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updated user preferences and tests

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This commit is contained in:
Aurthur Musendame 2024-10-27 08:25:31 +02:00
parent c09321a382
commit 0fe5f6da63
20 changed files with 200 additions and 119 deletions
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3
al_revision.sh Normal file
View file

@ -0,0 +1,3 @@
#!/bin/sh
alembic revision --autogenerate -m "$1"

2
felicity/alembic.ini → alembic.ini
View file

@ -2,7 +2,7 @@
[alembic]
# path to migration scripts
script_location = migrations
script_location = felicity/migrations
# template used to generate migration files
# file_template = %%(rev)s_%%(slug)s

3
felicity/al_revision.sh
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@ -1,3 +0,0 @@
#!/bin/sh
alembic revision --autogenerate -m $1

70
felicity/api/gql/user/mutations.py
View file

@ -88,16 +88,16 @@ def simple_task(message: str):
class UserMutations:
@strawberry.mutation(permission_classes=[IsAuthenticated])
async def create_user(
self,
info,
first_name: str,
last_name: str,
email: str,
user_name: str,
password: str,
passwordc: str,
group_uid: str | None = None,
open_reg: bool | None = False,
self,
info,
first_name: str,
last_name: str,
email: str,
user_name: str,
password: str,
passwordc: str,
group_uid: str | None = None,
open_reg: bool | None = False,
) -> UserResponse:
user_service = UserService()
group_service = GroupService()
@ -124,6 +124,7 @@ class UserMutations:
"user_name": user_name,
"password": password,
"is_superuser": False,
"login_retry": 0,
"created_by_uid": felicity_user.uid,
"updated_by_uid": felicity_user.uid,
}
@ -135,11 +136,10 @@ class UserMutations:
user = await user_service.save(user)
# initial user-preferences
pref_in = user_schemas.UserPreferenceCreate(expanded_menu=False, theme="LIGHT")
preference = await user_preference_service.create(pref_in)
user = await user_service.link_preference(
user.uid, preference_uid=preference.uid
)
pref = user_preference_service.get(user_uid=user.uid)
if not pref:
pref_in = user_schemas.UserPreferenceCreate(user_uid=user.uid, expanded_menu=False, theme="LIGHT")
await user_preference_service.create(pref_in)
if user_in.email:
logger.info("Handle email sending in a standalone service")
@ -147,17 +147,17 @@ class UserMutations:
@strawberry.mutation(permission_classes=[IsAuthenticated])
async def update_user(
self,
info,
user_uid: str,
first_name: str | None,
last_name: str | None,
mobile_phone: str | None,
email: str | None,
group_uid: str | None,
is_active: bool | None,
password: str | None = None,
passwordc: str | None = None,
self,
info,
user_uid: str,
first_name: str | None,
last_name: str | None,
mobile_phone: str | None,
email: str | None,
group_uid: str | None,
is_active: bool | None,
password: str | None = None,
passwordc: str | None = None,
) -> UserResponse:
user_service = UserService()
group_service = GroupService()
@ -202,7 +202,7 @@ class UserMutations:
@strawberry.mutation
async def authenticate_user(
self, info, username: str, password: str
self, info, username: str, password: str
) -> AuthenticatedDataResponse:
user_service = UserService()
@ -248,7 +248,7 @@ class UserMutations:
@strawberry.mutation()
async def validate_password_reset_token(
self, info, token: str
self, info, token: str
) -> PasswordResetValidityResponse:
user_service = UserService()
email = verify_password_reset_token(token)
@ -265,11 +265,11 @@ class UserMutations:
@strawberry.mutation()
async def reset_password(
self,
info,
user_uid: str,
password: str,
passwordc: str,
self,
info,
user_uid: str,
password: str,
passwordc: str,
) -> MessageResponse:
user_service = UserService()
@ -311,7 +311,7 @@ class UserMutations:
@strawberry.mutation(permission_classes=[IsAuthenticated])
async def update_group(
self, info, uid: str, payload: GroupInputType
self, info, uid: str, payload: GroupInputType
) -> GroupResponse:
group_service = GroupService()
@ -336,7 +336,7 @@ class UserMutations:
@strawberry.mutation(permission_classes=[IsAuthenticated])
async def update_group_permissions(
self, info, group_uid: str, permission_uid: str
self, info, group_uid: str, permission_uid: str
) -> UpdatedGroupPermsResponse:
group_service = GroupService()
permission_service = PermissionService()

