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merge: build-fix into staging
* fix: allow config from pytest to be ran in app.py * dx: ignore deprecation warnings with pytest * feat: update tests for server, study api * dx: ignore dependency warnings for all pytest commands * style: 🎨 fix code style issues with Black * wip: adding more tests to pytest * feat: added pyfixture for test_client * feat: have create_app use pytest-config or config based on testing * feat: use pytest-config for pytest * chore: clean app.py * feat: setup tests and fixtures for study api, create dataset api tests * wip: share pytest fixtures across tests with updated value * style: 🎨 fix code style issues with Black * feat: clear database fixture for testing * feat: pytest functions added for study, study metadata, datasets * style: 🎨 fix code style issues with Black * fix: study arm from new entry is patched * fix: patched and cleaned arm metadata api (post) * chore: clean test study api file * feat: track arm id * feat: tests added for central contact, ipd, arm metadata * feat: track arm id through testing * feat: added file for dataset metadata testing * fix: removed for loop and just check for id one time for POST cc endpoint * feat: tests added for collab, cond, desc, design, eligi, id, inter, ipd, link * style: 🎨 fix code style issues with Black * fix: central contact tests fixed, one found bug in response * feat: global variables added for study metadata tests * chore: remove print statements * refactor: /study POST endpoint returns content rather than 204 * wip: modifying login to handle config file for pytest * wip: reworking pytest to login in user once for testing * style: 🎨 fix code style issues with Black * refactor: allow login to use different configuration for testing * style: 🎨 fix code style issues with Black * refactor: use FAIRHUB_SECRET rather than secret for configuration * refactor: create user right after database is cleared * refactor: isort tests folder * fix: resolve unused arguments for pylint * chore: remove prints * feat: add description and payload requirements to ipd endpoint in swagger * feat: add description and payload requirements to arm endpoint in swagger * feat: add more tests for pytest * style: 🎨 fix code style issues with Black * feat: POST, PUT, DELETE tests added for study metadata * style: 🎨 fix code style issues with Black * feat: more tests added for study metadata * style: 🎨 fix code style issues with Black * fix: fix intervention metadata test * chore: gather information on endpoints that aren't working * fix: failed tests corrected * 🚨 fix: fix all linter warnings * 🐛 fix: update secret config * 👷 ci: add test workflow * 💚 test: ci workflow --------- Co-authored-by: Lint Action <lint-action@samuelmeuli.com> Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>
* feat: validation schema for sign up endpoint * style: 🎨 fix code style issues with Black * feat: validate email with email_validator * feat: schema validation for login * feat: schema validation for user details PUT * feat: POST, PUT schemas added for /study endpoint * feat: schema validation added for arm metadata * style: 🎨 fix code style issues with Black * feat: schema validation for available ipd * style: 🎨 fix code style issues with Black * feat: study contact schema validation added * feat: schema validation for collaborators * style: 🎨 fix code style issues with Black * feat: conditions schema validation added" * style: 🎨 fix code style issues with Black * feat: send better error message for invalid email * feat: schema validation for study description * feat: schema validation for study design * feat: schema validation for study intervention * schema validation for ipd sharing * feat: schema validation for study link * fix: fixed import typo * feat: schema validation for other metadata * feat: schema validation for study location * feat: schema validation for oversight endpoint * feat: schema validation for study reference * feat: schema validation for sponsors collaborators * feat: schema validate password meets all criterias on signup * wip: additional requirements/checks for schema validations * style: 🎨 fix code style issues with Black * feat: study design carries additional validations * feat: study contact carries additional validations * feat: study eligibility carries additional validations * feat: study intervention carries additional validations * feat: overal official has enums and other validations * feat: enums and other validations for location endpoint * feat: enums and additional validations for ipd sharing * feat: additional validations for study_status * feat: additional validations for study reference * feat: additional validations for available ipds * feat: enums added and additional validations for sponsor collaborators * additional enums and validations for study links * refactor: removed marshal_with for validation errors * feat: additional validations added for study contact * feat: enums added for enrollment_type in design endpoint * refactor: other metadata validation formatted * feat: minimum length added for validating sponsor collaborators * fix: remove double imports * refactor: isort imports * style: 🎨 fix code style issues with Black * feat: intervention schema validation added * feat: conditional requirements added to status metadata * feat: conditional validations added for sponsor collaborators * refactor: endpoint comment added * feat: additional validations for study identification * style: 🎨 fix code style issues with Black * feat: conditional validations and enums added for final endpoints * style: 🎨 fix code style issues with Black * fix: re-add study type for conditions endpoint * fix: remove last marshal_with on put, fix type def for data (overall-official) * fix: update pytest fixtures for validation schemas * style: 🎨 fix code style issues with Black * fix: updated pytests for schema validations * style: 🎨 fix code style issues with Black * fix: fix: invalid characters for regex * fix: update flake8 errors * style: 🎨 fix code style issues with Black * fix: update for flake8 errors * style: 🎨 fix code style issues with Black * fix: updating for flake8 issues * style: 🎨 fix code style issues with Black * fix: correct issues for pyflake8 * style: 🎨 fix code style issues with Black * fix: type def for request.json * fix: update for pylint issue * 🐛 fix: update schemas --------- Co-authored-by: Lint Action <lint-action@samuelmeuli.com> Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>
