From 762a8a05bff666e058bf4063b03f9219695778e4 Mon Sep 17 00:00:00 2001 From: Vadim Laletin Date: Tue, 22 Oct 2024 19:58:23 +0200 Subject: [PATCH] Add working example --- example/.dockerignore | 14 + example/.env.example | 10 + example/.env.tests.local.example | 1 + example/.env.tpl | 31 - example/.gitignore | 30 +- example/Dockerfile | 26 +- example/LICENSE | 21 + example/Makefile | 8 + example/Pipfile | 53 - example/Pipfile.lock | 1519 ----------- example/README.md | 34 +- example/app/__init__.py | 4 - example/app/access_policy/__init__.py | 25 - example/app/app_keys.py | 8 + example/app/config.py | 31 +- example/app/contrib/aidboxpy_ext.py | 122 - example/app/contrib/db_ext.py | 59 - example/app/contrib/sdk_ext.py | 73 - example/app/contrib/utils.py | 38 - example/app/fhirdate.py | 81 - example/app/manifest.py | 78 - example/app/notification.py | 183 -- example/app/operations/__init__.py | 1 + example/app/operations/example.py | 17 + example/app/periodic_tasks.py | 8 - example/app/sdk.py | 22 +- example/app/subscriptions.py | 25 - example/app/timeout.py | 17 - example/app/version.py | 6 + example/compose.test-env.yaml | 40 + example/compose.yaml | 16 + example/{app => }/contrib/__init__.py | 0 example/contrib/fhirpy.py | 30 + example/docker-compose.tests.yaml | 48 - example/docker-compose.yaml | 34 - example/env_tests | 22 - example/env_tests/aidbox | 17 + example/env_tests/app | 10 + example/env_tests/db | 3 + example/main.py | 80 +- example/poetry.lock | 2220 +++++++++++++++++ example/pyproject.toml | 100 +- example/resources/entities/.gitkeep | 0 example/resources/migrations/.gitkeep | 0 .../email/email-example.html | 9 - .../email/email-layout.html | 8 - example/resources/seeds/.gitkeep | 0 example/run_test.sh | 14 +- example/{app/utils.py => tests/__init__.py} | 0 example/tests/conftest.py | 21 +- example/tests/test_base.py | 45 - example/tests/test_db_isolation.py | 25 + example/tests/test_example.py | 10 + example/tests/test_timeout.py | 21 - example/tests_zen_project/zen-package.edn | 1 + example/tests_zen_project/zrc/main.edn | 5 + example/update-commit-hash.sh | 7 + example/update-version.sh | 7 + 58 files changed, 2686 insertions(+), 2652 deletions(-) create mode 100644 example/.dockerignore create mode 100644 example/.env.example create mode 100644 example/.env.tests.local.example delete mode 100644 example/.env.tpl create mode 100644 example/LICENSE create mode 100644 example/Makefile delete mode 100644 example/Pipfile delete mode 100644 example/Pipfile.lock delete mode 100644 example/app/access_policy/__init__.py create mode 100644 example/app/app_keys.py delete mode 100644 example/app/contrib/aidboxpy_ext.py delete mode 100644 example/app/contrib/db_ext.py delete mode 100644 example/app/contrib/sdk_ext.py delete mode 100644 example/app/contrib/utils.py delete mode 100644 example/app/fhirdate.py delete mode 100644 example/app/manifest.py delete mode 100644 example/app/notification.py create mode 100644 example/app/operations/__init__.py create mode 100644 example/app/operations/example.py delete mode 100644 example/app/periodic_tasks.py delete mode 100644 example/app/subscriptions.py delete mode 100644 example/app/timeout.py create mode 100644 example/app/version.py create mode 100644 example/compose.test-env.yaml create mode 100644 example/compose.yaml rename example/{app => }/contrib/__init__.py (100%) create mode 100644 example/contrib/fhirpy.py delete mode 100644 example/docker-compose.tests.yaml delete mode 100644 example/docker-compose.yaml delete mode 100644 example/env_tests create mode 100644 example/env_tests/aidbox create mode 100644 example/env_tests/app create mode 100644 example/env_tests/db create mode 100644 example/poetry.lock delete mode 100644 example/resources/entities/.gitkeep delete mode 100644 example/resources/migrations/.gitkeep delete mode 100644 example/resources/notificationtemplates/email/email-example.html delete mode 100644 example/resources/notificationtemplates/email/email-layout.html delete mode 100644 example/resources/seeds/.gitkeep rename example/{app/utils.py => tests/__init__.py} (100%) delete mode 100644 example/tests/test_base.py create mode 100644 example/tests/test_db_isolation.py create mode 100644 example/tests/test_example.py delete mode 100644 example/tests/test_timeout.py create mode 100644 example/tests_zen_project/zen-package.edn create mode 100644 example/tests_zen_project/zrc/main.edn create mode 100755 example/update-commit-hash.sh create mode 100755 example/update-version.sh diff --git a/example/.dockerignore b/example/.dockerignore new file mode 100644 index 0000000..2d6b48b --- /dev/null +++ b/example/.dockerignore @@ -0,0 +1,14 @@ +__pycache__ +.mypy_cache +.pytest_cache +.ruff_cache +.history +.vscode + +.coverage + +htmlcov +coverage.xml +report.xml + +.DS_Store \ No newline at end of file diff --git a/example/.env.example b/example/.env.example new file mode 100644 index 0000000..6a3853b --- /dev/null +++ b/example/.env.example @@ -0,0 +1,10 @@ +APP_INIT_CLIENT_ID=root +APP_INIT_CLIENT_SECRET=secret +APP_INIT_URL=http://host.docker.internal:8080 + +APP_ID=file-uploader +APP_SECRET=secret +APP_URL=http://host.docker.internal:8081 +APP_PORT=8081 +AIO_PORT=8081 +AIO_HOST=0.0.0.0 diff --git a/example/.env.tests.local.example b/example/.env.tests.local.example new file mode 100644 index 0000000..c7984fd --- /dev/null +++ b/example/.env.tests.local.example @@ -0,0 +1 @@ +AIDBOX_LICENSE_TEST= \ No newline at end of file diff --git a/example/.env.tpl b/example/.env.tpl deleted file mode 100644 index c7dd349..0000000 --- a/example/.env.tpl +++ /dev/null @@ -1,31 +0,0 @@ -APP_FAST_START_MODE=True -AIDBOX_LICENSE= - -AIDBOX_CLIENT_ID=root -AIDBOX_CLIENT_SECRET=secret -AIDBOX_ADMIN_PASSWORD=password - -AIDBOX_BASE_URL=http://devbox:8080 -AIDBOX_PORT=8080 -AIDBOX_FHIR_VERSION=4.0.0 - -APP_INIT_CLIENT_ID=root -APP_INIT_CLIENT_SECRET=secret -APP_INIT_URL=http://devbox:8080 - -APP_ID=app-example -APP_SECRET=secret -APP_URL=http://backend:8081 -APP_PORT=8081 -AIO_PORT=8081 -AIO_HOST=0.0.0.0 - -PGHOST=database -PGDATABASE=devbox -PGPORT=5432 -PGUSER=postgres -PGPASSWORD=postgres - -OPENID_RSA=/var/config/jwtRS256.key -OPENID_RSA_PUB=/var/config/jwtRS256.key.pub - diff --git a/example/.gitignore b/example/.gitignore index 92d54db..1cdd3e7 100644 --- a/example/.gitignore +++ b/example/.gitignore @@ -1,17 +1,17 @@ -config/jwtRS256.key -config/jwtRS256.key.pub -beta -.cpcache -.volumes -app.log -.idea/ -pom.xml -ui/*.iml -*.iml +__pycache__ +.mypy_cache +.pytest_cache +.ruff_cache +.history +.vscode + .env -__pycache__/ -.DS_Store -venv/ -env/ -htmlcov/ +.env.tests.local + .coverage + +htmlcov +coverage.xml +report.xml + +.DS_Store diff --git a/example/Dockerfile b/example/Dockerfile index edeedb7..5b2a545 100644 --- a/example/Dockerfile +++ b/example/Dockerfile @@ -1,14 +1,22 @@ -FROM python:3.10 -RUN mkdir /app +FROM python:3.12-slim + +RUN addgroup --gid 1000 dockeruser +RUN adduser --disabled-login --uid 1000 --gid 1000 dockeruser +RUN mkdir -p /app/ +RUN chown -R dockeruser:dockeruser /app/ + +RUN pip install poetry + +USER dockeruser + WORKDIR /app -RUN pip install pipenv safety +COPY pyproject.toml . +COPY poetry.lock . +RUN poetry install -COPY Pipfile . -COPY Pipfile.lock . -RUN pipenv install -RUN pipenv check COPY . . -CMD ["pipenv", "run", "gunicorn", "main:create_app", "--worker-class", "aiohttp.worker.GunicornWebWorker", "-b", "0.0.0.0:8081"] -EXPOSE 8081 +RUN poetry run mypy + +CMD ["poetry", "run", "gunicorn", "main:create_gunicorn_app", "--worker-class", "aiohttp.worker.GunicornWebWorker", "-b", "0.0.0.0:8081"] diff --git a/example/LICENSE b/example/LICENSE new file mode 100644 index 0000000..4be8c56 --- /dev/null +++ b/example/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2024 beda.software + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/example/Makefile b/example/Makefile new file mode 100644 index 0000000..21a811d --- /dev/null +++ b/example/Makefile @@ -0,0 +1,8 @@ +build-test: + docker compose -f compose.test-env.yaml build + +stop-test: + docker compose -f compose.test-env.yaml stop + +down-test: + docker compose -f compose.test-env.yaml down diff --git a/example/Pipfile b/example/Pipfile deleted file mode 100644 index b76b988..0000000 --- a/example/Pipfile +++ /dev/null @@ -1,53 +0,0 @@ -[[source]] -name = "pypi" -url = "https://pypi.org/simple" -verify_ssl = true - -[dev-packages] -anaconda = "*" -jedi = ">=0.18.0" -json-rpc = ">=1.13.0" -service-factory = ">=0.1.6" -black = "*" -autohooks = "*" -autohooks-plugin-black = "*" -autohooks-plugin-isort = "*" -isort = "*" -autoflake = "*" -importmagic = "*" -epc = "*" -pep8 = "*" -flake8 = "*" -ipython = "*" - -[packages] -pytest-aiohttp = "==0.3.0" -pytest-cov = "==3.0.0" -pytest = "==6.2.5" -pytest-mock = "==3.6.1" -Faker = "==9.8.0" -aioresponses = "==0.7.2" -python-dateutil = "==2.8.2" -aiocron = "==1.7" -funcy = "==1.16" -gunicorn = "==20.1.0" -aiosmtplib = "==1.1.6" -aiohttp = ">=3.8.0" -premailer = "==3.10.0" -sentry-sdk = "==1.4.3" -coloredlogs = ">=15.0.1" -boto3 = "==1.20.0" -PyYAML = "==6.0" -Jinja2 = "==3.0.2" -SQLAlchemy = ">=1.4.26" -fhirpy = "==1.2.1" -aidboxpy = "==1.2.0" -aidbox-python-sdk = {git = "https://github.com/Aidbox/aidbox-python-sdk.git",ref = "ef6b5c7492c470cc0559ab586651ea7661b8f061"} -fhirpathpy = {git = "https://github.com/beda-software/fhirpath-py.git",ref = "aaac1a4209e3e3cbce6f62246c0822c6cdaf5af5"} - - - - - -[requires] -python_version = "3.10" diff --git a/example/Pipfile.lock b/example/Pipfile.lock deleted file mode 100644 index 1563f68..0000000 --- a/example/Pipfile.lock +++ /dev/null @@ -1,1519 +0,0 @@ -{ - "_meta": { - "hash": { - "sha256": "890ead2c77764e473dcd340f72ec41191214e27c919c874ba1034cd108f14e7b" - }, - "pipfile-spec": 6, - "requires": { - "python_version": "3.10" - }, - "sources": [ - { - "name": "pypi", - "url": "https://pypi.org/simple", - "verify_ssl": true - } - ] - }, - "default": { - "aidbox-python-sdk": { - "git": "https://github.com/Aidbox/aidbox-python-sdk.git", - "ref": "ef6b5c7492c470cc0559ab586651ea7661b8f061" - }, - "aidboxpy": { - "hashes": [ - "sha256:05f0989198ccccf27a31add98c15e12c517bf1830d5698ef8492526229b62b77", - "sha256:f4969bc4a2accde874d053bde0c3dcf1eebdb6502d454a60e24c84807b5d95b0" - ], - "index": "pypi", - "version": "==1.2.0" - }, - "aiocron": { - "hashes": [ - "sha256:ad7d3b9bd88897934ffd18937ff235ab9fb01358280fd40e01461fd5f76348bd", - "sha256:f06d7b84b86d6cb7156c01e640b4122da86afaa4873c6bcf79e57c4762e48789" - ], - "index": "pypi", - "version": "==1.7" - }, - "aiohttp": { - "hashes": [ - "sha256:01d7bdb774a9acc838e6b8f1d114f45303841b89b95984cbb7d80ea41172a9e3", - "sha256:03a6d5349c9ee8f79ab3ff3694d6ce1cfc3ced1c9d36200cb8f08ba06bd3b782", - "sha256:04d48b8ce6ab3cf2097b1855e1505181bdd05586ca275f2505514a6e274e8e75", - 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Install pyenv and poetry globally +2. Install python3.12 python globally using pyenv +3. Inside the app directory, run `poetry env use /path/to/python312` +4. Run `poetry install` +5. Run `poetry shell` to activate virtual environment +6. Run `autohooks activate` to activate git hooks -Build images using `docker compose -f docker-compose.tests.yaml build`. +## Local deployment +0. Run Aidbox anywhere but make `host.docker.internal` available from the Aidbox to access the host machine +1. Run `cp .env.example .env` +2. `docker-compose up` +## Testing -After that, just start `./run_test.sh` or `./run_test.sh tests/test_base.py` (if you want to run the particular file/test). -The first run may take about a minute because it prepares the db and devbox. +1. Run `cp .env.tests.local.example .env.tests.local` +2. Put your dev aidbox license key into `AIDBOX_LICENSE_TEST` in `.env.tests.local` +3. Run `docker compose -f compose.test-env.yaml build` at the first time and every time once dependencies are updated/added +4. Run `./run_test.sh` +5. You can kill the containers when complete to work with tests by run: + `docker compose -f compose.test-env.yaml down` +## IDE setup -If you have updated some requirements, you need to re-run `docker-compose -f docker-compose.tests.yaml build` +Strongly recommended to use ruff and mypy plugins for IDE diff --git a/example/app/__init__.py b/example/app/__init__.py index 517da37..e69de29 100644 --- a/example/app/__init__.py +++ b/example/app/__init__.py @@ -1,4 +0,0 @@ - - -import app.notification -import app.timeout diff --git a/example/app/access_policy/__init__.py b/example/app/access_policy/__init__.py deleted file mode 100644 index d1bb314..0000000 --- a/example/app/access_policy/__init__.py +++ /dev/null @@ -1,25 +0,0 @@ -user_required_policy = {"engine": "json-schema", "schema": {"required": ["user"]}} - -super_admin_policy = { - "engine": "json-schema", - "schema": { - "required": ["user"], - "properties": { - "user": { - "anyOf": [ - {"required": ["id"], "properties": {"id": {"constant": "admin"}}}, - { - "required": ["data"], - "properties": {"data": {"required": ["superAdmin"]}}, - }, - ], - } - }, - }, -} - -strict_access_policies = { - "super_admin": super_admin_policy, -} - -access_policies = strict_access_policies diff --git a/example/app/app_keys.py b/example/app/app_keys.py new file mode 100644 index 0000000..6c5f13a --- /dev/null +++ b/example/app/app_keys.py @@ -0,0 +1,8 @@ +from aidbox_python_sdk.app_keys import client, sdk, settings +from aiohttp import ClientSession, web +from fhirpy import AsyncFHIRClient + +fhir_client: web.AppKey[AsyncFHIRClient] = web.AppKey("fhir_client", AsyncFHIRClient) +session = web.AppKey("session", ClientSession) + +__all__ = ["fhir_client", "client", "sdk", "settings", "session"] diff --git a/example/app/config.py b/example/app/config.py index 1e813f1..97e26c3 100644 --- a/example/app/config.py +++ b/example/app/config.py @@ -1,32 +1,3 @@ -import pytz import os -app_superadmin_email = os.environ.get("APP_SUPERADMIN_EMAIL", "admin@health-samurai.io") -app_superadmin_password = os.environ.get( - "APP_SUPERADMIN_PASSWORD", os.environ.get("AIDBOX_ADMIN_PASSWORD") -) - -secret_key = os.environ.get("SECRET_KEY", "").encode() -local_tz = pytz.timezone(os.environ.get("LOCAL_TZ", "US/Central")) - -from_email = os.environ.get("FROM_EMAIL", "donotreply@example.com") - -frontend_url = os.environ.get("FRONTEND_URL", "http://localhost:3000") -backend_public_url = os.environ.get("BACKEND_PUBLIC_URL", "http://localhost:8080") - - - - - - - - - - - - - -root_dir = os.path.dirname(os.path.abspath(__name__)) - -dev_init = os.environ.get("DEV_INIT", "False") == "True" -environment_name = os.environ.get("SENTRY_ENVIRONMENT", "") +is_test_environment = os.environ.get("TEST_ENV", False) diff --git a/example/app/contrib/aidboxpy_ext.py b/example/app/contrib/aidboxpy_ext.py deleted file mode 100644 index 67e0628..0000000 --- a/example/app/contrib/aidboxpy_ext.py +++ /dev/null @@ -1,122 +0,0 @@ -# TODO: refactor it after fhir-py#23 -from aidboxpy import AsyncAidboxResource - - -def extract_resources_from_bundle(bundle): - client = _get_client() - - return [ - client.resource(entry["resource"]["resourceType"], **entry["resource"]) - for entry in bundle["entry"] - ] - - -async def get_previous_version(resource): - """ - Returns previous version of the resource or None if it is the first version - """ - client = _get_client() - - # TODO: refactor it after fhir-py#23 - resource_history = extract_resources_from_bundle( - await client._fetch_resource( - "{0}/{1}/_history".format(resource.resource_type, resource.id), - {"_count": 2}, - ) - ) - if len(resource_history) == 2: - return resource_history.pop() - - return None - - -async def get_historic_version(resource, history_id): - """ - Returns historic version of the resource - """ - client = _get_client() - - historic_resource = await client._fetch_resource( - "{0}/{1}/_history/{2}".format(resource.resource_type, resource.id, history_id) - ) - if historic_resource: - return client.resource(historic_resource["resourceType"], **historic_resource) - - return None - - -async def aidbox_query(name, **params): - client = _get_client() - - return (await client._fetch_resource("$query/{0}".format(name), params=params)).get( - "data", None - ) - - -async def aidbox_mapping_apply(name, **payload): - client = _get_client() - - return await client._do_request( - "post", "Mapping/{0}/$apply".format(name), data=payload - ) - - -# TODO: cover with tests -def set_by_path(obj, path, value): - cursor = obj - last_part = path.pop() - - for index, part in enumerate(path): - if isinstance(cursor, dict) and part not in cursor: - nextpart = (path + [last_part])[index + 1] - try: - nnextpart = (path + [last_part])[index + 2] - except IndexError: - nnextpart = "" - - if isinstance(nextpart, int): - cursor[part] = [[] if isinstance(nnextpart, int) else {}] - else: - cursor[part] = {} - - cursor = cursor[part] - cursor[last_part] = value - - -def make_bundle(resources, type_="searchset", **kwargs): - client = _get_client() - - entries = [] - for resource in resources: - serialized_resource = ( - resource.serialize() - if isinstance(resource, AsyncAidboxResource) - else resource - ) - entry = {"resource": serialized_resource} - if type_ in ["transaction", "batch"]: - if resource.id: - entry["request"] = { - "method": "PUT", - "url": "/{0}/{1}".format( - serialized_resource["resourceType"], serialized_resource["id"] - ), - } - else: - entry["request"] = { - "method": "POST", - "url": "/{0}".format(serialized_resource["resourceType"]), - } - entries.append(entry) - - return client.resource("Bundle", type=type_, entry=entries, **kwargs) - - -def make_search_token(system="", code=""): - return f"{system}|{code}" - - -def _get_client(): - from app.sdk import sdk - - return sdk.client diff --git a/example/app/contrib/db_ext.py b/example/app/contrib/db_ext.py deleted file mode 100644 index 6d4d531..0000000 --- a/example/app/contrib/db_ext.py +++ /dev/null @@ -1,59 +0,0 @@ -from sqlalchemy.ext.compiler import compiles -from sqlalchemy.sql.expression import FunctionElement - - -# TODO: refactor after https://github.com/Aidbox/aidbox-python-sdk/issues/21 - - -class knife_extract_text(FunctionElement): - name = "knife_extract_text" - - -@compiles(knife_extract_text) -def compile_knife_extract_text(element, compiler, **kw): - return "knife_extract_text(%s)" % compiler.process(element.clauses, **kw) - - -class knife_extract_max_numeric(FunctionElement): - name = "knife_extract_max_numeric" - - -@compiles(knife_extract_max_numeric) -def compile_knife_extract_max_numeric(element, compiler, **kw): - return "knife_extract_max_numeric(%s)" % compiler.process(element.clauses, **kw) - - -class knife_extract_min_timestamptz(FunctionElement): - name = "knife_extract_min_timestamptz" - - -@compiles(knife_extract_min_timestamptz) -def compile_knife_extract_min_timestamptz(element, compiler, **kw): - return "knife_extract_min_timestamptz(%s)" % compiler.process(element.clauses, **kw) - - -class knife_date_bound(FunctionElement): - name = "knife_date_bound" - - -@compiles(knife_date_bound) -def compile_knife_date_bound(element, compiler, **kw): - return "knife_date_bound(%s)" % compiler.process(element.clauses, **kw) - - -class aidbox_text_search(FunctionElement): - name = "aidbox_text_search" - - -@compiles(aidbox_text_search) -def compile_aidbox_text_search(element, compiler, **kw): - return "aidbox_text_search(%s)" % compiler.process(element.clauses, **kw) - - -class unaccent(FunctionElement): - name = "unaccent" - - -@compiles(unaccent) -def compile_unaccent(element, compiler, **kw): - return "unaccent(%s)" % compiler.process(element.clauses, **kw) diff --git a/example/app/contrib/sdk_ext.py b/example/app/contrib/sdk_ext.py deleted file mode 100644 index a459b19..0000000 --- a/example/app/contrib/sdk_ext.py +++ /dev/null @@ -1,73 +0,0 @@ -import os - -import yaml - - -def merge_resources(*objs): - resources = {} - for obj in objs: - if not obj: - continue - - for resource_type, resources_by_id in obj.items(): - if resource_type not in resources: - resources[resource_type] = {} - for resource_id, resource in resources_by_id.items(): - resources[resource_type][resource_id] = resource - - return resources - - -def load_resources_by_ids(abs_path): - resources = {} - - for filename in os.listdir(abs_path): - if not filename.endswith(".yaml"): - continue - - resource_id = filename[:-5] - with open(os.path.join(abs_path, filename)) as f: - resources[resource_id] = yaml.safe_load(f) - return resources - - -def load_resources(abs_path): - resources = {} - - for resource_type in os.listdir(abs_path): - if not os.path.isdir(os.path.join(abs_path, resource_type)): - continue - if resource_type not in resources: - resources[resource_type] = {} - - resources[resource_type] = load_resources_by_ids( - os.path.join(abs_path, resource_type) - ) - return resources - - -def load_notification_templates(abs_path): - resources = {} - - for filename in os.listdir(abs_path): - if not filename.endswith(".html") and not filename.endswith(".txt"): - continue - - resource_id = filename.rsplit(".", 1)[0] - with open(os.path.join(abs_path, filename)) as f: - resources[resource_id] = {"template": f.read()} - return resources - - -def load_sql_migrations(abs_path): - migrations = [] - - for file in os.scandir(abs_path): - if not file.name.endswith(".sql"): - continue - with open(file.path) as f: - migrations.append( - {"id": os.path.splitext(file.name)[0], "sql": f.read(),} - ) - - return sorted(migrations, key=lambda x: x["id"]) diff --git a/example/app/contrib/utils.py b/example/app/contrib/utils.py deleted file mode 100644 index 18a8d7c..0000000 --- a/example/app/contrib/utils.py +++ /dev/null @@ -1,38 +0,0 @@ -import asyncio -import concurrent.futures -import logging -from functools import wraps, partial - - -def sync_to_async(fn): - @wraps(fn) - async def _wrapper(*args, **kwargs): - loop = asyncio.get_running_loop() - pfn = partial(fn, *args, **kwargs) - with concurrent.futures.ThreadPoolExecutor() as pool: - return await loop.run_in_executor(pool, pfn) - - return _wrapper - - -def robust_fn(coro_fn): - max_tries = 10 - - async def _fn(*args, **kwargs): - tries = 0 - while True: - try: - return await coro_fn(*args, **kwargs) - except Exception as exc: - tries += 1 - if tries == max_tries: - raise - - delay = 3 * tries - logging.debug( - "Caught an exception in `robust_call`\n{0}\n" - "Repeating the function call in {1} seconds...".format(exc, delay) - ) - await asyncio.sleep(delay) - - return _fn diff --git a/example/app/fhirdate.py b/example/app/fhirdate.py deleted file mode 100644 index fc1e810..0000000 --- a/example/app/fhirdate.py +++ /dev/null @@ -1,81 +0,0 @@ -import pytz -import datetime - -from dateutil.relativedelta import relativedelta - -from app.config import local_tz - - -FHIR_DATE_TIME_FORMAT = "%Y-%m-%dT%H:%M:%SZ" -FHIR_TIME_FORMAT = "%H:%M:%S" -FHIR_DATE_FORMAT = "%Y-%m-%d" -HUMAN_DATE_FORMAT = "%m.%d.%Y" -HUMAN_DATE_TIME_FORMAT = "%m.%d.%Y %H:%M" - - -def get_now(): - return local_tz.normalize( - pytz.utc.localize(datetime.datetime.utcnow().replace(microsecond=0)) - ) - - -def parse_time(time): - return datetime.datetime.strptime(time, FHIR_TIME_FORMAT).time() - - -def parse_date_time(date): - try: - return local_tz.normalize( - pytz.utc.localize(datetime.datetime.strptime(date, FHIR_DATE_TIME_FORMAT)) - ) - except ValueError: - return local_tz.localize(datetime.datetime.strptime(date, FHIR_DATE_FORMAT)) - - -def parse_date(date): - return datetime.datetime.strptime(date, FHIR_DATE_FORMAT).date() - - -def tz_min(date: datetime.datetime): - return date.replace(hour=0, minute=0, second=0) - - -def tz_max(date: datetime.datetime): - return date.replace(hour=23, minute=59, second=59) - - -def format_date_time(date: datetime.datetime): - return pytz.utc.normalize(date).strftime(FHIR_DATE_TIME_FORMAT) - - -def format_date(date: datetime.date): - return date.strftime(FHIR_DATE_FORMAT) - - -def format_local_date(date: str): - return parse_date_time(date).strftime(HUMAN_DATE_FORMAT) - - -def format_local_date_time(date: str): - # TODO: use user locale and tz - return parse_date_time(date).strftime(HUMAN_DATE_TIME_FORMAT) - - -def fhir_dayofweek_to_python(fhir_repr: str): - return {"mon": 0, "tue": 1, "wed": 2, "thu": 3, "fri": 4, "sat": 5, "sun": 6}[ - fhir_repr - ] - - -def fhir_period_to_timedelta(period: int, fhir_period_unit: str): - delta_key = { - "s": "seconds", - "min": "minutes", - "h": "hours", - "d": "days", - "wk": "weeks", - "mo": "months", - "a": "years", - }[fhir_period_unit] - - return relativedelta(**{delta_key: period}) diff --git a/example/app/manifest.py b/example/app/manifest.py deleted file mode 100644 index ed7f868..0000000 --- a/example/app/manifest.py +++ /dev/null @@ -1,78 +0,0 @@ -import os - -from app import config -from app.access_policy import access_policies -from app.contrib.sdk_ext import ( - merge_resources, - load_notification_templates, - load_resources, - load_sql_migrations, -) - -meta_resources = merge_resources( - { - "Client": { - "SPA": {"secret": "123456", "grant_types": ["password"]}, - }, - "AidboxConfig": { - "provider": { - "provider": {"console": {"type": "console"}, "default": "console"}, - } - }, - "AccessPolicy": access_policies, - "NotificationTemplate": { - **load_notification_templates( - os.path.join(config.root_dir, "resources/notificationtemplates/email") - ), - }, - "SearchParameter": { - # Place custom search parameters here - }, - "PGSequence": { - # Don't forget to add new sequence to new migration - # Remove this comment after https://github.com/Aidbox/Issues/issues/167 is solved - }, - "Attribute": { - # TODO: remove when Aidbox adds this status - "Notification.status": { - "path": ["status"], - "type": {"resourceType": "Entity", "id": "code"}, - "resource": {"resourceType": "Entity", "id": "Notification"}, - "module": "auth", - "enum": ["delivered", "error", "failure"], - }, - }, - }, - load_resources(os.path.join(config.root_dir, "resources/entities")), -) - -seeds = merge_resources( - { - "User": { - "superadmin": { - "password": config.app_superadmin_password, - "email": config.app_superadmin_email, - "data": { - "givenName": "Super", - "familyName": "Admin", - "superAdmin": {"resourceType": "Practitioner", "id": "superadmin"}, - }, - }, - }, - "Practitioner": { - "superadmin": { - "name": [{"given": ["Super"], "family": "Admin"}], - "telecom": [{"system": "email", "value": config.app_superadmin_email,}], - }, - }, - } - if config.dev_init - else {}, - load_resources(os.path.join(config.root_dir, "resources/seeds")), -) - -entities = { - #Put your custom resource definition here -} - -migrations = load_sql_migrations(os.path.join(config.root_dir, "resources/migrations")) diff --git a/example/app/notification.py b/example/app/notification.py deleted file mode 100644 index 74ef750..0000000 --- a/example/app/notification.py +++ /dev/null @@ -1,183 +0,0 @@ -import logging - -from jinja2 import Undefined, Environment -from jinja2.ext import Extension -from premailer import transform - -from app import config -from app.sdk import sdk -from app.fhirdate import get_now, format_date as format_date_fhir - - -async def send_email(to, template_id, payload, attachments=None, *, save=True): - provider = "console" - - notification = sdk.client.resource( - "Notification", - provider=default_provider, - providerData={ - "fromApp": True, - "type": "email", - "to": to, - "payload": payload, - "template": {"resourceType": "NotificationTemplate", "id": template_id}, - "attachments": attachments or [], - }, - ) - if save: - await notification.save() - return notification - - -async def send_sms(to, body): - provider = "console" - provider_data = {"fromApp": True, "type": "sms", "to": to, "body": body} - - notification = sdk.client.resource( - "Notification", provider=provider, providerData=provider_data - ) - await notification.save() - - -class SilentUndefined(Undefined): - def _fail_with_undefined_error(self, *args, **kwargs): - return None - - -class RenderBlocksExtension(Extension): - def __init__(self, environment): - super(RenderBlocksExtension, self).