Batch CURIE validation requests and fix Ubergraph TLS#46
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Fix #13
CURIE validation was sending one giant SPARQL query no matter how long the term list was, which slows things down and times out on large inputs. I added chunking so both validation and obsolete-term lookups break their queries into manageable batches, plus new tests to assert the chunking behavior. While running tests I kept hitting TLS errors against Ubergraph, so I pulled in certifi and wired the CA bundle into our SPARQL helper. Finally, I cleaned up docstrings/type hints across the touched modules and expanded .gitignore so local IDE/OS files stay out of git status.