comments and minor code orga

draeger-lab · Aug 18, 2024 · f433465 · f433465
1 parent 9518897
commit f433465
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Showing 8 changed files with 17 additions and 18 deletions.
diff --git a/src/main/java/edu/ucsd/sbrg/ModelPolisherCLILauncher.java b/src/main/java/edu/ucsd/sbrg/ModelPolisherCLILauncher.java
@@ -148,7 +148,13 @@ public void commandLineMode(AppConf appConf) {
         }
       }
       else {
+        long startTime = System.currentTimeMillis();
+
         processFile(parameters.input(), parameters.output());
+
+        // Log the time taken to process the file
+        long timeTaken = TimeUnit.MILLISECONDS.toSeconds(System.currentTimeMillis() - startTime);
+        logger.info(String.format(MESSAGES.getString("FINISHED_TIME"), (timeTaken / 60), (timeTaken % 60)));
       }
 
     } catch (ModelValidatorException | ModelWriterException | IOException |
@@ -196,20 +202,20 @@ private void validateIOParameters() throws IOException {
 
 
   private void processFile(File input, File output) throws ModelReaderException, ModelWriterException, ModelValidatorException, AnnotationException, SQLException {
-    long startTime = System.currentTimeMillis();
-
     SBMLDocument doc = new ModelReader(parameters.sboParameters(), registry).read(input);
 
-    // TODO: hier wäre es jetzt angebracht das Ding zu validieren, geht aber nicht, weil es keinen Validator in JSBML gibt
+    // TODO: validieren und ggf. fixer aufrufen
 
     Model model = doc.getModel();
 
+    // TODO: das sollte sich durch JSBML UpdateListener ersetzen lassen
     List<ProgressObserver> polishingObservers = List.of(new PolisherProgressBar());
     int count = getPolishingTaskCount(model);
     for (var o : polishingObservers) {
       o.initialize(new ProgressInitialization(count));
     }
 
+    // TODO: dispatch abhängig von level und version
     new SBMLPolisher(
             parameters.polishingParameters(),
             parameters.sboParameters(),
@@ -219,17 +225,20 @@ private void processFile(File input, File output) throws ModelReaderException, M
       o.finish(null);
     }
 
+    // TODO: das sollte sich durch JSBML UpdateListener ersetzen lassen
     List<ProgressObserver> annotationObservers = List.of(new PolisherProgressBar());
     int annotationTaskCount = getAnnotationTaskCount(model);
     for (var o : annotationObservers) {
       o.initialize(new ProgressInitialization(annotationTaskCount));
     }
 
+    // TODO: dispatch abhängig von level und version
     if (parameters.annotationParameters().biggAnnotationParameters().annotateWithBiGG()) {
       new BiGGSBMLAnnotator(new BiGGDB(), parameters.annotationParameters().biggAnnotationParameters(), parameters.sboParameters(),
               registry, annotationObservers).annotate(doc);
     }
 
+    // TODO: dispatch abhängig von level und version
     if (parameters.annotationParameters().adbAnnotationParameters().annotateWithAdb()) {
       new ADBSBMLAnnotator(new AnnotateDB(), parameters.annotationParameters().adbAnnotationParameters()).annotate(doc);
     }
@@ -246,10 +255,6 @@ private void processFile(File input, File output) throws ModelReaderException, M
       // use offline validation
       mv.validate(output);
     }
-
-    // Log the time taken to process the file
-    long timeTaken = TimeUnit.MILLISECONDS.toSeconds(System.currentTimeMillis() - startTime);
-    logger.info(String.format(MESSAGES.getString("FINISHED_TIME"), (timeTaken / 60), (timeTaken % 60)));
   }
 
   private int getPolishingTaskCount(Model model) {

diff --git a/src/main/java/edu/ucsd/sbrg/fixing/ReactionFixer.java b/src/main/java/edu/ucsd/sbrg/fixing/ReactionFixer.java
@@ -12,6 +12,8 @@ public void fix(Reaction reaction, int index) {
         fixMissingReactionId(reaction, index);
         setFastProperty(reaction);
         setReversibleProperty(reaction);
+        new SpeciesReferenceFixer().fix(reaction.getListOfReactants());
+        new SpeciesReferenceFixer().fix(reaction.getListOfProducts());
     }
 
     private void fixMissingReactionId(Reaction reaction, int index) {

diff --git a/src/main/java/edu/ucsd/sbrg/fixing/SpeciesReferenceFixer.java b/src/main/java/edu/ucsd/sbrg/fixing/SpeciesReferenceFixer.java
@@ -2,7 +2,7 @@
 
 import org.sbml.jsbml.SpeciesReference;
 
