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ReproNim / segstats_jsonld

Script to Export Freesurfer-based Parcellation/Segmentation Stats and Provenance as JSON-LD and NIDM
MIT License
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setup.py not copying XLS file #20

Open dbkeator opened 5 years ago

dbkeator commented 5 years ago

Hi @adswa ,

After installing package with python setup.py install, I find that the script can't be run without supplying a the jsonmap.json file with the command line parameter -jmap because the ReproNimCDEs.xlsx file in mapping_data isn't copied into the site_packages directory (see below). Any ideas?

[~/Documents/Coding/segstats_jsonld]$ segstats2nidm -f "https://fcp-indi.s3.amazonaws.com/data/Projects/ABIDE/Outputs/mindboggle_swf/mindboggle/freesurfer_subjects/sub-0050190/stats/aseg.stats" -subjid 0050190 -n /Users/dbkeator/Documents/Coding/simple2_NIDM_examples/datasets.datalad.org/abide/RawDataBIDS/SDSU/nidm.ttl -o /Users/dbkeator/Documents/Coding/simple2_NIDM_examples/datasets.datalad.org/abide/RawDataBIDS/SDSU/nidm.ttl Traceback (most recent call last): File "/miniconda3/bin/segstats2nidm", line 11, in load_entry_point('segstats-jsonld==0.0.1', 'console_scripts', 'segstats2nidm')() File "/miniconda3/lib/python3.7/site-packages/segstats_jsonld-0.0.1-py3.7.egg/segstats_jsonld/fs_to_nidm.py", line 916, in main fs_stat_file=stats_file) File "/miniconda3/lib/python3.7/site-packages/segstats_jsonld-0.0.1-py3.7.egg/segstats_jsonld/fs_to_nidm.py", line 458, in remap2json xls = pd.ExcelFile(xlsxfile) File "/miniconda3/lib/python3.7/site-packages/pandas/io/excel.py", line 653, in init self._reader = self._enginesengine File "/miniconda3/lib/python3.7/site-packages/pandas/io/excel.py", line 424, in init self.book = xlrd.open_workbook(filepath_or_buffer) File "/miniconda3/lib/python3.7/site-packages/xlrd/init.py", line 111, in open_workbook with open(filename, "rb") as f: FileNotFoundError: [Errno 2] No such file or directory: '/miniconda3/lib/python3.7/site-packages/segstats_jsonld-0.0.1-py3.7.egg/segstats_jsonld/mapping_data/ReproNimCDEs.xlsx'

adswa commented 5 years ago

will finally look into this today, sorry for the delay.

adswa commented 5 years ago

I'm for now including the xlxs file in the distribution. You should be able to pip uninstall segstats_jsonld and subsequently install the fresh release with pip install -i https://test.pypi.org/simple/ segstats-jsonld.

Please let me know whether this fixes it, @dbkeator