__init__(environment) - environment.extend(render_blocks=[]) - - def filter_stream(self, stream): - block_level = 0 - skip_level = 0 - in_endblock = False - - for token in stream: - if token.type == "block_begin": - if stream.current.value == "block": - block_level += 1 - if stream.look().value not in self.environment.render_blocks: - skip_level = block_level - - if token.value == "endblock": - in_endblock = True - - if skip_level == 0: - yield token - - if token.type == "block_end": - if in_endblock: - in_endblock = False - block_level -= 1 - - if skip_level == block_level + 1: - skip_level = 0 - - -jinja_env = Environment(undefined=SilentUndefined) - -jinja_subject_env = Environment( - undefined=SilentUndefined, extensions=[RenderBlocksExtension] -) -jinja_subject_env.render_blocks = ["subject"] - -jinja_body_env = Environment( - undefined=SilentUndefined, extensions=[RenderBlocksExtension] -) -jinja_body_env.render_blocks = ["body"] - - -class SendNotificationException(Exception): - pass - - -async def send_console(to, subject, body, attachments=None): - logging.debug( - "New notification:\nTo: {}\nSubject: {}\n{}\nattachments: {}".format( - to, subject, body, attachments or [] - ) - ) - return - - - - - - - - -providers = { - "console": send_console, - - -} - - -async def notification_sub(action, resource): - if action == "create": - provider_data = resource["providerData"] - - # Skip processing for non-app notifications - if not provider_data.get("fromApp"): - return - - payload = { - **provider_data["payload"], - "frontend_url": config.frontend_url, - "backend_url": config.backend_public_url, - "current_date": format_date_fhir(get_now()), - } - - template = await provider_data["template"].to_resource() - subject_template = jinja_subject_env.from_string(template["template"]) - body_template = jinja_body_env.from_string(template["template"]) - subject = subject_template.render(payload) - body = body_template.render(payload) - - notification_type = provider_data.get("type") - if notification_type == "email": - layout = await sdk.client.resources("NotificationTemplate").get( - id="email-layout" - ) - body = transform( - jinja_env.from_string(layout["template"]).render( - {"body": body, **payload} - ) - ) - elif notification_type == "sms": - pass - else: - raise Exception( - "Notification type `{}` is not supported".format(notification_type) - ) - - props = { - "subject": subject.strip(), - "body": body.strip(), - "to": provider_data["to"], - } - if "attachments" in provider_data: - props["attachments"] = provider_data["attachments"] - provider = resource["provider"] - - send_fn = providers.get(provider) - if not send_fn: - logging.warning("Unhandled notification for provider {}".format(provider)) - return - - try: - await send_fn(**props) - - resource["status"] = "delivered" - await resource.save() - except SendNotificationException as exc: - logging.debug(exc) - resource["status"] = "error" - await resource.save() - except Exception as exc: - logging.exception(exc) - resource["status"] = "failure" - await resource.save() - raise diff --git a/example/app/operations/__init__.py b/example/app/operations/__init__.py new file mode 100644 index 0000000..8f99451 --- /dev/null +++ b/example/app/operations/__init__.py @@ -0,0 +1 @@ +from . import example # noqa: F401 diff --git a/example/app/operations/example.py b/example/app/operations/example.py new file mode 100644 index 0000000..be7f39b --- /dev/null +++ b/example/app/operations/example.py @@ -0,0 +1,17 @@ +import fhirpy_types_r4b as r4b +from aidbox_python_sdk.types import SDKOperation, SDKOperationRequest +from aiohttp import web + +from app import app_keys as ak +from app.sdk import sdk + + +@sdk.operation(["POST"], ["$example"]) +async def example_op(_operation: SDKOperation, request: SDKOperationRequest) -> web.Response: + fhir_client = request["app"][ak.fhir_client] + + await fhir_client.save(r4b.Patient(id="example")) + patient: r4b.Patient = await fhir_client.get(r4b.Patient, "example") + + return web.json_response({"status": "ok", "patient": patient.model_dump()}) + diff --git a/example/app/periodic_tasks.py b/example/app/periodic_tasks.py deleted file mode 100644 index 40b3db1..0000000 --- a/example/app/periodic_tasks.py +++ /dev/null @@ -1,8 +0,0 @@ -import logging - -from aiocron import crontab - - -@crontab("*/1 * * * *") -def test_task(): - logging.debug("Example task") diff --git a/example/app/sdk.py b/example/app/sdk.py index 9d4d416..80a40a6 100644 --- a/example/app/sdk.py +++ b/example/app/sdk.py @@ -1,23 +1,5 @@ from aidbox_python_sdk.sdk import SDK from aidbox_python_sdk.settings import Settings -from aiohttp import web - -from app.manifest import entities, meta_resources, seeds, migrations - - -sdk_settings = Settings(**{}) -sdk = SDK( - sdk_settings, - entities=entities, - resources=meta_resources, - seeds=seeds, - migrations=migrations, -) - - -@sdk.operation( - ["GET"], ["healthcheck"], public=True, -) -async def healthcheck(operation, request): - return web.json_response({"is_ready": True}) +settings = Settings(**{}) +sdk = SDK(settings) diff --git a/example/app/subscriptions.py b/example/app/subscriptions.py deleted file mode 100644 index 5388ce7..0000000 --- a/example/app/subscriptions.py +++ /dev/null @@ -1,25 +0,0 @@ -import asyncio - -from app.sdk import sdk -from app.notification import notification_sub - - -subscriptions = { - "Notification": [notification_sub], -} - - -# TODO: refactor after https://github.com/Aidbox/aidbox-python-sdk/issues/22 -def register_subscription(resource_type, subs): - async def _common_sub(event): - resource = sdk.client.resource( - event["resource"]["resourceType"], **event["resource"] - ) - await asyncio.gather(*[sub(event["action"], resource) for sub in subs]) - - _common_sub.