[WIP] ENH: RESTful API to serve the data format #4

api/README.md

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+# API 
+
+This is a RESTful API  to serve the data format.
+
+
+## Usage
+
+### Store
+
+You must send a post request to: http://localhost:5000/store 
+The body of your request must match the following template 
+
+{
+	"output_format": "json", 
+	"fhir_resource_name": "patient"
+}
+
+### Mapping
+
+You must send a post request to: http://localhost:5000/mapping 
+The body of your request must match the following template 
+
+{
+	"output_format": "json", 
+	"fhir_resource_name": "patient"
+	"database": "CW"
+}

api/app.py

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+from flask import Flask, jsonify
+from flask_restful import Api
+
+from api.resources import Mapping, Store
+
+
+app = Flask(__name__)
+api = Api(app)
+
+api.add_resource(Store, '/store')
+api.add_resource(Mapping, '/mapping')
+
+@app.route('/')
+def index():
+    return jsonify(
+        {'message': 'Welcome to Fhir API'}
+    )
+
+
+if __name__ == '__main__':
+    app.run(debug=True)

api/common/utils.py

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+import glob
+import re
+
+
+def fhir_resource_path(fhir_resource, parent_folder):
+    # this is highly inefficient, since we need to scan the entire folder.
+    # It might be interesting to cache the folder structure
+
+    # case insensitive glob
+    # source: https://medium.com/@tylercubell/python-case-insensitive-glob-80ba7306b327
+    pattern = ".*/{}.yml".format(fhir_resource)
+    matching_files = [file for file in glob.glob(f'../{parent_folder}/**', recursive=True) if re.match(pattern, file, flags=re.IGNORECASE)]
+    if not matching_files:
+        return None
+    else:
+        return matching_files[0]

api/resources/__init__.py

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+from .resources import Mapping, Store

api/resources/resources.py

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+from flask import jsonify, send_from_directory
+# note: prefer send_from_directory to send_file  as send_file is not secured.
+# From the official documentation : "Please never pass filenames to this function from user sources;
+# you should use send_from_directory() instead."
+from flask_restful import Resource, reqparse
+import os
+import yaml
+
+from api.common.utils import fhir_resource_path
+
+
+class Store(Resource):
+    def post(self):
+
+        parser = reqparse.RequestParser()
+        parser.add_argument('output_format', required=True, type=str, choices=('json', 'yml'))
+        parser.add_argument('fhir_resource_name', required=True, type=str)
+
+        args = parser.parse_args()
+
+        file_path = fhir_resource_path(args['fhir_resource_name'], parent_folder='yml')
+        if not file_path:
+            return jsonify(
+                {"message": "Fhir resource not found."}
+            )
+
+        folder = os.path.dirname(file_path)
+        file = os.path.basename(file_path)
+        if args['output_format'] == 'json':
+            return jsonify(yaml.load(open(file_path)))
+
+        elif args['output_format'] == 'yml':
+            return send_from_directory(folder, file)
+
+
+class Mapping(Resource):
+    def post(self):
+
+        parser = reqparse.RequestParser()
+        parser.add_argument('output_format', required=True, type=str, choices=('sql', 'yml'))
+        parser.add_argument('fhir_resource_name', required=True, type=str)
+        parser.add_argument('database', required=True, type=str)
+
+        args = parser.args()
+
+        file_path = fhir_resource_path(args['fhir_resource_name'], parent_folder=args['database'])
+        if not file_path:
+            return jsonify(
+                {"message": "Fhir resource not found."}
+            )
+
+        folder = os.path.dirname(file_path)
+        file = os.path.basename(file_path)
+
+        if args['output_format'] == 'json':
+            return jsonify(yaml.load(open(file_path)))
+
+        elif args['output_format'] == 'yml':
+            return send_from_directory(folder, file)