| Age | Commit message (Expand) | Author |
|---|
| 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 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 |
| 2024-04-12 | 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...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 |
| 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`...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`.
| Frederick Muriuki Muriithi |
| 2024-03-15 | Move defaults settings into qc_app module. | Frederick Muriuki Muriithi |
| 2024-03-12 | Build up correct path to default settings...The assumption has been that the application will be started in the
root of the repository, and uses that to source the default
settings. It is, however, possible that the application is started in
a totally different working directory, which leads to an error during
startup.
This commit sources the default settings relative to a know file, in
this case the module __init__.py file for qc_app module.
| Frederick Muriuki Muriithi |
| 2024-03-04 | Use `Id` rather than `ProbeFreezeId`. | Frederick Muriuki Muriithi |
| 2024-03-04 | Display flash messages correctly. | Frederick Muriuki Muriithi |
| 2024-02-28 | Remove last vestiges of flask's "instance path" configurations. | Frederick Muriuki Muriithi |
| 2024-02-27 | Remove use of instance path in configurations. | Frederick Muriuki Muriithi |
| 2024-02-15 | Refactor checking for user input errors. | Frederick Muriuki Muriithi |
| 2024-02-15 | Verify that the file actually exist...In case a filename is provided, verify that the file actually exists
in the upload directory.
| Frederick Muriuki Muriithi |
