Revert "mfinder second commit, most functions moved to util file. Modified in…"

api/resources/interactions.py

@@ -5,10 +5,9 @@
 """
 
 from flask_restx import Namespace, Resource, fields
-from flask import request, jsonify
+from flask import request
 from markupsafe import escape
 from api.utils.bar_utils import BARUtils
-from api.utils.mfinder_utils import MfinderUtils
 from marshmallow import Schema, ValidationError, fields as marshmallow_fields
 from api import db
 from api.models.rice_interactions import Interactions as RiceInteractions
@@ -157,26 +156,3 @@ def post(self):
             return BARUtils.success_exit(res)
         else:
             return BARUtils.error_exit("No data for the given species/genes"), 400
-
-
-@itrns.route("/mfinder")
-class MFinder(Resource):
-    @itrns.expect(post_int_data)
-    def post(self):
-        """This endpoint was originally written by Vincent Lau to return mFinder
-        results to AGENT in his express node.JS app. However Tianhui Zhao refactored
-        to the BAR_API
-        """
-        data = request.get_json()
-        # Validate json
-        try:
-            data = MFinderDataSchema().load(data)
-        except ValidationError as err:
-            return BARUtils.error_exit(err.messages), 400
-
-        filtered_valid_arr = MfinderUtils.input_validation(data["data"])
-        if isinstance(filtered_valid_arr, str):
-            return BARUtils.error_exit(filtered_valid_arr), 400
-        settings = MfinderUtils.settings_validation(data.get("options", {}))
-        ret_json = MfinderUtils.create_files_and_mfinder(filtered_valid_arr, settings)
-        return jsonify(MfinderUtils.beautify_results(ret_json))

tests/resources/test_interactions.py

@@ -1,7 +1,6 @@
 from api import app
 from unittest import TestCase
 import json
-from json import load
 
 
 class TestIntegrations(TestCase):
@@ -132,57 +131,3 @@ def test_post_itrns(self):
             "error": "No data for the given species/genes",
         }
         self.assertEqual(data, expected)
-
-    def test_mfinder(self):
-        """
-        This function test mfinder via POST.
-        """
-        # Valid request
-        with open("tests/data/mfinder_input.json") as json_file_1:
-            input_data = load(json_file_1)
-        response = self.app_client.post(
-            "/interactions/mfinder",
-            json=input_data,
-        )
-        data = json.loads(response.get_data(as_text=True))
-        with open("tests/data/mfinder_output.json") as json_file_2:
-            expected = load(json_file_2)
-        self.assertEqual(data, expected)
-
-        # Invalid data structure
-        response = self.app_client.post("/interactions/mfinder", json={"data": {}})
-        data = json.loads(response.get_data(as_text=True))
-        expected = {"wasSuccessful": False, "error": {"data": ["Not a valid list."]}}
-        self.assertEqual(data, expected)
-
-        response = self.app_client.post("/interactions/mfinder", json={"data": []})
-        data = json.loads(response.get_data(as_text=True))
-        expected = {"wasSuccessful": False, "error": "arr length 0!"}
-        self.assertEqual(data, expected)
-
-        response = self.app_client.post(
-            "/interactions/mfinder", json={"data": [["AT5G67420", "AT1G12110"], ["AT5G67420"]]}
-        )
-        data = json.loads(response.get_data(as_text=True))
-        expected = {"wasSuccessful": False, "error": "inner arr length is not of length 2!"}
-        self.assertEqual(data, expected)
-
-        response = self.app_client.post("/interactions/mfinder", json={"data": [["AT5G67420", "AT1G12110"], 1]})
-        data = json.loads(response.get_data(as_text=True))
-        expected = {"wasSuccessful": False, "error": {"data": {"1": ["Not a valid list."]}}}
-        self.assertEqual(data, expected)
-
-        response = self.app_client.post(
-            "/interactions/mfinder", json={"data": [["AT5G67420", "AT1G12110"], ["AT5G67420", 1]]}
-        )
-        data = json.loads(response.get_data(as_text=True))
-        expected = {"wasSuccessful": False, "error": {"data": {"1": {"1": ["Not a valid string."]}}}}
-        self.assertEqual(data, expected)
-
-        # Invalid gene ID
-        response = self.app_client.post(
-            "/interactions/mfinder", json={"data": [["AT1G01010", "AT5G01010"], ["001G01030", "AT2G03240"]]}
-        )
-        data = json.loads(response.get_data(as_text=True))
-        expected = {"wasSuccessful": False, "error": "Invalid gene ID contained!"}
-        self.assertEqual(data, expected)