34
felicity/apps/abstract/repository.py
View file

@ -217,7 +217,7 @@ class BaseRepository(Generic[M]):
await session.flush()
async def query_table(
self, table: Table, columns: list[str] | None = None, **kwargs
self, table: Table, columns: list[str] | None = None, **kwargs
):
"""
Query a specific table with optional column selection and filters.
@ -444,11 +444,11 @@ class BaseRepository(Generic[M]):
return list(combined)
async def filter(
self,
filters: dict | list[dict],
sort_attrs: list[str] | None = None,
limit: int | None = None,
either: bool = False,
self,
filters: dict | list[dict],
sort_attrs: list[str] | None = None,
limit: int | None = None,
either: bool = False,
) -> list[M]:
"""
Filter model instances based on the given conditions.
@ -471,13 +471,13 @@ class BaseRepository(Generic[M]):
return found
async def paginate(
self,
page_size: int | None,
after_cursor: str | None,
before_cursor: str | None,
filters: dict | list[dict] | None,
sort_by: list[str] | None,
**kwargs,
self,
page_size: int | None,
after_cursor: str | None,
before_cursor: str | None,
filters: dict | list[dict] | None,
sort_by: list[str] | None,
**kwargs,
) -> PageCursor:
"""
Paginate model instances based on the given conditions.
@ -575,10 +575,10 @@ class BaseRepository(Generic[M]):
@staticmethod
def build_page_info(
start_cursor: str | None = None,
end_cursor: str | None = None,
has_next_page: bool = False,
has_previous_page: bool = False,
start_cursor: str | None = None,
end_cursor: str | None = None,
has_next_page: bool = False,
has_previous_page: bool = False,
) -> PageInfo:
"""
Build a PageInfo object with the given parameters.

1
felicity/apps/client/schemas.py
View file

@ -77,7 +77,6 @@ class ClientContactBaseInDB(ClientContactBase):
class ClientContactCreate(ClientContactBase):
client_uid: str
email: str
user_name: str
# Properties to receive via API on update

30
felicity/apps/common/utils/serializer.py
View file

@ -3,11 +3,11 @@ from enum import Enum
def _marshall_object(
obj,
path: list[str] | None = None,
memoize: dict | None = None,
exclude: list[str] | None = None,
depth: int = 2,
obj,
path: list[str] | None = None,
memoize: dict | None = None,
exclude: list[str] | None = None,
depth: int = 2,
) -> dict | str:
"""
Custom marshaller function to convert objects to dictionaries or strings with proper handling for
@ -62,18 +62,18 @@ def _marshall_object(
def marshaller(
obj,
path: list[str] | None = None,
memoize: dict | None = None,
exclude: list[str] | None = None,
depth: int = 2,
obj,
path: list[str] | None = None,
memoize: dict | None = None,
exclude: list[str] | None = None,
depth: int = 2,
) -> dict:
if isinstance(obj, str):
raise TypeError("Unsupported object of type 'str'")
# if isinstance(obj, str):
# return obj
output = _marshall_object(obj, path, memoize, exclude, depth)
if isinstance(output, str):
raise TypeError("Unexpected return type 'str' while marshalling")
#
# if isinstance(output, str):
# raise TypeError("Unexpected return type 'str' while marshalling")
return output

