Api tutorial

REQUIREMENTS.txt

@@ -6,16 +6,17 @@ flask-log
 flask-mail
 flask-restful
 gunicorn
-biocommons.seqrepo>=0.5.1
-httplib2>=0.9.0
-configparser>=3.5.0
-pyliftover>=0.3
-biotools>=0.3.0
+biocommons.seqrepo
+httplib2
+configparser
+pyliftover
+biotools
 mysql-connector-python
 requests
-pytest>=3.6
+pytest
 pytest-cov
 codecov
+dicttoxml
 
 
 

application/app_v1.py

@@ -0,0 +1,31 @@
+"""
+Simple rest interface for VariantVlidator built using Flask Flask-RESTPlus and Swagger UI
+"""
+
+# Import modules
+from flask import Flask
+from flask_restx import Api, Resource
+
+# Define the application as a Flask app with the name defined by __name__ (i.e. the name of the current module)
+# Most tutorials define application as "app", but I have had issues with this when it comes to deployment,
+# so application is recommended
+application = Flask(__name__)
+
+# Define the API as api
+api = Api(app = application)
+
+# Define a name-space to be read Swagger UI which is built in to Flask-RESTPlus
+# The first variable is the path of the namespace the second variable describes the space
+hello_space = api.namespace('hello', description='Simple API that returns a greeting')
+@hello_space.route("/")
+class HelloClass(Resource):
+	def get(self):
+		return {
+			"greeting": "Hello World"
+		}
+
+
+# Allows app to be run in debug mode
+if __name__ == '__main__':
+	application.debug = True # Enable debugging mode
+	application.run(host="127.0.0.1", port=5000) # Specify a host and port fot the app

application/app_v2.py

@@ -0,0 +1,40 @@
+"""
+Simple rest interface for VariantVlidator built using Flask Flask-RESTPlus and Swagger UI
+"""
+
+# Import modules
+from flask import Flask
+from flask_restx import Api, Resource
+
+# Define the application as a Flask app with the name defined by __name__ (i.e. the name of the current module)
+# Most tutorials define application as "app", but I have had issues with this when it comes to deployment,
+# so application is recommended
+application = Flask(__name__)
+
+# Define the API as api
+api = Api(app = application)
+
+# Define a name-space to be read Swagger UI which is built in to Flask-RESTPlus
+# The first variable is the path of the namespace the second variable describes the space
+hello_space = api.namespace('hello', description='Simple API that returns a greeting')
+@hello_space.route("/")
+class HelloClass(Resource):
+    def get(self):
+        return {
+            "greeting": "Hello World"
+        }
+
+
+name_space = api.namespace('name', description='Return a name provided by the user')
+@name_space.route("/<string:name>")
+class NameClass(Resource):
+    def get(self, name):
+        return {
+            "My name is" : name
+        }
+
+
+# Allows app to be run in debug mode
+if __name__ == '__main__':
+    application.debug = True # Enable debugging mode
+    application.run(host="127.0.0.1", port=5000) # Specify a host and port fot the app

application/app_v3.py

@@ -0,0 +1,51 @@
+"""
+Simple rest interface for VariantVlidator built using Flask Flask-RESTPlus and Swagger UI
+"""
+
+# Import modules
+from flask import Flask
+from flask_restx import Api, Resource
+import _____
+
+# Define the application as a Flask app with the name defined by __name__ (i.e. the name of the current module)
+# Most tutorials define application as "app", but I have had issues with this when it comes to deployment,
+# so application is recommended
+application = Flask(__name__)
+
+# Define the API as api
+api = Api(app = application)
+
+# Define a name-space to be read Swagger UI which is built in to Flask-RESTPlus
+# The first variable is the path of the namespace the second variable describes the space
+hello_space = api.namespace('hello', description='Simple API that returns a greeting')
+@hello_space.route("/")
+class HelloClass(Resource):
+    def get(self):
+        return {
+            "greeting": "Hello World"
+        }
+
+
+name_space = api.namespace('name', description='Return a name provided by the user')
+@name_space.route("/<string:name>")
+class NameClass(Resource):
+    def get(self, name):
+        return {
+            "My name is" : name
+        }
+
+vv_space = api.namespace('VariantValidator', description='VariantValidator APIs')
+@vv_space.route("/variantvalidator/_____")
+class VariantValidatorClass(Resource):
+    def get(self, _____):
+
+        # Make a request to the curent VariantValidator rest-API
+        url = _____
+        validation = _____
+        content = _____
+        return _____
+
+# Allows app to be run in debug mode
+if __name__ == '__main__':
+    application.debug = True # Enable debugging mode
+    application.run(host="127.0.0.1", port=5000) # Specify a host and port fot the app

