8 Commits

Author SHA1 Message Date
Bruce Martin
32f60a1547 clean up type inferencing (#2332)
* unit tests for 64 bit conversion

* clean up type handling

* type inference tests

* more type inference fixes

* use schema to determine user intent for data typing

* stop using deprecated API

* fbs type encoding test

* add missing test

* add more tests

* correctly infer X type for CXG adaptor

* lint

* fix typo

* ts migration

* cleanup from PR review

* lint

* PR review changes
2021-07-28 15:10:12 -07:00
Bruce Martin
1140676106 Correctly handle non-finite numbers in heuristic determination of X distribution (#2342)
* handle non-finites explicitly

* improve and test edge case handling for distribution estimation

* revert debugging changes

* code readability
2021-07-28 14:34:29 -07:00
Bruce Martin
0b1ab02a60 rename X_approx_distribution to X_approximate_distribution (#2337) 2021-07-27 13:43:04 -07:00
Bruce Martin
1ea2b7fe80 fix for incorrect stats computation in diff exp t-test (#2318)
* 2211 fixes

* lint

* lint

* add missing test and bug found by test

* change terminology for count distribution

* update scanpy requirement

* update scanpy requirement
2021-07-23 11:36:26 -07:00
Bruce Martin
e334fbe96e remove experimental ontology support (#2300)
* remove experimental ontology support

* lint

* remove ontologies from unit tests

* additional test changes
2021-07-14 07:23:38 -07:00
Severiano Badajoz
28b526b3fc feat: diffexp returns two genesets (#2230)
* feat: return two lists for diffexp (#2221)

* sp

* split out derive sort order, tests passing

* sp

* return diff exp results in two lists

* update

* copy implementation over to desktop

* add tests for two lists

* small fixes to complete backend implementation

* accept new diffexp response

* map diff exp response to genesets

* delete )

* name diffexp genesets with population names

* take constants out of state and allow width prop to override

* shorten mini-histo properly truncate and resize depending on expansion

* prepend new genesets

* rename data within diffexp action

* backend

* move diffexp ttest to common code module, update tests

* update for unit tests

* reference actual var

Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>
Co-authored-by: Madison Dunitz <dunitzm@gmail.com>
2021-06-08 21:02:19 +00:00
Bruce Martin
f2e9aecebe hosted gene sets routes, plus a few bug fixes (#2155)
* first cut at hosted gs routes

* lint

* update tests to match csv parser changes

* update tests to new API

* update gene set name validation rules to match requirements

* add path mapping from dataset to geneset

* add test cases for geneset GET route

* fix test assertion

* remove debugging code

* update gene set uri mapping function

* fix error message

* allow extra user-specified headers in gene set csv file

* clarify comment
2021-04-27 13:58:58 -07:00
Madison Dunitz
78c9d24ed4 Refactor czi_hosted and server into backend directory, pull common code into backend/common, refactor tests (#2102)
* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands
2021-03-26 00:27:07 -05:00