| Age | Commit message (Expand) | Author |
|---|
| 2024-07-02 | Call correct method. | Frederick Muriuki Muriithi |
| 2024-07-02 | Add URL information to debug information...To help with error reporting, as the user to also provide the URL of
the error page to help with debugging issues that the user encounters.
| Frederick Muriuki Muriithi |
| 2024-07-02 | Ensure no duplicated values for the query. | Frederick Muriuki Muriithi |
| 2024-07-01 | Respond with JSON. Handle error messages on UI. | Frederick Muriuki Muriithi |
| 2024-07-01 | Display error better.test-resumablejs | Frederick Muriuki Muriithi |
| 2024-07-01 | Check for genotype samples in the database...Check for genotype samples in both the R/qtl2 file and in the
database.
| Frederick Muriuki Muriithi |
| 2024-06-27 | Remove unnecessary debugging statements. | Frederick Muriuki Muriithi |
| 2024-06-27 | Handle chunks on backend and update UI with progress...Handle the uploaded chunks, enabling resumption of the upload if
incomplete.
Update the UI with the progress of the upload.
| Frederick Muriuki Muriithi |
| 2024-06-27 | Fix bug with the logging setup. | Frederick Muriuki Muriithi |
| 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...* 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.
| Frederick Muriuki Muriithi |
| 2024-06-25 | Add route to fetch node-js modules. | Frederick Muriuki Muriithi |
| 2024-06-20 | Check for special files that might share names/extensions...Check for special files and hidden files that might be inadvertently
added to the zip bundle by the operating system in use that might
share names and/or extensions with the main bundle files.
| 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 | Commit missing test. | 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...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.
| Frederick Muriuki Muriithi |
| 2024-06-14 | jquery, bootstrap: update page dependencies...* Add jquery which is needed for bootstrap plugins.
* Add the default bootstrap theme.
* Provide route to serve up jquery libraries.
| Frederick Muriuki Muriithi |
| 2024-06-14 | Move the modal to top of page to avoid display issues...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.
| Frederick Muriuki Muriithi |
| 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...Leave only data upload type selection on landing page.
| Frederick Muriuki Muriithi |
| 2024-06-13 | Update html templates to use bootstrap for styling | Frederick Muriuki Muriithi |
| 2024-06-12 | Update documentation | 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...Use bootstrap to eliminate a myriad of UI styling headaches.
| Frederick Muriuki Muriithi |
| 2024-06-12 | Make URI and UI correspond to each other....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.
| Frederick Muriuki Muriithi |
| 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...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.
| Frederick Muriuki Muriithi |
| 2024-04-17 | Use `cursor.lastrowid` to get row identifier...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.
| Frederick Muriuki Muriithi |
| 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!...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.
| Frederick Muriuki Muriithi |
| 2024-04-15 | Include images: Useful for favicon image. | Frederick Muriuki Muriithi |
| 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 | Move entry-point module to scripts package....This ensures the entry-point script/module is actually installed
together with the rest of the code.
| Frederick Muriuki Muriithi |
| 2024-04-12 | Add missing return. | Frederick Muriuki Muriithi |
| 2024-04-12 | Consistently check for possibly non-existent data...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.
| Frederick Muriuki Muriithi |
| 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...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.
| Frederick Muriuki Muriithi |
| 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 |
