Changeset 20758

Timestamp:

02/03/10 11:01:32 (2 years ago)

Author:

julie

Message:

move methods to helper class as they are shared with the portal and ajax

Location:

trunk

Files:

• bio/webapp/src/org/intermine/bio/web/logic/OrthologueConverter.java (modified) (12 diffs)
• intermine/web/main/src/org/intermine/dwr/AjaxServices.java (modified) (6 diffs)
• intermine/web/main/src/org/intermine/web/logic/PortalHelper.java (added)
• intermine/web/main/src/org/intermine/web/struts/PortalQueryAction.java (modified) (5 diffs)
• intermine/webapp/main/resources/webapp/js/imdwr.js (modified) (3 diffs)

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

@@ -15 +15 @@
 import java.util.ArrayList;
 import java.util.List;
-import java.util.regex.Pattern;
 
 import org.apache.commons.lang.StringUtils;
@@ -26 +25 @@
 import org.intermine.api.results.WebResults;
 import org.intermine.metadata.Model;
+import org.intermine.model.InterMineObject;
+import org.intermine.objectstore.ObjectStoreException;
 import org.intermine.pathquery.Constraints;
 import org.intermine.pathquery.PathQuery;
@@ -37 +38 @@
 public class OrthologueConverter extends BagConverter
 {
-
-    // D. melanogaster, C. lupus familiaris
-    private static final Pattern ORGANISM_SHORTNAME_MATCHER = Pattern.compile("([a-zA-Z]\\..+)");
     private Model model;
 
@@ -51 +49 @@
     }
 
-    private PathQuery constructPathQuery(String bagType, String bagName, String organismName) {
+    private PathQuery constructPathQuery(String organismName) {
         PathQuery q = new PathQuery(model);
 
@@ -61 +59 @@
         q.addConstraint("Gene.homologues.type", Constraints.eq("orthologue"));
 
-        q.addConstraint(bagType, Constraints.in(bagName));
         return q;
     }
@@ -67 +64 @@
     /**
      * runs the orthologue conversion pathquery and returns a comma-delimited list of identifiers
-     * used on list analysis page for intermine linking
+     * used on list analysis page for intermine linking, called via Ajax
      * @param profile the user's profile
      * @param bagType the class of the list, has to be gene I think
@@ -74 +71 @@
      * @return commadelimited list of identifiers, eg. eve,zen
      */
-    public String getConvertedObjectFields(Profile profile, String bagType,
-            String bagName, String organismName) {
+    public String getConvertedObjectFields(Profile profile, String bagType, String bagName,
+            String organismName) {
         StringBuffer orthologues = null;
-        PathQuery pathQuery = constructPathQuery(bagType, bagName, organismName);
+        PathQuery pathQuery = constructPathQuery(organismName);
+        pathQuery.addConstraint(bagType, Constraints.in(bagName));
         pathQuery.setView("Gene.homologues.homologue.primaryIdentifier");
         pathQuery.syncLogicExpression("and");
@@ -99 +97 @@
     /**
      * runs the orthologue conversion pathquery and returns list of intermine IDs
-     * used in the portal 
+     * used in the portal
      * @param profile the user's profile
      * @param bagType the class of the list, has to be gene I think
-     * @param bagName name of list
+     * @param bagList list of intermine object IDs
      * @param organismName name of homologue's organism
      * @return list of intermine IDs
      */
     public List<Integer> getConvertedObjectIds(Profile profile, String bagType,
-            String bagName, String organismName) {
-        PathQuery pathQuery = constructPathQuery(bagType, bagName, organismName);
+            List<Integer> bagList, String organismName) {
+        PathQuery pathQuery = constructPathQuery(organismName);
+        List<InterMineObject> objectList = null;
+        try {
+            objectList = im.getObjectStore().getObjectsByIds(bagList);
+        } catch (ObjectStoreException e) {
+            e.printStackTrace();
+            return null;
+        }
+        pathQuery.addConstraint(bagType, Constraints.in(objectList));
         pathQuery.setView(bagType + ".id");
         pathQuery.syncLogicExpression("and");
@@ -125 +131 @@
      */
     public ActionMessage getActionMessage(String externalids, int convertedSize, String type,
-            String ... parameters)
-                    throws UnsupportedEncodingException {
-
-        String organism = null, dataset = null;
-
-        for (String param : parameters) {
-            if (StringUtils.isEmpty(param)) {
-                continue;
-            }
-            if (ORGANISM_SHORTNAME_MATCHER.matcher(param).matches()) {
-                organism = param;
-            } else {
-                dataset = param;
-            }
+            String parameter) throws UnsupportedEncodingException {
+        if (StringUtils.isEmpty(parameter)) {
+            return null;
         }
 
