Added soft deletes to all deletion functions and added deleted_at filters as required

gatehouse_app/api/v1/external_auth/admin.py

@@ -21,7 +21,7 @@ def admin_list_app_providers():
         return api_response(success=False, message="Admin access required", status=403, error_type="FORBIDDEN")
 
     PROVIDERS = [{"id": "google", "name": "Google"}, {"id": "github", "name": "GitHub"}, {"id": "microsoft", "name": "Microsoft"}]
-    db_configs = {c.provider_type: c for c in ApplicationProviderConfig.query.all()}
+    db_configs = {c.provider_type: c for c in ApplicationProviderConfig.query.filter_by(deleted_at=None).all()}
 
     result = []
     for p in PROVIDERS:
@@ -64,7 +64,7 @@ def admin_configure_app_provider(provider: str):
     if not client_id:
         return api_response(success=False, message="client_id is required", status=400, error_type="VALIDATION_ERROR")
 
-    cfg = ApplicationProviderConfig.query.filter_by(provider_type=provider).first()
+    cfg = ApplicationProviderConfig.query.filter_by(provider_type=provider, deleted_at=None).first()
     if cfg:
         cfg.client_id = client_id
         if client_secret:
@@ -90,7 +90,6 @@ def admin_delete_app_provider(provider: str):
     from gatehouse_app.models.auth.authentication_method import ApplicationProviderConfig
     from gatehouse_app.models import OrganizationMember
     from gatehouse_app.utils.constants import OrganizationRole
-    from gatehouse_app.extensions import db
 
     admin_memberships = OrganizationMember.query.filter(
         OrganizationMember.user_id == g.current_user.id,
@@ -100,10 +99,9 @@ def admin_delete_app_provider(provider: str):
     if not admin_memberships:
         return api_response(success=False, message="Admin access required", status=403, error_type="FORBIDDEN")
 
-    cfg = ApplicationProviderConfig.query.filter_by(provider_type=provider).first()
+    cfg = ApplicationProviderConfig.query.filter_by(provider_type=provider, deleted_at=None).first()
     if not cfg:
         return api_response(success=False, message=f"Provider '{provider}' is not configured", status=404, error_type="NOT_FOUND")
 
-    db.session.delete(cfg)
-    db.session.commit()
+    cfg.delete()
     return api_response(message=f"{provider.capitalize()} OAuth provider configuration removed")

gatehouse_app/api/v1/external_auth/oauth.py

@@ -174,6 +174,7 @@ def select_organization():
 
         auth_method = AuthenticationMethod.query.filter_by(
             method_type=state_record.provider_type,
+            deleted_at=None,
         ).order_by(AuthenticationMethod.created_at.desc()).first()
 
         if not auth_method:
@@ -181,11 +182,11 @@ def select_organization():
 
         user = auth_method.user
 
-        org = Organization.query.get(organization_id)
+        org = Organization.query.filter_by(id=organization_id, deleted_at=None).first()
         if not org:
             return api_response(success=False, message="Organization not found", status=404, error_type="NOT_FOUND")
 
-        member = OrganizationMember.query.filter_by(user_id=user.id, organization_id=organization_id).first()
+        member = OrganizationMember.query.filter_by(user_id=user.id, organization_id=organization_id, deleted_at=None).first()
         if not member:
             return api_response(success=False, message="You are not a member of this organization", status=403, error_type="FORBIDDEN")
 

gatehouse_app/api/v1/external_auth/providers.py

@@ -14,13 +14,13 @@ from gatehouse_app.api.v1.external_auth._helpers import get_provider_type, _get_
 def list_providers():
     from gatehouse_app.models.auth.authentication_method import ApplicationProviderConfig
 
