Changeset 20740

Timestamp:

26/02/10 16:15:13 (2 years ago)

Author:

julie

Message:

refactor portal to use new method that returns list of object IDs instead of webresults. remove obsolete section of code referring to collapsed item collection. remove references to PORTAL_QUERY_FLAG, it's not used anymore either. refactor main method into several smaller ones.

Location:

trunk

Files:

• bio/webapp/src/org/intermine/bio/web/logic/OrthologueConverter.java (modified) (3 diffs)
• intermine/web/main/src/org/intermine/dwr/AjaxServices.java (modified) (1 diff)
• intermine/web/main/src/org/intermine/web/logic/Constants.java (modified) (1 diff)
• intermine/web/main/src/org/intermine/web/logic/bag/BagConverter.java (modified) (4 diffs)
• intermine/web/main/src/org/intermine/web/struts/ObjectDetailsController.java (modified) (1 diff)
• intermine/web/main/src/org/intermine/web/struts/PortalQueryAction.java (modified) (12 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.Matcher;
 import java.util.regex.Pattern;
 
-import javax.servlet.ServletContext;
-import javax.servlet.http.HttpSession;
-
 import org.apache.commons.lang.StringUtils;
-import org.apache.log4j.Logger;
 import org.apache.struts.action.ActionMessage;
-import org.directwebremoting.WebContextFactory;
 import org.intermine.api.InterMineAPI;
 import org.intermine.api.profile.Profile;
 import org.intermine.api.query.PathQueryExecutor;
-import org.intermine.api.query.WebResultsExecutor;
 import org.intermine.api.results.ExportResultsIterator;
 import org.intermine.api.results.ResultElement;
 import org.intermine.api.results.WebResults;
 import org.intermine.metadata.Model;
-import org.intermine.model.InterMineObject;
-import org.intermine.objectstore.ObjectStore;
-import org.intermine.objectstore.ObjectStoreException;
 import org.intermine.pathquery.Constraints;
-import org.intermine.pathquery.Path;
-import org.intermine.pathquery.PathException;
 import org.intermine.pathquery.PathQuery;
 import org.intermine.web.logic.bag.BagConverter;
 import org.intermine.web.logic.config.WebConfig;
-import org.intermine.web.logic.pathqueryresult.PathQueryResultHelper;
-import org.intermine.web.logic.session.SessionMethods;
 
 /**
@@ -52 +38 @@
 {
 
-    private static final Logger LOG = Logger.getLogger(OrthologueConverter.class);
+    
     // D. melanogaster, C. lupus familiaris
     private static final Pattern ORGANISM_SHORTNAME_MATCHER = Pattern.compile("([a-zA-Z]\\..+)");
-    private static InterMineAPI im;
-    private static Model model;
-    private static WebConfig webConfig;
-    private static ObjectStore os;
+    private Model model;
+    
 
-    public OrthologueConverter() {
-        super();
-        ServletContext servletContext = WebContextFactory.get().getServletContext();
-        HttpSession session = WebContextFactory.get().getSession();
-        im = SessionMethods.getInterMineAPI(session);
-        webConfig = SessionMethods.getWebConfig(servletContext);
+    /**
+     * @param im intermine api
+     * @param webConfig the webconfig
+     */
+    public OrthologueConverter(InterMineAPI im, WebConfig webConfig) {
+        super(im, webConfig);
         model = im.getModel();
-        os = im.getObjectStore();
-    }
-    
-    /**
-     * {@inheritDoc}
-     * @throws PathException
-     */
-    public WebResults getConvertedObjects (Profile profile, List<Integer> fromList, String type,
-            String ... parameters) throws ObjectStoreException, PathException {
-        String organism = null, dataset = null;
 
-        for (String param : parameters) {
-            if (StringUtils.isEmpty(param)) {
-                continue;
-            }
-            Matcher m = ORGANISM_SHORTNAME_MATCHER.matcher(param);
-            if (m.matches()) {
-                organism = param;
-            } else {
-                dataset = param;
-            }
-        }
-        List<InterMineObject> objectList = os.getObjectsByIds(fromList);
-        PathQuery q = generateQuery(objectList, type, organism, dataset);
-
-        LOG.info("PATH QUERY:" + q.toXml(PathQuery.USERPROFILE_VERSION));
-        WebResultsExecutor executor = im.getWebResultsExecutor(profile);
-
-        return executor.execute(q);
     }
 
