| Age | Commit message (Expand) | Author |
|---|
| 2024-02-20 | Read samples from geno file. | Frederick Muriuki Muriithi |
| 2024-02-20 | Read each file separately...Provide the function 'read_file_data' in the 'r_qtl.r_qtl2' module to
read each file in the bundle separately.
The function 'file_data' in the 'r_qtl.r_qtl2' module reads *ALL* the
files of a particular type (e.g. geno files) and returns a single
generator object with the data from *ALL* the files. This does not
render itself very useful for error checking.
We needed a way to check for errors, and report them for each and
every file in the bundle, for easier tracking and fixing.
| Frederick Muriuki Muriithi |
| 2024-02-20 | Stand-alone function to read control file...Add a function that, given the path to the zip file, will read the
control data. It creates its own context manager.
| Frederick Muriuki Muriithi |
| 2024-02-16 | Replace genotype codes with values in control file. | Frederick Muriuki Muriithi |
| 2024-02-16 | Convert missing value codes to None | Frederick Muriuki Muriithi |
| 2024-02-16 | Strip comment lines. | Frederick Muriuki Muriithi |
| 2024-02-16 | Read raw text data from a file in the zip bundle | Frederick Muriuki Muriithi |
| 2024-02-16 | Documentation: Add section on configurations. | Frederick Muriuki Muriithi |
| 2024-02-15 | Filter out NULL values | Frederick Muriuki Muriithi |
| 2024-02-15 | Refactor checking for user input errors. | Frederick Muriuki Muriithi |
| 2024-02-15 | Only log out information if the check is actually run. | 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 | Add some parallelism to the QC Checks | Frederick Muriuki Muriithi |
| 2024-02-13 | Provide nice UI progress indicators. | Frederick Muriuki Muriithi |
| 2024-02-13 | Make "FILE_TYPES" part of public interface for module/package. | Frederick Muriuki Muriithi |
| 2024-02-12 | Refactor: Use new decimal places checker. | Frederick Muriuki Muriithi |
| 2024-02-12 | Build generic decimal places checker. | 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 | 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 |
