chado qualifier updates

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3302 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/chado/ChadoTransaction.java

@@ -46,7 +46,7 @@ public class ChadoTransaction
   /** properties store */
   protected Hashtable properties; 
   /** old properties store */
-  protected Hashtable old_properties;
+  protected Hashtable constraint;
 
   /** type of statement */
   protected int type;
@@ -114,16 +114,11 @@ public class ChadoTransaction
     properties.put(name, value);
   }
 
-  /**
-  * 
-  *  Add a property to this transaction that will be changed.
-  *
-  */
-  public void addOldProperty(String name, String old_value)
+  public void setConstraint(String name, String value)
   {
-    if (properties == null)
-      old_properties = new Hashtable();
-    old_properties.put(name, old_value);
+    if(constraint == null)
+      constraint = new Hashtable();
+    constraint.put(name, value);
   }
 
   public String getSqlQuery()
@@ -146,8 +141,19 @@ public class ChadoTransaction
         if(enum_prop.hasMoreElements())
           sqlBuff.append(" , ");
       }
-      sqlBuff.append(" WHERE feature.feature_id=featureloc.feature_id AND feature.uniquename='");
+      sqlBuff.append(" WHERE feature.feature_id="+chadoTable+".feature_id AND feature.uniquename='");
       sqlBuff.append(uniquename+"'");
+
+      if(constraint != null)
+      {
+        Enumeration enum_constraint = constraint.keys();
+        while(enum_constraint.hasMoreElements())
+        {
+          name  = (String)enum_constraint.nextElement();
+          value = (String)constraint.get(name);
+          sqlBuff.append(" AND "+name+"="+value);
+        }
+      }
     }
 //  else if(type == INSERT)
 //  else

uk/ac/sanger/artemis/chado/ChadoTransactionManager.java

@@ -176,15 +176,23 @@ public class ChadoTransactionManager
           final StringVector qualifier_strings =
                        StreamQualifier.toStringVector(null, this_qualifier);
 
-          long cvterm_id = DatabaseDocument.getCvtermID(name);
+          String cvterm_id = DatabaseDocument.getCvtermID(name).toString();
           
           for(int value_index = 0; value_index < qualifier_strings.size();
               ++value_index)
           {
-            final String qualifier_string = qualifier_strings.elementAt(value_index);
-//          tsn.addProperty("value", qualifier_string);
+            String qualifier_string = qualifier_strings.elementAt(value_index);
+            int index = qualifier_string.indexOf("=");
+            if(index > -1)
+              qualifier_string = qualifier_string.substring(index+1);
+
+            tsn.addProperty("value", "'"+qualifier_string+"'");
           }
+          tsn.setConstraint("featureprop.type_id", cvterm_id);
+          sql.add(tsn);
  
+          System.out.println("******** "+DatabaseDocument.getCvtermID(name));
+          System.out.println(tsn.getSqlQuery());
         }
         else                                                   // insert qualifier
         {}

uk/ac/sanger/artemis/util/DatabaseDocument.java

@@ -295,16 +295,16 @@ public class DatabaseDocument extends Document
     return cdsBuffer.toString();
   }
 
-  public static long getCvtermID(String name)
+  public static Long getCvtermID(String name)
   {
     Enumeration enum_cvterm = cvterm.keys();
     while(enum_cvterm.hasMoreElements())
     {
       Long key = (Long)enum_cvterm.nextElement();
       if(name.equals(cvterm.get(key)))
-        return key.longValue();
+        return key;
     }
-    return (long)-1.;
+    return new Long("-1.");
   }
 
   private String getCvtermName(Connection conn, long id)