| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-06-21 | Test the progress indication feature | Frederick Muriuki Muriithi | |
| 2022-06-21 | Rename fixture: fixture gives back the redis url, not a server | Frederick Muriuki Muriithi | |
| 2022-06-21 | Update tests: Ensure errors return status code 400 | Frederick Muriuki Muriithi | |
| 2022-06-21 | Test the upload of zip files works as expected | Frederick Muriuki Muriithi | |
| - Ensure errors respond with status code 400 - Ensure error messages are displayed for any invalid zip file that is uploaded. | |||
| 2022-06-17 | Add configs for pytest | Frederick Muriuki Muriithi | |
| 2022-06-17 | Test endpoint '/parse/parse' | Frederick Muriuki Muriithi | |
| * Ensure error messages are displayed if a request is made to the '/parse/parse' endpoint with invalid, or missing data. | |||
| 2022-06-16 | Add more UI tests | Frederick Muriuki Muriithi | |
| - Test upload with missing or invalid data - Test triggering the parsing of the file | |||
| 2022-06-15 | Fix linting and type errors | Frederick Muriuki Muriithi | |
| 2022-06-15 | Setup test fixtures and initial tests for web-UI | Frederick Muriuki Muriithi | |
| 2022-06-13 | Add upload progress indicator | Frederick Muriuki Muriithi | |
| 2022-06-10 | Enable upload of zipfiles | Frederick Muriuki Muriithi | |
| 2022-06-10 | Update tests: Accept zeroes as valid values | Frederick Muriuki Muriithi | |
| 2022-06-02 | Enable user abortion of file parsing | Frederick Muriuki Muriithi | |
| Enable the user to abort the background parsing of the file. | |||
| 2022-06-02 | Expire the jobs in 14 days by default | Frederick Muriuki Muriithi | |
| 2022-06-02 | Add an error display to the progress status report | Frederick Muriuki Muriithi | |
| Enable the progress status page to show all the errors found at any point during the processing of the file. | |||
| 2022-06-02 | Provide missing argument | Frederick Muriuki Muriithi | |
| 2022-05-27 | Update documentation | Frederick Muriuki Muriithi | |
| 2022-05-27 | Remove unnecessary print statement | Frederick Muriuki Muriithi | |
| 2022-05-27 | Accept zeroes | Frederick Muriuki Muriithi | |
| 2022-05-27 | Revert "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. | |||
| 2022-05-20 | Accept exponential notation for standard-error files | Frederick Muriuki Muriithi | |
| 2022-05-20 | Use standard-error rather than standard_error for consistency | Frederick Muriuki Muriithi | |
| The CLI scripts use "standard-error" so update the web version to fit in with that. | |||
| 2022-05-20 | Fix minor bugs | Frederick Muriuki Muriithi | |
| 2022-05-20 | Handle errors | Frederick Muriuki Muriithi | |
| Implement code to handle errors in the processing of files. | |||
| 2022-05-19 | Update Web-UI: use new error collection paradigm | Frederick 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 | |||
| 2022-05-19 | Extract progress indication from the parsing | Frederick 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. | |||
| 2022-05-18 | Update CLI: use new error collection code | Frederick Muriuki Muriithi | |
| Use the new code that collects the errors in the CLI client. | |||
| 2022-05-18 | Remove obsoleted code. Fix linting errors. | Frederick Muriuki Muriithi | |
| Remove the old code that relied on exceptions to parse errors in the uploaded files. | |||
| 2022-05-18 | Simplify slot names and fix namedtuple type name | Frederick 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 | |||
| 2022-05-18 | Parse files with new non-exception functions | Frederick Muriuki Muriithi | |
| Parse the files with the new functions that return error objects instead of raising exceptions | |||
| 2022-05-18 | Return errors when found or None otherwise | Frederick 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. | |||
| 2022-05-11 | 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 | Frederick 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 | |||
| 2022-05-05 | 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 | Frederick Muriuki Muriithi | |
| - Use a way faster way of parsing the strains file | |||
| 2022-04-28 | Use sqlite3 to save the jobs metadata | Frederick Muriuki Muriithi | |
| * Use sqlite to save the jobs metadata and enable UI update of the progress for large files | |||
| 2022-04-28 | Update queuing and display results of file parsing | Frederick 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. | |||
| 2022-04-27 | Enable managing app via setup.py | Frederick 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. | |||
| 2022-04-27 | Implement command-line interface for QC of files | Frederick Muriuki Muriithi | |
| 2022-04-26 | Fix issues caught processing the jobs | Frederick Muriuki Muriithi | |
| * Create and push the application context for the worker functions * Fix the update of meta fields | |||
| 2022-04-26 | Queue file parsing jobs | Frederick 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 | |||
| 2022-04-25 | Call 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 | |||
| 2022-04-25 | Implement file upload | Frederick Muriuki Muriithi | |
| 2022-04-25 | Advance seek_position on error | Frederick 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. | |||
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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