Fix some LGTM errors

.pylintrc

@@ -52,6 +52,7 @@ disable=all
 
 enable=import-error,
        import-self,
+       cyclic-import,
        reimported,
        misplaced-future,
        relative-import,

atst/domain/permission_sets.py

@@ -1,7 +1,8 @@
 from sqlalchemy.orm.exc import NoResultFound
 
 from atst.database import db
-from atst.models import PermissionSet, Permissions
+from atst.models.permissions import Permissions
+from atst.models.permission_set import PermissionSet
 from .exceptions import NotFoundError
 
 

atst/models/__init__.py

@@ -1,8 +1,4 @@
-from sqlalchemy.ext.declarative import declarative_base
-
-Base = declarative_base()
-
-
+from .base import Base
 from .application import Application
 from .application_invitation import ApplicationInvitation
 from .application_role import ApplicationRole, Status as ApplicationRoleStatus

atst/models/application.py

@@ -1,7 +1,7 @@
 from sqlalchemy import and_, Column, ForeignKey, String
 from sqlalchemy.orm import relationship, synonym
 
-from atst.models import Base
+from atst.models.base import Base
 from atst.models.application_role import ApplicationRole
 from atst.models.environment import Environment
 from atst.models import mixins

atst/models/application_invitation.py

@@ -2,11 +2,13 @@ from sqlalchemy import Column, ForeignKey
 from sqlalchemy.dialects.postgresql import UUID
 from sqlalchemy.orm import relationship, backref
 
-from atst.models import Base
-from atst.models.mixins import TimestampsMixin, AuditableMixin, InvitesMixin
+from atst.models.base import Base
+import atst.models.mixins as mixins
 
 
-class ApplicationInvitation(Base, TimestampsMixin, AuditableMixin, InvitesMixin):
+class ApplicationInvitation(
+    Base, mixins.TimestampsMixin, mixins.AuditableMixin, mixins.InvitesMixin
+):
     __tablename__ = "application_invitations"
 
     application_role_id = Column(

atst/models/application_role.py

@@ -5,10 +5,11 @@ from sqlalchemy.orm import relationship
 from sqlalchemy.event import listen
 
 from atst.utils import first_or_none
-from atst.models import Base, mixins
+from atst.models.base import Base
+import atst.models.mixins as mixins
+import atst.models.types as types
 from atst.models.environment_role import EnvironmentRole
 from atst.models.mixins.auditable import record_permission_sets_updates
-from .types import Id
 
 
 class Status(Enum):
@@ -36,7 +37,7 @@ class ApplicationRole(
 ):
     __tablename__ = "application_roles"
 
-    id = Id()
+    id = types.Id()
     application_id = Column(
         UUID(as_uuid=True), ForeignKey("applications.id"), index=True, nullable=False
     )

atst/models/attachment.py

@@ -2,7 +2,9 @@ from sqlalchemy import Column, String
 from sqlalchemy.dialects.postgresql import UUID
 from sqlalchemy.orm.exc import NoResultFound
 
-from atst.models import Base, types, mixins
+from atst.models.base import Base
+import atst.models.mixins as mixins
+import atst.models.types as types
 from atst.database import db
 from atst.domain.exceptions import NotFoundError
 

atst/models/audit_event.py

@@ -2,7 +2,8 @@ from sqlalchemy import String, Column, ForeignKey, inspect
 from sqlalchemy.dialects.postgresql import UUID, JSONB
 from sqlalchemy.orm import relationship
 
-from atst.models import Base, types
+from atst.models.base import Base
+import atst.models.types as types
 from atst.models.mixins.timestamps import TimestampsMixin
 
 

atst/models/base.py

@@ -0,0 +1,3 @@
+from sqlalchemy.ext.declarative import declarative_base
+
+Base = declarative_base()

atst/models/clin.py

@@ -2,7 +2,9 @@ from enum import Enum
 from sqlalchemy import Column, Date, Enum as SQLAEnum, ForeignKey, Numeric, String
 from sqlalchemy.orm import relationship
 
-from atst.models import Base, mixins, types
+from atst.models.base import Base
+import atst.models.mixins as mixins
+import atst.models.types as types
 
 
 class JEDICLINType(Enum):

atst/models/environment.py

@@ -3,9 +3,9 @@ from sqlalchemy.orm import relationship
 from sqlalchemy.dialects.postgresql import JSONB
 from enum import Enum
 
