started with the query endpoint and request's errors

cgbeacon2/constants/__init__.py

@@ -1,2 +1,3 @@
 from .consent_codes import CONSENT_CODES
 from .variant_constants import CHROMOSOMES
+from .response_objs import MISSING_PARAMS_ERROR

cgbeacon2/constants/response_objs.py

@@ -0,0 +1,7 @@
+# Error objects
+MISSING_PARAMS_ERROR = dict(
+    error=dict(
+        errorCode=400,
+        errorMessage="Missing one or more mandatory parameters (referenceName, referenceBases, assemblyId)"
+    )
+)

cgbeacon2/server/blueprints/api_v1/controllers.py

@@ -0,0 +1,34 @@
+# -*- coding: utf-8 -*-
+import logging
+from flask import request
+from cgbeacon2.constants import MISSING_PARAMS_ERROR
+
+LOG = logging.getLogger(__name__)
+
+def set_query(req):
+    """Create a a query dictionary from GET or POST requests sent to the query endpoint.
+
+    Accepts:
+        req(flask.request)
+
+    Returns:
+        query(dict)
+    """
+    data = None
+    query = {}
+    if request.method == "GET":
+        data = req.args
+    else: # POST method
+        data = req.data
+
+    # check if the minimal required params were provided in query
+    if None in [data.get("referenceName"), data.get("referenceBases"), data.get("assemblyId")]:
+        # return a bad request 400 error with explanation message
+        return MISSING_PARAMS_ERROR
+
+
+    query = dict(
+
+    )
+
+    return data

cgbeacon2/server/blueprints/api_v1/views.py

@@ -1,13 +1,12 @@
 # -*- coding: utf-8 -*-
 import logging
-from flask import Blueprint, current_app, jsonify
+from flask import Blueprint, current_app, jsonify, request
 from cgbeacon2.models import Beacon
+from .controllers import set_query
 
 LOG = logging.getLogger(__name__)
-
 api1_bp = Blueprint("api_v1", __name__,)
 
-
 @api1_bp.route("/apiv1.0/", methods=["GET"])
 def info():
     """Returns Beacon info data as a json object"""
@@ -18,3 +17,21 @@ def info():
     resp = jsonify(beacon_obj.__dict__)
     resp.status_code = 200
     return resp
+
+
+@api1_bp.route("/apiv1.0/query", methods=["GET", "POST"])
+def query():
+    """Create a query from params provided in the request and return a response with eventual results"""
+
+    resp_obj = {}
+    # test query:  http://127.0.0.1:5000/apiv1.0/query?assemblyId=GRCh37&referenceName=1&start=1138913&alternateBases=T&includeDatasetResponses=true
+    query = set_query(request)
+
+    if "error" in query:
+        # query was not valid return error response
+        resp_obj["message"] = dict(query)
+        resp = jsonify(resp_obj)
+        resp.status_code = query["error"]["errorCode"]
+        return resp
+
+    return "HELLO THERE"

tests/conftest.py

@@ -34,6 +34,20 @@ def mock_app(database):
     return app
 
 
+@pytest.fixture
+def query_snv():
+    """A dictionary containing test query params"""
+    query = dict(
+        assembly = "GRCh37",
+        chrom = "1",
+        start = 235850063,
+        ref = "C",
+        alt = "A",
+        include_ds_resp = "ALL"
+    )
+    return query
+
+
 @pytest.fixture
 def test_dataset_cli():
     """A test dataset dictionary"""

tests/server/blueprints/api_v1/test_views.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 import json
+from cgbeacon2.constants import MISSING_PARAMS_ERROR
 
 
 def test_info(mock_app):
@@ -14,3 +15,28 @@ def test_info(mock_app):
     fields = ["id", "name", "apiVersion", "organisation", "datasets"]
     for field in fields:
         assert data[field] is not None
+
+
+def test_query_get_request_missing_params(mock_app):
+    """Test the query endpoint by sending a request without required params"""
+
+    # When a request missing one or more required params is sent to the server
+    response = mock_app.test_client().get("/apiv1.0/query?")
+
+    # Then it should return error
+    assert response.status_code == 400
+    data = json.loads(response.data)
+    assert data["message"]["error"] == MISSING_PARAMS_ERROR["error"]
+
+
+
+"""
+def test_query_get_request(mock_app, query_snv):
+    Test the query endpoint by sending a GET request
+
+    query_string = f'query?assemblyId={query_snv["assembly"]}&referenceName={query_snv["chrom"]}&start={query_snv["start"]}&alternateBases={query_snv["alt"]}&includeDatasetResponses={query_snv["include_ds_resp"]}'
+
+    response = mock_app.test_client().get("".join(["/apiv1.0/", query_string]))
+    assert response.status_code == 200
+
+"""