Adds BioSimulators Test Suite originating Omex archives for CLI execution tests

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

@@ -3,7 +3,7 @@
 import cbit.vcell.parser.ExpressionException;
 import cbit.vcell.solver.ode.ODESolverResultSet;
 
-import org.vcell.cli.CLIRecorder;
+import org.vcell.cli.CLIRecordable;
 import org.vcell.cli.PythonStreamException;
 import org.vcell.cli.vcml.VCMLHandler;
 import org.vcell.util.FileUtils;
@@ -22,7 +22,7 @@ public class ExecuteImpl {
 
     private final static Logger logger = LogManager.getLogger(ExecuteImpl.class);
 
-    public static void batchMode(File dirOfArchivesToProcess, File outputDir, CLIRecorder cliLogger,
+    public static void batchMode(File dirOfArchivesToProcess, File outputDir, CLIRecordable cliLogger,
                                  boolean bKeepTempFiles, boolean bExactMatchOnly, boolean bSmallMeshOverride) {
         FilenameFilter filter = (f, name) -> name.endsWith(".omex") || name.endsWith(".vcml");
         File[] inputFiles = dirOfArchivesToProcess.listFiles(filter);
@@ -67,7 +67,7 @@ public static void batchMode(File dirOfArchivesToProcess, File outputDir, CLIRec
         }
     }
 
-    public static void singleMode(File inputFile, File rootOutputDir, CLIRecorder cliLogger,
+    public static void singleMode(File inputFile, File rootOutputDir, CLIRecordable cliLogger,
             boolean bKeepTempFiles, boolean bExactMatchOnly, boolean bEncapsulateOutput, boolean bSmallMeshOverride) throws Exception {
         // Build statuses
         String bioModelBaseName = FileUtils.getBaseName(inputFile.getName()); // bioModelBaseName = input file without the path
@@ -81,7 +81,7 @@ public static void singleMode(File inputFile, File rootOutputDir, CLIRecorder cl
         ExecuteImpl.singleExecOmex(inputFile, rootOutputDir, cliLogger, bKeepTempFiles, bExactMatchOnly, bEncapsulateOutput, bSmallMeshOverride);
     }
 
-    public static void singleMode(File inputFile, File outputDir, CLIRecorder cliLogger) throws Exception {
+    public static void singleMode(File inputFile, File outputDir, CLIRecordable cliLogger) throws Exception {
         final boolean bKeepTempFiles = false;
         final boolean bExactMatchOnly = false;
         final boolean bEncapsulateOutput = false;
@@ -91,7 +91,7 @@ public static void singleMode(File inputFile, File outputDir, CLIRecorder cliLog
     }
 
     @Deprecated
-    public static void singleExecVcml(File vcmlFile, File outputDir, CLIRecorder cliLogger) {
+    public static void singleExecVcml(File vcmlFile, File outputDir, CLIRecordable cliLogger) {
         logger.warn("Using deprecated function to execute vcml");
         VCMLHandler.outputDir = outputDir.getAbsolutePath();
         logger.debug("Executing VCML file " + vcmlFile);
@@ -143,7 +143,7 @@ public static void singleExecVcml(File vcmlFile, File outputDir, CLIRecorder cli
         }
     }
 
-    private static void singleExecOmex(File inputFile, File rootOutputDir, CLIRecorder cliRecorder,
+    private static void singleExecOmex(File inputFile, File rootOutputDir, CLIRecordable cliRecorder,
             boolean bKeepTempFiles, boolean bExactMatchOnly, boolean bEncapsulateOutput, boolean bSmallMeshOverride) 
             throws ExecutionException, PythonStreamException, IOException, InterruptedException {
         ExecutionJob requestedExecution = new ExecutionJob(inputFile, rootOutputDir, cliRecorder, 

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

@@ -1,10 +1,6 @@
 package org.vcell.cli.run;
 
 public class ExecutionException extends Exception {
-    public ExecutionException(){
-        super();
-    }
-
     public ExecutionException(String message){
         super(message);
     }

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

@@ -1,6 +1,6 @@
 package org.vcell.cli.run;
 
-import org.vcell.cli.CLIRecorder;
+import org.vcell.cli.CLIRecordable;
 import org.vcell.cli.PythonStreamException;
 import org.vcell.util.FileUtils;
 
@@ -32,7 +32,7 @@ public class ExecutionJob {
     private Path sedmlPath2d3d;
     private File inputFile;
 
-    private CLIRecorder cliRecorder;
+    private CLIRecordable cliRecorder;
 
     /** 
      * Constructor to provide all necessary info.
@@ -45,7 +45,7 @@ public class ExecutionJob {
      * @param bEncapsulateOutput whether to provide a sub-folder for outputs (needed for batch jobs)
      * @param bSmallMeshOverride whether to use small meshes or standard meshes.
      */
-    public ExecutionJob(File inputFile, File rootOutputDir, CLIRecorder cliRecorder,
+    public ExecutionJob(File inputFile, File rootOutputDir, CLIRecordable cliRecorder,
             boolean bKeepTempFiles, boolean bExactMatchOnly, boolean bEncapsulateOutput, boolean bSmallMeshOverride){
         this();
         this.inputFile = inputFile;
@@ -139,8 +139,9 @@ public void executeArchive() throws InterruptedException, PythonStreamException,
             logger.error("Python-processing encountered fatal error. Execution is unable to properly continue.", e);
             throw e;
         } catch(InterruptedException|IOException e){
-            logger.error("System IO encountered a fatal error");
-            throw new ExecutionException();
+            String message = "System IO encountered a fatal error";
+            logger.error(message, e);
+            throw new ExecutionException(message, e);
         } 
     }
 

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

@@ -1,14 +1,15 @@
 package org.vcell.cli.run;
 
