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sorgerlab / indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
http://indra.bio
BSD 2-Clause "Simplified" License
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Journal info #1416

Closed kkaris closed 1 year ago

kkaris commented 1 year ago

This PR extends the pubmed client to be able to extract publication as well as issue information from pubmed medline XML data. Two new namespaces are also added for validation.

todo

kkaris commented 1 year ago

All the failing tests seem to be related to the uniprot client and not to the code in this PR

kkaris commented 1 year ago

At least some of the access to uniprot seem to have moved to https://rest.uniprot.org/uniprotkb/ from https://legacy.uniprot.org/uniprot/ - 30 of 31 tests pass when updating uniprot_url to https://rest.uniprot.org/uniprotkb/ at https://github.com/gyorilab/protmapper/blob/master/protmapper/uniprot_client.py#L18

https://www.uniprot.org/help/api_retrieve_entries

kkaris commented 1 year ago

I see now that there is an open PR for this in protmapper: https://github.com/gyorilab/protmapper/pull/45

kkaris commented 1 year ago

Hmm, I reran the tests because the previous failed tests seemed to be related to temporary connection issues (they passed locally), but now the tests stop at the build phase before running the test with this error:

Collecting kappy==4.1.2 (from indra==1.22.0)
  Downloading kappy-4.1.2-cp38-cp38-manylinux2010_x86_64.whl (12.3 MB)
     ━━━━━━━━━━                               3.1/12.3 MB 1.9 MB/s eta 0:00:05
ERROR: THESE PACKAGES DO NOT MATCH THE HASHES FROM THE REQUIREMENTS FILE. If you have updated the package versions, please update the hashes. Otherwise, examine the package contents carefully; someone may have tampered with them.
    kappy==4.1.2 from https://files.pythonhosted.org/packages/ac/a4/306c4aa4aa178df434a56be20225b3429db20e901c38939047436d0fe2f6/kappy-4.1.2-cp38-cp38-manylinux2010_x86_64.whl (from indra==1.22.0):
        Expected sha256 b8de8bcd857823215fcc3c184f68de5f1d80dc3b3352107749b8156f85d32ff4
             Got        08ec5ddf5296036acf34a806f5e47957a61774715842ba9c824ee4897e84f21b