14
felicity/apps/reflex/services.py
View file

@ -2,7 +2,7 @@ import logging
from operator import gt, lt, eq, ge, le, ne
from typing import List, Optional
from cachetools import TTLCache, cached
from cachetools import TTLCache
from felicity.apps.abstract.service import BaseService
from felicity.apps.analysis.entities.analysis import Analysis, Sample
@ -173,9 +173,9 @@ class ReflexEngineService:
logger.info(f"Reflex actions set for {result}")
@staticmethod
@cached(cache=reflex_action_cache)
# @cached(cache=reflex_action_cache)
async def get_reflex_action(
analysis_uid: str, level: int
analysis_uid: str, level: int
) -> Optional[ReflexAction]:
"""
Get reflex action with caching to improve performance.
@ -278,7 +278,7 @@ class ReflexEngineService:
await self.apply_actions(brain.actions, results_pool)
async def evaluate(
self, conditions: list[ReflexBrainCondition], results_pool: List[AnalysisResult]
self, conditions: list[ReflexBrainCondition], results_pool: List[AnalysisResult]
) -> bool:
"""
Evaluate conditions for decision-making.
@ -298,7 +298,7 @@ class ReflexEngineService:
@staticmethod
async def _eval_condition(
condition: ReflexBrainCondition, results_pool: List[AnalysisResult]
condition: ReflexBrainCondition, results_pool: List[AnalysisResult]
) -> bool:
"""
Evaluate a single condition against the results pool.
@ -401,7 +401,7 @@ class ReflexEngineService:
return all(evaluations)
async def apply_actions(
self, actions: list[ReflexBrainAction], results_pool: List[AnalysisResult]
self, actions: list[ReflexBrainAction], results_pool: List[AnalysisResult]
) -> None:
"""
Execute actions for a matching reflex brain.
@ -436,7 +436,7 @@ class ReflexEngineService:
await self.analysis_result_service.hide_report(r.uid)
async def get_results_pool(
self, conditions: list[ReflexBrainCondition]
self, conditions: list[ReflexBrainCondition]
) -> List[AnalysisResult]:
"""
Get a pool of relevant analysis results for the given conditions.

25
felicity/apps/user/entities.py
View file

@ -4,16 +4,13 @@ from sqlalchemy import Boolean, Column, ForeignKey, String, Table
from sqlalchemy.orm import Mapped, relationship
from felicity.apps.abstract.entity import BaseEntity
from .abstract import AbstractBaseUser
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
# TODO: Refactor User to LaboratoryContact, UserAuth to ContactAuth
"""
Many to Many Link between Group and User
"""
@ -38,13 +35,19 @@ permission_groups = Table(
class User(AbstractBaseUser):
__tablename__ = "user"
# One-to-one relationship with UserPreference
preference: Mapped["UserPreference"] = relationship(
"UserPreference",
back_populates="user",
lazy="selectin",
uselist=False,
cascade="all, delete-orphan",
foreign_keys="[UserPreference.user_uid]"
)
groups = relationship(
"Group", secondary=user_groups, back_populates="members", lazy="selectin"
)
preference_uid = Column(String, ForeignKey("user_preference.uid"))
preference = relationship(
"UserPreference", foreign_keys=[preference_uid], lazy="selectin"
)
class Permission(BaseEntity):
@ -85,6 +88,14 @@ class UserPreference(BaseEntity):
__tablename__ = "user_preference"
user_uid = Column(String, ForeignKey("user.uid", ondelete="CASCADE"), unique=True)
user: Mapped["User"] = relationship(
"User",
back_populates="preference",
foreign_keys=[user_uid],
single_parent=True
)
expanded_menu = Column(Boolean(), default=False)
departments = relationship(
"Department", secondary=department_preference, lazy="selectin"

2
felicity/apps/user/schemas.py
View file

@ -5,6 +5,7 @@ from pydantic import ConfigDict, EmailStr
from felicity.apps.common.schemas import BaseAuditModel, BaseModel
#
# Permission Schema
#
@ -87,6 +88,7 @@ class GroupInDB(GroupInDBBase):
# User Preferences
#
class UserPreferenceBase(BaseAuditModel):
user_uid: str
expanded_menu: bool | None = False
theme: str | None = "light"

