docs(Accessing Data): Fixed broken link to #create-user-access-file #881
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Pull Request Test Coverage Report for Build 10535
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rolinge
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Mar 10, 2021
* 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>
rolinge
added a commit
to rolinge/fence
that referenced
this pull request
Mar 10, 2021
* 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>
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closes #879
thanks @ndjones!
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