Extension to the temp directory usage

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

@@ -9,11 +9,14 @@
 import org.vcell.cli.CLIRecorder;
 import org.vcell.cli.run.ExecuteImpl;
 import org.vcell.cli.trace.Tracer;
+import org.vcell.util.FileUtils;
 import org.vcell.util.exe.Executable;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
 
 import java.io.File;
+import java.nio.file.Files;
+import java.util.Date;
 import java.util.concurrent.Callable;
 
 @Command(name = "biosimulations", description = "BioSimulators-compliant command-line interface to the vcell simulation program <https://vcell.org>.")
@@ -90,18 +93,17 @@ 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, OUT_DIR, cliRecorder, true);
-                if (Tracer.hasErrors()){
-                    if (!bQuiet) {
-                        logger.error("Errors occurred during execution");
-                        Tracer.reportErrors(bDebug);
-                    }
-                    return 1;
-                } else {
-                    return 0;
+                ExecuteImpl.singleMode(ARCHIVE, tmpDir, cliRecorder, true);
+                FileUtils.copyDirectoryContents(tmpDir, OUT_DIR, true, null);
+                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

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

@@ -493,22 +493,22 @@ public static void drawBreakLine(String breakString, int times) {
 
 
     public static boolean removeAndMakeDirs(File f) {
-        boolean removalSuccess = true;
-        if (f.exists()) {
-            boolean isRemoved = CLIUtils.removeDirs(f);
-            if (!isRemoved)
-                removalSuccess = false;
-                // we don't throw an exception up the stack here for two reasons:
-                // 1) deletion of files differs on different OS. Punishing users for their OS or their understanding thereof seems wrong.
-                // 2) the user may be using software that is necessarily holding resources; by blocking on failed deletion, we are
-                //      denying the potential use cases of VCell.
-                try{
-                    throw new Exception("File '" + f.getCanonicalPath() + "' could not be deleted!");
-                } catch (Exception e){
-                    logger.error(e);
-                }
+        if (!f.exists()) return f.mkdirs();
+        String filePath = "";
+        try {
+            filePath += f.getCanonicalPath();
+            org.vcell.util.FileUtils.deleteDirectoryContents(f, true, null);
+        } catch (IOException e) {
+            // if we got to here, we've tried to clear the contents of a directory a failed.
+            // we don't throw an exception up the stack here for two reasons:
+            // 1) deletion of files differs on different OS. Punishing users for their OS or their understanding thereof seems wrong.
+            // 2) the user may be using software that is necessarily holding resources; by blocking on failed deletion, we are
+            //      denying the potential use cases of VCell.
+            String msg = "File '" + filePath + "' could not be deleted!";
+            logger.error(msg, e);
+            return false;
         }
-        return f.mkdirs() && removalSuccess;
+        return true;
     }
 
     public static void createCSVFromODEResultSet(ODESolverResultSet resultSet, File f) throws ExpressionException {

