Wrapped the search functionality

egonw · Jan 11, 2012 · bb3ba81 · bb3ba81
1 parent 0f99580
commit bb3ba81
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Showing 2 changed files with 32 additions and 4 deletions.
diff --git a/plugins/net.bioclipse.bridgedb/src/net/bioclipse/bridgedb/business/BridgedbManager.java b/plugins/net.bioclipse.bridgedb/src/net/bioclipse/bridgedb/business/BridgedbManager.java
@@ -48,6 +48,24 @@ public Set<String> listAllSources() {
     	return sourceCodes;
     }
 
+    public Set<String> search(String restService, String query, int limit) throws BioclipseException {
+    	logger.debug("doing stuff...");
+
+    	// now we connect to the driver and create a IDMapper instance.
+    	IDMapper mapper;
+		try {
+			mapper = BridgeDb.connect(restService);
+		} catch (IDMapperException exception) {
+			throw new BioclipseException("Could not connect to the REST service at: " + restService);
+		}
+
+		try {
+			return extractIdentifierStrings(mapper.freeSearch(query, limit));
+		} catch (IDMapperException exception) {
+			throw new BioclipseException("Could not search the REST service: " + exception);
+		}
+    }
+
     public Set<String> map(String restService, String identifier, String source) throws BioclipseException {
     	return map(restService, identifier, source, null);
     }
@@ -90,10 +108,13 @@ public Set<String> map(String restService, String identifier, String source, Str
     	}
 
     	// and create a list of found, mapped URNs
-    	Set<String> results = new HashSet<String>();
+    	return extractIdentifierStrings(dests);
+    }
+
+	private Set<String> extractIdentifierStrings(Set<Xref> dests) {
+		Set<String> results = new HashSet<String>();
     	for (Xref dest : dests)
     	    results.add(dest.getURN());
-
-    	return results;
-    }
+		return results;
+	}
 }
diff --git a/plugins/net.bioclipse.bridgedb/src/net/bioclipse/bridgedb/business/IBridgedbManager.java b/plugins/net.bioclipse.bridgedb/src/net/bioclipse/bridgedb/business/IBridgedbManager.java
@@ -42,6 +42,13 @@ public interface IBridgedbManager extends IBioclipseManager {
     )
     public Set<String> map(String restService, String identifier, String source) throws BioclipseException;
 
+    @Recorded
+    @PublishedMethod(
+        methodSummary="Searches a BridgeDB REST service for the given query string, if the service supports searching.",
+        params="String restService, String query, int limit"
+    )
+    public Set<String> search(String restService, String query, int limit) throws BioclipseException;
+
     @Recorded
     @PublishedMethod(
         methodSummary="Return a BioDataSource for the given string. It throws a BioclipseException when an" +