Merge pull request #198 from sartography/feature/safety

Feature/safety

.github/workflows/backend_tests.yml

@@ -16,10 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          # FIXME: https://github.com/mysql/mysql-connector-python/pull/86
+          - { python: "3.11", os: "ubuntu-latest", session: "safety" }
-          # put back when poetry update protobuf mysql-connector-python updates protobuf
-          # right now mysql is forcing protobuf to version 3
-          # - { python: "3.11", os: "ubuntu-latest", session: "safety" }
           - { python: "3.11", os: "ubuntu-latest", session: "mypy" }
           - { python: "3.10", os: "ubuntu-latest", session: "mypy" }
           - { python: "3.9", os: "ubuntu-latest", session: "mypy" }

pyproject.toml

@@ -13,71 +13,8 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = ">=3.11,<3.12"
-click = "^8.0.1"
-flask = "2.2.2"
-flask-admin = "*"
-flask-bcrypt = "*"
-flask-cors = "*"
-flask-mail = "*"
-flask-marshmallow = "*"
-flask-migrate = "*"
-flask-restful = "*"
-werkzeug = "*"
-# go back to main once https://github.com/sartography/SpiffWorkflow/pull/241 is merged
-SpiffWorkflow = {git = "https://github.com/sartography/SpiffWorkflow", rev = "main"}
-# SpiffWorkflow = {develop = true, path = "/Users/kevin/projects/github/sartography/SpiffWorkflow"}
-# SpiffWorkflow = {develop = true, path = "/home/jason/projects/github/sartography/SpiffWorkflow"}
-sentry-sdk = "^1.10"
-sphinx-autoapi = "^2.0"
-# flask-bpmn = {develop = true, path = "/home/jason/projects/github/sartography/flask-bpmn"}
-# flask-bpmn = {develop = true, path = "/Users/kevin/projects/github/sartography/flask-bpmn"}
-flask-bpmn = {git = "https://github.com/sartography/flask-bpmn", rev = "main"}
-mysql-connector-python = "^8.0.29"
-pytest-flask = "^1.2.0"
-pytest-flask-sqlalchemy = "^1.1.0"
-psycopg2 = "^2.9.3"
-typing-extensions = "^4.4.0"
-connexion = {extras = [ "swagger-ui",], version = "^2"}
-lxml = "^4.9.1"
-marshmallow-enum = "^1.5.1"
-marshmallow-sqlalchemy = "^0.28.0"
-PyJWT = "^2.6.0"
-gunicorn = "^20.1.0"
-python-keycloak = "^2.5.0"
-APScheduler = "^3.9.1"
-Jinja2 = "^3.1.2"
-RestrictedPython = "^6.0"
-Flask-SQLAlchemy = "^3"
-
-# type hinting stuff
-# these need to be in the normal (non dev-dependencies) section
-# because if not then poetry export won't have them and nox -s mypy --pythons 3.10
-# will fail
-types-Werkzeug = "^1.0.9"
-types-PyYAML = "^6.0.12"
-types-Flask = "^1.1.6"
-types-requests = "^2.28.6"
-types-pytz = "^2022.1.1"
-
-# https://github.com/dropbox/sqlalchemy-stubs/pull/251
-# someday get off github
-# sqlalchemy-stubs = "^0.4"
-# sqlalchemy-stubs = { git = "https://github.com/dropbox/sqlalchemy-stubs.git", rev = "master" }
-# sqlalchemy-stubs = {develop = true, path = "/Users/kevin/projects/github/sqlalchemy-stubs"}
-# for now use my fork
-sqlalchemy-stubs = { git = "https://github.com/burnettk/sqlalchemy-stubs.git", rev = "scoped-session-delete" }
-simplejson = "^3.17.6"
-
 
