| Age | Commit message (Expand) | Author |
|---|
| 2024-12-09 | Prevent errors' table header from scrolling away. | Frederick Muriuki Muriithi |
| 2024-12-09 | Handle common typo likely to exist in control files. | Frederick Muriuki Muriithi |
| 2024-12-03 | Display the files metadata in progress section. | Frederick Muriuki Muriithi |
| 2024-12-03 | Retrieve job files metadata. | Frederick Muriuki Muriithi |
| 2024-12-03 | Fix some linting and mypy issues. | Frederick Muriuki Muriithi |
| 2024-12-03 | UI Styling: make table body text slightly smaller. | Frederick Muriuki Muriithi |
| 2024-12-03 | UI: Clip text that is too long. | Frederick Muriuki Muriithi |
| 2024-12-03 | Improve error text...Move the list to the end of the text to make it easier to clip text in
the UI.
| Frederick Muriuki Muriithi |
| 2024-12-03 | Update file metadata using a mapping...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.
| Frederick Muriuki Muriithi |
| 2024-12-03 | Provide consistent way to build file-specific fully-qualified keys | Frederick Muriuki Muriithi |
| 2024-12-03 | Improve UI: stdout/stderr output...Add styling to section and limit the height of the content.
| Frederick Muriuki Muriithi |
| 2024-12-03 | Display cell value...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).
| Frederick Muriuki Muriithi |
| 2024-12-03 | Improve UI: Move if check out of table...Create a new section for the errors display, and only display the
table if there is at least one error.
| Frederick Muriuki Muriithi |
| 2024-12-03 | Enable limiting of number of errors to fetch. | Frederick Muriuki Muriithi |
| 2024-12-03 | Save 'pheno' errors in redis as they are found. | Frederick Muriuki Muriithi |
| 2024-12-03 | Add some phenocovar metadata. | Frederick Muriuki Muriithi |
| 2024-12-03 | Fetch a jobs errors from its errors lists. | Frederick Muriuki Muriithi |
| 2024-12-03 | Save phenocovar errors in redis as they are found. | Frederick Muriuki Muriithi |
| 2024-12-03 | Pass the redis connection and fully qualified job id...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.
| Frederick Muriuki Muriithi |
| 2024-12-03 | Cleanup linting and type (mypy) errors. | Frederick Muriuki Muriithi |
| 2024-12-03 | Wrap everything in try-catch to handle errors gracefully....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.
| Frederick Muriuki Muriithi |
| 2024-12-02 | Add emphasis to important point. | Frederick Muriuki Muriithi |
| 2024-12-02 | Fix typo. | Frederick Muriuki Muriithi |
| 2024-12-02 | Send logs to STDOUT too. | Frederick Muriuki Muriithi |
| 2024-12-02 | Launch job and redirect to job status page. | Frederick Muriuki Muriithi |
| 2024-12-02 | Add UI to view status of the job as it runs. | Frederick Muriuki Muriithi |
| 2024-12-02 | Return 0 on completion of QC processing. | Frederick Muriuki Muriithi |
| 2024-12-02 | Change from 'pending' to 'started' on entry to script....Update the status of the job from 'pending' to 'started' at the
entry-point of the script.
| Frederick Muriuki Muriithi |
| 2024-11-22 | Remove local code that does db connection....Reuse the code in gn-libs for connecting to the database, rather than
using the replicated local code.
| Frederick Muriuki Muriithi |
| 2024-11-22 | Use gn-libs code for db connection....Use the code in gn-libs to connect to the database, rather than a
local module.
| Frederick Muriuki Muriithi |
| 2024-11-22 | Add gn-libs as a dependency. | Frederick Muriuki Muriithi |
| 2024-10-24 | Reduce number of local variables created in function....Use the values in the argparse.Namespace object directly to avoid
creating many local variables.
| Frederick Muriuki Muriithi |
| 2024-10-24 | Add `jobid` to extraction directory...Add the job id to help "group" files that belong to the same job.
| Frederick Muriuki Muriithi |
| 2024-10-24 | Check pheno, phenose, and phenonum files with logging...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.
| Frederick Muriuki Muriithi |
| 2024-10-24 | Check phenocovar files with logging...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.
| Frederick Muriuki Muriithi |
| 2024-10-24 | Fix linting and typing errors. | Frederick Muriuki Muriithi |
| 2024-10-24 | Add a `--loglevel` argument to select loglevel in scripts...To enable selection of log levels within scripts, this commit adds the
`--loglevel` argument to the list of arguments that can be passed to
scripts.
| Frederick Muriuki Muriithi |
| 2024-10-24 | Parse entire namespace object rather than individual values. | Frederick Muriuki Muriithi |
| 2024-10-24 | Move logger creation to `build_main` function...Since the module-level loggers are built mostly the same, move the
creation of the logger to the more general function to reduce
repetition.
| Frederick Muriuki Muriithi |
| 2024-10-24 | Add handler to send log messages to specific Redis list...Class `RedisMessageListHandler` builds a log handler that pushes any
messages logged out to the redis list specified by its
`fullyqualifiedkey` argument.
| Frederick Muriuki Muriithi |
| 2024-10-24 | Update Redis prefix settings. | Frederick Muriuki Muriithi |
| 2024-10-24 | Don't compute settings in configuration file. | Frederick Muriuki Muriithi |
| 2024-10-23 | Add documentation on background jobs. | Frederick Muriuki Muriithi |
| 2024-10-22 | Document emergent general QC structure for CSV files. | Frederick Muriuki Muriithi |
| 2024-10-22 | Refactor `qc_pheno_file` and reuse it for different file types....The QC/QA steps taken by the `qc_pheno_file` function are very
similar across the "pheno", "phenose" and "phenonum" files. This
commit makes the `qc_pheno_file` function a higher-order function and
we pass the file-type specific check(s) as a callable (function) to be
used for the QC/QA process.
| Frederick Muriuki Muriithi |
| 2024-10-22 | Check for errors in `pheno` files. | Frederick Muriuki Muriithi |
| 2024-10-21 | Check `phenocovar` files for errors. | Frederick Muriuki Muriithi |
| 2024-10-21 | Add utilities for reading text files and csv files...The function `read_text_file(…)` will read the raw text file and
return the content line by line.
The function `read_csv_file(…)` builds on `read_text_file(…)` to read
a file as a character-separated-values file. The field separator, and
comment_char characters can be provided to customise how the CSV file
is read.
| Frederick Muriuki Muriithi |
| 2024-10-17 | UI: Create background job when user uploads file. | Frederick Muriuki Muriithi |
| 2024-10-17 | Cleanup: Delete all extracted files after processing. | Frederick Muriuki Muriithi |
