parameter rework, logging and exception handling

src/main/java/edu/ucsd/sbrg/ModelPolisherCLILauncher.java

@@ -8,25 +8,21 @@
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
+import java.sql.SQLException;
 import java.util.Calendar;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.ResourceBundle;
 import java.util.concurrent.TimeUnit;
 import java.util.logging.Logger;
 
-import javax.xml.stream.XMLStreamException;
-
+import edu.ucsd.sbrg.annotation.AnnotationException;
 import edu.ucsd.sbrg.annotation.adb.ADBSBMLAnnotator;
 import edu.ucsd.sbrg.annotation.bigg.BiGGSBMLAnnotator;
+import edu.ucsd.sbrg.io.*;
 import edu.ucsd.sbrg.parameters.CommandLineParameters;
 import edu.ucsd.sbrg.db.adb.AnnotateDB;
 import edu.ucsd.sbrg.db.bigg.BiGGDB;
-import edu.ucsd.sbrg.io.IOOptions;
-import edu.ucsd.sbrg.io.ModelReader;
-import edu.ucsd.sbrg.io.ModelWriter;
-import edu.ucsd.sbrg.io.SBMLFileUtils;
-import edu.ucsd.sbrg.parameters.OutputParameters;
 import edu.ucsd.sbrg.polishing.SBMLPolisher;
 import edu.ucsd.sbrg.reporting.PolisherProgressBar;
 import edu.ucsd.sbrg.reporting.ProgressInitialization;
@@ -62,7 +58,7 @@
  * - HTML tag correction in SBML files.
  * - SBML document validation and conversion.
  * - Annotation of models using external databases.
- * - Output management including file writing, COMBINE archive creation, and compression.
+ * - Output management including file writing, COMBINE archive creation, and outputType.
  * <p>
  * This class also handles error logging and provides detailed logging of the processing steps.
  * 
@@ -118,12 +114,7 @@ public ModelPolisherCLILauncher(String... args) {
   public void commandLineMode(AppConf appConf) {
     SBProperties args = appConf.getCmdArgs();
 
-    try {
-        parameters = new CommandLineParameters(args);
-    } catch (IllegalArgumentException exc1) {
-      throw new IllegalArgumentException(exc1.getLocalizedMessage());
-    }
-
+    parameters = new CommandLineParameters(args);
     registry = new IdentifiersOrg();
 
     if (parameters.annotationParameters().biggAnnotationParameters().annotateWithBiGG()) {
@@ -136,7 +127,7 @@ public void commandLineMode(AppConf appConf) {
 
     try {
       var input = parameters.input();
-      var output = parameters.outputParameters().outputFile();
+      var output = parameters.output();
 
       // Check if the input exists, throw an exception if it does not
       if (!input.exists()) {
@@ -154,10 +145,18 @@ public void commandLineMode(AppConf appConf) {
       // Ensure the output directory or file's parent directory exists
       SBMLFileUtils.checkCreateOutDir(output);
 
-      batchProcess(input, parameters.outputParameters().outputFile());
+      batchProcess(input, parameters.output());
 
-    } catch (XMLStreamException | IOException exc) {
-      exc.printStackTrace();
+    } catch (ModelReaderException | ModelValidatorException | ModelWriterException | IOException |
+             AnnotationException e) {
+      // TODO: produce some user-friendly output and log to a file that can be provided for trouble-shooting
+      throw new RuntimeException(e);
+    } catch (IllegalArgumentException exc1) {
+      // TODO: produce some user-friendly output and log to a file that can be provided for trouble-shooting
+      throw new IllegalArgumentException(exc1.getLocalizedMessage());
+    } catch (SQLException e) {
+      // TODO: produce some user-friendly output and log to a file that can be provided for trouble-shooting
+      throw new RuntimeException(e);
     }
   }
 