@@ -155 +150 @@
 
         // organism
-        q.addConstraint("Gene.organism", Constraints.lookup(organism));
+        q.addConstraint("Gene.organism", Constraints.lookup(parameter));
 
         // if the XML is too long, the link generates "HTTP Error 414 - Request URI too long"
         if (externalids.length() < 4000) {
             q.addConstraint("Gene.homologues.homologue", Constraints.lookup(externalids));
-        }
-
-        if (!StringUtils.isEmpty(dataset)) {
-            // homologue.dataSets = dataset
-            q.addConstraint("Gene.homologues.dataSet.title", Constraints.eq(dataset));
         }
 
@@ -175 +165 @@
             {
                 String.valueOf(convertedSize),
-                organism,
+                parameter,
                 String.valueOf(externalids.split(",").length),
                 type,
@@ -186 +176 @@
     @Override
     public WebResults getConvertedObjects(Profile profile, List<Integer> fromList, String type,
-            String... parameters) {
+            String parameters) {
         // TODO Auto-generated method stub
         return null;

trunk/intermine/web/main/src/org/intermine/dwr/AjaxServices.java

@@ -13 +13 @@
 import java.io.IOException;
 import java.io.UnsupportedEncodingException;
-import java.lang.reflect.Constructor;
-import java.lang.reflect.InvocationTargetException;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -81 +79 @@
 import org.intermine.web.autocompletion.AutoCompleter;
 import org.intermine.web.logic.Constants;
+import org.intermine.web.logic.PortalHelper;
 import org.intermine.web.logic.bag.BagConverter;
 import org.intermine.web.logic.config.Type;
@@ -121 +120 @@
     private static final String INVALID_NAME_MSG = "Invalid name.  Names may only contain letters, "
         + "numbers, spaces, and underscores.";
+    private PortalHelper portalHelper = new PortalHelper();
+    
     /**
      * Creates a favourite Tag for the given templateName
@@ -1329 +1330 @@
         return defaultList;
     }
-    
+
     /**
      * used on list analysis page to convert list contents to orthologues.  then forwarded to
      * another intermine instance
-     * @param bagName bag of genes to convert
-     * @param selectedValue organism to convert to
+     * @param bagType class of bag
+     * @param bagName name of bag
+     * @param selectedValue orthologue organism
      * @return converted list of orthologues
-     * @throws UnsupportedEncodingException if we can't encode the name of the organism
-     * @throws ClassNotFoundException 
-     * @throws NoSuchMethodException 
-     * @throws SecurityException 
-     * @throws InvocationTargetException 
-     * @throws IllegalAccessException 
-     * @throws InstantiationException 
-     * @throws IllegalArgumentException 
-     */
-    public static String convertObjects(String bagType, String bagName, String selectedValue)
-    throws UnsupportedEncodingException, ClassNotFoundException, SecurityException, 
-    NoSuchMethodException, IllegalArgumentException, InstantiationException, IllegalAccessException, 
-    InvocationTargetException {
-        
+     * @throws UnsupportedEncodingException bad encoding
+     */
+    public String convertObjects(String bagType, String bagName, String selectedValue) 
+    throws UnsupportedEncodingException {
+        ServletContext servletContext = WebContextFactory.get().getServletContext();
         HttpServletRequest request = getRequest();
         HttpSession session = request.getSession();
         final InterMineAPI im = SessionMethods.getInterMineAPI(session);
         Profile profile = SessionMethods.getProfile(session);
-        
+        WebConfig webConfig = SessionMethods.getWebConfig(servletContext);
+
         BagQueryConfig bagQueryConfig = im.getBagQueryConfig();
+
         // Use custom converters
         Map<String, String []> additionalConverters =
@@ -1361 +1356 @@
         if (additionalConverters != null) {
             for (String converterClassName : additionalConverters.keySet()) {
-                Class clazz = Class.forName(converterClassName);
-                Constructor constructor = clazz.getConstructor();
-                BagConverter bagConverter = (BagConverter) constructor.newInstance();
-                return bagConverter.getConvertedObjectFields(profile, bagType, bagName, 
+
+                String addparameter = PortalHelper.getAdditionalParameter(request,
+                        additionalConverters.get(converterClassName));
+
+                if (StringUtils.isNotEmpty(addparameter)) {
+
+                    BagConverter bagConverter = portalHelper.getBagConverter(im, webConfig, 
+                            converterClassName);
+
+
+                return bagConverter.getConvertedObjectFields(profile, bagType, bagName,
                         selectedValue);
+                }
             }
         }
@@ -1371 +1374 @@
     }
 
