merging upstream changes from uc-cdis (#5)

* annotate spot for fix

* try overwrite roles, if fail, then create

* test exception handling

* catch arborist error

* log info failed put role

* test gen3authz patch

* fix git requirement line

* debug requirements load from git

* specify test gen3authz by commit

* test no git

* debug gen3authz tag

* clear cache in quay

* debug import test gen3authz lib

* test

* test

* revert dockerfile and requirements to master

* hack test poetry install gen3authz

* debug poetry install

* debug test dockerfile

* clear quay cache

* comment out gen3authz from setup.py

* tell poetry we don't need a virtual env thanks

* add gen3authz name to setup.py package list

* bump cdiserrors version

* add cdiserrors to setup.py

* bump gen3config

* fix ArboristError import path

* await get users from arborist

* don't await; catch attribute error

* h4ck dockerfile

* revert dockerfile

* use new release of gen3authz lib

* update httplib2

* remove comment

* fix conftest mock arborist patch method

* fix conftest request import path

* async magic mock arborist client

* add asynctest to dev-requirements

* revert testing stuff..

* fix tests - replace gen3authz requests.request with httpx.request

* revert

* fix requests import path in tests

* revert

* update dep versions

* bump authutils..

* revert deps..

* update dep versions

* bump authutils

* delete old poetry lock file

* test import cdispyutils branch

* add test lock file

* update tests

* update tests

* update tests

* debug tests

* revert

* reset

* Parse RAS visas

* chore(fence): New parent image pybase3-1.4.2 (uc-cdis#853)

* parse all users

* feat(userinfo): include identity provider name in userinfo response for clients

* feat(userinfo): safely graph idp name even if relationship doesn't exist

* docs(openapi): add idp to userinfo response docs

* visa update cron job

* initialize

* notes

* fix(dependencies): Fix poetry lock command (uc-cdis#858)

* fix(dependencies): Fix poetry lock

* new lock file

* Update pyproject.toml

Cool

Co-authored-by: Pauline Ribeyre <ribeyre@uchicago.edu>

Co-authored-by: Pauline Ribeyre <ribeyre@uchicago.edu>

* draft flow

* Dependency Fix New

* chore(builds): Speed up poetry commands by setting proper botocore version (uc-cdis#859)

* fix(dependencies): Fix poetry lock

* new lock file

* chore(build): Speed up docker build nby setting proper botocore version

* add new lock file

* removing line from the other PR

* more notes

* gen3authz use branch

* pkg

* async

* new fix

* new authz

* print

* stuff

* print

* new endpoint

* async

* prints

* updated

* remove prints

* update

* authutils

* testing

* testing

* update dependencies

* poetry update

* account for empty url list

* add window method

* updated as designed

* chore(google-manage-keys): Handle key deletion attempt that returns 400 FAILED_PRECONDITION (uc-cdis#868)

* chore(google-manage-keys): Handle key deletion with FAILED_PRECONDITION

* somem logging

* fence-create+logging

* fix asyncio

* fix asyncio for python<3.6

* db session fixes

* small fixes

* fixes

* try

* remove grant type

* remove try

* add not

* return for when no urls are present

* add variables

* fix

* check update

* int

* fix

* change small things

* add single visa processing

* loop through all urls

* rerun

* lock update

* add unit test

* fix parse_consent_code

* remove test

* finishing up + fence create update

* fix user yaml

* fix get

* add test cases

* comments

* feat(cookies): always set httponly flag on cookies (also update deps)

* add test case reformat

* remove redundent code

* adding fallback logic

* fix things

* add help

* feat(cookies): add httponly flag to missing spots

* test and such

* lock update

* fix things

* cahnge config

* lgos + black

* remove invalid visas

* db_session

* smoll fix

* add logs

* add logs

* #):
fix(no_force_sign): add regression test for urls with no_force_sign=False

* fix(no_force_sign): parse truthiness from no_force_sign param, rather than check if exists

