Merge pull request #19 from Project-OMOTES/18-work-flow-configuration…

…-in-one-location

workflows in one place working

.env.template

@@ -1,3 +1,5 @@
+OMOTES_ID=omotes-rest
+
 RABBITMQ_HOSTNAME=localhost
 RABBITMQ_PORT=5672
 RABBITMQ_USERNAME=omotes

dev-requirements.txt

@@ -1,14 +1,14 @@
 #
-# This file is autogenerated by pip-compile with Python 3.11
+# This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
 #    pip-compile --constraint=requirements.txt --extra=dev --output-file=dev-requirements.txt pyproject.toml
 #
-aio-pika==9.3.1
+aio-pika==9.4.2
     # via
     #   -c requirements.txt
     #   omotes-sdk-python
-aiormq==6.7.7
+aiormq==6.8.0
     # via
     #   -c requirements.txt
     #   aio-pika
@@ -63,6 +63,8 @@ colorama==0.4.6
     #   omotes-rest (pyproject.toml)
 coverage[toml]==7.4.4
     # via pytest-cov
+exceptiongroup==1.2.1
+    # via pytest
 flake8==6.0.0
     # via
     #   flake8-docstrings
@@ -121,19 +123,10 @@ kombu==5.3.5
     # via
     #   -c requirements.txt
     #   celery
-mako==1.3.2
-    # via
-    #   -c requirements.txt
-    #   pdoc3
-markdown==3.6
-    # via
-    #   -c requirements.txt
-    #   pdoc3
 markupsafe==2.1.3
     # via
     #   -c requirements.txt
     #   jinja2
-    #   mako
     #   werkzeug
 marshmallow==3.20.1
     # via
@@ -168,11 +161,11 @@ mypy-extensions==1.0.0
     #   black
     #   mypy
     #   typing-inspect
-omotes-sdk-protocol==0.0.8
+omotes-sdk-protocol==0.1.1
     # via
     #   -c requirements.txt
     #   omotes-sdk-python
-omotes-sdk-python==0.0.14
+omotes-sdk-python==2.0.2
     # via
     #   -c requirements.txt
     #   omotes-rest (pyproject.toml)
@@ -186,16 +179,12 @@ packaging==23.1
     #   pytest
     #   setuptools-git-versioning
     #   webargs
-pamqp==3.2.1
+pamqp==3.3.0
     # via
     #   -c requirements.txt
     #   aiormq
 pathspec==0.12.1
     # via black
-pdoc3==0.10.0
-    # via
-    #   -c requirements.txt
-    #   streamcapture
 platformdirs==4.2.0
     # via black
 pluggy==1.4.0
@@ -246,24 +235,35 @@ sqlalchemy[mypy]==2.0.28
     # via
     #   -c requirements.txt
     #   omotes-rest (pyproject.toml)
-streamcapture==1.2.2
+streamcapture==1.2.5
     # via
     #   -c requirements.txt
     #   omotes-sdk-python
 structlog==23.1.0
     # via
     #   -c requirements.txt
     #   omotes-rest (pyproject.toml)
+toml==0.10.2
+    # via setuptools-git-versioning
 tomli==2.0.1
-    # via black
+    # via
+    #   black
+    #   build
+    #   coverage
+    #   flake8-pyproject
+    #   mypy
+    #   pyproject-hooks
+    #   pytest
 types-flask-cors==4.0.0.20240405
     # via omotes-rest (pyproject.toml)
 types-protobuf==4.24.0.20240311
     # via omotes-rest (pyproject.toml)
-typing-extensions==4.7.1
+typing-extensions==4.11.0
     # via
     #   -c requirements.txt
+    #   marshmallow-dataclass
     #   mypy
+    #   omotes-sdk-python
     #   sqlalchemy
     #   typing-inspect
 typing-inspect==0.9.0

docker-compose.yml

@@ -17,7 +17,7 @@ services:
 
   omotes-rest:
 #    build: .
-    image: ghcr.io/project-omotes/omotes_rest:0.0.8
+    image: ghcr.io/project-omotes/omotes_rest:0.0.9
     networks:
       - omotes
       - mapeditor-net

pyproject.toml

@@ -37,7 +37,7 @@ dependencies = [
     "python-dotenv ~= 1.0.0",
     "structlog ~= 23.1.0",
     "SQLAlchemy == 2.0.28",
-    "omotes-sdk-python ~= 0.0.14",
+    "omotes-sdk-python ~= 2.0.2",
 ]
 