-    app_configs = {c.provider_type.lower(): c for c in ApplicationProviderConfig.query.filter_by(is_enabled=True).all()}
+    app_configs = {c.provider_type.lower(): c for c in ApplicationProviderConfig.query.filter_by(is_enabled=True, deleted_at=None).all()}
 
     user_orgs = g.current_user.get_organizations()
     org_configs = {}
     if user_orgs:
         organization_id = user_orgs[0].id
-        org_level = ExternalProviderConfig.query.filter_by(organization_id=organization_id).all()
+        org_level = ExternalProviderConfig.query.filter_by(organization_id=organization_id, deleted_at=None).all()
         org_configs = {c.provider_type.lower(): c for c in org_level}
 
     def provider_info(provider_id, name):
@@ -50,11 +50,11 @@ def get_provider_config(provider: str):
         return api_response(success=False, message="No organizations found for user", status=400, error_type="BAD_REQUEST")
 
     organization_id = user_orgs[0].id
-    member = OrganizationMember.query.filter_by(user_id=g.current_user.id, organization_id=organization_id).first()
+    member = OrganizationMember.query.filter_by(user_id=g.current_user.id, organization_id=organization_id, deleted_at=None).first()
     if not member or member.role not in [OrganizationRole.OWNER, OrganizationRole.ADMIN]:
         return api_response(success=False, message="Admin access required", status=403, error_type="FORBIDDEN")
 
-    config = ExternalProviderConfig.query.filter_by(organization_id=organization_id, provider_type=provider_type.value).first()
+    config = ExternalProviderConfig.query.filter_by(organization_id=organization_id, provider_type=provider_type.value, deleted_at=None).first()
     if not config:
         return api_response(success=False, message=f"{provider.title()} OAuth is not configured", status=404, error_type="NOT_FOUND")
 
@@ -74,7 +74,7 @@ def create_or_update_provider_config(provider: str):
         return api_response(success=False, message="No organizations found for user", status=400, error_type="BAD_REQUEST")
 
     organization_id = user_orgs[0].id
-    member = OrganizationMember.query.filter_by(user_id=g.current_user.id, organization_id=organization_id).first()
+    member = OrganizationMember.query.filter_by(user_id=g.current_user.id, organization_id=organization_id, deleted_at=None).first()
     if not member or member.role not in [OrganizationRole.OWNER, OrganizationRole.ADMIN]:
         return api_response(success=False, message="Admin access required", status=403, error_type="FORBIDDEN")
 
@@ -85,7 +85,7 @@ def create_or_update_provider_config(provider: str):
     if not client_id:
         return api_response(success=False, message="client_id is required", status=400, error_type="VALIDATION_ERROR")
 
-    config = ExternalProviderConfig.query.filter_by(organization_id=organization_id, provider_type=provider_type.value).first()
+    config = ExternalProviderConfig.query.filter_by(organization_id=organization_id, provider_type=provider_type.value, deleted_at=None).first()
     is_new = config is None
 
     if config:
@@ -137,11 +137,11 @@ def delete_provider_config(provider: str):
         return api_response(success=False, message="No organizations found for user", status=400, error_type="BAD_REQUEST")
 
     organization_id = user_orgs[0].id
-    member = OrganizationMember.query.filter_by(user_id=g.current_user.id, organization_id=organization_id).first()
+    member = OrganizationMember.query.filter_by(user_id=g.current_user.id, organization_id=organization_id, deleted_at=None).first()
     if not member or member.role not in [OrganizationRole.OWNER, OrganizationRole.ADMIN]:
         return api_response(success=False, message="Admin access required", status=403, error_type="FORBIDDEN")
 
