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AgeCommit message (Expand)Author
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 files...* Set up error objects. * Read the control data. Frederick Muriuki Muriithi
2023-12-20Add `pyyaml` as a dependency....Needed when reading/parsing the R/qtl2 control files. Frederick Muriuki Muriithi
2023-12-20Provide instance_path at client creation.Frederick Muriuki Muriithi
2023-12-20Stop relying on "GUIX_ENVIRONMENT" envvar...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. Frederick Muriuki Muriithi
2023-12-20Reduce table columns...Reduce the table columns displayed by javascript for the platforms. Frederick Muriuki Muriithi
2023-12-20Fix ID column key...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. Frederick Muriuki Muriithi
2023-12-20Add favicon...Add a favicon to reduce noise in the logs due to failed requests. Frederick Muriuki Muriithi
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....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. Frederick Muriuki Muriithi
2023-12-11samples: Fix bugs in code saving samples to db...* Check whether first row in file is for headings * Break infinite loop: check batch has content * Update saving of uploaded files Frederick Muriuki Muriithi
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/Cases...Implements the code enabling the upload of the samples/cases to the database. Frederick Muriuki Muriithi
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 error...Fix a bug that was causing the data insertion to fail. Frederick Muriuki Muriithi
2023-11-30Handle duplicate dataset creation error...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. Frederick Muriuki Muriithi
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 exceptions...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. Frederick Muriuki Muriithi
2023-11-24QC: Check for only one decimal place.Frederick Muriuki Muriithi
2023-11-15Log out DB errors even when handled...Log out any DB errors that occur to help with tracking and debugging failures. Frederick Muriuki Muriithi
2023-11-15Remove debugging statement.Frederick Muriuki Muriithi
2023-11-15Bug: Insert ProbeSets before average data and cross-refs...Insert the ProbeSets first before inserting the average data and cross-referencing it. Frederick Muriuki Muriithi
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....* 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. Frederick Muriuki Muriithi
2023-10-18Link to `ProbeSet.Id` in XRef Table...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. Frederick Muriuki Muriithi
2023-10-18Explicitly specify columns...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. Frederick Muriuki Muriithi
2023-10-16Fix bug: Insert ProbeSets if they do not exist.Frederick Muriuki Muriithi
2023-10-16Fix bug: Provide the platform_id to `insert_means`Frederick Muriuki Muriithi
2023-10-16Fix bug: parsing fields from query.Frederick Muriuki Muriithi
2023-10-16Indicate progress for data insert.Frederick Muriuki Muriithi
2023-10-16Link study to ProbeSetFreeze table.Frederick Muriuki Muriithi
2023-01-17Add link back to index page on abort or errorsFrederick Muriuki Muriithi
2023-01-17upload: Enable cancelling an upload.Frederick Muriuki Muriithi
2022-12-23Help: Provide some help content for end userFrederick Muriuki Muriithi
2022-11-16ui: provide error messaging if file is not selected.Frederick Muriuki Muriithi
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