| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-06-27 | Handle chunks on backend and update UI with progress | Frederick Muriuki Muriithi | |
| Handle the uploaded chunks, enabling resumption of the upload if incomplete. Update the UI with the progress of the upload. | |||
| 2024-06-27 | Fix bugs in error-reporting. | Frederick Muriuki Muriithi | |
| 2024-06-27 | Upload chunking: Provide UI and code for drag&drop and chunking | Frederick Muriuki Muriithi | |
| * Use resumable.js to handle the drag-and-drop feature, and chunking. * Add styling for the drag-and-drop area, and provide visual indication when a file is successfully dropped and added to the upload list. | |||
| 2024-06-25 | Add route to fetch node-js modules. | Frederick Muriuki Muriithi | |
| 2024-06-14 | Add banner similar to GeneNetwork2 | Frederick Muriuki Muriithi | |
| 2024-06-14 | Fix minor UI bugs | Frederick Muriuki Muriithi | |
| 2024-06-14 | Update page headings | Frederick Muriuki Muriithi | |
| 2024-06-14 | Remove unused template imports | Frederick Muriuki Muriithi | |
| 2024-06-14 | Use bootstrap for displaying progress widget | Frederick Muriuki Muriithi | |
| This commit converts the progress indication widget into a bootstrap modal dialog, and updates the javascript to prevent the code from interacting with bootstrap in unpredictable ways. | |||
| 2024-06-14 | jquery, bootstrap: update page dependencies | Frederick Muriuki Muriithi | |
| * Add jquery which is needed for bootstrap plugins. * Add the default bootstrap theme. * Provide route to serve up jquery libraries. | |||
| 2024-06-14 | Move the modal to top of page to avoid display issues | Frederick Muriuki Muriithi | |
| According to https://getbootstrap.com/docs/3.3/javascript/#callout-modal-markup-placement the bootstrap modal dialogs should be placed at the top of the page to avoid other components affecting their display and/or functionality. | |||
| 2024-06-13 | Fix tests and issues caught by tests.update-templates-for-bootstrap | Frederick Muriuki Muriithi | |
| 2024-06-13 | Handle HTTP errors gracefully. | Frederick Muriuki Muriithi | |
| 2024-06-13 | Update the help text. | Frederick Muriuki Muriithi | |
| 2024-06-13 | Clean up landing page | Frederick Muriuki Muriithi | |
| Leave only data upload type selection on landing page. | |||
| 2024-06-13 | Update html templates to use bootstrap for styling | Frederick Muriuki Muriithi | |
| 2024-06-12 | Update templates to use bootstrap classes. | Frederick Muriuki Muriithi | |
| 2024-06-12 | Use bundled bootstrap for styling the UI | Frederick Muriuki Muriithi | |
| Use bootstrap to eliminate a myriad of UI styling headaches. | |||
| 2024-06-12 | Make URI and UI correspond to each other. | Frederick Muriuki Muriithi | |
| Formerly, the URI and UI were not corresponding to each other, e.g. the URI /upload/samples/select_species would display the UI for selecting/creating the population. This was very confusing. This commit fixes that. The commit also adds in user input validation to catch input errors. | |||
| 2024-06-12 | Bug: Provide missing argument. Remove unused verr variable. | Frederick Muriuki Muriithi | |
| 2024-06-12 | Validate input before attempting to use it. | Frederick Muriuki Muriithi | |
| 2024-06-12 | Provide an input validation module. | Frederick Muriuki Muriithi | |
| 2024-05-05 | Fix indentation. | Frederick Muriuki Muriithi | |
| 2024-05-05 | Provide default for InbredSetId | Frederick Muriuki Muriithi | |
| The `InbredSetId` field in the `InbredSet` table in MariaDB is in some instances a required field, so we need to provide a value. This value should be the same as that for the `Id` field, that we do not previously know. This commit provides a value of zero (0) as the default. This value is subsequently updated to be same as that of the `Id` field. | |||
