fix in CLI mode

draeger-lab · Oct 12, 2024 · 6692356 · 6692356
1 parent a0934bf
commit 6692356
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Showing 2 changed files with 21 additions and 18 deletions.
diff --git a/app/src/main/java/de/uni_halle/informatik/biodata/mp/ModelPolisherCLILauncher.java b/app/src/main/java/de/uni_halle/informatik/biodata/mp/ModelPolisherCLILauncher.java
@@ -216,6 +216,9 @@ private void validateIOParameters() throws ParametersException {
       throw new ParametersException(format(MESSAGES.getString("READ_FILE_ERROR"), input), parameters);
     }
 
+    // Ensure the output directory or file's parent directory exists
+    SBMLFileUtils.checkCreateOutDir(output);
+
     // If the input is a directory but the output is not, exit with error
     if (input.isDirectory() && !output.isDirectory()) {
       throw new ParametersException(format(MESSAGES.getString("WRITE_DIR_TO_FILE_ERROR"),
@@ -232,8 +235,6 @@ private void validateIOParameters() throws ParametersException {
               parameters);
     }
 
-    // Ensure the output directory or file's parent directory exists
-    SBMLFileUtils.checkCreateOutDir(output);
   }
 
 

diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/io/SBMLFileUtils.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/io/SBMLFileUtils.java
@@ -93,23 +93,25 @@ public static boolean isDirectory(File file) {
      */
     public static void checkCreateOutDir(File output) {
         logger.debug(format(MESSAGES.getString("OUTPUT_FILE_DESC"), isDirectory(output) ? "directory" : "file"));
-        // ModelPolisher.isDirectory() checks if output location contains ., if so it is assumed to be a file
-        // output is directory
-        if (isDirectory(output) && !output.exists()) {
-            logger.debug(format(MESSAGES.getString("CREATING_DIRECTORY"), output.getAbsolutePath()));
-            if (!output.mkdirs()) {
-                // TODO: grace
-                throw new RuntimeException(format(MESSAGES.getString("DIRECTORY_CREATION_FAILED"), output.getAbsolutePath()));
-            }
-        }
-        // output is a file
-        else {
-            // check if directory of outfile exist and create if required
-            if (!output.getParentFile().exists()) {
-                logger.debug(format(MESSAGES.getString("CREATING_DIRECTORY"), output.getParentFile().getAbsolutePath()));
-                if (!output.getParentFile().mkdirs()) {
+        if (!output.exists()) {
+            // ModelPolisher.isDirectory() checks if output location contains ., if so it is assumed to be a file
+            // output is directory
+            if (isDirectory(output)) {
+                logger.debug(format(MESSAGES.getString("CREATING_DIRECTORY"), output.getAbsolutePath()));
+                if (!output.mkdirs()) {
                     // TODO: grace
-                    throw new RuntimeException(format(MESSAGES.getString("DIRECTORY_CREATION_FAILED"), output.getParentFile().getAbsolutePath()));
+                    throw new RuntimeException(format(MESSAGES.getString("DIRECTORY_CREATION_FAILED"), output.getAbsolutePath()));
+                }
+            }
+            // output is a file
+            else {
+                // check if directory of outfile exist and create if required
+                if (!output.getParentFile().exists()) {
+                    logger.debug(format(MESSAGES.getString("CREATING_DIRECTORY"), output.getParentFile().getAbsolutePath()));
+                    if (!output.getParentFile().mkdirs()) {
+                        // TODO: grace
+                        throw new RuntimeException(format(MESSAGES.getString("DIRECTORY_CREATION_FAILED"), output.getParentFile().getAbsolutePath()));
+                    }
                 }
             }
         }