-    config = ExternalProviderConfig.query.filter_by(organization_id=organization_id, provider_type=provider_type.value).first()
+    config = ExternalProviderConfig.query.filter_by(organization_id=organization_id, provider_type=provider_type.value, deleted_at=None).first()
     if not config:
         return api_response(success=False, message=f"{provider.title()} OAuth is not configured", status=404, error_type="NOT_FOUND")
 

gatehouse_app/api/v1/oidc.py

@@ -819,9 +819,9 @@ def oidc_register():
 
     org_id = data.get("organization_id")
     if org_id:
-        organization = Organization.query.get(org_id)
+        organization = Organization.query.filter_by(id=org_id, deleted_at=None).first()
     else:
-        organization = Organization.query.filter_by(is_active=True).first()
+        organization = Organization.query.filter_by(is_active=True, deleted_at=None).first()
 
     if not organization:
         organization = Organization(

gatehouse_app/api/v1/organizations/members.py

@@ -158,7 +158,7 @@ def send_mfa_reminder(org_id, user_id):
     if not user:
         return api_response(success=False, message="User not found", status=404)
 
-    compliance = MfaPolicyCompliance.query.filter_by(user_id=user_id, organization_id=org_id).first()
+    compliance = MfaPolicyCompliance.query.filter_by(user_id=user_id, organization_id=org_id, deleted_at=None).first()
     policy = OrganizationSecurityPolicy.query.filter_by(organization_id=org_id).first()
 
     if compliance and policy and compliance.deadline_at:

gatehouse_app/api/v1/ssh/certs.py

@@ -68,7 +68,7 @@ def sign_certificate():
     )
 
     allowed_principal_names = set()
-    memberships = OrganizationMember.query.filter_by(user_id=user_id).all()
+    memberships = OrganizationMember.query.filter_by(user_id=user_id, deleted_at=None).all()
     for om in memberships:
         org = om.organization
         if not org or org.deleted_at is not None:

gatehouse_app/models/auth/authentication_method.py

@@ -374,7 +374,7 @@ class OAuthState(BaseModel):
     def cleanup_expired(cls) -> None:
         """Remove expired OAuth states."""
         now = datetime.now(timezone.utc)
-        cls.query.filter(cls.expires_at < now).delete()
+        cls.query.filter(cls.expires_at < now).filter(cls.deleted_at == None).update({"deleted_at": now}, synchronize_session=False)
         db.session.commit()
 
     def to_dict(self, exclude=None):

gatehouse_app/models/auth/email_verification_token.py

@@ -32,7 +32,8 @@ class EmailVerificationToken(BaseModel):
 
         Any existing unused tokens for this user are invalidated first.
         """
-        cls.query.filter_by(user_id=user_id, used_at=None).delete()
+        now = datetime.now(timezone.utc)
+        cls.query.filter_by(user_id=user_id, used_at=None).filter(cls.deleted_at == None).update({"deleted_at": now}, synchronize_session=False)
         db.session.flush()
 
         token_value = secrets.token_urlsafe(48)

gatehouse_app/models/auth/password_reset_token.py

@@ -33,7 +33,8 @@ class PasswordResetToken(BaseModel):
         Any existing unused tokens for this user are invalidated first.
         """
         # Invalidate any existing unused tokens for this user
-        cls.query.filter_by(user_id=user_id, used_at=None).delete()
+        now = datetime.now(timezone.utc)
+        cls.query.filter_by(user_id=user_id, used_at=None).filter(cls.deleted_at == None).update({"deleted_at": now}, synchronize_session=False)
         db.session.flush()
 
         token_value = secrets.token_urlsafe(48)

gatehouse_app/services/auth_service.py

@@ -36,9 +36,9 @@ class AuthService:
         Raises:
             EmailAlreadyExistsError: If email is already registered
         """
-        # Check if email already exists
-        existing_user = User.query.filter_by(email=email.lower()).first()
-        if existing_user and existing_user.deleted_at is None:
+# Check if email already exists
+        existing_user = User.query.filter_by(email=email.lower(), deleted_at=None).first()
+        if existing_user:
             raise EmailAlreadyExistsError()
 
         # Create user
@@ -280,12 +280,11 @@ class AuthService:
             raise ConflictError("TOTP is already enabled for this account")
 
