| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-02-02 | Fix R/qtl covar bug | zsloan | |
| The rqtl_wrapper script was throwing an error when only a single categorical covariate was used. This is apparently because "covars[,name]" throws an error in such a situation. Using just "covars" in such a situation prevents the error. So I just added an if statement checking the number of covariates. There might be some better way to deal with this in R, but this is the best I could come up with. | |||
| 2022-02-02 | Remove PublishFreeze from retrieve_publish_trait_info query | zsloan | |
| The PublishFreeze table isn't necessary in phenotype queries, since PublishFreeze.Id = InbredSet.Id (for the purposes of identifying traits, at least) | |||
| 2022-02-02 | Fix bug where sample values of 0 were being treated as False | zsloan | |
| In line 91 of gn3/db/traits.py, there was an if statement "if record[key] else 'x'" that was treating values of 0 as False, so I changed it to explicitly check that values aren't None | |||
| 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. | |||
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