vcell-util/src/main/java/org/vcell/util/FileUtils.java

@@ -15,6 +15,7 @@
 import java.net.URL;
 import java.nio.ByteBuffer;
 import java.nio.channels.FileChannel;
+import java.nio.file.Files;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -44,7 +45,7 @@ public final class FileUtils {
      * @author Logan Drescher
      */
     public static void copyDirectoryContents(File sourceDir, File destDir, boolean performRecursive, FileFilter filter) throws IOException {
-        if (!(sourceDir.isDirectory())){
+        if (!sourceDir.isDirectory()){
             throw new IOException("Arguments for FileUtils.copyDirectory must be directories.  Problem with Source dir: "+sourceDir.getCanonicalPath());
         }
         if ((destDir.exists()) && !(destDir.isDirectory())) {
@@ -70,7 +71,40 @@ public static void copyDirectoryContents(File sourceDir, File destDir, boolean p
                 }
             }
         }
-}
+    }
+
+    /**
+     * Convenience method to copy a directory from a source to a destination.
+     * Overwrite is allowed, and the last modified is kept, 4k buffer used.
+     * @param targetDir the directory to delete the files inside of
+     * @param performRecursive whether to recursively copy directory contents, or keep surface level
+     * @param filter FileFilter settings to selectively filter types of files
+     * @throws IOException If the files are not the correct types, or an IO problem was encountered
+     * @author Ed Boyce
+     * @author Logan Drescher
+     */
+    public static void deleteDirectoryContents(File targetDir, boolean performRecursive, FileFilter filter) throws IOException {
+        if (!targetDir.isDirectory()){
+            throw new IOException("Argument for parameter `targetDir`" + targetDir.getCanonicalPath() + " is not a directory");
+        }
+
+        // We need all 3 to delete!
+        if (!targetDir.canWrite() || !targetDir.canExecute() || !targetDir.canRead()) {
+            throw new IOException("Cannot write to directory `" + targetDir.getCanonicalPath() + "`");
+        }
+
+        for (File currentFile : targetDir.listFiles()) { // Will not return a null because we already checked for directory!
+            if (filter != null && !filter.accept(currentFile)) continue;
+            if (currentFile.isDirectory() && performRecursive) {
+                deleteDirectoryContents(currentFile, true, filter);
+                if (!currentFile.delete()) throw new IOException("Failed to delete empty directory " + currentFile.getCanonicalPath());
+                continue;
+            }
+            if (currentFile.isFile()) {
+                deleteFile(currentFile);
+            }
+        }
+    }
 
 /**
 * Convenience method to copy a file from a source to a destination.
@@ -243,49 +277,34 @@ public static void saveUrlToFile(File file, String urlString) throws MalformedUR
     }
 }
 
+    public static void deleteFile(File f) throws IOException {
+        if (!f.exists()) throw new IOException("File \"" + f.getCanonicalPath() + "\" does not exist.");
+        if (!f.canWrite()) throw new IOException("File \"" + f.getCanonicalPath() + "\" is write protected.");
+        if (f.isDirectory()) throw new IOException("File \"" + f.getCanonicalPath() + "\" is a directory, not a single file.");
+        if (!f.delete()) throw new IOException("File \"" + f.getCanonicalPath() + "\" deletion attempt failed.");
+    }
+
 public static void deleteFile(String filePath) throws IOException {
-	File f = new File(filePath);
-	if (!f.exists()) {
-		throw new IOException("File \""+filePath+"\" does not exist.");
-	}
-	if (!f.canWrite()) {
-		throw new IOException("File \""+filePath+"\" is write protected.");
-	}	
-	if (f.isDirectory()) {
-		throw new IOException("File \""+filePath+"\" is a directory, and I'm currently programmed to balk at deleting whole directories.");
-	}
-	boolean bSuccess = f.delete();
-	if (!bSuccess) {
-		throw new IOException("File \""+filePath+"\" deletion attempt failed.");
-	}
+    deleteFile(new File(filePath));
 }
 
 public static void writeByteArrayToFile(byte[] byteArray, File outputFile) throws IOException {
-    FileOutputStream fileOutputStream = new FileOutputStream(outputFile);
-    try {
+    try (FileOutputStream fileOutputStream = new FileOutputStream(outputFile)) {
         ByteBuffer byteBuffer = ByteBuffer.wrap(byteArray);
         byteBuffer.put(byteArray);
         byteBuffer.flip();
         FileChannel fileChannel = fileOutputStream.getChannel();
         fileChannel.write(byteBuffer);
-    } finally {
-        fileOutputStream.close();
     }
 }
 
 
 public static byte[] readByteArrayFromFile(File inputFile)throws IOException  {
     byte [] inputFileByteArrayBuffer = new byte[(int) inputFile.length()];
-    InputStream inputStream = null;
-    try {
-        inputStream = new FileInputStream(inputFile);
-        if ( inputStream.read(inputFileByteArrayBuffer) == -1 ) {
-            throw new IOException("EOF character reached while trying to read the whole file:"+inputFile.getAbsolutePath());
-        }        
-    } finally { 
-         if ( inputStream != null ) {
-              inputStream.close();
-         }
+    try (InputStream inputStream = new FileInputStream(inputFile)) {
+        if (inputStream.read(inputFileByteArrayBuffer) == -1) {
+            throw new IOException("EOF character reached while trying to read the whole file:" + inputFile.getAbsolutePath());
+        }
     }
     return inputFileByteArrayBuffer;
 }