| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-06-23 | Change jsonable in GeneralTrait so that it passes all necessary table | zsloan | |
| information | |||
| 2022-06-23 | Convert trait.view to string for conversion to JSON | zsloan | |
| It's originally a boolean, which causes an error when passed to the JS code as JSON | |||
| 2022-06-13 | Check for chromosome of 'Un' and print location as 'Not available' in such cases | zsloan | |
| 2022-04-14 | Add group code to loading pages when applicable | zsloan | |
| This adds the group code to phenotype traits on loading pages, and also sets the group code as an attribute of the dataset.group class. | |||
| 2022-03-25 | Fix issues that prevented genotype traits from being added to collections | zsloan | |
| Some of this was caused by heatmaps supporting code; that code should probably pass the traits differently than the way it does in the "trait_info_str" function | |||
| 2022-02-21 | Fix incorrect dataset trait data caching | zsloan | |
| Trait data caching wasn't working correctly because it didn't account for the samplelist, causing caching to work incorrect in any situation where the target dataset's samplelist wasn't the same as that of the trait being correlated against. Trait data is stored as a dictionary where the keys are trait IDs and values are *lists* of sample values. This means that the caching needs to account for the exact same set of samples; otherwise you'll end up with samples being mismatched (since "the third sample with a value" for one dataset's trait might not be the same as "the third sample with a value" for another dataset's trait). To fix this, I added the samplelist to the functions that generate and fetch the hash file. This will require more cache files, though, so this should probably be reexamined later to make the code work with only a single cache file for each dataset. | |||
| 2021-11-25 | Delete noisy logging | BonfaceKilz | |
| 2021-11-23 | resolve merge conflicts | Alexander Kabui | |
| 2021-11-23 | pep8 formatting remove dead variables | Alexander Kabui | |
| 2021-11-17 | refactor sql query & date formatting | Alexander Kabui | |
| 2021-11-17 | replace redis fetch for cached timestamp with a query | Alexander Kabui | |
| 2021-11-17 | isolate SQL_URI parse to a function | Alexander Kabui | |
| 2021-11-17 | use a dynamic value for the db_name | Alexander Kabui | |
| 2021-11-17 | temp disable query caching | Alexander Kabui | |
| 2021-11-16 | use comprehension list;fix typo | Alexander Kabui | |
| 2021-11-16 | pep8 formatting remove debug statements | Alexander Kabui | |
| 2021-11-16 | test generate new files | Alexander Kabui | |
| 2021-11-16 | refactor:fix on the query :modify cache point | Alexander Kabui | |
| 2021-11-04 | check for null timestamp | Alexander Kabui | |
| 2021-11-04 | store table timestamp on redis | Alexander Kabui | |
| 2021-11-04 | init function to get the table timestamp | Alexander Kabui | |
| 2021-11-04 | pep8 formatting ,minor fixes | Alexander Kabui | |
| 2021-11-04 | generate filename hash | Alexander Kabui | |
| 2021-11-04 | fetch cached results | Alexander Kabui | |
| 2021-11-04 | function to cache sample results | Alexander Kabui | |
| 2021-10-22 | Replace hardcoded GN proxy URLs in trait.py with one pulled from settings | zsloan | |
| 2021-08-20 | Fixed some logic in trait.py that could cause a problem if a dataset_name ↵ | zsloan | |
| was passed that wasn't Temp | |||
| 2021-08-17 | Merge pull request #598 from zsloan/feature/add_filter_by_study_samples | zsloan | |
| Feature/add filter by study samples | |||
| 2021-08-13 | base: data_set: Remove unnecessary comments and logging statements | BonfaceKilz | |
| 2021-08-12 | Return empty list instead of None in get_study_samplelists | zsloan | |
| 2021-08-12 | Fix the way the study_sample_lists path is set and checked | zsloan | |
| 2021-08-12 | add function for reading in JSON file that lists sample lists unique to each ↵ | zsloan | |
| study within a group (in this case only BXD Longevity for now) | |||
| 2021-06-17 | delete loggers and comments | Alexander Kabui | |
| 2021-06-17 | sort sample name by sample_ids | Alexander Kabui | |
| 2021-06-17 | remove unused functions + minor fixes | Alexander Kabui | |
| 2021-06-17 | minor fix | Alexander Kabui | |
| 2021-06-17 | pep8 formatting | Alexander Kabui | |
| 2021-06-17 | add query for fetching probeset data | Alexander Kabui | |
| 2021-06-16 | Changed the function jsonable in trait.py to return a couple extra fields + ↵ | zsloan | |
| take dataset as an optional argument (to avoid having to pointlessly create it) | |||
| 2021-06-16 | Added function as_dict to data_set.py for situations where we don't want to ↵ | zsloan | |
| pass around the whole dataset object | |||
| 2021-05-10 | Merge branch 'testing' into feature/integrate-correlation-api | Alexander Kabui | |
| 2021-05-10 | add previous endpoint for correlation | Alexander Kabui | |
| 2021-05-05 | base: species: Remove redundant assignment | BonfaceKilz | |
| 2021-05-05 | base: chromosomes: Fetch the chromosomes lazily | BonfaceKilz | |
| 2021-05-05 | base: species: Rewrite Chromosomes using a dataclass | BonfaceKilz | |
| 2021-05-05 | base: species: Rewrite IndChromosome using a dataclass | BonfaceKilz | |
| 2021-05-05 | base: trait: Remove logging information | BonfaceKilz | |
| The log adds unnecessary noise in addition to creating unwanted side-effects. | |||
| 2021-05-05 | base: species: Rewrite TheSpecies class using a dataclass | BonfaceKilz | |
| 2021-05-05 | base: species: Remove unused import | BonfaceKilz | |
| 2021-05-05 | base: species: Format SQL queries | BonfaceKilz | |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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