* feat: add session table * feat: add session table * chore: add/remove session in logout/change password * chore: add session in login * fix: session removal logic * chore: convert user removal into function * style: format * feat: add logout test functions * feat: add logout test functions * style: format * style: format * style: format * fix: expiration nullability * fix: alembic table removed * style: format * style: format * fix: change token storage for sessions * style: format * fix: session remove for pass change * fix: remove alembic table * style: format * fix: check session * fix: session authentication * fix: change email verified type * fix: session extension time * chore: fix session time * style: format * fix: token session * fix: destroy schema * feat: u[date poetry --------- Co-authored-by: aydawka <aydan.gasimova2@gmail.com>
* fix: update study acronym to short description * fix: update study acronym to short description
* feat: added invitation templates * fix: added invitation function * fix: email invitation templates * style: 🎨 fix code style issues with Black * chore: added flask mail * fix: refactor invited_contributors table name to invite * fix: study invitation templates * fix: email verification * fix: database changes through migrations * fix: model changes for verification * fix: alembic revisions for email verification table * fix: email verification ands resend endpoint * wip: notification endpoint * style: 🎨 fix code style issues with Black * fix: alembic email verification revision * style: 🎨 fix code style issues with Black * feat: added checkings to the alembic revisions * fix: format * style: 🎨 fix code style issues with Black * fix: revisions * style: 🎨 fix code style issues with Black * fix: testing * fix: docker file * fix: model class and docker file * fix: testing constraint added * fix: testing environment added for notifications * fix: added test env to contributors * fix: deleted script from template * style: 🎨 fix code style issues with Black * fix: final revisions for testing * style: 🎨 fix code style issues with Black * fix: modify db using alembic * fix: set up config file for localhost * fix: invitation templates * style: 🎨 fix code style issues with Black * fix: email invitations * fix: added feature flag * fix: flask mailman * fix: remove auth duplication * fix: final revisions for emails * style: 🎨 fix code style issues with Black * fix: poetry lock * fix: authentication for email verification * fix: disabled alembic revisions * fix: removed comment * fix: upgrade destroy schema to remove alembic table * style: 🎨 fix code style issues with Black * fix: format * fix: sort testing files * fix: sort testing files * fix: additional details from staging * fix: modify template style * style: minor email sending typo * feat: add azure EmailClient system * style: format * ➕ chore: add dependency * ➕ chore: add dependency * style: template formats * fix: email confirmation direction if verification is False * fix: test issue * fix: test issue * chore: replace email names * style: format * fix: logic for sending verification * fix: add check api * fix: modify expiration * fix: authentication * fix: update alembic * fix: unverfied contributors * fix: class name * feat: email verification test * feat: set authentication for testing * fix: comment statement * fix: update poetrly lock * style: lint errors * fix: authentication * fix: alembic * fix: email verification for bypassed emails --------- Co-authored-by: Lint Action <lint-action@samuelmeuli.com> Co-authored-by: Sanjay Soundarajan <sanjay.16@live.com>
* fix: comment out the verification logic * fix: comment out the testing * fix: comment out confirm and resent api
* fix: format * fix: team api * fix: comment out unused api * fix: description * fix: identification * wip: test * wip: test team api * wip: test description page * ci: update workflow * ci: update workflow * style: format fix * fix: minlength rule * fix: uncomment testing * fix: uncomment testing * fix: study metadata * fix: version study metadata tedting * fix: minor issues
* fix: general information endpoint * fix: update general information * fix: update general information * fix: update schema for the general information * fix: update team * fix: update team schema * fix: rename contributoir to team * fix: access and rights * fix: restructure dataset metadata * feat: dataset metadata test * fix: format * fix: flask restx validation * fix: flask restx validation * fix: study team * style: format * style: format * fix: dataset metadata version test
* fix: study metadata folders * fix: format * fix: enambe restx validation for study metadata * fix: study metadata restx validation
* feat: add forgot&reset endpoints * fix: update forgot password auth * feat: add test to forgot password * fix: add test to forgot password * chore: modify dependencies * chore: modify dependencies * fix: dependencies * fix: dependencies * feat: add token column * feat: add token column * feat: add token column * fix: change receiver and msg * fix: add forgot and reset password * fix: comment out forgot and reset password * style: format
* fix: uploaded files * fix: uploaded files * fix: comment out recursion api * fix: error handling * fix: error handling * fix: error handling * style: format * feat: add azure storage datalake * style: format * fix: remove package-mode * fix: restore azure storage datalake * fix: study testing * fix: rename container name
* feat: add integration to models * feat: add integration for intervention * wip: integrations * fix: update models * fix: creating study check * style: format * style: format * fix: study add * fix: minor testing * style: format * style: format * fix: error handling * fix: comments * fix: minor issue
* fix: status error handling * fix: error handling
fix: huge etl upgrades
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