-from atst.models import Base
-from atst.models.types import Id
-from atst.models import mixins
+from atst.models.base import Base
+import atst.models.mixins as mixins
+import atst.models.types as types
 
 
 class Environment(
@@ -13,7 +13,7 @@ class Environment(
 ):
     __tablename__ = "environments"
 
-    id = Id()
+    id = types.Id()
     name = Column(String, nullable=False)
 
     application_id = Column(ForeignKey("applications.id"), nullable=False)

atst/models/environment_role.py

@@ -3,7 +3,9 @@ from sqlalchemy import Index, ForeignKey, Column, String, TIMESTAMP, Enum as SQL
 from sqlalchemy.dialects.postgresql import UUID
 from sqlalchemy.orm import relationship
 
-from atst.models import Base, types, mixins
+from atst.models.base import Base
+import atst.models.mixins as mixins
+import atst.models.types as types
 
 
 class CSPRole(Enum):

atst/models/job_failure.py

@@ -1,7 +1,7 @@
 from sqlalchemy import Column, ForeignKey
 
-from atst.models import Base
-from atst.models import mixins
+from atst.models.base import Base
+import atst.models.mixins as mixins
 
 
 class EnvironmentJobFailure(Base, mixins.JobFailureMixin):

atst/models/notification_recipient.py

@@ -1,6 +1,8 @@
 from sqlalchemy import String, Column
 
-from atst.models import Base, types, mixins
+from atst.models.base import Base
+import atst.models.types as types
+import atst.models.mixins as mixins
 
 
 class NotificationRecipient(Base, mixins.TimestampsMixin):

atst/models/permission_set.py

@@ -1,7 +1,9 @@
 from sqlalchemy import String, Column
 from sqlalchemy.dialects.postgresql import ARRAY
 
-from atst.models import Base, types, mixins
+from atst.models.base import Base
+import atst.models.mixins as mixins
+import atst.models.types as types
 
 
 class PermissionSet(Base, mixins.TimestampsMixin):

atst/models/portfolio.py

@@ -1,9 +1,11 @@
-from sqlalchemy import and_, Column, String
+from sqlalchemy import Column, String
 from sqlalchemy.orm import relationship
 from sqlalchemy.types import ARRAY
 from itertools import chain
 
-from atst.models import Base, Application, mixins, types
+from atst.models.base import Base
+import atst.models.types as types
+import atst.models.mixins as mixins
 from atst.models.portfolio_role import PortfolioRole, Status as PortfolioRoleStatus
 from atst.domain.permission_sets import PermissionSets
 from atst.utils import first_or_none
@@ -31,7 +33,7 @@ class Portfolio(
     applications = relationship(
         "Application",
         back_populates="portfolio",
-        primaryjoin=and_(Application.portfolio_id == id, Application.deleted == False),
+        primaryjoin="and_(Application.portfolio_id == Portfolio.id, Application.deleted == False)",
     )
     roles = relationship("PortfolioRole")
 

atst/models/portfolio_invitation.py

@@ -2,11 +2,13 @@ from sqlalchemy import Column, ForeignKey
 from sqlalchemy.dialects.postgresql import UUID
 from sqlalchemy.orm import relationship, backref
 
-from atst.models import Base
-from atst.models.mixins import TimestampsMixin, AuditableMixin, InvitesMixin
+from atst.models.base import Base
+import atst.models.mixins as mixins
 
 
-class PortfolioInvitation(Base, TimestampsMixin, InvitesMixin, AuditableMixin):
+class PortfolioInvitation(
+    Base, mixins.TimestampsMixin, mixins.InvitesMixin, mixins.AuditableMixin
+):
     __tablename__ = "portfolio_invitations"
 
     portfolio_role_id = Column(

atst/models/portfolio_role.py

@@ -4,8 +4,9 @@ from sqlalchemy.dialects.postgresql import UUID
 from sqlalchemy.orm import relationship
 from sqlalchemy.event import listen
 
-from atst.models import Base, mixins
-from .types import Id
+from atst.models.base import Base
+import atst.models.types as types
+import atst.models.mixins as mixins
 
 from atst.utils import first_or_none
 from atst.models.mixins.auditable import record_permission_sets_updates
@@ -41,7 +42,7 @@ class PortfolioRole(
 ):
     __tablename__ = "portfolio_roles"
 
