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2022-04-14Add group code to loading pages when applicablezsloan
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.
2022-03-25Fix issues that prevented genotype traits from being added to collectionszsloan
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
2022-02-21Fix incorrect dataset trait data cachingzsloan
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.
2021-11-25Delete noisy loggingBonfaceKilz
2021-11-23resolve merge conflictsAlexander Kabui
2021-11-23pep8 formatting remove dead variablesAlexander Kabui
2021-11-17refactor sql query & date formattingAlexander Kabui
2021-11-17replace redis fetch for cached timestamp with a queryAlexander Kabui
2021-11-17isolate SQL_URI parse to a functionAlexander Kabui
2021-11-17use a dynamic value for the db_nameAlexander Kabui
2021-11-17temp disable query cachingAlexander Kabui
2021-11-16use comprehension list;fix typoAlexander Kabui
2021-11-16pep8 formatting remove debug statementsAlexander Kabui
2021-11-16test generate new filesAlexander Kabui
2021-11-16refactor:fix on the query :modify cache pointAlexander Kabui
2021-11-04check for null timestampAlexander Kabui
2021-11-04store table timestamp on redisAlexander Kabui
2021-11-04init function to get the table timestampAlexander Kabui
2021-11-04pep8 formatting ,minor fixesAlexander Kabui
2021-11-04generate filename hashAlexander Kabui
2021-11-04fetch cached resultsAlexander Kabui
2021-11-04function to cache sample resultsAlexander Kabui
2021-10-22Replace hardcoded GN proxy URLs in trait.py with one pulled from settingszsloan
2021-08-20Fixed some logic in trait.py that could cause a problem if a dataset_name ↵zsloan
was passed that wasn't Temp
2021-08-17Merge pull request #598 from zsloan/feature/add_filter_by_study_sampleszsloan
Feature/add filter by study samples
2021-08-13base: data_set: Remove unnecessary comments and logging statementsBonfaceKilz
2021-08-12Return empty list instead of None in get_study_samplelistszsloan
2021-08-12Fix the way the study_sample_lists path is set and checkedzsloan
2021-08-12add 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)
2021-06-17delete loggers and commentsAlexander Kabui
2021-06-17sort sample name by sample_idsAlexander Kabui
2021-06-17remove unused functions + minor fixesAlexander Kabui
2021-06-17minor fixAlexander Kabui
2021-06-17pep8 formattingAlexander Kabui
2021-06-17add query for fetching probeset dataAlexander Kabui
2021-06-16Changed 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)
2021-06-16Added function as_dict to data_set.py for situations where we don't want to ↵zsloan
pass around the whole dataset object
2021-05-10Merge branch 'testing' into feature/integrate-correlation-apiAlexander Kabui
2021-05-10add previous endpoint for correlationAlexander Kabui
2021-05-05base: species: Remove redundant assignmentBonfaceKilz
2021-05-05base: chromosomes: Fetch the chromosomes lazilyBonfaceKilz
2021-05-05base: species: Rewrite Chromosomes using a dataclassBonfaceKilz
2021-05-05base: species: Rewrite IndChromosome using a dataclassBonfaceKilz
2021-05-05base: trait: Remove logging informationBonfaceKilz
The log adds unnecessary noise in addition to creating unwanted side-effects.
2021-05-05base: species: Rewrite TheSpecies class using a dataclassBonfaceKilz
2021-05-05base: species: Remove unused importBonfaceKilz
2021-05-05base: species: Format SQL queriesBonfaceKilz
2021-04-30autopep8: Run autopep8 100 times with target rulesBonfaceKilz
Rules used are: E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,E242, E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306, E401,E501,E70,E701,W291,W292,W293,W391,W504,E101,E11,E121, E122,E123,E124,E125,E126,E127,E128,E129,E131,E133
2021-04-30autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133BonfaceKilz
2021-04-30autopep8: Fix W504BonfaceKilz
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