Upgraded Solver Handler and fixed bugs in CLI Container

vcell-cli/src/main/java/org/vcell/cli/CLIStandalone.java

@@ -11,6 +11,7 @@
 import org.apache.logging.log4j.Logger;
 
 import cbit.vcell.mongodb.VCMongoMessage;
+import org.vcell.cli.run.RunUtils;
 import org.vcell.util.VCellUtilityHub;
 import org.vcell.util.document.KeyValue;
 import org.vcell.util.document.User;
@@ -36,6 +37,7 @@ public class CLIStandalone {
     private final static Logger logger = LogManager.getLogger(CLIStandalone.class);
     public static void main(String[] args) {
         int exitCode = -1;
+        RunUtils.drawBreakLine("-", 100);
         try{
             logger.info("Starting Vcell...");
             if (logger.isDebugEnabled()) logger.debug("!!!DEBUG Mode Active!!!");

vcell-cli/src/main/java/org/vcell/cli/messaging/CLIRecordable.java

@@ -5,16 +5,16 @@
 
 public interface CLIRecordable {
 
-    public void writeDetailedErrorList(Exception e, String message) throws IOException;
+    void writeDetailedErrorList(Exception e, String message) throws IOException;
 
-    public void writeFullSuccessList(String message) throws IOException;
+    void writeFullSuccessList(String message) throws IOException;
 
-    public void writeErrorList(Exception e, String message) throws IOException;
+    void writeErrorList(Exception e, String message) throws IOException;
 
-    public void writeDetailedResultList(String message) throws IOException;
+    void writeDetailedResultList(String message) throws IOException;
 
     // we make a list with the omex files that contain (some) spatial simulations (FVSolverStandalone solver)
-    public void writeSpatialList(String message) throws IOException;
+//    void writeSpatialList(String message) throws IOException;
 
-    public void writeImportErrorList(Exception e, String message) throws IOException;
+    void writeImportErrorList(Exception e, String message) throws IOException;
 }

vcell-cli/src/main/java/org/vcell/cli/messaging/CLIRecorder.java

@@ -17,7 +17,7 @@
 public class CLIRecorder extends Recorder implements CLIRecordable {
     protected final static boolean DEFAULT_SHOULD_PRINT_LOG_FILES = false, DEFAULT_SHOULD_FLUSH_LOG_FILES = false;
     protected boolean shouldPrintLogFiles, shouldFlushLogFiles;
-    protected TextFileRecord detailedErrorLog, fullSuccessLog, errorLog, detailedResultsLog, spatialLog, importErrorLog;
+    protected TextFileRecord detailedErrorLog, fullSuccessLog, errorLog, detailedResultsLog, /*spatialLog,*/ importErrorLog;
     protected File outputDirectory;
 
     // Note: this constructor is not public
@@ -86,7 +86,7 @@ public CLIRecorder(File outputDirectory, boolean forceLogFiles, boolean shouldFl
         this.fullSuccessLog = logManager.requestNewRecord(Paths.get(this.outputDirectory.getAbsolutePath(), "fullSuccessLog.txt").toString());
         this.errorLog = logManager.requestNewRecord(Paths.get(this.outputDirectory.getAbsolutePath(), "errorLog.txt").toString());
         this.detailedResultsLog = logManager.requestNewRecord(Paths.get(this.outputDirectory.getAbsolutePath(), "detailedResultLog.txt").toString());
-        this.spatialLog = logManager.requestNewRecord(Paths.get(this.outputDirectory.getAbsolutePath(), "hasSpatialLog.txt").toString());
+        //this.spatialLog = logManager.requestNewRecord(Paths.get(this.outputDirectory.getAbsolutePath(), "hasSpatialLog.txt").toString());
         this.importErrorLog = logManager.requestNewRecord(Paths.get(this.outputDirectory.getAbsolutePath(), "importErrorLog.txt").toString());
 
         this.createHeader();
@@ -162,10 +162,10 @@ public void writeDetailedResultList(String message) throws IOException {
      * 
      * @param message string to write to file
      */
-    public void writeSpatialList(String message) throws IOException {
-        // we make a list with the omex files that contain (some) spatial simulations (FVSolverStandalone solver)
-        this.writeToFileLog(this.spatialLog, message);
-    }
+//    public void writeSpatialList(String message) throws IOException {
+//        // we make a list with the omex files that contain (some) spatial simulations (FVSolverStandalone solver)
+//        this.writeToFileLog(this.spatialLog, message);
+//    }
 
