├── .gitignore ├── LICENSE ├── README.md ├── docker-compose.yml ├── img ├── hexagona_architecture_schemma.png └── send_file.png ├── samples ├── dummy.pdf └── sample_report.txt └── src ├── .dockerignore ├── .isort.cfg ├── Dockerfile ├── application ├── __init__.py ├── exceptions.py └── services │ ├── __init__.py │ ├── acquire_pdf_file.py │ └── anonymize_txt_file.py ├── controller ├── __init__.py ├── app.py ├── exceptions.py └── utils.py ├── domain ├── __init__.py ├── models │ ├── __init__.py │ └── report.py └── repositories │ ├── __init__.py │ └── report_repository_interface.py ├── infrastructure ├── __init__.py ├── database.py └── repositories │ ├── __init__.py │ ├── base_repository.py │ └── report_repository.py ├── lint.sh ├── requirements.txt └── test ├── __init__.py ├── application ├── __init__.py └── test_services.py ├── base_test_case.py ├── controller ├── __init__.py └── test_app.py └── infrastructure ├── __init__.py └── test_repositories.py /.gitignore: -------------------------------------------------------------------------------- 1 | 2 | # Created by https://www.toptal.com/developers/gitignore/api/python 3 | # Edit at https://www.toptal.com/developers/gitignore?templates=python 4 | 5 | ### Python ### 6 | # Byte-compiled / optimized / DLL files 7 | __pycache__/ 8 | *.py[cod] 9 | *$py.class 10 | 11 | # C extensions 12 | *.so 13 | 14 | # Distribution / packaging 15 | .Python 16 | build/ 17 | develop-eggs/ 18 | dist/ 19 | downloads/ 20 | eggs/ 21 | .eggs/ 22 | lib/ 23 | lib64/ 24 | parts/ 25 | sdist/ 26 | var/ 27 | wheels/ 28 | pip-wheel-metadata/ 29 | share/python-wheels/ 30 | *.egg-info/ 31 | .installed.cfg 32 | *.egg 33 | MANIFEST 34 | 35 | # PyInstaller 36 | # Usually these files are written by a python script from a template 37 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 38 | *.manifest 39 | *.spec 40 | 41 | # Installer logs 42 | pip-log.txt 43 | pip-delete-this-directory.txt 44 | 45 | # Unit test / coverage reports 46 | htmlcov/ 47 | .tox/ 48 | .nox/ 49 | .coverage 50 | .coverage.* 51 | .cache 52 | nosetests.xml 53 | coverage.xml 54 | *.cover 55 | *.py,cover 56 | .hypothesis/ 57 | .pytest_cache/ 58 | pytestdebug.log 59 | 60 | # Translations 61 | *.mo 62 | *.pot 63 | 64 | # Django stuff: 65 | *.log 66 | local_settings.py 67 | db.sqlite3 68 | db.sqlite3-journal 69 | 70 | # Flask stuff: 71 | instance/ 72 | .webassets-cache 73 | 74 | # Scrapy stuff: 75 | .scrapy 76 | 77 | # Sphinx documentation 78 | docs/_build/ 79 | doc/_build/ 80 | 81 | # PyBuilder 82 | target/ 83 | 84 | # Jupyter Notebook 85 | .ipynb_checkpoints 86 | 87 | # IPython 88 | profile_default/ 89 | ipython_config.py 90 | 91 | # pyenv 92 | .python-version 93 | 94 | # pipenv 95 | # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. 96 | # However, in case of collaboration, if having platform-specific dependencies or dependencies 97 | # having no cross-platform support, pipenv may install dependencies that don't work, or not 98 | # install all needed dependencies. 99 | #Pipfile.lock 100 | 101 | # PEP 582; used by e.g. github.com/David-OConnor/pyflow 102 | __pypackages__/ 103 | 104 | # Celery stuff 105 | celerybeat-schedule 106 | celerybeat.pid 107 | 108 | # SageMath parsed files 109 | *.sage.py 110 | 111 | # Environments 112 | .env 113 | .venv 114 | env/ 115 | venv/ 116 | ENV/ 117 | env.bak/ 118 | venv.bak/ 119 | pythonenv* 120 | 121 | # Spyder project settings 122 | .spyderproject 123 | .spyproject 124 | 125 | # Rope project settings 126 | .ropeproject 127 | 128 | # mkdocs documentation 129 | /site 130 | 131 | # mypy 132 | .mypy_cache/ 133 | .dmypy.json 134 | dmypy.json 135 | 136 | # Pyre type checker 137 | .pyre/ 138 | 139 | # pytype static type analyzer 140 | .pytype/ 141 | 142 | # profiling data 143 | .prof 144 | 145 | # End of https://www.toptal.com/developers/gitignore/api/python 146 | 147 | tmp/ 148 | 149 | # Editors 150 | *.sublime-workspace 151 | *.sublime-project 152 | .vscode 153 | .vscode/* 154 | .idea -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Python API example (SOLID & Hexagonal Arch.) 2 | 3 | 4 | ## Overview 5 | 6 | Example of an API built with Python3, followin Hexagonal architecture (*ports & adapters*) and SOLID principles. 7 | It uses some well known packages as Flask and SQLAlchemy. 