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2021-04-17add sort for correlation resultsAlexander Kabui
refactor return data type for tissue and lit
2021-04-16add benchmark function for sample rAlexander Kabui
2021-04-16benchmark normal function for sample rAlexander Kabui
2021-04-15optimization for sample correlationAlexander Kabui
2021-04-15test endpoint for fetching probeset data typesAlexander Kabui
2021-04-12replace experimental dbAlexander Kabui
2021-04-12fix tests for lit correlationAlexander Kabui
2021-04-12fix merge conflictAlexander Kabui
2021-04-12Integrate correlation APIAlexander Kabui
- add new api for gn2-gn3 sample r integration - delete map for sample list to values - add db util file - add python msql-client dependency - add db for fetching lit correlation results - add unittests for db utils - add tests for db_utils - modify api for fetching lit correlation results - refactor Mock Database Connector and unittests - add sql url parser - add SQL URI env variable - refactor code for db utils - modify return data for lit correlation - refactor tissue correlation endpoint - replace db_instance with conn
2021-04-06add mock db for testsAlexander Kabui
2021-04-06fix DocstringsAlexander Kabui
2021-04-06delete unnecessary functions and commentsAlexander Kabui
2021-04-05fix for fetching dataset traits dataAlexander Kabui
2021-04-04refactor code for trait dataAlexander Kabui
modify unittest and integration tests for datasets
2021-04-04fix:db connectionAlexander Kabui
2021-04-03add tests for getting trait dataAlexander Kabui
2021-04-01add mysqclient to requirements fileAlexander Kabui
2021-03-31add mysqlclient in guixAlexander Kabui
add env variable for GN2_URL
2021-03-31add fetch dataset strain id,strain name and unittestsAlexander Kabui
2021-03-31add temp_db setup and integration testsAlexander Kabui
2021-03-31add datasets functions and endpointsAlexander Kabui
2021-03-30refactor retrieve trait sample data and testsAlexander Kabui
2021-03-30modify getting sample data from dbAlexander Kabui
2021-03-30register trait blueprintAlexander Kabui
2021-03-30initial commit for creating datasetAlexander Kabui
2021-03-30initial commit for creating trait and datasetsAlexander Kabui
2021-03-23Convert Path object to a strBonfaceKilz
* gn3/file_utils.py (cache_ipfs_file): Return a str instead of a path object. * tests/unit/test_file_utils.py: Update failing tests.
2021-03-23Update Gemma docsBonfaceKilz
2021-03-23Update where cached file is storedBonfaceKilz
2021-03-23Use ipfs to get genotype filesBonfaceKilz
2021-03-23Apply auto-pep8 formattingBonfaceKilz
2021-03-23guix.scm: Add missing moduleBonfaceKilz
2021-03-23Add function to cache ipfs filesBonfaceKilz
2021-03-23Apply autopep-8BonfaceKilz
2021-03-23Re-add mypy conf fileBonfaceKilz
Deleted in 56ce88a
2021-03-17gn3: computations: correlations: Apply autopep-8.BonfaceKilz
2021-03-17gn3: file_utils: Apply autopep-8BonfaceKilz
2021-03-17guix.scm: Add ipfs-httpclient & sqlalchemy-stubs and sort the inputsBonfaceKilz
2021-03-17README: Update instructions on how to freeze packagesBonfaceKilz
2021-03-17Add python-ipfshttpclient and it's depsBonfaceKilz
2021-03-17README: Add extra note on depsBonfaceKilz
2021-03-17README: Add note on how to force install things in venvBonfaceKilz
2021-03-16delete unwanted correlation stuff (#5)Alexander Kabui
* delete unwanted correlation stuff * Refactor/clean up correlations (#4) * initial commit for Refactor/clean-up-correlation * add python scipy dependency * initial commit for sample correlation * initial commit for sample correlation endpoint * initial commit for integration and unittest * initial commit for registering correlation blueprint * add and modify unittest and integration tests for correlation * Add compute compute_all_sample_corr method for correlation * add scipy to requirement txt file * add tissue correlation for trait list * add unittest for tissue correlation * add lit correlation for trait list * add unittests for lit correlation for trait list * modify lit correlarion for trait list * add unittests for lit correlation for trait list * add correlation metho in dynamic url * add file format for expected structure input while doing sample correlation * modify input data structure -> add trait id * update tests for sample r correlation * add compute all lit correlation method * add endpoint for computing lit_corr * add unit and integration tests for computing lit corr * add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation * add unittest and integration tests for tissue correlation Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com> * update guix scm file * fix pylint error for correlations api Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>
2021-03-16Refactor/clean up correlations (#4)Alexander Kabui
* initial commit for Refactor/clean-up-correlation * add python scipy dependency * initial commit for sample correlation * initial commit for sample correlation endpoint * initial commit for integration and unittest * initial commit for registering correlation blueprint * add and modify unittest and integration tests for correlation * Add compute compute_all_sample_corr method for correlation * add scipy to requirement txt file * add tissue correlation for trait list * add unittest for tissue correlation * add lit correlation for trait list * add unittests for lit correlation for trait list * modify lit correlarion for trait list * add unittests for lit correlation for trait list * add correlation metho in dynamic url * add file format for expected structure input while doing sample correlation * modify input data structure -> add trait id * update tests for sample r correlation * add compute all lit correlation method * add endpoint for computing lit_corr * add unit and integration tests for computing lit corr * add /api/correlation/tissue_corr/{corr_method} endpoint for tissue correlation * add unittest and integration tests for tissue correlation Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>
2021-03-15Remove undefined variableBonfaceKilz
2021-03-15Bump up numpy to 1.20.1BonfaceKilz
This version has relevant mypy stubs.
2021-03-15Add sqlalchemy-stubs as a requirementBonfaceKilz
2021-03-15Add a basic mypy init fileBonfaceKilz
2021-03-15Apply pep-8 formattingBonfaceKilz
2021-03-15Delete redundant gn3/config.pyBonfaceKilz
All default confs should go to one place: gn3/setting.py * gn3/app.py: Delete get_config. Apply pep-8 formatting. * gn3/config.py: Delete it. Move conf options to... * gn3/settings.py: ... here.
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