Removed Python from CLI

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

@@ -46,7 +46,10 @@ public class CLIPythonManager {
     /**
      * Retrieve the Python Manager, or create and return if it doesn't exist.
      * @return the manager
+     * @deprecated CLIPythonManager is no longer used in CLI, and has no current use; should this be used again
+     * you need to check whether there are still bugs with Arm Macs, and whether single-instance python shells are not a viable alternative
      */
+    @Deprecated
     public static CLIPythonManager getInstance(){
         lg.trace("Getting Python instance");
         if (instance == null){
@@ -62,7 +65,9 @@ public static CLIPythonManager getInstance(){
      * @param arguments the arguments to provide to the function call, each as their own string, in the correct order
      * @return the return response from Python
      * @throws PythonStreamException if there is any exception encountered in this exchange.
+     * @deprecated See getInstance()
      */
+    @Deprecated
     public String callPython(String functionName, String... arguments) throws PythonStreamException {
         String command = this.formatPythonFunctionCall(functionName, arguments);
         try {
@@ -82,7 +87,9 @@ public String callPython(String functionName, String... arguments) throws Python
      * @param cliCommand the command to run
      * @throws InterruptedException if the python process was interrupted
      * @throws IOException if there was a system IO failure
+     * @deprecated See getInstance()
      */
+    @Deprecated
     private static String callNonSharedPython(String cliCommand)
             throws InterruptedException, IOException, PythonStreamException {
         Path cliWorkingDir = Paths.get(PropertyLoader.getRequiredProperty(PropertyLoader.cliWorkingDir));
@@ -96,7 +103,9 @@ private static String callNonSharedPython(String cliCommand)
      * Shuts down the python session and cleans up.
      * 
      * @throws IOException if there is a system IO issue.
+     * @deprecated See getInstance()
      */
+    @Deprecated
     public void closePythonProcess() throws IOException {
         // Exit the living Python Process
         lg.debug("Closing Python Instance");
@@ -122,7 +131,9 @@ public void closePythonProcess() throws IOException {
      * as means of installation verification.
      * 
      * @throws IOException if there is a problem with System I/O
+     * @deprecated this entire system is unstable on ARM Macs, and still a bit slow.
      */
+    @Deprecated
     public void instantiatePythonProcess() throws IOException, PythonStreamException {
         if (this.pythonProcess != null) return; // prevent override
         lg.info("Initializing Python...");
@@ -338,10 +349,26 @@ private static String runAndPrintProcessStreams(ProcessBuilder pb, String outStr
         return os;
     }
 
+    /**
+     * Checks whether python returned successfully or not
+     * @param returnedString
+     * @throws PythonStreamException
+     * @deprecated See getInstance()
+     */
+    @Deprecated
     public void parsePythonReturn(String returnedString) throws PythonStreamException {
        this.parsePythonReturn(returnedString, null, null);
     }
 
+    /**
+     * Checks whether python returned successfully or not
+     * @param returnedString
+     * @param outString
+     * @param errString
+     * @throws PythonStreamException
+     * @deprecated See getInstance()
+     */
+    @Deprecated
     public void parsePythonReturn(String returnedString, String outString, String errString) throws PythonStreamException {
         boolean DEBUG_NORMAL_OUTPUT = lg.isTraceEnabled(); // Consider getting rid of this, currently redundant
         String ERROR_PHRASE1 = "Traceback", ERROR_PHRASE2 = "File \"<stdin>\"";

vcell-cli/src/main/java/org/vcell/cli/biosimulation/BiosimulationsCommand.java

@@ -42,10 +42,10 @@ public class BiosimulationsCommand implements Callable<Integer> {
     private boolean help;
 
     public Integer call() {
-        CLIRecorder cliRecorder = null;
+        CLIRecorder cliRecorder;
         int returnCode;
 
-        if ((returnCode = this.noFurtherActionNeeded(bQuiet, bDebug, bVersion)) != -1)
+        if ((returnCode = BiosimulationsCommand.noFurtherActionNeeded(bQuiet, bDebug, bVersion)) != -1)
             return returnCode;
 
         try {
@@ -94,21 +94,14 @@ public Integer call() {
             logger.info("Beginning execution");
             File tmpDir = Files.createTempDirectory("VCell_CLI_" + Long.toHexString(new Date().getTime())).toFile();
             try {
-                CLIPythonManager.getInstance().instantiatePythonProcess();
                 ExecuteImpl.singleMode(ARCHIVE, tmpDir, cliRecorder, true);
-                CLIPythonManager.getInstance().closePythonProcess(); // Give the process time to finish
                 if (!Tracer.hasErrors()) return 0;
                 if (!bQuiet) {
                     logger.error("Errors occurred during execution");
                     Tracer.reportErrors(bDebug);
                 }
                 return 1;
             } finally {
-                try {
-                    CLIPythonManager.getInstance().closePythonProcess(); // WARNING: Python will need reinstantiation after this is called
-                } catch (Exception e) {
-                    logger.error(e.getMessage(), e);
-                }
                 logger.debug("Finished all execution.");
                 FileUtils.copyDirectoryContents(tmpDir, OUT_DIR, true, null);
             }
@@ -121,7 +114,7 @@ public Integer call() {
         }
     }
 
-    private int noFurtherActionNeeded(boolean bQuiet, boolean bDebug, boolean bVersion){
+    private static int noFurtherActionNeeded(boolean bQuiet, boolean bDebug, boolean bVersion){
         logger.debug("Validating CLI arguments");
         if (bVersion) {
             String version = PropertyLoader.getRequiredProperty(PropertyLoader.vcellSoftwareVersion);

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

@@ -110,8 +110,6 @@ public Integer call() {
                 System.err.println("cannot specify both debug and quiet, try --help for usage");
                 return 1;
             }
-
-            CLIPythonManager.getInstance().instantiatePythonProcess();
 
 
             Executable.setGlobalTimeoutMS(EXECUTABLE_MAX_WALLCLOCK_MILLIS);
@@ -132,7 +130,7 @@ public Integer call() {
                             bEncapsulateOutput, bSmallMeshOverride);
                 }
             }
-            CLIPythonManager.getInstance().closePythonProcess();
+
             // WARNING: Python needs re-instantiation once the above line is called!
             FileUtils.copyDirectoryContents(tmpDir, outputFilePath, true, null);
             return 0;

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

@@ -108,7 +108,8 @@ public static void batchMode(File dirOfArchivesToProcess, File outputDir, CLIRec
 
     private static void runSingleExecOmex(File inputFile, File outputDir, CLIRecordable cliLogger, boolean bKeepTempFiles,
                                           boolean bExactMatchOnly, boolean bSmallMeshOverride)
-            throws IOException, ExecutionException, PythonStreamException, InterruptedException, BiosimulationsHdfWriterException {
+            throws IOException, ExecutionException, PythonStreamException, BiosimulationsHdfWriterException {
+
         String bioModelBaseName = inputFile.getName().substring(0, inputFile.getName().indexOf(".")); // ".omex"??
         Files.createDirectories(Paths.get(outputDir.getAbsolutePath() + File.separator + bioModelBaseName)); // make output subdir
         final boolean bEncapsulateOutput = true;

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

@@ -93,16 +93,14 @@ public Integer call() {
             config.updateLoggers();
 
 
-            CLIPythonManager.getInstance().instantiatePythonProcess();
-
             Executable.setGlobalTimeoutMS(EXECUTABLE_MAX_WALLCLOCK_MILLIS);
             logger.info("Beginning execution");
             File tmpDir = Files.createTempDirectory("VCell_CLI_" + Long.toHexString(new Date().getTime())).toFile();
 
