Changeset 509 for trunk

Timestamp:

03/22/11 12:23:07 (14 months ago)

Author:

martijn

Message:

Start defining aliases, using a new xml configuration format

Location:

trunk

Files:

• org.bridgedb.bio/resources/org/bridgedb/bio/datasources.xml (added)
• org.bridgedb.bio/src/org/bridgedb/bio/BioDataSource.java (modified) (3 diffs)
• org.bridgedb.bio/test/org/bridgedb/bio/Test.java (modified) (1 diff)
• org.bridgedb/src/org/bridgedb/DataSource.java (modified) (3 diffs)
• org.bridgedb/src/org/bridgedb/impl/InternalUtils.java (modified) (2 diffs)

trunk/org.bridgedb.bio/src/org/bridgedb/bio/BioDataSource.java

@@ -25 +25 @@
 import java.util.regex.Pattern;
 
+import javax.xml.parsers.ParserConfigurationException;
+
 import org.bridgedb.DataSource;
 import org.bridgedb.DataSourcePatterns;
+import org.bridgedb.impl.InternalUtils;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
 
 /**
@@ -532 +537 @@
                                 if (fields.length > 8) builder.urnBase(fields[8]);
                         }
+                        
+                        InternalUtils.readXmlConfig(
+                                        new InputSource(
+                                                        BioDataSource.class.getClassLoader().getResourceAsStream(
+                                                                        "org/bridgedb/bio/datasources.xml")));
+                        
                 }
                 catch (IOException ex)
@@ -537 +548 @@
                         throw new Error(ex);
                 }
+                catch (ParserConfigurationException e)
+                {
+                        throw new Error(e);
+                }
+                catch (SAXException e)
+                {
+                        throw new Error(e);
+                }
+                
         }
-        
 }

trunk/org.bridgedb.bio/test/org/bridgedb/bio/Test.java

@@ -124 +124 @@
         }
         
+        @org.junit.Test
+        public void testAlias()
+        {
+                DataSource ds = DataSource.getByAlias("ensembl_gene_id");
+                assertSame(ds, BioDataSource.ENSEMBL);
+        }
+        
 }

trunk/org.bridgedb/src/org/bridgedb/DataSource.java

@@ -59 +59 @@
         private static Map<String, DataSource> byFullName = new HashMap<String, DataSource>();
         private static Set<DataSource> registry = new HashSet<DataSource>();
+        private static Map<String, DataSource> byAlias = new HashMap<String, DataSource>();
         
         private String sysCode = null;
@@ -321 +322 @@
         }
         
+        public void registerAlias(String alias)
+        {
+                byAlias.put (alias, this);
+        }
+        
         /**
          * Helper method to determine if a String is allowed as key for bySysCode and byFullname hashes.
@@ -363 +369 @@
         }
         
+        public static DataSource getByAlias(String alias)
+        {
+                return byAlias.get(alias);
+        }
+
         /**
                 get all registered datasoures as a set.

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

@@ -29 +29 @@
 import java.util.Set;
 
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.parsers.SAXParser;
+import javax.xml.parsers.SAXParserFactory;
+
 import org.bridgedb.DataSource;
 import org.bridgedb.IDMapper;
 import org.bridgedb.IDMapperException;
 import org.bridgedb.Xref;
+import org.xml.sax.Attributes;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+import org.xml.sax.XMLReader;
+import org.xml.sax.helpers.DefaultHandler;
 
 /**
@@ -261 +270 @@
         }
 
+        /** read a configuration file in the bridgedb xml format */
+        public static void readXmlConfig(InputSource is) throws ParserConfigurationException, SAXException, IOException
+        {       
+                SAXParserFactory spf = SAXParserFactory.newInstance();
+        spf.setNamespaceAware(true);
+        SAXParser saxParser = spf.newSAXParser();
+
+        XMLReader xmlReader = saxParser.getXMLReader();
+        xmlReader.setContentHandler(new ConfigXmlHandler());
+        xmlReader.parse(is);
+        }
+        
+        private static class ConfigXmlHandler extends DefaultHandler
+        {
+                DataSource current = null;
+                
+                @Override
+                public void startElement(String namespaceURI, String localName,
+                                String qName, Attributes atts)
+                throws SAXException
+                {
+                        if ("datasource".equals (localName))
+                        {
+                                String fullname = atts.getValue("fullname");
+                                if (fullname == null) throw new SAXException ("missing attribute fullname");
+                                current = DataSource.getByFullName(fullname);
+                        }
+                        
+                        if ("alias".equals (localName))
+                        {
+                                String alias = atts.getValue ("name");
+                                if (alias != null && current != null)
+                                        current.registerAlias(alias);
+                        }
+                }
+                
+                @Override
+                public void endElement(String namespaceURI, String localName, String qName) throws SAXException
+                {
+                        if ("datasource".equals (localName))
+                        {
+                                current = null;
+                        }
+                }
+
+        }
+
 }