| Age | Commit message (Expand) | Author |
|---|
| 2022-05-18 | Return errors when found or None otherwise...This commit adds a number of functions that return the error object
when an error is found, or `None` otherwise. It avoids the use of
exceptions as control flow constructs.
| Frederick Muriuki Muriithi |
| 2022-05-11 | Remove unnecessary packages for the CLI version | Frederick Muriuki Muriithi |
| 2022-05-11 | Update the guix definitions for the application | Frederick Muriuki Muriithi |
| 2022-05-11 | Document generating and running qc for/with docker | Frederick Muriuki Muriithi |
| 2022-05-11 | Tag string as a python f-string to fix error display bug | Frederick Muriuki Muriithi |
| 2022-05-09 | Update documentation and license...Add documentation on how to run the development version of the
GeneNetwork Quality Control application.
Update the license to the agpl3+ license used by genenetwork3
| Frederick Muriuki Muriithi |
| 2022-05-05 | Add a guix definition to enable installation | Frederick Muriuki Muriithi |
| 2022-05-05 | Add the long_description field for setuptools | Frederick Muriuki Muriithi |
| 2022-05-05 | Add `etc' as a package so that files underneath it are installed | Frederick Muriuki Muriithi |
| 2022-05-05 | Add package management configs | Frederick Muriuki Muriithi |
| 2022-05-02 | Optimise strain names parsing...- Use a way faster way of parsing the strains file
| Frederick Muriuki Muriithi |
| 2022-04-28 | Use sqlite3 to save the jobs metadata...* Use sqlite to save the jobs metadata and enable UI update of the
progress for large files
| Frederick Muriuki Muriithi |
| 2022-04-28 | Update queuing and display results of file parsing...* Make the 'worker' functions free from needing the application
context by passing all the details they need as arguments.
* Enable the display of parsing results.
| Frederick Muriuki Muriithi |
| 2022-04-27 | Enable managing app via setup.py...While the application is developed with GNU Guix, the end user might
not be using it, and therefore, this commit provides a way for the
user to install the application with the usual python package
management systems.
| Frederick Muriuki Muriithi |
| 2022-04-27 | Implement command-line interface for QC of files | Frederick Muriuki Muriithi |
| 2022-04-26 | Fix issues caught processing the jobs...* Create and push the application context for the worker functions
* Fix the update of meta fields
| Frederick Muriuki Muriithi |
| 2022-04-26 | Queue file parsing jobs...Enable the queuing of file parsing jobs, since the files could be
really large and take a long time to parse and present results.
* etc/default_config.py: Add default config for redis server
* manifest.scm: Add redis, and rq as dependencies
* qc_app/__init__.py
* qc_app/jobs.py: module to hold utilities for management of the jobs
* qc_app/parse.py: Enqueue the job - extract file-parsing code to
callable function
* qc_app/templates/base.html: Enable addition of extra meta tags
* qc_app/templates/job_progress.html: template to display job progress
* qc_app/templates/no_such_job.html: template to indicate when a job
id is invalid
* quality_control/parsing.py: Add the total size parsed so far
| Frederick Muriuki Muriithi |
| 2022-04-25 | Call parsing function. Fix a few issues....* qc_app/entry.py: Pass filetype onward to parsing endpoint
* qc_app/parse.py: Call the function(s) necessary to parse a file
* quality_control/errors.py: Fix argument passing to super class
| Frederick Muriuki Muriithi |
| 2022-04-25 | Implement file upload | Frederick Muriuki Muriithi |
| 2022-04-25 | Advance seek_position on error...Advance the seek position, once we have yielded up an error to causing
an infinite loop in certain conditions, where the `parse_errors`
function ends up resuming the gile in the same position once it
experiences an error.
| Frederick Muriuki Muriithi |
| 2022-04-25 | `take`: function to select a few items from an iterable...To avoid processing all the items in an iterable, the `take` function
is added in this commit. It realised a limited number (specified at
call time) of items from the iterable given.
| Frederick Muriuki Muriithi |
| 2022-04-25 | docs: update documentation on checks | Frederick Muriuki Muriithi |
| 2022-04-25 | UI: Add index page and basic styling...Add template(s) for the index page and some basic styling to get
started with.
| Frederick Muriuki Muriithi |
| 2022-04-25 | Ignore the instance directory if present in the repository...Ignore the flask instance directory if it is present in the
repository. The directory being present in the repository is mostly a
development convenience feature.
| Frederick Muriuki Muriithi |
| 2022-04-21 | Collect all the errors...Build a function to collect all the parsing errors into a "sequence"
of dict objects containing the issues found.
| Frederick Muriuki Muriithi |
| 2022-04-20 | Add scaffolding for web app...Add a basic scaffolding for the web interface to the quality-control
application.
| Frederick Muriuki Muriithi |
| 2022-04-20 | Update parameters for tests...Derive a "correct" sample file from an existing sample file with
errors for testing with large files.
Fix issue caught by test.
| Frederick Muriuki Muriithi |
| 2022-04-20 | Fix linting issues | Frederick Muriuki Muriithi |
| 2022-04-13 | Implement remaining file parsing tests...* Implement remaining file parsing tests and some helpers functions
needed for ensuring the tests work.
| Frederick Muriuki Muriithi |
| 2022-04-13 | Check for `DuplicateHeader` errors in `parse_file` function | Frederick Muriuki Muriithi |
| 2022-04-13 | Update `valid_header` to pass check for duplicated headers | Frederick Muriuki Muriithi |
| 2022-04-13 | Add test for duplicate headers | Frederick Muriuki Muriithi |
| 2022-04-13 | Implement test for parsing that fails...* Improve tests that ensure parsing fails in case the file has errors
* Add strains.csv file
* Implement minimum viable functionality that passes the implemented tests
| Frederick Muriuki Muriithi |
| 2022-04-13 | Add tests outline for file parsing...Add dummy failing tests and a stub for the parsing of the files
| Frederick Muriuki Muriithi |
| 2022-04-13 | Update Exception name...Change the exception name to be more descriptive.
| Frederick Muriuki Muriithi |
| 2022-04-13 | Add sample files for tests...Add some sample files to be used for testing that the parsing works as
expected.
| Frederick Muriuki Muriithi |
| 2022-04-11 | Add missing `__init__.py` to prevent import errors...Without the `tests/__init__.py` file, the tests directory was not
considered a package and therefore, running:
$ pytest
would fail with import error notifications. This fixes that.
| Frederick Muriuki Muriithi |
| 2022-04-11 | Implement MVI for headers validity checking function...Add a minimum viable implementation that passes the tests for the
function that checks for the validity of the headers
| Frederick Muriuki Muriithi |
| 2022-04-11 | Add tests for headers...* Add tests to check for validity of the headers
* Add stubs for the tests
| Frederick Muriuki Muriithi |
| 2022-04-11 | Implement MVP for valid_value functions...* Implement the minimum viable functions for the average and standard
error `valid_value` functions.
| Frederick Muriuki Muriithi |
| 2022-04-11 | Implement tests and stubs for functions under test | Frederick Muriuki Muriithi |
| 2022-04-11 | Set up initial, failing tests for cell values | Frederick Muriuki Muriithi |
| 2022-04-11 | Initialise the QC repository | Frederick Muriuki Muriithi |
