| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2024-02-15 | Provide only the file name, not full path....There are 2 reasons to provide only the filename and not the full
path:
* Security: We do not want to inadvertently expose the paths to the
outside world, or allow users to enter file system paths for this
system.
* The code does not assume a complete path, rather, it builds the path
to the upload directory using the filename received from the user.
| Frederick Muriuki Muriithi |
| 2024-02-15 | Provide the log messages to the status page. | Frederick Muriuki Muriithi |
| 2024-02-14 | Provide endpoint to send data to. | Frederick Muriuki Muriithi |
| 2024-02-14 | Extract upload progress indication code...* Extract the UI elements and code for indicating upload progress into
separate, reusable "modules".
* Fix bugs arising from changes.
| Frederick Muriuki Muriithi |
| 2024-02-13 | Provide nice UI progress indicators. | Frederick Muriuki Muriithi |
| 2024-02-12 | Check for errors in the 'phenose' file. | Frederick Muriuki Muriithi |
| 2024-02-12 | Check for errors in the 'pheno' file. | Frederick Muriuki Muriithi |
| 2024-02-12 | Improve error display for generic errors | Frederick Muriuki Muriithi |
| 2024-02-12 | Collect and display errors on 'geno' files in the bundle. | Frederick Muriuki Muriithi |
| 2024-02-12 | UI: Provide QC successful results page | Frederick Muriuki Muriithi |
| 2024-02-12 | Retrive and display generic bundle errors...Implement the first QC check for generic errors e.g. missing files in
bundle, etc. Display retrieved errors on UI.
| Frederick Muriuki Muriithi |
| 2024-02-12 | Raise error if file is missing rather than returning a Union value. | Frederick Muriuki Muriithi |
| 2024-02-12 | R/qtl2 QC: Set up scaffolding for QC UI...Set up the scaffolding for the flows and UI that will be used when
running QC against the uploaded R/qtl2 bundle.
This will be fleshed out later, and the UI is likely to change
somewhat, down the line.
| Frederick Muriuki Muriithi |
| 2024-02-07 | ShortName is optional, remove check and set default...The ShortName is optional, and can be set to the same value as
Name. This commit removes the check that made it mandatory.
| Frederick Muriuki Muriithi |
| 2024-02-07 | Prevent infinite redirect. | Frederick Muriuki Muriithi |
| 2024-02-07 | Fix error display: setup correct error class | Frederick Muriuki Muriithi |
| 2024-02-07 | Set up limits for inputs in UI | Frederick Muriuki Muriithi |
| 2024-02-06 | Bug: Fix routing issues...Fix the routing issues that were redirecting the flow to the wrong
endpoints.
| Frederick Muriuki Muriithi |
| 2024-02-05 | Run QC on the 'geno' file in R/qtl2 bundle. | Frederick Muriuki Muriithi |
| 2024-02-05 | Fix linting and type errors. | Frederick Muriuki Muriithi |
| 2024-02-05 | Do general bundle validation and show errors...* Display any and all errors on the UI
* Move `validate_bundle` to QC module and refactor to use
`missing_files`
| Frederick Muriuki Muriithi |
| 2024-02-05 | Update UI documentation...Improve the UI documentation by making it more explicit what each
section deals with to help aleviate confusion of what the different
features do.
| Frederick Muriuki Muriithi |
| 2024-02-02 | Bug: Specify DictCursor class to return dict-like result...Without specifying the `cursorclass`, the result is a tuple of the
form:
((query_col01_val, query_col02_val, ...), ...)
where the ellipsis specify the possibility of more than one of the
previous form.
We specify the DictCursor class instead so that the form changes to:
({query_col01_name: query_col01_val, ...}, ...)
which allows us to pick the value we want with a string index.
| Frederick Muriuki Muriithi |
| 2024-01-24 | Checks: Update code and tests to ensure all checks pass. | Frederick Muriuki Muriithi |
| 2024-01-24 | redis-prefix: update "upload samples" path | Frederick Muriuki Muriithi |
| 2024-01-24 | redis-prefix: Update "insert data" path. | Frederick Muriuki Muriithi |
| 2024-01-24 | redis-prefix: Update file validation code...Update the file validation script and routes to use the redis prefix
for jobs.
| Frederick Muriuki Muriithi |
| 2024-01-23 | Update scripts to use redis prefix. | Frederick Muriuki Muriithi |
| 2024-01-23 | Add prefix to redis keys...Since the GNQC application might find itself sharing the same redis
server and/or database with other applications, add a prefix to its
keys.
| Frederick Muriuki Muriithi |
| 2024-01-22 | UI: Fix some UI bugs. | Frederick Muriuki Muriithi |
| 2024-01-22 | scripts: Pass in logger to get detailed updates. | Frederick Muriuki Muriithi |
| 2024-01-22 | UI: Show progress of R/qtl2 bundle processing. | Frederick Muriuki Muriithi |
| 2024-01-20 | Fetch sample/case names from database...Fetch the sample/case names from the database rather than from a
static file in the repository.
Issue:
https://issues.genenetwork.org/issues/quality-control/read-samples-from-database-by-species
| Frederick Muriuki Muriithi |
| 2024-01-19 | scripts: Process R/qtl2 bundle...Build script to start the processing of the R/qtl2 bundle.
| Frederick Muriuki Muriithi |
| 2024-01-19 | UI: Present entry point for R/qtl2 bundles upload. | Frederick Muriuki Muriithi |
| 2024-01-18 | UI: Display summary information. | Frederick Muriuki Muriithi |
