Initial commit based on agent barebone.

Signed-off-by: Marcel Parciak <marcel.parciak@gmail.com>

.gitignore

+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/

.gitlab-ci.yml

+stages:
+  - test
+  - publish
+
+build_image:
+  stage: test
+  tags:
+    - shell
+    - medic
+    - umg
+
+  before_script:
+    - docker info
+
+  script:
+    - docker build -t $CI_REGISTRY_IMAGE:latest .
+
+run_tests:
+  stage: test
+  tags:
+    - shell
+    - medic
+    - umg
+
+  before_script:
+    - pip3 install --user pytest
+
+  script:
+    - pytest --junitxml=report.xml
+
+  artifacts:
+    reports:
+      junit: report.xml
+
+dryrun_publish_image:
+  stage: test
+  tags:
+    - shell
+    - medic
+    - umg
+
+  except:
+    refs:
+      - master
+
+  before_script:
+    - docker login --username $CI_REGISTRY_USER --password $CI_REGISTRY_PASSWORD $CI_REGISTRY
+    - AGENTVERSION=`python3 setup.py --version`
+
+  script:
+    - docker build -t $CI_REGISTRY_IMAGE:latest .
+    - docker tag $CI_REGISTRY_IMAGE:latest $CI_REGISTRY_IMAGE:$AGENTVERSION
+
+dryrun_publish_to_harbor:
+  stage: test
+  tags:
+    - shell
+    - medic
+    - wisslan
+    - umg
+    - harbor
+
+  except:
+    refs:
+      - master
+
+  before_script:
+    - docker login --username marcelparciak --password $HARBOR_PUSH_TOKEN https://harbor.umg.eu
+    - AGENTVERSION=`python3 setup.py --version`
+
+  script:
+    - docker build -t harbor.umg.eu/medic/$CI_PROJECT_NAME:latest .
+    - docker tag harbor.umg.eu/medic/$CI_PROJECT_NAME:latest harbor.umg.eu/medic/$CI_PROJECT_NAME:$AGENTVERSION
+
+publish_image:
+  stage: publish
+  tags:
+    - shell
+    - medic
+    - umg
+
+  only:
+    refs:
+      - master
+
+  before_script:
+    - docker login --username $CI_REGISTRY_USER --password $CI_REGISTRY_PASSWORD $CI_REGISTRY
+    - AGENTVERSION=`python3 setup.py --version`
+
+  script:
+    - docker build -t $CI_REGISTRY_IMAGE:latest .
+    - docker tag $CI_REGISTRY_IMAGE:latest $CI_REGISTRY_IMAGE:$AGENTVERSION
+    - docker push $CI_REGISTRY_IMAGE:latest
+    - docker push $CI_REGISTRY_IMAGE:$AGENTVERSION
+
+publish_to_harbor:
+  stage: publish
+  tags:
+    - shell
+    - medic
+    - wisslan
+    - umg
+    - harbor
+
+  only:
+    refs:
+      - master
+
+  before_script:
+    - docker login --username marcelparciak --password $HARBOR_PUSH_TOKEN https://harbor.umg.eu
+    - AGENTVERSION=`python3 setup.py --version`
+
+  script:
+    - docker build -t harbor.umg.eu/medic/$CI_PROJECT_NAME:latest .
+    - docker tag harbor.umg.eu/medic/$CI_PROJECT_NAME:latest harbor.umg.eu/medic/$CI_PROJECT_NAME:$AGENTVERSION
+    - docker push harbor.umg.eu/medic/$CI_PROJECT_NAME:latest
+    - docker push harbor.umg.eu/medic/$CI_PROJECT_NAME:$AGENTVERSION

.vscode/settings.json

+{
+    "python.pythonPath": "/home/marcel/.local/share/virtualenvs/annotation-agent-1DIG_x-f/bin/python",
+    "editor.formatOnSave": true,
+    "python.linting.enabled": true,
+    "python.formatting.provider": "black"
+}
\ No newline at end of file

Dockerfile

+FROM docker.io/tiangolo/uvicorn-gunicorn-fastapi:python3.8
+
+ENV MODULE_NAME="annotator.main"
+
+COPY ./requirements.txt /app/requirements.txt
+RUN pip3.8 install -r requirements.txt
+
+COPY ./prestart.sh /app/prestart.sh
+COPY ./setup.py /app/setup.py
+COPY ./annotator /app/annotator
+COPY ./Readme.md /app/Readme.md
\ No newline at end of file

Pipfile

+[[source]]
+name = "pypi"
+url = "https://pypi.org/simple"
+verify_ssl = true
+
+[dev-packages]
+fastapi = "*"
+uvicorn = "*"
+black = "*"
+
+[packages]
+cloudant = "*"
+sqlalchemy = "*"
+alembic = "*"
+pytest = "*"
+pycdstar3 = {git = "https://gitlab.gwdg.de/cdstar/pycdstar3"}
+
+[requires]
+python_version = "3.8"
+
+[pipenv]
+allow_prereleases = true

