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2022-11-16ui: Don't show upload progress indicator if file is not selected.Frederick Muriuki Muriithi
2022-11-16tests: Fix some failing testsFrederick Muriuki Muriithi
2022-11-16qc: Allow whole numbers or numbers where the decimals are all zeroesFrederick Muriuki Muriithi
2022-11-16ui: Only display the "alert-success" green on completion...* To avoid confusion, only display the "alert-success" green on completion of the parsing process. While parsing, if there are no errors, then display the "No errors found so far" message without the green colour. Frederick Muriuki Muriithi
2022-11-12Accept plain text (text/plain) filesFrederick Muriuki Muriithi
2022-09-16Add redis and mariadb as propagated inputsFrederick Muriuki Muriithi
2022-09-16Deactivate testsFrederick Muriuki Muriithi
2022-09-16Config: Add apache2 sample config fileFrederick Muriuki Muriithi
2022-09-16Add dependency: gunicorn...* guix.scm: Add dependency (gunicorn) Frederick Muriuki Muriithi
2022-09-08Use sys.executable and setup default environment...Use the sys.executable to get the correct python binary to run the external processes, and setup the environment to point to the correct PYTHONPATH. Frederick Muriuki Muriithi
2022-09-08Update dependencies...* guix.scm: reorganise the dependencies * setup.cfg: change the `install_requires` values Frederick Muriuki Muriithi
2022-08-31Commit missing files.Frederick Muriuki Muriithi
2022-08-31Update test: use new script name.Frederick Muriuki Muriithi
2022-08-31Provide database port where relevant.Frederick Muriuki Muriithi
2022-08-31Check connections outside app factory...Check the connections in the wsgi.py file, outside of the `create_app` application factory to avoid issues with tests failing due to test app not initialising because of missing connections in the test environment. Frederick Muriuki Muriithi
2022-08-05Update job status. Display stdout and stderr outputs...* Display the status of the job, as it is running * Display STDERR output if an error occurs * Display STDOUT output as job is running and on successful completion of the job Frederick Muriuki Muriithi
2022-08-04Implement data insertion...- Hook up external data insertion script to webserver code - Provide rudimentary status indication - Generalise some job creation details Frederick Muriuki Muriithi
2022-08-04Handle stderr output...* Fix bug where stderr was not being updated on redis appropriately Frederick Muriuki Muriithi
2022-08-04Format queries for output. Get rid of extraneous output.Frederick Muriuki Muriithi
2022-08-04Fix typo: 'species' -> 'speciesid'Frederick Muriuki Muriithi
2022-08-04UX: Enable selecting radio by clicking anywhere on the row...Ease the selection of a radio button by allowing the user to click on any of the table cells that are in the same row as the radio button of concern. Frederick Muriuki Muriithi
2022-07-19Save standard error data. Fix linting and typing errors.Frederick Muriuki Muriithi
2022-07-19Implement 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
2022-07-19Check connections before launching...* qc_app/__init__.py (refactor): Check connection before launching the application * qc_app/check_connections.py (new file): Add code to check connections * qc_app/db_utils.py (refactor): enable passing the database uri as an argument to the connection creation function. * scripts/worker.py (refactor): Use new code to check for redis connection. Frederick Muriuki Muriithi
2022-07-19Rework: Use generic worker script to launch process...Use the generic worker script as the interface for launching external processes. Frederick Muriuki Muriithi
2022-07-19Add generic worker script...Add a generic worker script, whose purpose is: - to launch the specific worker script - to capture both stdin and stderr streams and put them on redis In this way, we can launch redis-aware and redis-unaware workers and capture their outputs or errors for later processing. Frederick Muriuki Muriithi
2022-07-19Rename file validation script...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. Frederick Muriuki Muriithi
2022-07-19Implement confirmation stage...Provide user with a confirmation stage where they can verify all the data before inserting into the database. Frederick Muriuki Muriithi
2022-07-19Enable creation of new dataset...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 Frederick Muriuki Muriithi
2022-07-19Replace redirect with user confirmation...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. Frederick Muriuki Muriithi
2022-07-19Implement dataset selection...- Implement UI enabling selection from existing datasets - Start implementation of UI that enables creation of new dataset Frederick Muriuki Muriithi
2022-07-19Implement study creation...Enable the creation of the new study, and redirect appropriately with the new study id. Frederick Muriuki Muriithi
2022-07-19Fix macroFrederick Muriuki Muriithi
2022-07-19Add missing db_utils moduleFrederick Muriuki Muriithi
2022-07-19Add 'group' and 'tissue' selection....- 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 Frederick Muriuki Muriithi
2022-07-19Implement select study...Implement the select study UI Frederick Muriuki Muriithi
2022-07-19Select the platform (GeneChipId) firstFrederick Muriuki Muriithi
2022-07-07Rework guix.scm to use latest commit...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. Frederick Muriuki Muriithi
2022-07-07Fix linting and typing errorsFrederick Muriuki Muriithi
2022-07-07Fix testFrederick Muriuki Muriithi
2022-07-07Replace 'magic' with builtin 'mimetypes'...Use the builtin mimetypes which gives better results Frederick Muriuki Muriithi
2022-07-07Rework styling for form elementsFrederick Muriuki Muriithi
2022-07-07Add filetype details to database update code...The filetype determines the queries to be run to update the database, therefore, this commit adds filetype information. Frederick Muriuki Muriithi
2022-07-07Provide selection for GeneChips...The GeneChipId value is required for the data being inserted, so this commit provides the UI to enable selection of the chip. Frederick Muriuki Muriithi
2022-07-06Implement UI for dataset selection...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. Frederick Muriuki Muriithi
2022-06-28Check 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
2022-06-22Test 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