improve logs

remove duplicated lines + easier to parse (cpd or rxn ids extraction)

src/main/java/groupId/IsoMet/ParseSbml.java

@@ -70,7 +70,7 @@ public class ParseSbml {
 					i++;
 				} catch (CDKException e) {
 					cpd=new Compound(s);
-					logger.error("[SMILES] SMILES of compound "+s.getId()+" couldn't been parsed");
+					logger.error("[SMILES] "+s.getId()+": SMILES couldn't been parsed");
 					logger.debug("[SMILES] "+s.getId()+": "+smile);
 				}
 
@@ -79,7 +79,7 @@ public class ParseSbml {
 				//Since H atoms are ignored during atom mapping, this kind of species are removed from reactions
 				if(!smile.matches(".*[A-Za-z&&[^H]].*")){
 					cpd=null;
-					logger.warn("[SMILES] Compound "+s.getId()+" ignored: SMILES only contain Hydrogen");
+					logger.warn("[SMILES] "+s.getId()+" ignored: SMILES only contain Hydrogen");
 					logger.debug("[SMILES] "+s.getId()+": "+smile);
 				}
 
@@ -121,7 +121,7 @@ public class ParseSbml {
 				IsoMetReaction reaction = new IsoMetReaction(rEntry, substrates, products);
 				reactions.put(rEntry.getId(), reaction);
 			}catch (Exception e){
-				logger.error("[RXN] not able to create reaction "+rEntry.getId());
+				logger.error("[RXN] "+rEntry.getId()+": not able to create reaction");
 				logger.trace("",e);
 			}
 		});
@@ -258,15 +258,17 @@ public class ParseSbml {
 				.build();
 		for(IsoMetReaction reaction : reactions.values()){
 			f.checkAndFlag(reaction);
-			for(Flag flag : reaction.getFlags()){
-				logger.debug("[RXN] "+reaction.getSbmlReaction().getId()+": "+flag.toString());
+			if(!reaction.getFlags().isEmpty()){
+				for(Flag flag : reaction.getFlags()){
+					logger.debug("[RXN] "+reaction.getSbmlReaction().getId()+": "+flag.toString());
+				}
 				logger.debug("[RXN] "+reaction.getSbmlReaction().getId()+": "+ reaction.getEquation());
 			}
+
 			if(f.keep(reaction)) {
 				validReactions.add(reaction);
 			}else {
-				logger.warn("[RXN] "+reaction.getSbmlReaction().getId()+" not selected for AAM, doesn't match filtering criteria");
-				logger.debug("[RXN] "+reaction.getSbmlReaction().getId()+": "+ reaction.getEquation());
+				logger.warn("[RXN] "+reaction.getSbmlReaction().getId()+": not selected for AAM");
 			}
 		}
 		logger.info(model.getListOfReactions().size()+" reactions in SBML");
@@ -297,7 +299,7 @@ public class ParseSbml {
 				RxnSmiles = aamBuilder.compute(reactionSet.get(0));
 			} catch (Exception e) {
 				for(IsoMetReaction r : reactionSet){
-					logger.error("[AAM] error while computing " + r.getSbmlReaction().getId()+" atom mapping");
+					logger.error("[AAM] "+r.getSbmlReaction().getId()+": error while computing atom mapping");
 					logger.debug("[AAM] "+r.getSbmlReaction().getId()+": "+ r.getEquation());
 					logger.debug("[AAM] "+r.getSbmlReaction().getId()+": "+r.getRxnSmiles());
 				}
@@ -314,7 +316,7 @@ public class ParseSbml {
 						aamParser.parseMapping(r.getSubstrates(), r.getProducts(), finalRxnSmiles, aam);
 						r.setAtomMapping(aam);
 					} catch (Exception e) {
-						logger.error("[AAM] error while computing " + r.getSbmlReaction().getId()+" atom mapping");
+						logger.error("[AAM] "+ r.getSbmlReaction().getId()+": error while computing atom mapping");
 						logger.debug("[AAM] "+r.getSbmlReaction().getId()+": "+ r.getEquation());
 						logger.debug("[AAM] "+r.getSbmlReaction().getId()+": "+r.getRxnSmiles());
 						logger.trace("",e);