-public class SpeciesReferenceFixer implements IFixSpeciesReferences{
+public class SpeciesReferenceFixer implements IFixSpeciesReferences {
 
     @Override
     public void fix(SpeciesReference sr) {

diff --git a/src/main/java/edu/ucsd/sbrg/fixing/ext/groups/GroupsFixer.java b/src/main/java/edu/ucsd/sbrg/fixing/ext/groups/GroupsFixer.java
@@ -16,10 +16,6 @@ public class GroupsFixer {
     private static final Logger logger = LoggerFactory.getLogger(GroupsFixer.class);
     private static final ResourceBundle MESSAGES = ResourceManager.getBundle("edu.ucsd.sbrg.polisher.Messages");
 
-    /**
-     * Set group kind where required
-     *
-     */
     public static void fixGroups(Model model) {
         GroupsModelPlugin gPlug = (GroupsModelPlugin) model.getExtension(GroupsConstants.shortLabel);
         if ((gPlug != null) && gPlug.isSetListOfGroups()) {

diff --git a/src/main/java/edu/ucsd/sbrg/polishing/CompartmentPolisher.java b/src/main/java/edu/ucsd/sbrg/polishing/CompartmentPolisher.java
@@ -9,9 +9,7 @@
 import edu.ucsd.sbrg.reporting.ProgressObserver;
 import edu.ucsd.sbrg.resolver.Registry;
 import org.sbml.jsbml.Compartment;
-import org.sbml.jsbml.Model;
 import org.sbml.jsbml.SBO;
-import org.sbml.jsbml.Unit;
 
 import de.zbit.util.ResourceManager;
 import edu.ucsd.sbrg.db.bigg.BiGGId;

diff --git a/src/main/java/edu/ucsd/sbrg/polishing/SBMLPolisher.java b/src/main/java/edu/ucsd/sbrg/polishing/SBMLPolisher.java
@@ -44,8 +44,7 @@ public SBMLPolisher(PolishingParameters parameters, SBOParameters sboParameters,
     @Override
     public void polish(SBMLDocument doc) {
         logger.debug(format("Polish doc: {0}", doc.toString()));
-        // Ensure the document is at the correct SBML level and version
-        if (!doc.isSetLevelAndVersion() || (doc.getLevelAndVersion().compareTo(ValuePair.of(3, 1)) < 0)) {
+	if (!doc.isSetLevelAndVersion() || (doc.getLevelAndVersion().compareTo(ValuePair.of(3, 1)) < 0)) {
             logger.debug(MESSAGES.getString("TRY_CONV_LVL3_V1"));
             SBMLtools.setLevelAndVersion(doc, 3, 1);
         }

diff --git a/src/main/java/edu/ucsd/sbrg/polishing/SpeciesReferencesPolisher.java b/src/main/java/edu/ucsd/sbrg/polishing/SpeciesReferencesPolisher.java
@@ -2,7 +2,7 @@
 
 import org.sbml.jsbml.SpeciesReference;
 
-public class SpeciesReferencesPolisher implements IPolishSpeciesReferences{
+public class SpeciesReferencesPolisher implements IPolishSpeciesReferences {
 
     private final Integer defaultSBOterm;
 

diff --git a/src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/GeneProductAssociationsProcessor.java b/src/main/java/edu/ucsd/sbrg/polishing/ext/fbc/GeneProductAssociationsProcessor.java
@@ -2,7 +2,6 @@
 
 import de.zbit.util.ResourceManager;
 import edu.ucsd.sbrg.db.bigg.BiGGId;
-import org.sbml.jsbml.Annotation;
 import org.sbml.jsbml.Model;
 import org.sbml.jsbml.Reaction;
 import org.sbml.jsbml.ext.fbc.*;