Comments (3)
joewandy
commented on July 19, 2024
As a temporary fix, we've handled the KeyError here 55573d9.
But it would be better to do some kind of KEGG/HMDB/ChEBI lookup, instead of just skipping over the missing compounds.
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kmcluskey
commented on July 19, 2024
Chebi lookup is not much good as I think the std_cmpds coming from PiMP appear to have KEGG names. Can we lookup KEGG names and get the ID somehow?
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kmcluskey
commented on July 19, 2024
This now searches Kegg for a matching ID and issues a warning if one is not found.
bioservices needs to be installed and has been added to the Pipfile.
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Related Issues (20)
- Make pathway analysis species configurable
- Peak explorer M/F page is broken for FlyMet
- Refactor PiMP-export codes
- Refactor pipeline codes
- Allow the uploading of metabolomics data not coming from PiMP
- The gene explorer page needs to be made more generic.
- Optimise queries
- Support multiple projects
- Dockerise this
- Link metabolites back to genes HOT 1
- Metabolite explorer page slow HOT 1
- Add groupings for side tables HOT 2
- Fix Pathway Explorer page Tissue and Age tabs
- Reactome Pathway diagram HOT 2
- Comprehensive metabolite search
- STDs? HOT 2
- Gene names problems on Metabolite Page HOT 1
- Pathway metabolite list doesn't match diagram.
- Add Pathway descriptions to Pathway pages
- When the page is compressed the menu toggle no longer works HOT 1
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