             Tracer.clearTraceEvents();
             ExecuteImpl.singleMode(inputFilePath, tmpDir, cliTracer, bKeepTempFiles, bExactMatchOnly,
                             bEncapsulateOutput, bSmallMeshOverride);
-            CLIPythonManager.getInstance().closePythonProcess();
+
             // WARNING: Python needs re-instantiation once the above line is called!
             FileUtils.copyDirectoryContents(tmpDir, outputFilePath, true, null);
             final OmexExecSummary omexExecSummary;

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

@@ -26,8 +26,7 @@ public class ExecutionJob {
 
     private long startTime_ms, endTime_ms;
     private boolean bExactMatchOnly, bSmallMeshOverride, bKeepTempFiles;
-    private StringBuilder logOmexMessage;
-    private String inputFilePath;
+    private final StringBuilder logOmexMessage;
     private String bioModelBaseName;
     private String outputDir;
     private boolean anySedmlDocumentHasSucceeded = false;    // set to true if at least one sedml document run is successful
@@ -56,8 +55,7 @@ public ExecutionJob(File inputFile, File rootOutputDir, CLIRecordable cliRecorde
         this();
         this.inputFile = inputFile;
         this.cliRecorder = cliRecorder;
-
-        this.inputFilePath = inputFile.getAbsolutePath();
+
         this.bioModelBaseName = FileUtils.getBaseName(inputFile.getName()); // input file without the path
         String outputBaseDir = rootOutputDir.getAbsolutePath();
         this.outputDir = bEncapsulateOutput ? Paths.get(outputBaseDir, bioModelBaseName).toString() : outputBaseDir;
@@ -67,7 +65,7 @@ public ExecutionJob(File inputFile, File rootOutputDir, CLIRecordable cliRecorde
     }
 
     private ExecutionJob(){
-        this.logOmexMessage = new StringBuilder("");
+        this.logOmexMessage = new StringBuilder();
     }
 
     /**
@@ -77,29 +75,29 @@ private ExecutionJob(){
      * @throws PythonStreamException if calls to the python-shell instance are not working correctly
      * @throws IOException if there are system I/O issues.
      */
-    public void preprocessArchive() throws PythonStreamException, IOException {
+    public void preprocessArchive() throws IOException {
         // Start the clock
         this.startTime_ms = System.currentTimeMillis();
 
         // Beginning of Execution
         logger.info("Executing OMEX archive `{}`", this.inputFile.getName());
-        logger.info("Archive location: {}", this.inputFilePath);
+        logger.info("Archive location: {}", this.inputFile.getAbsolutePath());
         RunUtils.drawBreakLine("-", 100);
 
         // 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.inputFilePath, this.outputDir);
+            this.omexHandler = new OmexHandler(this.inputFile.getAbsolutePath(), this.outputDir);
             this.omexHandler.extractOmex();
             this.sedmlLocations = this.omexHandler.getSedmlLocationsAbsolute();
         } catch (IOException e){
-            String error = e.getMessage() + ", error for OmexHandler with " + this.inputFilePath;
+            String error = e.getMessage() + ", error for OmexHandler with " + this.inputFile.getAbsolutePath();
             this.cliRecorder.writeErrorList(e, this.bioModelBaseName);
             this.cliRecorder.writeDetailedResultList(this.bioModelBaseName + ", " + "IO error with OmexHandler");
             logger.error(error);
             throw new RuntimeException(error, e);
         } catch (Exception e) {
-            String error = e.getMessage() + ", error for archive " + this.inputFilePath;
+            String error = e.getMessage() + ", error for archive " + this.inputFile.getAbsolutePath();
             logger.error(error);
             if (this.omexHandler != null) this.omexHandler.deleteExtractedOmex();
             this.cliRecorder.writeErrorList(e, this.bioModelBaseName);

