No such file or directory: 'downloads/mixs6_core.tsv'

[turbomam]

I'm just making this for the first time! The download to downloads/mixs6.tsv works, but some subsequent step can't find downloads/mixs6_core.tsv

pipenv run python -m gsctools.mixs_converter

Traceback (most recent call last): File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/Users/MAM/Documents/gitrepos/mixs-source/gsctools/mixs_converter.py", line 495, in cli() File "/Users/MAM/.local/share/virtualenvs/mixs-source-ag2AQfeD/lib/python3.9/site-packages/click/core.py", line 829, in call return self.main(args, kwargs) File "/Users/MAM/.local/share/virtualenvs/mixs-source-ag2AQfeD/lib/python3.9/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/Users/MAM/.local/share/virtualenvs/mixs-source-ag2AQfeD/lib/python3.9/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, ctx.params) File "/Users/MAM/.local/share/virtualenvs/mixs-source-ag2AQfeD/lib/python3.9/site-packages/click/core.py", line 610, in invoke return callback(args, *kwargs) File "/Users/MAM/Documents/gitrepos/mixs-source/gsctools/mixs_converter.py", line 491, in cli cv.convert_and_save('model/schema/mixs.yaml') File "/Users/MAM/Documents/gitrepos/mixs-source/gsctools/mixs_converter.py", line 144, in convert_and_save obj = self.convert() File "/Users/MAM/Documents/gitrepos/mixs-source/gsctools/mixs_converter.py", line 271, in convert core_df = pd.read_csv(self.core_filename, sep="\t").fillna("").applymap(trim_strings) File "/Users/MAM/.local/share/virtualenvs/mixs-source-ag2AQfeD/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(args, kwargs) File "/Users/MAM/.local/share/virtualenvs/mixs-source-ag2AQfeD/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv return _read(filepath_or_buffer, kwds) File "/Users/MAM/.local/share/virtualenvs/mixs-source-ag2AQfeD/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 482, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/Users/MAM/.local/share/virtualenvs/mixs-source-ag2AQfeD/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 811, in init self._engine = self._make_engine(self.engine) File "/Users/MAM/.local/share/virtualenvs/mixs-source-ag2AQfeD/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1040, in _make_engine return mapping[engine](self.f, **self.options) # type: ignore[call-arg] File "/Users/MAM/.local/share/virtualenvs/mixs-source-ag2AQfeD/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 51, in init self._open_handles(src, kwds) File "/Users/MAM/.local/share/virtualenvs/mixs-source-ag2AQfeD/lib/python3.9/site-packages/pandas/io/parsers/base_parser.py", line 222, in _open_handles self.handles = get_handle( File "/Users/MAM/.local/share/virtualenvs/mixs-source-ag2AQfeD/lib/python3.9/site-packages/pandas/io/common.py", line 702, in get_handle handle = open( FileNotFoundError: [Errno 2] No such file or directory: 'downloads/mixs6_core.tsv'

[turbomam]

make downloads/mixs6_core.tsv fixes the above, but ... #5

[turbomam]

How should I interpret this, from downloads/README.md

@only1chunts uploaded new clean versions of the v6 checklist and package TSV files MIxSv6_checklists_14Sep2021_CIH.tsv MIxSv6_packages_14Sep2021_CIH.tsv

I don't see that file in the downloads folder.

BTW Should I be using this repo or https://github.com/GenomicsStandardsConsortium/mixs ?

[only1chunts]

Hi, apparently there is a script somewhere that will actually take the mixs google sheet and create the relevant tsv files in that download folder, I was not aware of that script when I manually uploaded some new TSV files on 14th Sept, you can ignore those files even if you find them! @cmungall should be able to help with the script to parse the google sheet, but the plan is to not do that until the next RDF call on 11Oct as I will have completed all the v6 changes by then!

[turbomam]

Thanks @only1chunts . I'm going to remove the remark I mentioned above in downloads/README.md because the Makefile does a good job of pulling all of the relevant Google Sheets now.