8 | 9 | Available endpoints: 10 | 11 | - `/acquire/pdf` 12 | - input: PDF file, by `POST`, as *form-data*. Expected POST param name is: `file`. 13 | - output: JSON like `{"plain_text": "All plain text extracted from PDF file"}`. 14 | 15 | - `/anonymize/txt` 16 | - input: txt plain text file, by `POST`, as *form-data*. Expected POST param name is: `file`. See an example of file structure on [this sample file](samples/sample_report.txt). 17 | - output: JSON like `{"patient_id": "1234", "document_text": "She's in good health!"}`. 18 | 19 | 20 | 21 | ## Installation 22 | 23 | ### Requirements 24 | 25 | Install [docker](https://docs.docker.com/install/linux/docker-ce/ubuntu/), and [docker-compose](https://docs.docker.com/compose/install/). 26 | 27 | ### Setup 28 | 29 | Clone this repo and build Docker containers with docker-compose 30 | 31 | 32 | ``` 33 | git clone git@github.com:serfer2/flask-hexagonal-architecture-api.git 34 | cd flask-hexagonal-architecture-api 35 | docker-compose up -d 36 | ``` 37 | Now, API is listening at localhost port 8000. Available endpoints are: 38 | 39 | - [http://localhost:8000/acquire/pdf](http://localhost:8000/acquire/pdf) 40 | - [http://localhost:8000/anonymize/txt](http://localhost:8000/anonymize/txt) 41 | 42 | ## Architecture 43 | 44 | Code architecture follows hexagonal architecture principles, also known as *ports and adapters*. 45 | 46 | This architecture is divided in three main layers: 47 | 48 | - **Infrastructure**: The outer layer. Controllers and all I/O related stuff (web framework, DB, ...). Anything that can change by an "external" cause (not by your decision), is in this layer. It includes repositories specific implementation, known as *adapters*. 49 | 50 | - **Application**: Use cases. Actions triggered by API calls, represented by application services. 51 | 52 | - **Domain**: Inner layer. Business context and rules goes here, represented by models and domain services. Repositories Interfaces, known as *ports*, belongs to this layer. 53 | 54 | 55 | ![hexagona_architecture_schemma](img/hexagona_architecture_schemma.png) 56 | 57 | ### Code structure 58 | 59 | Source code directory tree looks like this: 60 | 61 | ``` 62 | . 63 | ├── application 64 | │   ├── exceptions.py 65 | │   ├── __init__.py 66 | │   └── services 67 | │   ├── acquire_pdf_file.py 68 | │   ├── anonymize_txt_file.py 69 | │   └── __init__.py 70 | ├── controller 71 | │   ├── app.py ---------------> API entry point 72 | │   ├── exceptions.py 73 | │   ├── __init__.py 74 | │   └── utils.py 75 | ├── Dockerfile 76 | ├── domain 77 | │   ├── __init__.py 78 | │   ├── models 79 | │   │   ├── __init__.py 80 | │   │   └── report.py 81 | │   └── repositories 82 | │   ├── __init__.py 83 | │   └── report_repository_interface.py 84 | ├── infrastructure 85 | │   ├── database.py 86 | │   ├── __init__.py 87 | │   └── repositories 88 | │   ├── base_repository.py 89 | │   ├── __init__.py 90 | │   └── report_repository.py 91 | ├── lint.sh 92 | ├── requirements.txt 93 | └── test 94 | ├── application 95 | │   ├── __init__.py 96 | │   └── test_services.py 97 | ├── base_test_case.py 98 | ├── controller 99 | │   ├── __init__.py 100 | │   └── test_app.py 101 | ├── infrastructure 102 | │   ├── __init__.py 103 | │   └── test_repositories.py 104 | └── __init__.py 105 | ``` 106 | 107 | ## Testing 108 | 109 | 110 | ### Running tests 111 | 112 | Tests have been built with [Unittest](https://docs.python.org/3/library/unittest.html). Running tests is as simple as: 113 | 114 | ``` 115 | docker-compose exec api python -m unittest discover 116 | ``` 117 | 118 | ### Testing strategy 119 | 120 | - We're testing full API call lifetime cycle, see `test/controller/test_app.py`. These tests are not **acceptance** tests but close to be. 121 | 122 | - Application services have been tested trough `test/controller/test_app.py`, but some extra **unit** tests have been needed, these tests are in `test/application/test__services.py`. 123 | 124 | - Since API is very simple, we don't have *domain services*. *Models* are close to be *DTOs*, so there's no logic to be tested. This is why there's no `test/domain/` folder. 