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2021-06-18db: phenotypes: Add Publication dataclass and mappingBonfaceKilz
2021-06-18db: phenotypes: Update failing testsBonfaceKilz
2021-06-18db: phenotypes: Generalise the update functionBonfaceKilz
* gn3/db/phenotypes.py (update_phenotype): Delete it. (update): New, more general function.
2021-06-18db: phenotypes: Map a table to it's relevant dict mappingBonfaceKilz
2021-06-18db: phenotypes: Add type for DataclassBonfaceKilz
See: https://www.py4u.net/discuss/188952
2021-06-18db: phenotypes: Put mapping def after dataclassBonfaceKilz
2021-06-18db: phenotypes: Add phenotype table mappingBonfaceKilz
2021-06-18db: phenotypes: Add dataclass to represent PublishXRefBonfaceKilz
2021-06-18db: phenotype: Make "pylint: disable=[R0902]" global for fileBonfaceKilz
2021-06-18tests: test_phenotypes: New test cases for loading phenotypesBonfaceKilz
2021-06-18db: 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.
2021-06-18Fixed issue where all bool kwargs were always being passed to ↵zsloan
generate_rqtl_cmd and also made code check if output file already exists (so caching works)
2021-06-18Added option for enabling permutation stratazsloan
Fixed issue where covariates with numerical names were being ignored Fixed issue where the hash filename wasn't being used for the permutation output
2021-06-18Add rqtl_wrapper.R script and necessary imports to guix.scmzsloan
2021-06-18Fix R/qtl command and the way keyword arguments are passedzsloan
2021-06-16Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into mainzsloan
2021-06-16Fixed spelling of coeffient to coefficientzsloan
2021-06-16add r-wgna packageAlexander Kabui
2021-06-16minor fixAlexander Kabui
2021-06-16refactor script and add testsAlexander Kabui
2021-06-16add r_testthatpackageAlexander Kabui
2021-06-16add fetch args functionAlexander Kabui
2021-06-15fix script path issuesAlexander Kabui
2021-06-14fix missing call to bicorAndPvalueAlexander Kabui
2021-06-14add biweight r script and testsAlexander Kabui
2021-06-11minor fixesAlexander Kabui
2021-06-11remove ununsed variablesAlexander Kabui
2021-06-11refactor perf query functionsAlexander Kabui
2021-06-11rename perf query fileAlexander Kabui
2021-06-11pep8 formattingAlexander Kabui
2021-06-11add tests to setup packagesAlexander Kabui
2021-06-11add types and dataset namesAlexander Kabui
2021-06-11initial commit for queries perfomance testsAlexander Kabui
2021-06-07db: test_db: Add extra variable in test data for "id"BonfaceKilz
2021-06-07Rename json_data column to json_diff_dataBonfaceKilz
2021-06-07gn3: db: Fix how columns from tables is resolvedBonfaceKilz
2021-06-07gn3: db: Add "id_" property to metadata_audit class and mappingBonfaceKilz
2021-06-07tests: test_db: Add a test-case for fetchallBonfaceKilz
2021-06-07gn3: db: Add "fetchall" method.BonfaceKilz
2021-06-07gn3: metadata_audit: Make props for MetadataAudit class optionalBonfaceKilz
2021-06-07gn3: db: Make "WHERE" clause optionalBonfaceKilz
* gn3/db/__init__.py (fetchone): Make "WHERE" an Optional arg.
2021-06-07gn3: db: Use correct DATACLASSMAP entry from metadata_auditBonfaceKilz
2021-06-07tests: test_db: Rename TestPhenotypeBonfaceKilz
2021-06-07tests: test_phenotype: Rename to test_dbBonfaceKilz
2021-06-07gn3: db: sort importsBonfaceKilz
2021-06-03gn3: db: Remove "escape_string" from importsBonfaceKilz
We use prepared statements, so no need to have this.
2021-06-03Use prepared statements for FETCH sql functionBonfaceKilz
2021-06-03gn3: db: Replace items() with keys()BonfaceKilz
* gn3/db/__init__.py (diff_from_dict): We only use the keys of the dict!
2021-06-03Use prepared statements for UPDATE sql functionBonfaceKilz
2021-06-03tests: test_audit: Update test case to check for prepared statementsBonfaceKilz
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