| Age | Commit message (Expand) | Author |
|---|
| 2022-02-02 | Fix R/qtl covar bug...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.
| zsloan |
| 2022-02-02 | Remove PublishFreeze from retrieve_publish_trait_info query...The PublishFreeze table isn't necessary in phenotype queries, since
PublishFreeze.Id = InbredSet.Id (for the purposes of identifying traits,
at least)
| zsloan |
| 2022-02-02 | Fix bug where sample values of 0 were being treated as False...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
| zsloan |
| 2022-02-02 | Fix retrieve_publish_trait_data query...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)
| zsloan |
| 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"...This reverts commit f676c291967f8a81836b73c5a5dcd3c65e02552c.
| BonfaceKilz |
| 2022-01-27 | Use guix shell shortcut with guix.scm file | jgart |
| 2022-01-24 | README: Add pylint and mypy CI badges....We now have separate CI jobs for the pylint and mypy tests.
* README.md: Add pylint and mypy CI badges.
| Arun Isaac |
| 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....The CI has been moved to penguin2, and this is accompanied by a URI change.
* README.md: Update link to CI badge.
| Arun Isaac |
| 2022-01-12 | Update return type. Remove duplicate import....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.
| Frederick Muriuki Muriithi |
| 2022-01-12 | Indent code correctly...Indent the code correctly.
| Frederick Muriuki Muriithi |
| 2022-01-12 | Deduplicate query to fetch data for 'Publish' traits...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.
| Frederick Muriuki Muriithi |
| 2022-01-10 | Check for path existence...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2022-01-10 | Fix dataset retrieval query for `Geno` traits...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2022-01-10 | Use the correct letter case for the keys...* Use the correct case for the keys inorder to retrieve the correct values.
| Frederick Muriuki Muriithi |
| 2022-01-10 | Surround statement with parens for readability | Frederick Muriuki Muriithi |
| 2022-01-10 | Indicate that string is an f-string...* 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.
| Frederick Muriuki Muriithi |
| 2022-01-10 | Convert keys to string...* 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.
| Frederick Muriuki Muriithi |
| 2022-01-10 | Remove all pairs with 'None' as the value...* Remove all key-value pairs whose value is None.
| Frederick Muriuki Muriithi |
| 2022-01-10 | Fix error in query: Replace '=' with 'IN' | Frederick Muriuki Muriithi |
| 2022-01-10 | Replace unoptimised function with optimised one...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.
| Frederick Muriuki Muriithi |