@@ -166,12 +165,9 @@ public void commandLineMode(AppConf appConf) {
    * Processes the specified input and output paths. If the input is a directory, it recursively processes each file within.
    *
    * @param input  Path to the input file or directory to be processed. This should correspond to {@link CommandLineParameters#input()}.
-   * @param output Path to the output file or directory where processed files should be saved.
-   *               This should correspond to {@link OutputParameters#outputFile()}.
-   * @throws IOException if the input file or directory does not exist, or if no files are found within the directory.
-   * @throws XMLStreamException if an error occurs during file processing, propagated from {@link ModelPolisherCLILauncher#processFile(File, File)}.
+   * @param output Path to the output file or directory where processed files should be saved. This should correspond to {@link CommandLineParameters#output()}.
    */
-  private void batchProcess(File input, File output) throws IOException, XMLStreamException {
+  private void batchProcess(File input, File output) throws ModelReaderException, ModelWriterException, ModelValidatorException, AnnotationException, SQLException {
     // If the input is a directory, process each file within it
     if (input.isDirectory()) {
       File[] files = input.listFiles();
@@ -195,7 +191,7 @@ private void batchProcess(File input, File output) throws IOException, XMLStream
   }
 
 
-  private void processFile(File input, File output) throws XMLStreamException, 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);
@@ -214,7 +210,10 @@ private void processFile(File input, File output) throws XMLStreamException, IOE
       o.initialize(new ProgressInitialization(count));
     }
 
-    new SBMLPolisher(parameters.polishingParameters(), parameters.sboParameters(), registry, polishingObservers).polish(doc);
+    new SBMLPolisher(
+            parameters.polishingParameters(),
+            parameters.sboParameters(),
+            registry, polishingObservers).polish(doc);
 
     for (var o : polishingObservers) {
       o.finish(null);
@@ -227,8 +226,8 @@ private void processFile(File input, File output) throws XMLStreamException, IOE
     }
 
     if (parameters.annotationParameters().biggAnnotationParameters().annotateWithBiGG()) {
-        new BiGGSBMLAnnotator(bigg, parameters.annotationParameters().biggAnnotationParameters(), parameters.sboParameters(),
-                registry, annotationObservers).annotate(doc);
+      new BiGGSBMLAnnotator(bigg, parameters.annotationParameters().biggAnnotationParameters(), parameters.sboParameters(),
+              registry, annotationObservers).annotate(doc);
     }
 
     if (parameters.annotationParameters().adbAnnotationParameters().addADBAnnotations()) {
@@ -239,12 +238,12 @@ private void processFile(File input, File output) throws XMLStreamException, IOE
       o.finish(null);
     }
 
-    new ModelWriter(parameters.outputParameters()).write(doc, output, getVersionNumber());
+    output = new ModelWriter(parameters.outputType()).write(doc, output);
 
     if (parameters.SBMLValidation()) {
-      var mv = new ModelValidator(parameters.outputParameters());
+      var mv = new ModelValidator();
       // use offline validation
-      mv.validate(output, false);
+      mv.validate(output);
     }
 
     // Log the time taken to process the file

src/main/java/edu/ucsd/sbrg/ModelPolisherOptions.java

@@ -24,20 +24,20 @@ public interface ModelPolisherOptions extends KeyProvider {
   /**
    * @author Andreas Dräger
    */
-  enum Compression {
+  enum OutputType {
 
-    GZIP("gz"),
-    NONE("none"),
-    ZIP("zip");
+    SBML("xml"),
+    JSON("json"),
+    COMBINE("combine");
 
     @JsonValue
     private final String extension;
 
-    Compression() {
-      this(null);
+     OutputType() {
+       this(null);
     }
 
-    Compression(String extension) {
+    OutputType(String extension) {
       this.extension = extension;
     }
 
@@ -74,8 +74,8 @@ public String getFileExtension() {
    * so, which archive type should be used.
    */
   @SuppressWarnings("unchecked")
-  Option<Compression> COMPRESSION_TYPE =
-    new Option<>("COMPRESSION_TYPE", Compression.class, MESSAGES.getString("COMPR_DESC"), Compression.NONE);
+  Option<OutputType> OUTPUT_TYPE =
+    new Option<>("OUTPUT_TYPE", OutputType.class, MESSAGES.getString("COMPR_DESC"), OutputType.SBML);
   /**
    * This XHTML file defines alternative document notes and makes them
    * exchangeable.

