Refactor dataservice to be more modular

Create common module for common code among resources
Create new folder for person tests, move all person tests into it
Separate out model code, resource code, serialization code for Person
resources
Refactor and replace Flask-Script with built in CLI
Add support for api versioning
Clean up Flask CLI commands
Change api prefix from /api/v1 to /v1
Remove Flask-Script dependenct
Replace relative imports with absolute imports

dataservice/__init__.py

@@ -1,19 +1,69 @@
-import os
-from flask import Flask, jsonify
-from flask_sqlalchemy import SQLAlchemy
-from flask_restplus import Api
-from config import config, DevelopmentConfig
+# -*- coding: utf-8 -*-
+"""The app module, containing the app factory function."""
+from flask import Flask
 
-db = SQLAlchemy()
+from dataservice import commands
+from dataservice.extensions import db, migrate
+from dataservice.api.person.models import Person
+from config import config
 
 
 def create_app(config_name):
+    """
+    An application factory
+    """
     app = Flask(__name__)
+    app.url_map.strict_slashes = False
     app.config.from_object(config[config_name])
-    config[config_name].init_app(app)
 
-    db.init_app(app)
-    from dataservice.api import api
-    api.init_app(app)
+    # Register Flask extensions
+    register_extensions(app)
+    register_shellcontext(app)
+    register_commands(app)
+    register_blueprints(app)
 
     return app
+
+
+def register_shellcontext(app):
+    """
+    Register shell context objects
+    """
+
+    def shell_context():
+        """Shell context objects."""
+        return {'db': db,
+                'Person': Person}
+
+    app.shell_context_processor(shell_context)
+
+
+def register_commands(app):
+    """
+    Register Click commands
+    """
+    app.cli.add_command(commands.test)
+
+
+def register_extensions(app):
+    """
+    Register Flask extensions
+    """
+
+    # SQLAlchemy
+    db.init_app(app)
+
+    # Migrate
+    migrate.init_app(app, db)
+
+
+def register_error_handlers(app):
+    """
+    Register error handlers
+    """
+    pass
+
+
+def register_blueprints(app):
+    from dataservice.api import api_v1
+    app.register_blueprint(api_v1)

dataservice/api/__init__.py

@@ -1,7 +1,11 @@
+from flask import Blueprint
 from flask_restplus import Api
-from .person import person_api
+from dataservice.api.person import person_api
 
-api = Api(title='Kids First Data Service',
+api_v1 = Blueprint('api', __name__, url_prefix='/v1')
+
+api = Api(api_v1,
+          title='Kids First Data Service',
           description=open('dataservice/api/README.md').read(),
           version='0.1',
           default='',

dataservice/model.py → dataservice/api/common/model.py

@@ -1,9 +1,8 @@
-from sqlalchemy.ext.declarative import declared_attr
-
 from datetime import datetime
-from . import db
+from sqlalchemy.ext.declarative import declared_attr
 
-from .id_service import assign_id
+from dataservice.extensions import db
+from dataservice.api.common.id_service import assign_id
 
 
 class IDMixin:
@@ -48,17 +47,3 @@ class File(Base):
     name = db.Column(db.String(32))
     data_type = db.Column(db.String(32))
     size = db.Column(db.Integer(), default=0)
-
-
-class Person(Base):
-    """
-    Person entity.
-
-    :param _id: Unique id assigned by RDBMS
-    :param kf_id: Unique id given by the Kid's First DCC
-    :param external_id: Name given to person by contributor
-    :param created_at: Time of object creation
-    :param modified_at: Last time of object modification
-    """
-    __tablename__ = "person"
-    external_id = db.Column(db.String(32))

