Merge pull request #1377 from virtualcell/New7_7Container

Attempting to enforce needed permissions
virtualcell · Nov 8, 2024 · d53f86f · d53f86f
2 parents 9f29879 + 47c619e
commit d53f86f
Showing 1 changed file with 30 additions and 22 deletions.
diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java b/vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java
@@ -14,6 +14,7 @@
 import java.nio.file.*;
 import java.text.ParseException;
 import java.util.*;
+import java.util.stream.Stream;
 
 public class OmexHandler {
     String tempPath;
@@ -56,30 +57,37 @@ public OmexHandler(String omexPath, String outDir) throws IOException {
     }
 
     private void replaceMetadataRdfFiles(Path zipFilePath) throws IOException {
+        if (!zipFilePath.toFile().exists() || !zipFilePath.toFile().isFile())
+            throw new IllegalArgumentException("ZipFile supposedly at `" + zipFilePath + "` is invalid");
+        if (!zipFilePath.toFile().canWrite()) if (!zipFilePath.toFile().setWritable(true))
+            throw new IllegalArgumentException("ZipFile at `" + zipFilePath + "` can not be written to.");
+        if (!zipFilePath.toFile().canExecute()) if (!zipFilePath.toFile().setExecutable(true))
+            throw new IllegalArgumentException("ZipFile at `" + zipFilePath + "` does not allow execution.");
         try( FileSystem fs = FileSystems.newFileSystem(zipFilePath) ) {
             for (Path root : fs.getRootDirectories()) {
-                Files.walk(root)
-                        .filter(Files::isRegularFile)
-                        .filter(path -> path.toString().endsWith(".rdf"))
-                        .forEach(path -> {
-                            try {
-                                // write empty RDF file to temp file and replace the file inside the zip
-                                Path tempFile = Files.createTempFile("temp", ".rdf");
-                                String new_rdf_content =
-                                    """
-                                    <?xml version='1.0' encoding='UTF-8'?>
-                                    <rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'>
-                                    </rdf:RDF>
-                                    """;
-                                Files.write(tempFile, new_rdf_content.getBytes());
-                                // replace fileInsideZipPath with temp file
-                                Files.delete(path);
-                                Files.copy(tempFile, path);
-                                Files.delete(tempFile);
-                            } catch (IOException e) {
-                                logger.error("Unable to delete metadata.rdf file from OMEX archive: " + e.getMessage(), e);
-                            }
-                        });
+                try (Stream<Path> contents = Files.walk(root)) {
+                    contents.filter(Files::isRegularFile)
+                            .filter(path -> path.toString().endsWith(".rdf"))
+                            .forEach(path -> {
+                                try {
+                                    // write empty RDF file to temp file and replace the file inside the zip
+                                    Path tempFile = Files.createTempFile("temp", ".rdf");
+                                    String new_rdf_content =
+                                            """
+                                            <?xml version='1.0' encoding='UTF-8'?>
+                                            <rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'>
+                                            </rdf:RDF>
+                                            """;
+                                    Files.write(tempFile, new_rdf_content.getBytes());
+                                    // replace fileInsideZipPath with temp file
+                                    Files.delete(path);
+                                    Files.copy(tempFile, path);
+                                    Files.delete(tempFile);
+                                } catch (IOException e) {
+                                    logger.error("Unable to delete metadata.rdf file from OMEX archive: " + e.getMessage(), e);
+                                }
+                            });
+                }
             }
 
         }