7
felicity/apps/user/services.py
View file

@ -27,7 +27,7 @@ class UserService(BaseService[User, UserCreate, UserUpdate]):
super().__init__(UserRepository())
async def create(
self, user_in: UserCreate, related: list[str] | None = None
self, user_in: UserCreate, related: list[str] | None = None
) -> User:
by_username = await self.get_by_username(user_in.user_name)
if by_username:
@ -119,11 +119,6 @@ class UserService(BaseService[User, UserCreate, UserUpdate]):
user_in = UserUpdate(**{**user_obj, "is_active": False})
await super().update(user_uid, user_in)
async def link_preference(self, user_uid: str, preference_uid):
_update = {"preference_uid": preference_uid}
update_in = UserUpdate(**_update)
return await super().update(user_uid, update_in)
class GroupService(BaseService[Group, GroupCreate, GroupUpdate]):
def __init__(self):

3
felicity/database/base.py
View file

@ -1,4 +1,3 @@
from felicity.apps.abstract.entity import BaseEntity # noqa
from felicity.apps.analysis.entities.analysis import Analysis # noqa
from felicity.apps.analysis.entities.analysis import AnalysisCategory # noqa
from felicity.apps.analysis.entities.analysis import AnalysisCoding # noqa
@ -32,7 +31,6 @@ from felicity.apps.client.entities import Client # noqa
from felicity.apps.client.entities import ClientContact # noqa
from felicity.apps.idsequencer.entities import IdSequence # noqa
from felicity.apps.impress.entities import ReportImpress # noqa
# from felicity.apps.setup.entities import MethodValidation # noqa
# from felicity.apps.setup.entities import InstrumentCompetence # noqa
from felicity.apps.instrument.entities import CalibrationCertificate # noqa
@ -88,3 +86,4 @@ from felicity.apps.user.entities import User # noqa
from felicity.apps.user.entities import UserPreference # noqa
from felicity.apps.worksheet.entities import WorkSheet # noqa
from felicity.apps.worksheet.entities import WorkSheetTemplate # noqa
from felicity.apps.abstract.entity import BaseEntity # noqa

20
felicity/lims/seeds/superusers.py
View file

@ -3,7 +3,6 @@ import logging
from felicity.apps.user import schemas
from felicity.apps.user.services import GroupService, UserPreferenceService, UserService
from felicity.core.config import get_settings
from .groups_perms import FGroup
settings = get_settings()
@ -39,13 +38,10 @@ async def seed_daemon_user() -> None:
await user_service.save(system_daemon)
# initial user-preferences
if not system_daemon.preference_uid:
pref_in = schemas.UserPreferenceCreate(expanded_menu=False, theme="light")
preference = await preference_service.create(pref_in)
logger.info(
f"linking system daemon {system_daemon.uid} to preference {preference.uid}"
)
await user_service.link_preference(system_daemon.uid, preference.uid)
preference = preference_service.get(user_uid=system_daemon.uid)
if not preference:
pref_in = schemas.UserPreferenceCreate(user_uid=system_daemon.uid, expanded_menu=False, theme="light")
await preference_service.create(pref_in)
logger.info("Done Setting up system daemon")
@ -78,9 +74,9 @@ async def seed_super_user() -> None:
await user_service.save(super_user)
# initial user-preferences
if not super_user.preference_uid:
pref_in = schemas.UserPreferenceCreate(expanded_menu=False, theme="light")
preference = await preference_service.create(pref_in)
await user_service.link_preference(super_user.uid, preference.uid)
preference = preference_service.get(user_uid=super_user.uid)
if not preference:
pref_in = schemas.UserPreferenceCreate(user_uid=super_user.uid, expanded_menu=False, theme="light")
await preference_service.create(pref_in)
logger.info("Done Setting up system admin")

72
felicity/migrations/versions/9d42a09f0754_remodelled_user_preferences.py Normal file
View file

