Added appropriate exception catching for SBML errors when exproting to SEDML.

vcell-cli/src/main/java/org/vcell/cli/run/hdf5/Hdf5Writer.java

@@ -72,7 +72,7 @@ public static void writeHdf5(Hdf5DataContainer hdf5DataWrapper, File outDirForCu
                         masterHdf5.insertNumericAttributes(currentDatasetId, "times", Hdf5DataPreparer.getSpatialHdf5Attribute_Times(data));
                     }  
                     masterHdf5.insertFixedStringAttribute(currentDatasetId, "_type", data.datasetMetadata._type);
-                    masterHdf5.insertFixedStringAttributes(currentDatasetId, "scanParameterNames", Arrays.asList(data.dataSource.scanParameterNames));
+                    //masterHdf5.insertFixedStringAttributes(currentDatasetId, "scanParameterNames", Arrays.asList(data.dataSource.scanParameterNames));
                     masterHdf5.insertFixedStringAttributes(currentDatasetId, "sedmlDataSetDataTypes", data.datasetMetadata.sedmlDataSetDataTypes);
                     masterHdf5.insertFixedStringAttributes(currentDatasetId, "sedmlDataSetIds", data.datasetMetadata.sedmlDataSetIds);
 

vcell-cli/src/main/java/org/vcell/cli/vcml/ExportOmexBatchCommand.java

@@ -1,5 +1,6 @@
 package org.vcell.cli.vcml;
 
+import org.vcell.cli.vcml.ExportOmexCommand;
 import cbit.vcell.resource.PropertyLoader;
 
 import org.apache.logging.log4j.Level;
@@ -10,12 +11,18 @@
 import org.vcell.admin.cli.CLIDatabaseService;
 import org.vcell.cli.CLIRecorder;
 import org.vcell.sedml.ModelFormat;
+import org.vcell.sedml.SEDMLEventLog;
+import org.vcell.sedml.SEDMLEventLogFile;
 import org.vcell.util.DataAccessException;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.sql.SQLException;
 import java.util.concurrent.Callable;
 
@@ -64,23 +71,88 @@ public class ExportOmexBatchCommand implements Callable<Integer> {
     private boolean help;
 
     public Integer call() {
-        Level logLevel = bDebug ? Level.DEBUG : logger.getLevel();
+        Level logLevel = this.bDebug ? Level.DEBUG : logger.getLevel();
 
         LoggerContext config = (LoggerContext)(LogManager.getContext(false));
         config.getConfiguration().getLoggerConfig(LogManager.getLogger("org.vcell").getName()).setLevel(logLevel);
         config.getConfiguration().getLoggerConfig(LogManager.getLogger("cbit").getName()).setLevel(logLevel);
         config.updateLoggers();
-
+        final SEDMLEventLog sedmlEventLog;
         try {
-
             logger.debug("Batch export of omex files requested");
             PropertyLoader.loadProperties();
-            if (inputFilePath == null || !inputFilePath.exists() || !inputFilePath.isDirectory())
-                throw new RuntimeException("inputFilePath '" + (inputFilePath == null ? "" : inputFilePath) + "' is not a 'valid directory'");
-
-            if (outputFilePath.exists() && !outputFilePath.isDirectory())
-                throw new RuntimeException("outputFilePath '" + outputFilePath + "' is not a 'valid directory'");
+            File parentDir = new File(outputFilePath.getParent()).getCanonicalFile();
+            if (this.inputFilePath == null || !this.inputFilePath.exists() || !this.inputFilePath.isDirectory())
+                throw new RuntimeException("inputFilePath '" + (this.inputFilePath == null ? "" : this.inputFilePath) + "' is not a valid VCML archive");
+            if (this.outputFilePath == null || !this.outputFilePath.isDirectory())
+                throw new RuntimeException("outputFilePath '" + (this.outputFilePath == null ? "" : this.outputFilePath) + "' is not a valid target for OMEX archive");
+            if (parentDir.exists() && !parentDir.isDirectory()) {
+                throw new RuntimeException("directory for output '" + parentDir.getCanonicalPath() + "' is not a valid directory for OMEX archive");
+            }
+            if (!parentDir.exists())
+                if (!parentDir.mkdirs())
+                    throw new RuntimeException("Output dir doesn't exist and could not be made!");
+
+
+            if (bWriteLogFiles) {
+                sedmlEventLog = new SEDMLEventLogFile(new File(outputFilePath, "jobLog.txt"));
+            } else {
+                sedmlEventLog = (String entry) -> {};
+            }
+        } catch (IOException e){
+            throw new RuntimeException("Error in setting up batch execution:\n\t", e);
+        }
 
