| Age | Commit message (Expand) | Author |
|---|
| 2024-12-03 | Fix some linting and mypy issues. | 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 | 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 | 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 | 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 | Fix typo. | Frederick Muriuki Muriithi |
| 2024-12-02 | Send logs to STDOUT too. | 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 | 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 |
| 2024-10-24 | 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 |
| 2024-10-22 | 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 |
| 2024-10-17 | Cleanup: Delete all extracted files after processing. | Frederick Muriuki Muriithi |
| 2024-10-17 | Leave TODO notes for what needs to be done. | Frederick Muriuki Muriithi |
| 2024-10-17 | Fetch samples from database...Fetch the samples from the database. These will be used to verify
that the samples in the phenotype files already exist in the database
and are valid.
| Frederick Muriuki Muriithi |
| 2024-10-17 | Undo transpose for any transposed files...To reduce the complexity involved in the processing of the files, we
undo any transposition of the CSV files for those files that are
marked as transposed.
| Frederick Muriuki Muriithi |
| 2024-10-17 | Pass new arguments to QC function. | Frederick Muriuki Muriithi |
| 2024-10-17 | Add `speciesid` and `populationid` arguments to the script. | Frederick Muriuki Muriithi |
| 2024-10-17 | Add the working directory argument to the script....Add a `--working-dir` argument to allow passing a directory where the
script process the files within. If not provided, it defaults to a
directory within the systems temporary directory.
| Frederick Muriuki Muriithi |
| 2024-10-17 | Extract the R/qtl2 bundle for processing....To enable processing of the files individually, this commit will
enable the extraction of the files into a known working directory in
which all further processing will take place.
| Frederick Muriuki Muriithi |
| 2024-10-17 | Extract common functions. | Frederick Muriuki Muriithi |
| 2024-10-17 | Save errors for each file in lists. Parallelise error checking....* Save the errors for each file in a redis list for that file.
* Make error checking parallel, i.e. ensure every file of a particular
type is checked completely independent of other files of the same
type.
| Frederick Muriuki Muriithi |
| 2024-10-17 | Rewrite the QC code for R/qtl2 | Frederick Muriuki Muriithi |
| 2024-10-14 | Initialise background script for running QC on phenotype bundles. | Frederick Muriuki Muriithi |
| 2024-10-14 | BugFix: Use provided prefix...Use the provided prefix rather than calling `jobs.jobsnamespace()`
function that depends of an app context existing.
| Frederick Muriuki Muriithi |
| 2024-10-14 | Make addition of arguments independent of each other. | Frederick Muriuki Muriithi |
| 2024-09-09 | Enable samples uploads. | Frederick Muriuki Muriithi |
| 2024-09-03 | Initialise the populations package and update references. | Frederick Muriuki Muriithi |
| 2024-08-28 | Move code handling expression data upload into new module. | Frederick Muriuki Muriithi |
| 2024-08-16 | Log out correct parameters. | Frederick Muriuki Muriithi |
| 2024-08-13 | Bug: cross reference with NULL cM when "gmap" file is absent...The "gmap" file might not exist in some bundles. In those instances,
cross-reference the data without including the genotypes' physical
positions (cM).
| Frederick Muriuki Muriithi |
| 2024-08-12 | Rename module: Module contains exceptions classes. | Frederick Muriuki Muriithi |
| 2024-08-08 | Fix bugs and pass in logger to functions. | Frederick Muriuki Muriithi |
| 2024-08-06 | Pass logger on to inner functions...Pass the logger forward to inner functions to help with debugging things.
| Frederick Muriuki Muriithi |
| 2024-07-25 | Fix typing and linting errors. | Frederick Muriuki Muriithi |
| 2024-07-25 | Rename module: qc_app --> uploader | Frederick Muriuki Muriithi |