-    id = Id()
+    id = types.Id()
     portfolio_id = Column(
         UUID(as_uuid=True), ForeignKey("portfolios.id"), index=True, nullable=False
     )

atst/models/task_order.py

@@ -5,7 +5,10 @@ from sqlalchemy import Column, DateTime, ForeignKey, String
 from sqlalchemy.ext.hybrid import hybrid_property
 from sqlalchemy.orm import relationship
 
-from atst.models import Attachment, Base, mixins, types
+from atst.models.base import Base
+import atst.models.types as types
+import atst.models.mixins as mixins
+from atst.models.attachment import Attachment
 from atst.utils.clock import Clock
 
 

atst/models/user.py

@@ -1,9 +1,11 @@
-from sqlalchemy import and_, String, ForeignKey, Column, Date, Boolean, Table, TIMESTAMP
+from sqlalchemy import String, ForeignKey, Column, Date, Boolean, Table, TIMESTAMP
 from sqlalchemy.orm import relationship
 from sqlalchemy.dialects.postgresql import UUID
 from sqlalchemy.event import listen
 
-from atst.models import Base, ApplicationRole, types, mixins
+from atst.models.base import Base
+import atst.models.types as types
+import atst.models.mixins as mixins
 from atst.models.portfolio_invitation import PortfolioInvitation
 from atst.models.application_invitation import ApplicationInvitation
 from atst.models.mixins.auditable import (
@@ -35,9 +37,7 @@ class User(
     application_roles = relationship(
         "ApplicationRole",
         backref="user",
-        primaryjoin=and_(
-            ApplicationRole.user_id == id, ApplicationRole.deleted == False
-        ),
+        primaryjoin="and_(ApplicationRole.user_id == User.id, ApplicationRole.deleted == False)",
     )
 
     portfolio_invitations = relationship(

atst/routes/applications/__init__.py

@@ -1,18 +1,14 @@
-from flask import Blueprint, current_app as app, g, redirect, url_for
-
-applications_bp = Blueprint("applications", __name__)
+from flask import current_app as app, g, redirect, url_for
 
 from . import index
 from . import new
 from . import settings
 from . import invitations
+from .blueprint import applications_bp
 from atst.domain.environment_roles import EnvironmentRoles
 from atst.domain.exceptions import UnauthorizedError
 from atst.domain.authz.decorator import user_can_access_decorator as user_can
 from atst.models.permissions import Permissions
-from atst.utils.context_processors import portfolio as portfolio_context_processor
-
-applications_bp.context_processor(portfolio_context_processor)
 
 
 def wrap_environment_role_lookup(user, environment_id=None, **kwargs):

atst/routes/applications/blueprint.py

@@ -0,0 +1,6 @@
+from flask import Blueprint
+
+from atst.utils.context_processors import portfolio as portfolio_context_processor
+
+applications_bp = Blueprint("applications", __name__)
+applications_bp.context_processor(portfolio_context_processor)

atst/routes/applications/index.py

@@ -1,6 +1,6 @@
 from flask import render_template
 
-from . import applications_bp
+from .blueprint import applications_bp
 from atst.domain.authz.decorator import user_can_access_decorator as user_can
 from atst.models.permissions import Permissions
 

atst/routes/applications/invitations.py

@@ -1,6 +1,6 @@
 from flask import redirect, url_for, g
 
-from . import applications_bp
+from .blueprint import applications_bp
 from atst.domain.invitations import ApplicationInvitations
 
 

atst/routes/applications/new.py

@@ -1,6 +1,6 @@
 from flask import redirect, render_template, request as http_request, url_for, g
 
-from . import applications_bp
+from .blueprint import applications_bp
 from atst.domain.applications import Applications
 from atst.domain.portfolios import Portfolios
 from atst.forms.application import NameAndDescriptionForm, EnvironmentsForm

atst/routes/applications/settings.py

@@ -1,6 +1,6 @@
 from flask import redirect, render_template, request as http_request, url_for, g
 