+        try {
+            PropertyLoader.loadProperties();
+
+            logger.debug("Batch export of omex files requested");
+            int numSuccessfulExports = 0, numTotalFiles = 0;
+            Path inputDirPath = this.inputFilePath.getCanonicalFile().toPath();
+            try (DirectoryStream<Path> dirStream = Files.newDirectoryStream(inputDirPath)){
+                for (Path child : dirStream){
+                    // Begin Setup
+                    File childFile, targetOutputFile;
+                    try {
+                        childFile = child.toFile();
+                        if (childFile.isDirectory()){
+                            continue;
+                        }
+                        if (!child.toString().endsWith(".vcml")){
+                            continue;
+                        }
+                        numTotalFiles++;
+
+                        String childFileFullName = childFile.getName();
+                        String outputFileName = childFileFullName.substring(0, childFileFullName.length() - 5);
+                        targetOutputFile = Paths.get(this.outputFilePath.getCanonicalPath(), outputFileName).toFile();
+                    } catch (IOException e){
+                        logger.error("Error setting up '" + child.getFileName() + "':\n\t", e);
+                        continue;
+                    }
+
+                    // Setup Complete, Begin Conversion.
+                    try {
+                        ExportOmexCommand.exportVCMLFile(childFile, targetOutputFile, this.outputModelFormat, sedmlEventLog,
+                                this.bWriteLogFiles, this.bValidateOmex, this.bSkipUnsupportedApps);
+                        logger.info("Conversion from '" + child.getFileName()
+                                + "' to '" + targetOutputFile.getName() + "' succeeded");
+                        numSuccessfulExports++;
+                    } catch (Exception e){
+                        logger.error("Conversion for '" + child.getFileName() + "' failed:\n\t", e);
+                    }
+                    logger.error("Continuing to next file to convert.\n\n");
+                }
+                logger.info(String.format("Batch mode complete.\n\t"
+                        + " %d/%d exports were successful.", numSuccessfulExports, numTotalFiles));
+            }
+
+        } catch (Exception e){
+            logger.error("Unexpected IO Error occurred, ending batch conversion");
+            throw new RuntimeException("Unexpected IO error occurred:\n\t", e);
+        }
+        return 0;
+        /* old methodology
             if (bOffline) this.runInOfflineMode();
             else this.run();
 
@@ -91,6 +163,7 @@ public Integer call() {
         } finally {
             logger.debug("Batch export completed");
         }
+        */
     }
 
     private void runInOfflineMode() throws IOException {

vcell-cli/src/main/java/org/vcell/cli/vcml/ExportOmexCommand.java

@@ -7,6 +7,7 @@
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.core.LoggerContext;
 import org.vcell.sedml.ModelFormat;
+import org.vcell.sedml.SEDMLEventLog;
 import org.vcell.util.DataAccessException;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
@@ -42,8 +43,8 @@ public class ExportOmexCommand implements Callable<Integer> {
     boolean bValidateOmex;
 
     public Integer call() {
-        Level logLevel = bDebug ? Level.DEBUG : logger.getLevel(); 
-        
+        Level logLevel = bDebug ? Level.DEBUG : logger.getLevel();
+
         LoggerContext config = (LoggerContext)(LogManager.getContext(false));
         config.getConfiguration().getLoggerConfig(LogManager.getLogger("org.vcell").getName()).setLevel(logLevel);
         config.getConfiguration().getLoggerConfig(LogManager.getLogger("cbit").getName()).setLevel(logLevel);
@@ -52,15 +53,35 @@ public Integer call() {
         try {
             PropertyLoader.loadProperties();
 
