Api tutorial - Unit Checkpint 3

application/app_v1.py

@@ -4,7 +4,7 @@
 
 # Import modules
 from flask import Flask
-from flask_restplus import Api, Resource
+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,
@@ -27,5 +27,7 @@ def get(self):
 
 # Allows app to be run in debug mode
 if __name__ == '__main__':
+	#from waitress import serve
 	application.debug = True # Enable debugging mode
+	#serve(application, host = "127.0.0.1", port=5000)
 	application.run(host="127.0.0.1", port=5000) # Specify a host and port fot the app

application/app_v2.py

@@ -4,7 +4,7 @@
 
 # Import modules
 from flask import Flask
-from flask_restplus import Api, Resource
+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,

application/app_v3.py

@@ -3,9 +3,10 @@
 """
 
 # Import modules
-from flask import Flask
-from flask_restplus import Api, Resource
-import _____
+from flask import Flask, make_response
+from flask_restx import Api, Resource, reqparse
+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,
@@ -15,6 +16,28 @@
 # Define the API as api
 api = Api(app = application)
 
+# Define a parser:
+parser = reqparse.RequestParser()
+parser.add_argument('content-type',
+                    type = str,
+                    help = 'Accepted:\n- application/json\n- text/xml')
+
+# Add API representations:
+# For xml:
+@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
+
+# For json:
+@api.representation('application/json')
+def json(data, code, headers):
+    resp = make_response(data, code)
+    resp.headers['Content-Type'] = 'application/json'
+    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')
@@ -33,17 +56,37 @@ def get(self, name):
         return {
             "My name is" : name
         }
-
+
+# Exercise 2 part 1:
 vv_space = api.namespace('VariantValidator', description='VariantValidator APIs')
-@vv_space.route("/variantvalidator/_____")
+@vv_space.route("/variantvalidator/<string:genome_build>/<string:var_desc>/<string:select_transcripts>")
 class VariantValidatorClass(Resource):
-    def get(self, _____):
+
+    @api.doc(parser = parser)
+
+    def get(self, genome_build, var_desc, select_transcripts):
 
         # Make a request to the curent VariantValidator rest-API
-        url = _____
-        validation = _____
-        content = _____
-        return _____
+        url = f"https://rest.variantvalidator.org/{genome_build}/{var_desc}/{select_transcripts}"
+        validation = requests.get(url)
+        content = validation.json()
+
+        # Collect arguments from the parser:
+        args = parser.parse_args()
+
+        # If content-type specified - return the content object in that format:
+        if args['content-type'] == 'application/json':
+            return json(content, 200, None)
+
+        elif args['content-type'] == 'text/xml':
+            return xml(content, 200, None)
+
+        # Return in the default format:
+        else:
+            return content
+
+# Exercise 2 part 3:
+
 
 # Allows app to be run in debug mode
 if __name__ == '__main__':

application/app_v4.py

@@ -4,7 +4,7 @@
 
 # Import modules
 from flask import Flask, make_response
-from flask_restplus import Api, Resource
+from flask_restx import Api, Resource
 import requests
 from dicttoxml import dicttoxml
 

application/app_v5.py

@@ -4,7 +4,7 @@
 
 # Import modules
 from flask import Flask, make_response
-from flask_restplus import Api, Resource, reqparse
+from flask_restx import Api, Resource, reqparse
 import requests
 from dicttoxml import dicttoxml
 

application/app_v6.py

@@ -4,7 +4,7 @@
 
 # Import modules
 from flask import Flask, make_response, request
-from flask_restplus import Api, Resource, reqparse, fields, abort
+from flask_restx import Api, Resource, reqparse, fields, abort
 import requests
 from requests.exceptions import ConnectionError
 from dicttoxml import dicttoxml