 [tool.poetry.dev-dependencies]
-pytest = "^7.1.2"
-coverage = {extras = ["toml"], version = "^6.1"}
-safety = "^2.3.1"
-mypy = ">=0.961"
-typeguard = "^2.13.2"
-xdoctest = {extras = ["colors"], version = "^1.0.1"}
-sphinx = "^5.0.2"
-sphinx-autobuild = ">=2021.3.14"
 pre-commit = "^2.20.0"
 flake8 = "^4.0.1"
 black = ">=21.10b0"
@@ -89,71 +26,9 @@ bandit = "1.7.2"
 flake8-bugbear = "^22.10.25"
 flake8-docstrings = "^1.6.0"
 flake8-rst-docstrings = "^0.2.7"
-# flask-sqlalchemy-stubs = "^0.2"
-pep8-naming = "^0.13.2"
-darglint = "^1.8.1"
 reorder-python-imports = "^3.9.0"
 pre-commit-hooks = "^4.0.1"
-sphinx-click = "^4.3.0"
-Pygments = "^2.10.0"
 pyupgrade = "^3.1.0"
-furo = ">=2021.11.12"
-
-[tool.poetry.scripts]
-spiffworkflow-backend = "spiffworkflow_backend.__main__:main"
 
 [tool.poetry.group.dev.dependencies]
 tomli = "^2.0.1"
-
-[tool.pytest.ini_options]
-# ignore deprecation warnings from various packages that we don't control
-filterwarnings = [
-    # note the use of single quote below to denote "raw" strings in TOML
-    # kombu/utils/compat.py:82
-    'ignore:SelectableGroups dict interface is deprecated. Use select.',
-    # flask_marshmallow/__init__.py:34
-    # marshmallow_sqlalchemy/convert.py:17
-    'ignore:distutils Version classes are deprecated. Use packaging.version instead.',
-    # connexion/spec.py:50
-    'ignore:Passing a schema to Validator.iter_errors is deprecated and will be removed in a future release',
-    # connexion/decorators/validation.py:16
-    'ignore:Accessing jsonschema.draft4_format_checker is deprecated and will be removed in a future release.',
-    # connexion/apis/flask_api.py:236
-    "ignore:'_request_ctx_stack' is deprecated and will be removed in Flask 2.3",
-    "ignore:Setting 'json_encoder' on the app or a blueprint is deprecated and will be removed in Flask 2.3",
-    "ignore:'JSONEncoder' is deprecated and will be removed in Flask 2.3",
-    "ignore:'app.json_encoder' is deprecated and will be removed in Flask 2.3"
-]
-
-[tool.coverage.paths]
-source = ["src", "*/site-packages"]
-tests = ["tests", "*/tests"]
-
-[tool.coverage.run]
-branch = true
-source = ["spiffworkflow_backend", "tests"]
-
-[tool.coverage.report]
-show_missing = true
-fail_under = 50
-
-[tool.mypy]
-strict = true
-disallow_any_generics = false
-warn_unreachable = true
-pretty = true
-show_column_numbers = true
-show_error_codes = true
-show_error_context = true
-plugins = "sqlmypy"
-
-# We get 'error: Module has no attribute "set_context"' for sentry-sdk without this option
-implicit_reexport = true
-
-# allow for subdirs to NOT require __init__.py
-namespace_packages = true
-explicit_package_bases = false
-
-[build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"

spiffworkflow-backend/conftest.py

@@ -45,8 +45,8 @@ def app() -> Flask:
 def with_db_and_bpmn_file_cleanup() -> None:
     """Do it cleanly!"""
     meta = db.metadata
-    db.session.execute(db.update(BpmnProcessModel, values={"top_level_process_id": None}))
+    db.session.execute(db.update(BpmnProcessModel).values(top_level_process_id=None))
-    db.session.execute(db.update(BpmnProcessModel, values={"direct_parent_process_id": None}))
+    db.session.execute(db.update(BpmnProcessModel).values(direct_parent_process_id=None))
 
     for table in reversed(meta.sorted_tables):
         db.session.execute(table.delete())

