| Age | Commit message (Expand) | Author |
|---|---|---|
| 2021-05-08 | Add method to fetch riset name and id | BonfaceKilz |
| 2021-05-08 | Add endpoints for (batch) entering phenotypes and genotypes | BonfaceKilz |
| 2021-05-08 | Add extra procedure for parsing a genotype file...* gn3/computations/parsers.py (parse_genofile): New procedure. * tests/unit/computations/test_parsers.py: New test files for above. | BonfaceKilz |
| 2021-05-03 | add default no of cores | Alexander Kabui |
| 2021-05-03 | modify default SQL_URI | Alexander Kabui |
| 2021-05-03 | add trait_id fix mypy issues | Alexander Kabui |
| 2021-05-03 | minor fixes for tiss correlation tests and naming | Alexander Kabui |
| 2021-05-03 | replace database with conn | Alexander Kabui |
| 2021-05-02 | remove trait and dataset blueprint | Alexander Kabui |
| 2021-05-02 | delete dataset and trait files | Alexander Kabui |
| 2021-04-20 | pep8 formatting | Alexander Kabui |
| 2021-04-20 | add experiment function for computing tissue correlation using multiprocessing | Alexander Kabui |
| 2021-04-18 | refactor:return trait_name in corr_results | Alexander Kabui |
| 2021-04-17 | ad pep8 formatting | Alexander Kabui |
| 2021-04-17 | add sort for correlation results...refactor return data type for tissue and lit | Alexander Kabui |
| 2021-04-16 | add benchmark function for sample r | Alexander Kabui |
| 2021-04-16 | benchmark normal function for sample r | Alexander Kabui |
| 2021-04-15 | optimization for sample correlation | Alexander Kabui |
| 2021-04-15 | test endpoint for fetching probeset data types | Alexander Kabui |
| 2021-04-12 | replace experimental db | Alexander Kabui |
| 2021-04-12 | fix merge conflict | Alexander Kabui |
| 2021-04-12 | Integrate correlation API...- 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 | Alexander Kabui |
| 2021-04-06 | fix Docstrings | Alexander Kabui |
| 2021-04-06 | delete unnecessary functions and comments | Alexander Kabui |
| 2021-04-05 | fix for fetching dataset traits data | Alexander Kabui |
| 2021-04-04 | refactor code for trait data...modify unittest and integration tests for datasets | Alexander Kabui |
| 2021-04-04 | fix:db connection | Alexander Kabui |
| 2021-04-03 | add tests for getting trait data | Alexander Kabui |
| 2021-03-31 | add mysqlclient in guix...add env variable for GN2_URL | Alexander Kabui |
| 2021-03-31 | add fetch dataset strain id,strain name and unittests | Alexander Kabui |
| 2021-03-31 | add temp_db setup and integration tests | Alexander Kabui |
| 2021-03-31 | add datasets functions and endpoints | Alexander Kabui |
| 2021-03-30 | refactor retrieve trait sample data and tests | Alexander Kabui |
| 2021-03-30 | modify getting sample data from db | Alexander Kabui |
| 2021-03-30 | register trait blueprint | Alexander Kabui |
| 2021-03-30 | initial commit for creating dataset | Alexander Kabui |
| 2021-03-30 | initial commit for creating trait and datasets | Alexander Kabui |
| 2021-03-23 | Convert Path object to a str...* gn3/file_utils.py (cache_ipfs_file): Return a str instead of a path object. * tests/unit/test_file_utils.py: Update failing tests. | BonfaceKilz |
| 2021-03-23 | Update where cached file is stored | BonfaceKilz |
| 2021-03-23 | Use ipfs to get genotype files | BonfaceKilz |
| 2021-03-23 | Apply auto-pep8 formatting | BonfaceKilz |
| 2021-03-23 | Add function to cache ipfs files | BonfaceKilz |
| 2021-03-23 | Re-add mypy conf file...Deleted in 56ce88a | BonfaceKilz |
| 2021-03-17 | gn3: computations: correlations: Apply autopep-8. | BonfaceKilz |
| 2021-03-17 | gn3: file_utils: Apply autopep-8 | BonfaceKilz |
| 2021-03-16 | delete unwanted correlation stuff (#5)...* 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> | Alexander Kabui |
| 2021-03-16 | 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> | Alexander Kabui |
| 2021-03-15 | Remove undefined variable | BonfaceKilz |
| 2021-03-15 | Apply pep-8 formatting | BonfaceKilz |
| 2021-03-15 | Delete redundant gn3/config.py...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. | BonfaceKilz |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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