| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-02-02 | Fix retrieve_publish_trait_data query | zsloan | |
| The PublishFreeeze table is actually unnecessary for this query, since the group ID (inbred_set_id) should be passed in and that ID is in the PublishXRef table (so no neeed to join with PublishFreeze) | |||
| 2022-02-02 | response object error fix | Alexander Kabui | |
| 2022-02-02 | pep8 formatting | Alexander Kabui | |
| 2022-02-02 | remove comments | Alexander Kabui | |
| 2022-02-02 | return 401 on request fail | Alexander Kabui | |
| 2022-02-02 | refactor code for invoking ctl script | Alexander Kabui | |
| 2022-02-02 | pep8 formatting | Alexander Kabui | |
| 2022-02-02 | match case string input to boolean | Alexander Kabui | |
| 2022-02-02 | fix for parametric input | Alexander Kabui | |
| 2022-02-02 | use user input significance | Alexander Kabui | |
| 2022-02-02 | new line fix | Alexander Kabui | |
| 2022-02-02 | add new json output | Alexander Kabui | |
| 2022-02-02 | fix comprehension list | Alexander Kabui | |
| 2022-02-02 | Revert "Use guix shell shortcut with guix.scm file" | BonfaceKilz | |
| This reverts commit f676c291967f8a81836b73c5a5dcd3c65e02552c. | |||
| 2022-01-27 | Use guix shell shortcut with guix.scm file | jgart | |
| 2022-01-24 | README: Add pylint and mypy CI badges. | Arun Isaac | |
| We now have separate CI jobs for the pylint and mypy tests. * README.md: Add pylint and mypy CI badges. | |||
| 2022-01-22 | minor refactoring | Alexander Kabui | |
| 2022-01-22 | function override:fix target specific output file for network | Alexander Kabui | |
| 2022-01-22 | generate network | Alexander Kabui | |
| 2022-01-22 | process ctl plot data img | Alexander Kabui | |
| 2022-01-22 | generate ctl plots for each trait | Alexander Kabui | |
| 2022-01-22 | read stdout data;handle exceptions | Alexander Kabui | |
| 2022-01-22 | generate required json data for ctl api | Alexander Kabui | |
| 2022-01-22 | fixes for ctl script:generate ctl ctl_significant json | Alexander Kabui | |
| 2022-01-22 | bugfixes for script;create pheno and geno objects | Alexander Kabui | |
| 2022-01-22 | add endpoint for ctl | Alexander Kabui | |
| 2022-01-22 | init file to call ctl script | Alexander Kabui | |
| 2022-01-22 | generate lineplot | Alexander Kabui | |
| 2022-01-22 | minor fix:read input data from json file | Alexander Kabui | |
| 2022-01-22 | export json data | Alexander Kabui | |
| 2022-01-22 | get significant interactions | Alexander Kabui | |
| 2022-01-22 | perform the ctl scan | Alexander Kabui | |
| 2022-01-22 | fetch genotypes and phenotype files | Alexander Kabui | |
| 2022-01-22 | init script ctl analysis | Alexander Kabui | |
| 2022-01-21 | README: Update link to CI badge. | Arun Isaac | |
| The CI has been moved to penguin2, and this is accompanied by a URI change. * README.md: Update link to CI badge. | |||
| 2022-01-12 | Update return type. Remove duplicate import. | Frederick Muriuki Muriithi | |
| The function is a generator function, since it uses a `yield` statement, and thus returns a generator object, that contains a tuple object. This fixes that. We also remove a duplicate import. | |||
| 2022-01-12 | Indent code correctly | Frederick Muriuki Muriithi | |
| Indent the code correctly. | |||
| 2022-01-12 | Deduplicate query to fetch data for 'Publish' traits | Frederick Muriuki Muriithi | |
| The queries run in the `get_trait_csv_sample_data` and `retrieve_publish_trait_data` functions in the `gn3.db.traits` module were mostly similar. This commit changes that, by making the `get_trait_csv_sample_data` function make use of the results from calling the `retrieve_publish_trait_data` function. | |||
| 2022-01-10 | Check for path existence | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi | |||
| 2022-01-10 | Fix dataset retrieval query for `Geno` traits | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi | |||
| 2022-01-10 | Use the correct letter case for the keys | Frederick Muriuki Muriithi | |
| * Use the correct case for the keys inorder to retrieve the correct values. | |||
| 2022-01-10 | Surround statement with parens for readability | Frederick Muriuki Muriithi | |
| 2022-01-10 | Indicate that string is an f-string | Frederick Muriuki Muriithi | |
| * The string had the f-string syntax to format the values to be inserted into the string, but was missing the 'f' before the opening quotes to signify to python that this was an f-string. This commit fixes that. | |||
| 2022-01-10 | Convert keys to string | Frederick Muriuki Muriithi | |
| * Some traits have a name composed of all numerals, which leads to the names being interpreted as numbers. This commit forces them to string to avoid subtle bugs where the code fails. | |||
| 2022-01-10 | Remove all pairs with 'None' as the value | Frederick Muriuki Muriithi | |
| * Remove all key-value pairs whose value is None. | |||
| 2022-01-10 | Fix error in query: Replace '=' with 'IN' | Frederick Muriuki Muriithi | |
| 2022-01-10 | Replace unoptimised function with optimised one | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Replace unoptimised function with one optimised to give better performance. The optimisation done here is to fetch multiple items/traits from the database per query, rather than the original form, which fetched a single item/trait from the database per query. | |||
| 2022-01-10 | Silence `duplicate-code` linting notifications | Frederick Muriuki Muriithi | |
| 2022-01-10 | Convert NaN to None | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Comment: https://github.com/genenetwork/genenetwork3/pull/67#issuecomment-1000828159 * Convert NaN values to None to avoid possible bugs with the string replace method used before. | |||
| 2022-01-10 | Add optimised entry for partial correlations | Frederick Muriuki Muriithi | |
| Issue: * Function `gn3.computations.partial_correlations_optimised.partial_correlations_entry` is a copy of the `gn3.computations.partial_correlation.partial_correlations_entry` function that is optimised for better performance. The optimised function is intended to replace the unoptimised one, but it is included in this commit for comparison purposes, and to maintain some historical context for doing it this way. | |||
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