[MOBY-guts] biomoby commit

[Gary Schlitz]

gss
Wed Jul 21 18:01:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db
In directory pub.open-bio.org:/tmp/cvs-serv12905/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db

Modified Files:
	StorageManager.java 
Log Message:
Many changes prior to BOSC

moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db StorageManager.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java	2004/07/15 20:27:17	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/smoby/ref/tools/db/StorageManager.java	2004/07/21 22:01:20	1.2
@@ -9,6 +9,8 @@
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.shared.*;
 import com.hp.hpl.jena.vocabulary.*;
+import java.sql.Connection;
+import java.sql.SQLException;
 import java.util.*;
 
 /**
@@ -60,7 +62,7 @@
 	{
 	    Model model = ((MOBYProviderImpl) provider).getUnderlying();
         Model dbModel = null;
-        String uriString = provider.getURI();
+        String uriString = provider.getResource().getURI();
         Resource uri = model.createResource(uriString);
         
         try
@@ -100,6 +102,12 @@
             	dbModel.add(uri, MOBY.lastModifiedDate, lastModifiedDate.getTime());
             }
             
+            // Add keywords associated with the provider
+            //
+            KeywordFinder finder = new KeywordFinder(provider, model);
+            addKeywords(provider.getResource().getURI(),
+            		    finder.getKeywords(), dbModel);
+            
             // Commit the transaction on the database model
             //
             dbModel.commit();
@@ -116,6 +124,73 @@
             }
         }
     }
+	
+	private void addKeywords(String providerURI, KeywordList list, Model model)
+		throws StorageException
+	{
+		try
+		{
+			ModelRDB dbModel = (ModelRDB) model;
+			Connection conn = dbModel.getConnection().getConnection();
+			
+			java.sql.Statement sql = conn.createStatement();
+			
+			doAddKeywords(providerURI, list.getProviderKeywords(), "P", sql);
+			doAddKeywords(providerURI, list.getSubjectKeywords(), "S", sql);
+			doAddKeywords(providerURI, list.getObjectKeywords(), "O", sql);
+			
+		}
+		catch (Throwable t)
+		{
+			throw new StorageException(t);
+		}
+	}
+	
+	private void doAddKeywords(String providerURI, Iterator it,
+			                   String appliesTo, java.sql.Statement sql)
+		throws SQLException
+	{
+		while (it.hasNext())
+		{
+			String keyword = it.next().toString();
+			
+			StringBuffer sb = new StringBuffer();
+			
+			sb.append("INSERT INTO MOBY_KEYWORD\n");
+			sb.append("       (keyword, provider_uri, applies_to)\n");
+			sb.append("values ('");
+			sb.append(keyword.toLowerCase().trim());
+			sb.append("', '");
+			sb.append(providerURI);
+			sb.append("', '");
+			sb.append(appliesTo);
+			sb.append("')");
+			
+			String queryString = sb.toString();
+			
+			sql.execute(queryString);
+		}
+	}
+	
+	private void removeKeywords(String providerURI, Model model)
+		throws StorageException
+	{
+		try
+		{
+			ModelRDB dbModel = (ModelRDB) model;
+			Connection conn = dbModel.getConnection().getConnection();
+			
+			java.sql.Statement sql = conn.createStatement();
+			
+			sql.execute("DELETE FROM MOBY_KEYWORD WHERE provider_uri = '"
+					    + providerURI + "'");
+			
+		}
+		catch (Throwable t)
+		{
+			throw new StorageException(t);
+		}
+	}
     
     /**
      * Remove all the statements registered by a given provider URI
@@ -143,6 +218,10 @@
             //
             ProviderRemover.remove(dbModel, providerURI);
             
+            // Remove keywords associated with the provider URI
+            //
+            removeKeywords(providerURI, dbModel);
+            
             // Commit the transaction on the database
             //
             dbModel.commit();