[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/chado ChadoAdapter.java, 1.50, 1.51 XmlConfigFileParser.java, 1.38, 1.39

[elee <gk...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv25306/dataadapter/chado

Modified Files:
	ChadoAdapter.java XmlConfigFileParser.java 
Log Message:
+ Added lookups by synonyms



Index: ChadoAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/ChadoAdapter.java,v
retrieving revision 1.50
retrieving revision 1.51
diff -C2 -d -r1.50 -r1.51
*** ChadoAdapter.java	3 Apr 2008 00:02:45 -0000	1.50
--- ChadoAdapter.java	13 Aug 2008 15:14:46 -0000	1.51
***************
*** 217,220 ****
--- 217,221 ----
      //String seqId = this.stateInfo.getProperty(INPUT_ID);
      String seqId = dataInput.getSeqId();
+     StringBuilder realSeqId = new StringBuilder();
  
      // Create a JdbcChadoAdapter; all the actual database communication is delegated
***************
*** 231,235 ****
      // Throws DataAdapterException if conn or seq invalid
      logger.info("checking that the database contains a sequence of type " + soType + " with name=" + seqId);
!     jdbcAdap.validateConnectionAndSequence(soType, seqId);
      fireProgressEvent(new ProgressEvent(this, new Double(100.0), "Connecting to chado database"));
  
--- 232,236 ----
      // Throws DataAdapterException if conn or seq invalid
      logger.info("checking that the database contains a sequence of type " + soType + " with name=" + seqId);
!     jdbcAdap.validateConnectionAndSequence(soType, seqId, realSeqId);
      fireProgressEvent(new ProgressEvent(this, new Double(100.0), "Connecting to chado database"));
  
***************
*** 240,244 ****
      }
      else {
!       cset = jdbcAdap.getCurationSet(this, soType, seqId);
      }
  
--- 241,246 ----
      }
      else {
!       // if realSeqId is populated, that means we did a search by synonym, need to use the actual id
!       cset = jdbcAdap.getCurationSet(this, soType, realSeqId.length() > 0 ? realSeqId.toString() : seqId);
      }
  

Index: XmlConfigFileParser.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/XmlConfigFileParser.java,v
retrieving revision 1.38
retrieving revision 1.39
diff -C2 -d -r1.38 -r1.39
*** XmlConfigFileParser.java	6 Dec 2007 01:40:41 -0000	1.38
--- XmlConfigFileParser.java	13 Aug 2008 15:14:46 -0000	1.39
***************
*** 268,271 ****
--- 268,272 ----
      Boolean copyGeneModelsIntoResultTier = null;
      List seqTypeList = null;
+     Boolean useSynonyms = null;
  
      for (int i = 0; i < size; i++) {
***************
*** 445,448 ****
--- 446,454 ----
        }
        
+       // USE SYNONYMS FOR LOOKING UP FEATURES
+       else if (nodeName.equals("useSynonyms")) {
+         useSynonyms = getTextNodeBooleanObj(node);
+       }
+       
        else {
          logger.error("Unknown xml element in chado config file: "+nodeName);
***************
*** 534,537 ****
--- 540,547 ----
          if (queryFeatureIdWithName != null)
            inst.setQueryFeatureIdWithName(queryFeatureIdWithName.booleanValue());
+         
+         if (useSynonyms != null) {
+           inst.setUseSynonyms(useSynonyms.booleanValue());
+         }
        }
        catch (UnsupportedOperationException e) {