diff --git a/api/.flake8 b/.flake8 similarity index 100% rename from api/.flake8 rename to .flake8 diff --git a/.github/workflows/api.yaml b/.github/workflows/api.yaml index 56c67b0..4126086 100644 --- a/.github/workflows/api.yaml +++ b/.github/workflows/api.yaml @@ -4,7 +4,7 @@ on: push: paths: - ".github/workflows/api*" - - "api/**/*" + - "./**/*" jobs: lint: @@ -21,14 +21,12 @@ jobs: - name: Set up dependencies run: | - cd api/ pip install -U pip poetry poetry config virtualenvs.create false poetry install --with dev - name: Run linters run: | - cd api/ task lint tests: @@ -56,20 +54,17 @@ jobs: - name: Set up dependencies run: | - cd api/ pip install -U pip poetry poetry config virtualenvs.create false poetry install --with dev - name: Set up database run: | - cd api/ aerich init-db || true aerich upgrade || true - name: Run tests run: | - cd api/ task test deploy: @@ -109,8 +104,8 @@ jobs: - name: Build and push image uses: docker/build-push-action@v2 with: - context: api/ - file: api/Dockerfile + context: . + file: ./Dockerfile push: true tags: | us-central1-docker.pkg.dev/rj-sms/docker/prontuario-integrado:${{ github.sha }} diff --git a/.github/workflows/lib-docs.yaml b/.github/workflows/lib-docs.yaml deleted file mode 100644 index 753b60a..0000000 --- a/.github/workflows/lib-docs.yaml +++ /dev/null @@ -1,42 +0,0 @@ -name: Lib - Docs - -on: - push: - branches: - - main - paths: - - ".github/workflows/lib-*" - - "lib/**/*" - -jobs: - docs: - name: Deploy docs - runs-on: ubuntu-latest - steps: - - name: Checkout - uses: actions/checkout@v2 - - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: "3.10.x" - - - name: Upgrade pip - run: | - pip install -U pip poetry - - - name: Install package and doc dependencies - run: | - cd lib/ - poetry install - - - name: Generate docs - run: | - cd lib/ - poetry run docs - - - name: Deploy docs - uses: JamesIves/github-pages-deploy-action@v4.2.3 - with: - branch: gh-pages - folder: lib/docs/fhir_utils diff --git a/.github/workflows/lib-lint.yaml b/.github/workflows/lib-lint.yaml deleted file mode 100644 index db02a5c..0000000 --- a/.github/workflows/lib-lint.yaml +++ /dev/null @@ -1,41 +0,0 @@ -name: Lib - Lint - -on: - push: - paths: - - ".github/workflows/lib-*" - - "lib/**/*" - -jobs: - lint: - name: ${{ matrix.os }}${{ matrix.arch }} - Python ${{ matrix.python-version }} - lint - runs-on: ${{ matrix.os }} - strategy: - matrix: - os: [ubuntu-latest] - arch: [x64] - python-version: ["3.10.x"] - steps: - - name: Checkout - uses: actions/checkout@v2 - - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - architecture: ${{ matrix.arch }} - - - name: Set up Poetry and upgrade pip - run: | - cd lib/ - pip install -U pip poetry - - - name: Install this package - run: | - cd lib/ - poetry install - - - name: Run tests - run: | - cd lib/ - poetry run lint diff --git a/.github/workflows/lib-tests.yaml b/.github/workflows/lib-tests.yaml deleted file mode 100644 index 74e5efa..0000000 --- a/.github/workflows/lib-tests.yaml +++ /dev/null @@ -1,41 +0,0 @@ -name: Lib - Tests - -on: - push: - paths: - - ".github/workflows/lib-*" - - "lib/**/*" - -jobs: - tests: - name: ${{ matrix.os }}${{ matrix.arch }} - Python ${{ matrix.python-version }} - tests - runs-on: ${{ matrix.os }} - strategy: - matrix: - os: [ubuntu-latest] - arch: [x64] - python-version: ["3.10.x"] - steps: - - name: Checkout - uses: actions/checkout@v2 - - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - architecture: ${{ matrix.arch }} - - - name: Set up Poetry and upgrade pip - run: | - cd lib/ - pip install -U pip poetry - - - name: Install this package - run: | - cd lib/ - poetry install - - - name: Run tests - run: | - cd lib/ - poetry run test diff --git a/.gitignore b/.gitignore index 6e0981f..6159340 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,135 @@ -.vscode/launch.json -.env +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +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/ + +# 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 +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.