__name__ = f"{resource_type}_sub" - sdk.subscription(resource_type)(_common_sub) - - -for rt, rt_subs in subscriptions.items(): - register_subscription(rt, rt_subs) diff --git a/example/app/timeout.py b/example/app/timeout.py deleted file mode 100644 index 338247d..0000000 --- a/example/app/timeout.py +++ /dev/null @@ -1,17 +0,0 @@ -import asyncio -from aiohttp import web - -from app.sdk import sdk - - -@sdk.operation(["GET"], ["$default-timeout"]) -async def operation_handler_with_default_timeout(operation, request): - await asyncio.sleep(1) - return web.json_response({"result": "success"}) - - -@sdk.operation(["GET"], ["$sleep", {"name": "sleep-ms"}], timeout=2000) -async def operation_handler_with_custom_timeout(operation, request): - sleep_duration = int(request["route-params"]["sleep-ms"]) - await asyncio.sleep(sleep_duration) - return web.json_response({"result": "success"}) diff --git a/example/app/version.py b/example/app/version.py new file mode 100644 index 0000000..652e96f --- /dev/null +++ b/example/app/version.py @@ -0,0 +1,6 @@ +""" +NOTE: this file is automatically generated +""" + +__version__ = '0.0.1' +__build_commit_hash__ = "local" diff --git a/example/compose.test-env.yaml b/example/compose.test-env.yaml new file mode 100644 index 0000000..2bcd2cb --- /dev/null +++ b/example/compose.test-env.yaml @@ -0,0 +1,40 @@ +name: aidbox-python-sdk-example-tests +services: + aidbox-db: + image: "healthsamurai/aidboxdb:16.1" + env_file: + - ./env_tests/db + healthcheck: + test: ["CMD", "pg_isready", "-U", "postgres"] + interval: 5s + timeout: 5s + retries: 10 + aidbox: + image: healthsamurai/aidboxone:stable + depends_on: + aidbox-db: + condition: service_healthy + env_file: + - ./env_tests/aidbox + volumes: + - "./tests_zen_project:/aidbox-project" + environment: + AIDBOX_LICENSE: ${AIDBOX_LICENSE_TEST} + healthcheck: + test: curl --fail http://localhost:8080/health || exit 1 + interval: 5s + timeout: 30s + retries: 50 + app: + image: ${BUILD_IMAGE} + build: . + depends_on: + aidbox: + condition: service_healthy + env_file: + - ./env_tests/app + volumes: + - ./:/app + command: ["poetry", "run", "pytest"] + environment: + TEST_ENV: True diff --git a/example/compose.yaml b/example/compose.yaml new file mode 100644 index 0000000..4560e87 --- /dev/null +++ b/example/compose.yaml @@ -0,0 +1,16 @@ +name: aidbox-python-sdk-example +services: + app: + image: ${BUILD_IMAGE} + build: . + env_file: + - .env + volumes: + - ./:/app + extra_hosts: + - "host.docker.internal:host-gateway" + ports: + - "8081:8081" + command: ["poetry", "run", "gunicorn", "main:create_gunicorn_app", "--worker-class", "aiohttp.worker.GunicornWebWorker", "-b", "0.0.0.0:8081", "--reload"] + environment: + TEST_ENV: True diff --git a/example/app/contrib/__init__.py b/example/contrib/__init__.py similarity index 100% rename from example/app/contrib/__init__.py rename to example/contrib/__init__.py diff --git a/example/contrib/fhirpy.py b/example/contrib/fhirpy.py new file mode 100644 index 0000000..ccc5a29 --- /dev/null +++ b/example/contrib/fhirpy.py @@ -0,0 +1,30 @@ +import fhirpy_types_r4b as r4b +from fhirpy import AsyncFHIRClient +from fhirpy.base import ResourceProtocol +from typing_extensions import TypeVar + +TResource = TypeVar("TResource") + + +def make_reference_str(resource: ResourceProtocol) -> str: + assert resource.id, "Field `id` must be presented" + return f"{resource.resourceType}/{resource.id}" + + +def to_reference(resource: ResourceProtocol) -> r4b.Reference: + return r4b.Reference(reference=make_reference_str(resource)) + + +async def to_resource( + client: AsyncFHIRClient, resource_type: type[TResource], reference: r4b.Reference +) -> TResource: + assert reference.reference, "Field `reference` must be presented" + resource_dict = await client.get(reference.reference) + + return resource_type(**resource_dict) + + +def get_resource_type(reference: r4b.Reference) -> str: + assert reference.reference + + return reference.reference.split("/")[0] diff --git a/example/docker-compose.tests.yaml b/example/docker-compose.tests.yaml deleted file mode 100644 index a94b1aa..0000000 --- a/example/docker-compose.tests.yaml +++ /dev/null @@ -1,48 +0,0 @@ -version: '3.1' -services: - backend: - image: ${BUILD_IMAGE:-example-backend-test} - build: . - command: ${TEST_COMMAND} - env_file: - - env_tests - environment: - APP_FAST_START_MODE: ${APP_FAST_START_MODE} - depends_on: - devbox-healthcheck: - condition: - service_healthy - links: - - devbox - volumes: - - .:/app - # Colored logs - tty: true - devbox-healthcheck: - image: curlimages/curl - entrypoint: /bin/sleep 10000 - links: - - devbox - depends_on: - - devbox - healthcheck: - test: curl --fail http://devbox:8080 || exit 1 - interval: 1s - timeout: 20s - retries: 100 - devbox: - image: "healthsamurai/aidboxone:stable" - depends_on: - - devbox-db - links: - - "devbox-db:database" - env_file: - - env_tests - environment: - AIDBOX_LICENSE: ${TESTS_AIDBOX_LICENSE} - devbox-db: - image: "healthsamurai/aidboxdb:14.5" - environment: - POSTGRES_USER: postgres - POSTGRES_PASSWORD: postgres - POSTGRES_DB: devbox diff --git a/example/docker-compose.yaml b/example/docker-compose.yaml deleted file mode 100644 index 1513590..0000000 --- a/example/docker-compose.yaml +++ /dev/null @@ -1,34 +0,0 @@ -version: '3.1' -services: - backend: - build: . - command: ["pipenv", "run", "gunicorn", "main:create_app", "--worker-class", "aiohttp.worker.GunicornWebWorker", "-b", "0.0.0.0:8081", "--reload"] - depends_on: - - devbox - links: - - devbox - env_file: - - .env - volumes: - - ./:/app:cached - - ./config:/var/config:cached - # Colored logs - tty: true - devbox: - image: "healthsamurai/aidboxone:stable" - depends_on: - - devbox-db - links: - - "devbox-db:database" - ports: - - "8080:8080" - env_file: - - .env - volumes: - - ./config:/var/config:cached - devbox-db: - image: "healthsamurai/aidboxdb:14.5" - environment: - POSTGRES_USER: postgres - POSTGRES_PASSWORD: postgres - POSTGRES_DB: devbox diff --git a/example/env_tests b/example/env_tests deleted file mode 100644 index 19c9d99..0000000 --- a/example/env_tests +++ /dev/null @@ -1,22 +0,0 @@ -AIDBOX_CLIENT_ID=root -AIDBOX_CLIENT_SECRET=secret -AIDBOX_BASE_URL=http://devbox:8080 -AIDBOX_PORT=8080 -AIDBOX_FHIR_VERSION=4.0.0 -APP_INIT_CLIENT_ID=root -APP_INIT_CLIENT_SECRET=secret -APP_INIT_URL=http://devbox:8080 -APP_SUPERADMIN_PASSWORD=password -APP_SUPERADMIN_EMAIL=superadmin@example.com -APP_ID=app-example-test -APP_SECRET=secret -APP_URL=http://backend:8081 -APP_PORT=8081 -AIO_PORT=8081 -AIO_HOST=0.0.0.0 -AIO_APP_PATH=. -PGHOST=database -PGDATABASE=devbox -PGPORT=5432 -PGUSER=postgres -PGPASSWORD=postgres diff --git a/example/env_tests/aidbox b/example/env_tests/aidbox new file mode 100644 index 0000000..cd7c3b3 --- /dev/null +++ b/example/env_tests/aidbox @@ -0,0 +1,17 @@ +AIDBOX_STDOUT_PRETTY=all +AIDBOX_CLIENT_ID=root +AIDBOX_CLIENT_SECRET=secret +AIDBOX_BASE_URL=http://aidbox:8080 +AIDBOX_PORT=8080 +AIDBOX_FHIR_VERSION=4.0.0 + +PGHOST=aidbox-db +PGPORT=5432 +PGDATABASE=aidbox-tests +PGUSER=postgres +PGPASSWORD=postgres + +BOX_PROJECT_GIT_TARGET__PATH=/aidbox-project +AIDBOX_ZEN_ENTRYPOINT=main/box +AIDBOX_DEV_MODE=true +AIDBOX_ZEN_DEV_MODE=true \ No newline at end of file diff --git a/example/env_tests/app b/example/env_tests/app new file mode 100644 index 0000000..551ef0d --- /dev/null +++ b/example/env_tests/app @@ -0,0 +1,10 @@ +APP_INIT_CLIENT_ID=root +APP_INIT_CLIENT_SECRET=secret +APP_INIT_URL=http://aidbox:8080 + +APP_ID=aidbox-python-sdk-tests +APP_SECRET=secret +APP_URL=http://app:8081 +APP_PORT=8081 +AIO_PORT=8081 +AIO_HOST=0.0.0.0 \ No newline at end of file diff --git a/example/env_tests/db b/example/env_tests/db new file mode 100644 index 0000000..24b18d5 --- /dev/null +++ b/example/env_tests/db @@ -0,0 +1,3 @@ +POSTGRES_USER=postgres +POSTGRES_PASSWORD=postgres +POSTGRES_DB=aidbox-tests \ No newline at end of file diff --git a/example/main.py b/example/main.py index 7771964..2e5173f 100644 --- a/example/main.py +++ b/example/main.py @@ -1,36 +1,68 @@ import logging -import coloredlogs -from asyncio import get_event_loop +from collections.abc import AsyncGenerator -import sentry_sdk -from sentry_sdk.integrations.logging import LoggingIntegration -from sentry_sdk.integrations.aiohttp import AioHttpIntegration -from aidbox_python_sdk.main import create_app as _create_app +from aidbox_python_sdk.main import init_client, register_app, setup_routes +from aidbox_python_sdk.settings import Settings +from aiohttp import BasicAuth, ClientSession, web +from fhirpy import AsyncFHIRClient -# Don't remove these imports -from app.sdk import sdk_settings, sdk -import app.subscriptions +from app import app_keys as ak +from app import config, operations # noqa: F401 +from app.sdk import sdk - - -coloredlogs.install( - level="DEBUG", fmt="%(asctime)s - %(name)s - %(levelname)s - %(message)s" -) logging.basicConfig( - format="%(asctime)s - %(name)s - %(levelname)s - %(message)s", level=logging.DEBUG + format="%(asctime)s - %(name)s - %(levelname)s - %(message)s", level=logging.INFO ) -logging.getLogger("aidbox_sdk").setLevel(logging.INFO) -logging.getLogger("urllib3").setLevel(logging.INFO) -sentry_logging = LoggingIntegration( - level=logging.DEBUG, # Capture info and above as breadcrumbs - event_level=logging.WARNING, # Send warnings as events -) -sentry_sdk.init(integrations=[AioHttpIntegration(), sentry_logging]) +async def init_fhir_client(settings: Settings, prefix: str = "") -> AsyncFHIRClient: + basic_auth = BasicAuth( + login=settings.APP_INIT_CLIENT_ID, + password=settings.APP_INIT_CLIENT_SECRET, + ) + + return AsyncFHIRClient( + f"{settings.APP_INIT_URL}{prefix}", + authorization=basic_auth.encode(), + dump_resource=lambda x: x.model_dump(), + ) + + +async def fhir_client_ctx(app: web.Application) -> AsyncGenerator[None, None]: + app[ak.fhir_client] = await init_fhir_client(app[ak.settings], "/fhir") + yield + + +async def client_ctx(app: web.Application) -> AsyncGenerator[None, None]: + app[ak.client] = await init_client(app[ak.settings]) + yield + + +async def app_ctx(app: web.Application) -> AsyncGenerator[None, None]: + await register_app(app[ak.sdk], app[ak.client]) + yield + + +async def client_session_ctx(app: web.Application) -> AsyncGenerator[None, None]: + session = ClientSession() + app[ak.session] = session + yield + await session.close() + + +def create_app() -> web.Application: + app = web.Application() + app[ak.sdk] = sdk + app[ak.settings] = sdk.settings + app.cleanup_ctx.append(client_session_ctx) + app.cleanup_ctx.append(client_ctx) + app.cleanup_ctx.append(fhir_client_ctx) + 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"poetry.core.masonry.api" + [tool.black] +target-version = ["py312"] line-length = 100 -target-version = ['py38'] -exclude = ''' -( - /( - | \.git - | \.pytest_cache - | htmlcov - | locales - | resources - | requirements - | embed - )/ -) -''' - -[tool.isort] -multi_line_output = 3 -include_trailing_comma = true -use_parentheses = true -line_length = 100 -default_section = "THIRDPARTY" -known_first_party = ["app"] + +[tool.ruff] +target-version = "py312" +line-length = 100 +extend-exclude = ["emded"] + +[tool.ruff.lint] +select = ["I", "E", "F", "N", "B", "C4", "PT", "UP", "I001", "A", "RET", "TID251", "RUF", "SIM", "PYI", "T20", "PIE", "G", "ISC", "PL", "ANN"] +# E501 is disabled because line limit is controlled by black +# RUF015 is disabled because index access is preferred way for us +# PIE804 is disabled because we often use FHIR like camelCase variables +# SIM102 is disabled because nested if's are more readable +# SIM117 is disabled because nested with's are more readable +ignore = ["E501", "RUF006", "RUF015", "PIE804", "SIM102", "SIM117"] +unfixable = ["F401"] [tool.autohooks] -mode = "pythonpath" -pre-commit = ["autohooks.plugins.black", "autohooks.plugins.isort"] +mode = "poetry" +pre-commit = ["autohooks.plugins.mypy", "autohooks.plugins.ruff", "autohooks.plugins.black"] [tool.pytest.ini_options] -minversion = "6.0" -addopts = "-ra -q --color=yes --junitxml=report.xml --cov-report html --cov-report term:skip-covered --doctest-modules" -testpaths = ["tests"] +minversion = "8.0" +addopts = "-ra --color=yes --cov app --cov-report xml:coverage.xml --cov-report term --cov-report html --junitxml=report.xml" +testpaths = [ + "tests" +] +asyncio_mode = "auto" log_cli = true -log_cli_level = "INFO" -norecursedirs = "embed" \ No newline at end of file +log_cli_level = "WARNING" + +[tool.mypy] +exclude = [ + ".history", + "embed" +] +files = ["app", "tests"] +ignore_missing_imports = true +check_untyped_defs = true +plugins = ["pydantic.mypy"] + +[tool.pydantic-mypy] +init_typed = true diff --git a/example/resources/entities/.gitkeep b/example/resources/entities/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/example/resources/migrations/.gitkeep b/example/resources/migrations/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/example/resources/notificationtemplates/email/email-example.html b/example/resources/notificationtemplates/email/email-example.html deleted file mode 100644 index 8aa9869..0000000 --- a/example/resources/notificationtemplates/email/email-example.html +++ /dev/null @@ -1,9 +0,0 @@ - -{% block subject %} -Subject -{% endblock %} - -{% block body %} -Body -{% endblock %} - diff --git a/example/resources/notificationtemplates/email/email-layout.html b/example/resources/notificationtemplates/email/email-layout.html deleted file mode 100644 index 5326c01..0000000 --- a/example/resources/notificationtemplates/email/email-layout.html +++ /dev/null @@ -1,8 +0,0 @@ - - - -
- {{ body }} -
