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AJ's work on for data library#1

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AlbertSnows merged 207 commits intofeat/originuc-cdis/gen3-user-data-library:feat/originfrom users/ajs/devuc-cdis/gen3-user-data-library:users/ajs/devCopy head branch name to clipboardDec 4, 2024

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Commits on Sep 9, 2024

• add redoc

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• parent 0aeb863

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• various cleanup

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Commits on Sep 10, 2024

• fix route type

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• changed post to put

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Commits on Sep 11, 2024

• corrected type

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Commits on Sep 12, 2024

• add replace list and extend items

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• add some typing

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Commits on Sep 16, 2024

• add type to auth

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• move authz endpoints to lambdas

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Commits on Sep 17, 2024

• finishing tests

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• fixing the user id thing

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Commits on Sep 18, 2024

• minor fixes to test

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• minor fixes to db

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• update get lists

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• fixing circular import

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Commits on Sep 19, 2024

• working on tests

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• stop using frozen sets

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• add todo

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• change /lists from replace to update

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Commits on Sep 20, 2024

• fixing db update to rely on orm instead of dict

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• moved lists file

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• adding data file

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Commits on Sep 23, 2024

• get list tests

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• more route cleanup

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Commits on Sep 24, 2024

• change route schema

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• fix data

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Commits on Sep 25, 2024

• fix route input expectation

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• adding some todos

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• beginning inspection

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Commits on Sep 26, 2024

• moving files around

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• renaming files

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• breaking up functions

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• more doc work

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• adding more documentation for routes

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• adding more tests for lists

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• adding helpers test file

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Commits on Sep 30, 2024

• working on fixes tests after migration

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• minor switch to endpoint

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• fix the loss of arborist

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Commits on Oct 1, 2024

• SAFE: all tests passing again

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• test reading lists success

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• minor data change, cf

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• blacklist test

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Commits on Oct 2, 2024

• more test writing, adding lots of todos

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• better read lists test

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• finished tests for now

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• formatting cleanup

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• minor format

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Commits on Oct 3, 2024

• reformatting commit

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• minor, more format changes

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• working on endpoint refactor

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Commits on Oct 4, 2024

• moving some code to helper

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• minor formatting

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Commits on Oct 5, 2024

• unsatisfying error handler abstraction, works for now though

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• cleaning up by id

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• fixing test that works now for some reason

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• fixing spooky variable behavior

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Commits on Oct 7, 2024

• saving alex's suggestions

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Commits on Oct 8, 2024

• saving alex's suggestions p2

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• remove malicious test todo

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• add config readme

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• moving schema to config

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Commits on Oct 9, 2024

• moved items_schema

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• document update structure

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• renaming test configs a bit

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• renaming things

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• more name changes

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• remove unused

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• more fixes to get new config

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• schema location notes

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• trying to add middleware

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Commits on Oct 10, 2024

• middleware + remove endpoint

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• revert to conftest

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• adding future considerations

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• middleware done(?) needs test

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• working on middleware test

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• regex_key_matcher test (not working)

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• key matcher works

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Commits on Oct 11, 2024

• working on ensuring middleware is hit

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• middleware works

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• adding lib

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Commits on Oct 14, 2024

• adding max limits checks

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• test_docs fixed

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• on update added to column

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• more tests

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Commits on Oct 15, 2024

• fixing issues in by id, including auth

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• most tests fixed by updating .env

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• TESTS STABLE

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• STABLE v0.2: fix config

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• all todo's moved to docs

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• minor format

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• formatting todo doc

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• UNSAFE: in the middle of various fixes

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Commits on Oct 16, 2024

• fixing tests

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• STABLE: fixed tests

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• STABLE: fixed tests, v2

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• added some docs

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• fixed base test router missing router

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• STABLE: adding middleware validation!

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• minor doc update

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Commits on Oct 17, 2024

• switching to dependencies

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• STABLE: terminal and pycharm work

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• changing data structure

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• migrating helpers to folder

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• STABLE: tests fixed again after switching to deps

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Commits on Oct 18, 2024

• STABLE: working on dependencies

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• add validate lists

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Commits on Oct 21, 2024

• validate lists works?