-    private static PathQuery constructPathQuery(String organism, String dataset) {
+    private PathQuery constructPathQuery(String bagType, String bagName, String organismName) {
         PathQuery q = new PathQuery(model);
 
         // organism
-        q.addConstraint("Gene.homologues.homologue.organism", Constraints.lookup(organism));
+        q.addConstraint("Gene.homologues.homologue.organism.shortName", 
+                Constraints.eq(organismName));
 
         // homologue.type = "orthologue"
         q.addConstraint("Gene.homologues.type", Constraints.eq("orthologue"));
 
-        if (StringUtils.isNotEmpty(dataset)) {
-            // homologue.dataSets = dataset
-            q.addConstraint("Gene.homologues.dataSets.title", Constraints.eq(dataset));
-        }
+        q.addConstraint(bagType, Constraints.in(bagName));
         return q;
     }
 
-    private PathQuery generateQuery(List<InterMineObject> objectList, String type, String organism,
-            String dataset)
-    throws PathException {
-        PathQuery q = constructPathQuery(organism, dataset);
-
-        List<Path> view = PathQueryResultHelper.getDefaultView(type, model, webConfig,
-                        "Gene.homologues.homologue", false);
-        view = getFixedView(view);
-        q.setViewPaths(view);
-
-        q.addConstraint(type, Constraints.in(objectList));
-
-        q.syncLogicExpression("and");
-        return q;
-    }
-
-
-    private static PathQuery generateQuery(String bagType, String bagName, String organismName) {
-        PathQuery q = constructPathQuery(organismName, null);
-        q.setView("Gene.homologues.homologue.primaryIdentifier");
-        q.addConstraint(bagType, Constraints.in(bagName));
-        q.syncLogicExpression("and");
-        return q;
-    }
-
-    public String getFieldsFromConvertedObjects(Profile profile, String bagType,
+    /**
+     * runs the orthologue conversion pathquery and returns a comma-delimited list of identifiers
+     * @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 organismName name of homologue's organism
+     * @return commadelimited list of identifiers, eg. eve,zen
+     */
+    public String getConvertedObjectFields(Profile profile, String bagType,
             String bagName, String organismName) {
-        String orthologues = "";
-        PathQuery pathQuery = generateQuery(bagType, bagName, organismName);
+        StringBuffer orthologues = null;
+        PathQuery pathQuery = constructPathQuery(bagType, bagName, organismName);
+        pathQuery.setView("Gene.homologues.homologue.primaryIdentifier");
+        pathQuery.syncLogicExpression("and");
         PathQueryExecutor executor = im.getPathQueryExecutor(profile);
         ExportResultsIterator it = executor.execute(pathQuery);
-        
+
         while (it.hasNext()) {
             List<ResultElement> row = it.next();
             String orthologue = row.get(0).getField().toString();
-            if (StringUtils.isNotEmpty(orthologues)) {
-                orthologues += ",";
+            if (orthologues != null) {
+                orthologues.append(",");
             }
-            orthologues += orthologue;
+            orthologues.append(orthologue);
         }
-
-        return orthologues;
+        if (orthologues == null) {
+            return null;
+        }
+        return orthologues.toString();
     }
-
+    
     /**
-     * If view contains joined organism, this will make sure, that
-     * organism is joined as a inner join. Else constraint on organism doesn't work.
-     * @param pathQuery
-     * @param joinPath
-     * @throws PathException
+     * runs the orthologue conversion pathquery and returns list of intermine IDs
+     * @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 organismName name of homologue's organism
+     * @return list of intermine IDs
      */
-    private List<Path> getFixedView(List<Path> view) throws PathException {
-        String invalidPath = "Gene.homologues.homologue:organism";
-        String validPath = "Gene.homologues.homologue.organism";
-        List<Path> ret = new ArrayList<Path>();
-        for (Path path : view) {
-            if (path.toString().contains(invalidPath)) {
-                String newPathString = path.toString().replace(invalidPath, validPath);
-                path = new Path(path.getModel(), newPathString);
-            }
-            ret.add(path);
+    public List<Integer> getConvertedObjectIds(Profile profile, String bagType,
+            String bagName, String organismName) {
+        PathQuery pathQuery = constructPathQuery(bagType, bagName, organismName);
+        pathQuery.setView(bagType + ".id");
+        PathQueryExecutor executor = im.getPathQueryExecutor(profile);
+        ExportResultsIterator it = executor.execute(pathQuery);
+        List<Integer> ids = new ArrayList();
+        while (it.hasNext()) {
+            List<ResultElement> row = it.next();
+            ids.add((Integer) row.get(0).getField());
         }
-        return ret;
+        return ids;
     }
 