-            logger.debug("Beginning export");
-            VcmlOmexConverter.convertOneFile(
-                    inputFilePath, outputFilePath, outputModelFormat, bWriteLogFiles, bValidateOmex, bSkipUnsupportedApps);
-            return 0;
+            if (inputFilePath == null || !inputFilePath.exists() || !inputFilePath.isDirectory())
+                throw new RuntimeException("inputFilePath '" + (inputFilePath == null ? "" : inputFilePath) + "' is not a valid VCML archive");
+
+            if (outputFilePath == null || outputFilePath.isDirectory())
+                throw new RuntimeException("outputFilePath '" + (outputFilePath == null ? "" : outputFilePath) + "' is not a valid target for OMEX archive");
+
+            if (outputFilePath.exists())
+                this.logger.warn(String.format("File '%s' already exists."));
+
+            return ExportOmexCommand.exportVCMLFile(this.inputFilePath, this.outputFilePath,
+                    this.outputModelFormat, null, this.bWriteLogFiles, this.bValidateOmex, this.bSkipUnsupportedApps);
+
         } catch (Exception e) {
-            e.printStackTrace();
-            throw new RuntimeException(e.getMessage());
-        } finally {
-            logger.debug("Completed all exports");
+            throw new RuntimeException("Export failed with message:\n\t" + e.getMessage(), e);
+        }
+    }
+
+    public static int exportVCMLFile(File inputFilePath, File outputFilePath, ModelFormat outputModelFormat, SEDMLEventLog sedmlEventLog,
+                                     boolean bWriteLogFiles, boolean bValidateOmex, boolean bSkipUnsupportedApps)
+            throws Exception {
+        try {
+            logger.debug(String.format("Beginning export of '%s'", inputFilePath.getName()));
+            VcmlOmexConverter.convertOneFile(inputFilePath, outputFilePath, outputModelFormat, sedmlEventLog,
+                    bWriteLogFiles, bValidateOmex, bSkipUnsupportedApps);
+            logger.debug(String.format("Finished export of '%s'", inputFilePath.getName()));
+        } catch (Exception e){
+            logger.error(String.format("Error while exporting '%s'", inputFilePath.getName())); // We throw, no need to print error here
+            throw e;
         }
+        return 0;
     }
 }

vcell-cli/src/main/java/org/vcell/cli/vcml/VCMLConversionException.java

@@ -0,0 +1,19 @@
+package org.vcell.cli.vcml;
+
+public class VCMLConversionException extends Exception {
+    public VCMLConversionException(String message){
+        super(message);
+    }
+
+    public VCMLConversionException(String message, Throwable cause){
+        super(message, cause);
+    }
+
+    public VCMLConversionException(Throwable cause){
+        super(cause);
+    }
+
+    public VCMLConversionException(String message, Throwable cause, boolean enableSuppression, boolean writableStackTrace){
+        super(message, cause, enableSuppression, writableStackTrace);
+    }
+}

