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Fix CATH downloads: use https, and check the response before caching it #1136

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Fix CATH downloads: use https, and check the response before caching it #1136

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f061f57
Fix FileDownloadUtils validation and implement checksum verification
aalhossary Aug 15, 2026
80e9daa
Test that a 404 is neither cached nor recorded as valid
aalhossary Aug 15, 2026
66d27c7
Make LocalPDBDirectory.getLastModifiedTime public
aalhossary Aug 15, 2026
7244f21
Fix CATH downloads: use https, and check the response before caching it
aalhossary Aug 15, 2026
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Test that a 404 is neither cached nor recorded as valid 
Exercises the new status checking against the real wwPDB archive: downloadFile
must throw HttpStatusException rather than writing the error page to the
destination, and createValidationFiles must not record a .size for it. Without
the second half the cached error page would pass validateFile, since its
recorded size would match the error body exactly.
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aalhossary committed Aug 15, 2026
commit 80e9daab55d7269f380239acc7140bf8b1681703
25 changes: 25 additions & 0 deletions biojava-core/src/test/java/org/biojava/nbio/core/util/FileDownloadUtilsTest.java
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Expand Up @@ -214,6 +214,31 @@ void testValidationFiles() throws IOException{
}
}

@Nested
class HttpStatus {

@Test
void notFoundThrowsAndLeavesNothingBehind() throws IOException {
// A path that is guaranteed absent from the wwPDB archive.
URL missing = new URL("https://files.wwpdb.org/pub/pdb/data/structures/divided/mmCIF/zz/zzzz.cif.gz");
File dest = new File(System.getProperty("java.io.tmpdir"), "bj-missing.cif.gz");
File sizeFile = new File(dest.getParentFile(), dest.getName() + ".size");
dest.delete();
sizeFile.delete();

HttpStatusException e = assertThrows(HttpStatusException.class,
() -> FileDownloadUtils.downloadFile(missing, dest));
assertEquals(404, e.getStatusCode());
assertTrue(e.isNotFound());
assertFalse(dest.exists(), "a 404 body must never be written to the destination");

// ... and no validation metadata may be recorded for it either, or the
// cached error page would later pass validation.
FileDownloadUtils.createValidationFiles(missing, dest, null, FileDownloadUtils.Hash.UNKNOWN);
assertFalse(sizeFile.exists(), "no size file should be written for a 404 response");
}
}

@Nested
class Hashing {

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