 [project.optional-dependencies]
@@ -74,7 +74,7 @@ enabled = true
 
 [tool.pytest.ini_options]
 addopts = """--cov=omotes_rest --cov-report html --cov-report term-missing \
---cov-fail-under 2"""
+--cov-fail-under 40"""
 
 [tool.coverage.run]
 source = ["src"]

requirements.txt

@@ -1,12 +1,12 @@
 #
-# This file is autogenerated by pip-compile with Python 3.11
+# This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
 #    pip-compile --output-file=requirements.txt pyproject.toml
 #
-aio-pika==9.3.1
+aio-pika==9.4.2
     # via omotes-sdk-python
-aiormq==6.7.7
+aiormq==6.8.0
     # via aio-pika
 amqp==5.2.0
     # via kombu
@@ -57,14 +57,9 @@ jinja2==3.1.2
     # via flask
 kombu==5.3.5
     # via celery
-mako==1.3.2
-    # via pdoc3
-markdown==3.6
-    # via pdoc3
 markupsafe==2.1.3
     # via
     #   jinja2
-    #   mako
     #   werkzeug
 marshmallow==3.20.1
     # via
@@ -82,20 +77,18 @@ multidict==6.0.5
     # via yarl
 mypy-extensions==1.0.0
     # via typing-inspect
-omotes-sdk-protocol==0.0.8
+omotes-sdk-protocol==0.1.1
     # via omotes-sdk-python
-omotes-sdk-python==0.0.14
+omotes-sdk-python==2.0.2
     # via omotes-rest (pyproject.toml)
 packaging==23.1
     # via
     #   apispec
     #   gunicorn
     #   marshmallow
     #   webargs
-pamqp==3.2.1
+pamqp==3.3.0
     # via aiormq
-pdoc3==0.10.0
-    # via streamcapture
 prompt-toolkit==3.0.43
     # via click-repl
 protobuf==4.25.3
@@ -110,12 +103,14 @@ six==1.16.0
     # via python-dateutil
 sqlalchemy==2.0.28
     # via omotes-rest (pyproject.toml)
-streamcapture==1.2.2
+streamcapture==1.2.5
     # via omotes-sdk-python
 structlog==23.1.0
     # via omotes-rest (pyproject.toml)
-typing-extensions==4.7.1
+typing-extensions==4.11.0
     # via
+    #   marshmallow-dataclass
+    #   omotes-sdk-python
     #   sqlalchemy
     #   typing-inspect
 typing-inspect==0.9.0

scripts/install_dependencies.sh

@@ -1,3 +1,8 @@
-. .venv/bin/activate
+#!/bin/bash
 
-pip-sync requirements.txt
+if [[ "$OSTYPE" != "win32" && "$OSTYPE" != "msys" ]]; then
+  echo "Activating .venv first."
+  . .venv/bin/activate
+fi
+
+pip-sync ./dev-requirements.txt ./requirements.txt

scripts/update_dependencies.sh

@@ -1,3 +1,8 @@
 #!/bin/bash
-. .venv/bin/activate
-pip-compile -o requirements.txt ./pyproject.toml
+
+if [[ "$OSTYPE" != "win32" && "$OSTYPE" != "msys" ]]; then
+  . .venv/bin/activate
+fi
+
+pip-compile --output-file=requirements.txt pyproject.toml
+pip-compile --extra=dev -c requirements.txt --output-file=dev-requirements.txt pyproject.toml

src/omotes_rest/__init__.py

@@ -44,8 +44,10 @@ def create_app(object_name: str) -> Flask:
 
     # Register blueprints.
     from omotes_rest.apis.job import api as job_api
+    from omotes_rest.apis.workflow import api as workflow_api
 
     api.register_blueprint(job_api)
+    api.register_blueprint(workflow_api)
 
