OSX may break replay

[ChrisKeefe]

When replaying an extracted zip archive of files that was compressed on OSX, parsing fails because the included __MACOSX directory contains non-zipfiles named._something.qz*:

We need to:

• [x] confirm that this only impacts compressed and then decompressed ziparchives
• [x] check whether this behavior also occurs on MacOS - details below
• [ ] fix, possibly by ignoring hidden files, ignoring files within __MACOSX in the fp, removing __MACOSX, or catching BadZipFile("File is not a zip file") errors and looking more closely at them.

[ChrisKeefe]

@cherman2 helped diagnose this issue today. Thank you!

• Provenance Replay assumes that any file suffixed .qza or .qzv is a QIIME 2 Archive
• the default zip utility used by MacOS finder (Archive Utility') adds a_MACOSXdirectory when it zips things. Inside this directory are a collection of files named..qza` that are not QIIME 2 Archives.
• the zip command available from the MacOS terminal does not appear to do this
• when these problematic zip archives are unzipped on MacOS (via terminal and presumably also finder), the resulting decompressed directory does not contain a __MACOSX directory`.
• when unzipped on by nemo (and possibly other file browsers), the false .qzx files in the resulting __MACOSX directory break parsing with the confusing error message below. Unzipping in terminal with zip seems to drop the directory.

TLDR: this error only arises in cases where a mac user has zipped a collection of .qzx in their file browser and sent it to a non-MacOS machine where it was unzipped (probably again in the file browser) for parsing.

chris:~/src/provenance_lib (main)> replay reproducibility-supplement --i-in-fp testfiles-ahhh\ \(1\)/ --o-out-fp whatever.zip --p-recurse
Parsing testfiles-ahhh (1)/testfiles-ahhh/multiplexed-seqs.qza
Parsing testfiles-ahhh (1)/testfiles-ahhh/newdir/demux-paired-end-ahhhh.qza
Parsing testfiles-ahhh (1)/__MACOSX/testfiles-ahhh/._multiplexed-seqs.qza
Traceback (most recent call last):
  File "/home/chris/miniconda3/envs/q2-22.2/bin/replay", line 33, in <module>
    sys.exit(load_entry_point('provenance-lib', 'console_scripts', 'replay')())
  File "/home/chris/miniconda3/envs/q2-22.2/lib/python3.8/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/chris/miniconda3/envs/q2-22.2/lib/python3.8/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/chris/miniconda3/envs/q2-22.2/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/chris/miniconda3/envs/q2-22.2/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/chris/miniconda3/envs/q2-22.2/lib/python3.8/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/chris/src/provenance_lib/provenance_lib/click_commands.py", line 184, in reproducibility_supplement
    write_reproducibility_supplement(
  File "/home/chris/src/provenance_lib/provenance_lib/replay.py", line 722, in write_reproducibility_supplement
    dag = ProvDAG(artifact_data=payload, validate_checksums=validate_checksums,
  File "/home/chris/src/provenance_lib/provenance_lib/parse.py", line 108, in __init__
    parser_results = parse_provenance(cfg, artifact_data)
  File "/home/chris/src/provenance_lib/provenance_lib/parse.py", line 443, in parse_provenance
    return parser.parse_prov(cfg, payload)
  File "/home/chris/src/provenance_lib/provenance_lib/parse.py", line 382, in parse_prov
    with zipfile.ZipFile(archive) as zf:
  File "/home/chris/miniconda3/envs/q2-22.2/lib/python3.8/zipfile.py", line 1269, in __init__
    self._RealGetContents()
  File "/home/chris/miniconda3/envs/q2-22.2/lib/python3.8/zipfile.py", line 1336, in _RealGetContents
    raise BadZipFile("File is not a zip file")
zipfile.BadZipFile: File is not a zip file