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2022-07-19Rename file validation scriptFrederick Muriuki Muriithi
As preparation for building a new generic worker script, this commit renames the file validation script from 'worker.py' to 'validate_file.py' so as to ensure the name conforms better to what the script does.
2022-07-19Implement confirmation stageFrederick Muriuki Muriithi
Provide user with a confirmation stage where they can verify all the data before inserting into the database.
2022-07-19Enable creation of new datasetFrederick Muriuki Muriithi
Enable the user to create a new dataset should the need arise. A few extra fixes were done, such as: - Provide list of average methods to choose from - Provide input elements for some expected fields - Add a new confirmation step before doing the actual data update
2022-07-19Replace redirect with user confirmationFrederick Muriuki Muriithi
Rather than using the redirect, that led to exposing the study id as a get parameter, this commit adds an auxilliary step that allows the user to choose whether to continue with the new study or go back and select an existing study.
2022-07-19Implement dataset selectionFrederick Muriuki Muriithi
- Implement UI enabling selection from existing datasets - Start implementation of UI that enables creation of new dataset
2022-07-19Implement study creationFrederick Muriuki Muriithi
Enable the creation of the new study, and redirect appropriately with the new study id.
2022-07-19Fix macroFrederick Muriuki Muriithi
2022-07-19Add missing db_utils moduleFrederick Muriuki Muriithi
2022-07-19Add 'group' and 'tissue' selection.Frederick Muriuki Muriithi
- Build code to populate the "Group" and "Tissue" dropdown lists - Enable redirect with POST data (code 307) in case there is input error to enable the user fix their errors - Move hidden fields to macro to reduce repetition
2022-07-19Implement select studyFrederick Muriuki Muriithi
Implement the select study UI
2022-07-19Select the platform (GeneChipId) firstFrederick Muriuki Muriithi
2022-07-07Rework guix.scm to use latest commitFrederick Muriuki Muriithi
Rather than specifying a specific commit in the development guix.scm this commit has the system automatically get the latest commit and use that for building the package object.
2022-07-07Fix linting and typing errorsFrederick Muriuki Muriithi
2022-07-07Fix testFrederick Muriuki Muriithi
2022-07-07Replace 'magic' with builtin 'mimetypes'Frederick Muriuki Muriithi
Use the builtin mimetypes which gives better results
2022-07-07Rework styling for form elementsFrederick Muriuki Muriithi
2022-07-07Add filetype details to database update codeFrederick Muriuki Muriithi
The filetype determines the queries to be run to update the database, therefore, this commit adds filetype information.
2022-07-07Provide selection for GeneChipsFrederick Muriuki Muriithi
The GeneChipId value is required for the data being inserted, so this commit provides the UI to enable selection of the chip.
2022-07-06Implement UI for dataset selectionFrederick Muriuki Muriithi
As part of updating the database with the new data, there is a need to select the appropriate dataset that the data belongs to, and this commit provides the UI to assist the user do that.
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.
2022-06-22Test zipfiles uploads: commit forgotten testsFrederick Muriuki Muriithi
2022-06-22Test the results pagesFrederick Muriuki Muriithi
2022-06-21Test the progress indication featureFrederick Muriuki Muriithi
2022-06-21Rename fixture: fixture gives back the redis url, not a serverFrederick Muriuki Muriithi
2022-06-21Update tests: Ensure errors return status code 400Frederick Muriuki Muriithi
2022-06-21Test the upload of zip files works as expectedFrederick Muriuki Muriithi
- Ensure errors respond with status code 400 - Ensure error messages are displayed for any invalid zip file that is uploaded.
2022-06-17Add configs for pytestFrederick Muriuki Muriithi
2022-06-17Test 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.
2022-06-16Add more UI testsFrederick Muriuki Muriithi
- Test upload with missing or invalid data - Test triggering the parsing of the file
2022-06-15Fix linting and type errorsFrederick Muriuki Muriithi
2022-06-15Setup test fixtures and initial tests for web-UIFrederick Muriuki Muriithi
2022-06-13Add upload progress indicatorFrederick Muriuki Muriithi
2022-06-10Enable upload of zipfilesFrederick Muriuki Muriithi
2022-06-10Update tests: Accept zeroes as valid valuesFrederick Muriuki Muriithi
2022-06-02Enable user abortion of file parsingFrederick Muriuki Muriithi
Enable the user to abort the background parsing of the file.
2022-06-02Expire the jobs in 14 days by defaultFrederick Muriuki Muriithi
2022-06-02Add an error display to the progress status reportFrederick Muriuki Muriithi
Enable the progress status page to show all the errors found at any point during the processing of the file.
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.
generated by cgit v1.2.3 (git 2.44.0) at 2024-07-16 10:18:44 +0000