         # Clean up any existing unverified TOTP enrollment attempts
-        # Use hard delete for unverified methods since they're incomplete enrollment attempts
+        # Soft delete for unverified methods since they're incomplete enrollment attempts
         existing_totp_method = user.get_totp_method()
         if existing_totp_method and not existing_totp_method.verified:
             logger.debug(f"Removing existing unverified TOTP method for user {user.id}")
-            db.session.delete(existing_totp_method)  # Hard delete - unverified methods are temporary
-            db.session.commit()  # Commit to ensure deletion before creating new record
+            existing_totp_method.delete(soft=True)  # Soft delete - unverified methods are temporary
 
         # Generate TOTP secret
         secret = TOTPService.generate_secret()

gatehouse_app/services/billing_service.py

@@ -50,8 +50,8 @@ class BillingService:
         if not plan:
             raise ValueError("Plan not found")
         
-        # Check if subscription already exists
-        existing = Subscription.query.filter_by(organization_id=organization_id).first()
+                # Check if subscription already exists
+        existing = Subscription.query.filter_by(organization_id=organization_id, deleted_at=None).first()
         if existing:
             raise ValueError("Organization already has a subscription")
         
@@ -88,7 +88,7 @@ class BillingService:
         Returns:
             Updated subscription
         """
-        subscription = Subscription.query.filter_by(organization_id=organization_id).first()
+        subscription = Subscription.query.filter_by(organization_id=organization_id, deleted_at=None).first()
         if not subscription:
             raise ValueError("No subscription found for organization")
         
@@ -111,7 +111,7 @@ class BillingService:
         Returns:
             Updated subscription
         """
-        subscription = Subscription.query.filter_by(organization_id=organization_id).first()
+        subscription = Subscription.query.filter_by(organization_id=organization_id, deleted_at=None).first()
         if not subscription:
             raise ValueError("No subscription found for organization")
         
@@ -132,7 +132,7 @@ class BillingService:
         Returns:
             Updated subscription
         """
-        subscription = Subscription.query.filter_by(organization_id=organization_id).first()
+        subscription = Subscription.query.filter_by(organization_id=organization_id, deleted_at=None).first()
         if not subscription:
             raise ValueError("No subscription found for organization")
         
@@ -158,7 +158,7 @@ class BillingService:
         Returns:
             Overage calculation with details
         """
-        subscription = Subscription.query.filter_by(organization_id=organization_id).first()
+        subscription = Subscription.query.filter_by(organization_id=organization_id, deleted_at=None).first()
         if not subscription:
             return {"has_overage": False, "overage_cost": 0, "user_count": 0, "included_users": 0}
         

gatehouse_app/services/external_auth/__init__.py

@@ -42,7 +42,7 @@ class ExternalAuthService:
         provider_type_str = provider_type.value if isinstance(provider_type, AuthMethodType) else provider_type
 
         app_config = ApplicationProviderConfig.query.filter_by(
-            provider_type=provider_type_str
+            provider_type=provider_type_str, deleted_at=None
         ).first()
 
         if not app_config:
@@ -64,6 +64,7 @@ class ExternalAuthService:
             org_override_obj = OrganizationProviderOverride.query.filter_by(
                 organization_id=organization_id,
                 provider_type=provider_type_str,
+                deleted_at=None,
             ).first()
 
             if org_override_obj and not org_override_obj.is_enabled:

gatehouse_app/services/external_auth/app_provider.py

@@ -14,7 +14,7 @@ def create_app_provider_config(
     **kwargs,
 ) -> ApplicationProviderConfig:
     existing = ApplicationProviderConfig.query.filter_by(
-        provider_type=provider_type
+        provider_type=provider_type, deleted_at=None
     ).first()
 
     if existing:
@@ -51,7 +51,7 @@ def update_app_provider_config(
     **updates,
 ) -> ApplicationProviderConfig:
     config = ApplicationProviderConfig.query.filter_by(
-        provider_type=provider_type
+        provider_type=provider_type, deleted_at=None
     ).first()
 