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/ + +# VSCode project settings +.vscode/ + +# Generated API keys +api-key*.txt \ No newline at end of file diff --git a/api/.kubernetes.yaml b/.kubernetes.yaml similarity index 100% rename from api/.kubernetes.yaml rename to .kubernetes.yaml diff --git a/api/Dockerfile b/Dockerfile similarity index 100% rename from api/Dockerfile rename to Dockerfile diff --git a/api/.gitignore b/api/.gitignore deleted file mode 100644 index 6159340..0000000 --- a/api/.gitignore +++ /dev/null @@ -1,135 +0,0 @@ -# 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/ -pip-wheel-metadata/ -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/ - -# 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 -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# IPython -profile_default/ -ipython_config.py - -# pyenv -.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/ - -# VSCode project settings -.vscode/ - -# Generated API keys -api-key*.txt \ No newline at end of file diff --git a/api/app/__init__.py b/app/__init__.py similarity index 100% rename from api/app/__init__.py rename to app/__init__.py diff --git a/api/app/config/__init__.py b/app/config/__init__.py similarity index 100% rename from api/app/config/__init__.py rename to app/config/__init__.py diff --git a/api/app/config/base.py b/app/config/base.py similarity index 100% rename from api/app/config/base.py rename to app/config/base.py diff --git a/api/app/config/dev.py b/app/config/dev.py similarity index 100% rename from api/app/config/dev.py rename to app/config/dev.py diff --git a/api/app/config/prod.py b/app/config/prod.py similarity index 100% rename from api/app/config/prod.py rename to app/config/prod.py diff --git a/api/app/datalake/__init__.py b/app/datalake/__init__.py similarity index 100% rename from api/app/datalake/__init__.py rename to app/datalake/__init__.py diff --git a/api/app/datalake/formatters.py b/app/datalake/formatters.py similarity index 100% rename from api/app/datalake/formatters.py rename to app/datalake/formatters.py diff --git a/api/app/datalake/models.py b/app/datalake/models.py similarity index 100% rename from api/app/datalake/models.py rename to app/datalake/models.py diff --git a/api/app/datalake/uploader.py b/app/datalake/uploader.py similarity index 100% rename from api/app/datalake/uploader.py rename to app/datalake/uploader.py diff --git a/api/app/datalake/utils.py b/app/datalake/utils.py similarity index 100% rename from api/app/datalake/utils.py rename to app/datalake/utils.py diff --git a/api/app/db.py b/app/db.py similarity index 100% rename from api/app/db.py rename to app/db.py diff --git a/api/app/dependencies.py b/app/dependencies.py similarity index 100% rename from api/app/dependencies.py rename to app/dependencies.py diff --git a/api/app/enums.py b/app/enums.py similarity index 100% rename from api/app/enums.py rename to app/enums.py diff --git a/api/app/main.py b/app/main.py similarity index 100% rename from api/app/main.py rename to app/main.py diff --git a/api/app/models.py b/app/models.py similarity index 100% rename from api/app/models.py rename to app/models.py diff --git a/api/app/pydantic_models.py b/app/pydantic_models.py similarity index 100% rename from api/app/pydantic_models.py rename to app/pydantic_models.py diff --git a/api/app/routers/__init__.py b/app/routers/__init__.py similarity index 100% rename from api/app/routers/__init__.py rename to app/routers/__init__.py diff --git a/api/app/routers/auth.py b/app/routers/auth.py similarity index 100% rename from api/app/routers/auth.py rename to app/routers/auth.py diff --git a/api/app/routers/entities.py b/app/routers/entities.py similarity index 100% rename from api/app/routers/entities.py rename to app/routers/entities.py diff --git a/api/app/routers/entities_mrg.py b/app/routers/entities_mrg.py similarity index 100% rename from api/app/routers/entities_mrg.py rename to app/routers/entities_mrg.py diff --git a/api/app/routers/entities_raw.py b/app/routers/entities_raw.py similarity index 100% rename from api/app/routers/entities_raw.py rename to app/routers/entities_raw.py diff --git a/api/app/routers/entities_std.py b/app/routers/entities_std.py similarity index 100% rename from api/app/routers/entities_std.py rename to app/routers/entities_std.py diff --git a/api/app/utils.py b/app/utils.py