src/main/java/edu/ucsd/sbrg/ModelValidator.java

@@ -2,80 +2,39 @@
 
 import de.zbit.io.ZIPUtils;
 import de.zbit.util.ResourceManager;
-import edu.ucsd.sbrg.parameters.OutputParameters;
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.SBMLError;
 import org.sbml.jsbml.SBMLErrorLog;
 import org.sbml.jsbml.SBMLReader;
-import org.sbml.jsbml.validator.SBMLValidator;
 import org.sbml.jsbml.validator.offline.LoggingValidationContext;
 
 import javax.xml.stream.XMLStreamException;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.HashMap;
-import java.util.Map;
+import java.io.*;
 import java.util.ResourceBundle;
 import java.util.logging.Logger;
 
 import static java.text.MessageFormat.format;
 
 public class ModelValidator {
-    /**
-     * Bundle for ModelPolisher logger messages
-     */
     private static final ResourceBundle MESSAGES = ResourceManager.getBundle("edu.ucsd.sbrg.polisher.Messages");
-    /**
-     * A {@link Logger} for this class.
-     */
     private static final Logger logger = Logger.getLogger(ModelValidator.class.getName());
-    private final OutputParameters parameters;
 
-    public ModelValidator(OutputParameters parameters) {
-        this.parameters = parameters;
-    }
 
-    /**
-     * Validates an SBML file either online or offline based on the provided parameters.
-     * Online validation refers to checking the file against a remote service or database, using specific parameters for the validation process.
-     * Offline validation involves reading the file locally, handling different compression formats if necessary, and validating the SBML document against local constraints.
-     * Errors encountered during the validation process are logged for further analysis.
-     *
-     * @param outputFile The file object of the SBML file to be validated.
-     * @param online   A boolean flag indicating whether to perform online (true) or offline (false) validation.
-     */
-    public void validate(File outputFile, boolean online) {
-        String fileExtension = parameters.compression().getFileExtension();
-        String filename = outputFile.getAbsolutePath() + "." + fileExtension;
+    public void validate(File outputFile) throws ModelValidatorException {
+        try {
+            String filename = outputFile.getAbsolutePath();
 
-        if (online) {
-            logger.info(format(MESSAGES.getString("VAL_ONLINE"), filename));
-            String output = "xml";
-            String offcheck = "p,u";
-            Map<String, String> parameters = new HashMap<>();
-            parameters.put("output", output);
-            parameters.put("offcheck", offcheck);
-            logger.info("Validating " + filename + "\n");
-            SBMLErrorLog sbmlErrorLog = SBMLValidator.checkConsistency(filename, parameters);
-            handleErrorLog(sbmlErrorLog, filename);
-        } else {
             logger.info(format(MESSAGES.getString("VAL_OFFLINE"), filename));
             SBMLDocument doc = null;
-            try {
-                InputStream istream;
-                if (filename.endsWith(".gz")) {
-                    istream = ZIPUtils.GUnzipStream(filename);
-                } else if (filename.endsWith(".zip")) {
-                    istream = ZIPUtils.ZIPunCompressStream(filename);
-                } else {
-                    istream = new FileInputStream(filename);
-                }
-                doc = SBMLReader.read(istream);
-            } catch (XMLStreamException | IOException e) {
-                e.printStackTrace();
+            InputStream istream;
+            if (filename.endsWith(".gz")) {
+                istream = ZIPUtils.GUnzipStream(filename);
+            } else if (filename.endsWith(".zip")) {
+                istream = ZIPUtils.ZIPunCompressStream(filename);
+            } else {
+                istream = new FileInputStream(filename);
             }
+            doc = SBMLReader.read(istream);
             if (doc != null) {
                 LoggingValidationContext context = new LoggingValidationContext(doc.getLevel(), doc.getVersion());
                 context.loadConstraints(SBMLDocument.class);
@@ -85,6 +44,8 @@ public void validate(File outputFile, boolean online) {
             } else {
                 logger.severe(format(MESSAGES.getString("VAL_OFFLINE_FAIL"), filename));
             }
+        } catch (XMLStreamException | IOException e) {
+            throw new ModelValidatorException(e, outputFile);
         }
     }
 

src/main/java/edu/ucsd/sbrg/ModelValidatorException.java

@@ -0,0 +1,17 @@
+package edu.ucsd.sbrg;
+
+import java.io.File;
+
+public class ModelValidatorException extends Exception {
+
+    private final File outputFile;
+
+    public ModelValidatorException(Exception e, File outputFile) {
+        super(e);
+        this.outputFile = outputFile;
+    }
+
+    public File outputFile() {
+        return outputFile;
+    }
+}

src/main/java/edu/ucsd/sbrg/annotation/AbstractAnnotator.java

@@ -4,6 +4,7 @@
 import edu.ucsd.sbrg.reporting.ProgressUpdate;
 import edu.ucsd.sbrg.reporting.ReportType;
 
