| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | |
| 2021-08-17 | 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 | 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 | |
| 2021-04-30 | autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133 | BonfaceKilz | |
| 2021-04-30 | autopep8: Fix W504 | BonfaceKilz | |
| 2021-04-30 | autopep8: Fix E501 | BonfaceKilz | |
| 2021-04-30 | autopep8: Fix E301,E302,E303,E304,E305,E306 | BonfaceKilz | |
| 2021-04-30 | autopep8: Fix E20-E27 | BonfaceKilz | |
| Run: python -m autopep8 --in-place --recrusive ./ --select\ E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\ E242,E251,E252,E26,E265,E266,E27 -p 3 | |||
| 2021-04-29 | Run `sed -i 's/(object)//g'` | BonfaceKilz | |
| See: https://is.gd/pL7IJF Ran: find . \( -type d -name .git -prune \) -o -type f -print0 | xargs -0 sed -i 's/(object)//g' | |||
| 2021-04-29 | base: data_set: Remove unused method | BonfaceKilz | |
| * wqflask/base/data_set.py (Dataset.get_accession_id): Delete it. | |||
| 2021-04-29 | base: data_set: Apply pep-8 | BonfaceKilz | |
| 2021-04-29 | base: data_set: Remove unused method | BonfaceKilz | |
| * wqflask/base/data_set.py (riset): Delete class method. | |||
| 2021-04-29 | base: data_set: Rewrite data_set using @dataclass | BonfaceKilz | |
| @dataclasses should be used to hold only data. Since dataset only encapsulates data, re-writing it using a dataclass makes it more readable and easier to follow. | |||
| 2021-04-23 | debugging for fetching probe data | Alexander Kabui | |
| 2021-04-23 | Remove stale comments | BonfaceKilz | |
| 2021-02-11 | Removed some log statements | zsloan | |
| 2020-10-12 | Merge branch 'testing' into build/python3-migration | BonfaceKilz | |
| 2020-10-08 | Fixed remaining issue that applies to all dataset types | zsloan | |
| * wqflask/base/data_set.py - Fixed issue where there was an error when trying to take the len of the query results when there were no results | |||
| 2020-10-08 | Fixed issue where new phenotype groups wouldn't be saved to the ↵ | zsloan | |
| self.datasets property because the group name was used as the key (instead of the group name + "Publish", which is the full dataset name for phenotypes) * wqflask/base/data_set.py - Set "group_name" as a separate variable from "name" to avoid it being used as the key in self.datasets | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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