similarity index 100% rename from api/app/utils.py rename to app/utils.py diff --git a/api/app/validators.py b/app/validators.py similarity index 100% rename from api/app/validators.py rename to app/validators.py diff --git a/api/compose-entrypoint.sh b/compose-entrypoint.sh old mode 100755 new mode 100644 similarity index 100% rename from api/compose-entrypoint.sh rename to compose-entrypoint.sh diff --git a/api/data/city.csv b/data/city.csv similarity index 100% rename from api/data/city.csv rename to data/city.csv diff --git a/api/data/conditioncode.csv b/data/conditioncode.csv similarity index 100% rename from api/data/conditioncode.csv rename to data/conditioncode.csv diff --git a/api/data/country.csv b/data/country.csv similarity index 100% rename from api/data/country.csv rename to data/country.csv diff --git a/api/data/datasource.csv b/data/datasource.csv similarity index 100% rename from api/data/datasource.csv rename to data/datasource.csv diff --git a/api/data/gender.csv b/data/gender.csv similarity index 100% rename from api/data/gender.csv rename to data/gender.csv diff --git a/api/data/meta.json b/data/meta.json similarity index 100% rename from api/data/meta.json rename to data/meta.json diff --git a/api/data/nationality.csv b/data/nationality.csv similarity index 100% rename from api/data/nationality.csv rename to data/nationality.csv diff --git a/api/data/ocupacao_cbo.csv b/data/ocupacao_cbo.csv similarity index 100% rename from api/data/ocupacao_cbo.csv rename to data/ocupacao_cbo.csv diff --git a/api/data/ocupacao_familias.csv b/data/ocupacao_familias.csv similarity index 100% rename from api/data/ocupacao_familias.csv rename to data/ocupacao_familias.csv diff --git a/api/data/race.csv b/data/race.csv similarity index 100% rename from api/data/race.csv rename to data/race.csv diff --git a/api/data/state.csv b/data/state.csv similarity index 100% rename from api/data/state.csv rename to data/state.csv diff --git a/api/docker-compose.yaml b/docker-compose.yaml similarity index 100% rename from api/docker-compose.yaml rename to docker-compose.yaml diff --git a/api/kustomization.yaml b/kustomization.yaml similarity index 100% rename from api/kustomization.yaml rename to kustomization.yaml diff --git a/lib/.flake8 b/lib/.flake8 deleted file mode 100644 index 7da1f96..0000000 --- a/lib/.flake8 +++ /dev/null @@ -1,2 +0,0 @@ -[flake8] -max-line-length = 100 diff --git a/lib/.gitignore b/lib/.gitignore deleted file mode 100644 index f7c807f..0000000 --- a/lib/.gitignore +++ /dev/null @@ -1,132 +0,0 @@ -# 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/ -pip-wheel-metadata/ -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/ - -# 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 -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# IPython -profile_default/ -ipython_config.py - -# pyenv -.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/ - -# VS Code -.vscode/ \ No newline at end of file diff --git a/lib/README.md b/lib/README.md deleted file mode 100644 index 84b81ff..0000000 --- a/lib/README.md +++ /dev/null @@ -1,18 +0,0 @@ -# FHIR utilities - -This repository contains a set of utilities for working with FHIR resources. - -## Installation - -```bash -pip install fhir-utils -``` - -## Development - -```bash -git clone https://github.com/prefeitura-rio/fhir-utils -cd fhir-utils -poetry install -pre-commit install -``` diff --git a/lib/fhir_utils/__init__.py b/lib/fhir_utils/__init__.py deleted file mode 100644 index 4286211..0000000 --- a/lib/fhir_utils/__init__.py +++ /dev/null @@ -1,4 +0,0 @@ -# -*- coding: utf-8 -*- -from .conf import settings # noqa -from .version import __version__ # noqa -from fhir_utils.healthcare_api import HealthcareApi \ No newline at end of file diff --git a/lib/fhir_utils/conf.py b/lib/fhir_utils/conf.py deleted file mode 100644 index b59b552..0000000 --- a/lib/fhir_utils/conf.py +++ /dev/null @@ -1,64 +0,0 @@ -# -*- coding: utf-8 -*- -from os import getenv -from typing import Callable, Union - -from loguru import logger - - -def getenv_or_action( - key: str, action: Union[Callable[[str], str], str], default: str = None -) -> str: - """ - Get an environment variable or execute an action. - - Args: - key (str): The name of the environment variable. - action (Union[Callable[[str], str], str]): The action to execute if the - environment variable is not set. Can be a callable or a string. If a - callable is provided, it will be called with the key as the only - argument. If a string is provided, it will check if this callback - is implemented here and call it. If not, it will raise an exception. - default (str, optional): The default value to return if the environment - variable is not set and no action is provided. Defaults to None. - - Returns: - str: The value of the environment variable or the result of the action. - """ - - def _raise(key: str) -> str: - raise Exception( - f"Environment variable {key} is not set and no action is provided." - ) - - def _warn(key: str) -> str: - logger.warning(f"Environment variable {key} is not set. Using default value.") - return default - - def _pass(key: str) -> str: - return default - - _val = getenv(key) - if _val is None: - if action in [None, "pass"]: - return _pass(key) - elif callable(action): - return action(key) - elif isinstance(action, str): - if action == "raise": - return _raise(key) - elif action == "warn": - return _warn(key) - else: - raise ValueError( - f'Action "{action}" is not implemented in getenv_or_action.' - ) - else: - return default - return _val - - -class Settings: - __slots__ = () - - -settings = Settings() diff --git a/lib/fhir_utils/healthcare_api.py b/lib/fhir_utils/healthcare_api.py deleted file mode 100644 index 5b42cb5..0000000 --- a/lib/fhir_utils/healthcare_api.py +++ /dev/null @@ -1,180 +0,0 @@ -# -*- coding: utf-8 -*- -from google.auth.transport import requests -from google.oauth2 import service_account -import os - - -class HealthcareApi: - """ - This class provides the basic methods for interacting with FHIR resources in the Google Healthcare API. - Reference: - https://cloud.google.com/healthcare-api/docs/reference/rest - """ - - def __init__(self, project_id, location): - self.credentials = service_account.Credentials.from_service_account_file(os.environ["GOOGLE_APPLICATION_CREDENTIALS"]) - self.scoped_credentials = self.credentials.with_scopes(["https://www.googleapis.com/auth/cloud-platform"]) - self.session = requests.AuthorizedSession(self.scoped_credentials) - self.project_id = project_id - self.location = location - self.base_url = "https://healthcare.googleapis.com/v1" - self.url = (f"{self.base_url}/projects/{self.project_id}/locations/{self.location}") - self.header = {"Content-Type": "application/fhir+json;charset=utf-8"} - - def create( - self, - dataset_id: str, - fhir_store_id: str, - resource: str, - payload: dict - ) -> dict: - """Create a new resource in the FHIR store""" - resource_path = f"{self.url}/datasets/{dataset_id}/fhirStores/{fhir_store_id}/fhir/{resource}" - - response = self.session.post(resource_path, headers=self.header, json=payload) - - return {"status_code": response.status_code, "body": response.json()} - - def update( - self, - dataset_id: str, - fhir_store_id: str, - resource: str, - resource_id: str, - payload: dict, - ) -> dict: - """Update an existing resource in the FHIR store""" - resource_path = f"{self.url}/datasets/{dataset_id}/fhirStores/{fhir_store_id}/fhir/{resource}/{resource_id}" - - response = self.session.put(resource_path, headers=self.header, json=payload) - - return {"status_code": response.status_code, "body": response.json()} - - def update_conditional( - self, - dataset_id: str, - fhir_store_id: str, - resource: str, - condition: str, - payload: dict, - ) -> dict: - """ - If a resource is found based on the search criteria specified in the query parameters, - updates the entire contents of that resource. - If the search criteria identify zero matches, and the supplied resource body contains an id, - and the FHIR store has enableUpdateCreate set, creates the resource with the client-specified ID. - If the search criteria identify zero matches, and the supplied resource body does not contain an id, - the resource is created with a server-assigned ID as per the create method. - - Feature only available in beta endpoint. - See: - https://cloud.google.com/healthcare-api/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/conditionalUpdate - - Response code: - 200 Success - Updated or created successfully - 412 Precondition Failed - If the search criteria identify more than one match - - """ - - base_url_beta = "https://healthcare.googleapis.com/v1beta1" - url_beta = f"{base_url_beta}/projects/{self.project_id}/locations/{self.location}" - - resource_path = f"{url_beta}/datasets/{dataset_id}/fhirStores/{fhir_store_id}/fhir/{resource}" - resource_path += f"?