-from . import applications_bp
+from .blueprint import applications_bp
 from atst.domain.exceptions import AlreadyExistsError
 from atst.domain.environments import Environments
 from atst.domain.applications import Applications

atst/routes/portfolios/__init__.py

@@ -1,12 +1,7 @@
-from flask import Blueprint, request as http_request, g, render_template
+from flask import request as http_request, g, render_template
 from operator import attrgetter
 
-portfolios_bp = Blueprint("portfolios", __name__)
-
 from . import index
 from . import invitations
 from . import admin
-from atst.utils.context_processors import portfolio as portfolio_context_processor
-
-
-portfolios_bp.context_processor(portfolio_context_processor)
+from .blueprint import portfolios_bp

atst/routes/portfolios/admin.py

@@ -1,6 +1,6 @@
 from flask import render_template, request as http_request, g, redirect, url_for
 
-from . import portfolios_bp
+from .blueprint import portfolios_bp
 from atst.domain.portfolios import Portfolios
 from atst.domain.portfolio_roles import PortfolioRoles
 from atst.models.portfolio_role import Status as PortfolioRoleStatus

atst/routes/portfolios/blueprint.py

@@ -0,0 +1,5 @@
+from flask import Blueprint
+from atst.utils.context_processors import portfolio as portfolio_context_processor
+
+portfolios_bp = Blueprint("portfolios", __name__)
+portfolios_bp.context_processor(portfolio_context_processor)

atst/routes/portfolios/index.py

@@ -2,7 +2,7 @@ from datetime import date, timedelta
 
 from flask import redirect, render_template, url_for, request as http_request, g
 
-from . import portfolios_bp
+from .blueprint import portfolios_bp
 from atst.forms.portfolio import PortfolioCreationForm
 from atst.domain.reports import Reports
 from atst.domain.portfolios import Portfolios

atst/routes/portfolios/invitations.py

@@ -1,6 +1,6 @@
 from flask import g, redirect, url_for, render_template, request as http_request
 
-from . import portfolios_bp
+from .blueprint import portfolios_bp
 from atst.domain.authz.decorator import user_can_access_decorator as user_can
 from atst.domain.exceptions import AlreadyExistsError
 from atst.domain.invitations import PortfolioInvitations

atst/routes/task_orders/__init__.py

@@ -1,10 +1,4 @@
-from flask import Blueprint
-
-task_orders_bp = Blueprint("task_orders", __name__)
-
 from . import index
 from . import new
 from . import downloads
-from atst.utils.context_processors import portfolio as portfolio_context_processor
-
-task_orders_bp.context_processor(portfolio_context_processor)
+from .blueprint import task_orders_bp

atst/routes/task_orders/blueprint.py

@@ -0,0 +1,5 @@
+from flask import Blueprint
+from atst.utils.context_processors import portfolio as portfolio_context_processor
+
+task_orders_bp = Blueprint("task_orders", __name__)
+task_orders_bp.context_processor(portfolio_context_processor)

atst/routes/task_orders/downloads.py

@@ -1,6 +1,6 @@
 from flask import Response, current_app as app
 
-from . import task_orders_bp
+from .blueprint import task_orders_bp
 from atst.domain.task_orders import TaskOrders
 from atst.domain.exceptions import NotFoundError
 from atst.domain.authz.decorator import user_can_access_decorator as user_can

atst/routes/task_orders/index.py

@@ -1,6 +1,6 @@
 from flask import g, render_template, url_for, redirect
 
-from . import task_orders_bp
+from .blueprint import task_orders_bp
 from atst.domain.authz.decorator import user_can_access_decorator as user_can
 from atst.domain.portfolios import Portfolios
 from atst.domain.task_orders import TaskOrders

atst/routes/task_orders/new.py

@@ -8,7 +8,7 @@ from flask import (
     jsonify,
 )
 
-from . import task_orders_bp
+from .blueprint import task_orders_bp
 from atst.domain.authz.decorator import user_can_access_decorator as user_can
 from atst.domain.exceptions import NoAccessError
 from atst.domain.task_orders import TaskOrders

atst/utils/notification_sender.py

@@ -2,7 +2,7 @@ from sqlalchemy import select
 
 from atst.jobs import send_notification_mail
 from atst.database import db
-from atst.models import NotificationRecipient
+from atst.models.notification_recipient import NotificationRecipient
 
 
 class NotificationSender(object):