Improvement for ValueError message about pynmrstar HOT 6 CLOSED

Dear Masashi,

This is definitely a bug, you shouldn't see the "internaluse..." value. I will work today to fix it. Thank you for the report. Feel free to reach out with any other feedback on how we can improve the PyNMRSTAR library.

Thanks,
Jon

from pynmrstar.

Dear Masashi,

I cannot reproduce the error using the most recent versions of the PyNMR-STAR library (either v2 or v3 branch):

>>> import pynmrstar
>>> a = pynmrstar.Entry.from_string("""data_nef_D_800107
...  
... save_nef_nmr_meta_data
...  _Entry.Sf_category                    entry_information
...  _Entry.Sf_framecode                   nef_nmr_meta_data
...  _Entry.NMR_STAR_version               3.2.1.18
...  _Entry.Source_data_format             nmr_exchange_format
...  _Entry.Source_data_format_version     1.1
...  _Entry.Generated_software_name        PDBStat
...  _Entry.Generated_software_version     5.20-exp
...  _Entry.Generated_date                 2020-01-28T16:40:10
...  _Entry.UUID                           1580226010
...  _Entry.Related_coordinate_file_name   .
...  _Entry.ID                             2PNG
... # 
...  _pdbx_nmr_assigned_chem_shift_list.entry_id         ?
...  _pdbx_nmr_assigned_chem_shift_list.id               ?
...  _pdbx_nmr_assigned_chem_shift_list.data_file_name   2png.nef
... #
... save_""")
Traceback (most recent call last):
  File "<stdin>", line 20, in <module>
  File "/Users/jon/PycharmProjects/PyNMRSTAR/pynmrstar.py", line 1838, in from_string
    return cls(the_string=the_string)
  File "/Users/jon/PycharmProjects/PyNMRSTAR/pynmrstar.py", line 1599, in __init__
    parser.parse(star_buffer.read(), source=self.source)
  File "/Users/jon/PycharmProjects/PyNMRSTAR/pynmrstar.py", line 890, in parse
    curframe.add_tag(curtag, self.token, self.get_line_number())
  File "/Users/jon/PycharmProjects/PyNMRSTAR/pynmrstar.py", line 2625, in add_tag
    (self.tag_prefix, prefix))
ValueError: One saveframe cannot have tags with different categories (or tags that don't match the set category)! '_Entry' vs '_pdbx_nmr_assigned_chem_shift_list'.

Can you please provide the version you are using print(pynmrstar.__version__) and the exact code that is triggering this exception?

Thanks!

from pynmrstar.

Hi Jon,

The above message is expected one from the issue. I am using 2.6.4.1 and it was deployed sometime via pip command. So, I need to update the library?

Thank you and stay safe,

from pynmrstar.

Dear Masashi,

I reviewed the commit logs, and it doesn't appear that the behavior of this particular code has changed since 2.6.4.1 Something else must be triggering the incorrect error message. (Though I still suggest upgrading if you are able.)

Could you attach the file where this bug triggers (in case there is an issue with characters in the file that GitHub has stripped out) and the specific code that triggers it?

Hope you are both well and safe also.

Thanks,
Jon

from pynmrstar.

Dear Jon,

Thank you for your comment. I found that this problem was related to NEFtranslator implementation originally developed by Kumaran.

    def read_input_file(self, in_file):
        """ Read input NEF/NMR-STAR file.
            @param in_file: input NEF/NMR-STAR file path
            @return: status, Entry/Saveframe/Loop data type or message, data object
        """

        is_ok = True
        star_data = None

        try:
            print ('Entry')
            star_data = pynmrstar.Entry.from_file(in_file)
            msg = 'Entry'

        except ValueError as e:
            print (e)

            try:
                print ('Saveframe')
                star_data = pynmrstar.Saveframe.from_file(in_file)
                msg = 'Saveframe'

            except ValueError as e:
                print (e)

                try:
                    print ('Loop')
                    star_data = pynmrstar.Loop.from_file(in_file)
                    msg = 'Loop'

                except ValueError as e:
                    print (e)
                    is_ok = False
                    msg = str(e) # '%s contains no valid saveframe or loop. PyNMRSTAR ++ Error  - %s' % (os.path.basename(in_file), str(e))

        except Exception as e:
            is_ok = False
            msg = str(e)
            
        return is_ok, msg, star_data

The output was:

Entry
One saveframe cannot have tags with different categories (or tags that don't match the set category)! '_Entry' vs '_pdbx_nmr_assigned_chem_shift_list'.
Saveframe
("Only 'save_NAME' is valid in the body of a NMR-STAR file. Found 'data_nef_D_800107'.", 1)
Loop
("Invalid token found in saveframe 'internaluseyoushouldntseethis_frame': 'data_nef_D_800107'", 1)

NEFtranslator tries to read file as Entry, it fails, as Saveframe, and finally, as Loop. PyNMRSTAR library throws proper error message when parser class matches with the file. But, I received the last error message. Now, I could resolve this problem by changing my implementation which retains exceptions as e1, e2, and e3, respectively.

Could you please clarify the error message in pynmrstar.Loop class?

Best regards,
Masashi

from pynmrstar.

Dear Masashi,

Thank you for these additional details. I have improved the error message when attempting to parse a loop object from a block of text which is not a loop. If you update to version 2.6.5.1 of the library you should see the improved behavior.

Thanks for the report!

Take care,
Jon

from pynmrstar.