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11 daysPrompt for the files.Frederick Muriuki Muriithi
11 daysPrompt for file structure details.Frederick Muriuki Muriithi
12 daysAdd incomple template for uploading individual files.Frederick Muriuki Muriithi
12 daysCreate new base templates for upload of phenotype.Frederick Muriuki Muriithi
Implement the common UI features, for fetching publication details.
12 daysUpdate link text.Frederick Muriuki Muriithi
14 daysAdd menu entry for platforms in "View Species" page.Frederick Muriuki Muriithi
14 daysRetain population for "List Markers" pageFrederick Muriuki Muriithi
For UI consistency, and as a convenience to the users, retain the population details for the "List Markers" page to help them navigate more easily using the breadcrumbs.
14 daysReorder menus in the populations page.Frederick Muriuki Muriithi
Make the order of the menus a little closer to the likely order of data upload.
14 daysDeactivate access to incomplete/unimplemented features.Frederick Muriuki Muriithi
14 daysRedirect if there's only a single phenotype datasetFrederick Muriuki Muriithi
If a particular population has only a single phenotype dataset, redirect to the dataset view page rather than listing the only dataset.
14 daysUse specialised template renderer for phenotypes.Frederick Muriuki Muriithi
Use the specialised template renderer to keep the rendering consistent.
14 daysUI: Remove extraneous text in "View*" pages.Frederick Muriuki Muriithi
14 daysImprove breadcrumbsFrederick Muriuki Muriithi
Update the breadcrumb links such that each will lead back the parent section rather than to generic section pages. This is updated for the relevant parts of the UI.
2024-12-09Prevent user from continuing on error.Frederick Muriuki Muriithi
2024-12-09Prevent errors' table header from scrolling away.Frederick Muriuki Muriithi
2024-12-09Handle common typo likely to exist in control files.Frederick Muriuki Muriithi
2024-12-03Display the files metadata in progress section.Frederick Muriuki Muriithi
2024-12-03Retrieve job files metadata.Frederick Muriuki Muriithi
2024-12-03Fix some linting and mypy issues.Frederick Muriuki Muriithi
2024-12-03UI Styling: make table body text slightly smaller.Frederick Muriuki Muriithi
2024-12-03UI: Clip text that is too long.Frederick Muriuki Muriithi
2024-12-03Improve error textFrederick Muriuki Muriithi
Move the list to the end of the text to make it easier to clip text in the UI.
2024-12-03Update file metadata using a mappingFrederick Muriuki Muriithi
Update the metadata using a mapping rather than updating a field at a time to make it easier to ensure everything is updated in one go.
2024-12-03Provide consistent way to build file-specific fully-qualified keysFrederick Muriuki Muriithi
2024-12-03Improve UI: stdout/stderr outputFrederick Muriuki Muriithi
Add styling to section and limit the height of the content.
2024-12-03Display cell valueFrederick Muriuki Muriithi
Display the cell value to enable the user compare the error message to the actual value, in order to figure out how to fix the error(s).
2024-12-03Improve UI: Move if check out of tableFrederick Muriuki Muriithi
Create a new section for the errors display, and only display the table if there is at least one error.
2024-12-03Enable limiting of number of errors to fetch.Frederick Muriuki Muriithi
2024-12-03Save 'pheno' errors in redis as they are found.Frederick Muriuki Muriithi
2024-12-03Add some phenocovar metadata.Frederick Muriuki Muriithi
2024-12-03Fetch a jobs errors from its errors lists.Frederick Muriuki Muriithi
2024-12-03Save phenocovar errors in redis as they are found.Frederick Muriuki Muriithi
2024-12-03Pass the redis connection and fully qualified job idFrederick Muriuki Muriithi
Pass the redis connection on to the function used to build main since it might need to use a connection to redis. Also pass the computed fully qualified job id rather than recomputing it every time. Update dependent functions to take the new arguments.
2024-12-03Cleanup linting and type (mypy) errors.Frederick Muriuki Muriithi
2024-12-03Wrap everything in try-catch to handle errors gracefully.Frederick Muriuki Muriithi
Put everything in the build_main function within a try-catch block to ensure we capture all exceptions that might occur in different scripts and log them out. This helps with debugging errors in the asynchronous scripts.
2024-12-02Add emphasis to important point.Frederick Muriuki Muriithi
2024-12-02Fix typo.Frederick Muriuki Muriithi
2024-12-02Send logs to STDOUT too.Frederick Muriuki Muriithi
2024-12-02Launch job and redirect to job status page.Frederick Muriuki Muriithi
2024-12-02Add UI to view status of the job as it runs.Frederick Muriuki Muriithi
2024-12-02Return 0 on completion of QC processing.Frederick Muriuki Muriithi
2024-12-02Change from 'pending' to 'started' on entry to script.Frederick Muriuki Muriithi
Update the status of the job from 'pending' to 'started' at the entry-point of the script.
2024-11-22Remove local code that does db connection.Frederick Muriuki Muriithi
Reuse the code in gn-libs for connecting to the database, rather than using the replicated local code.
2024-11-22Use gn-libs code for db connection.Frederick Muriuki Muriithi
Use the code in gn-libs to connect to the database, rather than a local module.
2024-11-22Add gn-libs as a dependency.Frederick Muriuki Muriithi
2024-10-24Reduce number of local variables created in function.Frederick Muriuki Muriithi
Use the values in the argparse.Namespace object directly to avoid creating many local variables.
2024-10-24Add `jobid` to extraction directoryFrederick Muriuki Muriithi
Add the job id to help "group" files that belong to the same job.
2024-10-24Check pheno, phenose, and phenonum files with loggingFrederick Muriuki Muriithi
Add logging to the `qc_pheno_file` function so that we get the messages pushed to redis for every file that is being checked for errors.
2024-10-24Check phenocovar files with loggingFrederick Muriuki Muriithi
Build a function-scope logger using the new `scripts.redis_logger.RedisMessageListHandler` log handler to log-out the messages for each phenocovar file being processed in a more thread-safe way.
2024-10-24Fix linting and typing errors.Frederick Muriuki Muriithi