kids-first · dankolbman · Jan 17, 2018 · Jan 10, 2018 · Jan 11, 2018 · Jan 11, 2018
@@ -1,3 +1,5 @@
+*.sqlite
+*.swp
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

@@ -0,0 +1,69 @@
+import os
+basedir = os.path.abspath(os.path.dirname(__file__))
+
+
+class Config:
+    HOST = "0.0.0.0"
+    SSL_DISABLE = os.environ.get("SSL_DISABLE", False)
+
+    RESTPLUS_MASK_SWAGGER = False
+
+    @staticmethod
+    def init_app(app):
+        pass
+
+
+class DevelopmentConfig(Config):
+    DEBUG = True
+    SSL_DISABLE = True
+    SQLALCHEMY_DATABASE_URI = os.environ.get("DEV_DATABASE_URL") or \
+            "sqlite:///" + os.path.join(basedir, "data-dev.sqlite")
+    SQLALCHEMY_TRACK_MODIFICATIONS = True
+
+
+class TestingConfig(Config):
+    SERVER_NAME = "localhost"
+    TESTING = True
+    WTF_CSRF_ENABLED = False
+    SQLALCHEMY_DATABASE_URI = os.environ.get("TEST_DATABASE_URL") or \
+            "sqlite:///" + os.path.join(basedir, "data-test.sqlite")
+    SQLALCHEMY_TRACK_MODIFICATIONS = True
+
+
+class ProductionConfig(Config):
+    # Should use postgres
+    SQLALCHEMY_DATABASE_URI = os.environ.get("DATABASE_URL") or \
+            "sqlite:///" + os.path.join(basedir, "data.sqlite")
+
+    @classmethod
+    def init_app(cls, app):
+        Config.init_app(app)
+
+        # email errors to the administrators
+        import logging
+        from logging.handlers import SMTPHandler
+        credentials = None
+        secure = None
+
+
+class UnixConfig(ProductionConfig):
+    @classmethod
+    def init_app(cls, app):
+        ProductionConfig.init_app(app)
+
+        # log to syslog
+        import logging
+        from logging.handlers import SysLogHandler
+        syslog_handler = SysLogHandler()
+        syslog_handler.setLevel(logging.WARNING)
+        app.logger.addHandler(syslog_handler)
+
+
+config = {
+    "development": DevelopmentConfig,
+    "testing": TestingConfig,
+    "production": ProductionConfig,
+    "unix": UnixConfig,
+
+    "default": DevelopmentConfig
+}
@@ -0,0 +1,19 @@
+import os
+from flask import Flask, jsonify
+from flask_sqlalchemy import SQLAlchemy
+from flask_restplus import Api
+from config import config, DevelopmentConfig
+
+db = SQLAlchemy()
+
+
+def create_app(config_name):
+    app = Flask(__name__)
+    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)
+
+    return app
@@ -0,0 +1,49 @@
+Primary API for interacting with the Kid's First Data Model.
+
+## Service-Wide Standards and Functionality
+
+### Field Masking
+
+Partial data fetching is supported via the `X-Fields` header.
+To specifiy that only some fields are to be returned, include a bracketed,
+coma-delimited list under the `X-Fields` header:
+
+`X-Fields: {kf_id, name}`
+
+Brackets may be nested to filter on nested fields:
+
+`X-Fields: {kf_id, name, type{format, extension}}`
+
+An asterisk may be used to specify all fields:
+
+`X-Fields: *`
+
+Or all sub-fields:
+
+`X-Fields: {kf_id, type{*}}`
+
+Or all root fields, but with only some sub-fields:
+
+`X-Fields: {*, type{format}}`
+
+
+
+### Pagination
+
+```
+{
+  pages: [
+    { "doc_id": 30, "value": "Lorem" },
+    { "doc_id": 31, "value": "ipsum" },
+    { "doc_id": 32, "value": "dolor" },
+    ...
