Annotation loading error

[luli7]

Hi Everyone,

I am using PyPath dev version 0.8.20 under python 3.6. I have pickled annotation, however when loading it back, I got following error messages (I also got exactly the same message when loading annotation without pickle a=annot.AnnotationTable()):

a=annot.AnnotationTable(pickle_file='know/software/pypath/annot_31db_20190619.pickle') Traceback (most recent call last): File "", line 1, in File "/home/luli7/.local/lib/python3.6/site-packages/pypath/annot.py", line 2132, in init self.set_reference_set() File "/home/luli7/.local/lib/python3.6/site-packages/pypath/annot.py", line 2279, in set_reference_set swissprot_only = self.swissprot_only, File "/home/luli7/.local/lib/python3.6/site-packages/pypath/annot.py", line 605, in get_reference_set sorted(complex.all_complexes()) File "/home/luli7/.local/lib/python3.6/site-packages/pypath/complex.py", line 478, in all_complexes db = get_db() File "/home/luli7/.local/lib/python3.6/site-packages/pypath/complex.py", line 466, in get_db init_db(kwargs) File "/home/luli7/.local/lib/python3.6/site-packages/pypath/complex.py", line 455, in init_db globals()['db'] = ComplexAggregator(kwargs) File "/home/luli7/.local/lib/python3.6/site-packages/pypath/complex.py", line 377, in init name = 'OmniPath', File "/home/luli7/.local/lib/python3.6/site-packages/pypath/complex.py", line 94, in init self.load() File "/home/luli7/.local/lib/python3.6/site-packages/pypath/complex.py", line 412, in load processor = res() File "/home/luli7/.local/lib/python3.6/site-packages/pypath/complex.py", line 220, in init input_method = 'cellphonedb_complexes', File "/home/luli7/.local/lib/python3.6/site-packages/pypath/complex.py", line 94, in init self.load() File "/home/luli7/.local/lib/python3.6/site-packages/pypath/complex.py", line 99, in load resource.AbstractResource.load(self) File "/home/luli7/.local/lib/python3.6/site-packages/pypath/resource.py", line 77, in load self.load_data() File "/home/luli7/.local/lib/python3.6/site-packages/pypath/resource.py", line 114, in load_data self.data = self.input_method(**self.input_args) File "/home/luli7/.local/lib/python3.6/site-packages/pypath/dataio.py", line 6360, in cellphonedb_complexes annot = cellphonedb_complex_annotations() File "/home/luli7/.local/lib/python3.6/site-packages/pypath/dataio.py", line 6224, in cellphonedb_complex_annotations name_method = name_method, File "/home/luli7/.local/lib/python3.6/site-packages/pypath/dataio.py", line 6187, in _cellphonedb_annotations receptor = get_desc(rec, 'receptor'), File "/home/luli7/.local/lib/python3.6/site-packages/pypath/dataio.py", line 6171, in get_desc attr not in rec and not rec[desc] KeyError: 'receptor_desc'

[luli7]

Hi,

I looked at my log file. I feels like, even loading a pickle file, PyPath is still trying to down-load new files from github. last line of log file: [2019-06-25 10:53:03] [curl] File at https://raw.githubusercontent.com/Teichlab/cellphonedb/master/cellphonedb/src/core/data/complex.csv successfully retrieved. Resulted file type plain text, file object. Local file at /home/luli7/.pypath/cache/e77b828b6eb5ddaa1145375877d4b76a-complex.csv.

When I open this file from cache, it is empty containing only: 404: Not Found 404: Not Found 404: Not Found

I think Cellphonedb potentially changed their URL for this data set, and it feels like there are also some re-naming after looking at: https://github.com/Teichlab/cellphonedb/tree/master/cellphonedb/src/core/data

Could you please fix this issue?

Thank you so much! Best regards Lu

[npalacioescat]

Hi Lu,

We are aware that CellPhone DB recently updated its database and some fields and URLs have changed since the previous version. This issue will be addressed ASAP.

Cheers

[deeenes]

Hi Lu,

Thanks for reporting it, fixed in 148637a

Best,

Denes