[MOBY-guts] biomoby commit

[Eddie Kawas]

kawas
Wed Feb  9 13:26:41 EST 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv31128/org/biomoby/client/gui/serviceInstanceCreationTool

Modified Files:
	MobyUtilities.java 
Log Message:
Fixed GetRelations so that it executes quickly and doesnt spin off
into infinite loops with bad input - Eddie

moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyUtilities.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/08 01:50:31	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/MobyUtilities.java	2005/02/09 18:26:41	1.3
@@ -4,6 +4,7 @@
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.net.URL;
+import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.StringTokenizer;
@@ -12,6 +13,9 @@
 
 import javax.swing.tree.TreePath;
 
+import org.biomoby.client.gui.util.MobyObjectPrimitiveExtractor;
+import org.biomoby.client.gui.util.Triples;
+
 /**
  * Utilities that are useful for retrieving information about certain objects, parsing objects, etc.
  * @author Eddie Kawas
@@ -21,12 +25,6 @@
  */
 
 public class MobyUtilities {
-    // strings that when concatenated return the attributes, articlename, etc of an object
-    final private static String URL_OBJECT = new String(
-            "http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?name=");
-
-    final private static String URL_LSID = new String(
-            "http://mobycentral.cbr.nrc.ca/cgi-bin/types/Objects?lsid_name=");
 
     /**
      * PRE: None.<p>
@@ -40,44 +38,31 @@
     public static LinkedList GetRelations(String name) throws IOException {
         URL url = null;
         boolean isLSID = false;
-        // TODO check if name == lsid
-        Pattern p = Pattern.compile("(^urn:lsid:biomoby.org:objectclass:\\S+)",
+        Pattern p = Pattern.compile("(^urn:lsid:biomoby.org:objectclass:\\S+$)",
                 Pattern.CASE_INSENSITIVE);
         Matcher m = p.matcher(name);
         isLSID = m.matches();
+        if (isLSID) {
+            int x = name.lastIndexOf(":")+1;
+            name = name.substring(x);
+        }
 
-        if (!isLSID)
-            url = new URL(URL_OBJECT + name);
-        else
-            url = new URL(URL_LSID + name);
-        BufferedReader in = new BufferedReader(new InputStreamReader(url
-                .openStream()));
-        String input;
-        String parent = "Object";
         LinkedList llHas = new LinkedList();
         LinkedList llHasa = new LinkedList();
-
-        while ((input = in.readLine()) != null) {
-            StringTokenizer st = new StringTokenizer(input, "\t");
-            if (st.countTokens() > 2) {
-                st.nextToken(); // object name that was queried
-                StringTokenizer lsid = new StringTokenizer(st.nextToken(), ":");
-                String relation = "";
-                while (lsid.hasMoreTokens())
-                    relation = lsid.nextToken(); // isa, hasa, etc
-                if (relation.equalsIgnoreCase("isa"))
-                    parent = st.nextToken();
-                else if (relation.equalsIgnoreCase("has"))
-                    llHas.add(st.nextToken());
-                else if (relation.equalsIgnoreCase("hasa"))
-                    llHasa.add(st.nextToken());
+        MobyObjectPrimitiveExtractor mope = new MobyObjectPrimitiveExtractor();
+        ArrayList al = mope.getPrimitives(name);
+        for (Iterator x = al.iterator(); x.hasNext();) {
+            Triples t = (Triples)x.next();
+            if (t.getType() == Triples.HAS) {
+                llHas.add(t.getPrimitive());
+            }
+            if (t.getType() == Triples.HASA) {
+                llHasa.add(t.getPrimitive());
             }
         }
-        if (parent.equals("")) {
-            return null;
-        }
+        // set up the return list
         LinkedList listToReturn = new LinkedList();
-        listToReturn.addFirst(parent);
+        listToReturn.addFirst("Object");
         listToReturn.add(llHas);
         listToReturn.add(llHasa);
         return listToReturn;
@@ -172,9 +157,9 @@
     }
 
     public static void main(String[] args) throws IOException {
-        LinkedList ll = MobyUtilities.GetRelations("genbank-flatfile");
+        LinkedList ll = MobyUtilities.GetRelations("DNASequence");
         System.out.println(ll.toString());
-        ll = MobyUtilities.GetRelations("urn:lsid:biomoby.org:objectclass:Object");
+        ll = MobyUtilities.GetRelations("urn:lsid:biomoby.org:objectclass:DNASequence");
         System.out.println(ll.toString());
     }
 }
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