aboutsummaryrefslogtreecommitdiff
AgeCommit message (Collapse)Author
2021-06-18gn3: db: Remove "escape_string" from importsBonfaceKilz
We use prepared statements, so no need to have this.
2021-06-18Use prepared statements for FETCH sql functionBonfaceKilz
2021-06-18gn3: db: Replace items() with keys()BonfaceKilz
* gn3/db/__init__.py (diff_from_dict): We only use the keys of the dict!
2021-06-18Use prepared statements for UPDATE sql functionBonfaceKilz
2021-06-18tests: test_audit: Update test case to check for prepared statementsBonfaceKilz
2021-06-18gn3: db: Add new function for doing sql INSERTBonfaceKilz
2021-06-18sql: Add a new folder that houses sql statements for new tablesBonfaceKilz
2021-06-18Add data structures for the table metadata_auditBonfaceKilz
2021-06-18gn3: db: Add spacing before around "AND" in sql clauseBonfaceKilz
2021-06-18unit: test_phenotypes: Test for multiple "WHERE" clausesBonfaceKilz
2021-06-18Get the diff between 2 dicts and return that as a dictBonfaceKilz
2021-06-18gn3: db: Return None if data and where are emptyBonfaceKilz
2021-06-18fix index error (#16)Alexander Kabui
2021-06-18Move the methods, "update" and "fetch", to gn3.dbBonfaceKilz
2021-06-18db: phenotypes: Fix publication_mappingBonfaceKilz
2021-06-18db: phenotypes: Fix typoBonfaceKilz
2021-06-18tests: test_phenotype: Add function that tests "fetchone"BonfaceKilz
2021-06-18db: phenotypes: Add function for fetching a single resultBonfaceKilz
* gn3/db/phenotypes.py (fetchone): New function.
2021-06-18db: phenotypes: Add a dataclass mapBonfaceKilz
Maps a string to it's dataclass.
2021-06-18db: phenotypes: Add Publication table mappingBonfaceKilz
2021-06-18db: phenotypes: Rename phenotype_column_mappingBonfaceKilz
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
2021-05-25Include code that processes rqtl output files and returns actual results ↵zsloan
instead of just the output filename
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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 22:50:11 +0000