Changeset 315

Timestamp:

02/24/10 15:41:07 (5 months ago)

Author:

martijn

Message:

Accidentally checked in old version of GdbProvider?, reverted. Adjusted server start scripts.

Location:

trunk

Files:

• org.bridgedb.rdb/src/org/bridgedb/rdb/GdbProvider.java (modified) (6 diffs)
• org.bridgedb.server/build.xml (modified) (1 diff)
• org.bridgedb.server/src/org/bridgedb/server/IDMapperService.java (modified) (1 diff)
• start-server.sh (modified) (1 diff)

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

@@ -26 +26 @@
 import java.util.Map;
 
+import org.bridgedb.BridgeDb;
+import org.bridgedb.IDMapper;
 import org.bridgedb.IDMapperException;
 import org.bridgedb.bio.Organism;
-
 
 /**
@@ -39 +40 @@
  */
 public class GdbProvider {
-        Map<Organism, List<IDMapperRdb>> organism2gdb = new HashMap<Organism, List<IDMapperRdb>>();
-        List<IDMapperRdb> globalGdbs = new ArrayList<IDMapperRdb>();
+        Map<Organism, List<IDMapper>> organism2gdb = new HashMap<Organism, List<IDMapper>>();
+        List<IDMapper> globalGdbs = new ArrayList<IDMapper>();
         
-        public void addOrganismGdb(Organism organism, IDMapperRdb gdb) {
-                List<IDMapperRdb> l = organism2gdb.get(organism);
+        public void addOrganismGdb(Organism organism, IDMapper gdb) {
+                List<IDMapper> l = organism2gdb.get(organism);
                 if(l == null) {
-                        organism2gdb.put(organism, l = new ArrayList<IDMapperRdb>());
+                        organism2gdb.put(organism, l = new ArrayList<IDMapper>());
                 }
                 if(!l.contains(gdb)) {
@@ -53 +54 @@
         
         public void removeOrganismGdb(Organism organism, IDMapperRdb gdb) {
-                List<IDMapperRdb> l = organism2gdb.get(organism);
+                List<IDMapper> l = organism2gdb.get(organism);
                 if(l != null) {
                         l.remove(gdb);
@@ -59 +60 @@
         }
         
-        public void addGlobalGdb(IDMapperRdb gdb) {
+        public void addGlobalGdb(IDMapper gdb) {
                 if(!globalGdbs.contains(gdb)) globalGdbs.add(gdb);
         }
         
-        public void removeGlobalGdb(IDMapperRdb gdb) {
+        public void removeGlobalGdb(IDMapper gdb) {
                 globalGdbs.remove(gdb);
         }
         
-        public List<IDMapperRdb> getGdbs(Organism organism) {
-                List<IDMapperRdb> gdbs = organism2gdb.get(organism);
+        public List<IDMapper> getGdbs(Organism organism) {
+                List<IDMapper> gdbs = organism2gdb.get(organism);
                 if(gdbs == null) {
-                        gdbs = new ArrayList<IDMapperRdb>();
+                        gdbs = new ArrayList<IDMapper>();
                 }
                 gdbs.addAll(globalGdbs);
@@ -78 +79 @@
         static final String DB_GLOBAL = "*";
         
-        public static GdbProvider fromConfigFile(File f) throws IDMapperException, IOException {
-                System.out.println("Parsing gene database configuration: " + f);
+        public static GdbProvider fromConfigFile(File f) throws IDMapperException, IOException, ClassNotFoundException {
+                System.out.println("Parsing gene database configuration: " + f.getAbsolutePath());
                 GdbProvider gdbs = new GdbProvider();
                 BufferedReader in = new BufferedReader(new FileReader(f));
                 String line = in.readLine();
+                Class.forName ("org.bridgedb.rdb.IDMapperRdb");
+                Class.forName("org.bridgedb.file.IDMapperText");
+                try
+                {
+                        Class.forName ("com.mysql.jdbc.Driver");
+                }
+                catch (ClassNotFoundException ex)
+                {
+                        System.out.println ("MySQL driver not in classpath, mysql backend unavailable");
+                }
                 while(line != null) {
                         String[] kv = line.split("\t");
@@ -88 +99 @@
                                 String key = kv[0];
                                 String value = kv[1];
+                                
+                                if (!value.startsWith("idmapper")) value = "idmapper-pgdb:" + value;
+                                IDMapper mapper = BridgeDb.connect (value);
                                 Organism org = Organism.fromLatinName(key);
                                 if(org != null) {
-                                        DataDerby dbConn = new DataDerby();
-                                        SimpleGdb gdb = SimpleGdbFactory.createInstance(value, dbConn, DBConnector.PROP_NONE);
-                                        gdbs.addOrganismGdb(org, gdb);
+                                        gdbs.addOrganismGdb(org, mapper);
                                 } else if(DB_GLOBAL.equalsIgnoreCase(key)) {
-                                        DataDerby dbConn = new DataDerby();
-                                        SimpleGdb gdb = SimpleGdbFactory.createInstance(value, dbConn, DBConnector.PROP_NONE);
-                                        gdbs.addGlobalGdb(gdb);
+                                        gdbs.addGlobalGdb(mapper);
                                 } else {
                                         System.out.println("Unable to parse organism: " + key);

trunk/org.bridgedb.server/build.xml

@@ -33 +33 @@
         <jar jarfile="${jar.name}">
           <manifest>
-                <attribute name="Main-Class" value="org.bridgedb.rest.Server"/>
-                <attribute name="Class-Path" value="derby.jar bridgedb.jar bridgedb-bio.jar org.restlet.jar"/>
+                <attribute name="Main-Class" value="org.bridgedb.server.Server"/>
+                <attribute name="Class-Path" value="derby.jar org.bridgedb.jar org.bridgedb.bio.jar org.bridgedb.rdb.jar org.restlet.jar"/>
           </manifest>
           <fileset dir="build"/>

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

@@ -63 +63 @@
                 {
                         System.err.println ("Could not find config file " + configFile);
-                        System.err.println ("Please copy webservice/gdb.config.template and adjust it to your needs");
+                        System.err.println ("Please copy org.bridgedb.server/gdb.config.template and adjust it to your needs");
                         System.exit(1);
                 }

trunk/start-server.sh

@@ -1 +1 @@
 #!/bin/sh
 
-java -jar dist/bridgedb-webservice.jar "$@"
+java -jar dist/org.bridgedb.server.jar "$@"