Added support for loading local Derby databases

egonw · Feb 15, 2012 · 0bd8895 · 0bd8895
1 parent fe50b75
commit 0bd8895
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Showing 7 changed files with 44 additions and 4 deletions.
diff --git a/plugins/net.bioclipse.bridgedb/.classpath b/plugins/net.bioclipse.bridgedb/.classpath
@@ -1,10 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
+	<classpathentry exported="true" kind="lib" path="jar/derby.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5"/>
 	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
 	<classpathentry kind="src" path="src"/>
 	<classpathentry exported="true" kind="lib" path="jar/org.bridgedb.bio.jar"/>
 	<classpathentry exported="true" kind="lib" path="jar/org.bridgedb.jar"/>
 	<classpathentry kind="lib" path="jar/org.bridgedb.webservice.bridgerest.jar"/>
+	<classpathentry kind="lib" path="jar/org.bridgedb.rdb.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>
diff --git a/plugins/net.bioclipse.bridgedb/META-INF/MANIFEST.MF b/plugins/net.bioclipse.bridgedb/META-INF/MANIFEST.MF
@@ -17,5 +17,7 @@ Bundle-ActivationPolicy: lazy
 Bundle-ClassPath: .,
  jar/org.bridgedb.bio.jar,
  jar/org.bridgedb.jar,
- jar/org.bridgedb.webservice.bridgerest.jar
+ jar/org.bridgedb.webservice.bridgerest.jar,
+ jar/org.bridgedb.rdb.jar,
+ jar/derby.jar
 Bundle-RequiredExecutionEnvironment: J2SE-1.5
diff --git a/plugins/net.bioclipse.bridgedb/build.properties b/plugins/net.bioclipse.bridgedb/build.properties
@@ -5,4 +5,7 @@ bin.includes = plugin.xml,\
                .,\
                jar/org.bridgedb.bio.jar,\
                jar/org.bridgedb.jar,\
-               jar/org.bridgedb.webservice.bridgerest.jar
+               jar/org.bridgedb.webservice.bridgerest.jar,\
+               jar/org.bridgedb.rdb.jar,\
+               jar/bridgeDB_license.txt,\
+               jar/derby.jar
diff --git a/plugins/net.bioclipse.bridgedb/jar/derby.jar b/plugins/net.bioclipse.bridgedb/jar/derby.jar
diff --git a/plugins/net.bioclipse.bridgedb/jar/org.bridgedb.rdb.jar b/plugins/net.bioclipse.bridgedb/jar/org.bridgedb.rdb.jar
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
@@ -63,8 +63,14 @@ public Set<String> search(String restService, String query, int limit) throws Bi
 			throw new BioclipseException("Could not connect to the REST service at: " + restService);
 		}
 
+		return search(mapper, query, limit);
+    }
+
+    public Set<String> search(IDMapper database, String query, int limit) throws BioclipseException {
+    	logger.debug("doing stuff...");
+
 		try {
-			return extractIdentifierStrings(mapper.freeSearch(query, limit));
+			return extractIdentifierStrings(database.freeSearch(query, limit));
 		} catch (IDMapperException exception) {
 			throw new BioclipseException("Could not search the REST service: " + exception);
 		}
@@ -136,4 +142,17 @@ private Set<String> extractIdentifierStrings(Set<Xref> dests) {
 	public Xref xref(String identifier, String source) throws BioclipseException {
 		return new Xref(identifier, getSource(source));
 	}
+
+	public IDMapper loadRelationalDatabase(String location) throws BioclipseException {
+		try {
+			Class.forName ("org.bridgedb.rdb.IDMapperRdb");
+		} catch (ClassNotFoundException exception) {
+			throw new BioclipseException("Could not load the IDMapperRdb driver.", exception);
+		}
+		try {
+			return BridgeDb.connect("idmapper-pgdb:" + location);
+		} catch (IDMapperException exception) {
+			throw new BioclipseException("Could not the database at this location: " + location, exception);
+		}
+	}
 }
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
@@ -19,6 +19,7 @@
 import net.bioclipse.managers.business.IBioclipseManager;
 
 import org.bridgedb.DataSource;
+import org.bridgedb.IDMapper;
 import org.bridgedb.Xref;
 
 @PublishedClass(
@@ -50,6 +51,13 @@ public interface IBridgedbManager extends IBioclipseManager {
     )
     public Set<String> search(String restService, String query, int limit) throws BioclipseException;
 
+    @Recorded
+    @PublishedMethod(
+        methodSummary="Searches a local BridgeDB instance for the given query string.",
+        params="IDMapper database, String query, int limit"
+    )
+    public Set<String> search(IDMapper database, String query, int limit) throws BioclipseException;
+
     @Recorded
     @PublishedMethod(
         methodSummary="Return a BioDataSource for the given string. It throws a BioclipseException when an" +
@@ -79,5 +87,11 @@ public interface IBridgedbManager extends IBioclipseManager {
         params="String identifier, String source"
     )
     public Xref xref(String identifier, String source);
-
+
+    @Recorded
+    @PublishedMethod(
+        methodSummary="Loads a BridgeDB Rdb database from a file location.",
+        params="String location"
+    )
+    public IDMapper loadRelationalDatabase(String location) throws BioclipseException;
 }