     if not config:
@@ -90,7 +90,7 @@ def update_app_provider_config(
 
 def get_app_provider_config(provider_type: str) -> ApplicationProviderConfig:
     config = ApplicationProviderConfig.query.filter_by(
-        provider_type=provider_type
+        provider_type=provider_type, deleted_at=None
     ).first()
 
     if not config:
@@ -104,13 +104,13 @@ def get_app_provider_config(provider_type: str) -> ApplicationProviderConfig:
 
 
 def list_app_provider_configs() -> list:
-    configs = ApplicationProviderConfig.query.all()
+    configs = ApplicationProviderConfig.query.filter_by(deleted_at=None).all()
     return [config.to_dict() for config in configs]
 
 
 def delete_app_provider_config(provider_type: str) -> bool:
     config = ApplicationProviderConfig.query.filter_by(
-        provider_type=provider_type
+        provider_type=provider_type, deleted_at=None
     ).first()
 
     if not config:

gatehouse_app/services/external_auth/linking.py

@@ -219,10 +219,11 @@ def authenticate_with_provider(
     auth_method = AuthenticationMethod.query.filter_by(
         method_type=provider_type,
         provider_user_id=user_info["provider_user_id"],
+        deleted_at=None,
     ).first()
 
     if not auth_method:
-        existing_user = User.query.filter_by(email=user_info["email"]).first()
+        existing_user = User.query.filter_by(email=user_info["email"], deleted_at=None).first()
 
         if existing_user:
             AuditService.log_external_auth_login_failed(
@@ -286,12 +287,13 @@ def unlink_provider(
     auth_method = AuthenticationMethod.query.filter_by(
         user_id=user_id,
         method_type=provider_type,
+        deleted_at=None,
     ).first()
 
     if not auth_method:
         raise ExternalAuthError("Provider not linked", "PROVIDER_NOT_LINKED", 400)
 
-    other_methods = AuthenticationMethod.query.filter_by(user_id=user_id).count()
+    other_methods = AuthenticationMethod.query.filter_by(user_id=user_id, deleted_at=None).count()
     if other_methods <= 1:
         raise ExternalAuthError(
             "Cannot unlink the last authentication method",

gatehouse_app/services/external_auth/org_override.py

@@ -16,7 +16,7 @@ def create_org_provider_override(
     **kwargs,
 ) -> OrganizationProviderOverride:
     app_config = ApplicationProviderConfig.query.filter_by(
-        provider_type=provider_type
+        provider_type=provider_type, deleted_at=None
     ).first()
 
     if not app_config:
@@ -29,6 +29,7 @@ def create_org_provider_override(
     existing = OrganizationProviderOverride.query.filter_by(
         organization_id=organization_id,
         provider_type=provider_type,
+        deleted_at=None,
     ).first()
 
     if existing:
@@ -69,6 +70,7 @@ def update_org_provider_override(
     override = OrganizationProviderOverride.query.filter_by(
         organization_id=organization_id,
         provider_type=provider_type,
+        deleted_at=None,
     ).first()
 
     if not override:
@@ -110,6 +112,7 @@ def get_org_provider_override(
     override = OrganizationProviderOverride.query.filter_by(
         organization_id=organization_id,
         provider_type=provider_type,
+        deleted_at=None,
     ).first()
 
     if not override:
@@ -124,7 +127,7 @@ def get_org_provider_override(
 
 def list_org_provider_overrides(organization_id: str) -> list:
     overrides = OrganizationProviderOverride.query.filter_by(
-        organization_id=organization_id
+        organization_id=organization_id, deleted_at=None
     ).all()
     return [override.to_dict() for override in overrides]
 
@@ -133,6 +136,7 @@ def delete_org_provider_override(organization_id: str, provider_type: str) -> bo
     override = OrganizationProviderOverride.query.filter_by(
         organization_id=organization_id,
         provider_type=provider_type,
+        deleted_at=None,
     ).first()
 
     if not override:

gatehouse_app/services/network_access_service.py

@@ -1024,17 +1024,17 @@ def revoke_membership_soft(
 
 
 def hard_delete_membership(membership_id: str) -> None:
-    """Hard delete a membership after ZeroTier has been cleaned up.
+    """Soft delete a membership after ZeroTier has been cleaned up.
 
