +38 @@
 {
 
-
     // D. melanogaster, C. lupus familiaris
     private static final Pattern ORGANISM_SHORTNAME_MATCHER = Pattern.compile("([a-zA-Z]\\..+)");
     private Model model;
-
 
     /**
@@ -51 +49 @@
         super(im, webConfig);
         model = im.getModel();
-
     }
 
@@ -70 +67 @@
     /**
      * runs the orthologue conversion pathquery and returns a comma-delimited list of identifiers
+     * used on list analysis page for intermine linking
      * @param profile the user's profile
      * @param bagType the class of the list, has to be gene I think
@@ -101 +99 @@
     /**
      * runs the orthologue conversion pathquery and returns list of intermine IDs
+     * used in the portal 
      * @param profile the user's profile
      * @param bagType the class of the list, has to be gene I think
@@ -111 +110 @@
         PathQuery pathQuery = constructPathQuery(bagType, bagName, organismName);
         pathQuery.setView(bagType + ".id");
+        pathQuery.syncLogicExpression("and");
         PathQueryExecutor executor = im.getPathQueryExecutor(profile);
         ExportResultsIterator it = executor.execute(pathQuery);

trunk/intermine/web/main/src/org/intermine/web/struts/PortalQueryAction.java

@@ -49 +49 @@
 import org.intermine.pathquery.PathException;
 import org.intermine.pathquery.PathQuery;
+import org.intermine.util.StringUtil;
 import org.intermine.web.logic.Constants;
 import org.intermine.web.logic.bag.BagConverter;
@@ -114 +115 @@
         }
 
-
         String[] idList = extId.split(",");
 
@@ -130 +130 @@
 
         // If the class is not in the model, we can't continue
+        className = StringUtil.capitalise(className);
         if (model.getClassDescriptorByName(className) == null) {
             recordError(new ActionMessage("errors.badportalclass"), request);
@@ -166 +167 @@
             for (String converterClassName : additionalConverters.keySet()) {
 
-                String[] addparameters = getAdditionalParameters(request,
+                String addparameter = getAdditionalParameter(request,
                         additionalConverters.get(converterClassName));
 
-                if (addparameters.length > 0) {
+                if (StringUtils.isNotEmpty(addparameter)) {
 
                     BagConverter bagConverter = getBagConverter(im, webConfig, converterClassName);
@@ -175 +176 @@
                     imBag = profile.createBag(bagName, className, "");
                     List<Integer> converted = bagConverter.getConvertedObjectIds(profile,
-                            className, bagName, addparameters[0]);
+                            className, bagName, addparameter);
                     // No matches
                     if (converted.size() <= 0) {
                         actionMessages.add(Constants.PORTAL_MSG,
-                            new ActionMessage("portal.noorthologues", addparameters, extId));
+                            new ActionMessage("portal.noorthologues", addparameter, extId));
                         session.setAttribute(Constants.PORTAL_MSG, actionMessages);
                         return goToResults(mapping, session, webResults);
                     }
                     actionMessages.add(Constants.PORTAL_MSG, bagConverter.getActionMessage(extId,
-                            converted.size(), className, addparameters));
+                            converted.size(), className, addparameter));
                     session.setAttribute(Constants.PORTAL_MSG, actionMessages);
 
@@ -234 +235 @@
     }
 
-    private String[] getAdditionalParameters(HttpServletRequest request, String[] paramArray)
+    private String getAdditionalParameter(HttpServletRequest request, String[] paramArray)
     throws UnsupportedEncodingException {
 
-    String[] urlFields = paramArray[0].split(",");
-    String[] addparameters = new String[urlFields.length];
-    int i = 0;
-    for (String urlField : urlFields) {
-        // if one of the request vars matches the variables listed in the bagquery
-        // config, add the variable to be passed to the custom converter
-        String param = request.getParameter(urlField);
-        if (StringUtils.isNotEmpty(param)) {
-            // the spaces in organisms, eg. D.%20rerio, need to be handled
-            addparameters[i] = URLDecoder.decode(param, "UTF-8");
-        }
-    }
-    return addparameters;
-    }
-
-    private ActionForward goToResults(ActionMapping mapping,
-                                      HttpSession session, WebResults webResults) {
+        String[] urlFields = paramArray[0].split(",");
+        String addparameter = null;
+        for (String urlField : urlFields) {
+            // if one of the request vars matches the variables listed in the bagquery
+            // config, add the variable to be passed to the custom converter
+            String param = request.getParameter(urlField);
+            if (StringUtils.isNotEmpty(param)) {
+                // the spaces in organisms, eg. D.%20rerio, need to be handled
+                addparameter = URLDecoder.decode(param, "UTF-8");
+            }
+        }
+        return addparameter;
+    }
+
+    private ActionForward goToResults(ActionMapping mapping, HttpSession session,
+            WebResults webResults) {
         PagedTable pc = new PagedTable(webResults);
         String identifier = "col" + index++;
@@ -285 +285 @@
         if (bagListSize == 0 && bagQueryResultSize == 1) {
             ActionMessage msg = new ActionMessage("results.lookup.noresults.one",
-                    new Integer(bagQueryResultSize),
-                    className);
+                    new Integer(bagQueryResultSize), className);
             actionMessages.add(Constants.PORTAL_MSG, msg);
         } else if (bagListSize == 0 && bagQueryResultSize > 1) {
             ActionMessage msg = new ActionMessage("results.lookup.noresults.many",
-                    new Integer(bagQueryResultSize),
-                    className);
+                    new Integer(bagQueryResultSize), className);
             actionMessages.add(Constants.PORTAL_MSG, msg);
         } else if (bagListSize > 0) {