spiffworkflow-backend/pyproject.toml

@@ -39,10 +39,16 @@ pytest-flask = "^1.2.0"
 pytest-flask-sqlalchemy = "^1.1.0"
 psycopg2 = "^2.9.3"
 typing-extensions = "^4.4.0"
+
+# pinned to higher than 65.5.0 because of a vulnerability
+# and to lower than 67 because i didn't feel like addressing
+# new deprecation warnings. we don't need this library explicitly,
+# but at one time it was pulled in by various libs we depend on.
+setuptools = "^65.5.1"
+
 connexion = {extras = [ "swagger-ui",], version = "^2"}
 lxml = "^4.9.1"
 marshmallow-enum = "^1.5.1"
-marshmallow-sqlalchemy = "^0.28.0"
 PyJWT = "^2.6.0"
 gunicorn = "^20.1.0"
 APScheduler = "*"
@@ -75,7 +81,8 @@ flask-jwt-extended = "^4.4.4"
 pylint = "^2.15.10"
 flask-simple-crypt = "^0.3.3"
 cryptography = "^39.0.2"
-
+safety = "^2.3.5"
+sqlalchemy = "^2.0.7"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.1.2"

spiffworkflow-backend/src/spiffworkflow_backend/__init__.py

@@ -44,8 +44,9 @@ class MyJSONEncoder(DefaultJSONProvider):
             return obj.serialized
         elif isinstance(obj, sqlalchemy.engine.row.Row):  # type: ignore
             return_dict = {}
-            for row_key in obj.keys():
+            row_mapping = obj._mapping
-                row_value = obj[row_key]
+            for row_key in row_mapping.keys():
+                row_value = row_mapping[row_key]
                 if hasattr(row_value, "serialized"):
                     return_dict.update(row_value.serialized)
                 elif hasattr(row_value, "__dict__"):

spiffworkflow-backend/src/spiffworkflow_backend/models/process_instance.py

@@ -53,6 +53,7 @@ class ProcessInstanceModel(SpiffworkflowBaseDBModel):
     """ProcessInstanceModel."""
 
     __tablename__ = "process_instance"
+    __allow_unmapped__ = True
     id: int = db.Column(db.Integer, primary_key=True)
     process_model_identifier: str = db.Column(db.String(255), nullable=False, index=True)
     process_model_display_name: str = db.Column(db.String(255), nullable=False, index=True)

spiffworkflow-backend/src/spiffworkflow_backend/models/process_instance_report.py

@@ -8,7 +8,6 @@ from typing import Optional
 from typing import TypedDict
 
 from sqlalchemy import ForeignKey
-from sqlalchemy.orm import deferred
 from sqlalchemy.orm import relationship
 
 from spiffworkflow_backend.exceptions.process_entity_not_found_error import (
@@ -69,7 +68,7 @@ class ProcessInstanceReportModel(SpiffworkflowBaseDBModel):
 
     id: int = db.Column(db.Integer, primary_key=True)
     identifier: str = db.Column(db.String(50), nullable=False, index=True)
-    report_metadata: dict = deferred(db.Column(db.JSON))  # type: ignore
+    report_metadata: dict = db.Column(db.JSON)
     created_by_id = db.Column(ForeignKey(UserModel.id), nullable=False, index=True)  # type: ignore
     created_by = relationship("UserModel")
     created_at_in_seconds = db.Column(db.Integer)

spiffworkflow-backend/src/spiffworkflow_backend/models/task.py

@@ -47,6 +47,7 @@ class MultiInstanceType(enum.Enum):
 @dataclass
 class TaskModel(SpiffworkflowBaseDBModel):
     __tablename__ = "task"
+    __allow_unmapped__ = True
     id: int = db.Column(db.Integer, primary_key=True)
     guid: str = db.Column(db.String(36), nullable=False, unique=True)
     bpmn_process_id: int = db.Column(ForeignKey(BpmnProcessModel.id), nullable=False, index=True)  # type: ignore

spiffworkflow-backend/src/spiffworkflow_backend/routes/process_instances_controller.py

@@ -632,9 +632,10 @@ def process_instance_task_list(
                 status_code=400,
             )
 
-        _parent_bpmn_processes, task_models_of_parent_bpmn_processes = (
+        (
-            TaskService.task_models_of_parent_bpmn_processes(to_task_model)
+            _parent_bpmn_processes,
-        )
+            task_models_of_parent_bpmn_processes,
+        ) = TaskService.task_models_of_parent_bpmn_processes(to_task_model)
         task_models_of_parent_bpmn_processes_guids = [p.guid for p in task_models_of_parent_bpmn_processes if p.guid]
         task_model_query = task_model_query.filter(
             or_(

spiffworkflow-backend/src/spiffworkflow_backend/services/process_instance_processor.py

