| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-03-20 | Fix bug: correctly merge standard-error values in file to data in db | Frederick Muriuki Muriithi | |
| `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. | |||
| 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` | Frederick Muriuki Muriithi | |
| 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`. | |||
| 2024-03-15 | Move defaults settings into qc_app module. | Frederick Muriuki Muriithi | |
| 2024-03-14 | Update symbolic link | Frederick Muriuki Muriithi | |
| The module file was changed but the link to it was not updated. This commit fixes that. | |||
| 2024-03-12 | Build up correct path to default settings | Frederick Muriuki Muriithi | |
| 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. | |||
| 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 | Frederick Muriuki Muriithi | |
| 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. | |||
| 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 | Frederick Muriuki Muriithi | |
| Ensure that **ALL** samples/cases/individuals mentioned in any of the pheno files actually exist in at least one of the geno files. | |||
| 2024-02-21 | Pass 'filename' value to error checker function. | Frederick Muriuki Muriithi | |
| 2024-02-20 | Track filename in the errors | Frederick Muriuki Muriithi | |
| 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. | |||
| 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 | Frederick Muriuki Muriithi | |
| 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. | |||
| 2024-02-20 | Stand-alone function to read control file | Frederick Muriuki Muriithi | |
| Add a function that, given the path to the zip file, will read the control data. It creates its own context manager. | |||
| 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 | Frederick Muriuki Muriithi | |
| In case a filename is provided, verify that the file actually exists in the upload directory. | |||
| 2024-02-15 | Provide only the file name, not full path. | Frederick Muriuki Muriithi | |
| 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. | |||
| 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 | Frederick Muriuki Muriithi | |
| * Extract the UI elements and code for indicating upload progress into separate, reusable "modules". * Fix bugs arising from changes. | |||
| 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 | |
 |
index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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