[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/chado/jdbc JdbcChadoAdapter.java, 1.172, 1.173 PureJDBCTransactionWriter.java, 1.12, 1.13

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

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv15823

Modified Files:
	JdbcChadoAdapter.java PureJDBCTransactionWriter.java 
Log Message:
The PureJDBCTransactionWriter can manage the addition of synonyms.

New cv 'null' which contains the term :'synonym' used in the synonym table.
Should be changed when GMOD will change its strategy about that.


Two new functions in the JdbcChadoAdapter :
- insertSynonymRowIfNeeded : insert a synonym if it is not already stored in the
database.
- insertFeatureSynonymRow : the link between the feature table and the synonym
table.



Index: JdbcChadoAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/JdbcChadoAdapter.java,v
retrieving revision 1.172
retrieving revision 1.173
diff -C2 -d -r1.172 -r1.173
*** JdbcChadoAdapter.java	9 Feb 2007 03:15:06 -0000	1.172
--- JdbcChadoAdapter.java	13 Feb 2007 13:35:42 -0000	1.173
***************
*** 142,145 ****
--- 142,147 ----
    private Map propertyTypeCvTerms;
  
+   private Map nullCvTerms;
+   
    private ChadoInstance chadoInstance;
  
***************
*** 835,839 ****
--- 837,853 ----
      return h;
    }
+   // cvterm from the table cv 'null'
+   
+   public Long getNullCVTermId(String name) {
+     if (nullCvTerms == null) 
+       nullCvTerms = getCVTerms("null");
+ 
+     Long result = (Long)(nullCvTerms.get(name));
  
+     if (result == null) 
+       logger.error("lookup failed for cvterm_id for cvterm with name ='" + name + "'; " );
+     return result;  
+   } 
+   
    /** Returns null if name not present in cvterm table */
    Long getFeatureCVTermId(String name) {
***************
*** 3585,3588 ****
--- 3599,3603 ----
        pkcMap.put("feature_dbxref", "feature_dbxref_id");
        pkcMap.put("feature_synonym", "feature_synonym_id");
+       pkcMap.put("synonym", "synonym_id");
        pkcMap.put("feature_relationship", "feature_relationship_id");
  
***************
*** 3996,3999 ****
--- 4011,4087 ----
    }  
    
+   public Long insertSynonymRowIfNeeded(String name,Long typeId,String synonym_sgml) {
+   	Long synonymId = getSynonymId(name,typeId);
+ 	if(synonymId != null)
+ 		return synonymId;
+ 	
+ 	String tableName = "synonym";
+     	HashMap colValues = new HashMap();
+ 
+     	// TODO - add some error checking
+ 
+     	// add synonym_id
+     	long newSynonymId = addPrimaryKeyColumnValue(tableName, colValues);
+ 
+     	// non-NULLable columns
+     	colValues.put("name", name);
+     	colValues.put("type_id", typeId);
+     	colValues.put("synonym_sgml", synonym_sgml);
+ 
+ 	// Unquoted/hard-coded columns
+ 	HashMap unquotedCols =null;
+ 
+     	if (insertRow(tableName, colValues, unquotedCols)) {
+       		return new Long(newSynonymId);
+     	} else {
+       		return null;
+     	}  
+   }
+   
+   // allow to get synonym_id with the name and the type_id
+   
+   private Long getSynonymId(String name,Long typeId) {
+     Connection c = getConnectionUsedForLastTransaction();
+   
+     try {
+       String sql = "SELECT synonym_id FROM synonym WHERE name ='"+name+ "' AND type_id="+typeId;
+       ResultSet rs = executeLoggedSelectQuery("getSynonymId", c, sql);
+       if(rs.next()) 
+       	return rs.getLong("synonym_id");
+     } catch (SQLException sqle) {
+       logger.error("SQLException getting row id from getSynonymId() ResultSet", sqle);
+       return null;
+     }
+     return null;
+   }
+   
+   public Long insertFeatureSynonymRow(Long synId, Long featId,Integer pubId,boolean is_current ,boolean is_internal) {
+   	String tableName = "feature_synonym";
+     	HashMap colValues = new HashMap();
+ 
+     	// TODO - add some error checking
+ 
+     	// add feature_synonym_id
+     	long newFeatureSynonymId = addPrimaryKeyColumnValue(tableName, colValues);
+ 
+     	// non-NULLable columns
+     	colValues.put("synonym_id", synId);
+     	colValues.put("feature_id", featId);
+     	colValues.put("pub_id", pubId);
+ 	colValues.put("is_current", is_current);
+ 	colValues.put("is_internal", is_internal);
+ 
+ 	// Unquoted/hard-coded columns
+ 	HashMap unquotedCols =null;
+ 
+     	if (insertRow(tableName, colValues, unquotedCols)) {
+       		return new Long(newFeatureSynonymId);
+     	} else {
+       		return null;
+     	} 
+   
+   
+   }   
+   
    /**
     * @param featureId chado feature_id of the original feature

Index: PureJDBCTransactionWriter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/jdbc/PureJDBCTransactionWriter.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** PureJDBCTransactionWriter.java	9 Feb 2007 04:10:20 -0000	1.12
--- PureJDBCTransactionWriter.java	13 Feb 2007 13:35:42 -0000	1.13
***************
*** 613,618 ****
  	// synonym
  	if (subpart.isSynonym()) {
! 	  // TODO
! 	  logger.warn("add SYNONYM not yet implemented");
  	} else {
  	  logger.error("not yet implemented - gene AddTransaction with subpart = " + subpart);
--- 613,617 ----
  	// synonym
  	if (subpart.isSynonym()) {
! 	  addSucceeded = addSynonym(feature,t);
  	} else {
  	  logger.error("not yet implemented - gene AddTransaction with subpart = " + subpart);
***************
*** 1101,1105 ****
      return exonId;
    }
! 
    /**
     * Compute the chado featureloc.locgroup for an Apollo feature.
--- 1100,1132 ----
      return exonId;
    }
!   
!   protected boolean addSynonym (SeqFeatureI feature, AddTransaction t) {
!   	long featId = getChadoFeatureId(feature);
! 	
! 	String name=t.getNewSubpartValue().toString();
! 	if(name == null) {
! 		logger.error("Can't insert a synonym with a name null");
! 		return false;
! 	}
! 	
! 	Long synonymTypeId = this.jdbcAdapter.getNullCVTermId("synonym");
! 	Long synId = null;
! 	if (synonymTypeId == null) {
!       		logger.warn("database has no 'synonym' cvterm; cannot record synonym with name = " + name);
!         } else {
! 		synId = this.jdbcAdapter.insertSynonymRowIfNeeded(name,synonymTypeId,name);		
! 	}
! 	if(synId == null) return false; 
! 		
! 	// feature_synonym table
! 	Integer pubId = new Integer(1); //Need to be changed
! 	boolean is_current = true;
! 	boolean is_internal = false;
! 	Long featsynId = this.jdbcAdapter.insertFeatureSynonymRow(synId,featId,new Integer(1),is_current,is_internal);
! 	if(featsynId == null)
! 		return false; 
! 		   
!   	return true;
!   }
    /**
     * Compute the chado featureloc.locgroup for an Apollo feature.