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2024-01-03Refactor: Extract potentially reusable functionsFrederick Muriuki Muriithi
The processing of transposed files is probably going to be very similar, thus the need to extract some reusable code from the geno-file-specific function in preparation.
2024-01-02Inherit from `gnqc-py` in `guix-bioinformatics`.Frederick Muriuki Muriithi
2024-01-02Cleanup guix definitions in preparation for deployment.Frederick Muriuki Muriithi
2024-01-02Mark tests as unit tests.Frederick Muriuki Muriithi
2024-01-02Abstract away non-transposed file processingFrederick Muriuki Muriithi
Since the processing of non-transposed files is mostly similar, abstract away the common operations into a separate function and use the function instead of repeating the same pattern of code throughout the codebase.
2024-01-02Cleanup: Fix linting and typing errors and update docs.Frederick Muriuki Muriithi
2023-12-28Rework parsing of transposed geno files.Frederick Muriuki Muriithi
2023-12-28Handle transposed geno files.Frederick Muriuki Muriithi
2023-12-27Tests: Test parsing of non-transposed geno files.Frederick Muriuki Muriithi
Check that the parsing of non-transposed geno files. Leave in failing test for transposed geno files.
2023-12-27Tests: Test parsing of pmap files. Merge testing of map files.Frederick Muriuki Muriithi
2023-12-27Tests: Add tests for parsing gmap files.Frederick Muriuki Muriithi
2023-12-25Generalise to read both genetic and physical maps.Frederick Muriuki Muriithi
2023-12-25Read genetic map filesFrederick Muriuki Muriithi
2023-12-20Read genotype filesFrederick Muriuki Muriithi
2023-12-20Read R/qtl2 format filesFrederick Muriuki Muriithi
* Set up error objects. * Read the control data.
2023-12-20Add `pyyaml` as a dependency.Frederick Muriuki Muriithi
Needed when reading/parsing the R/qtl2 control files.
2023-12-20Provide instance_path at client creation.Frederick Muriuki Muriithi
2023-12-20Stop relying on "GUIX_ENVIRONMENT" envvarFrederick Muriuki Muriithi
While we run the service under GNU Guix, there is no telling where anyone else with access to the code (which is open-source) will run the application. This means we need a more dynamic way to get the paths for any commands we choose to run.
2023-12-20Reduce table columnsFrederick Muriuki Muriithi
Reduce the table columns displayed by javascript for the platforms.
2023-12-20Fix ID column keyFrederick Muriuki Muriithi
Fix the wrong assumption that the ID key will always be "ProbeSetID". The key for the ID column could change from study to study or dataset to dataset.
2023-12-20Add faviconFrederick Muriuki Muriithi
Add a favicon to reduce noise in the logs due to failed requests.
2023-12-19Commit missing templates.Frederick Muriuki Muriithi
2023-12-19Bug: Commit population before trying to upload data.Frederick Muriuki Muriithi
2023-12-18Samples: Hook-up external async script to upload the samples.Frederick Muriuki Muriithi
2023-12-14samples: Create external script and fix some bugs.Frederick Muriuki Muriithi
2023-12-14Pass connection to `species_by_id` function.Frederick Muriuki Muriithi
To make `species_by_id` function reusable even outside of the application context, pass in the database connection instead of creating the connection inside the function.
2023-12-11samples: Fix bugs in code saving samples to dbFrederick Muriuki Muriithi
* Check whether first row in file is for headings * Break infinite loop: check batch has content * Update saving of uploaded files
2023-12-07Samples: Read an save data to db.Frederick Muriuki Muriithi
2023-12-07Samples: Provide preview feature.Frederick Muriuki Muriithi
2023-12-06Feature: Upload Samples/CasesFrederick Muriuki Muriithi
Implements the code enabling the upload of the samples/cases to the database.
2023-11-30Remove link to non-existent file.Frederick Muriuki Muriithi
2023-11-30Error logging: Add more details to help with debugging.Frederick Muriuki Muriithi
2023-11-30Bug: Fix insertion errorFrederick Muriuki Muriithi
Fix a bug that was causing the data insertion to fail.
2023-11-30Handle duplicate dataset creation errorFrederick Muriuki Muriithi
Notify the user when they try to create a new dataset that has the same name as an existing dataset and give them the chance to fix it before continuing.
2023-11-30Fix errors caught by pylint and mypy.Frederick Muriuki Muriithi
2023-11-28Handle generic MySQL errors at the top-level.Frederick Muriuki Muriithi
2023-11-28Capture, log and handle generic exceptionsFrederick Muriuki Muriithi
Handle any and all unforeseen error conditions gracefully by capturing the exceptions, logging out for debug purposes and providing the user with a generic error page.
2023-11-24QC: Check for only one decimal place.Frederick Muriuki Muriithi
2023-11-15Log out DB errors even when handledFrederick Muriuki Muriithi
Log out any DB errors that occur to help with tracking and debugging failures.
2023-11-15Remove debugging statement.Frederick Muriuki Muriithi
2023-11-15Bug: Insert ProbeSets before average data and cross-refsFrederick Muriuki Muriithi
Insert the ProbeSets first before inserting the average data and cross-referencing it.
2023-11-15UI: Remove 'Full Name' and 'Short Name' fields for study.Frederick Muriuki Muriithi
2023-11-15UI: Only show GeneChipId and GeneChipNameFrederick Muriuki Muriithi
2023-11-15mypy: Fix typing errors.Frederick Muriuki Muriithi
2023-11-15Linting: Fix linting errors.Frederick Muriuki Muriithi
2023-11-15Commit changes on query success.Frederick Muriuki Muriithi
2023-11-15Provide default `AuthorisedUsers` value.Frederick Muriuki Muriithi
2023-10-30Prevent overwrite. Avoid inserting same probeset multiple times.Frederick Muriuki Muriithi
* Avoid overwriting existing data by adding a random string to the name of the ProbeSet * Read ProbeSet names separately from the means for the strains, to avoid entering the same ProbeSet record over and over with varying names.
2023-10-18Link to `ProbeSet.Id` in XRef TableFrederick Muriuki Muriithi
The "ProbeSetId" value in the file is actually stored in the database in the `ProbeSet.Name` field, whereas the `ProbeSetXRef` table actually uses the `ProbeSet.Id` value to define the relationships. This commit fixes that issue.
2023-10-18Explicitly specify columnsFrederick Muriuki Muriithi
Due to possible schema differences between local small db on development computer and those on CI/CD and Production, explicitly specify the columns being operated on by the queries.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-05 16:09:05 +0000