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2021-05-26db: phenotypes: Fix typoBonfaceKilz
2021-05-25Include code that processes rqtl output files and returns actual results ↵zsloan
instead of just the output filename
2021-05-20tests: test_phenotype: Add function that tests "fetchone"BonfaceKilz
2021-05-20db: phenotypes: Add function for fetching a single resultBonfaceKilz
* gn3/db/phenotypes.py (fetchone): New function.
2021-05-20db: phenotypes: Add a dataclass mapBonfaceKilz
Maps a string to it's dataclass.
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: Update failing testsBonfaceKilz
2021-05-20db: phenotypes: Generalise the update functionBonfaceKilz
* gn3/db/phenotypes.py (update_phenotype): Delete it. (update): New, more general function.
2021-05-20db: phenotypes: Map a table to it's relevant dict mappingBonfaceKilz
2021-05-20db: phenotypes: Add type for DataclassBonfaceKilz
See: https://www.py4u.net/discuss/188952
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
2021-05-20tests: test_phenotypes: New test cases for loading phenotypesBonfaceKilz
2021-05-20db: phenotypes: Add a way of updating the Phenotype tableBonfaceKilz
* gn3/db/phenotypes.py (Phenotype): New dataclass. (update_phenotype): New function. [phenotype_column_mapping]: New variable.
2021-05-19Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into ↵zsloan
feature/add_rqtl_endpoints
2021-05-19Add r-optparse to guix.scmPjotr Prins
2021-05-19Temporarily replace forward-slashes with underscores, since they can be ↵zsloan
included in the hashes used for filenames
2021-05-19Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into ↵zsloan
feature/add_rqtl_endpoints
2021-05-19Added R and r-qtlPjotr Prins
2021-05-19More SQL optimization trialsPjotr Prins
2021-05-19Fix SQL queryPjotr Prins
2021-05-19SQL query gives different resultPjotr Prins
2021-05-19New SQL approachPjotr Prins
2021-05-18Added test for compose_rqtl_cmd in tests/unit/test_commands.pyzsloan
2021-05-18Removed len from this if statement, since an empty list evaluates to False ↵zsloan
by itself
2021-05-18Added unit test for computations/rqtl.pyzsloan
2021-05-18Account for boolean kwargs in compute() by storing them in a list, since ↵zsloan
they don't have corresponding values
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 ↵zsloan
keywords and arguments + account for boolean kwargs without values (like --interval or --covar)
2021-05-18Slow SQL: add notePjotr Prins
2021-05-18Add original SQL queryPjotr Prins
2021-05-18Notes on SQL queryPjotr Prins
2021-05-18Fixed variety of issues detected by pylintzsloan
2021-05-17Created compose_rqtl_command and generate_rqtl_command to create the actual ↵zsloan
command to be run from the command line; used the same pattern as for GEMMA for consistency
2021-05-17Read in kwargs fromrequest and pass the command, tmpdir, and kwargs to ↵zsloan
generate_rqtl_cmd which returns the actual command and output path
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
2021-05-17Merge pull request #11 from genenetwork/feature/minor-fixesBonfaceKilz
Feature/minor fixes
2021-05-15resolve merge conflictAlexander Kabui
2021-05-15Merge branch 'main' into feature/minor-fixesAlexander Kabui
2021-05-15index lit tuple resultAlexander Kabui
2021-05-14READMEPjotr Prins
2021-05-13tests: test_general: Add test case for run_r_qtl endpointBonfaceKilz
2021-05-13Add end-point for running an rQTL programBonfaceKilz
* gn3/api/general.py (run_r_qtl): New function. * gn3/settings.py: New variable.
2021-05-13Rename file_utils to fs_helpersBonfaceKilz
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...
generated by cgit v1.2.3 (git 2.46.2) at 2024-12-05 01:55:54 +0000