KnowledgebaseManagers Meta Issue

[kkaris]

NOTE: this list is being updated as more sources are updated/fixed

This issue keeps track of issues and updates related to knowledgebase managers.

• TAS: Need a new TAS update - TAS maintainer has been sent a request for update
• Signor: Signor processor error sorgerlab/indra#1419
• Causal Bionet: CausalBioNet processing - KeyError while processing jgif file  sorgerlab/indra#1420
• BioGRID: No update needed
• Pathway Commons: No update needed
• CTD: New data available - switched to using from_web
• DrugBank: New data available - process new statements and put on S3
• VirHostNet: No update needed
• Phospho.ELM - Get ConnectionError to gilda web service after running a couple of thousand of calls Using local gilda instead
• HPRD: Assumes downloaded file exists - download from hprd.org errors
• BEL Large Corpus: Missing small_corpus.bel.nodelink.json.gz? cthoyt/selventa-knowledge#8 - resolved: small corpus file re-added
• Phosphosite Plus: New data available and copied to S3
• RLIMS-P: RLIMS-P invalid statement error sorgerlab/indra#1422
• TRRUST: No update needed
• DGI: Updated to call process_version() without explicit version number, this makes BeautifulSoup4 an indirect dependency via bioversions
• CRoG: No update needed
• CONIB: No update needed
• UbiBrowser: Ubibrowser KeyError sorgerlab/indra#1418

[kkaris]

Related PR in indra: sorgerlab/indra#1423

[kkaris]

Question for DGI:
I switched to using no version in the call to process_version() in indra_db.cli.knowledgebase. This does make BeautifulSoup4 a sub-dependency via the import and use of bioversions. If this is not desirable we can stick with hard coding the version instead, or looking up the latest version ourselves with e.g. xml's ElementTree or other built-in module.