+import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
+
 import cbit.vcell.parser.ExpressionException;
 import cbit.vcell.resource.OperatingSystemInfo;
 import cbit.vcell.xml.ExternalDocInfo;
-import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
-
-import org.jlibsedml.*;
-
 import org.apache.commons.io.FilenameUtils;
-import org.vcell.cli.CLIRecorder;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.jlibsedml.*;
+import org.vcell.cli.CLIRecordable;
 import org.vcell.cli.PythonStreamException;
 import org.vcell.cli.run.hdf5.Hdf5DatasetWrapper;
 import org.vcell.cli.run.hdf5.Hdf5FileWrapper;
@@ -17,13 +18,10 @@
 import org.vcell.util.FileUtils;
 import org.vcell.util.GenericExtensionFilter;
 
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
-
 import java.io.File;
-import java.io.IOException;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -33,13 +31,13 @@
 
 public class SedmlJob {
     private boolean somethingFailed, hasScans, hasOverrides, bKeepTempFiles, bExactMatchOnly, bSmallMeshOverride;
-    private String sedmlLocation, bioModelBaseName, resultsDirPath, logDocumentMessage, logDocumentError, sedmlName;
+    private String sedmlLocation, bioModelBaseName, resultsDirPath, logDocumentMessage, logDocumentError, sedmlName, problemsOccured;
     private StringBuilder logOmexMessage;
     private SedmlStatistics docStatistics;
     private SedML sedml;
     private File masterOmexArchive, rootOutputDir, plotsDirectory, plotFile;
     private List<Output> outputs;
-    private CLIRecorder cliRecorder;
+    private CLIRecordable cliRecorder;
     private File outDirForCurrentSedml;
 
     private final static Logger logger = LogManager.getLogger(SedmlJob.class);
@@ -60,7 +58,7 @@ public class SedmlJob {
      * @param logOmexMessage a string-builder to contain progress updates of omex execution
      */
     public SedmlJob(String sedmlLocation, OmexHandler omexHandler, File masterOmexArchive, File rootOutputDir, String resultsDirPath, String sedmlPath2d3dString,
-            CLIRecorder cliRecorder, boolean bKeepTempFiles, boolean bExactMatchOnly, boolean bSmallMeshOverride, StringBuilder logOmexMessage){
+                    CLIRecordable cliRecorder, boolean bKeepTempFiles, boolean bExactMatchOnly, boolean bSmallMeshOverride, StringBuilder logOmexMessage){
         this.somethingFailed = false;
         this.masterOmexArchive = masterOmexArchive;
         this.sedmlLocation = sedmlLocation;
@@ -77,6 +75,7 @@ public SedmlJob(String sedmlLocation, OmexHandler omexHandler, File masterOmexAr
         this.cliRecorder = cliRecorder;
         this.logDocumentMessage = "Initializing SED-ML document... ";
         this.logDocumentError = "";
+        this.problemsOccured = "";
 
     }
 
@@ -269,13 +268,13 @@ private void processOutputs(SolverHandler solverHandler) throws PythonStreamExce
             logDocumentError += e.getMessage();
             this.reportProblem(e);
             org.apache.commons.io.FileUtils.deleteDirectory(this.plotsDirectory);    // removing temp path generated from python
-            throw new ExecutionException();
+            throw new ExecutionException("error while processing outputs: "+e.getMessage(), e);
         }
     }
 
     private boolean evalulateResults() throws PythonStreamException, InterruptedException, IOException {
         if (this.somethingFailed) {        // something went wrong but no exception was fired
-            Exception e = new RuntimeException("Failure executing the sed document. ");
+            Exception e = new RuntimeException("Failure executing the sed document:\n" + this.problemsOccured);
             logDocumentError += e.getMessage();
             this.reportProblem(e);
             org.apache.commons.io.FileUtils.deleteDirectory(this.plotsDirectory);    // removing temp path generated from python
@@ -384,10 +383,11 @@ private static Path getRelativePath(String[] tokenizedPath){
         return null;
     }
 
-    private static boolean somethingDidFail(){
+    private boolean somethingDidFail(){
         StackTraceElement elem = new Exception().getStackTrace()[1];
-
-        logger.debug(String.format("Something failed in %s @ line %d", elem.getClassName(), elem.getLineNumber()));
+        String failString = String.format("Something failed in %s @ line %d", elem.getClassName(), elem.getLineNumber());
+        this.problemsOccured += failString + '\n';
+        logger.debug(failString);
         return true;
     }
 

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

@@ -37,7 +37,7 @@
 import org.jlibsedml.XPathTarget;
 import org.jlibsedml.modelsupport.SBMLSupport;
 import org.jmathml.ASTNode;
-import org.vcell.cli.CLIRecorder;
+import org.vcell.cli.CLIRecordable;
 import org.vcell.sbml.vcell.SBMLImportException;
 import org.vcell.sbml.vcell.SBMLImporter;
 import org.vcell.util.ISize;
@@ -281,7 +281,7 @@ public void initialize(List<BioModel> bioModelList, SedML sedml) throws Expressi
         System.out.println("topTaskToBaseTask: " + topTaskToBaseTask.size());
     }
 
-    public void simulateAllTasks(ExternalDocInfo externalDocInfo, SedML sedml, CLIRecorder cliLogger,
+    public void simulateAllTasks(ExternalDocInfo externalDocInfo, SedML sedml, CLIRecordable cliLogger,
                                  File outputDirForSedml, String outDir, String outputBaseDir, String sedmlLocation,
                                  boolean keepTempFiles, boolean exactMatchOnly, boolean bSmallMeshOverride) throws Exception {
         // create the VCDocument(s) (bioModel(s) + application(s) + simulation(s)), do sanity checks