application/app_v4.py

@@ -0,0 +1,68 @@
+"""
+Simple rest interface for VariantVlidator built using Flask Flask-RESTPlus and Swagger UI
+"""
+
+# Import modules
+from flask import Flask, make_response
+from flask_restx import Api, Resource
+import requests
+from dicttoxml import dicttoxml
+
+# Define the application as a Flask app with the name defined by __name__ (i.e. the name of the current module)
+# Most tutorials define application as "app", but I have had issues with this when it comes to deployment,
+# so application is recommended
+application = Flask(__name__)
+
+# Define the API as api
+api = Api(app = application)
+
+
+"""
+Representations
+ - Adds a response-type into the "Response content type" drop-down menu displayed in Swagger
+ - When selected, the APP will return the correct response-header and content type
+ - The default for flask-restx is aspplication/json
+"""
+# Add additional representations using the @api.representation decorator
+# Requires the module make_response from flask and json2xml
+@api.representation('text/xml')
+def xml(data, code, headers):
+    data = dicttoxml(data)
+    resp = make_response(data, code)
+    resp.headers['Content-Type'] = 'text/xml'
+    return resp
+
+
+# Define a name-space to be read Swagger UI which is built in to Flask-RESTPlus
+# The first variable is the path of the namespace the second variable describes the space
+hello_space = api.namespace('hello', description='Simple API that returns a greeting')
+@hello_space.route("/")
+class HelloClass(Resource):
+    def get(self):
+        return {
+            "greeting": "Hello World"
+        }
+
+name_space = api.namespace('name', description='Return a name provided by the user')
+@name_space.route("/<string:name>")
+class NameClass(Resource):
+    def get(self, name):
+        return {
+            "My name is" : name
+        }
+
+vv_space = api.namespace('VariantValidator', description='VariantValidator APIs')
+@vv_space.route("/variantvalidator/<string:genome_build>/<string:variant_description>/<string:select_transcripts>")
+class VariantValidatorClass(Resource):
+    def get(self, genome_build, variant_description, select_transcripts):
+
+        # Make a request to the curent VariantValidator rest-API
+        url = '/'.join(['http://rest.variantvalidator.org/variantvalidator', genome_build, variant_description, select_transcripts])
+        validation = requests.get(url)
+        content = validation.json()
+        return content
+
+# Allows app to be run in debug mode
+if __name__ == '__main__':
+    application.debug = True # Enable debugging mode
+    application.run(host="127.0.0.1", port=5000) # Specify a host and port fot the app

