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Correlations: Remove top_n argument#105

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fredmanglis wants to merge 64 commits intomaingenenetwork/genenetwork3:mainfrom correlation-return-fewer-resultsgenenetwork/genenetwork3:correlation-return-fewer-resultsCopy head branch name to clipboard

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Commits on Nov 3, 2022

• Add credentials checking

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Commits on Nov 8, 2022

• Tests: Separate *ALL* unit test fixtures from auth-specific ones

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• Tests: Test migration to create user_credentials table

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• Tests: Tests the credentials check system

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• Settings: Provide default AUTH_DB setting.

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• CLI: Provide apply-migrations command for flask

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• Tests: Generalise testing 'CREATE TABLE' migrations

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• Add migration to create the groups table.

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• Tests: Fix typo: remove variable from quotes.

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• Tests: Fix test name.

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• Migrations: Create privileges table.

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• Migrations: Create resource_categories table.

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• Migrations: Init resource_categories with initial categories

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• Migrations: Improve resource_categories data tests.

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• Fix issue where only primary samples were used when all samples are

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Commits on Nov 9, 2022

• Tests: Provide backend fixture to (apply|rollback)_single_migration

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• Migrations: Add resource_meta field to resource_categories table

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Commits on Nov 10, 2022

• Migrations: Add migration for 'resources' table

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• Migrations: Add migration for mrna_resources table

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• Migrations: Add migration for 'phenotype_resources' table

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• Migrations: migration for 'genotype_resources' table

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• Migrations: migration for 'roles' table

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• Migrations: migration for 'generic_roles' table

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• Migrations: migration for role_privileges table

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• Migrations: migration for role_privileges table

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• Tests: Generalise tests for adding/removing columns to/from tables

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• Migrations: Add columns to 'privileges' table

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Commits on Nov 13, 2022

• Documentation: Explain how to run migrations

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Commits on Nov 14, 2022

• Migrations: Migration for initial privileges

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• Migrations: Add generic_role_privileges table

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• Rename files for consistency

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• Migrations: Drop generic_role* tables

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• Migrations: Create group_roles table

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• Migrations: Create the group-leader role and give it privileges

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• Migrations: Add user_editable field to roles table

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• auth: Add test for create_group

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• Migrations: Create user_roles table

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• tests: split test app and test client

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• auth: Implement create_group

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Commits on Nov 15, 2022

• tests: Fix cause of DeprecationWarning

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• tests: Use gn3.auth.db functions for db connection and cursor

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• tests: typo: fix migration script file name

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• pylint: Fix linting errors.

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• auth: Reorganise package - move function to checks module

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• auth: Add some typing information to the functions

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• pylint: Fix a myriad of linting errors

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• Add missing module __init__.py to mitigate the mypy errors

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• auth: Specify types for privileges, roles, groups

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• auth: Return results of calling function directly

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• auth: Add create_group_role function.

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Commits on Nov 16, 2022

• Inject SPARQLWrapper as a parameter

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• tests: Test role creation

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• auth: fix bugs in the code

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• tests: Add tests for privileges

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• pylint: fix some linting errors

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Commits on Nov 17, 2022

• tests: test for addition of data to non-empty table

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• Migrations: Add column group_role_id to group_roles table

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• Tests: Make test failure messages clearer.

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• auth: Define the User type

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• tests: Add test to check creation of roles attached to groups

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• Migrations: Create group_users table

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• auth: Finish implementation of create_group_role

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Commits on Nov 20, 2022

• auth: Prevent group leader from being a member of multiple groups

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Commits on Nov 23, 2022

• Correlations: Remove top_n argument

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