     Called by the reconciliation job after successfully removing the member
-    from the ZeroTier controller. This is the final DB cleanup step.
+    from the ZeroTier controller. This marks the membership as deleted.
     """
     membership = DeviceNetworkMembership.query.filter(
         DeviceNetworkMembership.id == membership_id,
     ).first()
 
     if not membership:
-        logger.warning(f"[hard_delete_membership] Membership {membership_id} not found, skipping.")
+        logger.warning(f"[hard_delete_membership] Membership {membership_id} not found or already deleted, skipping.")
         return
 
     device = Device.query.get(membership.device_id)
@@ -1048,7 +1048,7 @@ def hard_delete_membership(membership_id: str) -> None:
         except Exception as exc:
             logger.warning(f"[hard_delete_membership] ZT delete failed for {device.node_id}: {exc}")
 
-    db.session.delete(membership)
+    membership.delete(soft=True)
     db.session.commit()
 
     AuditService.log_action(
@@ -1061,6 +1061,6 @@ def hard_delete_membership(membership_id: str) -> None:
             "device_node_id": device.node_id if device else None,
             "network_id": network.zerotier_network_id if network else None,
         },
-        description=f"Membership hard-deleted: device {device.node_id if device else 'unknown'} from network",
+        description=f"Membership deleted: device {device.node_id if device else 'unknown'} from network",
         success=True,
     )

gatehouse_app/services/oauth_flow/register.py

@@ -111,7 +111,7 @@ def handle_register_callback(
             access_token=tokens["access_token"],
         )
 
-        existing_user = User.query.filter_by(email=user_info["email"]).first()
+        existing_user = User.query.filter_by(email=user_info["email"], deleted_at=None).first()
         if existing_user:
             raise OAuthFlowError(
                 f"An account with email {user_info['email']} already exists. "

gatehouse_app/services/zerotier_reconciliation_service.py

@@ -283,9 +283,9 @@ def reconcile_deleted_memberships() -> dict:
             if not device or not network:
                 logger.warning(
                     f"[Reconciliation] Membership {membership.id}: missing "
-                    f"{'device' if not device else 'network'} — hard-deleting record only."
+                    f"{'device' if not device else 'network'} — soft-deleting record only."
                 )
-                db.session.delete(membership)
+                membership.delete(soft=True)
                 db.session.commit()
                 results["deleted"] += 1
                 continue
@@ -304,20 +304,20 @@ def reconcile_deleted_memberships() -> dict:
             except Exception as zt_exc:
                 logger.warning(
                     f"[Reconciliation] ZT delete failed for node {node_id} "
-                    f"on {network_label}: {zt_exc} — proceeding with DB hard-delete."
+                    f"on {network_label}: {zt_exc} — proceeding with DB soft-delete."
                 )
 
-            db.session.delete(membership)
+            membership.delete(soft=True)
             db.session.commit()
             results["deleted"] += 1
             logger.debug(
-                f"[Reconciliation] Hard-deleted membership {membership.id} "
+                f"[Reconciliation] Soft-deleted membership {membership.id} "
                 f"(node={node_id}, network={network_label})."
             )
 
         except Exception as exc:
             logger.error(
-                f"[Reconciliation] Failed to hard-delete membership {membership.id}: {exc}",
+                f"[Reconciliation] Failed to soft-delete membership {membership.id}: {exc}",
                 exc_info=True,
             )
             results["errors"] += 1