@@ -241 +183 @@
         return am;
     }
+
+    @Override
+    public WebResults getConvertedObjects(Profile profile, List<Integer> fromList, String type,
+            String... parameters) {
+        // TODO Auto-generated method stub
+        return null;
+    }
 }

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

@@ -1364 +1364 @@
                 Constructor constructor = clazz.getConstructor();
                 BagConverter bagConverter = (BagConverter) constructor.newInstance();
-                return bagConverter.getFieldsFromConvertedObjects(profile, bagType, bagName, 
+                return bagConverter.getConvertedObjectFields(profile, bagType, bagName, 
                         selectedValue);
             }

trunk/intermine/web/main/src/org/intermine/web/logic/Constants.java

@@ -105 +105 @@
 
     /**
-     * The name of the property that is set to TRUE in the PortalQueryAction Action to indicate
-     * to the ObjectDetailsController that we have come from a portal page.
-     */
-    public static final String PORTAL_QUERY_FLAG = "PORTAL_QUERY_FLAG";
-
-    /**
      * The name of the property to look up to find the maximum size of an inline table.
      */

trunk/intermine/web/main/src/org/intermine/web/logic/bag/BagConverter.java

@@ -14 +14 @@
 import java.util.List;
 
-import javax.servlet.ServletContext;
-import javax.servlet.http.HttpSession;
-
 import org.apache.struts.action.ActionMessage;
-import org.directwebremoting.WebContextFactory;
 import org.intermine.api.InterMineAPI;
 import org.intermine.api.profile.Profile;
 import org.intermine.api.results.WebResults;
-import org.intermine.metadata.Model;
-import org.intermine.objectstore.ObjectStore;
 import org.intermine.objectstore.ObjectStoreException;
 import org.intermine.pathquery.PathException;
 import org.intermine.web.logic.config.WebConfig;
-import org.intermine.web.logic.session.SessionMethods;
 
 
@@ -35 +28 @@
  *
  */
-public abstract class BagConverter {
-    
-    private static InterMineAPI im = null;
-    private static Model model = null;
-    private static WebConfig webConfig = null;
-    private static ObjectStore os = null;
-    
-    
+public abstract class BagConverter
+{
+
+    protected InterMineAPI im = null;
+    protected WebConfig webConfig = null;
+
+    /**
+     *
+     * @param im intermine API
+     * @param webConfig the webconfig
+     */
+    public BagConverter(InterMineAPI im, WebConfig webConfig) {
+        this.im = im;
+        this.webConfig = webConfig;
+    }
+
     /**
      * Returns a List<ResultRows> of converted objects
+     * @param profile user's profile
      * @param parameters the parameters
      * @param fromList the list to convert
@@ -53 +55 @@
      * @throws PathException bad path
      */
-    public abstract WebResults getConvertedObjects(Profile profile, List<Integer> fromList, String type, 
-            String ... parameters)
+    public abstract WebResults getConvertedObjects(Profile profile, List<Integer> fromList,
+            String type, String ... parameters)
         throws ClassNotFoundException, ObjectStoreException, PathException;
 
@@ -67 +69 @@
      * @throws UnsupportedEncodingException exception
      */
-    public abstract ActionMessage getActionMessage(String externalids, int convertedSize, String type, 
-            String ... parameters) 
+    public abstract ActionMessage getActionMessage(String externalids, int convertedSize,
+            String type, String ... parameters)
     throws ObjectStoreException, UnsupportedEncodingException;
-    
-    public abstract String getFieldsFromConvertedObjects(Profile profile, String bagType,
+
+    /**
+     *
+     * @param profile user's profile
+     * @param bagType class of list
+     * @param bagName name of list
+     * @param constraintValue value of constraint
+     * @return string of comma delimited identifiers
+     */
+    public abstract String getConvertedObjectFields(Profile profile, String bagType,
+            String bagName, String constraintValue);
+
+    /**
+    *
+    * @param profile user's profile
+    * @param bagType class of list
+    * @param bagName name of list
+    * @param constraintValue value of constraint
+    * @return list of intermine IDs
+    */
+    public abstract List<Integer> getConvertedObjectIds(Profile profile, String bagType,
             String bagName, String constraintValue);
 }

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

@@ -88 +88 @@
         request.setAttribute("object", dobj);
 