+
 }

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

@@ -11 +11 @@
  */
 
-import java.io.UnsupportedEncodingException;
-import java.lang.reflect.Constructor;
-import java.net.URLDecoder;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -51 +48 @@
 import org.intermine.util.StringUtil;
 import org.intermine.web.logic.Constants;
+import org.intermine.web.logic.PortalHelper;
 import org.intermine.web.logic.bag.BagConverter;
 import org.intermine.web.logic.config.WebConfig;
@@ -70 +68 @@
 {
     private static int index = 0;
+    private PortalHelper helper = new PortalHelper();
+    
 //    private static final Logger LOG = Logger.getLogger(PortalQueryAction.class);
-    private Map<String, BagConverter> bagConverters = new HashMap();
-
 
     /**
@@ -167 +165 @@
             for (String converterClassName : additionalConverters.keySet()) {
 
-                String addparameter = getAdditionalParameter(request,
+                String addparameter = PortalHelper.getAdditionalParameter(request,
                         additionalConverters.get(converterClassName));
 
                 if (StringUtils.isNotEmpty(addparameter)) {
 
-                    BagConverter bagConverter = getBagConverter(im, webConfig, converterClassName);
-
-                    imBag = profile.createBag(bagName, className, "");
+                    BagConverter bagConverter = helper.getBagConverter(im, webConfig, 
+                            converterClassName);
                     List<Integer> converted = bagConverter.getConvertedObjectIds(profile,
-                            className, bagName, addparameter);
+                            className, bagList, addparameter);
                     // No matches
                     if (converted.size() <= 0) {
@@ -216 +213 @@
     }
 
-    private BagConverter getBagConverter(InterMineAPI im, WebConfig webConfig,
-            String converterClassName) {
-
-        BagConverter bagConverter = bagConverters.get(converterClassName);
-
-        if (bagConverter == null) {
-            try {
-                Class clazz = Class.forName(converterClassName);
-                Constructor constructor = clazz.getConstructor(InterMineAPI.class, WebConfig.class);
-                bagConverter = (BagConverter) constructor.newInstance(im, webConfig);
-            } catch (Exception e) {
-                throw new RuntimeException("Failed to construct bagconverter for "
-                        + converterClassName, e);
-            }
-            bagConverters.put(converterClassName, bagConverter);
-        }
-        return bagConverter;
-    }
-
-    private String getAdditionalParameter(HttpServletRequest request, String[] paramArray)
-    throws UnsupportedEncodingException {
-
-        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) {

trunk/intermine/webapp/main/resources/webapp/js/imdwr.js

@@ -819 +819 @@
 
 function checkOrthologueMapping(statusCount, remoteMine, localMine) {
+
     var myForm = document.forms['orthologueLinkForm' + statusCount];
     var orthologueSelect = myForm.orthologueDatasets;
@@ -825 +826 @@
     var localMapping = bits[0];
     var remoteMapping = bits[1];
+
     var selectedOrganism = orthologueSelect.options[orthologueSelect.selectedIndex].text;
     myForm.orthologue.value = selectedOrganism;
 
+    // hide/show the radio button and name of intermine if they do/don't have orthologues
     if (localMapping != null && localMapping != "") {
         display('orthologueMappingLocalLabel' + statusCount, true);
@@ -846 +849 @@
         display('orthologueMappingLocalRadio' + statusCount, false);
     }
-}
+    // if there is only one option, don't show a dropdown
+//    if (orthologueSelect.length == 1) {
+//        display('orthologueSelectDisplay' + statusCount, true);
+//        display('orthologueSelect' + statusCount, false);
+//        // update text to be selected value
+//        document.getElementById('orthologueSelect' + statusCount).innerHtml
+//            = orthologueSelect.options[0].text;
+//    } else {
+//        // show dropdown
+//        display('orthologueSelectDisplay' + statusCount, false);
+//        display('orthologueSelect' + statusCount, true);
+//    }
+}