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2024-02-28Fix bug: fetch from cursor, not return from cursor.execute(…)load-raw-data-no-parsingFrederick Muriuki Muriithi
2024-02-27Remove use of instance path in configurations.Frederick Muriuki Muriithi
2024-02-21Check that samples/cases are consistentFrederick 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.
2024-02-21Pass 'filename' value to error checker function.Frederick Muriuki Muriithi
2024-02-20Track filename in the errorsFrederick 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.
2024-02-20Generalise fetching of samples/cases/individuals.Frederick Muriuki Muriithi
2024-02-20Read samples from geno file.Frederick Muriuki Muriithi
2024-02-20Read each file separatelyFrederick 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.
2024-02-20Stand-alone function to read control fileFrederick Muriuki Muriithi
Add a function that, given the path to the zip file, will read the control data. It creates its own context manager.
2024-02-16Replace genotype codes with values in control file.Frederick Muriuki Muriithi
2024-02-16Convert missing value codes to NoneFrederick Muriuki Muriithi
2024-02-16Strip comment lines.Frederick Muriuki Muriithi
2024-02-16Read raw text data from a file in the zip bundleFrederick Muriuki Muriithi
2024-02-16Documentation: Add section on configurations.Frederick Muriuki Muriithi
2024-02-15Filter out NULL valuesFrederick Muriuki Muriithi
2024-02-15Refactor checking for user input errors.Frederick Muriuki Muriithi
2024-02-15Only log out information if the check is actually run.Frederick Muriuki Muriithi
2024-02-15Verify that the file actually existFrederick Muriuki Muriithi
In case a filename is provided, verify that the file actually exists in the upload directory.
2024-02-15Provide 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.
2024-02-15Provide the log messages to the status page.Frederick Muriuki Muriithi
2024-02-14Provide endpoint to send data to.Frederick Muriuki Muriithi
2024-02-14Extract upload progress indication codeFrederick Muriuki Muriithi
* Extract the UI elements and code for indicating upload progress into separate, reusable "modules". * Fix bugs arising from changes.
2024-02-13Add some parallelism to the QC ChecksFrederick Muriuki Muriithi
2024-02-13Provide nice UI progress indicators.Frederick Muriuki Muriithi
2024-02-13Make "FILE_TYPES" part of public interface for module/package.Frederick Muriuki Muriithi
2024-02-12Refactor: Use new decimal places checker.Frederick Muriuki Muriithi
2024-02-12Build generic decimal places checker.Frederick Muriuki Muriithi
2024-02-12Check for errors in the 'phenose' file.Frederick Muriuki Muriithi
2024-02-12Check for errors in the 'pheno' file.Frederick Muriuki Muriithi
2024-02-12Improve error display for generic errorsFrederick Muriuki Muriithi
2024-02-12Collect and display errors on 'geno' files in the bundle.Frederick Muriuki Muriithi
2024-02-12Add scaffolding for running individual files' QC checksFrederick Muriuki Muriithi
2024-02-12UI: Provide QC successful results pageFrederick Muriuki Muriithi
2024-02-12Extract missing files check to external functionFrederick Muriuki Muriithi
2024-02-12Retrive and display generic bundle errorsFrederick Muriuki Muriithi
Implement the first QC check for generic errors e.g. missing files in bundle, etc. Display retrieved errors on UI.
2024-02-12Raise error if file is missing rather than returning a Union value.Frederick Muriuki Muriithi
2024-02-12Provide the key for each file listed in the control file.Frederick Muriuki Muriithi
2024-02-12R/qtl2 QC: Set up scaffolding for QC UIFrederick Muriuki Muriithi
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.
2024-02-12Provide better error messagingFrederick Muriuki Muriithi
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.
2024-02-08Generalise error retrieval: extract common structureFrederick Muriuki Muriithi
Extract the common structure into a separate function and pass in checkers that return the errors they find.
2024-02-08Use error objects rather than plain tuple values.Frederick Muriuki Muriithi
2024-02-07ShortName is optional, remove check and set defaultFrederick Muriuki Muriithi
The ShortName is optional, and can be set to the same value as Name. This commit removes the check that made it mandatory.
2024-02-07Prevent infinite redirect.Frederick Muriuki Muriithi
2024-02-07Fix error display: setup correct error classFrederick Muriuki Muriithi
2024-02-07Set up limits for inputs in UIFrederick Muriuki Muriithi
2024-02-06Check that pheno values are numerical and at least 3 decimal placesFrederick Muriuki Muriithi
2024-02-06Bug: Fix routing issuesFrederick Muriuki Muriithi
Fix the routing issues that were redirecting the flow to the wrong endpoints.
2024-02-05Run QC on the 'geno' file in R/qtl2 bundle.Frederick Muriuki Muriithi
2024-02-05Check that data in geno file is validFrederick Muriuki Muriithi
Add a function to ensure the values in the geno files are all listed in the control data under the "genotypes" key.
2024-02-05Add a QC step: Check all listed files existFrederick Muriuki Muriithi
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.