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2023-10-16Fix bug: Insert ProbeSets if they do not exist.Frederick Muriuki Muriithi
2023-10-16Fix bug: Provide the platform_id to `insert_means`Frederick Muriuki Muriithi
2023-10-16Fix bug: parsing fields from query.Frederick Muriuki Muriithi
2023-10-16Indicate progress for data insert.Frederick Muriuki Muriithi
2023-10-16Link study to ProbeSetFreeze table.Frederick Muriuki Muriithi
2023-01-17Add link back to index page on abort or errorsFrederick Muriuki Muriithi
2023-01-17upload: Enable cancelling an upload.Frederick Muriuki Muriithi
2022-12-23Help: Provide some help content for end userFrederick Muriuki Muriithi
2022-11-16ui: provide error messaging if file is not selected.Frederick Muriuki Muriithi
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 completionFrederick Muriuki Muriithi
* 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.
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: gunicornFrederick Muriuki Muriithi
* guix.scm: Add dependency (gunicorn)
2022-09-08Use sys.executable and setup default environmentFrederick Muriuki Muriithi
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.
2022-09-08Update dependenciesFrederick Muriuki Muriithi
* guix.scm: reorganise the dependencies * setup.cfg: change the `install_requires` values
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 factoryFrederick Muriuki Muriithi
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.
2022-08-05Update job status. Display stdout and stderr outputsFrederick Muriuki Muriithi
* 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
2022-08-04Implement data insertionFrederick Muriuki Muriithi
- Hook up external data insertion script to webserver code - Provide rudimentary status indication - Generalise some job creation details
2022-08-04Handle stderr outputFrederick Muriuki Muriithi
* Fix bug where stderr was not being updated on redis appropriately
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 rowFrederick Muriuki Muriithi
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.
2022-07-19Save standard error data. Fix linting and typing errors.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
2022-07-19Check connections before launchingFrederick Muriuki Muriithi
* 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.
2022-07-19Rework: Use generic worker script to launch processFrederick Muriuki Muriithi
Use the generic worker script as the interface for launching external processes.
2022-07-19Add generic worker scriptFrederick Muriuki Muriithi
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.
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
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