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2024-10-21Check `phenocovar` files for errors.Frederick Muriuki Muriithi
2024-10-21Add utilities for reading text files and csv filesFrederick Muriuki Muriithi
The function `read_text_file(…)` will read the raw text file and return the content line by line. The function `read_csv_file(…)` builds on `read_text_file(…)` to read a file as a character-separated-values file. The field separator, and comment_char characters can be provided to customise how the CSV file is read.
2024-10-17UI: Create background job when user uploads file.Frederick Muriuki Muriithi
2024-10-17Cleanup: Delete all extracted files after processing.Frederick Muriuki Muriithi
2024-10-17Leave TODO notes for what needs to be done.Frederick Muriuki Muriithi
2024-10-17Fetch samples from databaseFrederick Muriuki Muriithi
Fetch the samples from the database. These will be used to verify that the samples in the phenotype files already exist in the database and are valid.
2024-10-17Undo transpose for any transposed filesFrederick Muriuki Muriithi
To reduce the complexity involved in the processing of the files, we undo any transposition of the CSV files for those files that are marked as transposed.
2024-10-17Pass new arguments to QC function.Frederick Muriuki Muriithi
2024-10-17Add `speciesid` and `populationid` arguments to the script.Frederick Muriuki Muriithi
2024-10-17Add the working directory argument to the script.Frederick Muriuki Muriithi
Add a `--working-dir` argument to allow passing a directory where the script process the files within. If not provided, it defaults to a directory within the systems temporary directory.
2024-10-17Extract the R/qtl2 bundle for processing.Frederick Muriuki Muriithi
To enable processing of the files individually, this commit will enable the extraction of the files into a known working directory in which all further processing will take place.
2024-10-17Extract common functions.Frederick Muriuki Muriithi
2024-10-17Save errors for each file in lists. Parallelise error checking.Frederick Muriuki Muriithi
* Save the errors for each file in a redis list for that file. * Make error checking parallel, i.e. ensure every file of a particular type is checked completely independent of other files of the same type.
2024-10-17Rewrite the QC code for R/qtl2Frederick Muriuki Muriithi
2024-10-17Ignore comment lines.Frederick Muriuki Muriithi
2024-10-17Implement sha256 hashing over file contents.Frederick Muriuki Muriithi
2024-10-17Add test for function to compute file hash.Frederick Muriuki Muriithi
2024-10-17Rename test module.Frederick Muriuki Muriithi
2024-10-17mypy: Fix some typing issues.Frederick Muriuki Muriithi
2024-10-14Initialise background script for running QC on phenotype bundles.Frederick Muriuki Muriithi
2024-10-14Update typing information.Frederick Muriuki Muriithi
2024-10-14BugFix: Use provided prefixFrederick Muriuki Muriithi
Use the provided prefix rather than calling `jobs.jobsnamespace()` function that depends of an app context existing.
2024-10-14Make addition of arguments independent of each other.Frederick Muriuki Muriithi
2024-10-14Improve error messages for R/qtl2 code.Frederick Muriuki Muriithi
2024-10-14Improve UI copy: Add list of files used.Frederick Muriuki Muriithi
2024-10-14Improve layout and styling of sidebar contentFrederick Muriuki Muriithi
2024-10-10UI hints: Help user in choosing the appropriate option.Frederick Muriuki Muriithi
2024-10-10Build UI to add new phenotypes.Frederick Muriuki Muriithi
Build the UI and set up styling. This is not working currently.
2024-10-10Limit the length of the population descriptionFrederick Muriuki Muriithi
2024-10-07Handle "No linked resource" error cleanly.Frederick Muriuki Muriithi
Display the page even if there is no linked resource, but keep the sensitive information hidden in such cases.
2024-10-07Add phenotype units to UIFrederick Muriuki Muriithi
2024-10-07Reuse requests checks to fix "too many returns" linting errorFrederick Muriuki Muriithi
2024-10-07linting: Fix minor linting issues.Frederick Muriuki Muriithi
2024-10-07Create new phenotype dataset (PublishFreeze).Frederick Muriuki Muriithi
Provide the UI and code to create a new phenotype dataset.
2024-10-07Extract reusable input validation code.Frederick Muriuki Muriithi
2024-10-07Generalise pagination and paginate phenotypesFrederick Muriuki Muriithi
Generalise the code generating table pagination UI, and use it to paginate the list of phenotypes.
2024-10-02Add missing __init__.pyFrederick Muriuki Muriithi
2024-10-01Add UI elements for possible extra functionality.Frederick Muriuki Muriithi
2024-10-01Extract privileges and use them for access controlFrederick Muriuki Muriithi
2024-09-30BugFix: Ensure all data items show up.Frederick Muriuki Muriithi
2024-09-30Initialise views for a specific phenotypeFrederick Muriuki Muriithi
Each phenotype is independent, of all others, and they are only put into datasets mostly for easy coralling of phenotypes related to a specific populations. As such, the system will probably need to provide a way to view (and possibly edit) each phenotype independent of all the others. This also fits in with the auth.
2024-09-30Extract common check into decorator for reusability.Frederick Muriuki Muriithi
2024-09-27Remove unused placeholders for now.Frederick Muriuki Muriithi
2024-09-27Improve query for fetching a phenotype dataset's dataFrederick Muriuki Muriithi
2024-09-27Show some details for a phenotype dataset.Frederick Muriuki Muriithi
2024-09-27Extract common functionality into reusable function.Frederick Muriuki Muriithi
2024-09-26Start building up the view dataset endpointFrederick Muriuki Muriithi
2024-09-26List the phenotype datasets.Frederick Muriuki Muriithi
2024-09-26Enable selecting population for phenotypes.Frederick Muriuki Muriithi
2024-09-26Initialise the phenotypes section.Frederick Muriuki Muriithi