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2021-05-20db: phenotypes: Add function for fetching a single result...* gn3/db/phenotypes.py (fetchone): New function. BonfaceKilz
2021-05-20db: phenotypes: Add a dataclass map...Maps a string to it's dataclass. BonfaceKilz
2021-05-20db: phenotypes: Add Publication table mappingBonfaceKilz
2021-05-20db: phenotypes: Rename phenotype_column_mappingBonfaceKilz
2021-05-20db: phenotypes: Add Publication dataclass and mappingBonfaceKilz
2021-05-20db: phenotypes: Generalise the update function...* gn3/db/phenotypes.py (update_phenotype): Delete it. (update): New, more general function. BonfaceKilz
2021-05-20db: phenotypes: Map a table to it's relevant dict mappingBonfaceKilz
2021-05-20db: phenotypes: Add type for Dataclass...See: https://www.py4u.net/discuss/188952 BonfaceKilz
2021-05-20db: phenotypes: Put mapping def after dataclassBonfaceKilz
2021-05-20db: phenotypes: Add phenotype table mappingBonfaceKilz
2021-05-20db: phenotypes: Add dataclass to represent PublishXRefBonfaceKilz
2021-05-20db: phenotype: Make "pylint: disable=[R0902]" global for fileBonfaceKilz
2021-05-20db: phenotypes: Add a way of updating the Phenotype table...* gn3/db/phenotypes.py (Phenotype): New dataclass. (update_phenotype): New function. [phenotype_column_mapping]: New variable. BonfaceKilz
2021-05-19Temporarily replace forward-slashes with underscores, since they can be inclu...zsloan
2021-05-18Removed len from this if statement, since an empty list evaluates to False by...zsloan
2021-05-18Account for boolean kwargs in compute() by storing them in a list, since they...zsloan
2021-05-18Account for boolean kwargs in compose_rqtl_cmdzsloan
2021-05-18Fixed generate_rqtl_cmd to make the kwarg hash from a combination of keywords...zsloan
2021-05-18Fixed variety of issues detected by pylintzsloan
2021-05-17Created compose_rqtl_command and generate_rqtl_command to create the actual c...zsloan
2021-05-17Read in kwargs fromrequest and pass the command, tmpdir, and kwargs to genera...zsloan
2021-05-17Added RQTL_WRAPPER_CMD (which is fetched from environment) in settings.pyzsloan
2021-05-17Add rqtl.py for rqtl endpointszsloan
2021-05-17Register rqtl blueprintzsloan
2021-05-15resolve merge conflictAlexander Kabui
2021-05-15Merge branch 'main' into feature/minor-fixesAlexander Kabui
2021-05-15index lit tuple resultAlexander Kabui
2021-05-13Add end-point for running an rQTL program...* gn3/api/general.py (run_r_qtl): New function. * gn3/settings.py: New variable. BonfaceKilz
2021-05-13Rename file_utils to fs_helpers...Generally avoid naming things with a "utils" prefix/ suffix since it encourages contributors to dump any new functions there; and over time, as the code grows, things get messy... BonfaceKilz
2021-05-13computations: correlations: Apply pep-8BonfaceKilz
2021-05-12delete unused functionsAlexander Kabui
2021-05-12rename lit_correlation_for_trait_list to lit_correlation_for_traitAlexander Kabui
2021-05-12rename tissue_correlation_for_trait_list with tissue_correlation_for_traitAlexander Kabui
2021-05-12rename p_val ro tissue_p_value for tissue_resultsAlexander Kabui
2021-05-10db: species: Add method for fetching all speciesBonfaceKilz
2021-05-08db: species: Fetch chromosomes using a group or species name...* gn3/db/species.py (get_chromosome): New function. BonfaceKilz
2021-05-08gn3: db_utils: Remove mypy ignore stub...MySQLdb is already ignored in ".mypy.ini", added in 88c33df. BonfaceKilz
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 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
2021-05-03add default no of coresAlexander Kabui
2021-05-03modify default SQL_URIAlexander Kabui
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