| Age | Commit message (Expand) | Author |
|---|
| 2024-02-20 | Track filename in the errors...R/qtl2 bundles can contain more than one file, of the same type. When
errors are encountered in any of the files, we need to be able to
inform the user which file it is, in addition to the line and column
number.
| Frederick Muriuki Muriithi |
| 2024-01-20 | Fetch sample/case names from database...Fetch the sample/case names from the database rather than from a
static file in the repository.
Issue:
https://issues.genenetwork.org/issues/quality-control/read-samples-from-database-by-species
| Frederick Muriuki Muriithi |
| 2024-01-15 | Update imports: `take` was moved to different package. | Frederick Muriuki Muriithi |
| 2024-01-15 | Extract common functional tools to separate package. | Frederick Muriuki Muriithi |
| 2022-07-19 | Implement data insertion (averages/means)...* quality_control/file_utils.py (new file): extract common file
utilities.
* quality_control/parsing.py (refactor): extract common file
utilities.
* scripts/insert_data.py: Implement data insertion for averages/means
| Frederick Muriuki Muriithi |
| 2022-06-28 | Check for inconsistent columns...The number columns in each contents line should be equal to the nember
of columns in the header line.
| Frederick Muriuki Muriithi |
| 2022-06-15 | Fix linting and type errors | Frederick Muriuki Muriithi |
| 2022-06-10 | Enable upload of zipfiles | Frederick Muriuki Muriithi |
| 2022-06-02 | Enable user abortion of file parsing...Enable the user to abort the background parsing of the file.
| Frederick Muriuki Muriithi |
| 2022-05-19 | Extract progress indication from the parsing...Since progress indication is not part of the parsing, this commit
extracts the progress indication into functions with well defined
input arguments that hide the progress indication logic from the
parsing function.
| Frederick Muriuki Muriithi |
| 2022-05-18 | Remove obsoleted code. Fix linting errors....Remove the old code that relied on exceptions to parse errors in the
uploaded files.
| Frederick Muriuki Muriithi |
| 2022-05-18 | Parse files with new non-exception functions...Parse the files with the new functions that return error objects
instead of raising exceptions
| Frederick Muriuki Muriithi |
| 2022-05-02 | Optimise strain names parsing...- Use a way faster way of parsing the strains file
| Frederick Muriuki Muriithi |
| 2022-04-27 | Implement command-line interface for QC of files | 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 | 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 |
| 2022-04-21 | 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 | 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 | 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 |