application/app_v5.py

@@ -0,0 +1,68 @@
+"""
+Simple rest interface for VariantVlidator built using Flask Flask-RESTPlus and Swagger UI
+"""
+
+# Import modules
+from flask import Flask, make_response
+from flask_restx import Api, Resource
+import requests
+from dicttoxml import dicttoxml
+
+# Define the application as a Flask app with the name defined by __name__ (i.e. the name of the current module)
+# Most tutorials define application as "app", but I have had issues with this when it comes to deployment,
+# so application is recommended
+application = Flask(__name__)
+
+# Define the API as api
+api = Api(app = application)
+
+
+"""
+Representations
+ - Adds a response-type into the "Response content type" drop-down menu displayed in Swagger
+ - When selected, the APP will return the correct response-header and content type
+ - The default for flask-restx is aspplication/json
+"""
+# Add additional representations using the @api.representation decorator
+# Requires the module make_response from flask and json2xml
+@api.representation('text/xml')
+def xml(data, code, headers):
+    data = dicttoxml(data)
+    resp = make_response(data, code)
+    resp.headers['Content-Type'] = 'text/xml'
+    return resp
+
+
+# Define a name-space to be read Swagger UI which is built in to Flask-RESTPlus
+# The first variable is the path of the namespace the second variable describes the space
+hello_space = api.namespace('hello', description='Simple API that returns a greeting')
+@hello_space.route("/")
+class HelloClass(Resource):
+    def get(self):
+        return {
+            "greeting": "Hello World"
+        }
+
+name_space = api.namespace('name', description='Return a name provided by the user')
+@name_space.route("/<string:name>")
+class NameClass(Resource):
+    def get(self, name):
+        return {
+            "My name is" : name
+        }
+
+vv_space = api.namespace('VariantValidator', description='VariantValidator APIs')
+@vv_space.route("/variantvalidator/<string:genome_build>/<string:variant_description>/<string:select_transcripts>")
+class VariantValidatorClass(Resource):
+    def get(self, genome_build, variant_description, select_transcripts):
+
+        # Make a request to the curent VariantValidator rest-API
+        url = '/'.join(['http://rest.variantvalidator.org/variantvalidator', genome_build, variant_description, select_transcripts])
+        validation = requests.get(url)
+        content = validation.json()
+        return content
+
+# Allows app to be run in debug mode
+if __name__ == '__main__':
+    application.debug = True # Enable debugging mode
+    application.run(host="127.0.0.1", port=5000) # Specify a host and port fot the app

application/app_v6.py

@@ -0,0 +1,68 @@
+"""
+Simple rest interface for VariantVlidator built using Flask Flask-RESTPlus and Swagger UI
+"""
+
+# Import modules
+from flask import Flask, make_response
+from flask_restx import Api, Resource
+import requests
+from dicttoxml import dicttoxml
+
+# Define the application as a Flask app with the name defined by __name__ (i.e. the name of the current module)
+# Most tutorials define application as "app", but I have had issues with this when it comes to deployment,
+# so application is recommended
+application = Flask(__name__)
+
+# Define the API as api
+api = Api(app = application)
+
+
+"""
+Representations
+ - Adds a response-type into the "Response content type" drop-down menu displayed in Swagger
+ - When selected, the APP will return the correct response-header and content type
+ - The default for flask-restx is aspplication/json
+"""
+# Add additional representations using the @api.representation decorator
+# Requires the module make_response from flask and json2xml
+@api.representation('text/xml')
+def xml(data, code, headers):
+    data = dicttoxml(data)
+    resp = make_response(data, code)
+    resp.headers['Content-Type'] = 'text/xml'
+    return resp
+
+
+# Define a name-space to be read Swagger UI which is built in to Flask-RESTPlus
+# The first variable is the path of the namespace the second variable describes the space
+hello_space = api.namespace('hello', description='Simple API that returns a greeting')
+@hello_space.route("/")
+class HelloClass(Resource):
+    def get(self):
+        return {
+            "greeting": "Hello World"
+        }
+
+name_space = api.namespace('name', description='Return a name provided by the user')
+@name_space.route("/<string:name>")
+class NameClass(Resource):
+    def get(self, name):
+        return {
+            "My name is" : name
+        }
+
+vv_space = api.namespace('VariantValidator', description='VariantValidator APIs')
+@vv_space.route("/variantvalidator/<string:genome_build>/<string:variant_description>/<string:select_transcripts>")
+class VariantValidatorClass(Resource):
+    def get(self, genome_build, variant_description, select_transcripts):
+
+        # Make a request to the curent VariantValidator rest-API
+        url = '/'.join(['http://rest.variantvalidator.org/variantvalidator', genome_build, variant_description, select_transcripts])
+        validation = requests.get(url)
+        content = validation.json()
+        return content
+
+# Allows app to be run in debug mode
+if __name__ == '__main__':
+    application.debug = True # Enable debugging mode
+    application.run(host="127.0.0.1", port=5000) # Specify a host and port fot the app

application/requirements.txt

@@ -0,0 +1,3 @@
+flask==1.1.1
+flask_restplus
+Werkzeug==0.16.1