biopragmatics / obo-db-ingest

🗄️ Conversion of biomedical nomenclatures like HGNC to OBO
https://biopragmatics.github.io/obo-db-ingest/
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HGNC ingest fails as ingester assumes latest release is present #5

Closed cmungall closed 1 year ago

cmungall commented 1 year ago
py run-test: commands[0] | python build.py -x hgnc
INFO: [2023-02-03 11:33:41] pystow.utils - downloading with urllib from https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/json/hgnc_complete_set_2023-02-01.json to /Users/cjm/.data/pyobo/raw/hgnc/2023-02-01/hgnc_complete_set.json
Making OBO examples:   0%|                                                                                                                                                                                      | 0/1 [00:00<?, ?it/s, prefix=hgnc]
Traceback (most recent call last):
  File "/Users/cjm/repos/obo-db-ingest/build.py", line 143, in <module>
    main()

[...]

urllib.error.HTTPError: HTTP Error 404: Not Found
ERROR: InvocationError for command /Users/cjm/repos/obo-db-ingest/.tox/py/bin/python build.py -x hgnc (exited with code 1)
_____________________________________________________________________________________________________________________ summary _____________________________________________________________________________________________________________________
  lint: commands succeeded
ERROR:   py: commands failed

it looks like 2023-02-01 is not up yet (but it may be by the time you get to this issue):

https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/json/

image

not sure if this is a regular occurrence, but the assumption that there is always a release present for the 1st of the current month may be unreliable

cthoyt commented 1 year ago

This is fixed now