125 | 126 | - According to the architecture schema (see image above), **integration** tests are in `test/infrastructure/test_repositories.py`. 127 | 128 | ### Real test with Postman 129 | 130 | Postman is a great tool for playing with our API. 131 | Here's an example on how to send files by HTTP POST method to our API endpoints: 132 | 133 | ![Sending files with Postman](img/send_file.png) 134 | 135 | ## References 136 | 137 | - [ES] Curso de arquitectura Hexagonal de [codely.tv](https://pro.codely.tv/library/arquitectura-hexagonal/66748/about/) 138 | - [Flask](https://flask.palletsprojects.com/en/1.1.x/) development guide. 139 | - [SQLAlchemy](https://docs.sqlalchemy.org/en/13/) documentation. 140 | 141 | 142 | ## ToDo: 143 | 144 | Since this is a demo project, extracting plain text from PDF, is out of scope. This is why `AcquirePdfFile` application service is incomplete (actually returning a hardcoded string). Feel free to complete it :) 145 | 146 | -------------------------------------------------------------------------------- /docker-compose.yml: -------------------------------------------------------------------------------- 1 | version: '3' 2 | services: 3 | api: 4 | build: ./src/ 5 | volumes: 6 | - ./src/:/usr/src/app/ 7 | ports: 8 | - 8000:8000 9 | environment: 10 | DB_URI: "sqlite:////usr/src/app/tmp/api.db" 11 | HOST: "0.0.0.0" 12 | PORT: 8000 13 | FLASK_DEBUG: 1 14 | -------------------------------------------------------------------------------- /img/hexagona_architecture_schemma.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/serfer2/flask-hexagonal-architecture-api/56aa0ec6c7723377ee250103de2f60e19a9d1899/img/hexagona_architecture_schemma.png -------------------------------------------------------------------------------- /img/send_file.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/serfer2/flask-hexagonal-architecture-api/56aa0ec6c7723377ee250103de2f60e19a9d1899/img/send_file.png -------------------------------------------------------------------------------- /samples/dummy.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/serfer2/flask-hexagonal-architecture-api/56aa0ec6c7723377ee250103de2f60e19a9d1899/samples/dummy.pdf -------------------------------------------------------------------------------- /samples/sample_report.txt: -------------------------------------------------------------------------------- 1 | MD: 987654 2 | Patient report header 3 | 4 | This patient is feeling good. 5 | No sickness, no bad diseases symptoms. 6 | All alright! 7 | 8 | A random footer -------------------------------------------------------------------------------- /src/.dockerignore: -------------------------------------------------------------------------------- 1 | /tmp 2 | README.md 3 | STYLEGUIDE.md 4 | Makefile 5 | -------------------------------------------------------------------------------- /src/.isort.cfg: -------------------------------------------------------------------------------- 1 | [settings] 2 | line_length=99 3 | known_third_party=django,rest_framework,django_filters,model_utils,impersonate,chroniker,modeltranslation,pinax,rollbar,expects,pytz,unidecode,werkzeug,pdfminer,dateutil,simplejson,xlrd,reportlab,openpyxl,xlsxwriter,simple_value_object,celery,stripe,pinax,mock,doublex,simple_value_object,simple_ioc,domain_events,model_utils,freezegun,requests 4 | indent=4 5 | multi_line_output=3 6 | default_section=FIRSTPARTY 7 | order_by_type=true 8 | force_grid_wrap=true 9 | -------------------------------------------------------------------------------- /src/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM python:3.8 2 | WORKDIR /usr/src/app 3 | COPY . . 4 | RUN pip install --no-cache-dir -r requirements.txt \ 5 | && mkdir -p /usr/src/app/tmp 6 | VOLUME ["/usr/src/app/tmp"] 7 | ENV PYTHONPATH "${PYTHONPATH}:/usr/src/app" 8 | EXPOSE 8000 9 | CMD ["python", "controller/app.py"] 10 | -------------------------------------------------------------------------------- /src/application/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/serfer2/flask-hexagonal-architecture-api/56aa0ec6c7723377ee250103de2f60e19a9d1899/src/application/__init__.py -------------------------------------------------------------------------------- /src/application/exceptions.py: -------------------------------------------------------------------------------- 1 | class WrongFileStructureException(Exception): 2 | 3 | def __init__(self, data=None): 4 | Exception.