     /**
      * Write to `importErrorLog.txt`

vcell-cli/src/main/java/org/vcell/cli/messaging/CliTracer.java

@@ -20,7 +20,7 @@ public void writeErrorList(Exception e, String message) {
     public void writeDetailedResultList(String message) {
         Tracer.log("writeDetailedResultList(): "+message);
     }
-    @Override
+    //@Override
     public void writeSpatialList(String message) {
         Tracer.log("writeSpatialList(): "+message);
     }

vcell-cli/src/main/java/org/vcell/cli/run/CLISolverListener.java

@@ -0,0 +1,106 @@
+package org.vcell.cli.run;
+
+import cbit.vcell.parser.DivideByZeroException;
+import cbit.vcell.solver.SolverException;
+import cbit.vcell.solver.server.SolverEvent;
+import cbit.vcell.solver.server.SolverListener;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.vcell.util.Triplet;
+
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.TimeoutException;
+
+public class CLISolverListener implements SolverListener {
+    private static final Logger lg = LogManager.getLogger(CLISolverListener.class);
+
+    public final CompletableFuture<Triplet<Double, Integer, Exception>> solverResult;
+    private final StringBuilder solverLog;
+    private final String solverLabel;
+
+    /**
+     * Tracks a CLI execution of a solver, and offers a completable future for the result!
+     * @param solverLabel what to call the solver this class listens to
+     */
+    public CLISolverListener(String solverLabel) {
+        this.solverResult = new CompletableFuture<>();
+        this.solverLog = new StringBuilder();
+        this.solverLabel = solverLabel;
+    }
+
+    /**
+     * Invoked when the solver aborts a calculation (abnormal termination).
+     *
+     * @param event indicates the solver and the event type
+     */
+    @Override
+    public void solverAborted(SolverEvent event) {
+        Double progress = event.getProgress();
+        Exception fault = this.determineFault(event);
+        this.solverResult.complete(new Triplet<>(progress, SolverEvent.SOLVER_ABORTED, fault));
+    }
+
+    private Exception determineFault(SolverEvent event){
+        String sourceString = event.getSource().toString();
+        String errorString = event.getSimulationMessage().getDisplayMessage();
+        String formattedString = String.format("%s(%s): %s", this.solverLabel, sourceString, errorString);
+        if (errorString.toLowerCase().contains("timed out")) return new TimeoutException(formattedString);
+        else if (errorString.toLowerCase().contains("divide by zero")) return new DivideByZeroException(formattedString);
+        else return new SolverException(formattedString);
+    }
+
+    /**
+     * Invoked when the solver finishes a calculation (normal termination).
+     *
+     * @param event indicates the solver and the event type
+     */
+    @Override
+    public void solverFinished(SolverEvent event) {
+        Double progress = event.getProgress();
+        String sourceString = event.getSource().toString();
+        String successString = event.getSimulationMessage().toString();
+        lg.info("{}({}) Success Message: {}", this.solverLabel, sourceString, successString);
+        this.solverResult.complete(new Triplet<>(progress, SolverEvent.SOLVER_FINISHED, null));
+    }
+
+    /**
+     * Invoked when the solver stores values in the result set.
+     *
+     * @param event indicates the solver and the event type
+     */
+    @Override
+    public void solverPrinted(SolverEvent event) {
+        this.solverLog.append(event.getSimulationMessage()).append("\n");
+    }
+
+    /**
+     * Invoked when the solver stores values in the result set.
+     *
+     * @param event indicates the solver and the event type
+     */
+    @Override
+    public void solverProgress(SolverEvent event) {
+        lg.info("{}({}) progress: {}\t(\"{}\")", this.solverLabel, event.getSource().toString(), event.getProgress(), event.getSimulationMessage());
+    }
+
+    /**
+     * Invoked when the solver begins a calculation.
+     *
+     * @param event indicates the solver and the event type
+     */
+    @Override
+    public void solverStarting(SolverEvent event) {
+        lg.info("{}({}) Beginning Simulation (\"{}\")", this.solverLabel, event.getSource().toString(), event.getSimulationMessage());
+    }
+
+    /**
+     * Invoked when the solver stops a calculation, usually because
+     * of a user-initiated stop call.
+     *
+     * @param event indicates the solver and the event type
+     */
+    @Override
+    public void solverStopped(SolverEvent event) {
+        lg.info("{}({}) Ending Simulation: (\"{}\")", this.solverLabel, event.getSource().toString(), event.getSimulationMessage());
+    }
+}

vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java

@@ -35,7 +35,6 @@ public class ExecutionJob {
 
     private OmexHandler omexHandler = null;
     private List<String> sedmlLocations;
-    private Path sedmlPath2d3d;
     private File inputFile;
 
