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2022-06-02Provide missing argumentFrederick Muriuki Muriithi
2022-05-27Update documentationFrederick Muriuki Muriithi
2022-05-27Remove unnecessary print statementFrederick Muriuki Muriithi
2022-05-27Accept zeroesFrederick Muriuki Muriithi
2022-05-27Revert "Accept exponential notation for standard-error files"Frederick Muriuki Muriithi
This reverts commit 960c1a5b831d8761a3e1716f86ded4cc5b67eea0. After meeting with Arthur, it was confirmed that the CSV file should not have values in the exponential notation.
2022-05-20Accept exponential notation for standard-error filesFrederick Muriuki Muriithi
2022-05-20Use standard-error rather than standard_error for consistencyFrederick Muriuki Muriithi
The CLI scripts use "standard-error" so update the web version to fit in with that.
2022-05-20Fix minor bugsFrederick Muriuki Muriithi
2022-05-20Handle errorsFrederick Muriuki Muriithi
Implement code to handle errors in the processing of files.
2022-05-19Update Web-UI: use new error collection paradigmFrederick Muriuki Muriithi
- README.org: document how to run scripts manually - manifest.scm: remove python-rq as a dependency - qc_app/jobs.py: rework job launching and processing - qc_app/parse.py: use reworked job processing - qc_app/templates/job_progress.html: display progress correctly - qc_app/templates/parse_results.html: display final results - scripts/worker.py: new worker script
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.
2022-05-18Update CLI: use new error collection codeFrederick Muriuki Muriithi
Use the new code that collects the errors in the CLI client.
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.
2022-05-18Simplify slot names and fix namedtuple type nameFrederick Muriuki Muriithi
- replace `line_number` with `line` and `column_number` with `column` to save on slot name lengths. - Fix the type name for the `DuplicateHeading` namedtuple type
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
2022-05-18Return errors when found or None otherwiseFrederick Muriuki Muriithi
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.
2022-05-11Remove unnecessary packages for the CLI versionFrederick Muriuki Muriithi
2022-05-11Update the guix definitions for the applicationFrederick Muriuki Muriithi
2022-05-11Document generating and running qc for/with dockerFrederick Muriuki Muriithi
2022-05-11Tag string as a python f-string to fix error display bugFrederick Muriuki Muriithi
2022-05-09Update documentation and licenseFrederick Muriuki Muriithi
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
2022-05-05Add a guix definition to enable installationFrederick Muriuki Muriithi
2022-05-05Add the long_description field for setuptoolsFrederick Muriuki Muriithi
2022-05-05Add `etc' as a package so that files underneath it are installedFrederick Muriuki Muriithi
2022-05-05Add package management configsFrederick Muriuki Muriithi
2022-05-02Optimise strain names parsingFrederick Muriuki Muriithi
- Use a way faster way of parsing the strains file
2022-04-28Use sqlite3 to save the jobs metadataFrederick Muriuki Muriithi
* Use sqlite to save the jobs metadata and enable UI update of the progress for large files
2022-04-28Update queuing and display results of file parsingFrederick Muriuki Muriithi
* 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.
2022-04-27Enable managing app via setup.pyFrederick Muriuki Muriithi
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.
2022-04-27Implement command-line interface for QC of filesFrederick Muriuki Muriithi
2022-04-26Fix issues caught processing the jobsFrederick Muriuki Muriithi
* Create and push the application context for the worker functions * Fix the update of meta fields
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
2022-04-25Call parsing function. Fix a few issues.Frederick Muriuki Muriithi
* 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
2022-04-25Implement file uploadFrederick Muriuki Muriithi
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.
2022-04-25docs: update documentation on checksFrederick Muriuki Muriithi
2022-04-25UI: Add index page and basic stylingFrederick Muriuki Muriithi
Add template(s) for the index page and some basic styling to get started with.
2022-04-25Ignore the instance directory if present in the repositoryFrederick Muriuki Muriithi
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.
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.
2022-04-20Add scaffolding for web appFrederick Muriuki Muriithi
Add a basic scaffolding for the web interface to the quality-control application.
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
2022-04-13Update `valid_header` to pass check for duplicated headersFrederick Muriuki Muriithi
2022-04-13Add test for duplicate headersFrederick 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
2022-04-13Update Exception nameFrederick Muriuki Muriithi
Change the exception name to be more descriptive.