+    { "doc_id": 40, "value": "amet" }
+  ],
+  from: 30,
+  to: 40,
+  results: 10,
+  total: 1204,
+  message: "Success",
+  status: 200
+}
+```
@@ -0,0 +1,30 @@
+from flask_restplus import Api
+from .person import person_api
+
+api = Api(title='Kids First Data Service',
+          description=open('dataservice/api/README.md').read(),
+          version='0.1',
+          default='',
+          default_label='')
+
+api.add_namespace(person_api)
+
+
+@api.documentation
+def redoc_ui():
+    """ Uses ReDoc for swagger documentation """
+    docs_page = """<!DOCTYPE html>
+    <html>
+    <head>
+    <title>API Docs</title>
+    <!-- needed for mobile devices -->
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    </head>
+    <body>
+    <redoc spec-url="{}"></redoc>
+    <script src="https://rebilly.github.io/ReDoc/releases/latest/redoc.min.js">
+    </script>
+    </body>
+    </html>
+    """.format(api.specs_url)
+    return docs_page
@@ -0,0 +1,21 @@
+A person is one of the central entities of the Kid's First DCC.
+
+### Fields
+
+`kf_id` - the unique identifier assigned by Kid's First used as the primary
+reference to this Person
+
+`source_name` - the identifier used by the original contributor of the data
+
+`date_created` - the date the person`s record was created in the DCC
+
+`date_modified` - the last date that the record's fields were modified.
+Restricted to fields of the entity itself, not any of it's related entities.
+
+### Identifiers
+
+The Kid's First DCC assigns a unique, internal identifier of the form:
+`KF-P000000` on creation of a new Person. This identifier is used accross the
+Kids First Data Service and Data Resource Portal It is expected that the Person
+also have an identifier unique to the study it came from. This field is to be
+captured in the `source_name` property of the Person upon creation.
@@ -0,0 +1 @@
+from .person import person_api
diff --git a/dataservice/api/person/person.py b/dataservice/api/person/person.py
@@ -0,0 +1,137 @@
+from datetime import datetime
+from flask import request
+from flask_restplus import Namespace, Resource, fields, abort
+
+from ... import model
+from ... import db
+
+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')
+})
+
+
+@person_api.route('/')
+class PersonList(Resource):
+    @person_api.marshal_with(response_model)
+    def get(self):
+        """
+        Get all persons
+        """
+        persons = model.Person.query.all()
+        return {'status': 200,
+                'message': '{} persons'.format(len(persons)),
+                'content': {'persons': persons}}, 200
+
+    @person_api.marshal_with(response_model)
+    @person_api.doc(responses={201: 'person created',
+                               400: 'invalid data'})
+    @person_api.expect(person_model)
+    def post(self):
+        """
+        Create a new person
+
+        Creates a new person and assigns a Kids First id
+        """
+        body = request.json
+        person = model.Person(**body)
+        db.session.add(person)
+        db.session.commit()
+        return {'status': 201,
+                'message': 'person created',
+                'content': {'persons': [person]}}, 201
+
+
+@person_api.route('/<string:kf_id>')
+class Person(Resource):
+    @person_api.marshal_with(response_model)
+    @person_api.doc(responses={200: 'person found',
+                               404: 'person not found'})
+    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()
+        if not person:
+            self._not_found(kf_id)
+
+        return {'status': 200,
+                'message': 'person found',
+                'content': {'persons': [person]}}, 200
+
+    @person_api.marshal_with(response_model)
+    @person_api.doc(responses={201: 'person updated',
+                               400: 'invalid data',
+                               404: 'person not found'})
+    @person_api.expect(person_model)
+    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()
+        if not person:
+            self._not_found(kf_id)
+
+        person.external_id = body.get('external_id')
+        db.session.commit()
+
+        return {'status': 201,
+                'message': 'person updated',
+                'content': {'persons': [person]}}, 201
+
+    @person_api.marshal_with(response_model)
+    @person_api.doc(responses={204: 'person deleted',
+                               404: 'person not found'})
+    def delete(self, kf_id):
+        """
+        Delete person by id
+
+        Deletes a person given a Kids First id
+        """
+        person = model.Person.query.filter_by(kf_id=kf_id).one_or_none()
+        if not person:
+            self._not_found(kf_id)
+
+        db.session.delete(person)
+        db.session.commit()
+        return {'status': 200,
+                'message': 'person deleted',
+                'content': {'persons': [person]}}, 200
+
+    def _not_found(self, kf_id):
+        """
+        Temporary helper - will do error handling better later
+        """
+        status = 404
+        abort(status, "Person with kf_id '{}' not found".format(kf_id),
+              status=status, content=None)
diff --git a/dataservice/id_service.py b/dataservice/id_service.py
@@ -0,0 +1,5 @@
+import uuid
+
+
+def assign_id():
+    return str(uuid.uuid4())