[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/chado/jdbc JdbcChadoAdapter.java, 1.169, 1.170

[Jonathan C. <jcr...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv29541

Modified Files:
	JdbcChadoAdapter.java 
Log Message:
This should have been committed earlier (sorry).  It's been modified
to take the new cv/cvterm configuration parameters into account, and
to account for the fact that the featureprop.rank column is NOT nullable.


Index: JdbcChadoAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java,v
retrieving revision 1.169
retrieving revision 1.170
diff -C2 -d -r1.169 -r1.170
*** JdbcChadoAdapter.java	7 Feb 2007 21:14:14 -0000	1.169
--- JdbcChadoAdapter.java	9 Feb 2007 01:37:47 -0000	1.170
***************
*** 914,918 ****
--- 914,951 ----
      return (Long)(this.propertyTypeCvTerms.get(name));
    }
+ 
+   // -------------------------------------
+   // Retrieve an arbitrary cvterm
+   // -------------------------------------
      
+   // TODO - cache these results also
+   Long getCVTermId(String cvName, String cvTermName) {
+     Long result = null;
+     String cvNameCol = chadoVersion.getCvNameCol();
+ 
+     String sql = "SELECT cvt.cvterm_id " + 
+       "FROM cvterm cvt, cv c " + 
+       "WHERE c.cv_id = cvt.cv_id " +
+       "AND c." + cvNameCol + "='" + cvName + "' " +
+       "AND cvt.name = '" + cvTermName + "' ";
+       
+     try {
+       ResultSet rs = executeLoggedSelectQuery("getCVTermId", sql);
+       if (rs.next()) {
+         result = new Long(rs.getLong("cvterm_id"));
+       } else {
+ 	logger.warn("no cvterm_id found for cvterm '" + cvTermName + "' in CV '" + cvName + "'");
+       }
+       if (rs.next()) {
+ 	logger.error("multiple cvterm_ids found for cvterm '" + cvTermName + "' in CV '" + cvName + "'");
+       }
+     }
+     catch (SQLException sqle) {
+       logger.error("SQLException retrieving cvterms with cvname = " + cvTermName, sqle);
+     }
+ 
+     return result;
+   }
+ 
    // ------------------
    // Organism map/cache
***************
*** 1491,1494 ****
--- 1524,1531 ----
        "FROM featureprop fp, cvterm "+
        "WHERE fp.feature_id = "+feature_id+" AND fp.type_id = cvterm.cvterm_id";
+ 
+     String ownerTerm = chadoInstance.getFeatureOwnerPropertyTerm();    
+     String altDescrTerm = chadoInstance.getSeqDescriptionTerm();
+ 
      try {
        ResultSet rs = executeLoggedSelectQuery("addAnnotationFeatProps", sql);
***************
*** 1496,1500 ****
          String type = rs.getString("name");
          String value = rs.getString("value");
!         if (type.equals("owner")) // only makes sense for transcripts
            annot.setOwner(value);
          // "non-canonical_splice_site"?? Transcript ->AnnotatedFeat
--- 1533,1537 ----
          String type = rs.getString("name");
          String value = rs.getString("value");
!         if (type.equals(ownerTerm)) // only makes sense for transcripts
            annot.setOwner(value);
          // "non-canonical_splice_site"?? Transcript ->AnnotatedFeat
***************
*** 1508,1511 ****
--- 1545,1550 ----
          else if (type.equals("description"))
            annot.setDescription(value);
+ 	else if (type.equals(altDescrTerm)) 
+           annot.setDescription(value);
          else
            annot.addProperty(type,value);
***************
*** 1640,1644 ****
                                 boolean getTargetSeqsSeparately,
                                 boolean lazyTgtSeqs, boolean getTargetSeqDescriptions,
-                                String targetSeqDescriptionCVTerm,
                                 boolean joinWithFeatureProp, SequenceI refSeq, 
                                 StrandedFeatureSet sfs, String scoreColumn, 
--- 1679,1682 ----
***************
*** 1704,1708 ****
            tgtDescField = "tgtDescription";
            //tgtDescSelect = "tgt_fp.value as "+tgtDescField+", ";
!           Long descriptionTypeId = getPropertyTypeCVTermId(targetSeqDescriptionCVTerm);
            //tgtDescOuterJoin = "LEFT OUTER JOIN featureprop tgt_fp ON "+
            //"(tgtFeat.feature_id = tgt_fp.feature_id "
--- 1742,1750 ----
            tgtDescField = "tgtDescription";
            //tgtDescSelect = "tgt_fp.value as "+tgtDescField+", ";
! 
! 	  String seqDescrCv = chadoInstance.getSeqDescriptionCVName();
! 	  String seqDescrTerm = chadoInstance.getSeqDescriptionTerm();
! 	  Long descriptionTypeId = getCVTermId(seqDescrCv, seqDescrTerm);
! 
            //tgtDescOuterJoin = "LEFT OUTER JOIN featureprop tgt_fp ON "+
            //"(tgtFeat.feature_id = tgt_fp.feature_id "
***************
*** 3926,3930 ****
    }
    
!   public Long insertFeaturepropRow(Long featureId, Long typeId, String value, Long rank)
    {
      String tableName = "featureprop";
--- 3968,3972 ----
    }
    
!   public Long insertFeaturepropRow(Long featureId, Long typeId, String value, long rank)
    {
      String tableName = "featureprop";
***************
*** 3939,3946 ****
      colValues.put("feature_id", featureId);
      colValues.put("type_id", typeId);
!     
  
      // NULLable columns
-     if (rank != null) { colValues.put("rank", rank); }
      if (value != null) {  colValues.put("value", value); }
  
--- 3981,3987 ----
      colValues.put("feature_id", featureId);
      colValues.put("type_id", typeId);
!     colValues.put("rank", new Long(rank));
  
      // NULLable columns
      if (value != null) {  colValues.put("value", value); }