| 2024-04-17 | Use `cursor.lastrowid` to get row identifier | Frederick Muriuki Muriithi | |
| Use the more robust `cursor.lastrowid` to get the row identifier value, rather than using the `SELECT MAX(Id) …` form. With the `cursor.lastrowid` form, we do not have to remember to add 1 to the value to avoid conflict. | |||
| 2024-04-16 | Set InbredSet.InbredSetId value in a more robust way. | Frederick Muriuki Muriithi | |
| 2024-04-16 | bug: Set ProbeFreezeId for only new row! | Frederick Muriuki Muriithi | |
| Previously the extra ProbeFreezeId column was being updated for *ALL* rows, rather than just the newly inserted row, which is a bug. This commit fixes that. | |||
| 2024-04-12 | Provide more relevant error message. | Frederick Muriuki Muriithi | |
| 2024-04-12 | Provide defaults for required field. | Frederick Muriuki Muriithi | |
| 2024-04-12 | Add missing return. | Frederick Muriuki Muriithi | |
| 2024-04-12 | Consistently check for possibly non-existent data | Frederick Muriuki Muriithi | |
| The "geno-dataset", "tissue", "pheno-study" and "pheno-dataset" data "objects" might not exist for a particular uploaded bundle, so we check in a consistent manner to ensure they are provided when needed. | |||
| 2024-04-12 | Provide tissue-id details to probeset dataset templates | Frederick Muriuki Muriithi | |
| 2024-04-10 | linting: Fix linting errors. | Frederick Muriuki Muriithi | |
| 2024-04-10 | logging: Set up logging in wsgi.py | Frederick Muriuki Muriithi | |
| Make flask use the gunicorn loggers when run under gunicorn, otherwise, use our custom logging. Putting the logging setup inside `create_app(…)` would cause each worker to override the gunicorn loggers, meaning we were not receiving the logs, especially for `debug(…)` calls. | |||
| 2024-04-10 | Gracefully handle all `werkzeug.exceptions` errors. | Frederick Muriuki Muriithi | |
| 2024-04-10 | Use application logger, not root logger. | Frederick Muriuki Muriithi | |
| 2024-04-08 | Add logging for IntegrityError | Frederick Muriuki Muriithi | |
| 2024-04-08 | Refactor: Make error-checking more robust | Frederick Muriuki Muriithi | |
| Rather than maintaining a dictionary of possible error-checking functions, this commit allows passing in the error-checking functions necessary for each point. This makes the code easier to extend by simply defining a new error-checking function and passing it in to the error-checking "driver". | |||
| 2024-04-08 | Fix issues caught by integration tests. | Frederick Muriuki Muriithi | |
| 2024-04-08 | Fix pylint and mypy errors. | Frederick Muriuki Muriithi | |
| 2024-04-08 | bug: UI: Provide better error messaging. | Frederick Muriuki Muriithi | |
| 2024-04-08 | bug: Handle IntegrityError: Studies cannot have same name. | Frederick Muriuki Muriithi | |
| 2024-04-08 | bug: Check that Genotype dataset name is not duplicated. | Frederick Muriuki Muriithi | |
| 2024-04-05 | Handle exceptions creating ProbeSet datasets. | Frederick Muriuki Muriithi | |
| 2024-04-05 | Add explicit route for favicon to reduce noise in the logs. | Frederick Muriuki Muriithi | |
| 2024-03-29 | Add UI to select/create tissue. | Frederick Muriuki Muriithi | |
| 2024-03-20 | Use `url_for` to get icon. | Frederick Muriuki Muriithi | |
| 2024-03-19 | Set up application logging. | Frederick Muriuki Muriithi | |
| 2024-03-19 | Add debugging statements to track upload of R/qtl2 bundle. | Frederick Muriuki Muriithi | |
| 2024-03-19 | Query by `Id` rather than `ProbeFreezeId` | Frederick Muriuki Muriithi | |
| Previously `ProbeFreezeId` was set as 1 more than the largest `Id` value found, which might not end up being the same as the incremented Id. This commit, thus, queries by `Id` which is more robust, and does an actual update for the `ProbeFreezeId` column to make it same value as `Id`. | |||
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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