__init__(self) 5 | self.data = data or {} 6 | 7 | def to_dict(self): 8 | return self.data 9 | -------------------------------------------------------------------------------- /src/application/services/__init__.py: -------------------------------------------------------------------------------- 1 | from .acquire_pdf_file import AcquirePdfFile 2 | from .anonymize_txt_file import AnonymizeTxtFile 3 | -------------------------------------------------------------------------------- /src/application/services/acquire_pdf_file.py: -------------------------------------------------------------------------------- 1 | class AcquirePdfFile: 2 | 3 | def do(self, file_content): 4 | # TODO: Extract text from PDF file_content 5 | return 'Some plain text' 6 | -------------------------------------------------------------------------------- /src/application/services/anonymize_txt_file.py: -------------------------------------------------------------------------------- 1 | import hashlib 2 | import re 3 | 4 | from domain.models import Report 5 | from ..exceptions import WrongFileStructureException 6 | 7 | 8 | class AnonymizeTxtFile: 9 | # TODO: we're assuming MR is number with four digits or more. 10 | 11 | def __init__(self): 12 | self.section_split_rule = re.compile('\n{2}') 13 | self.medical_record_rule = re.compile(' \d{4,}') 14 | 15 | def do(self, file_content, repository): 16 | sections = [section.strip() for section in self.section_split_rule.split(file_content) if section.strip() != ''] 17 | 18 | if len(sections) < 2: 19 | error = {'file': 'wrong structure'} 20 | raise WrongFileStructureException(error) 21 | 22 | mr = self._mr(header=sections[0]) 23 | if not mr: 24 | error = {'file': 'MR not found'} 25 | raise WrongFileStructureException(error) 26 | 27 | report = Report( 28 | patient_id=self._patient_id(mr), 29 | document_text=sections[1] 30 | ) 31 | repository.insert(report) 32 | 33 | return { 34 | 'patient_id': report.patient_id, 35 | 'document_text': report.document_text 36 | } 37 | 38 | def _mr(self, header): 39 | match = self.medical_record_rule.search(header) 40 | if not match: 41 | return '' 42 | return match.group(0).strip() 43 | 44 | def _patient_id(self, mr): 45 | _hash = hashlib.new('ripemd160') 46 | _hash.update(bytes(mr, 'utf-8')) 47 | return _hash.hexdigest() 48 | -------------------------------------------------------------------------------- /src/controller/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/serfer2/flask-hexagonal-architecture-api/56aa0ec6c7723377ee250103de2f60e19a9d1899/src/controller/__init__.py -------------------------------------------------------------------------------- /src/controller/app.py: -------------------------------------------------------------------------------- 1 | import os 2 | 3 | from flask import ( 4 | Flask, 5 | g, 6 | jsonify, 7 | request 8 | ) 9 | 10 | from application.exceptions import WrongFileStructureException 11 | from application.services import ( 12 | AcquirePdfFile, 13 | AnonymizeTxtFile 14 | ) 15 | from controller.exceptions import BadRequestException 16 | from controller.utils import file_by_mimetype 17 | from infrastructure.database import ( 18 | close_db_connection, 19 | init_db_engine, 20 | db_connect 21 | ) 22 | from infrastructure.repositories import ReportRepository 23 | 24 | 25 | app = Flask(__name__) 26 | 27 | 28 | def get_db_connection(app): 29 | if 'db_con' not in g: 30 | db_engine = app.config.get('DB_ENGINE', None) or init_db_engine() 31 | g.db_con = db_connect(db_engine) 32 | return g.db_con 33 | 34 | 35 | @app.errorhandler(BadRequestException) 36 | @app.errorhandler(WrongFileStructureException) 37 | def handle_bad_request(error): 38 | response = jsonify(error.to_dict()) 39 | response.status_code = 400 40 | return response 41 | 42 | 43 | @app.route('/acquire/pdf', methods=['GET', 'POST']) 44 | def acquire_pdf(): 45 | if request.method == 'GET': 46 | return jsonify({'status': 'alive!'}) 47 | 48 | file = file_by_mimetype(request, 'application/pdf') 49 | plain_text = AcquirePdfFile().do( 50 | file_content=file.stream.read() 51 | ) 52 | 53 | return jsonify({'plain_text': plain_text}) 54 | 55 | 56 | @app.route('/anonymize/txt', methods=['GET', 'POST']) 57 | def anonymize_txt(): 58 | if request.method == 'GET': 59 | return jsonify({'status': 'alive!'