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• adding docs

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Commits on Oct 22, 2024

• reverting client change for tests

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• STABLE: comment out middleware code for now

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Commits on Oct 23, 2024

• moving test files around

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• add delete test

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• fixing more tests

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• fix: Move jsonschema to main dependencies

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• fix: app_instance -> app in main.py

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• Updates ImageBuildAndPush to only depend on Security

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Commits on Oct 24, 2024

• Use the right test-script

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• Debug - echo current_dir

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• starting to add max item tests

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• Merge pull request #6 from uc-cdis/fix/docker-fixes

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Commits on Oct 30, 2024

• fix config a tad plus test_dependencies

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• remove old migration

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• BLACK formatting

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Commits on Oct 31, 2024

• fix(bash): fix bash script paths and simplify logic

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• Merge pull request #8 from uc-cdis/fix/bash

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• fix .env and address question

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• fix faulty config switch for functions

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• removing some candidates that we may not need?

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• bring back pytest asyncio

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• P1: implmenting some of alex's suggestions

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Commits on Nov 1, 2024

• switch from helpers to utils folder

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• Running poetry lock

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• fix readme references

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Commits on Nov 4, 2024

• minor fix to config, remove token claims

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• Update docs/future_considerations.md

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• minor fixes to docs, move config

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• merge

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• ran pre-commit, changed whitelist, remove schema

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• delete middleware, add docs, update pre-commit

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Commits on Nov 5, 2024

• add type hints

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• more fixes from test branch

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Commits on Nov 6, 2024

• implementing alex's remaining suggestions

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• fix tests

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• fix ci, fix schema setup

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• fix sh files

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• fix migration stuff a bit, and config

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• TEST: test.sh under bin?

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• TEST: change location of references

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• remove redundant file

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Commits on Nov 13, 2024

• temp change coverage

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Commits on Nov 14, 2024

• Update config/item_schemas.json

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• implementing part of alex's changes

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• turn off skip auth test

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• Merge remote-tracking branch 'origin/users/ajs/dev' into users/ajs/dev

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• remove :param and :return

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• Update README.md

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• next chunk of changes per alex's suggestion

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• another chunk of changes per alex's review

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• Merge remote-tracking branch 'origin/users/ajs/dev' into users/ajs/dev

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• fix test.sh

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Commits on Nov 15, 2024

• fixing minor details in responses, as well as commits

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• possible fix for replace list

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• working on various fixes per Alex. these ones include adding slashes to by id tests

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Commits on Nov 18, 2024

• adding updated time to allow list

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• Disable UnitTest CI, reduce coverage to 0

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• Remove informational lint

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• Remove RequiredLint

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• Merge pull request #9 from uc-cdis/disable_unitest_ci

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• adding awaits, fixing tests

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• Merge remote-tracking branch 'origin/users/ajs/dev' into users/ajs/dev

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• adding type params to the docs

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• working on swagger docs

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Commits on Nov 19, 2024

• swagger docs, remove requirements from basic

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• fix remaining tests

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• finish docstring work

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• minor fix to create policy handler

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• gen3_data_library -> gen3_user_data_library

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• minor fix to json encoder

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• Merge remote-tracking branch 'origin/fix/arborist-resource-paths' into users/ajs/dev

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• adding debug lines

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Commits on Nov 20, 2024

• Add DEBUG_SKIP_AUTH to ensure_user_exists

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• Merge pull request #11 from uc-cdis/fix/disable-arborist

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Commits on Nov 26, 2024

• chore(lint): test linter fix

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• chore(admin): run black and isort, update deps by relocking

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• fix(metrics): update metrics handling, remove broken profiling

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• Merge remote-tracking branch 'origin/users/ajs/dev' into users/ajs/dev

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• chore(lock): relock

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• chore(poetry): relock with lib on new version

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• fix(whitespace): formating

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Commits on Dec 3, 2024

• switch to dict query

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• fix get_list_info

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• formatting, remove youtrack issue

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• working on docs

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• adding authz to readme

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• move derive changes.

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• fix get list query type

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• change db doc

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• TESTING: Revert "fix get list query type"

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• TESTING: trying 'fix get list query type' again

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• add details to readme

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