@ -0,0 +1,72 @@
"""remodelled user preferences
Revision ID: 9d42a09f0754
Revises: c03167691623
Create Date: 2024-10-27 06:28:17.903319
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '9d42a09f0754'
down_revision = 'c03167691623'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.drop_index('ix_analysis_result_level', table_name='analysis_result')
op.drop_index('ix_analysis_result_lft', table_name='analysis_result')
op.drop_index('ix_analysis_result_rgt', table_name='analysis_result')
op.create_index('analysis_result_level_idx', 'analysis_result', ['level'], unique=False)
op.create_index('analysis_result_lft_idx', 'analysis_result', ['lft'], unique=False)
op.create_index('analysis_result_rgt_idx', 'analysis_result', ['rgt'], unique=False)
op.drop_index('ix_message_level', table_name='message')
op.drop_index('ix_message_lft', table_name='message')
op.drop_index('ix_message_rgt', table_name='message')
op.create_index('message_level_idx', 'message', ['level'], unique=False)
op.create_index('message_lft_idx', 'message', ['lft'], unique=False)
op.create_index('message_rgt_idx', 'message', ['rgt'], unique=False)
op.drop_index('ix_sample_level', table_name='sample')
op.drop_index('ix_sample_lft', table_name='sample')
op.drop_index('ix_sample_rgt', table_name='sample')
op.create_index('sample_level_idx', 'sample', ['level'], unique=False)
op.create_index('sample_lft_idx', 'sample', ['lft'], unique=False)
op.create_index('sample_rgt_idx', 'sample', ['rgt'], unique=False)
op.drop_constraint('user_preference_uid_fkey', 'user', type_='foreignkey')
op.drop_column('user', 'preference_uid')
op.add_column('user_preference', sa.Column('user_uid', sa.String(), nullable=True))
op.create_unique_constraint(None, 'user_preference', ['user_uid'])
op.create_foreign_key(None, 'user_preference', 'user', ['user_uid'], ['uid'], ondelete='CASCADE')
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.drop_constraint(None, 'user_preference', type_='foreignkey')
op.drop_constraint(None, 'user_preference', type_='unique')
op.drop_column('user_preference', 'user_uid')
op.add_column('user', sa.Column('preference_uid', sa.VARCHAR(), autoincrement=False, nullable=True))
op.create_foreign_key('user_preference_uid_fkey', 'user', 'user_preference', ['preference_uid'], ['uid'])
op.drop_index('sample_rgt_idx', table_name='sample')
op.drop_index('sample_lft_idx', table_name='sample')
op.drop_index('sample_level_idx', table_name='sample')
op.create_index('ix_sample_rgt', 'sample', ['rgt'], unique=False)
op.create_index('ix_sample_lft', 'sample', ['lft'], unique=False)
op.create_index('ix_sample_level', 'sample', ['level'], unique=False)
op.drop_index('message_rgt_idx', table_name='message')
op.drop_index('message_lft_idx', table_name='message')
op.drop_index('message_level_idx', table_name='message')
op.create_index('ix_message_rgt', 'message', ['rgt'], unique=False)
op.create_index('ix_message_lft', 'message', ['lft'], unique=False)
op.create_index('ix_message_level', 'message', ['level'], unique=False)
op.drop_index('analysis_result_rgt_idx', table_name='analysis_result')
op.drop_index('analysis_result_lft_idx', table_name='analysis_result')
op.drop_index('analysis_result_level_idx', table_name='analysis_result')
op.create_index('ix_analysis_result_rgt', 'analysis_result', ['rgt'], unique=False)
op.create_index('ix_analysis_result_lft', 'analysis_result', ['lft'], unique=False)
op.create_index('ix_analysis_result_level', 'analysis_result', ['level'], unique=False)
# ### end Alembic commands ###

14
felicity/tests/integration/sample_workflow/test_07_results.py
View file

@ -1,9 +1,9 @@
import logging
import pytest
from felicity.tests.integration.utils.user import make_password, make_username
from felicity.apps.analysis.tasks import submit_results, verify_results
from felicity.tests.integration.utils.user import make_password, make_username
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
@ -12,7 +12,7 @@ logger = logging.getLogger(__name__)
@pytest.mark.asyncio
@pytest.mark.order(80)
async def test_submit_results(
app_gql, app_api, auth_data, samples, worksheets, laboratory_instruments, methods
app_gql, app_api, auth_data, samples, worksheets, laboratory_instruments, methods
):
add_gql = """
mutation SubmitAnalysisResults($analysisResults: [ARResultInputType!]!, $sourceObject: String!, $sourceObjectUid: String!) {
@ -404,6 +404,14 @@ async def test_verify_sample_results(app_gql, users, samples):
logger.info(f"samples::::::::::::::: {samples}")
results = samples[0]["analysisResults"]
sample = None
results = None
for _sample in samples:
results = list(filter(lambda r: r["status"] == "resulted", _sample["analysisResults"]))
if len(results) > 0:
sample = _sample
break
response = await app_gql.post(
"/felicity-gql",
json={
@ -411,7 +419,7 @@ async def test_verify_sample_results(app_gql, users, samples):
"variables": {
"analyses": [results[0]["uid"]],
"sourceObject": "sample",
"sourceObjectUid": samples[0]["uid"],
"sourceObjectUid": sample["uid"],
},
},
headers={"Authorization": f"bearer {user_data['token']}"},