     CORS(app, resources={r"/*": {"origins": "*"}})
 

src/omotes_rest/apis/api_dataclasses.py

@@ -8,6 +8,18 @@
 from marshmallow_dataclass import add_schema, dataclass
 
 
+@add_schema
+@dataclass
+class WorkflowResponse:
+    """Response with available workflows."""
+
+    Schema: ClassVar[Type[Schema]] = Schema
+
+    workflow_type_name: str
+    workflow_type_description_name: str
+    workflow_parameters: dict[str, Any] | None
+
+
 class JobRestStatus(Enum):
     """Possible job status."""
 

src/omotes_rest/apis/job.py

@@ -1,4 +1,3 @@
-import base64
 import logging
 import uuid
 
@@ -103,8 +102,6 @@ def get(self, job_id: str) -> JobResultResponse:
         """Return job result with output ESDL (can be None)."""
         job_uuid = uuid.UUID(job_id)
         output_esdl = current_app.rest_if.get_job_output_esdl(job_uuid)
-        if output_esdl:
-            output_esdl = base64.b64encode(bytes(output_esdl, "utf-8")).decode("utf-8")
         return JobResultResponse(job_id=job_uuid, output_esdl=output_esdl)
 
 

src/omotes_rest/apis/workflow.py

@@ -0,0 +1,26 @@
+import logging
+
+from flask_smorest import Blueprint
+from flask.views import MethodView
+from flask import jsonify, Response
+
+from omotes_rest.typed_app import current_app
+
+
+logger = logging.getLogger("omotes_rest")
+
+api = Blueprint(
+    "Workflow",
+    "Workflow",
+    url_prefix="/workflow",
+    description="Omotes workflows: retrieve the available workflow and their properties",
+)
+
+
+@api.route("/")
+class WorkflowAPI(MethodView):
+    """Requests."""
+
+    def get(self) -> Response:
+        """Return a summary of all workflows with parameter jsonforms format."""
+        return jsonify(current_app.rest_if.get_workflows_jsonforms_format())

src/omotes_rest/config.py

@@ -1,7 +1,7 @@
 import os
 
 
-class POSTGRESConfig:
+class PostgresConfig:
     """Retrieve POSTGRES configuration from environment variables."""
 
     host: str

src/omotes_rest/main.py

@@ -12,7 +12,6 @@
 from omotes_rest import create_app
 from omotes_rest.rest_interface import RestInterface
 from omotes_rest.settings import EnvSettings
-from omotes_rest.workflows import WORKFLOW_TYPE_MANAGER
 from omotes_rest.typed_app import current_app
 
 
@@ -87,7 +86,7 @@ def post_fork(_: Arbiter, __: SyncWorker) -> None:
     with app.app_context():
         """current_app is only within the app context"""
 
-        current_app.rest_if = RestInterface(WORKFLOW_TYPE_MANAGER)
+        current_app.rest_if = RestInterface()
         """Interface for this Omotes Rest service."""
 
         current_app.rest_if.start()

src/omotes_rest/postgres_interface.py

@@ -11,7 +11,7 @@
 import logging
 from omotes_rest.apis.api_dataclasses import JobRestStatus, JobInput
 from omotes_rest.db_models.job_rest import JobRest
-from omotes_rest.config import POSTGRESConfig
+from omotes_rest.config import PostgresConfig
 
 logger = logging.getLogger("omotes_rest")
 
@@ -60,7 +60,7 @@ def session_scope(do_expunge: bool = False) -> Generator[SQLSession, None, None]
         Session.remove()
 
 
-def initialize_db(application_name: str, config: POSTGRESConfig) -> Engine:
+def initialize_db(application_name: str, config: PostgresConfig) -> Engine:
     """Initialize the database connection by creating the engine.
 
     Also configure the default session maker.
@@ -112,12 +112,12 @@ class PostgresInterface:
     in this interface must set up a Session (scope) separately.
     """
 
-    db_config: POSTGRESConfig
+    db_config: PostgresConfig
     """Configuration on how to connect to the database."""
     engine: Engine
     """Engine for starting connections to the database."""
 
-    def __init__(self, postgres_config: POSTGRESConfig) -> None:
+    def __init__(self, postgres_config: PostgresConfig) -> None:
         """Create the PostgreSQL interface."""
         self.db_config = postgres_config