     private CLIRecordable cliRecorder;
@@ -59,7 +58,7 @@ public ExecutionJob(File inputFile, File rootOutputDir, CLIRecordable cliRecorde
 
         this.bioModelBaseName = FileUtils.getBaseName(inputFile.getName()); // input file without the path
         String outputBaseDir = rootOutputDir.getAbsolutePath();
-        this.outputDir = bEncapsulateOutput ? Paths.get(outputBaseDir, bioModelBaseName).toString() : outputBaseDir;
+        this.outputDir = bEncapsulateOutput ? Paths.get(outputBaseDir, this.bioModelBaseName).toString() : outputBaseDir;
         this.bKeepTempFiles = bKeepTempFiles;
         this.bExactMatchOnly = bExactMatchOnly;
         this.bSmallMeshOverride = bSmallMeshOverride;
@@ -86,7 +85,6 @@ public void preprocessArchive() throws IOException {
 
         // Unpack the Omex Archive
         try { // It's unlikely, but if we get errors here they're fatal.
-            this.sedmlPath2d3d = Paths.get(this.outputDir, "temp");
             this.omexHandler = new OmexHandler(this.inputFile.getAbsolutePath(), this.outputDir);
             this.omexHandler.extractOmex();
             this.sedmlLocations = this.omexHandler.getSedmlLocationsAbsolute();
@@ -136,17 +134,21 @@ public void executeArchive(boolean isBioSimSedml) throws BiosimulationsHdfWriter
         } catch (IOException e){
             logger.error("System IO encountered a fatal error");
             throw new ExecutionException(e);
+        } finally {
+            RunUtils.drawBreakLine("-", 100);
         }
+
     }
 
     private void executeSedmlDocument(String sedmlLocation, HDF5ExecutionResults cumulativeHdf5Results) throws IOException, PreProcessingException, ExecutionException {
         BiosimulationLog.instance().updateSedmlDocStatusYml(sedmlLocation, BiosimulationLog.Status.QUEUED);
-        SedmlJob job = new SedmlJob(sedmlLocation, this.omexHandler, this.inputFile, this.outputDir, this.sedmlPath2d3d.toString(), this.cliRecorder, this.bKeepTempFiles, this.bExactMatchOnly, this.bSmallMeshOverride, this.logOmexMessage);
+        SedmlJob job = new SedmlJob(sedmlLocation, this.omexHandler.getOutputPathFromSedml(sedmlLocation), this.inputFile, this.outputDir, this.cliRecorder, this.bKeepTempFiles, this.bExactMatchOnly, this.bSmallMeshOverride, this.logOmexMessage);
         SedmlStatistics stats = job.preProcessDoc();
         boolean hasSucceeded = job.simulateSedml(cumulativeHdf5Results);
         this.anySedmlDocumentHasSucceeded |= hasSucceeded;
         this.anySedmlDocumentHasFailed &= hasSucceeded;
         logger.log(hasSucceeded ? Level.INFO : Level.ERROR, "Processing of SedML ({}) {}", stats.getSedmlName(), hasSucceeded ? "succeeded." : "failed!");
+        RunUtils.drawBreakLine("-", 100);
     }
 
     /**
@@ -162,23 +164,23 @@ public void postProcessessArchive() throws IOException {
         this.endTime_ms = System.currentTimeMillis();
         long elapsedTime_ms = this.endTime_ms - this.startTime_ms;
         double duration_s = elapsedTime_ms / 1000.0;
-        logger.info("Omex `" + inputFile.getName() + "` processing completed (" + duration_s + "s)");
+        logger.info("Omex `" + this.inputFile.getName() + "` processing completed (" + duration_s + "s)");
         //
         // failure if at least one of the documents in the omex archive fails
         //
-        if (anySedmlDocumentHasFailed) {
+        if (this.anySedmlDocumentHasFailed) {
             String error = " All sedml documents in this archive failed to execute";
-            if (anySedmlDocumentHasSucceeded) {        // some succeeded, some failed
+            if (this.anySedmlDocumentHasSucceeded) {        // some succeeded, some failed
                 error = " At least one document in this archive failed to execute";
             }
             BiosimulationLog.instance().updateOmexStatusYml(BiosimulationLog.Status.FAILED, duration_s);
             logger.error(error);
-            logOmexMessage.append(error);
-            cliRecorder.writeErrorList(new Exception("exception not recorded"), bioModelBaseName);
+            this.logOmexMessage.append(error);
+            this.cliRecorder.writeErrorList(new Exception("exception not recorded"), this.bioModelBaseName);
         } else {
             BiosimulationLog.instance().updateOmexStatusYml(BiosimulationLog.Status.SUCCEEDED, duration_s);
-            cliRecorder.writeFullSuccessList(bioModelBaseName);
-            logOmexMessage.append(" Done");
+            this.cliRecorder.writeFullSuccessList(this.bioModelBaseName);
+            this.logOmexMessage.append(" Done");
 
