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MetabolicAtlas / data-files

Source data files used when deploying Metabolic Atlas
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feat: update all models #8

Closed mihai-sysbio closed 3 years ago

mihai-sysbio commented 3 years ago

This PR supersedes the other two PRs created with the same purpose, #4 an #7, which will be closed in favor of this one.

With this PR we fetch the latest (pre-)releases from all the models - model yml file and all existing annotation tsv files. The single exception is Yeast-GEM, where the latest release 8.5.0 changes the subsystems in a way that breaks compatibility with the maps. For this model, we will wait for the next release.

The file Yeast-GEM/subsystemSVG.tsv has been sorted alphabetically and the commented-out lines were removed.

From now on, all files in /integrated-models will be stored without Git LFS, in order to facilitate diff-ing and file content inspection.

mihai-sysbio commented 3 years ago

Thank you @inghylt for noticing this. There is a version field in both the integratedModels.json and each model yml file. Since this is an eager integration of the updated models, the yml files have an empty version. Commit 902e0b8 addresses this. In the normal case of integrating updates, this should not be a problem.

mihai-sysbio commented 3 years ago

Thank you all for the reviews. I hope the last commit isn't breaking things, so I'm going to merge. I still think it would be nicer to have an improved solution to how the *SVG.tsv files are handled, but let's do that in #9 to keep the focus of this PR on updating the model files.

mihai-sysbio commented 3 years ago

I could not find any SVG for Chondroitin sulfate degradation so the reference to it in Human-GEM as a subsystem SVG had to be removed in 811457d.