dataservice/api/person/__init__.py

@@ -1 +1 @@
-from .person import person_api
+from .resources import person_api

dataservice/api/person/models.py

@@ -0,0 +1,16 @@
+from dataservice.extensions import db
+from dataservice.api.common.model import Base
+
+
+class Person(Base):
+    """
+    Person entity.
+
+    :param _id: Unique id assigned by RDBMS
+    :param kf_id: Unique id given by the Kid's First DCC
+    :param external_id: Name given to person by contributor
+    :param created_at: Time of object creation
+    :param modified_at: Last time of object modification
+    """
+    __tablename__ = "person"
+    external_id = db.Column(db.String(32))

dataservice/api/person/person.py → dataservice/api/person/resources.py

@@ -1,42 +1,15 @@
-from datetime import datetime
 from flask import request
 from flask_restplus import Namespace, Resource, fields, abort
 
-from ... import model
-from ... import db
+from dataservice.extensions import db
+from dataservice.api.person import models
 
 description = open('dataservice/api/person/README.md').read()
 
 person_api = Namespace(name='persons', description=description)
 
-person_model = person_api.model('Person', {
-    'kf_id': fields.String(
-        example='KF00001',
-        description='ID assigned by Kids First'),
-    'created_at': fields.String(
-        example=datetime.now().isoformat(),
-        description='Date Person was registered in with the DCC'),
-    'modified_at': fields.String(
-        example=datetime.now().isoformat(),
-        description='Date of last update to the Persons data'),
-    'external_id': fields.String(
-        example='SUBJ-3993',
-        description='Identifier used in the original study data')
-})
-
-person_list = person_api.model("Persons", {
-    "persons": fields.List(fields.Nested(person_model))
-})
-
-response_model = person_api.model('Response', {
-    'content': fields.Nested(person_list),
-    'status': fields.Integer(
-        description='HTTP response status code',
-        example=200),
-    'message': fields.String(
-        description='Additional information about the response',
-        example='Success')
-})
+from dataservice.api.person.serializers import (person_model,
+                                                response_model)
 
 
 @person_api.route('/')
@@ -46,7 +19,7 @@ def get(self):
         """
         Get all persons
         """
-        persons = model.Person.query.all()
+        persons = models.Person.query.all()
         return {'status': 200,
                 'message': '{} persons'.format(len(persons)),
                 'content': {'persons': persons}}, 200
@@ -62,7 +35,7 @@ def post(self):
         Creates a new person and assigns a Kids First id
         """
         body = request.json
-        person = model.Person(**body)
+        person = models.Person(**body)
         db.session.add(person)
         db.session.commit()
         return {'status': 201,
@@ -80,7 +53,7 @@ def get(self, kf_id):
         Get a person by id
         Gets a person given a Kids First id
         """
-        person = model.Person.query.filter_by(kf_id=kf_id).one_or_none()
+        person = models.Person.query.filter_by(kf_id=kf_id).one_or_none()
         if not person:
             self._not_found(kf_id)
 
@@ -98,7 +71,7 @@ def put(self, kf_id):
         Update an existing person
         """
         body = request.json
-        person = model.Person.query.filter_by(kf_id=kf_id).one_or_none()
+        person = models.Person.query.filter_by(kf_id=kf_id).one_or_none()
         if not person:
             self._not_found(kf_id)
 
@@ -118,7 +91,7 @@ def delete(self, kf_id):
 
         Deletes a person given a Kids First id
         """
-        person = model.Person.query.filter_by(kf_id=kf_id).one_or_none()
+        person = models.Person.query.filter_by(kf_id=kf_id).one_or_none()
         if not person:
             self._not_found(kf_id)
 