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

@@ -172,7 +172,7 @@ public boolean preProcessDoc() throws PythonStreamException, InterruptedExceptio
             Path path = Paths.get(this.plotFile.getAbsolutePath());
             if (!Files.exists(path)){
                 // SED-ML file generated by python VCell_cli_util
-                PythonCalls.genSedmlForSed2DAnd3D(this.MASTER_OMEX_ARCHIVE.getAbsolutePath(), this.RESULTS_DIRECTORY_PATH);
+                //PythonCalls.genSedmlForSed2DAnd3D(this.MASTER_OMEX_ARCHIVE.getAbsolutePath(), this.RESULTS_DIRECTORY_PATH);
             }
             if (!Files.exists(path)) {
                 String message = "Failed to create plot file " + this.plotFile.getAbsolutePath();
@@ -379,7 +379,7 @@ private void generateCSV(SolverHandler solverHandler) throws DataAccessException
 
     private void generatePlots() throws PythonStreamException, InterruptedException, IOException {
         logger.info("Generating Plots... ");
-        PythonCalls.genPlotsPseudoSedml(this.SEDML_LOCATION, this.OUTPUT_DIRECTORY_FOR_CURRENT_SEDML.toString());    // generate the plots
+        //PythonCalls.genPlotsPseudoSedml(this.SEDML_LOCATION, this.OUTPUT_DIRECTORY_FOR_CURRENT_SEDML.toString());    // generate the plots
         // We assume if no exception is returned that the plots pass
         for (Output output : this.sedml.getOutputs()){
             if (!(output instanceof Plot2D plot)) continue;

vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java

@@ -43,13 +43,11 @@ public static void setup() throws PythonStreamException, IOException {
 		PropertyLoader.setProperty(PropertyLoader.cliWorkingDir, new File("../vcell-cli-utils").getAbsolutePath());
 		VCMongoMessage.enabled = false;
 
-		CLIPythonManager.getInstance().instantiatePythonProcess();
 		omexTestCases = OmexTestingDatabase.loadOmexTestCases();
 	}
 
 	@AfterAll
 	public static void teardown() throws Exception {
-		CLIPythonManager.getInstance().closePythonProcess();
 		VCellUtilityHub.shutdown();
 	}
 

vcell-cli/src/test/java/org/vcell/cli/run/ExecuteImplTest.java

@@ -26,7 +26,6 @@ public void test_singleExecOmex() throws Exception {
         PropertyLoader.setProperty(PropertyLoader.cliWorkingDir, new File("../vcell-cli-utils").getAbsolutePath());
         VCMongoMessage.enabled = false;
         try {
-            CLIPythonManager.getInstance().instantiatePythonProcess();
 
             InputStream omexInputStream = ExecuteImplTest.class.getResourceAsStream("/BioModel1.omex");
             File tempOutputDir = Files.createTempDirectory("ExecuteImplTest_temp").toFile();
@@ -46,7 +45,6 @@ public void test_singleExecOmex() throws Exception {
             tempOmexFile.delete();
 
         } finally {
-            CLIPythonManager.getInstance().closePythonProcess();
         }
     }
 }

vcell-cli/src/test/java/org/vcell/cli/run/QuantOmexExecTest.java

@@ -40,12 +40,10 @@ public static void setup() throws PythonStreamException, IOException {
 		PropertyLoader.setProperty(PropertyLoader.cliWorkingDir, new File("../vcell-cli-utils").getAbsolutePath());
 		VCMongoMessage.enabled = false;
 
-		CLIPythonManager.getInstance().instantiatePythonProcess();
 	}
 
 	@AfterAll
 	public static void teardown() throws Exception {
-		CLIPythonManager.getInstance().closePythonProcess();
 		VCellUtilityHub.shutdown();
 	}
 

vcell-cli/src/test/java/org/vcell/cli/run/SpatialExecTest.java

@@ -49,13 +49,10 @@ public static void setup() throws PythonStreamException, IOException {
         config.updateLoggers();
         config.getConfiguration().getLoggerConfig(LogManager.getLogger("io.jhdf").getName()).setLevel(Level.WARN);
         config.updateLoggers();
-
-        CLIPythonManager.getInstance().instantiatePythonProcess();
     }
 
     @AfterAll
     public static void teardown() throws Exception {
-        CLIPythonManager.getInstance().closePythonProcess();
         VCellUtilityHub.shutdown();
     }