-        if (session.getAttribute(Constants.PORTAL_QUERY_FLAG) != null) {
-            session.removeAttribute(Constants.PORTAL_QUERY_FLAG);
-            // FIXME see #1911
-            // setVerboseCollections(session, dobj);
-        }
-
         Map<String, Map> placementRefsAndCollections = new TreeMap<String, Map>();
         Set<String> aspects = new HashSet<String>(SessionMethods.getCategories(servletContext));

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;
@@ -36 +37 @@
 import org.intermine.api.profile.Profile;
 import org.intermine.api.query.WebResultsExecutor;
-import org.intermine.api.results.ResultElement;
 import org.intermine.api.results.WebResults;
-import org.intermine.api.results.flatouterjoins.MultiRow;
-import org.intermine.api.results.flatouterjoins.MultiRowValue;
 import org.intermine.api.template.TemplateManager;
 import org.intermine.api.template.TemplatePopulator;
@@ -45 +43 @@
 import org.intermine.api.util.NameUtil;
 import org.intermine.metadata.Model;
-import org.intermine.model.InterMineObject;
 import org.intermine.objectstore.ObjectStoreException;
 import org.intermine.objectstore.query.ConstraintOp;
-import org.intermine.objectstore.query.ResultsRow;
 import org.intermine.pathquery.Constraints;
 import org.intermine.pathquery.Path;
 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;
@@ -75 +70 @@
     private static int index = 0;
 //    private static final Logger LOG = Logger.getLogger(PortalQueryAction.class);
+    private Map<String, BagConverter> bagConverters = new HashMap();
+
+
     /**
      * Link-ins from other sites end up here (after some redirection).
@@ -95 +93 @@
         final InterMineAPI im = SessionMethods.getInterMineAPI(session);
         ServletContext servletContext = session.getServletContext();
-        String extId = request.getParameter("externalid");
+
         String origin = request.getParameter("origin");
         String className = request.getParameter("class");
-        //String organism = request.getParameter("organism");
+        String extId = request.getParameter("externalid");
         if ((extId == null) || (extId.length() <= 0)) {
             extId = request.getParameter("externalids");
         }
+
         // Add a message to welcome the user
         Properties properties = SessionMethods.getWebProperties(servletContext);
         String welcomeMsg = properties.getProperty("portal.welcome." + origin);
-        if (StringUtil.isEmpty(welcomeMsg)) {
+        if (StringUtils.isEmpty(welcomeMsg)) {
             welcomeMsg = properties.getProperty("portal.welcome");
         }
@@ -115 +114 @@
         }
 
-        session.setAttribute(Constants.PORTAL_QUERY_FLAG, Boolean.TRUE);
-
-        // Set collapsed/uncollapsed state of object details UI
-        // TODO This might not be used anymore
-        Map<String, Boolean> collapsed = SessionMethods.getCollapsedMap(session);
-        collapsed.put("fields", Boolean.TRUE);
-        collapsed.put("further", Boolean.FALSE);
-        collapsed.put("summary", Boolean.FALSE);
-
-        Profile profile = SessionMethods.getProfile(session);
+
         String[] idList = extId.split(",");
 
@@ -139 +129 @@
         BagQueryConfig bagQueryConfig = im.getBagQueryConfig();
 
-        // If the class is not in the model, we can't continue
-        try {
-            className = StringUtil.capitalise(className);
-            Class.forName(model.getPackageName() + "." + className);
-        } catch (ClassNotFoundException clse) {
+        // If the class is not in the model, we can't continue        
+        if (model.getClassDescriptorByName(className) == null) { 
             recordError(new ActionMessage("errors.badportalclass"), request);
             return goToNoResults(mapping, session);
         }
-        String bagName = NameUtil.generateNewName(profile.getSavedBags().keySet(), "link");
-
+             
         PathQuery pathQuery = new PathQuery(model);
         List<Path> view = PathQueryResultHelper.getDefaultView(className, model, webConfig, null,
@@ -157 +143 @@
 
