[Bug in v1.11.0] Need to check for the presence of failedIds key in uniprot.mapping #245
Description
Bug introduced in v1.11.0
It seems that the result of http_get(f"idmapping/status/{job_id}", frmt="json") does not contain the failedIds key if there are no failed ids:
bioservices/src/bioservices/uniprot.py
Line 476 in 07577b6
The changes introduced in the most recent release v1.11.0, 16 hours ago
result in a KeyError bug when that happens and the line responsible for that is the following:
bioservices/src/bioservices/uniprot.py
Line 482 in 07577b6
See the following example
In [1]: from bioservices.uniprot import UniProt
In [2]: u = UniProt(verbose=False, cache=False)
...: u.services.logging.setLevel("ERROR")
In [3]: u.mapping("UniProtKB_AC-ID", "KEGG", "P43403,P1
...: 23456")
0it [00:00, ?it/s]
Out[3]: {'results': [{'from': 'P43403', 'to': 'hsa:7535'}], 'failedIds': ['P123456']}
In [4]: u.mapping("UniProtKB_AC-ID", "KEGG", "P43403")
-------------------------------------------------------
KeyError Traceback (most recent call last)
<ipython-input-4-9022bf9c0b6c> in <module>
----> 1 u.mapping("UniProtKB_AC-ID", "KEGG", "P43403")
~/opt/miniconda3/envs/my_env/lib/python3.7/site-packages/bioservices/uniprot.py in mapping(self, fr, to, query, polling_interval_seconds, max_waiting_time, progress)
480 batches = results["results"]
481
--> 482 fails = results["failedIds"]
483
484 size = 25
KeyError: 'failedIds'Unfortunately, the existing test does not exercise the case where there are no failed ids:
bioservices/test/webservices/test_uniprot.py
Lines 46 to 52 in cce05ab