| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2024-04-08 | Refactor: Make error-checking more robust...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".
| Frederick Muriuki Muriithi |
| 2024-04-08 | Fix issues caught by integration tests. | Frederick Muriuki Muriithi |