+import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -19,18 +20,23 @@ public AbstractAnnotator(List<ProgressObserver> observers) {
         this.observers = observers;
     }
 
-    public void annotate(List<SBMLElement> elementsToAnnotate) {
+    public void annotate(List<SBMLElement> elementsToAnnotate) throws SQLException {
         throw new UnsupportedOperationException();
     }
 
-    abstract public void annotate(SBMLElement elementToAnnotate);
+    abstract public void annotate(SBMLElement elementToAnnotate) throws SQLException, AnnotationException;
 
     protected void statusReport(String text, Object element) {
         for (var o : observers) {
             o.update(new ProgressUpdate(text, element, ReportType.STATUS));
         }
     }
 
+    protected void diffReport(String elementType, Object element1, Object element2) {
+        for (var o : observers) {
+            o.update(new ProgressUpdate(elementType, List.of(element1, element2), ReportType.DATA));
+        }
+    }
     public List<ProgressObserver> getObservers() {
         return observers;
     }

src/main/java/edu/ucsd/sbrg/annotation/AnnotationException.java

@@ -0,0 +1,8 @@
+package edu.ucsd.sbrg.annotation;
+
+public class AnnotationException extends Exception{
+
+    public AnnotationException(String msg, Exception e) {
+        super(msg, e);
+    }
+}

src/main/java/edu/ucsd/sbrg/annotation/adb/ADBReactionsAnnotator.java

@@ -6,6 +6,7 @@
 import edu.ucsd.sbrg.db.bigg.BiGGId;
 import org.sbml.jsbml.Reaction;
 
+import java.sql.SQLException;
 import java.util.*;
 
 import static edu.ucsd.sbrg.db.adb.AnnotateDBContract.Constants.BIGG_REACTION;
@@ -17,15 +18,19 @@ public ADBReactionsAnnotator(AnnotateDB adb, ADBAnnotationParameters parameters)
     }
 
     @Override
-    public void annotate(List<Reaction> reactions) {
-        reactions.forEach(this::annotate);
+    public void annotate(List<Reaction> reactions) throws SQLException {
+        for (Reaction reaction : reactions) {
+            annotate(reaction);
+        }
     }
 
     @Override
-    public void annotate(Reaction reaction) {
+    public void annotate(Reaction reaction) throws SQLException {
         String id = reaction.getId();
         Optional<BiGGId> reactionId = BiGGId.createReactionId(id);
-        reactionId.ifPresent(biGGId -> addBQB_IS_AnnotationsFromADB(reaction.getAnnotation(), BIGG_REACTION, biGGId));
+        if (reactionId.isPresent()) {
+            addBQB_IS_AnnotationsFromADB(reaction.getAnnotation(), BIGG_REACTION, reactionId.get());
+        }
         if ((reaction.getCVTermCount() > 0) && !reaction.isSetMetaId()) {
             reaction.setMetaId(reaction.getId());
         }

src/main/java/edu/ucsd/sbrg/annotation/adb/ADBSBMLAnnotator.java

@@ -6,14 +6,16 @@
 import org.sbml.jsbml.Model;
 import org.sbml.jsbml.SBMLDocument;
 
+import java.sql.SQLException;
+
 public class ADBSBMLAnnotator extends AbstractADBAnnotator<SBMLDocument> {
 
     public ADBSBMLAnnotator(AnnotateDB adb, ADBAnnotationParameters parameters) {
         super(adb, parameters);
     }
 
     @Override
-    public void annotate(SBMLDocument doc) {
+    public void annotate(SBMLDocument doc) throws SQLException {
         Model model = doc.getModel();
 
         new ADBSpeciesAnnotator(adb, parameters).annotate(model.getListOfSpecies());