Cleanup metadata headers #1367
Merged
Cleanup metadata headers #1367
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
This commit cleans up naming of metadata headers in downloaded metadata TSV. It does the following: 1. Keeps headers as input into "augur export" rather than renaming by title. Thus it has "originating_lab" rather than "Originating lab", "pango_lineage" rather than "PANGO lineage", etc... This should make it easier for people to process downloaded metadata from Auspice alongside metadata provisioned by Nextstrain (via GISAID or via S3). 2. Makes "date" the second column as this is often what's most important. I couldn't figure out a way to intelligently order remaining fields. My first thought was to use metadata.colorings, but this isn't sorted. 3. Fixes "accession". It had been exporting as "[object Object]".
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Outdated suggestions cannot be applied.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
This commit cleans up naming of metadata headers in downloaded metadata TSV. It does the following:
augur exportrather than renaming by title. Thus it has "originating_lab" rather than "Originating lab", "pango_lineage" rather than "PANGO lineage", etc... This should make it easier for people to process downloaded metadata from Auspice alongside metadata provisioned by Nextstrain (via GISAID or via S3).Related issue(s)
I discovered these issues while working on #1366. However I thought it best to separate PRs.
Testing
I've tested locally with a number of datasets provisioned by
npm run get-data.