| Age | Commit message (Expand) | Author |
|---|
| 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 | Add scaffolding for running individual files' QC checks | Frederick Muriuki Muriithi |
| 2024-02-12 | UI: Provide QC successful results page | Frederick Muriuki Muriithi |
| 2024-02-12 | Extract missing files check to external function | 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 | Provide the key for each file listed in the control file. | 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 |
| 2024-02-12 | Provide better error messaging...Provide a better error message that can help the user figure out what
they did wrong and fix it for themselves instead of the older, cryptic
and extremely unhelpful error message.
| Frederick Muriuki Muriithi |
| 2024-02-08 | Generalise error retrieval: extract common structure...Extract the common structure into a separate function and pass in
checkers that return the errors they find.
| Frederick Muriuki Muriithi |
| 2024-02-08 | Use error objects rather than plain tuple values. | 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 | Check that pheno values are numerical and at least 3 decimal places | 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 | Check that data in geno file is valid...Add a function to ensure the values in the geno files are all listed
in the control data under the "genotypes" key.
| Frederick Muriuki Muriithi |
| 2024-02-05 | Add a QC step: Check all listed files exist...Add a QC step to the R/qtl2 bundle processing - check that all files
that are listed in the control file also exist in the 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 | Retrieve list of all files, and list of missing files...Add QC a function to list all files listed in the control file, and
another to list only the files missing from the bundle.
| 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 | List file types in a single place for easier reuse | Frederick Muriuki Muriithi |
| 2024-02-02 | Ensure control file defaults are set up in code. | 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 |
| 2024-01-23 | Tests: Use prefixes in tests rather than starting redis server...It's easier, and more robust to put the data under a prefix within a
redis database rather than try to run a redis server, especially
within the test environment. This commit updates the tests to use a
redis prefix instead.
| 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 |
| 2024-01-18 | UI: Create new ProbeSet dataset. | Frederick Muriuki Muriithi |
| 2024-01-18 | UI: Select from existing ProbeSet datasets. | Frederick Muriuki Muriithi |
| 2024-01-18 | Create new ProbeSet study. | Frederick Muriuki Muriithi |
| 2024-01-17 | UI: Select ProbeSet study. | Frederick Muriuki Muriithi |
| 2024-01-17 | UI: Implement creating new genotype datasets. | Frederick Muriuki Muriithi |
| 2024-01-17 | UI: Initialise summary page. | Frederick Muriuki Muriithi |
| 2024-01-17 | Enable selecting from existing genotype datasets. | Frederick Muriuki Muriithi |
