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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
2021-06-03gn3: db: Add new function for doing sql INSERTBonfaceKilz
2021-06-03sql: Add a new folder that houses sql statements for new tablesBonfaceKilz
2021-06-03Add data structures for the table metadata_auditBonfaceKilz
2021-06-03gn3: db: Add spacing before around "AND" in sql clauseBonfaceKilz
2021-06-03unit: test_phenotypes: Test for multiple "WHERE" clausesBonfaceKilz
2021-06-03Get the diff between 2 dicts and return that as a dictBonfaceKilz
2021-06-03gn3: db: Return None if data and where are emptyBonfaceKilz
2021-05-30fix index error (#16)Alexander Kabui
2021-05-26Move the methods, "update" and "fetch", to gn3.dbBonfaceKilz
2021-05-26db: phenotypes: Fix publication_mappingBonfaceKilz
2021-05-26db: phenotypes: Fix typoBonfaceKilz
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.
2021-05-19Add r-optparse to guix.scmPjotr Prins
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