| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 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 |
| 2024-10-17 | Ignore comment lines. | Frederick Muriuki Muriithi |
| 2024-10-17 | Implement sha256 hashing over file contents. | Frederick Muriuki Muriithi |
| 2024-10-17 | Add test for function to compute file hash. | Frederick Muriuki Muriithi |
| 2024-10-17 | Rename test module. | Frederick Muriuki Muriithi |
| 2024-10-17 | mypy: Fix some typing issues. | Frederick Muriuki Muriithi |
| 2024-10-14 | Initialise background script for running QC on phenotype bundles. | Frederick Muriuki Muriithi |
| 2024-10-14 | Update typing information. | 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 |
| 2024-10-14 | Improve error messages for R/qtl2 code. | Frederick Muriuki Muriithi |
| 2024-10-14 | Improve UI copy: Add list of files used. | Frederick Muriuki Muriithi |
| 2024-10-14 | Improve layout and styling of sidebar content | Frederick Muriuki Muriithi |
| 2024-10-10 | UI hints: Help user in choosing the appropriate option. | Frederick Muriuki Muriithi |
| 2024-10-10 | Build UI to add new phenotypes....Build the UI and set up styling. This is not working currently.
| Frederick Muriuki Muriithi |
| 2024-10-10 | Limit the length of the population description | Frederick Muriuki Muriithi |
| 2024-10-07 | Handle "No linked resource" error cleanly....Display the page even if there is no linked resource, but keep the
sensitive information hidden in such cases.
| Frederick Muriuki Muriithi |
| 2024-10-07 | Add phenotype units to UI | Frederick Muriuki Muriithi |
| 2024-10-07 | Reuse requests checks to fix "too many returns" linting error | Frederick Muriuki Muriithi |
| 2024-10-07 | linting: Fix minor linting issues. | Frederick Muriuki Muriithi |
| 2024-10-07 | Create new phenotype dataset (PublishFreeze)....Provide the UI and code to create a new phenotype dataset.
| Frederick Muriuki Muriithi |
| 2024-10-07 | Extract reusable input validation code. | Frederick Muriuki Muriithi |
| 2024-10-07 | Generalise pagination and paginate phenotypes...Generalise the code generating table pagination UI, and use it to
paginate the list of phenotypes.
| Frederick Muriuki Muriithi |
| 2024-10-02 | Add missing __init__.py | Frederick Muriuki Muriithi |
| 2024-10-01 | Add UI elements for possible extra functionality. | Frederick Muriuki Muriithi |
| 2024-10-01 | Extract privileges and use them for access control | Frederick Muriuki Muriithi |
| 2024-09-30 | BugFix: Ensure all data items show up. | Frederick Muriuki Muriithi |
