[Taverna-cvs] RestfulSBS/src/main/java/uk/org/mygrid/sogsa/sbs/semanticAnnotation BLASTReportAnnotator.java, 1.4, 1.5

[Paolo M. <pmi...@us...>]

Update of /cvsroot/taverna/RestfulSBS/src/main/java/uk/org/mygrid/sogsa/sbs/semanticAnnotation
In directory ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv8454/src/main/java/uk/org/mygrid/sogsa/sbs/semanticAnnotation

Modified Files:
	BLASTReportAnnotator.java 
Log Message:
post-demo check in

Index: BLASTReportAnnotator.java
===================================================================
RCS file: /cvsroot/taverna/RestfulSBS/src/main/java/uk/org/mygrid/sogsa/sbs/semanticAnnotation/BLASTReportAnnotator.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** BLASTReportAnnotator.java	29 Jan 2009 19:24:51 -0000	1.4
--- BLASTReportAnnotator.java	30 Jan 2009 17:04:15 -0000	1.5
***************
*** 85,90 ****
  	private static final String NCBI_BASE = "http://www.ebi.ac.uk/Tools/es/cgi-bin/result.cgi?tool=ncbiblast;jobid=";
  
! 	final String cachedReport = "src/main/resources/cachedUniprotBLASTReport.xml";  // cached report if we fail to retrieve it live
! //	final String cachedReport = "src/main/resources/cachedEMBLBLASTReport.xml";  // cached report if we fail to retrieve it live
  
  
--- 85,90 ----
  	private static final String NCBI_BASE = "http://www.ebi.ac.uk/Tools/es/cgi-bin/result.cgi?tool=ncbiblast;jobid=";
  
! //	final String cachedReport = "src/main/resources/cachedUniprotBLASTReport.xml";  // cached report if we fail to retrieve it live
! 	final String cachedReport = "src/main/resources/cachedEMBLBLASTReport.xml";  // cached report if we fail to retrieve it live
  
  
***************
*** 547,551 ****
  							while (rs.next()) {
  
! 								String termType = rs.getString("term_type");
  
  								GOID2GOTerm.put(GOID, termType);
--- 547,551 ----
  							while (rs.next()) {
  
! 								String termType = rs.getString("id");
  
  								GOID2GOTerm.put(GOID, termType);
***************
*** 688,694 ****
  				for (String GOA:GOAs) {
  					// literal or ontology class??
  					g.add(ACURI, 
  							dss.getValueFactory().createURI(HASGOA_PROPERTY), 
! 							dss.getValueFactory().createLiteral(GOA));
  				}
  
--- 688,697 ----
  				for (String GOA:GOAs) {
  					// literal or ontology class??
+ 					
+ 					String goTerm = GOID2GOTerm.get(GOA);
+ 
  					g.add(ACURI, 
  							dss.getValueFactory().createURI(HASGOA_PROPERTY), 
! 							dss.getValueFactory().createLiteral(goTerm));
  				}