[WIP] Returning solver handler results for recording

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

@@ -5,16 +5,18 @@
 
 public interface CLIRecordable {
 
-    public void writeDetailedErrorList(String message) throws IOException;
+    void writeDetailedErrorList(String message) throws IOException;
 
-    public void writeFullSuccessList(String message) throws IOException;
+    void writeFullSuccessList(String message) throws IOException;
 
-    public void writeErrorList(String message) throws IOException;
+    void writeErrorList(String message) throws IOException;
 
-    public void writeDetailedResultList(String message) throws IOException;
+    void writeDetailedResultList(String message) throws IOException;
+
+    void writeDetailedSimBreakdown(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(String message) throws IOException;
+    void writeImportErrorList(String message) throws IOException;
 }

vcell-cli/src/main/java/org/vcell/cli/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, detailedSimBreakdown, spatialLog, importErrorLog;
     protected File outputDirectory;
 
     // Note: this constructor is not public
@@ -86,6 +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.detailedSimBreakdown = logManager.requestNewRecord(Paths.get(this.outputDirectory.getAbsolutePath(), "detailedSimBreakdown.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());
 
@@ -152,6 +153,15 @@ public void writeDetailedResultList(String message) throws IOException {
         this.writeToFileLog(this.detailedResultsLog, message);
     }
 
+    /**
+     * Write to `detailedSimBreakdown.txt`
+     *
+     * @param message string to write to file
+     */
+    public void writeDetailedSimBreakdown(String message) throws IOException {
+        this.writeToFileLog(this.detailedSimBreakdown, message);
+    }
+
 
     /**
      * Write to `hasSpatialLog.txt`

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

@@ -16,7 +16,7 @@
 import java.util.concurrent.Callable;
 import java.util.Date;
 
-@Command(name = "execute", description = "run .vcml or .omex files via Python API")
+@Command(name = "execute", description = "run .vcml or .omex files")
 public class ExecuteCommand implements Callable<Integer> {
 
     private final static Logger logger = org.apache.logging.log4j.LogManager.getLogger(ExecuteCommand.class);
@@ -100,7 +100,7 @@ public Integer call() {
                     bKeepTempFiles, bExactMatchOnly, bEncapsulateOutput, 
                     EXECUTABLE_MAX_WALLCLOCK_MILLIS, help, bDebug, bQuiet
             );
-            logger.trace(trace_args);
+            logger.debug(trace_args);
 
             logger.debug("Validating CLI arguments");
             if (bDebug && bQuiet) {

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

@@ -44,7 +44,7 @@ public static void batchMode(File dirOfArchivesToProcess, File outputDir, CLIRec
 
             logger.info("Preparing output directory...");
             // we don't want to accidentally delete the input...
-            // if the output is a subset of the input file's housing directory, we shouldn't delete!!
+            // if the output directory is a subset of the input file's housing directory, we shouldn't delete!!
             if (!inputFile.getParentFile().getCanonicalPath().contains(adjustedOutputDir.getCanonicalPath()))
                 RunUtils.removeAndMakeDirs(adjustedOutputDir);
             try {

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

@@ -0,0 +1,67 @@
+package org.vcell.cli.run;
+
+import cbit.vcell.biomodel.BioModel;
+import cbit.vcell.solver.TempSimulation;
+import org.vcell.util.Pair;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class RunResults {
+    private final Map<BioModel, List<TempSimulation>> bioModelToListOfTemp;
+    private final Map<TempSimulation, Pair<Status, Integer>> tempSimulationToStatus;
+
+    public RunResults() {
+        this.bioModelToListOfTemp = new HashMap<>();
+        this.tempSimulationToStatus = new HashMap<>();
+    }
+
+    public List<TempSimulation> getTempSimulations(BioModel bioModel) {
+        return this.bioModelToListOfTemp.get(bioModel);
+    }
+
+    public Pair<Status, Integer> getStatus(BioModel bioModel, TempSimulation tempSimulation) {
+        return this.bioModelToListOfTemp.containsKey(bioModel) ? null : tempSimulationToStatus.get(tempSimulation);
+    }
+
+    public void setStatus(BioModel bioModel, TempSimulation tempSimulation, Integer duration) {
+        this.setStatus(bioModel, tempSimulation, null, duration);
+    }
+
+    public void setStatus(BioModel bioModel, TempSimulation tempSimulation, Status status) {
+        this.setStatus(bioModel, tempSimulation, status, null);
+    }
+
+    public void setStatus(BioModel bioModel, TempSimulation tempSimulation, Status status, Integer duration){
+        if (!this.bioModelToListOfTemp.containsKey(bioModel)) this.bioModelToListOfTemp.put(bioModel, new ArrayList<>());
+        List<TempSimulation> relevantSims = this.bioModelToListOfTemp.get(bioModel);
+        if (!relevantSims.contains(tempSimulation)) this.bioModelToListOfTemp.get(bioModel).add(tempSimulation);
+        if (!this.tempSimulationToStatus.containsKey(tempSimulation)) {
+            this.tempSimulationToStatus.put(tempSimulation, new Pair<>(status, duration));
+        }
+        Pair<Status, Integer> previousStatuses = this.tempSimulationToStatus.get(tempSimulation);
+        if (status != null){
+            this.tempSimulationToStatus.put(tempSimulation, new Pair<>(status, previousStatuses.two));
+            previousStatuses = this.tempSimulationToStatus.get(tempSimulation);
+        }
+
+        if (duration != null){
+            this.tempSimulationToStatus.put(tempSimulation, new Pair<>(previousStatuses.one, duration));
+        }
+    }
+
+    public List<IndividualResult> generateRecordsOfResults(){
+        List<IndividualResult> results = new ArrayList<>();
+        for (BioModel bm : this.bioModelToListOfTemp.keySet()) {
+            for (TempSimulation ts : this.bioModelToListOfTemp.get(bm)) {
+                Pair<Status, Integer> statusAndDuration = this.tempSimulationToStatus.get(ts);
+                results.add(new IndividualResult(bm, ts, statusAndDuration.one, statusAndDuration.two));
+            }
+        }
+        return results;
+    }
+
+    public record IndividualResult(BioModel bioModel, TempSimulation tempSimulation, Status status, Integer duration) {}
+}