@@ -1216,13 +1216,16 @@ class ProcessInstanceProcessor:
                 spiff_tasks_updated[task.id] = task
 
         for updated_spiff_task in spiff_tasks_updated.values():
-            bpmn_process, task_model, new_task_models, new_json_data_dicts = (
+            (
-                TaskService.find_or_create_task_model_from_spiff_task(
+                bpmn_process,
-                    updated_spiff_task,
+                task_model,
-                    self.process_instance_model,
+                new_task_models,
-                    self._serializer,
+                new_json_data_dicts,
-                    bpmn_definition_to_task_definitions_mappings=self.bpmn_definition_to_task_definitions_mappings,
+            ) = TaskService.find_or_create_task_model_from_spiff_task(
-                )
+                updated_spiff_task,
+                self.process_instance_model,
+                self._serializer,
+                bpmn_definition_to_task_definitions_mappings=self.bpmn_definition_to_task_definitions_mappings,
             )
             bpmn_process_to_use = bpmn_process or task_model.bpmn_process
             bpmn_process_json_data = TaskService.update_task_data_on_bpmn_process(

spiffworkflow-backend/src/spiffworkflow_backend/services/process_instance_report_service.py

@@ -309,11 +309,14 @@ class ProcessInstanceReportService:
     ) -> list[dict]:
         """Add_metadata_columns_to_process_instance."""
         results = []
-        for process_instance in process_instance_sqlalchemy_rows:
+        for process_instance_row in process_instance_sqlalchemy_rows:
-            process_instance_dict = process_instance["ProcessInstanceModel"].serialized
+            process_instance_mapping = process_instance_row._mapping
+            process_instance_dict = process_instance_row[0].serialized
             for metadata_column in metadata_columns:
                 if metadata_column["accessor"] not in process_instance_dict:
-                    process_instance_dict[metadata_column["accessor"]] = process_instance[metadata_column["accessor"]]
+                    process_instance_dict[metadata_column["accessor"]] = process_instance_mapping[
+                        metadata_column["accessor"]
+                    ]
 
             results.append(process_instance_dict)
         return results

spiffworkflow-backend/src/spiffworkflow_backend/services/workflow_execution_service.py

@@ -1,4 +1,3 @@
-import logging
 import time
 from typing import Callable
 from typing import Optional
@@ -123,13 +122,16 @@ class TaskModelSavingDelegate(EngineStepDelegate):
                 self.json_data_dicts[json_data_dict["hash"]] = json_data_dict
 
     def _update_task_model_with_spiff_task(self, spiff_task: SpiffTask, task_failed: bool = False) -> TaskModel:
-        bpmn_process, task_model, new_task_models, new_json_data_dicts = (
+        (
-            TaskService.find_or_create_task_model_from_spiff_task(
+            bpmn_process,
-                spiff_task,
+            task_model,
-                self.process_instance,
+            new_task_models,
-                self.serializer,
+            new_json_data_dicts,
-                bpmn_definition_to_task_definitions_mappings=self.bpmn_definition_to_task_definitions_mappings,
+        ) = TaskService.find_or_create_task_model_from_spiff_task(
-            )
+            spiff_task,
+            self.process_instance,
+            self.serializer,
+            bpmn_definition_to_task_definitions_mappings=self.bpmn_definition_to_task_definitions_mappings,
         )
         bpmn_process_json_data = TaskService.update_task_data_on_bpmn_process(
             bpmn_process or task_model.bpmn_process, spiff_task.workflow.data
@@ -280,10 +282,6 @@ class WorkflowExecutionService:
 
         finally:
             self.execution_strategy.save()
-            spiff_logger = logging.getLogger("spiff")
-            for handler in spiff_logger.handlers:
-                if hasattr(handler, "bulk_insert_logs"):
-                    handler.bulk_insert_logs()  # type: ignore
             db.session.commit()
 
             if save: