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2021-05-13computations: correlations: Apply pep-8BonfaceKilz
2021-05-10tests: test_species: Add test for `get_all_species`BonfaceKilz
2021-05-10db: species: Add method for fetching all speciesBonfaceKilz
2021-05-10tests: test_gemma: Add TMPDIR to test_client()BonfaceKilz
2021-05-10setup.py: Add gn3.api to packagesBonfaceKilz
2021-05-10setup.py: Remove gn3.utility from packagesBonfaceKilz
2021-05-10guix.scm: Add missing comma in propagated-inputBonfaceKilz
2021-05-08guix.scm: Add python-numpy and python-requestsBonfaceKilz
2021-05-08setup.py: Create basic setup fileBonfaceKilz
2021-05-08Fix typoBonfaceKilz
2021-05-08tests: test_species: New testsBonfaceKilz
2021-05-08db: species: Fetch chromosomes using a group or species nameBonfaceKilz
* gn3/db/species.py (get_chromosome): New function.
2021-05-08gn3: db_utils: Remove mypy ignore stubBonfaceKilz
MySQLdb is already ignored in ".mypy.ini", added in 88c33df.
2021-05-08Ignore missing stub imports from MySQLdbBonfaceKilz
2021-05-08Fix pep-8 errorsBonfaceKilz
2021-05-08db: traits: Add extra method for looking up webqtl datasetsBonfaceKilz
2021-05-08db: traits: Update method for inserting publication methodBonfaceKilz
2021-05-08Add method for inserting publication_dataBonfaceKilz
2021-05-08Add webqtlCaseData DS to keep track of case data in one traitBonfaceKilz
2021-05-08Replace namedtuple with a dataclassBonfaceKilz
2021-05-08Add method for inserting phenotypesBonfaceKilz
2021-05-08Add method for inserting publicationsBonfaceKilz
2021-05-08Add method to fetch riset name and idBonfaceKilz
2021-05-08Add endpoints for (batch) entering phenotypes and genotypesBonfaceKilz
2021-05-08Add issue and PR templatesBonfaceKilz
2021-05-08Add extra procedure for parsing a genotype fileBonfaceKilz
* gn3/computations/parsers.py (parse_genofile): New procedure. * tests/unit/computations/test_parsers.py: New test files for above.
2021-05-08Add extra genotype test fileBonfaceKilz
* tests/unit/test_data/genotype.txt: New file. * tests/unit/test_file_utils.py: Update failing test.
2021-05-08Add python-mysqlclient as a dependencyBonfaceKilz
2021-05-05Merge pull request #9 from genenetwork/Feature/speed-up-correlationBonfaceKilz
Feature/speed up correlation
2021-05-03add default no of coresAlexander Kabui
2021-05-03modify default SQL_URIAlexander Kabui
2021-05-03add trait_id fix mypy issuesAlexander Kabui
2021-05-03minor fixes for tiss correlation tests and namingAlexander Kabui
2021-05-03replace database with connAlexander Kabui
2021-05-02remove trait and dataset blueprintAlexander Kabui
2021-05-02delete dataset and trait filesAlexander Kabui
2021-04-20pep8 formattingAlexander Kabui
2021-04-20add experiment function for computing tissue correlation using multiprocessingAlexander Kabui
2021-04-18refactor:return trait_name in corr_resultsAlexander Kabui
2021-04-17ad pep8 formattingAlexander Kabui
2021-04-17refactor tests for litAlexander Kabui
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
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