Merge branch 'master' into Christian

.gitignore

@@ -26,6 +26,8 @@ bridgedb-*.gz
 # generated checkstyle warnings
 /org.bridgedb/warnings.txt
 
+# ignore temporary files
+gdb.config
 
 #DO NOT IGNORE 
 #src-axis   #While these are autogenerated removing them will break offline builds.

dbbuilder/src/org/bridgedb/extract/SpeciesList

@@ -46,8 +46,10 @@ Neisseria collection	Neisseria			Nx
 Pyrococcus collection	Pytococcus			Px
 Staphylococcus collection	Staphylococcus			Sx
 Streptococcus collection	Streptococcus			Tx
-Aspergillus niger	Black mold	5061	ani	An
+Aspergillus niger	Black Mold	5061	ani	An
 Clostridium thermocellum	Cthe		cth	Ct
-Gibberella zeae	Fusarium gramaninearum	5518		Gz
+Gibberella zeae	Fusarium graminearum	5518		Gz
 Solanum lycopersicum	Tomato	4081		Sl
 Glycine max	Soybean	3847		Gm	
+Beta vulgaris   Sugar Beet  3555  bvu Bv
+Hordeum vulgare Barley  4513  hvu Hv

org.bridgedb.bio/resources/org/bridgedb/bio/organisms.txt

@@ -2,6 +2,7 @@ Anopheles	gambiae	Mosquito_Ag	Ag
 Arabidopsis	thaliana	Arabidopsis	At
 Aspergillus	niger	Black mold	An
 Bacillus	subtilis	Bsubtilis	Bs
+Beta vulgaris Sugar Beet  Bv
 Bos	taurus	Cow	Bt
 Caenorhabditis	elegans	Celegans	Ce
 Canis	familiaris	Dog	Cf
@@ -17,6 +18,7 @@ Gallus	gallus	Chicken	Gg
 Glycine	max	Soybean	Gm
 Gibberella	zeae	Fusarium graminearum	Gz
 Homo	sapiens	Human	Hs
+Hordeum vulgare Barley  Hv
 Loxodonta	africana	Elephant	La
 Macaca	mulatta	Rhesus Monkey	Ml
 Monodelphis	domestica	Opossum	Md

org.bridgedb.bio/src/org/bridgedb/bio/DataSourceTxt.java

@@ -46,20 +46,22 @@ public static void init()
 			throw new Error(ex);
 		}
 	}
+
+	public static String datasourcesTxt = "";
 
-    public static void loadInputStream(InputStream is) throws IOException{
-        new DataSourceTxt().loadAnInputStream(is);
-    }
+	public static void loadInputStream(InputStream is) throws IOException{
+		new DataSourceTxt().loadAnInputStream(is);
+	}
 
-    protected void loadAnInputStream(InputStream is) throws IOException 
-	{
+	protected void loadAnInputStream(InputStream is) throws IOException {
 		BufferedReader reader = new BufferedReader (
 				new InputStreamReader (is));
 		String line;
-        while ((line = reader.readLine()) != null) {
-            String[] fields = line.split ("\\t");
-            loadLine(fields);
-        }		
+   		while ((line = reader.readLine()) != null) {
+			datasourcesTxt = datasourcesTxt + line + "\n";
+            		String[] fields = line.split ("\\t");
+            		loadLine(fields);
+        	}		
 	}
 
 	protected void loadLine(String[] fields) throws IOException 

org.bridgedb.bio/src/org/bridgedb/bio/Organism.java

@@ -40,6 +40,7 @@ public enum Organism
 	ArabidopsisThaliana("Arabidopsis thaliana", "At", 3702),
 	Aspergillusniger("Aspergillus niger", "An", "Black mold", 5061),
 	BacillusSubtilis("Bacillus subtilis", "Bs", 1423),
+	BetaVulgaris("Beta vulgaris", "Bv", "Sugar Beet", 3555),
 	BosTaurus("Bos taurus", "Bt", "Cow", 9913),
 	CaenorhabditisElegans("Caenorhabditis elegans", "Ce", "Worm", 6239),
 	CanisFamiliaris("Canis familiaris", "Cf", "Dog", 9615),
@@ -58,6 +59,7 @@ public enum Organism
 	GlycineMax("Glycine max", "Gm", "Soybean", 3847),
 	GibberellaZeae("Gibberella zeae", "Gz", "Fusarium graminearum", 5518),
 	HomoSapiens("Homo sapiens", "Hs", "Human", 9606),
+	HordeumVulgare("Hordeum vulgare", "Hv", "Barley", 4513),
 	LoxodontaAfricana ("Loxodonta africana", "La", "Elephant", 9785),
 	MacacaMulatta ("Macaca mulatta", "Ml", "Rhesus Monkey", 9544),
 	MusMusculus("Mus musculus", "Mm", "Mouse", 10090),

org.bridgedb.server/src/org/bridgedb/server/DataSources.java

@@ -0,0 +1,17 @@
+package org.bridgedb.server;
+
+import org.bridgedb.bio.DataSourceTxt;
+import org.restlet.resource.Get;
+import org.restlet.resource.ServerResource;
+
+public class DataSources extends ServerResource {
+
+	protected void doInit() {
+		DataSourceTxt.init();
+	}
+
+	@Get
+	public String getDataSources() {
+		return DataSourceTxt.datasourcesTxt;	
+	}
+}

org.bridgedb.server/src/org/bridgedb/server/IDMapperService.java

@@ -37,6 +37,7 @@ public class IDMapperService extends Application {
 	public static final String PAR_ID = "id";
 	public static final String PAR_SYSTEM = "system";
 	public static final String PAR_QUERY = "query";
+	public static final String PAR_DATASOURCES = "datasources";
 
 	public static final String PAR_TARGET_SYSTEM = "dataSource";
 	public static final String PAR_TARGET_ATTR_NAME = "attrName";
@@ -220,6 +221,11 @@ public IDMapperService(File aConfigFile, boolean transitive)
 	public static final String URL_BACK_PAGE_TEXT = "/{" + PAR_ORGANISM + "}/backPageText/{" + PAR_SYSTEM + "}/{" + 
 		PAR_ID + "}";
 
+	/**
+	 * URL pattern for getting the datasources.txt file
+	 */
+	public static final String URL_DATASOURCES = "/" + PAR_DATASOURCES;
+
 	private GdbProvider gdbProvider;
 
 	public synchronized void start() throws Exception {
@@ -234,6 +240,7 @@ public Restlet createRoot() {
 		//router.setDefaultMatchingMode(Router.BEST);		
 		//System.out.println("MatchingMode: "+ router.getDefaultMatchingMode() + " : "+ router.getRequiredScore());
 
+		router.attach(URL_DATASOURCES, DataSources.class);
 
 		//Register the route for the home page url pattern
 		String target = "http://bridgedb.org/wiki/BridgeWebservice";