Changeset 473

Timestamp:

01/24/11 12:50:33 (16 months ago)

Author:

martijn

Message:

Alternative freeAttributeSearch method, Patch by Ferry

Location:

trunk

Files:

• org.bridgedb.rdb/src/org/bridgedb/rdb/SimpleGdbImplCommon.java (modified) (2 diffs)
• org.bridgedb.webservice.biomart/src/org/bridgedb/webservice/biomart/IDMapperBiomart.java (modified) (1 diff)
• org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java (modified) (1 diff)
• org.bridgedb.webservice.picr/src/org/bridgedb/webservice/picr/IDMapperPicr.java (modified) (1 diff)
• org.bridgedb/src/org/bridgedb/AttributeMapper.java (modified) (2 diffs)
• org.bridgedb/src/org/bridgedb/IDMapperStack.java (modified) (2 diffs)

trunk/org.bridgedb.rdb/src/org/bridgedb/rdb/SimpleGdbImplCommon.java

@@ -17 +17 @@
 import org.bridgedb.IDMapperException;
 import org.bridgedb.Xref;
+import org.bridgedb.impl.InternalUtils;
 
 /**
@@ -321 +322 @@
                 }
         }
+        
+        public Map<Xref, Set<String>> freeAttributeSearchEx (String query, String attrType, int limit) throws IDMapperException
+        {
+                Map<Xref, Set<String>> result = new HashMap<Xref, Set<String>>();
+                final QueryLifeCycle pst = (MATCH_ID.equals (attrType)) ? 
+                                qIdSearchWithAttributes : qAttributeSearch;
+                synchronized (pst) { 
+                        try {
+                                pst.init(limit);
+                                pst.setString(1, attrType);
+                                pst.setString(2, "%" + query.toLowerCase() + "%");
+                                ResultSet r = pst.executeQuery();
+        
+                                while(r.next()) 
+                                {
+                                        String id = r.getString("id");
+                                        String code = r.getString("code");
+                                        String symbol = r.getString("attrValue");
+                                        Xref ref = new Xref (id, DataSource.getBySystemCode(code));
+                                        InternalUtils.multiMapPut(result, ref, symbol);
+                                }
+                        } catch (SQLException e) {
+                                throw new IDMapperException (e);
+                        }
+                        finally { pst.cleanup(); }
+                        return result;
+                }
+        }
 
         /** {@inheritDoc} */

trunk/org.bridgedb.webservice.biomart/src/org/bridgedb/webservice/biomart/IDMapperBiomart.java

@@ -388 +388 @@
      * {@inheritDoc}
      */
+    public Map<Xref, Set<String>> freeAttributeSearchEx (String query, String attrType, int limit) throws IDMapperException {
+        throw new UnsupportedOperationException("Free attribute search not supported.");
+    }
+
+    /**
+     * {@inheritDoc}
+     */
     public Set<String> getAttributeSet() throws IDMapperException {
         return stub.availableTgtAttributes(mart, dataset);

trunk/org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java

@@ -513 +513 @@
                 } 
         }
+
+        @Override
+        public Map<Xref, Set<String>> freeAttributeSearchEx(String query, String attrType, int limit)
+                        throws IDMapperException
+        {
+                try {
+                        Map<Xref, Set<String>> result = new HashMap<Xref, Set<String>>();
+                        
+                        BufferedReader in = new UrlBuilder("attributeSearch")
+                                .ordered (query).named("limit", "" + limit)
+                                .named ("attrName", attrType)
+                                .openReader();
+                        String line;
+                        while ((line = in.readLine()) != null) {
+                                String[] cols = line.split("\t", -1);
+                                Xref x = new Xref (cols[0], DataSource.getByFullName(cols[1]));
+                                String value = cols[2];
+                                InternalUtils.multiMapPut(result, x, value);
+                        }
+                        in.close();
+                        return result;
+                } catch (IOException ex) {
+                        throw new IDMapperException (ex);
+                } 
+        }
         
 }

trunk/org.bridgedb.webservice.picr/src/org/bridgedb/webservice/picr/IDMapperPicr.java

@@ -272 +272 @@
                 return result;
         }
+
+        @Override
+        public Map<Xref, Set<String>> freeAttributeSearchEx(String query, String attrType, int limit)
+                        throws IDMapperException
+        {
+                throw new UnsupportedOperationException();
+        }
 }

trunk/org.bridgedb/src/org/bridgedb/AttributeMapper.java

@@ -51 +51 @@
 
         /**
-         * free text search for matching symbols.
+         * free text search for matching attributes.
          * @return map references and attribute values that match the query
          * @param query The text to search for
@@ -61 +61 @@
         public Map<Xref, String> freeAttributeSearch (String query, String attrType, int limit) throws IDMapperException;
 
+        /**
+         * Improved version of free text search for matching attributes.
+         * Unlike freeAttributeSearch, this method may return multiple results per xref.
+         * @return map of references and attribute values that match the query
+         * @param query The text to search for
+         * @param attrType the attribute to look for, e.g. 'Symbol' or 'Description'. 
+         *      If you use the special MATCH_ID constant, it will query the identifier instead.
+         * @param limit The number of results to limit the search to
+         * @throws IDMapperException if the mapping service is (temporarily) unavailable 
+         */
+        public Map<Xref, Set<String>> freeAttributeSearchEx (String query, String attrType, int limit) throws IDMapperException;
+        
         /** use this magic constant as the attrType parameter to also search for identifiers. */
         public static final String MATCH_ID = "org.bridgedb.MATCH_ID";

trunk/org.bridgedb/src/org/bridgedb/IDMapperStack.java

@@ -386 +386 @@
         }
         
+        public Map<Xref, Set<String>> freeAttributeSearchEx (String query, String attrType, int limit) throws IDMapperException
+        {
+                Map<Xref, Set<String>> result = new HashMap<Xref, Set<String>>();
+                for (IDMapper child : gdbs)
+                {
+                        if (child != null && child instanceof AttributeMapper && child.isConnected()
+                                && ((AttributeMapper)child).isFreeAttributeSearchSupported())
+                        {
+                                Map<Xref, Set<String>> childResult = 
+                                        ((AttributeMapper)child).freeAttributeSearchEx(query, attrType, limit);
+                                if (result == null) 
+                                        result = childResult;
+                                else
+                                {
+                                        for (Xref ref : childResult.keySet())
+                                        {
+                                                if (!result.containsKey(ref))
+                                                        result.put (ref, childResult.get(ref));
+                                        }
+                                }
+                        }
+                }
+                return result;
+        }
+        
         /** @return concatenation of toString of each child */
         @Override public String toString()
@@ -533 +558 @@
                 return result;
         }
-        
 }