Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

downloads of ontology in csv format results in error if new submission is created but not yet processed #170

Open
alexskr opened this issue Aug 14, 2023 · 1 comment

Comments

@alexskr
Copy link
Member

alexskr commented Aug 14, 2023

When a new submission is created .csv.gz file is removed from the previous submission before the latest submission gets parsed and becomes ready. Downloading ontology in csv format will results in 500 error until latest submission is successfully parsed.
see ncbo/ontologies_api#123

This problem is usually not noticeable because latest submission typically gets parsed within a few minutes after it is created. However, in some edge cases this becomes a problem:

  1. adding an a new UMLS release can take multiple days so downloads of csv is broken at that time.
  2. if latest ontology fails to parse then downloads of csv files will result in error even though it is possible to browse ontology classes in the UI

possible solutions:

  1. delay removing artifacts for previous submissions until after the latest submission is successfully parsed
  2. at the bare minimum api should respond with 404 status instead of 500.
@jvendetti
Copy link
Member

The generation of CSV representations of ontologies is interleaved with indexing. If an ontology fails to index, the CSV will not be generated.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants