Changeset 161 for trunk/corelib/src/org/bridgedb/webservice/biomart/util/BiomartClient.java

Timestamp:

08/19/09 05:53:32 (3 years ago)

Author:

jgao

Message:

IDMapperBiomart refactor to clean the interface

Location:

trunk/corelib/src/org/bridgedb/webservice/biomart/util

Files:

• . (added)
• BiomartClient.java (copied) (copied from trunk/corelib/src/org/bridgedb/webservice/biomart/BiomartStub.java) (14 diffs)

trunk/corelib/src/org/bridgedb/webservice/biomart/util/BiomartClient.java

@@ -16 +16 @@
 //
 
-package org.bridgedb.webservice.biomart;
+package org.bridgedb.webservice.biomart.util;
 
 import java.io.BufferedReader;
@@ -30 +30 @@
 import java.util.HashMap;
 import java.util.Map;
-import java.util.Vector;
 
 import javax.xml.parsers.DocumentBuilder;
@@ -45 +44 @@
  * BioMart service class, adapted from BioMart client in Cytoscape.
  */
-public final class BiomartStub {
+public final class BiomartClient {
     public static final String defaultBaseURL = "http://www.biomart.org/biomart/martservice";
     
     private final String baseURL;
-    private static final String RESOURCE = "/org/bridgedb/webservice/biomart/filterconversion.txt";
+    private static final String RESOURCE = "/org/bridgedb/webservice/biomart/util/filterconversion.txt";
 
     //private Map<String, Map<String, String>> databases = null;
-    private Map<String, Database> databases = null;
+    private Map<String, Database> marts = null;
 
     private Map<String, Dataset> datasets = new HashMap();
-    private Map<String, Vector<Dataset>> mapDbDss = new HashMap();
+    private Map<String, Map<String,Dataset>> mapDbDss = new HashMap();
     private Map<String, Map<String, Filter>> mapDsFilters = new HashMap();
     private Map<String, Map<String, Attribute>> mapDsAttrs = new HashMap();
@@ -62 +61 @@
 
     private static final int BUFFER_SIZE = 81920;
-
-    // one instance per base url
-    private static Map<String, BiomartStub> instances = new HashMap();
-
-    /**
-     * Get a BioMartStub with the default base URL.
-     * @return BiomartStub
-     * @throws IOException if failed to read local resource
-     */
-    public static BiomartStub getInstance() throws IOException {
-        return getInstance(defaultBaseURL);
-    }
-
-    /**
-     * Get a BioMartStub with the base URL.
-     * @param baseURL base URL of BioMart
-     * @return BioMartStub
-     * @throws IOException if failed to read local resource
-     */
-    public static BiomartStub getInstance(String baseURL) throws IOException {
-        if (baseURL==null) {
-            throw new IllegalArgumentException("base url cannot be null");
-        }
-
-        BiomartStub instance = instances.get(baseURL);
-        if (instance==null) {
-            instance = new BiomartStub(baseURL);
-            instances.put(baseURL, instance);
-        }
-
-        return instance;
-   }
-
 
     /**
@@ -102 +68 @@
      * @throws IOException if failed to read local resource
      */
-    private BiomartStub(String baseURL) throws IOException {
+    public BiomartClient(String baseURL) throws IOException {
         this.baseURL = baseURL + "?";
         loadConversionFile();
@@ -149 +115 @@
      * @return converted attribute
      */
-    public Attribute filterToAttributeName(String dsName, String dbName,
+    private Attribute filterToAttribute(String dsName, String dbName,
                 String filterID) {
         if (filterConversionMap.get(dbName) == null) {
@@ -160 +126 @@
 
     /**
+     *
+     * @param dataset
+     * @param filter
+     * @return
+     */
+    public Attribute filterToAttribute(String dataset, String filter) {
+        Attribute attr;
+        if (dataset.contains("REACTOME")) {
+            attr = filterToAttribute(dataset, "REACTOME", filter);
+        } else if (dataset.contains("UNIPROT")) {
+            attr = filterToAttribute(dataset, "UNIPROT", filter);
+        } else if (dataset.contains("VARIATION")) {
+            attr = getAttribute(dataset, filter + "_stable_id");
+        } else {
+            attr = getAttribute(dataset, filter);
+        }
+
+        return attr;
+    }
+
+    /**
      *  Get the registry information from the base URL.
      *
@@ -170 +157 @@
             throws IOException, ParserConfigurationException, SAXException {
         // If already loaded, just return it.
-        if (databases != null)
-            return databases;
+        if (marts != null)
+            return marts;
 
         // Initialize database map.
-        databases = new HashMap<String, Database>();
+        marts = new HashMap<String, Database>();
 
         // Prepare URL for the registry status
@@ -208 +195 @@
             }
 
-            databases.put(dbID, new Database(dbID,entry));
+            marts.put(dbID, new Database(dbID,entry));
         }
 
@@ -214 +201 @@
         is = null;
 
-        return databases;
+        return marts;
     }
 
@@ -223 +210 @@
      * @throws IOException if failed to read
      */
-    public Vector<Dataset> getAvailableDatasets(final String martName)
+    public Map<String, Dataset> getAvailableDatasets(final String martName)
             throws IOException {
-        Vector<Dataset> result = mapDbDss.get(martName);
+        Map<String, Dataset> result = mapDbDss.get(martName);
         if (result!=null) {
             return result;
@@ -239 +226 @@
 
         //final Map<String, String> datasources = new HashMap<String, String>();
-        result = new Vector();
-
-        Database database = databases.get(martName);
+        result = new HashMap();
+
+        Database database = marts.get(martName);
 
         if (database==null) {
@@ -266 +253 @@
             if ((parts.length > 4) && parts[3].equals("1")) {
                 Dataset dataset = new Dataset(parts[1], parts[2], database);
-                result.add(dataset);
+                result.put(dataset.getName(),dataset);
                 //datasourceMap.put(parts[1], martName);
                 datasets.put(parts[1], dataset);
@@ -498 +485 @@
      * @return database
      */
-    public Database getDatabase(final String dbname) {
-        return databases.get(dbname);
+    public Database getMart(final String dbname) {
+        return marts.get(dbname);
     }