Readme.md

+An agent barebone for Active Workflow agents. 
+
+# Active Workflow Barebone Agent
+
+This Agent complies to the [external REST-API](https://github.com/automaticmode/active_workflow/blob/master/docs/remote_agent_api.md) of [ActiveWorkflow](https://github.com/automaticmode/active_workflow). 
+
+# How to use
+
+In the first step, you should rename the `app` directory to something meaningful (although this needs many modification in each file). Do not forget to change it in setup.py, too. 
+
+After renaming, you can start to work on the main.py, which is the main entrypoint for this agent. This barebone provides you with [pydantic](https://pydantic-docs.helpmanual.io/) models for Active Workflow requests and responses. In the models_activeworkflow.py file, the "Application specifics" models allow to tailor the models to your needs. Namely, you should modify `PayloadInput`, `MessageOutput`, `OptionsCommon`, `MemoryCommon` and `CredentialsCommon`.
+
+`config.py` holds the configuration according to [FastAPI](https://fastapi.tiangolo.com/) (i.e. it can be set via environment variables when starting uvicorn or the provided Dockerfile). Use it to make your agent configurable.
+
+Use the `__version__.py` for versioning of your module, setup.py will try to access this value to determine the version. Also, this will add versions to the .gitlab-ci.yml for automatic creation of tagged images. For now, this is a manual process, i.e. you have to change the `VERSION` tuple in `__version__.py` to assign a version.
+
+Keep in mind you may need to add lines to the Dockerfile if you expand you agent, e.g. by implementing a SQL backend (using [sqlalchemy](https://www.sqlalchemy.org/) and [alembic](https://alembic.sqlalchemy.org/en/latest/) of course). Also, this repo uses pipenv for package management, the Dockerfile uses pip3 instead. Do not forget to freeze manually using pipenv or use a package like [pipenv_to_requirements](https://github.com/gsemet/pipenv-to-requirements).
+
+Last but not least, change this Readme.md and add all necessary information to it. This Readme is used in the agent description part of the Active Workflow register response, meaning that a AW-user will see it as the description of this agent.
+
+## API Caller Configurations
+
+### Register
+
+This is what happens when you call register:
+
+#### Example
+
+```
+{
+    "some": "option"
+}
+```
+
+### Receive
+
+This is what happens when you call receive:
+
+#### Example
+
+Full request:
+```
+{
+    "method": "receive",
+    "params": {
+        "message": {
+            "payload": {
+                "context": {
+                    "test_val": 12
+                }
+            }
+        },
+        "options": {
+            "job_name": "DummyJob",
+            "job_version": "1.0",
+            "context": {
+                "test_val": 8
+            }
+        }, 
+        "memory": {
+            "jobs": []
+        },
+        "credentials": {}
+    }
+}
+```
+
+Full response:
+```
+{
+    "result": {
+        "errors": [],
+        "logs": ["Job DummyJob has been started with id 21."],
+        "memory": {
+            "jobs": [21]
+        },
+        "messages": [],
+    }
+}
+```
+
+### Check
+
+This is what happens when you call check:
+
+#### Example
+
+Full request:
+```
+{
+    "method": "check",
+    "params": {
+        "message": null
+        "options": {
+            "job_name": "DummyJob",
+            "job_version": "1.0",
+            "context": {
+                "test_val": 8
+            }
+        },
+        "memory": {
+            "jobs": [21]
+        },
+        "credentials": [],
+    }
+}
+```
+
+Full response:
+```
+
+    "result": {
+        "errors": [],
+        "logs": [
+            "25|2pdwaA|QvVW2g6IdzHS|key.compareTo(25) != 0 failed\n"
+        ],
+        "memory": {
+            "jobs": []
+        },
+        "messages": [
+            {
+                "job_run_id": 21,
+                "job_id": 4,
+                "job_name": "DummyJob",
+                "job_version": "1.0",
+                "completed": true,
+                "returncode": 0,
+                "runtime": 1.036232,
+                "response": {
+                    "data": [
+                        {
+                            "entity": 1,
+                            "attribute": "wARNk5",
+                            "value": "7riXpzHPFECz"
+                        }
+                    ]
+                }
+            }
+        ]
+    }
+}
+```
+### Additional API Calls
+
+Any non-active workflow based API endpoints can be explained here.
+
+## Service Configuration
+
+Configuration can be done using environment variables. It does not matter whether done locally or given to docker.
+
+* `example_setting`: Some setting that configures your agent. Default: `"Unset"`
\ No newline at end of file

annotator/.gitignore

+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/

annotator/__init__.py

+import logging
+
+access_log = logging.getLogger("gunicorn.access")
+error_log = logging.getLogger("gunicorn.error")

annotator/__version__.py

+VERSION = (0, 1, 0)
+
+__version__ = ".".join(map(str, VERSION))

annotator/config.py

+from pydantic import BaseSettings
+import os
+
+from annotator import __version__
+
+
+class BasicSettings(BaseSettings):
+    application_name: str = "CouchDB Annotation Agent"
+    application_version: str = __version__.__version__
+    cdstar_uri: str = "http://localhost:8082/v3"
+    cdstar_user: str = "medic1"
+    cdstar_pass: str = "medIC!umG!9"
+    cdstar_vault: str = "medic"
+    couch_uri: str = "http://localhost:5984"
+    couch_user: str = "medic"
+    couch_pass: str = "medic2020"
+    couch_db: str = "medic"
+
+
+def get_version():
+    return BasicSettings().application_version
+
+
+agent_description = ""
+with open(
+    os.path.join(os.path.abspath(os.path.dirname(__file__)), os.pardir, "Readme.md")
+) as readme:
+    agent_description = readme.read()

annotator/errors.py

+class ActiveWorkflowException(Exception):
+    def __init__(self, name: str, message: str):
+        self.name = name
+        self.message = message

annotator/main.py

+import datetime
+
+from annotator import access_log, error_log
+from annotator import stores
+from annotator import models_activeworkflow as awmodels
+from annotator.config import BasicSettings
+from annotator.errors import ActiveWorkflowException
+
+from fastapi import BackgroundTasks, FastAPI, Request
+import fastapi
+import fastapi.responses
+
+app = FastAPI()
+
+# TODO: specify your endpoint name here!
+endpoint_name = "annotator"