vcell-cli/src/main/java/org/vcell/cli/vcml/VcmlOmexConverter.java

@@ -14,6 +14,7 @@
 import org.apache.logging.log4j.Logger;
 import org.vcell.admin.cli.CLIDatabaseService;
 import org.vcell.sbml.OmexPythonUtils;
+import org.vcell.sbml.UnsupportedSbmlExportException;
 import org.vcell.sedml.*;
 import org.vcell.util.DataAccessException;
 import org.vcell.util.document.BioModelInfo;
@@ -42,6 +43,7 @@ public class VcmlOmexConverter {
 	public static void convertOneFile(File input,
 									  File outputDir,
 									  ModelFormat modelFormat,
+									  SEDMLEventLog passedInSedmlEventLog,
 									  boolean bWriteLogFiles,
 									  boolean bValidateOmex,
 									  boolean bSkipUnsupportedApps)
@@ -53,12 +55,15 @@ public static void convertOneFile(File input,
 		logger.debug("Beginning conversion of `" + input + "`");
 		Predicate<Simulation> simulationExportFilter = simulation -> true;
 		BioModelInfo bioModelInfo = null;
-		final SEDMLEventLog sedmlEventLog;
-		if (bWriteLogFiles) {
+		SEDMLEventLog sedmlEventLog;
+		if (passedInSedmlEventLog != null){
+			sedmlEventLog = passedInSedmlEventLog;
+		} else if (bWriteLogFiles) {
 			sedmlEventLog = new SEDMLEventLogFile(new File(outputDir, jobLogFileName));
 		} else {
 			sedmlEventLog = (String entry) -> {};
 		}
+
 		boolean bHasPython = true;
 		List<SEDMLTaskRecord> sedmlTaskRecords = SEDMLExporter.writeBioModel(
 				input,
@@ -204,19 +209,22 @@ public static void convertFilesNoDatabase(File inputDir, File outputDir, ModelFo
 						bSkipUnsupportedApps,
 						bHasPython,
 						bValidateOmex);
-				if (!sedmlTaskRecords.stream().anyMatch((SEDMLTaskRecord r) -> r.getTaskResult() == TaskResult.FAILED)) {
+				if (sedmlTaskRecords.stream().noneMatch((SEDMLTaskRecord r) -> r.getTaskResult() == TaskResult.FAILED)) {
 					logger.info("Combine archive created for `" + inputFileName + "`");
 				} else {
 					List<String> errorList = sedmlTaskRecords.stream()
 							.filter((SEDMLTaskRecord r) -> r.getTaskResult() == TaskResult.FAILED)
-							.map((SEDMLTaskRecord r) -> r.getCSV())
+							.map(SEDMLTaskRecord::getCSV)
 							.collect(Collectors.toList());
 					String msg = "Failed converting VCML to OMEX archive for `" + inputFileName + "`, errors: " + errorList;
 					logger.error(msg);
-					throw new RuntimeException(msg);
+					throw new VCMLConversionException(msg);
 				}
-			} catch (SEDMLExporter.SEDMLExportException | OmexPythonUtils.OmexValidationException e) {
+			} catch (SEDMLExporter.SEDMLExportException | OmexPythonUtils.OmexValidationException | VCMLConversionException e) {
 				logger.error("Failed converting VCML to OMEX archive for `" + inputFileName + "`", e);
+			} catch (Exception e){
+				logger.error("Unexpected Exception occurred while converting VCML:\n\t", e);
+				throw e;
 			}
 		}
 		logger.debug("Completed conversion of files in `" + inputDir + "`");

vcell-core/src/main/java/cbit/vcell/resource/PropertyLoader.java

@@ -247,6 +247,8 @@ public class PropertyLoader {
 	public static final String cmdSrvcSshCmdRestoreTimeoutFactor = record("vcell.ssh.cmd.restoretimeout", ValueType.GEN);
 
 	public static final String cliWorkingDir = record("cli.workingDir", ValueType.DIR);
+
+	public static final String vcellVcmlLocation = record("vcell.vcmlLocation", ValueType.DIR);
 
 	public static final String enableSpringSaLaD = record("vcell.enableSpringSaLaD", ValueType.BOOL);
 

vcell-core/src/main/java/org/vcell/sbml/OmexPythonUtils.java

@@ -77,8 +77,7 @@ private static List<OmexValidationError> getErrorsFromReport(JsonObject reportRo
     }
 
     private static int callCLIPython(String command, Path omexFile, Path tempDir, Path reportJsonFile) throws InterruptedException, IOException {
-        File installDir = PropertyLoader.getRequiredDirectory(PropertyLoader.installationRoot);
-        File cliPythonDir = Paths.get(installDir.getAbsolutePath(), "vcell-cli-utils").toAbsolutePath().toFile();
+        File cliPythonDir = PropertyLoader.getRequiredDirectory(PropertyLoader.cliWorkingDir).getCanonicalFile();
         ProcessBuilder pb = new ProcessBuilder(
                 "poetry", "run", "python",
                 "-m", "vcell_cli_utils.wrapper",