10
felicity/tests/unit/apps/abstract/test_abstract_service.py
View file

@ -1,7 +1,7 @@
from pydantic import BaseModel
import pytest
from unittest.mock import AsyncMock, create_autospec
import pytest
from pydantic import BaseModel
from sqlalchemy import String
from sqlalchemy.orm import Mapped, mapped_column
@ -85,7 +85,7 @@ async def test_get(test_service):
test_service.repository.get = AsyncMock(return_value=mock_entity)
result = await test_service.get(uid="1")
assert result == mock_entity
test_service.repository.get.assert_awaited_once_with(uid="1")
test_service.repository.get.assert_awaited_once_with(uid="1", related=None)
@pytest.mark.asyncio
@ -103,10 +103,10 @@ async def test_get_by_uids(test_service):
@pytest.mark.asyncio
async def test_get_related(test_service):
mock_entity = MockEntity(uid="1", name="test", bio="test bio")
test_service.repository.get_related = AsyncMock(return_value=mock_entity)
test_service.repository.get = AsyncMock(return_value=mock_entity)
result = await test_service.get(related=["related1"], uid="1")
assert result == mock_entity
test_service.repository.get_related.assert_awaited_once_with(
test_service.repository.get.assert_awaited_once_with(
related=["related1"], uid="1"
)

2
felicity/tests/unit/apps/user/test_user_service.py
View file

@ -35,7 +35,7 @@ class UserServiceTestCase(unittest.IsolatedAsyncioTestCase):
)
result = await self.user_service.create(UserCreate(**self.user_data))
self.repository.get.assert_called_once_with(
user_name=self.user_data["user_name"]
user_name=self.user_data["user_name"], related=None
)
self.repository.create.assert_called_once()
self.assertIsNotNone(result.return_value.uid)

3
felicity/tests/unit/apps/user/test_user_service2.py
View file

@ -44,7 +44,7 @@ async def test_add_user(user_service, mocker, user_data):
result = await user_service.create(UserCreate(**user_data))
user_service.repository.get.assert_called_once_with(
user_name=user_data["user_name"]
user_name=user_data["user_name"], related=None
)
user_service.repository.create.assert_called_once()
@ -84,7 +84,6 @@ async def test_add_user_password_policy_weak(user_service, mocker, user_data):
)
)
# @pytest.mark.asyncio
# async def test_add_user_password_mismatch(user_service, mocker, user_data):
# mocker.patch.object(user_service.repository, "get", return_value=None)

2
felicity/tests/unit/core/test_security.py
View file

@ -52,7 +52,7 @@ async def test_access_token(trial_data):
@pytest.mark.asyncio
async def test_access_token_timedelta(trial_data):
with pytest.raises(TypeError):
create_access_token(trial_data["username"], timedelta(minutes=5))
create_access_token(trial_data["username"], 5)
@pytest.mark.asyncio

2
requirements.txt
View file

@ -7,7 +7,7 @@ python-jose[cryptography]==3.3.0
passlib[bcrypt]==1.7.4
emails==0.6
apscheduler==3.10.4
sqlalchemy_mptt==0.2.5
sqlalchemy_mptt@git+https://github.com/lowatt/sqlalchemy_mptt@sqlalchemy
sqlalchemy_mixins@git+https://github.com/absent1706/sqlalchemy-mixins
tenacity==8.2.3
pydantic[email]==2.5.3