Atomimu should not depend on `strptime` for parse date in PDB

[Czaki]

For Bug Reports

Expected behaviour

Read PDB file if using non English locale

Actual behaviour

~/.pyenv/versions/3.8.3/envs/partseg3.8/lib/python3.8/site-packages/atomium/utilities.py in open(path, *args, **kwargs)
     39         except:
     40             with builtins.open(path, "rb") as f: filestring = f.read()
---> 41         return parse_string(filestring, path, *args, **kwargs)
     42 
     43 

~/.pyenv/versions/3.8.3/envs/partseg3.8/lib/python3.8/site-packages/atomium/utilities.py in parse_string(filestring, path, file_dict, data_dict)
    122     parsed = file_func(filestring)
    123     if not file_dict:
--> 124         parsed = data_func(parsed)
    125         if not data_dict:
    126             filetype = data_func.__name__.split("_")[0].replace("mmc", "c")

~/.pyenv/versions/3.8.3/envs/partseg3.8/lib/python3.8/site-packages/atomium/pdb.py in pdb_dict_to_data_dict(pdb_dict)
     80       "geometry": {"assemblies": [], "crystallography": {}}, "models": []
     81     }
---> 82     update_description_dict(pdb_dict, data_dict)
     83     update_experiment_dict(pdb_dict, data_dict)
     84     update_quality_dict(pdb_dict, data_dict)

~/.pyenv/versions/3.8.3/envs/partseg3.8/lib/python3.8/site-packages/atomium/pdb.py in update_description_dict(pdb_dict, data_dict)
     95     :param dict data_dict: The data dictionary to update."""
     96 
---> 97     extract_header(pdb_dict, data_dict["description"])
     98     extract_title(pdb_dict, data_dict["description"])
     99     extract_keywords(pdb_dict, data_dict["description"])

~/.pyenv/versions/3.8.3/envs/partseg3.8/lib/python3.8/site-packages/atomium/pdb.py in extract_header(pdb_dict, description_dict)
    174         line = pdb_dict["HEADER"][0]
    175         if line[50:59].strip():
--> 176             description_dict["deposition_date"] = datetime.strptime(
    177              line[50:59], "%d-%b-%y"
    178             ).date()

~/.pyenv/versions/3.8.3/lib/python3.8/_strptime.py in _strptime_datetime(cls, data_string, format)
    566     """Return a class cls instance based on the input string and the
    567     format string."""
--> 568     tt, fraction, gmtoff_fraction = _strptime(data_string, format)
    569     tzname, gmtoff = tt[-2:]
    570     args = tt[:6] + (fraction,)

~/.pyenv/versions/3.8.3/lib/python3.8/_strptime.py in _strptime(data_string, format)
    347     found = format_regex.match(data_string)
    348     if not found:
--> 349         raise ValueError("time data %r does not match format %r" %
    350                          (data_string, format))
    351     if len(data_string) != found.end():

ValueError: time data '24-JUL-96' does not match format '%d-%b-%y'

For my case

In[11]: date(1996, 6, 15).strftime("%d-%b-%y")
Out[11]: '15-cze-96'

Not '15-Jun-96'

Example code to reproduce

On non-English OS:

import atomium
import locale

locale.setlocale(local.LC_ALL, "")
atomium.open("/home/czaki/Pobrane/tmp/3mht.pdb")

https://docs.python.org/3/library/datetime.html#strftime-and-strptime-format-codes directly told that strptime will use local abrev.

Python Version/Operating System

Python 3.8.3, Ubuntu 21.10

[samirelanduk]

Thanks for pointing this out, I hadn't even realised. This will be fixed in atomium v2.0, released in a few weeks.