Changeset 513 for trunk

Timestamp:

05/09/11 12:09:58 (13 months ago)

Author:

martijn

Message:

Improvements to server config file: allow comments, allow specification of extra driver classes

Location:

trunk

Files:

• org.bridgedb.bio/resources/org/bridgedb/bio/datasources.xml (modified) (1 diff)
• org.bridgedb.rdb/src/org/bridgedb/rdb/GdbProvider.java (modified) (3 diffs)
• org.bridgedb.rdb/src/org/bridgedb/rdb/impl (added)
• org.bridgedb.rdb/src/org/bridgedb/rdb/impl/ConfigFile.java (added)
• org.bridgedb/src/org/bridgedb/impl/InternalUtils.java (modified) (3 diffs)

trunk/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.xml

@@ -1 @@
-<datasources>
-        <datasource fullname="Ensembl">
-                <alias name="ensembl_gene_id"/>
-        </datasource>
-        <datasource fullname="Entrez Gene">
-                <alias name="entrezgene"/>
-        </datasource>
-        <datasource fullname="Affy">
-                <alias name="affy_hg_u133a_2"/>
-        </datasource>
-</datasources>
+<?xml version="1.0"?>
+<bridgedb>
+        <datasources>
+                <datasource fullname="Ensembl">
+                        <alias name="ensembl_gene_id"/>
+                </datasource>
+                <datasource fullname="Entrez Gene">
+                        <alias name="entrezgene"/>
+                </datasource>
+                <datasource fullname="Affy">
+                        <alias name="affy_hg_u133a_2"/>
+                </datasource>
+        </datasources>
+        <properties>
+                <property key="org.bridgedb.webservice.synergizer.DefaultUrl" value="http://...."/>
+        </properties>
+</bridgedb>

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

@@ -32 +32 @@
 import org.bridgedb.IDMapperStack;
 import org.bridgedb.bio.Organism;
+import org.bridgedb.rdb.impl.ConfigFile;
 
 /**
@@ -107 +108 @@
         }
         
-        public static GdbProvider fromConfigFile(File f, boolean transitive) throws IDMapperException, IOException, ClassNotFoundException {
-                System.out.println("Parsing gene database configuration: " + f.getAbsolutePath());
+        public static GdbProvider fromConfigFile(File f, boolean transitive) throws IDMapperException, IOException, ClassNotFoundException 
+        {       
+                ConfigFile cf = new ConfigFile(f);      
                 GdbProvider gdbs = new GdbProvider(transitive);
-                BufferedReader in = new BufferedReader(new FileReader(f));
-                String line = in.readLine();
-                Class.forName ("org.bridgedb.rdb.IDMapperRdb");
-                Class.forName("org.bridgedb.file.IDMapperText");
-                try
+                List<String> drivers = cf.getDrivers();
+                
+                // add a few defaults that will always be loaded
+                drivers.add("org.bridgedb.rdb.IDMapperRdb");
+                drivers.add("org.bridgedb.file.IDMapperText");
+                drivers.add("com.mysql.jdbc.Driver");
+                
+                for (String driver : drivers)
                 {
-                        Class.forName ("com.mysql.jdbc.Driver");
+                        try
+                        {
+                                Class.forName (driver);
+                                System.out.println ("Loaded driver: " + driver);
+                        }
+                        catch (ClassNotFoundException ex)
+                        {
+                                System.out.println ("Warning: driver '" + driver + "'  not in classpath, some features may not be available.");
+                        }
                 }
-                catch (ClassNotFoundException ex)
+
+                for (String key : cf.getMappers().keySet())
                 {
-                        System.out.println ("MySQL driver not in classpath, mysql backend unavailable");
-                }
-                while(line != null) {
-                        String[] kv = line.split("\t");
-                        if(kv.length == 2) {
-                                String key = kv[0];
-                                String value = kv[1];
-                                
-                                if (!value.startsWith("idmapper")) value = "idmapper-pgdb:" + value;
+                        for (String value : cf.getMappers().get(key))
+                        {
                                 IDMapper mapper = BridgeDb.connect (value);
                                 Organism org = Organism.fromLatinName(key);
@@ -138 +145 @@
                                         System.out.println("Unable to parse organism: " + key);
                                 }
-                        } else {
-                                System.out.println("Invalid key/value pair in gene database configuration: " + line);
                         }
-                        line = in.readLine();
                 }
-                in.close();
+
                 return gdbs;
         }

trunk/org.bridgedb/src/org/bridgedb/impl/InternalUtils.java

@@ -21 +21 @@
 import java.net.URL;
 import java.net.URLConnection;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -26 +27 @@
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -229 +231 @@
      * will not be discared.
      * <p>
+     * This is like multiMapPut, but uses a list instead of a set for each value of the map. 
+     * @param <T> key type of multimap
+     * @param <U> value type of multimap
+     * @param map multimap to work on
+     * @param key key of the value to insert
+     * @param val value to insert.
+    */
+    public static <T, U> void multiMapAdd(Map<T, List<U>> map, T key, U val)
+    {
+        List<U> list;
+        if (map.containsKey (key))
+        {
+                list = map.get(key);
+        }
+        else
+        {
+                list = new ArrayList<U>();
+                map.put(key, list);
+        }
+        list.add (val);
+    }
+
+    /**
+     * Generic method for multimaps, a map that can contain multiple values per key.
+     * Unlike a regular map, if you insert a value for a key that already exists, the previous value 
+     * will not be discared.
+     * <p>
      * multiMapPutAll let's you insert a collection of items at once. 
      * @param <T> key type of multimap