- diff --git a/example/resources/seeds/.gitkeep b/example/resources/seeds/.gitkeep deleted file mode 100644 index e69de29..0000000 diff --git a/example/run_test.sh b/example/run_test.sh index d275e28..579cb59 100755 --- a/example/run_test.sh +++ b/example/run_test.sh @@ -1,14 +1,16 @@ #!/bin/sh -if [ -f ".env" ]; then - export `cat .env` +if [ -f ".env.tests.local" ]; then + export `cat .env.tests.local` fi -if [ -z "${TESTS_AIDBOX_LICENSE}" ]; then - echo "TESTS_AIDBOX_LICENSE is required to run tests" +if [ -z "${AIDBOX_LICENSE_TEST}" ]; then + echo "AIDBOX_LICENSE_TEST is required to run tests" exit 1 fi -export TEST_COMMAND="pipenv run pytest --cov app ${@:-tests/}" -docker compose -f docker-compose.tests.yaml up --exit-code-from backend backend + +docker compose -f compose.test-env.yaml pull --quiet +docker compose -f compose.test-env.yaml up --exit-code-from app app + exit $? diff --git a/example/app/utils.py b/example/tests/__init__.py similarity index 100% rename from example/app/utils.py rename to example/tests/__init__.py diff --git a/example/tests/conftest.py b/example/tests/conftest.py index 8548ce0..95071a8 100644 --- a/example/tests/conftest.py +++ b/example/tests/conftest.py @@ -1,8 +1,21 @@ +from typing import Protocol + import pytest +from aiohttp import web +from aiohttp.test_utils import TestClient +from fhirpy import AsyncFHIRClient + +from app import app_keys as ak + +pytest_plugins = ["aidbox_python_sdk.pytest_plugin"] + + +class SafeDBFixture(Protocol): + pass -pytest_plugins = ["aidbox_python_sdk.pytest_plugin", "pytester"] +@pytest.fixture() +def fhir_client(client: TestClient) -> AsyncFHIRClient: + app: web.Application = client.server.app # type: ignore -@pytest.fixture(scope="session") -def sdk(client): - return client.server.app["sdk"] + return app[ak.fhir_client] diff --git a/example/tests/test_base.py b/example/tests/test_base.py deleted file mode 100644 index 3f07b67..0000000 --- a/example/tests/test_base.py +++ /dev/null @@ -1,45 +0,0 @@ -# The next 4 tests check that the system works correctly -# Both client and aidbox available via HTTP on runtime -# Each save_db transaction separated from other -# Please keep all this test and don't remove them -# If any of this test fails that mean -# that system is in the inconsistent state and all tests become flaky - - -async def test_health_check(client): - resp = await client.get("/health") - assert resp.status == 200 - json = await resp.json() - assert json == {"status": "OK"} - - -async def test_live_health_check(client): - resp = await client.get("/live") - assert resp.status == 200 - json = await resp.json() - assert json == {"status": "OK"} - - -async def test_database_isolation__1(sdk, safe_db): - patients = await sdk.client.resources("Patient").fetch_all() - assert len(patients) == 0 - - patient = sdk.client.resource("Patient") - await patient.save() - - patients = await sdk.client.resources("Patient").fetch_all() - assert len(patients) == 1 - - -async def test_database_isolation__2(sdk, safe_db): - patients = await sdk.client.resources("Patient").fetch_all() - assert len(patients) == 0 - - patient = sdk.client.resource("Patient") - await patient.save() - - patient = sdk.client.resource("Patient") - await patient.save() - - patients = await sdk.client.resources("Patient").fetch_all() - assert len(patients) == 2 diff --git a/example/tests/test_db_isolation.py b/example/tests/test_db_isolation.py new file mode 100644 index 0000000..5f49628 --- /dev/null +++ b/example/tests/test_db_isolation.py @@ -0,0 +1,25 @@ +import fhirpy_types_r4b as r4b +from fhirpy import AsyncFHIRClient + +from tests.conftest import SafeDBFixture + + +async def test_database_isolation__1(fhir_client: AsyncFHIRClient, safe_db: SafeDBFixture) -> None: + patients = await fhir_client.resources(r4b.Patient).fetch_all() + assert len(patients) == 0 + + await fhir_client.create(r4b.Patient()) + + patients = await fhir_client.resources(r4b.Patient).fetch_all() + assert len(patients) == 1 + + +async def test_database_isolation__2(fhir_client: AsyncFHIRClient, safe_db: SafeDBFixture) -> None: + patients = await fhir_client.resources(r4b.Patient).fetch_all() + assert len(patients) == 0 + + await fhir_client.create(r4b.Patient()) + await fhir_client.create(r4b.Patient()) + + patients = await fhir_client.resources(r4b.Patient).fetch_all() + assert len(patients) == 2 # noqa: PLR2004 diff --git a/example/tests/test_example.py b/example/tests/test_example.py new file mode 100644 index 0000000..3fb2900 --- /dev/null +++ b/example/tests/test_example.py @@ -0,0 +1,10 @@ +from aidbox_python_sdk.aidboxpy import AsyncAidboxClient + +from tests.conftest import SafeDBFixture + + +async def test_example(safe_db: SafeDBFixture, aidbox_client: AsyncAidboxClient) -> None: + example_output = await aidbox_client.execute("$example", method="POST") + + assert example_output["status"] == "ok" + assert example_output["patient"]["id"] == "example" diff --git a/example/tests/test_timeout.py b/example/tests/test_timeout.py deleted file mode 100644 index 102b1ff..0000000 --- a/example/tests/test_timeout.py +++ /dev/null @@ -1,21 +0,0 @@ -import logging -import asyncio -import pytest - -import fhirpy - - -async def test_default_timout_works(sdk, safe_db): - response = await sdk.client.execute("$default-timeout", "GET") - assert response == {"result": "success"} - - -async def test_sleep_operation_fails(sdk, safe_db): - with pytest.raises(fhirpy.base.exceptions.OperationOutcome) as timeout_exc: - await sdk.client.execute("$sleep/2500", "GET") - assert "idle timeout" in str(timeout_exc) - - -async def test_sleep_operation_succeeds(sdk, safe_db): - response = await sdk.client.execute("$sleep/1", "GET") - assert response == {"result": "success"} diff --git a/example/tests_zen_project/zen-package.edn b/example/tests_zen_project/zen-package.edn new file mode 100644 index 0000000..5aeab72 --- /dev/null +++ b/example/tests_zen_project/zen-package.edn @@ -0,0 +1 @@ +{:deps {}} diff --git a/example/tests_zen_project/zrc/main.edn b/example/tests_zen_project/zrc/main.edn new file mode 100644 index 0000000..cafe36b --- /dev/null +++ b/example/tests_zen_project/zrc/main.edn @@ -0,0 +1,5 @@ +{ns main + import #{aidbox + hl7-fhir-r4-core} + box + {:zen/tags #{aidbox/system}}} diff --git a/example/update-commit-hash.sh b/example/update-commit-hash.sh new file mode 100755 index 0000000..9b19280 --- /dev/null +++ b/example/update-commit-hash.sh @@ -0,0 +1,7 @@ +#!/bin/sh +# NOTE: This file is run before build! Never run it locally! + +BUILD_COMMIT_HASH=$CI_COMMIT_SHORT_SHA + +# Shared +sed -i -e "s/__build_commit_hash__ = .*/__build_commit_hash__ = '$BUILD_COMMIT_HASH'/g" app/version.py \ No newline at end of file diff --git a/example/update-version.sh b/example/update-version.sh new file mode 100755 index 0000000..1156e66 --- /dev/null +++ b/example/update-version.sh @@ -0,0 +1,7 @@ +#!/bin/sh +# NOTE: This file is run before build! Never run it locally! + +VERSION=$1 + +# Shared +sed -i -e "s/__version__ = .*/__version__ = '$VERSION'/g" app/version.py