         }
         BiosimulationLog.instance().setOutputMessage("null", "null", "omex", logOmexMessage.toString());

vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java

@@ -94,29 +94,6 @@ private void replaceMetadataRdfFiles(Path zipFilePath) throws IOException {
         }
     }
 
-    public static void rename(String zipFileName, String entryOldName, String entryNewName) throws Exception {
-
-        /* Define ZIP File System Properties in HashMap */
-        Map<String, String> zip_properties = new HashMap<>();
-        /* We want to read an existing ZIP File, so we set this to False */
-        zip_properties.put("create", "false");
-
-        /* Specify the path to the ZIP File that you want to read as a File System */
-        URI zip_disk = URI.create("jar:file:/" + zipFileName);
-
-        /* Create ZIP file System */
-        try (FileSystem zipfs = FileSystems.newFileSystem(zip_disk, zip_properties)) {
-            /* Access file that needs to be renamed */
-            Path pathInZipfile = zipfs.getPath(entryOldName);
-            /* Specify new file name */
-            Path renamedZipEntry = zipfs.getPath(entryNewName);
-            logger.trace("About to rename an entry from ZIP File" + pathInZipfile.toUri());
-            /* Execute rename */
-            Files.move(pathInZipfile, renamedZipEntry, StandardCopyOption.ATOMIC_MOVE);
-            logger.trace("File successfully renamed");
-        }
-    }
-
     public List<String> getSedmlLocationsRelative(){
         Collection<ArchiveEntry> entries = this.archive.getEntries();
 
@@ -135,26 +112,16 @@ public List<String> getSedmlLocationsRelative(){
             sedmlMap.get(isMaster ? MASTER : REGULAR).add(entry);
         }
 
+        if (!sedmlMap.get(MASTER).isEmpty()) return sedmlMap.get(MASTER).stream().map(ArchiveEntry::getFilePath).toList();
+
         // Test corner cases
-        if (sedmlMap.get(MASTER).isEmpty()){
-            if (sedmlMap.get(REGULAR).isEmpty()) {
-                throw new RuntimeException("There are no SED-MLs in the archive to execute");
-            }
-            if (masterCount > 0) {
-                logger.warn("No SED-MLs are marked as master, so will run them all");
-            }
-            return sedmlMap.get(REGULAR).stream().map(ArchiveEntry::getFilePath).toList();
-        }
+        if (sedmlMap.get(REGULAR).isEmpty()) throw new RuntimeException("There are no SED-MLs in the archive to execute");
 
-        return sedmlMap.get(MASTER).stream().map(ArchiveEntry::getFilePath).toList();
-    }
+        if (masterCount > 0) logger.warn("No SED-MLs are marked as master, so will run them all");
 
-    private boolean isSedmlFormat(ArchiveEntry entry) {
-        URI format = entry.getFormat();
-        return format.getPath().contains("sedml") || format.getPath().contains("sed-ml");
+        return sedmlMap.get(REGULAR).stream().map(ArchiveEntry::getFilePath).toList();
     }
 
-
     public ArrayList<String> getSedmlLocationsAbsolute(){
         ArrayList<String> sedmlListAbsolute = new ArrayList<>();
         List<String> sedmlListRelative = this.getSedmlLocationsRelative();
@@ -165,9 +132,13 @@ public ArrayList<String> getSedmlLocationsAbsolute(){
         return sedmlListAbsolute;
     }
 
+    private boolean isSedmlFormat(ArchiveEntry entry) {
+        URI format = entry.getFormat();
+        return format.getPath().contains("sedml") || format.getPath().contains("sed-ml");
+    }
+
     public String getOutputPathFromSedml(String absoluteSedmlPath) {
         String outputPath = "";
-        //String sedmlName = absoluteSedmlPath.substring(absoluteSedmlPath.lastIndexOf(File.separator) + 1);
         List<String> sedmlListRelative = this.getSedmlLocationsRelative();
         for (String sedmlFileRelative : sedmlListRelative) {
             boolean check = absoluteSedmlPath.contains(Paths.get(sedmlFileRelative).normalize().toString());