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path: root/quality_control/parsing.py
AgeCommit message (Collapse)Author
2024-01-15Extract common functional tools to separate package.Frederick Muriuki Muriithi
2022-07-19Implement data insertion (averages/means)Frederick Muriuki Muriithi
* 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
2022-06-28Check for inconsistent columnsFrederick Muriuki Muriithi
The number columns in each contents line should be equal to the nember of columns in the header line.
2022-06-15Fix linting and type errorsFrederick Muriuki Muriithi
2022-06-10Enable upload of zipfilesFrederick Muriuki Muriithi
2022-06-02Enable user abortion of file parsingFrederick Muriuki Muriithi
Enable the user to abort the background parsing of the file.
2022-05-19Extract progress indication from the parsingFrederick Muriuki Muriithi
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.
2022-05-18Remove obsoleted code. Fix linting errors.Frederick Muriuki Muriithi
Remove the old code that relied on exceptions to parse errors in the uploaded files.
2022-05-18Parse files with new non-exception functionsFrederick Muriuki Muriithi
Parse the files with the new functions that return error objects instead of raising exceptions
2022-05-02Optimise strain names parsingFrederick Muriuki Muriithi
- Use a way faster way of parsing the strains file
2022-04-27Implement command-line interface for QC of filesFrederick Muriuki Muriithi
2022-04-26Queue file parsing jobsFrederick Muriuki Muriithi
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
2022-04-25Advance seek_position on errorFrederick Muriuki Muriithi
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.
2022-04-25`take`: function to select a few items from an iterableFrederick Muriuki Muriithi
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.
2022-04-21Collect all the errorsFrederick Muriuki Muriithi
Build a function to collect all the parsing errors into a "sequence" of dict objects containing the issues found.
2022-04-20Update parameters for testsFrederick Muriuki Muriithi
Derive a "correct" sample file from an existing sample file with errors for testing with large files. Fix issue caught by test.
2022-04-20Fix linting issuesFrederick Muriuki Muriithi
2022-04-13Implement remaining file parsing testsFrederick Muriuki Muriithi
* Implement remaining file parsing tests and some helpers functions needed for ensuring the tests work.
2022-04-13Check for `DuplicateHeader` errors in `parse_file` functionFrederick Muriuki Muriithi
2022-04-13Implement test for parsing that failsFrederick Muriuki Muriithi
* 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
2022-04-13Add tests outline for file parsingFrederick Muriuki Muriithi
Add dummy failing tests and a stub for the parsing of the files