| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 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 |
| 2024-03-11 | Rename module | Frederick Muriuki Muriithi |
| 2024-03-11 | Fix package name: gnqc-py to gn-uploader | Frederick Muriuki Muriithi |
| 2024-03-11 | Add guix-past as a channel dependency | Frederick Muriuki Muriithi |
| 2024-03-11 | Make guix-bioinformatics a dependency for this channel. | Frederick Muriuki Muriithi |
| 2024-03-08 | Update packaging and distribution declarations. | Frederick Muriuki Muriithi |
| 2024-03-08 | Rename package for guix | 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 | tests: test with just the message - don't include markup...Markup can, and will change as improvements are made, but the error
messages will not change that often, plus that is what we want to
actually test for, not the markup.
| Frederick Muriuki Muriithi |
| 2024-02-28 | tests: Update unit tests: remove use of obsoleted functions. | Frederick Muriuki Muriithi |
| 2024-02-28 | Remove last vestiges of flask's "instance path" configurations. | Frederick Muriuki Muriithi |
| 2024-02-28 | Fix bug: fetch from cursor, not return from cursor.execute(…)load-raw-data-no-parsing | Frederick Muriuki Muriithi |
| 2024-02-27 | Remove use of instance path in configurations. | Frederick Muriuki Muriithi |
| 2024-02-21 | Check that samples/cases are consistent...Ensure that **ALL** samples/cases/individuals mentioned in any of the
pheno files actually exist in at least one of the geno files.
| Frederick Muriuki Muriithi |
| 2024-02-21 | Pass 'filename' value to error checker function. | Frederick Muriuki Muriithi |
| 2024-02-20 | Track filename in the errors...R/qtl2 bundles can contain more than one file, of the same type. When
errors are encountered in any of the files, we need to be able to
inform the user which file it is, in addition to the line and column
number.
| Frederick Muriuki Muriithi |
| 2024-02-20 | Generalise fetching of samples/cases/individuals. | Frederick Muriuki Muriithi |
| 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 |