{condition}" - - response = self.session.put(resource_path, headers=self.header, json=payload) - - return {"status_code": response.status_code, "body": response.json()} - - def read( - self, - dataset_id: str, - fhir_store_id: str, - resource: str, - resource_id: str - ) -> dict: - """Read the contents of a specific resource in the FHIR store""" - resource_path = f"{self.url}/datasets/{dataset_id}/fhirStores/{fhir_store_id}/fhir/{resource}/{resource_id}" - - response = self.session.get(resource_path, headers=self.header) - - return {"status_code": response.status_code, "body": response.json()} - - def read_conditional( - self, - dataset_id: str, - fhir_store_id: str, - resource: str, - condition: str - ) -> dict: - """ - If a resource is found based on the search criteria specified in the query parameters, - read the entire contents of that resource. - """ - resource_path = f"{self.url}/datasets/{dataset_id}/fhirStores/{fhir_store_id}/fhir/{resource}" - resource_path += f"?{condition}" - - response = self.session.get(resource_path, headers=self.header) - - return {"status_code": response.status_code, "body": response.json()} - - def delete( - self, - dataset_id: str, - fhir_store_id: str, - resource: str, - resource_id: str - ) -> dict: - """ - Delete a resource from the FHIR store - - Response code: - 200 Success - If the resource was deleted or not found - """ - resource_path = f"{self.url}/datasets/{dataset_id}/fhirStores/{fhir_store_id}/fhir/{resource}/{resource_id}" - - response = self.session.delete(resource_path, headers=self.header) - - return {"status_code": response.status_code, "body": response.json()} - - -class FastCRUD(HealthcareApi): - """The FastCRUD class is a subclass of HealthcareApi that provides additional convenience methods for most common CRUD actions.""" - - def __init__(self, project_id, location): - super().__init__(project_id, location) - - def resource_search_lastupdated( - self, - dataset_id: str, - fhir_store_id: str, - resource: str, - since: str - ) -> dict: - """Read the entries from a resource in the FHIR store that were last updated after a specific date and time""" - parameter = f"_lastUpdated=gt{since}" - return self.read_conditional(dataset_id, fhir_store_id, resource, parameter) - - def patient_search( - self, - dataset_id: str, - fhir_store_id: str, - cpf: str - ) -> dict: - """Read the entries from Patient resource in the FHIR store based on tax id (CPF)""" - parameter = f"identifier=https://rnds-fhir.saude.gov.br/NamingSystem/cpf|{cpf}" - return self.read_conditional(dataset_id, fhir_store_id, "Patient", parameter) - - def patient_update( - self, - dataset_id: str, - fhir_store_id: str, - cpf: str, - payload: dict - ) -> dict: - """Update the entries from Patient resource in the FHIR store based on tax id (CPF)""" - parameter = f"identifier=https://rnds-fhir.saude.gov.br/NamingSystem/cpf|{cpf}" - return self.update_conditional(dataset_id, fhir_store_id, "Patient", parameter, payload) diff --git a/lib/fhir_utils/utils.py b/lib/fhir_utils/utils.py deleted file mode 100644 index 661943c..0000000 --- a/lib/fhir_utils/utils.py +++ /dev/null @@ -1,33 +0,0 @@ -# -*- coding: utf-8 -*- -import json -import xmltodict - -def json_to_dict(json_file_path): - try: - with open(json_file_path, 'r') as file: - data = json.load(file) - return data - except FileNotFoundError: - print(f"File '{json_file_path}' not found.") - except json.JSONDecodeError: - print(f"Unable to parse JSON file: '{json_file_path}'.") - except Exception as e: - print(f"An error occurred while importing JSON: {e}") - - -def xml_to_dict(xml_file_path): - try: - with open(xml_file_path, 'r') as file: - xml_data = file.read() - return xmltodict.parse(xml_data) - except FileNotFoundError: - print(f"Error: XML file not found at '{xml_file_path}'") - return None - except Exception as e: - print(f"Error: Unable to parse XML file. Reason: {str(e)}") - return None - - -def save_to_json(dict, json_path,): - with open(json_path, "w") as file: - json.dump(dict, file) \ No newline at end of file diff --git a/lib/fhir_utils/version.py b/lib/fhir_utils/version.py deleted file mode 100644 index 2ad579c..0000000 --- a/lib/fhir_utils/version.py +++ /dev/null @@ -1,4 +0,0 @@ -# -*- coding: utf-8 -*- -import importlib.metadata - -__version__ = importlib.metadata.version("fhir_utils") diff --git a/lib/poetry.lock b/lib/poetry.lock deleted file mode 100644 index 283399a..0000000 --- a/lib/poetry.lock +++ /dev/null @@ -1,1042 +0,0 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. - -[[package]] -name = "black" -version = "24.4.2" -description = "The uncompromising code formatter." -optional = false -python-versions = ">=3.8" -files = [ - {file = "black-24.4.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:dd1b5a14e417189db4c7b64a6540f31730713d173f0b63e55fabd52d61d8fdce"}, - {file = "black-24.4.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8e537d281831ad0e71007dcdcbe50a71470b978c453fa41ce77186bbe0ed6021"}, - 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"^3.0.0" -flake8 = "^4.0.1" -pdoc3 = "^0.10.0" -mako = "^1.2.4" -markdown = "^3.4.3" - -[build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" diff --git a/lib/pytest.ini b/lib/pytest.ini deleted file mode 100644 index 77409e9..0000000 --- a/lib/pytest.ini +++ /dev/null @@ -1,9 +0,0 @@ -[pytest] -testpaths = - tests -norecursedirs=dist build .tox scripts -addopts = - --doctest-modules - --cov=fhir_utils - -r a - -v diff --git a/lib/scripts/__init__.py b/lib/scripts/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/lib/scripts/docs.py b/lib/scripts/docs.py deleted file mode 100644 index ce36515..0000000 --- a/lib/scripts/docs.py +++ /dev/null @@ -1,10 +0,0 @@ -# -*- coding: utf-8 -*- -import subprocess - - -def main(): - """ - Lint all python files in the project. - """ - command = "pdoc3 --html --html-dir docs fhir_utils" - subprocess.run(command, shell=True) diff --git a/lib/scripts/lint.py b/lib/scripts/lint.py deleted file mode 100644 index c3bf29f..0000000 --- a/lib/scripts/lint.py +++ /dev/null @@ -1,11 +0,0 @@ -# -*- coding: utf-8 -*- -from glob import glob -import subprocess - - -def main(): - """ - Lint all python files in the project. - """ - files = glob("**/*.py", recursive=True) - subprocess.run(["flake8", *files]) diff --git a/lib/scripts/test.py b/lib/scripts/test.py deleted file mode 100644 index b2203d0..0000000 --- a/lib/scripts/test.py +++ /dev/null @@ -1,6 +0,0 @@ -# -*- coding: utf-8 -*- -import pytest - - -def main(): - pytest.main([]) diff --git a/lib/tests/__init__.py b/lib/tests/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/lib/tests/test_sanity.py b/lib/tests/test_sanity.py deleted file mode 100644 index 7fcfa18..0000000 --- a/lib/tests/test_sanity.py +++ /dev/null @@ -1,3 +0,0 @@ -# -*- coding: utf-8 -*- -def test_sanity(): - assert True diff --git a/api/migrations/app/0_20240311091535_init.py b/migrations/app/0_20240311091535_init.py similarity index 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rename to migrations/app/20_20240708144217_update.py diff --git a/api/migrations/app/21_20240708152253_update.py b/migrations/app/21_20240708152253_update.py similarity index 100% rename from api/migrations/app/21_20240708152253_update.py rename to migrations/app/21_20240708152253_update.py diff --git a/api/migrations/app/22_20240709095718_update.py b/migrations/app/22_20240709095718_update.py similarity index 100% rename from api/migrations/app/22_20240709095718_update.py rename to migrations/app/22_20240709095718_update.py diff --git a/api/migrations/app/23_20240722102840_update.py b/migrations/app/23_20240722102840_update.py similarity index 100% rename from api/migrations/app/23_20240722102840_update.py rename to migrations/app/23_20240722102840_update.py diff --git a/api/migrations/app/2_20240401095822_update.py b/migrations/app/2_20240401095822_update.py similarity index 100% rename from api/migrations/app/2_20240401095822_update.py rename to 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