application/my_requests.py

@@ -0,0 +1,91 @@
+# import the requests module
+import requests
+import urllib.parse
+
+# Create the class
+class MyRequests:
+
+    def __init__(self):
+        self.base_url = None
+        self.url = None
+
+    # method that makes the call to the API using the get method:
+    def request_data(self, prms = None):
+        return requests.get(self.url, params = prms)
+
+    # method that assembles the url to request data from the hello endpoint:
+    def hello(self):
+        self.url = f"{self.base_url}hello"
+        return self.request_data()
+
+    # method to get data from the name endpoint:
+    def name_get(self, name):
+        self.url = f"{self.base_url}name/{name}"
+        return self.request_data()
+
+    # method to get data from the VariantValidator endpoint: ## Have been quite confused about what the last two bits of exercise 2 are asking for - is it make changes to app v3 to add requesting diff. content types and then to here?
+    def VV_get(self, gbuild, vdesc, seltrans, content_type = None):
+
+        # If want to request as xml:
+        if content_type == 'xml':
+            self.url = f"{self.base_url}VariantValidator/variantvalidator/{gbuild}/{vdesc}/{seltrans}?content-type=text/xml"
+
+        # If want to request as json:
+        elif content_type == 'json':
+            self.url = f"{self.base_url}VariantValidator/variantvalidator/{gbuild}/{vdesc}/{seltrans}?content-type=application/json"
+
+        # Else use default url:
+        else:
+            self.url = f"{self.base_url}VariantValidator/variantvalidator/{gbuild}/{vdesc}/{seltrans}"
+
+        return self.request_data()
+
+
+
+if __name__ == "__main__":
+    mrq = MyRequests()
+
+    # Set the base url
+    mrq.base_url = "http://127.0.0.1:5000/"
+
+    ### hello endpoint:
+    # request the data
+    response_hello = mrq.hello()
+
+    # print the 3 response sections
+    print(response_hello.status_code)
+    print(response_hello.headers)
+    print(response_hello.text)
+    print(response_hello.json())
+
+    ### name endpoint:
+    name = 'Tom'
+    response_nm = mrq.name_get(name)
+    print(response_nm.status_code)
+    print(response_nm.headers)
+    print(response_nm.text)
+    print(response_nm.json())
+
+    ## VariantValidator endpoint - left these blank for now:
+    gbuild = 'hg19'
+    #gbuild = 'xxx'
+    vdesc = 'NM_000088.3:c.589G>T'
+    #vdesc = 'xxx'
+    seltrans = 'NM_000088.3'
+    #seltrans = ''
+    content_type = ''
+
+    # Need to do some url parsing as varint descriptions and transcripts can have reserved characters:
+    url_vdesc = urllib.parse.quote(vdesc)
+    url_seltrans = urllib.parse.quote(seltrans)
+
+    print(url_seltrans, url_vdesc)
+
+    response_VV = mrq.VV_get(gbuild, url_vdesc, url_seltrans, content_type)
+
+    print(response_VV.status_code)
+
+    if content_type == 'xml':
+        print(response_VV.text)
+    else:
+        print(response_VV.json())

application/requirements.txt

@@ -1,3 +1,6 @@
-flask==1.1.1
-flask_restplus
-Werkzeug==0.16.1
+flask==2.3.0
+flask-restx==1.0.0
+Werkzeug==2.3.3
+requests==2.31.0
+urllib
+dicttoxml

application/rest_api/app.py

@@ -4,7 +4,8 @@
 
 # Import modules
 from flask import Flask, request
-from endpoints import api, representations, exceptions, request_parser
+from endpoints import api
+from utils import representations, exceptions, request_parser
 import logging
 from logging import handlers
 import time

application/rest_api/endpoints/__init__.py

@@ -1,4 +1,4 @@
-from flask_restplus import Api
+from flask_restx import Api
 
 from .hello import api as ns_hello
 from .name import api as ns_name

application/rest_api/endpoints/hello.py

@@ -1,6 +1,6 @@
-from flask_restplus import Namespace, Resource
-from . import request_parser
-from . import representations
+from flask_restx import Namespace, Resource
+from utils import request_parser
+from utils import representations
 
 
 """

application/rest_api/endpoints/name.py

@@ -1,6 +1,6 @@
-from flask_restplus import Namespace, Resource
-from . import request_parser
-from . import representations
+from flask_restx import Namespace, Resource
+from utils import request_parser
+from utils import representations
 
 
 """

application/rest_api/endpoints/variantvalidator_endpoints.py

@@ -1,9 +1,9 @@
-from flask_restplus import Namespace, Resource
-from . import request_parser
-from . import representations
+from flask_restx import Namespace, Resource
+from utils import request_parser
+from utils import representations
 import requests
 from requests.exceptions import ConnectionError
-from . import exceptions
+from utils import exceptions
 
 """
 Create a parser object locally

application/rest_api/endpoints/request_parser.py → application/rest_api/utils/request_parser.py

@@ -1,4 +1,4 @@
-from flask_restplus import reqparse
+from flask_restx import reqparse
 
 
 # Create a RequestParser object to identify specific content-type requests in HTTP URLs

environment.yml

@@ -0,0 +1,4 @@
+name: tl1_vv_env
+dependencies:
+  - python==3.12
+  - pip

rest_variantValidator/app.py

@@ -7,7 +7,7 @@
 
 # IMPORT FLASK MODULES
 from flask import Flask ,request, jsonify, abort, url_for, g, send_file, redirect, Blueprint #, session, g, redirect, , abort, render_template, flash, make_response, abort
-from flask_restful import Resource, Api, reqparse, abort, fields, marshal_with
+from flask_restx import Resource, Api, reqparse, abort, fields, marshal_with
 from vv_flask_restful_swagger import swagger
 from flask_log import Logging
 from flask_mail import Mail, Message