jamesjeffryes / pyclassyfire

A python client for the ClassyFire API

pyclassyfire

This package provides a set of helper functions in python for annotating chemical structures with the chemical ontology developed by Djoumbou et. al using the ClassyFire API

pyclassyfire's Issues

Unicode decoding problem with function client.sdf_query()

Dear James,

Thank you for having written such a Python interface to Classyfire!

I submitted the unzipped file
buffer16.zip
to function call client.sdf_query(filenameBuffer, filenameOut) and an exception was raised:

1 queries submitted to ClassyFire API
0 percent complete
Traceback (most recent call last):
File "run2.py", line 93, in
client.sdf_query(filenameBuffer, filenameOut)
File "C:\Users\jmn\Documents\CNRS20\Publis\PNMRNP_STARTED\Biblio\pyclassyfire-master\pyclassyfire\client.py", line 223, in sdf_query
outfile.write(get_results(query_ids[i], return_format='sdf'))
File "C:\Users\jmn\Anaconda3\envs\rdkit3\lib\encodings\cp1252.py", line 19, in encode
return codecs.charmap_encode(input,self.errors,encoding_table)[0]
UnicodeEncodeError: 'charmap' codec can't encode character '\u03b1' in position 8847: character maps to

It looks like classification by classyfire was successful but some unicode character cannot be inserted in the resulting .sdf file.

\u03b1 is the unicode encoding for the greek letter alpha, not so uncommon in chemistry.

Could you please indicate a fix or a workaround?

Many thanks in advance.
Best regards,

Jean-Marc

KeyError: 'number_of_pages'

Hello,

Do you know why i get the following error with the test file?:

Line of code:
open("test_datatable_result_inchi.json", "w").write(json.dumps(get_results_multientry_multipage_patient(query_ids, return_format="json")))

Thanks a lot in advance!!
Best, Michelle

DEBUG:urllib3.connectionpool:http://classyfire.wishartlab.com:80 "GET /queries/6188679.json HTTP/1.1" 500 48

KeyError Traceback (most recent call last)
in
----> 1 open("test_datatable_result_inchi.json", "w").write(json.dumps(get_results_multientry_multipage_patient(query_ids, return_format="json")))

~\anaconda3\lib\site-packages\pybatchclassyfire\pybatchclassyfire.py in get_results_multientry_multipage_patient(query_ids_list, return_format)
596
597 result = json.loads(r.text)
--> 598 num_pages = result["number_of_pages"]
599
600

KeyError: 'number_of_pages'

ClassyFire Server Down

Hi,
the ClassyFire server connected to GNPS and used by your script (posted on the following page https://pypi.org/project/pybatchclassyfire/ and redirecting to this GitHub repository) is down:
https://gnps-classyfire.ucsd.edu

Can you fix this?
Find attached the txt version of the script, with the the link to the server inside.

pybatchclassyfire.txt

Thanks

batch queries (SMILES)

Hi! I am new using this classyfire API. I just wanna know how to do queries with multiple SMILES.
Is that possible?

For example: O=Cc1ccc(O)c(OC)c1, CC(=O)NCCC1=CNc2c1cc(OC)cc2, CN1CCC[C@H]1c2cccnc2

Can I use this 3 SMILES in the same input file? I didn´t find how to do it.

thanks!

regards!

"0 percent complete" forever

Dear James,

I am facing a new problem now.
After a successful trial of client.sdf_query() with a batch of 1000 molecules in about 1 minute,
running a second batch of 1000 molecules resulted after about 15 minutes (still running...)
in many "0 percent complete" lines (about 1 per minute).
Is this a problem from the server side?
Is there some usage quota?

Best regards,

Jean-Marc