Switch Andersen lab metadata #54
Merged
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
Previous metadata file in the Andersen lab repo is no longer getting updated. It was last updated April 26, 2024.¹ The repo now automatically updates a new metadata CSV file since andersen-lab/avian-influenza#2 ¹ https://github.com/andersen-lab/avian-influenza/blob/f04267ba8d2fcace275bd5b01e120abf036e3fec/metadata/PRJNA1102327_metadata.csv
Fixes critical errors that prevented the andersen-lab ingest workflow from running due to the switch to the new automated CSV file in the previous commit. There will be a a series of other improvements in subsequent commits to clean up the workflow.
The automated CSV file from Andersen lab includes the region and country columns as `geo_loc_name_country_continent` and `geo_loc_name_country` respectively, so we no longer have to hardcode their values.
Preparing for using the same script for the Andersen lab ingest, where the `old_name` for host values include more variations on capitalizations.
The automated metadata has a lot more host values so it makes more sense to use the same `transform-host` script as the NCBI ingest. This also helps to ensure that they all use the same standard hosts.
Instead of doing custom date transformations in `curate-andersen-lab-data`, just use `augur curate format-dates`.
Allow users to add annotations for the Andersen lab data.
I didn't want to use the user annotations for 150+ records' date and division data, so I opted to just join the old metadata with the new automated metadata.
trvrb
approved these changes
Jun 10, 2024
|
I triggered the ingest-ncbi GH Action workflow after merging to update the S3 data. |
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.
Description of proposed changes
Uses the latest automated metadata for the Andersen lab ingest workflow and includes small improvements for the Andersen lab ingest.
I ran the workflow locally then compared the output metadata with the production metadata on S3. There were no differences in the previous records, but I do see an addition of 382 records from the Andersen lab ingest.
Related issue(s)
Resolves #53
Checklist