"Fixed" uncaught exception issue (by just replacing the problematic file

virtualcell · Sep 11, 2024 · 32b379a · 32b379a
1 parent 0a31023
commit 32b379a
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Showing 2 changed files with 3 additions and 2 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
@@ -5,6 +5,7 @@
 import de.unirostock.sems.cbarchive.CombineArchiveException;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.jdom2.IllegalNameException;
 import org.jdom2.JDOMException;
 import org.vcell.cli.CLIUtils;
 
@@ -52,9 +53,9 @@ public OmexHandler(String omexPath, String outDir) throws IOException {
             if ((initiallyEncounteredErrors && omexFile.canWrite() && initialArchive.getErrors().contains(".rdf"))
                 || initialArchive.getEntries().stream().map(ArchiveEntry::getFileName).noneMatch(name->name.endsWith(".rdf")))
                 this.replaceMetadataRdfFiles(Paths.get(omexPath)); // Replace the offending files
-        } catch (CombineArchiveException | JDOMException | ParseException e) {
+        } catch (CombineArchiveException | JDOMException | IllegalNameException | ParseException e) {
             // Alright, we got errors, AND an exception. Let's try a hail mary.
-            if (omexFile.canWrite() && e.getMessage().contains(".rdf"))
+            if (omexFile.canWrite())
                 this.replaceMetadataRdfFiles(Paths.get(omexPath));
         }
 

diff --git a/vcell-cli/src/test/resources/BioModel1.omex b/vcell-cli/src/test/resources/BioModel1.omex