[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/chado/jdbc JdbcChadoWriter.java, 1.2, 1.3 PureJDBCTransactionWriter.java, 1.30, 1.31

[arnaiz <oli...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv9312

Modified Files:
	JdbcChadoWriter.java PureJDBCTransactionWriter.java 
Log Message:
Added transaction (with the new system) for the status (isFinished and isProblematic)


Index: JdbcChadoWriter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoWriter.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** JdbcChadoWriter.java	22 May 2008 01:19:15 -0000	1.2
--- JdbcChadoWriter.java	22 May 2008 12:17:34 -0000	1.3
***************
*** 162,165 ****
--- 162,166 ----
          updateSynonyms(annot1, annot2);
          updateComments(annot1, annot2);
+ 	updateStatus(annot1, annot2);
          processFeatures(annot1.getFeatures(), annot2.getFeatures(), refSeq);
        }
***************
*** 478,481 ****
--- 479,507 ----
    }
    
+     
+     /** Update the status for a AnnotatedFeatureI object.
+    *
+    *  @param annot1 - AnnotatedFeatureI object being edited.
+    *  @param annot2 - AnnotatedFeatureI object stored in database.
+    */
+   private void updateStatus(AnnotatedFeatureI annot1, AnnotatedFeatureI annot2)
+   {
+      boolean isFinished1 = annot1.isFinished();
+      boolean isFinished2 = annot2.isFinished();
+      
+      long annotId = getChadoFeatureId(annot1);
+      
+      if(isFinished1 != isFinished2) {
+        updateStatus(annotId,"status",annot1.getProperty("status"),annot2.getProperty("status"));     
+      }
+   
+      boolean isProblematic1 = annot1.isProblematic();
+      boolean isProblematic2 = annot2.isProblematic();
+      if(isProblematic1 != isProblematic2) {
+        updateStatus(annotId,"problem",""+isProblematic1,""+isProblematic2);
+      }
+   }
+   
+   
    /** Process the sequence edits associated with a SequenceI object.
     *

Index: PureJDBCTransactionWriter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/PureJDBCTransactionWriter.java,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** PureJDBCTransactionWriter.java	22 May 2008 01:19:16 -0000	1.30
--- PureJDBCTransactionWriter.java	22 May 2008 12:17:35 -0000	1.31
***************
*** 889,893 ****
  	logger.warn("database has no 'problem' cvterm; cannot store problem featureprop for transcript with id = " + transId);
        } else {
! 	Long transProbFpId = this.jdbcAdapter.insertFeaturepropRow(transId, problemTypeId, "false", 0);
  	if (transProbFpId == null) return null;
        }
--- 889,893 ----
  	logger.warn("database has no 'problem' cvterm; cannot store problem featureprop for transcript with id = " + transId);
        } else {
! 	Long transProbFpId = this.jdbcAdapter.insertFeaturepropRow(transId, problemTypeId,""+transcript.isProblematic(), 0);
  	if (transProbFpId == null) return null;
        }
***************
*** 899,903 ****
  	logger.warn("database has no 'status' cvterm; cannot store status featureprop for transcript with id = " + transId);
        } else {
! 	Long transStatusFpId = this.jdbcAdapter.insertFeaturepropRow(transId, statusTypeId, "in	progress", 0);
  	if (transStatusFpId == null) return null;
        }
--- 899,903 ----
  	logger.warn("database has no 'status' cvterm; cannot store status featureprop for transcript with id = " + transId);
        } else {
! 	Long transStatusFpId = this.jdbcAdapter.insertFeaturepropRow(transId, statusTypeId, transcript.getProperty("status"), 0);
  	if (transStatusFpId == null) return null;
        }
***************
*** 2313,2316 ****
--- 2313,2335 ----
    }
    
+   protected boolean updateStatus(long annotId, String statusTerm, String newStatus, String oldStatus)
+   {
+     Long typeId = jdbcAdapter.getPropertyTypeCVTermId(statusTerm);
+     if (typeId == null) {
+       logger.warn("database has no " + statusTerm + " cvterm");
+       return false;
+     }
+     Connection c = jdbcAdapter.getConnectionUsedForLastTransaction();
+     ChadoFeatureProp dbFeatProp = new ChadoFeatureProp(annotId, typeId, oldStatus, c);
+     int rank = dbFeatProp.getRank();
+     if(dbFeatProp != null) { 
+       logger.info("updating property '" + statusTerm + "' to '" + newStatus + "' from '" + oldStatus+"'");
+       return this.jdbcAdapter.updateFeaturepropRow(dbFeatProp.getFeaturepropId(),dbFeatProp,annotId, typeId, newStatus, rank);
+     }         
+     return false;
+   }  
+   
+   
+   
    protected String getChadoCdsName(ApolloNameAdapterI nameAdapter, String name)
    {