Merged
Conversation
Co-authored-by: Ben Capodanno <31941502+bencap@users.noreply.github.com>
Co-authored-by: Ben Capodanno <31941502+bencap@users.noreply.github.com>
The current column marks whether the mapped variant is considered the most current mapped version of a given variant in the mapped_variants table. This is necessary because we may store multiple mapped versions of a variant. This commit also adds a default value of "1.3" for the VRS version, since all the mapped variants currently in the database use VRS 1.3, and adds a default value of the date of execution for the modification date, since the modification date should keep track of when the row was last updated.
These columns will store metadata about the hashed ids used to store the target sequence, if applicable, in Seqrepo during mapping, as well as hashed ids that point to the accession id of the target gene or mapped reference in Seqrepo. Also stores human-readable labels for mapped reference sequences.
Logging now requires jobs to be retained, so instead of using the same job id for all mapping jobs, instead track the job id of the currently running mapping job and check whether that job has completed before queueing a new job. Also, add more exception handling to worker mapping job.
Previously used processing state enum for mapping state field, but this caused database constraint issues.
Merged
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
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
No description provided.