Closed e0 closed 3 years ago
In theory, using the organism is more generic, but in practice it does not make a difference for us. I haven't tested this but the change looks good.
It looks like the organism
field is missing from the newer data files. For example: https://github.com/MetabolicAtlas/data-files/blob/feat/more-models/integrated-models/Human-GEM/Human-GEM.yml
I assume the feat/more-models
branch represents the new format going forward so I made this change. The short_name
also exists in both versions so it looks like the safer option for both cases.
Edit: updated PR description to reflect this as well.
Perhaps silly question, but how can I recreate the problem? I assume it's related to what's shown in Interaction Partners?
Perhaps silly question, but how can I recreate the problem? I assume it's related to what's shown in Interaction Partners?
Sorry, I should have been more specific in the PR description. You could checkout the feat/more-models
branch from the data-files
repo and rebuild the stack. After this if you try to go to the 3D map viewer and apply some RNA levels, all the circle nodes should be gray.
The
isHuman
fromconst isHuman = metadataSection.organism === 'Homo sapiens';
is used to populate the HPA RNA levels. In the newer data files, theorganism
field is missing, which meansisHuman
is always false, which in turn means the HPA RNA levels do not get populated. This PR uses theshort_name
field instead, which exists in both the older and newer data files.