* ras login

* fixes

* small fixes

* stop revoke

* revoke

* black

* small change

* sess

* init sync

* blargh

* add session

* revert

* add to config

* black + spaces

* fix tests

* add to config

* Update bin/fence_create.py

Co-authored-by: Pauline Ribeyre <ribeyre@uchicago.edu>

* Update fence/scripting/fence_create.py

Co-authored-by: Pauline Ribeyre <ribeyre@uchicago.edu>

* Update fence/sync/sync_users.py

Co-authored-by: Pauline Ribeyre <ribeyre@uchicago.edu>

* Update fence/sync/sync_users.py

Co-authored-by: Pauline Ribeyre <ribeyre@uchicago.edu>

* Update fence/job/visa_update_cronjob.py

Co-authored-by: Pauline Ribeyre <ribeyre@uchicago.edu>

* review changes

* black

* resolve again

* remove comments

* black

* small fix

* login

* revoke control

* close session

* refactor

* PXP-7696 Fix/renew access token (uc-cdis#874)

* ix: always mint new token

* fix: wrong logic

* fix: add config

* run the hook

* set default to false

* resolve comments

* Update tests/dbgap_sync/test_user_sync.py

Co-authored-by: Pauline Ribeyre <ribeyre@uchicago.edu>

* Update tests/dbgap_sync/test_user_sync.py

Co-authored-by: Pauline Ribeyre <ribeyre@uchicago.edu>

* fix(empty idp): always commit user/idp to db

* Update fence/sync/sync_users.py

Co-authored-by: Pauline Ribeyre <ribeyre@uchicago.edu>

* update black

* fix typo

* Feat/refresh expires in (uc-cdis#848)

* store expires_in param from authz request in flask session

* take expires_in value from session if present for generating refresh tokens

* fix key check

* debug

* revert

* add exp col to auth code db table model

* extract expires_in param from authorize request and put in db record

* add refresh_token_expires_in logic to token response

* add code for db migration authorization_code table add col

* remove comment

* reformat

* handle pre-db migration case

* undo last change

* handle pre-db-migration case

* fix init auth code record

* undo last change

* revert

* try reflecting db to enable backwards compatibility with previous db schema

* add ref to relevant doc

* fix db reflection

* add scope handling

* reflect auth code table at token endpoint

* revert

* Accommodate variously named query params for expiration times

* expiry does not always refer to access token

* Refactor get-and-validate-requested-expiration pattern into util fn

* Clearer intentions, better names, less repetition, less cognitive load, etc

Co-authored-by: vpsx <19900057+vpsx@users.noreply.github.com>

* test(login_user): ensure logged in users have idp

* docs(login_user): add a docstring

* format black

* fix(login_user): dont log in if already configured

* chore(login_user): remove unused flask.request arg

* chore(login_user): trigger build

* fix(oauth): allow fence oauth w/o LOGIN_OPTIONS

* docs(Accessing Data): Fixed broken link to #create-user-access-file (uc-cdis#881)

Co-authored-by: mattgarvin1 <mattgarvin1@gmail.com>
Co-authored-by: Alexander VanTol <Avantol13@users.noreply.github.com>
Co-authored-by: BinamB <numb.baj@gmail.com>
Co-authored-by: Marcelo R Costa <marceloc@uchicago.edu>
Co-authored-by: Alexander VT <alexander.m.vantol@gmail.com>
Co-authored-by: Binam Bajracharya <44302895+BinamB@users.noreply.github.com>
Co-authored-by: Pauline Ribeyre <ribeyre@uchicago.edu>
Co-authored-by: mattreex <mattreex.9@gail.com>
Co-authored-by: Mattreex <45504048+mattreex@users.noreply.github.com>
Co-authored-by: Matthew Cannalte <mcannalte@uchicago.edu>
Co-authored-by: Mingfei Shao <2475897+mfshao@users.noreply.github.com>
Co-authored-by: John McCann <johnmccann@uchicago.edu>
Co-authored-by: vpsx <19900057+vpsx@users.noreply.github.com>