| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-12-06 | Feature: Upload Samples/Cases | Frederick Muriuki Muriithi | |
| Implements the code enabling the upload of the samples/cases to the database. | |||
| 2023-11-30 | Remove link to non-existent file. | Frederick Muriuki Muriithi | |
| 2023-11-30 | Error logging: Add more details to help with debugging. | Frederick Muriuki Muriithi | |
| 2023-11-30 | Bug: Fix insertion error | Frederick Muriuki Muriithi | |
| Fix a bug that was causing the data insertion to fail. | |||
| 2023-11-30 | Handle duplicate dataset creation error | Frederick Muriuki Muriithi | |
| Notify the user when they try to create a new dataset that has the same name as an existing dataset and give them the chance to fix it before continuing. | |||
| 2023-11-30 | Fix errors caught by pylint and mypy. | Frederick Muriuki Muriithi | |
| 2023-11-28 | Handle generic MySQL errors at the top-level. | Frederick Muriuki Muriithi | |
| 2023-11-28 | Capture, log and handle generic exceptions | Frederick Muriuki Muriithi | |
| Handle any and all unforeseen error conditions gracefully by capturing the exceptions, logging out for debug purposes and providing the user with a generic error page. | |||
| 2023-11-24 | QC: Check for only one decimal place. | Frederick Muriuki Muriithi | |
| 2023-11-15 | Log out DB errors even when handled | Frederick Muriuki Muriithi | |
| Log out any DB errors that occur to help with tracking and debugging failures. | |||
| 2023-11-15 | Remove debugging statement. | Frederick Muriuki Muriithi | |
| 2023-11-15 | Bug: Insert ProbeSets before average data and cross-refs | Frederick Muriuki Muriithi | |
| Insert the ProbeSets first before inserting the average data and cross-referencing it. | |||
| 2023-11-15 | UI: Remove 'Full Name' and 'Short Name' fields for study. | Frederick Muriuki Muriithi | |
| 2023-11-15 | UI: Only show GeneChipId and GeneChipName | Frederick Muriuki Muriithi | |
| 2023-11-15 | mypy: Fix typing errors. | Frederick Muriuki Muriithi | |
| 2023-11-15 | Linting: Fix linting errors. | Frederick Muriuki Muriithi | |
| 2023-11-15 | Commit changes on query success. | Frederick Muriuki Muriithi | |
| 2023-11-15 | Provide default `AuthorisedUsers` value. | Frederick Muriuki Muriithi | |
| 2023-10-30 | Prevent overwrite. Avoid inserting same probeset multiple times. | Frederick Muriuki Muriithi | |
| * Avoid overwriting existing data by adding a random string to the name of the ProbeSet * Read ProbeSet names separately from the means for the strains, to avoid entering the same ProbeSet record over and over with varying names. | |||
| 2023-10-18 | Link to `ProbeSet.Id` in XRef Table | Frederick Muriuki Muriithi | |
| The "ProbeSetId" value in the file is actually stored in the database in the `ProbeSet.Name` field, whereas the `ProbeSetXRef` table actually uses the `ProbeSet.Id` value to define the relationships. This commit fixes that issue. | |||
| 2023-10-18 | Explicitly specify columns | Frederick Muriuki Muriithi | |
| Due to possible schema differences between local small db on development computer and those on CI/CD and Production, explicitly specify the columns being operated on by the queries. | |||
| 2023-10-16 | Fix bug: Insert ProbeSets if they do not exist. | Frederick Muriuki Muriithi | |
| 2023-10-16 | Fix bug: Provide the platform_id to `insert_means` | Frederick Muriuki Muriithi | |
| 2023-10-16 | Fix bug: parsing fields from query. | Frederick Muriuki Muriithi | |
| 2023-10-16 | Indicate progress for data insert. | Frederick Muriuki Muriithi | |
| 2023-10-16 | Link study to ProbeSetFreeze table. | Frederick Muriuki Muriithi | |
| 2023-01-17 | Add link back to index page on abort or errors | Frederick Muriuki Muriithi | |
| 2023-01-17 | upload: Enable cancelling an upload. | Frederick Muriuki Muriithi | |
| 2022-12-23 | Help: Provide some help content for end user | Frederick Muriuki Muriithi | |
| 2022-11-16 | ui: provide error messaging if file is not selected. | Frederick Muriuki Muriithi | |
| 2022-11-16 | ui: Don't show upload progress indicator if file is not selected. | Frederick Muriuki Muriithi | |
| 2022-11-16 | tests: Fix some failing tests | Frederick Muriuki Muriithi | |
| 2022-11-16 | qc: Allow whole numbers or numbers where the decimals are all zeroes | Frederick Muriuki Muriithi | |
| 2022-11-16 | ui: Only display the "alert-success" green on completion | Frederick 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. | |||
| 2022-11-12 | Accept plain text (text/plain) files | Frederick Muriuki Muriithi | |
| 2022-09-16 | Add redis and mariadb as propagated inputs | Frederick Muriuki Muriithi | |
| 2022-09-16 | Deactivate tests | Frederick Muriuki Muriithi | |
| 2022-09-16 | Config: Add apache2 sample config file | Frederick Muriuki Muriithi | |
| 2022-09-16 | Add dependency: gunicorn | Frederick Muriuki Muriithi | |
| * guix.scm: Add dependency (gunicorn) | |||
| 2022-09-08 | Use sys.executable and setup default environment | Frederick 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. | |||
| 2022-09-08 | Update dependencies | Frederick Muriuki Muriithi | |
| * guix.scm: reorganise the dependencies * setup.cfg: change the `install_requires` values | |||
| 2022-08-31 | Commit missing files. | Frederick Muriuki Muriithi | |
| 2022-08-31 | Update test: use new script name. | Frederick Muriuki Muriithi | |
| 2022-08-31 | Provide database port where relevant. | Frederick Muriuki Muriithi | |
| 2022-08-31 | Check connections outside app factory | Frederick 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. | |||
| 2022-08-05 | Update job status. Display stdout and stderr outputs | Frederick 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 | |||
| 2022-08-04 | Implement data insertion | Frederick Muriuki Muriithi | |
| - Hook up external data insertion script to webserver code - Provide rudimentary status indication - Generalise some job creation details | |||
| 2022-08-04 | Handle stderr output | Frederick Muriuki Muriithi | |
| * Fix bug where stderr was not being updated on redis appropriately | |||
| 2022-08-04 | Format queries for output. Get rid of extraneous output. | Frederick Muriuki Muriithi | |
| 2022-08-04 | Fix typo: 'species' -> 'speciesid' | Frederick Muriuki Muriithi | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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