[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Wed Apr 18 11:55:18 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv12197/src/main/ca/ucalgary/seahawk/util

Modified Files:
	MobyUtils.java 
Log Message:
Added binary data support, and create GlobalKeyword only if data is not also a sequence
moby-live/Java/src/main/ca/ucalgary/seahawk/util MobyUtils.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyUtils.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyUtils.java	2007/02/08 16:59:58	1.5
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyUtils.java	2007/04/18 15:55:18	1.6
@@ -2,17 +2,21 @@
 
 import ca.ucalgary.seahawk.gui.MobyContentGUI;
 import ca.ucalgary.seahawk.gui.MobyServicesGUI;
+import ca.ucalgary.seahawk.services.MobyClient;
 
 import org.biomoby.shared.data.*;
 import org.biomoby.shared.MobyDataType;
 import org.biomoby.shared.MobyNamespace;
 
+import java.io.ByteArrayOutputStream;
+import java.io.InputStream;
+import java.net.URL;
 import java.util.Vector;
 import javax.swing.JLabel;
 
 /**
  * Contains utility methods for Moby Object creation from unstructured data, and for
- * creating the Seahawk GUI.
+ * creating the Seahawk GUI. 
  */
 
 public class MobyUtils{
@@ -21,6 +25,41 @@
     private static MobyContentGUI mobyContentGUI = null;
     private static MobyServicesGUI mobyServicesGUI = null;
     
+    /**
+     * The purpose of this method is to create a MOBY document to encapsulate
+     * a binary data object stored at the given URL.  If the data does
+     * not represent a single binary MOBY object, the method returns null.
+     * If the provided client or URL is null, null will be returned too.
+     */
+    public static MobyContentInstance convertURLtoMobyBinaryData(MobyClient client, URL url)throws Exception{
+	if(url == null || client == null){
+	    return null;
+	}
+
+	ByteArrayOutputStream bytes = new ByteArrayOutputStream();
+	InputStream is = url.openStream();
+
+	// Slurp up the file as bytes
+	byte[] buffer = new byte[4096];
+	for(int bytesRead = is.read(buffer); bytesRead != -1; bytesRead = is.read(buffer)){
+	    bytes.write(buffer, 0, bytesRead);
+	}
+
+	// Find MOBY Objects in it
+	MobyDataObject[] foundObjects = client.getMobyObjects(bytes.toByteArray(), 
+							      MobyDataType.getDataType(MobyDataBytes.BASE64_DATATYPE));
+	// Did we unambiguously find one binary object?
+	if(foundObjects != null && foundObjects.length == 1){
+	    MobyContentInstance mci = new MobyContentInstance();
+	    String[] dataName = url.getPath().split("/");
+	    MobyDataJob job = new MobyDataJob();
+	    job.put(dataName[dataName.length-1], foundObjects[0]);
+	    mci.put(dataName[dataName.length-1], job); // name the data by the last part of the URL path
+	    return mci;
+	}
+	return null;
+    }
+
     public static MobyDataInstance[] convertStringToObjects(String data, boolean reverseSelected){
 	if(data == null){
 	    return new MobyDataInstance[0];
@@ -39,14 +78,6 @@
 	strObject.setPrimaryNamespace(new MobyNamespace("seahawk"));
 	objects.add(strObject);
 
-	// If it's a single word, give keyword options
-	if(data.trim().matches("^[A-Za-z0-9_-]{3,}$")){
-	    objects.add(new MobyDataComposite("Global_Keyword",
-					      "dummy_name", 
-					      "seahawk", 
-					      data.trim()));
-        }
-
 	// See if it's sequence
 	MobyDataComposite mdc = createMobySequence(data, "user-selection");
 	if(mdc != null){
@@ -63,6 +94,16 @@
 	    mdc.setName(objectName);
 	    objects.add(mdc);
 	}
+	// If it's a single word, give keyword options
+	else{
+	    if(data.trim().matches("^[A-Za-z0-9_-]{3,35}$")){
+		objects.add(new MobyDataComposite("Global_Keyword",
+						  "dummy_name", 
+						  "seahawk", 
+						  data.trim()));
+	    }
+	}
+
 
 	return (MobyDataInstance[]) objects.toArray(new MobyDataInstance[objects.size()]);
     }