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

@@ -1,5 +1,6 @@
 package org.vcell.cli.run;
 
+import cbit.vcell.biomodel.BioModel;
 import cbit.vcell.resource.OperatingSystemInfo;
 import cbit.vcell.xml.ExternalDocInfo;
 import org.apache.commons.io.FilenameUtils;
@@ -228,7 +229,6 @@ public boolean simulateSedml(HDF5ExecutionResults masterHdf5File) throws Interru
         ExternalDocInfo externalDocInfo = new ExternalDocInfo(this.MASTER_OMEX_ARCHIVE, true);
 
         this.runSimulations(solverHandler, externalDocInfo);
-        this.recordRunDetails(solverHandler);
         Span span = null;
         try {
             span = Tracer.startSpan(Span.ContextType.PROCESSING_SIMULATION_OUTPUTS, "processOutputs", null);
@@ -244,7 +244,7 @@ public boolean simulateSedml(HDF5ExecutionResults masterHdf5File) throws Interru
         return this.evaluateResults();
     }
 
-    private void runSimulations(SolverHandler solverHandler, ExternalDocInfo externalDocInfo) throws IOException {
+    private void runSimulations(SolverHandler solverHandler, ExternalDocInfo externalDocInfo) {
         /*
          * - Run solvers and make reports; all failures/exceptions are being caught
          * - we send both the whole OMEX file and the extracted SEDML file path
@@ -256,10 +256,11 @@ private void runSimulations(SolverHandler solverHandler, ExternalDocInfo externa
             String str = "Building solvers and starting simulation of all tasks... ";
             logger.info(str);
             this.logDocumentMessage += str;
-            solverHandler.simulateAllTasks(externalDocInfo, this.sedml, this.CLI_RECORDER,
+            RunResults results = solverHandler.simulateAllTasks(externalDocInfo, this.sedml, this.CLI_RECORDER,
                     this.OUTPUT_DIRECTORY_FOR_CURRENT_SEDML, this.RESULTS_DIRECTORY_PATH,
                     this.ROOT_OUTPUT_DIR.getAbsolutePath(), this.SEDML_LOCATION, this.SHOULD_KEEP_TEMP_FILES,
                     this.ACCEPT_EXACT_MATCH_ONLY, this.SHOULD_OVERRIDE_FOR_SMALL_MESH);
+            this.recordRunDetails(solverHandler, results);
         } catch (Exception e) {
             Throwable currentTierOfException = e;
             StringBuilder errorMessage = new StringBuilder();
@@ -277,8 +278,6 @@ private void runSimulations(SolverHandler solverHandler, ExternalDocInfo externa
                 span.close();
             }
         }
-
-        this.recordRunDetails(solverHandler);
     }
 
     private void processOutputs(SolverHandler solverHandler, HDF5ExecutionResults masterHdf5File) throws InterruptedException, ExecutionException, PythonStreamException {
@@ -466,17 +465,27 @@ private void reportProblem(Exception e) throws PythonStreamException, Interrupte
         PythonCalls.updateSedmlDocStatusYml(this.SEDML_LOCATION, Status.FAILED, this.RESULTS_DIRECTORY_PATH);
     }
 
-    private void recordRunDetails(SolverHandler solverHandler) throws IOException {
-        String message = this.DOC_STATISTICS.getNumModels() + ",";
-        message += this.DOC_STATISTICS.getNumSimulations() + ",";
-        message += this.DOC_STATISTICS.getNumTasks() + ",";
-        message += this.DOC_STATISTICS.getNumOutputs() + ",";
+    private void recordRunDetails(SolverHandler solverHandler, RunResults results) throws IOException {
+        StringBuilder generalMessage = new StringBuilder(this.BIOMODEL_BASE_NAME + ",");
+        generalMessage.append(this.DOC_STATISTICS.getNumModels()).append(",");
+        generalMessage.append(this.DOC_STATISTICS.getNumSimulations()).append(",");
+        generalMessage.append(this.DOC_STATISTICS.getNumTasks()).append(",");
+        generalMessage.append(this.DOC_STATISTICS.getNumOutputs()).append(",");
 
-        message += solverHandler.countBioModels + ",";
-        message += this.hasOverrides + ",";
-        message += this.hasScans + ",";
-        message += solverHandler.countSuccessfulSimulationRuns;
-        this.CLI_RECORDER.writeDetailedResultList(this.BIOMODEL_BASE_NAME + "," + message);
-        logger.debug(message);
+        generalMessage.append(solverHandler.countBioModels).append(",");
+        generalMessage.append(this.hasOverrides).append(",");
+        generalMessage.append(this.hasScans).append(",");
+        generalMessage.append(solverHandler.countSuccessfulSimulationRuns);
+        this.CLI_RECORDER.writeDetailedResultList(generalMessage.toString());
+
+        for (RunResults.IndividualResult result : results.generateRecordsOfResults()){
+            String individualMessage = result.bioModel() + "," +
+                    result.tempSimulation() + "," +
+                    result.duration() + "," +
+                    result.status() + ",";
+            this.CLI_RECORDER.writeDetailedSimBreakdown(individualMessage);
+        }
+
+        logger.debug(generalMessage.toString());
     }
 }