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Do not automatically try downloading from a .gz URL from known broken servers. #41

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gouttegd wants to merge 1 commit into from
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Do not automatically try downloading from a .gz URL from known broken servers. #41

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28 changes: 25 additions & 3 deletions src/incatools/odk/helper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -177,14 +177,36 @@ def info(tools) -> None:
then fallback to "U". This is enabled by default, unless the
provided URL already points to a compressed file.""",
)
def download(url, output, reference, cache_info, max_retry, try_gzip) -> None:
@click.option(
"--broken-hosts-file",
default="config/broken-hosts.txt",

@matentzn matentzn Oct 16, 2026

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hmmm, not so much a fan of a list.. Cant we just try and fail to decompress?

type=click.Path(path_type=Path, dir_okay=False),
help="""A file containing a list of known broken HTTP hosts, from
which downloading a gzipped file shall not be attempted
despite --try-gzip.""",
)
def download(
url, output, reference, cache_info, max_retry, try_gzip, broken_hosts_file
) -> None:
"""Download a file."""

urlpath = Path(urlparse(url).path)
urlobj = urlparse(url)
urlpath = Path(urlobj.path)
compression = Compression.from_extension(urlpath)

broken_hosts: List[str] = []

@matentzn matentzn Oct 16, 2026

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GzipFile.read() on some cases raises gzip.BadGzipFile (an OSError), not DownloadError, so the except DownloadError in the attempts loop below never catches it (like http://www.ebi.ac.uk/efo/efo.owl.gz). so we crash instead of falling back to the plain URL.

If _handle_successful_download in download.py caught the decompression error, deleted the tmp file and raised DownloadError, the existing fallback would just work, for EBI and any other server that answers 200 for things that don't exist (something like this, to get the idea):

try:
    with tmpfile.open("wb") as fd:
        for chunk in _ResponseWrapper.maybe_wrap(response, comp).iter_content(512):
            h.update(chunk)
            fd.write(chunk)
except (OSError, EOFError) as e:
    tmpfile.unlink(missing_ok=True)
    raise DownloadError(f"Cannot decompress file from {response.url}: {e}")

(EOFError is for truncated gzip. OSError also catches real disk-write errors, so maybe catch only around the decompression if you want to keep those apart.)

@gouttegd gouttegd Oct 17, 2026

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That’s a good idea, thanks!

if try_gzip and broken_hosts_file.exists():
with broken_hosts_file.open("r") as f:
for line in [line.strip() for line in f]:
if line and not line.startswith("#"):
broken_hosts.append(line)

attempts: List[Tuple[str, Compression]] = []
if compression == Compression.NONE and try_gzip:
if (
compression == Compression.NONE
and try_gzip
and urlobj.netloc not in broken_hosts

@matentzn matentzn Oct 16, 2026

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netloc includes the port and userinfo, and it's case-sensitive, so http://www.ebi.ac.uk:80/efo/efo.owl or WWW.EBI.AC.UK gets past this check. Maybe urlobj.hostname?

):
attempts.append((url + ".gz", Compression.GZIP))
attempts.append((url, compression))

Expand Down
6 changes: 6 additions & 0 deletions src/incatools/odk/templates/src/ontology/config/broken-hosts.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
# Broken HTTP hosts; these servers are known to cause issues when
# attempting to download gzipped files from them.

# The EBI server returns a homepage with a 200 status code,
# instead of a proper 404, for any unknown URL.
www.ebi.ac.uk
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