         Map<String, BagQueryResult> returnBagQueryResults = new HashMap();
+        Profile profile = SessionMethods.getProfile(session);
         WebResultsExecutor executor = im.getWebResultsExecutor(profile);
         WebResults webResults = executor.execute(pathQuery, returnBagQueryResults);
-
+        
+        String bagName = NameUtil.generateNewName(profile.getSavedBags().keySet(), "link");
         InterMineBag imBag = profile.createBag(bagName, className, "");
         List<Integer> bagList = new ArrayList();
@@ -177 +165 @@
         if (additionalConverters != null) {
             for (String converterClassName : additionalConverters.keySet()) {
-                Class clazz = Class.forName(converterClassName);
-                Constructor constructor = clazz.getConstructor();
-                String[] paramArray = additionalConverters.get(converterClassName);
-                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");
-                    }
-                }
+
+                String[] addparameters = getAdditionalParameters(request,
+                        additionalConverters.get(converterClassName));
+
                 if (addparameters.length > 0) {
-                    BagConverter bagConverter = (BagConverter) constructor.newInstance();
-                    WebResults convertedWebResult = bagConverter.getConvertedObjects(profile,
-                            bagList, className, addparameters);
+
+                    BagConverter bagConverter = getBagConverter(converterClassName);
+
                     imBag = profile.createBag(bagName, className, "");
-                    List<Integer> converted = new ArrayList<Integer>();
-                    for (MultiRow<ResultsRow<MultiRowValue<ResultElement>>> resRow
-                            : convertedWebResult) {
-                        ResultElement resElement = resRow.get(0).get(0).getValue();
-                        Object obj = resElement.getObject();
-                        if (obj instanceof InterMineObject) {
-                            converted.add(((InterMineObject) obj).getId());
-                        }
-                    }
+                    List<Integer> converted = bagConverter.getConvertedObjectIds(profile, 
+                            className, bagName, addparameters[0]);
                     // No matches
                     if (converted.size() <= 0) {
@@ -224 +194 @@
             }
         }
-        // Attach messages
-        if (bagList.size() == 0 && bagQueryResult.getMatches().size() == 1) {
-            ActionMessage msg = new ActionMessage("results.lookup.noresults.one",
-                                                  new Integer(bagQueryResult.getMatches().size()),
-                                                  className);
-            actionMessages.add(Constants.PORTAL_MSG, msg);
-        } else if (bagList.size() == 0 && bagQueryResult.getMatches().size() > 1) {
-            ActionMessage msg = new ActionMessage("results.lookup.noresults.many",
-                                                  new Integer(bagQueryResult.getMatches().size()),
-                                                  className);
-            actionMessages.add(Constants.PORTAL_MSG, msg);
-        } else if (bagList.size() > 0) {
-            ActionMessage msg = new ActionMessage("results.lookup.matches.many",
-                                                  new Integer(bagList.size()));
-            actionMessages.add(Constants.PORTAL_MSG, msg);
-        } else if (bagList.size() == 0) {
-            ActionMessage msg = new ActionMessage("portal.nomatches", extId);
-            actionMessages.add(Constants.PORTAL_MSG, msg);
-        }
+
+        attachMessages(actionMessages, className, bagQueryResult.getMatches().size(),
+                bagList.size(), extId);
+
         session.setAttribute(Constants.PORTAL_MSG, actionMessages);
 
@@ -260 +215 @@
     }
 
+    private BagConverter getBagConverter(String converterClassName) {
+
+        BagConverter bagConverter = bagConverters.get(converterClassName);
+
+        if (bagConverter == null) {
+            try {
+                Class clazz = Class.forName(converterClassName);
+                Constructor constructor = clazz.getConstructor();
+                bagConverter = (BagConverter) constructor.newInstance();
+            } catch (Exception e) {
+                throw new RuntimeException("Failed to construct bagconverter for "
+                        + converterClassName, e);
+            }
+            bagConverters.put(converterClassName, bagConverter);
+        }
+        return bagConverter;
+    }
+
+    private String[] getAdditionalParameters(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) {
@@ -287 +278 @@
     }
 
+    private void attachMessages(ActionMessages actionMessages, String className,
+            int bagQueryResultSize,
+            int bagListSize, String extId) {
+        // Attach messages
+        if (bagListSize == 0 && bagQueryResultSize == 1) {
+            ActionMessage msg = new ActionMessage("results.lookup.noresults.one",
+                    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);
+            actionMessages.add(Constants.PORTAL_MSG, msg);
+        } else if (bagListSize > 0) {
+            ActionMessage msg = new ActionMessage("results.lookup.matches.many",
+                    new Integer(bagListSize));
+            actionMessages.add(Constants.PORTAL_MSG, msg);
+        } else if (bagListSize == 0) {
+            ActionMessage msg = new ActionMessage("portal.nomatches", extId);
+            actionMessages.add(Constants.PORTAL_MSG, msg);
+        }
+    }
+
     /**
-     * @deprecated Use the BagQueryRunner instead
+     * @deprecated Use the quicksearch action instead
      */
     private String loadObjectDetails(ServletContext servletContext, HttpSession session,