Fix the epidemology DKG construction pipeline and docker container startup #376
Conversation
This file contains 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
nanglo123
force-pushed
the
fix_dkg_construct
branch
from
6aec354 to
7346375
Compare
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Outdated suggestions cannot be applied.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.
This PR fixes a bug where we incorrectly test for
Xrefobjects from themira.dkg.modelsmodule instead ofXrefobjects from thebioontologies.obographmodule in the DKG construction pipeline. We also remove resources that do not contain any graph data and remove duplicate xref edges.We now test to see if white spaced stripped gilda normalized text evaluates to a truthy value before creating a corresponding
gildaterm as opposed to regular gilda normalized text. The reason for this is that some non-english characters when grounded, return a string with only spaces which would cause the docker container to crash