NationalSecurityAgency/ghidra · error · IOException

{inputFile.getAbsolutePath()} is not an XML file

Error message

{inputFile.getAbsolutePath()} is not an XML file

What it means

Thrown by queryPair when the inputFile argument does not satisfy isFile() — meaning the path does not exist, is a directory, or is otherwise not a readable regular file. Despite the message text saying 'is not an XML file', the check is purely a filesystem existence/type test; it does not inspect file contents.

Source

Thrown at Ghidra/Features/BSim/src/main/java/ghidra/features/bsim/query/ingest/BulkSignatures.java:889

			pairs.add(pairInput);
		}
		return count;
	}

	/**
	 * Compares pairs of functions specified in an input (XML) file, and writes
	 * the results to an output file.
	 * 
	 * @param inputFile input XML file
	 * @param outputFile output XML file
	 * @throws IOException if there is a problem establishing the server connection
	 * @throws SAXException if an XML parse error occurs
	 * @throws LSHException if there is a problem querying the database
	 */
	protected void queryPair(File inputFile, File outputFile)
			throws IOException, SAXException, LSHException {
		if (!inputFile.isFile()) {
			throw new IOException(inputFile.getAbsolutePath() + " is not an XML file");
		}
		if (outputFile.isFile()) {
			Msg.info(this, "Overwriting file " + outputFile.getAbsolutePath());
			outputFile.delete();
		}
		establishQueryServerConnection(true);
		QueryPair query = new QueryPair();
		query.pairs = new ArrayList<PairInput>();
		ErrorHandler handler = SpecXmlUtils.getXmlHandler();
		XmlPullParser parser = XmlPullParserFactory.create(inputFile, handler, false);
		parser.start("querypair");

		try (FileWriter writer = new FileWriter(outputFile)) {
			writer.append("<responsepair>\n");
			ResponsePair.Accumulator accumulator = new ResponsePair.Accumulator();
			ResponsePair finalResponse = new ResponsePair();
			int count = readQueryPairs(parser, 20, query.pairs);
			while (count != 0) {

View on GitHub (pinned to d5f144c24d)

Solutions

1. Verify the path exists and is a regular file before calling queryPair (check inputFile.isFile() in the caller).
2. Use absolute paths to avoid ambiguity about the working directory.
3. Check file permissions on the path and parent directory.
4. If the file should have been generated by a prior step, verify that step completed successfully.

Example fix

// before
if (!inputFile.isFile()) {
    throw new IOException(inputFile.getAbsolutePath() + " is not an XML file");
}

// after — clearer message distinguishing missing vs wrong type
if (!inputFile.exists()) {
    throw new IOException("Input file does not exist: " + inputFile.getAbsolutePath());
}
if (!inputFile.isFile()) {
    throw new IOException("Input path is not a regular file: " + inputFile.getAbsolutePath());
}

// Validate the input file before calling queryPair
if (inputFile == null || !inputFile.isFile()) {
    throw new IllegalArgumentException(
        "Input file must exist and be a regular file: " +
        (inputFile != null ? inputFile.getAbsolutePath() : "null"));
}
// Optionally check XML header
try (var r = new java.io.BufferedReader(new java.io.FileReader(inputFile))) {
    String firstLine = r.readLine();
    if (firstLine != null && !firstLine.startsWith("<?xml") && !firstLine.startsWith("<querypair")) {
        // warn: file exists but may not be valid BSim pair XML
    }
}

// Check before calling queryPair
public static boolean isValidPairInputFile(File f) {
    return f != null && f.isFile() && f.canRead();
}

try {
    bulk.queryPair(inputFile, outputFile);
} catch (IOException e) {
    if (e.getMessage().contains("is not an XML file")) {
        // File path issue — verify path and retry
        System.err.println("Check input path: " + inputFile.getAbsolutePath());
    }
    throw e;
}

When it happens

Trigger: Calling queryPair(inputFile, outputFile) where inputFile points to a directory, a non-existent path, or a path the process cannot stat. The check is inputFile.isFile() returning false.

Common situations: Typo or wrong relative path in a command-line invocation; passing a directory path instead of the intended XML file; the file was cleaned up by another process before this method runs; insufficient permissions causing isFile() to return false.

Related errors

• {resultFolder.getAbsolutePath()} is not a valid directory
• Executable
• Expecting privilege option (admin or user)
• host required
• Non-empty dbName required

AI-assisted analysis of NationalSecurityAgency/ghidra@d5f144c24d (2026-08-14). Data as JSON: /api/errors/71a7ee04e339bee7. Report an issue: GitHub.