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Push BCOs to https://data.tst.glygen.org/ #1581

Closed katewarner closed 2 months ago

katewarner commented 2 months ago

All BCOs for 2.6 have been created and reviewed. Push to TST. #1502

All BCOs have been created and passed the error check, except the user dataset human_proteoform_glycosylation_sites_platelet_olinked.csv which is still being created.

rykahsay commented 2 months ago

Then why do I still get this?

$ python3 /software/glygen/check-bco2filename-mapping.py  | grep ERROR
NO-BCO,mouse_protein_pdb_map.csv,ERROR,in_fs
NO-BCO,sarscov1_protein_pdb_map.csv,ERROR,in_fs
NO-BCO,yeast_protein_pdb_map.csv,ERROR,in_fs
NO-BCO,rat_protein_pdb_map.csv,ERROR,in_fs
NO-BCO,fruitfly_protein_pdb_map.csv,ERROR,in_fs
NO-BCO,sarscov2_protein_pdb_map.csv,ERROR,in_fs
NO-BCO,fruitfly_proteoform_glycosylation_sites_carbbank.csv,ERROR,in_fs
NO-BCO,human_protein_pdb_map.csv,ERROR,in_fs
NO-BCO,protein_reaction2ec_rhea.csv,ERROR,in_fs
NO-BCO,chicken_proteoform_glycosylation_sites_carbbank.csv,ERROR,in_fs
NO-BCO,pig_proteoform_glycosylation_sites_carbbank.csv,ERROR,in_fs
NO-BCO,dicty_proteoform_glycosylation_sites_carbbank.csv,ERROR,in_fs
NO-BCO,hcv1a_protein_pdb_map.csv,ERROR,in_fs
NO-BCO,pig_protein_pdb_map.csv,ERROR,in_fs
NO-BCO,hcv1b_protein_pdb_map.csv,ERROR,in_fs
NO-BCO,chicken_protein_pdb_map.csv,ERROR,in_fs
NO-BCO,dicty_protein_pdb_map.csv,ERROR,in_fs
NO-BCO,arabidopsis_protein_pdb_map.csv,ERROR,in_fs
ubhuiyan commented 2 months ago

@rykahsay All BCOs for 2.6 have been created. Please push to tst.

rykahsay commented 2 months ago

@ubhuiyan are you running "python3 /software/glygen/check-bco2filename-mapping.py"? When I do that, I still see some ERRORs:

$ python3 /software/glygen/check-bco2filename-mapping.py | grep ERROR
NO-BCO,fruitfly_proteoform_glycosylation_sites_carbbank.csv,ERROR,in_fs
NO-BCO,chicken_proteoform_glycosylation_sites_carbbank.csv,ERROR,in_fs
NO-BCO,pig_proteoform_glycosylation_sites_carbbank.csv,ERROR,in_fs
NO-BCO,dicty_proteoform_glycosylation_sites_carbbank.csv,ERROR,in_fs
katewarner commented 2 months ago

Sorry Robel, you can ignore those datasets as they are empty. Urnisha has removed these organisms for this dataset from the dataset-masterlist.json. Would you like us to delete these datasets?

ubhuiyan commented 2 months ago

I don't think I have permission to remove those empty files from the unreviewed folder. If they do need to be removed, Robel you can remove those files and continue with pushing to tst.

rykahsay commented 2 months ago

Please close this ticket