| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 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 |
| 2024-04-04 | Remove unused database connection. | Frederick Muriuki Muriithi |
| 2024-04-03 | Reduce size of data inserted per query...Reduce the size of data inserted per query since MariDB allows a
packet with a maximum size of 1GB. This should hopefully resolve the
…OperationalError: (2006, 'Server has gone away')
error.
| Frederick Muriuki Muriithi |
| 2024-03-29 | Quiet linter. | Frederick Muriuki Muriithi |
| 2024-03-29 | Add UI to select/create tissue. | Frederick Muriuki Muriithi |
| 2024-03-22 | Notify user if identifiers are not consistent. | Frederick Muriuki Muriithi |
| 2024-03-22 | Map names in files to names in database. | Frederick Muriuki Muriithi |
| 2024-03-22 | Fix linting issue. | Frederick Muriuki Muriithi |
| 2024-03-21 | Improve channel definition documentation. | Frederick Muriuki Muriithi |
| 2024-03-20 | Use `url_for` to get icon. | Frederick Muriuki Muriithi |
| 2024-03-20 | Fix bug: correctly merge standard-error values in file to data in db...`read_datavalues(…)` function returns a dict of the form:
```
{
ProbeSetName01: ({…}, …),
ProbeSetName02: ({…}, …),
︙
}
```
Previously, the generator would thus try to index into the keys of the
datavalues, which were strings, leading to an error.
This commit changes the generator to return the values of the
datavalues dict as a flattened list of values.
| 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 |
| 2024-03-14 | Update symbolic link...The module file was changed but the link to it was not updated. This
commit fixes that.
| Frederick Muriuki Muriithi |
