JOSS Review: `match_parser` does not work if `magic` is not installed
Closed this issue · 3 comments
In parsers.py, the _compressions variable remains undefined if python-magic (and some other imports) are not imported. However, _compressions is used on line 80 regardless and you get the following error until you install python-magic:
Cell In[1], line 5
2 from nomad.client import parse, normalize_all
4 # match and run the parser
----> 5 archive = parse('vasprun.xml')
6 # run all normalizers
7 normalize_all(archive)
File ~/anaconda3/envs/nomad/lib/python3.9/site-packages/nomad/client/processing.py:49, in parse(mainfile_path, parser_name, backend_factory, strict, logger)
47 else:
48 mainfile_path = os.path.abspath(mainfile_path)
---> 49 parser = parsers.match_parser(mainfile_path, strict=strict)
50 if isinstance(parser, parsing.MatchingParser):
51 parser_name = parser.name
File ~/anaconda3/envs/nomad/lib/python3.9/site-packages/nomad/parsing/parsers.py:71, in
match_parser(mainfile_path, strict)
68 return None
70 with open(mainfile_path, 'rb') as f:
---> 71 compression, open_compressed = _compressions.get(f.read(3), (None, open))
73 with open_compressed(mainfile_path, 'rb') as cf: # type: ignore
74 buffer = cf.read(config.parser_matching_size)
NameError: name '_compressions' is not defined
magic is needed to determine file types. It should be installed with parsing as in
Line 50 in 3e7d2cf
Since you are running on a win machine, is libmagic available such that pythoin-magic is successfully installed? Just FYI, win is not officially supported/maintained, there could be more errors here and there.
This was actually on Ubuntu. I'll dig into what happened here and report back, but either way I think the logic is still broken regardless because _compressions remains undefined if the try/except block goes to except.
I started using the main branch instead of an older version and this issue no longer remains.