}) 60 | 61 | file = file_by_mimetype(request, 'text/plain') 62 | anonymized_data = AnonymizeTxtFile().do( 63 | file_content=file.stream.read().decode("utf-8"), 64 | repository=ReportRepository(get_db_connection(app)) 65 | ) 66 | 67 | return jsonify(anonymized_data) 68 | 69 | 70 | @app.teardown_appcontext 71 | def teardown_db(exception=None): 72 | db_con = g.pop('db_con', None) 73 | if db_con is not None: 74 | close_db_connection(db_con) 75 | 76 | 77 | if __name__ == '__main__': 78 | app.run(host=os.getenv('HOST'), port=os.getenv('PORT')) 79 | -------------------------------------------------------------------------------- /src/controller/exceptions.py: -------------------------------------------------------------------------------- 1 | class BadRequestException(Exception): 2 | 3 | def __init__(self, data=None): 4 | Exception.__init__(self) 5 | self.data = data or {} 6 | 7 | def to_dict(self): 8 | return self.data 9 | -------------------------------------------------------------------------------- /src/controller/utils.py: -------------------------------------------------------------------------------- 1 | from controller.exceptions import BadRequestException 2 | 3 | 4 | def file_by_mimetype(request, mimetype): 5 | if 'file' not in request.files: 6 | raise BadRequestException({'file': 'mandatory'}) 7 | 8 | file = request.files['file'] 9 | if file.mimetype != mimetype: 10 | raise BadRequestException({'file': 'wrong file type'}) 11 | 12 | return file 13 | -------------------------------------------------------------------------------- /src/domain/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/serfer2/flask-hexagonal-architecture-api/56aa0ec6c7723377ee250103de2f60e19a9d1899/src/domain/__init__.py -------------------------------------------------------------------------------- /src/domain/models/__init__.py: -------------------------------------------------------------------------------- 1 | from .report import Report 2 | -------------------------------------------------------------------------------- /src/domain/models/report.py: -------------------------------------------------------------------------------- 1 | class Report: 2 | 3 | def __init__(self, patient_id, document_text): 4 | self.patient_id = patient_id 5 | self.document_text = document_text 6 | 7 | def __repr__(self): 8 | return f'' 9 | 10 | def as_dict(self): 11 | return { 12 | 'patient_id': self.patient_id, 13 | 'document_text': self.document_text 14 | } 15 | -------------------------------------------------------------------------------- /src/domain/repositories/__init__.py: -------------------------------------------------------------------------------- 1 | from .report_repository_interface import ReportRepositoryInterface -------------------------------------------------------------------------------- /src/domain/repositories/report_repository_interface.py: -------------------------------------------------------------------------------- 1 | from abc import ( 2 | ABCMeta, 3 | abstractmethod 4 | ) 5 | 6 | 7 | class ReportRepositoryInterface: 8 | __metaclass__ = ABCMeta 9 | 10 | @abstractmethod 11 | def insert(self, report): 12 | pass 13 | -------------------------------------------------------------------------------- /src/infrastructure/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/serfer2/flask-hexagonal-architecture-api/56aa0ec6c7723377ee250103de2f60e19a9d1899/src/infrastructure/__init__.py -------------------------------------------------------------------------------- /src/infrastructure/database.py: -------------------------------------------------------------------------------- 1 | import os 2 | 3 | from sqlalchemy import ( 4 | Column, 5 | MetaData, 6 | String, 7 | Table, 8 | Text, 9 | create_engine, 10 | ) 11 | 12 | metadata = MetaData() 13 | 14 | reports_table = Table( 15 | 'report', metadata, 16 | Column('patient_id', String(250), primary_key=True), 17 | Column('document_text', Text, nullable=False) 18 | ) 19 | 20 | 21 | def init_db_engine(db_uri=None): 22 | uri = db_uri or os.getenv('DB_URI') 23 | db_engine = create_engine(uri, convert_unicode=True) 24 | __create_tables_if_not_exists(db_engine) 25 | return db_engine 26 | 27 | 28 | def db_connect(db_engine): 29 | return db_engine.connect() 30 | 31 | 32 | def close_db_connection(db_connection): 33 | try: 34 | db_connection.close() 35 | except: 36 | pass 37 | 38 | 39 | def __create_tables_if_not_exists(db_engine): 40 | # NOTE: use Alembic for migrations (https://alembic.sqlalchemy.org/en/latest/) 41 | reports_table.create(db_engine, checkfirst=True) 42 | -------------------------------------------------------------------------------- /src/infrastructure/repositories/__init__.py: -------------------------------------------------------------------------------- 1 | from .base_repository import BaseRepository 2 | from .report_repository import ReportRepository 3 | -------------------------------------------------------------------------------- /src/infrastructure/repositories/base_repository.py: -------------------------------------------------------------------------------- 1 | class BaseRepository(): 2 | 3 | def __init__(self, db_connection): 4 | self.db_connection = db_connection 5 | -------------------------------------------------------------------------------- /src/infrastructure/repositories/report_repository.py: -------------------------------------------------------------------------------- 1 | from domain.repositories import ReportRepositoryInterface 2 | from infrastructure.database import reports_table 3 | from infrastructure.repositories import BaseRepository 4 | 5 | 6 | class ReportRepository(BaseRepository, ReportRepositoryInterface): 7 | 8 | def insert(self, report): 9 | with self.db_connection.begin(): 10 | self.db_connection.execute( 11 | reports_table.insert(), 12 | report.as_dict() 13 | ) 14 | -------------------------------------------------------------------------------- /src/lint.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -e 3 | flake8 . --exclude=migrations,apps.py,settings,__init__.py,.venv --ignore=E501,E722,W605 4 | -------------------------------------------------------------------------------- /src/requirements.txt: -------------------------------------------------------------------------------- 1 | expects==0.9.0 2 | flake8==3.8.4 3 | flask==1.1.2 4 | ipdb==0.13.4 5 | sqlalchemy==1.3.20 -------------------------------------------------------------------------------- /src/test/__init__.py: -------------------------------------------------------------------------------- 1 | from .base_test_case import BaseTestCase 2 | -------------------------------------------------------------------------------- /src/test/application/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/serfer2/flask-hexagonal-architecture-api/56aa0ec6c7723377ee250103de2f60e19a9d1899/src/test/application/__init__.py -------------------------------------------------------------------------------- /src/test/application/test_services.py: -------------------------------------------------------------------------------- 1 | from expects import ( 2 | equal, 3 | expect, 4 | raise_error 5 | ) 6 | 7 | from application.exceptions import WrongFileStructureException 8 | from application.services import AnonymizeTxtFile 9 | from domain.repositories import ReportRepositoryInterface 10 | from test import BaseTestCase 11 | 12 | 13 | class FakeReportRepository(ReportRepositoryInterface): 14 | 15 | def __init__(self): 16 | self.__reports = {} 17 | 18 | def insert(self, report): 19 | self.__reports[report.patient_id] = report 20 | 21 | def get_by_patient_id(self, patient_id): 22 | return self.__reports[patient_id] 23 | 24 | 25 | class AnonymizeTxtFileTestCase(BaseTestCase): 26 | 27 | def test_it_raises_exception_when_wrong_file_content_structure(self): 28 | wrong_file_content = 'Bad news.\nThis is wrong.' 29 | 30 | expect(lambda: AnonymizeTxtFile().do( 31 | file_content=wrong_file_content, 32 | repository=FakeReportRepository() 33 | )).to(raise_error(WrongFileStructureException)) 34 | 35 | def test_it_raises_exception_when_no_mr_in_report_header(self): 36 | wrong_header = ( 37 | 'Random data\n' 38 | 'Some other header data\n' 39 | ) 40 | free_text = ( 41 | 'Free text body, full of important data and\n' 42 | 'annotations that we should save.\n' 43 | 'We hope this report is good news for patient :)\n' 44 | ) 45 | 46 | expect(lambda: AnonymizeTxtFile().do( 47 | file_content=f'{wrong_header}\n{free_text}', 48 | repository=FakeReportRepository() 49 | )).to(raise_error(WrongFileStructureException)) 50 | 51 | def test_it_rerturns_free_text_and_hashed_medical_record_number(self): 52 | mr = '1234567890' 53 | hashed_mr = '9d752daa3fb4df29837088e1e5a1acf74932e074' 54 | header = ( 55 | f'MR: {mr}\n' 56 | 'Some other header data\n' 57 | ) 58 | free_text = ( 59 | 'Free text body, full of important data and\n' 60 | 'annotations that we should save.\n' 61 | 'We hope this report is good news for patient :)' 62 | ) 63 | 64 | result = AnonymizeTxtFile().do( 65 | file_content=f'{header}\n{free_text}', 66 | repository=FakeReportRepository() 67 | ) 68 | 69 | expect(result['patient_id']).to(equal(hashed_mr)) 70 | expect(result['document_text']).to(equal(free_text)) 71 | 72 | def test_it_persists_report_in_repository(self): 73 | mr = '1234567890' 74 | hashed_mr = '9d752daa3fb4df29837088e1e5a1acf74932e074' 75 | header = ( 76 | f'MR: {mr}\n' 77 | 'Some other header data\n' 78 | ) 79 | free_text = ( 80 | 'Free text body, full of important data and\n' 81 | 'annotations that we should save.\n' 82 | 'We hope this report is good news for patient :)' 83 | ) 84 | repository = FakeReportRepository() 85 | 86 | result = AnonymizeTxtFile().do( 87 | file_content=f'{header}\n{free_text}', 88 | repository=repository 89 | ) 90 | 91 | report = repository.get_by_patient_id(result['patient_id']) 92 | expect(report.patient_id).to(equal(hashed_mr)) 93 | expect(report.document_text).to(equal(free_text)) 94 | -------------------------------------------------------------------------------- /src/test/base_test_case.py: -------------------------------------------------------------------------------- 1 | import os 2 | import tempfile 3 | import unittest 4 | 5 | from controller.app import app 6 | from infrastructure.database import ( 7 | db_connect, 8 | init_db_engine 9 | ) 10 | 11 | 12 | class BaseTestCase(unittest.TestCase): 13 | 14 | def setUp(self): 15 | db_engine = self._build_test_db() 16 | self.app = app 17 | self.app.config.update( 18 | TESTING=True, 19 | DEBUG=True, 20 | WTF_CSRF_ENABLED=False, 21 | DB_ENGINE=db_engine 22 | ) 23 | self.client = self.app.test_client() 24 | self.db_connection = db_connect(db_engine) 25 | 26 | def tearDown(self): 27 | os.close(self.db_file_descriptor) 28 | os.unlink(self.db_file_path) 29 | 30 | def _build_test_db(self): 31 | self.db_file_descriptor, self.db_file_path = tempfile.mkstemp() 32 | return init_db_engine(db_uri=f"sqlite:///{self.db_file_path}") 33 | -------------------------------------------------------------------------------- /src/test/controller/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/serfer2/flask-hexagonal-architecture-api/56aa0ec6c7723377ee250103de2f60e19a9d1899/src/test/controller/__init__.py -------------------------------------------------------------------------------- /src/test/controller/test_app.py: -------------------------------------------------------------------------------- 1 | import io 2 | from unittest.mock import patch 3 | 4 | from expects import ( 5 | be_true, 6 | equal, 7 | expect, 8 | have_keys 9 | ) 10 | 11 | from infrastructure.repositories import ReportRepository 12 | from test import BaseTestCase 13 | 14 | 15 | class AcquirePdfEndpointTestCase(BaseTestCase): 16 | 17 | def test_endpoint_status_can_be_checked(self): 18 | response = self.client.get('/acquire/pdf') 19 | 20 | expect(response.status_code).to(equal(200)) 21 | expect(response.json).to(equal({'status': 'alive!'