| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-02-08 | db: traits: Enable deletion of individual sample values | BonfaceKilz | |
| If a user replaces an individual value with an "x", delete that date entry from the respective table. Deletion here is the only option since by default the Nstrain, PublishData and PublishSE don't accept null values. Note that deleting all 3 values is equivalent to removing the sample from the CSV file. * gn3/db/traits.py (update_sample_data): If a value is "x", delete it from the respective table. | |||
| 2022-02-08 | db: traits: Allow insertions of "0" in resp. sample values tables | BonfaceKilz | |
| When editing values from "x" to "0"(or any other value) when editing data, an "update" statement was being run; thereby no new value was being inserted. To the end user, modifying an "x" value to something else meant that no value was being inserted. This commit fixes that by doing an insert whenever a change from "x" to "0" is performed. * gn3/db/traits.py (update_sample_data): Add insert statements whenever an "update" statement returns a 0 row-count. | |||
| 2022-02-08 | db: traits: Insert "count" instead of "error" in "NStrain" table | BonfaceKilz | |
| 2022-02-03 | db: Fetch correct sample data | BonfaceKilz | |
| 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. | |||
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