dataservice/api/person/serializers.py

@@ -0,0 +1,33 @@
+from datetime import datetime
+from flask_restplus import fields
+
+from dataservice.api.person.resources import person_api
+
+person_model = person_api.model('Person', {
+    'kf_id': fields.String(
+        example='KF00001',
+        description='ID assigned by Kids First'),
+    'created_at': fields.String(
+        example=datetime.now().isoformat(),
+        description='Date Person was registered in with the DCC'),
+    'modified_at': fields.String(
+        example=datetime.now().isoformat(),
+        description='Date of last update to the Persons data'),
+    'external_id': fields.String(
+        example='SUBJ-3993',
+        description='Identifier used in the original study data')
+})
+
+person_list = person_api.model("Persons", {
+    "persons": fields.List(fields.Nested(person_model))
+})
+
+response_model = person_api.model('Response', {
+    'content': fields.Nested(person_list),
+    'status': fields.Integer(
+        description='HTTP response status code',
+        example=200),
+    'message': fields.String(
+        description='Additional information about the response',
+        example='Success')
+})

dataservice/commands.py

@@ -0,0 +1,12 @@
+# -*- coding: utf-8 -*-
+"""Click commands."""
+
+import click
+
+
+@click.command()
+def test():
+    """ Run the unit tests and pep8 checks """
+    from subprocess import call
+    call(["python", "-m", "pytest", "tests"])
+    call(["python", "-m", "pytest", "--pep8", "dataservice"])

dataservice/extensions.py

@@ -0,0 +1,7 @@
+from flask_migrate import Migrate
+from flask_sqlalchemy import SQLAlchemy, Model
+
+
+db = SQLAlchemy()
+
+migrate = Migrate()

manage.py

@@ -1,39 +1,9 @@
-#!/usr/bin/env python
-import os
+#! /usr/bin/env python
 
-from dataservice import create_app, db
-from flask_script import Manager, Shell
-from flask_migrate import Migrate, MigrateCommand
+import os
+from dataservice import create_app
 
 app = create_app(os.getenv('FLASK_CONFIG') or 'default')
-manager = Manager(app)
-migrate = Migrate(app, db)
-
-
-def make_shell_context():
-    return dict(app=app, db=db)
-
-
-manager.add_command("shell", Shell(make_context=make_shell_context))
-manager.add_command('db', MigrateCommand)
-
-
-@manager.command
-def test(coverage=False):
-    """ Run the unit tests and pep8 checks """
-    from subprocess import call
-    call(["python","-m","pytest","tests"])
-    call(["python","-m","pytest","--pep8","dataservice"])
-
-
-@manager.command
-def deploy():
-    """ Run deployment tasks """
-    from flask.ext.migrate import upgrade
-
-    # migrate database to latest revision
-    upgrade()
-
 
 if __name__ == '__main__':
-    manager.run()
+    app.run()

requirements.txt

@@ -5,7 +5,6 @@ Flask==0.12.2
 Flask-Migrate==2.1.1
 Flask-Profile==0.2
 flask-restplus==0.10.1
-Flask-Script==2.0.6
 Flask-SQLAlchemy==2.3.2
 itsdangerous==0.24
 Jinja2==2.8

tests/test_person_model.py → tests/person/test_models.py

@@ -1,10 +1,9 @@
 from datetime import datetime
 import uuid
 
-from dataservice import db
-from dataservice.model import Person
-
-from utils import FlaskTestCase
+from dataservice.extensions import db
+from dataservice.api.person.models import Person
+from tests.utils import FlaskTestCase
 
 
 class ModelTest(FlaskTestCase):

tests/test_person_api.py → tests/person/test_resources.py

@@ -1,10 +1,10 @@
 import json
 from flask import url_for
 
-from dataservice.model import Person
-from utils import FlaskTestCase
+from dataservice.api.person.models import Person
+from tests.utils import FlaskTestCase
 
-PERSONS_PREFIX = 'persons'
+PERSONS_PREFIX = 'api.persons'
 PERSON_URL = '{}_{}'.format(PERSONS_PREFIX, 'person')
 PERSON_LIST_URL = '{}_{}'.format(PERSONS_PREFIX, 'person_list')
 

tests/utils.py

@@ -1,6 +1,7 @@
 import json
 import unittest
-from dataservice import create_app, db
+from dataservice import create_app
+from dataservice.extensions import db
 from flask import url_for