})) 22 | 23 | def test_it_returns_bad_request_when_no_file_posted(self): 24 | response = self.client.post('/acquire/pdf', data={}) 25 | 26 | expect(response.status_code).to(equal(400)) 27 | expect(response.json).to(equal({'file': 'mandatory'})) 28 | 29 | def test_it_returns_bad_request_when_invalid_file_type(self): 30 | wrong_file = (io.BytesIO(b"Some text"), 'report.doc') 31 | data = {'file': wrong_file} 32 | 33 | response = self.client.post('/acquire/pdf', data=data) 34 | 35 | expect(response.status_code).to(equal(400)) 36 | expect(response.json).to(equal({'file': 'wrong file type'})) 37 | 38 | @patch('controller.app.AcquirePdfFile.do') 39 | def test_it_calls_application_service_with_pdf_file_content(self, application_service): 40 | pdf_file = (io.BytesIO(b"Some text"), 'report.pdf') 41 | data = {'file': pdf_file} 42 | application_service.return_value = "Doesn't matter" 43 | 44 | self.client.post('/acquire/pdf', data=data) 45 | 46 | application_service.assert_called_with( 47 | file_content=b"Some text", 48 | ) 49 | 50 | def test_it_returns_extracted_plain_text(self): 51 | pdf_file = (io.BytesIO(b"Some plain text"), 'report.pdf') 52 | data = {'file': pdf_file} 53 | 54 | response = self.client.post('/acquire/pdf', data=data) 55 | 56 | expect(response.status_code).to(equal(200)) 57 | expect(response.json).to(equal( 58 | {'plain_text': 'Some plain text'}) 59 | ) 60 | 61 | 62 | class AnonymizeTxtEndpointTestCase(BaseTestCase): 63 | 64 | def test_endpoint_status_can_be_checked(self): 65 | response = self.client.get('/anonymize/txt') 66 | 67 | expect(response.status_code).to(equal(200)) 68 | expect(response.json).to(equal({'status': 'alive!'})) 69 | 70 | def test_it_returns_bad_request_when_no_file_posted(self): 71 | response = self.client.post('/anonymize/txt', data={}) 72 | 73 | expect(response.status_code).to(equal(400)) 74 | expect(response.json).to(equal({'file': 'mandatory'})) 75 | 76 | def test_it_returns_bad_request_when_invalid_file_type(self): 77 | wrong_file = (io.BytesIO(b"Some text"), 'report.pdf') 78 | data = {'file': wrong_file} 79 | 80 | response = self.client.post('/anonymize/txt', data=data) 81 | 82 | expect(response.status_code).to(equal(400)) 83 | expect(response.json).to(equal({'file': 'wrong file type'})) 84 | 85 | @patch('controller.app.AnonymizeTxtFile.do') 86 | def test_it_calls_application_service(self, application_service): 87 | pdf_file = (io.BytesIO(b"Some text"), 'Report1.txt') 88 | data = {'file': pdf_file} 89 | application_service.return_value = "Doesn't matter" 90 | 91 | self.client.post('/anonymize/txt', data=data) 92 | 93 | kwargs = application_service.call_args.kwargs 94 | expect(kwargs['file_content']).to(equal("Some text")) 95 | expect( 96 | isinstance(kwargs['repository'], ReportRepository) 97 | ).to(be_true) 98 | 99 | @patch('controller.app.AnonymizeTxtFile.do') 100 | def test_it_returns_anonymized_content(self, application_service): 101 | pdf_file = (io.BytesIO(b"Some text"), 'Report1.txt') 102 | data = {'file': pdf_file} 103 | application_service.return_value = { 104 | 'patient_id': '1234', 105 | 'document_text': 'She\'s in good health!' 106 | } 107 | 108 | response = self.client.post('/anonymize/txt', data=data) 109 | expect(response.status_code).to(equal(200)) 110 | expect(response.json).to(have_keys({ 111 | 'patient_id': '1234', 112 | 'document_text': 'She\'s in good health!' 113 | })) 114 | -------------------------------------------------------------------------------- /src/test/infrastructure/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/serfer2/flask-hexagonal-architecture-api/56aa0ec6c7723377ee250103de2f60e19a9d1899/src/test/infrastructure/__init__.py -------------------------------------------------------------------------------- /src/test/infrastructure/test_repositories.py: -------------------------------------------------------------------------------- 1 | from expects import ( 2 | equal, 3 | expect 4 | ) 5 | 6 | from infrastructure.repositories import ReportRepository 7 | from test import BaseTestCase 8 | 9 | 10 | class StubReport: 11 | 12 | def as_dict(self): 13 | return { 14 | 'patient_id': '123456', 15 | 'document_text': 'Any random text' 16 | } 17 | 18 | 19 | class ReportRepositoryTestCase(BaseTestCase): 20 | 21 | def test_it_inserts_a_report(self): 22 | report = StubReport() 23 | repository = ReportRepository(self.db_connection) 24 | query = "SELECT * FROM report WHERE patient_id = '123456'" 25 | 26 | repository.insert(report) 27 | 28 | expect(self._read_from_db(query)).to( 29 | equal({ 30 | 'patient_id': '123456', 31 | 'document_text': 'Any random text' 32 | }) 33 | ) 34 | 35 | def _read_from_db(self, sql_query): 36 | registry = self.db_connection.execute(sql_query).first() 37 | return dict(registry.items()) 38 | --------------------------------------------------------------------------------