Implement tiledb_soma_healthcheck component #1055
Open
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
dorien-er
requested changes
Aug 21, 2025
CHANGELOG.md
Outdated
Comment on lines
23
to
27
| * (Experimental) Added `from_h5mu_or_h5ad_to_tiledb` component. Warning: the functionality in this component is experimental | ||
| and its behavior may change in future releases (PR #1034). | ||
|
|
||
| * (Experimental) Added `tiledb_soma_healthcheck` component (PR #1055). | ||
|
|
There was a problem hiding this comment.
Can this be moved to the ## EXPERIMENTAL section of the changelog?
| roles: [ author, maintainer ] | ||
| argument_groups: | ||
| - name: Input database | ||
| description: "Open CellxGene Census by URI." |
There was a problem hiding this comment.
Is this always CxG-specific? Could it not apply to e.g. private TileDB databases?
| ) | ||
| with tiledbsoma.open(par["input_uri"], "w", context=context) as _: | ||
| logger.info("Connection successful!") | ||
| logger.info("Component finished") |
There was a problem hiding this comment.
Can a logger statement be added with some information in case the health check is unsuccesful?
There was a problem hiding this comment.
I could; what extra information are you looking for? Mostly tiledbsoma already adds information in the error message.
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Outdated suggestions cannot be applied.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.
Changelog
Implement tiledb_soma_healthcheck component
Issue ticket number and link
Closes #xxxx (Replace xxxx with the GitHub issue number)Checklist before requesting a review
I have performed a self-review of my code
Conforms to the Contributor's guide
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
CI tests succeed!