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2021-06-23minor fixes for biweight scriptAlexander Kabui
2021-06-20minor fix docstringAlexander Kabui
2021-06-20merge mainAlexander Kabui
2021-06-20make requested changes to biweightAlexander Kabui
2021-06-18Fixed pylint issueszsloan
2021-06-18Resolve mypy errors in computations/rqtl.pyzsloan
2021-06-18Fixed spelling of coeffient to coefficientzsloan
2021-06-18Rename json_data column to json_diff_dataBonfaceKilz
2021-06-18gn3: db: Fix how columns from tables is resolvedBonfaceKilz
2021-06-18gn3: db: Add "id_" property to metadata_audit class and mappingBonfaceKilz
2021-06-18gn3: db: Add "fetchall" method.BonfaceKilz
2021-06-18gn3: metadata_audit: Make props for MetadataAudit class optionalBonfaceKilz
2021-06-18gn3: db: Make "WHERE" clause optionalBonfaceKilz
* gn3/db/__init__.py (fetchone): Make "WHERE" an Optional arg.
2021-06-18gn3: db: Use correct DATACLASSMAP entry from metadata_auditBonfaceKilz
2021-06-18gn3: db: sort importsBonfaceKilz
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
2021-06-18gn3: db: Add new function for doing sql INSERTBonfaceKilz
2021-06-18Add data structures for the table metadata_auditBonfaceKilz
2021-06-18gn3: db: Add spacing before around "AND" in sql clauseBonfaceKilz
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
2021-06-18db: 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: 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
2021-06-18db: 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)
2021-06-18Fix R/qtl command and the way keyword arguments are passedzsloan
2021-06-16add r-wgna packageAlexander Kabui
2021-06-16minor fixAlexander Kabui
2021-06-16refactor script and add testsAlexander 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
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