Merge pull request #18 from Knox-AAU/architecture_fix

Architecture fix

.vscode/settings.json

@@ -0,0 +1,11 @@
+{
+ "python.testing.unittestArgs": [
+ "-v",
+ "-s",
+ ".",
+ "-p",
+ "test_*.py"
+ ],
+ "python.testing.pytestEnabled": false,
+ "python.testing.unittestEnabled": true
+}

relation_extraction/API_handler.py

@@ -0,0 +1,17 @@
+
+from abc import ABCMeta, abstractmethod
+
+class APIHandler(metaclass=ABCMeta):
+ @property
+ @classmethod
+ @abstractmethod
+ def API_endpoint():
+ """Property used to define the API_endpoint for the subclass of APIHandler"""
+ pass
+
+ @classmethod 
+ @abstractmethod
+ def send_request(request): 
+ pass
+
+

relation_extraction/LessNaive/lessNaive.py

@@ -1,12 +1,12 @@
+from relation_extraction.ontology_messenger import OntologyMessenger
+from relation_extraction.knowledge_graph_messenger import KnowledgeGraphMessenger
 from .openie import POST_corenlp
 import json
 import sys 
 
 import urllib.parse
 from strsimpy.normalized_levenshtein import NormalizedLevenshtein
 from rapidfuzz.distance import Levenshtein
-from relation_extraction.output import format_output
-from relation_extraction.get_relations import extract_specific_relations
 
 
 def find_best_ontology_match(api_relation, ontology_relations):
@@ -68,11 +68,11 @@ def do_relation_extraction(data, ontology_relations):
  relations.extend(val["relations"])
 
  tuples = [[r["subject"], r["relation"], r["object"]] for r in relations]
- format_output(tuples)
+ KnowledgeGraphMessenger.format_output(tuples)
  return tuples
 
 def main():
- ontology_relations = extract_specific_relations()
+ ontology_relations = OntologyMessenger.send_request()
  do_relation_extraction(json.load(open("inputSentences.json")), ontology_relations) 
 
 

relation_extraction/NaiveMVP/main.py

@@ -1,9 +1,9 @@
 import json
+from relation_extraction.knowledge_graph_messenger import KnowledgeGraphMessenger
 import strsimpy
 import sys
 from strsimpy.normalized_levenshtein import NormalizedLevenshtein
-from relation_extraction.output import send_to_database_component
-from relation_extraction.get_relations import extract_specific_relations
+from relation_extraction.ontology_messenger import OntologyMessenger
 import datetime
 import multiprocessing as mp
 from functools import partial
@@ -71,7 +71,7 @@ def parse_data(data, relations):
 
 def handle_relation_post_request(data):
  try:
- relations = extract_specific_relations()
+ relations = OntologyMessenger.send_request()
  except Exception as E:
  print(f"Exception during retrieval of relations: {str(E)}")
  raise Exception(f"Exception during retrieval of relations")
@@ -83,19 +83,19 @@ def handle_relation_post_request(data):
  raise Exception("Incorrectly formatted input. Exception during parsing")
 
  try:
- send_to_database_component(parsed_data)
+ KnowledgeGraphMessenger.send_request(parsed_data)
  except Exception as E:
  print(f"Exception during request to database. {str(E)}")
  raise Exception("Data was not sent to database due to connection error")
 
 
 def main():
- relations = extract_specific_relations()
+ relations = OntologyMessenger.send_request()
  # Opening JSON file
  with open('inputSentences.json', 'r') as f:
  # returns JSON object as a dictionary 
  data = json.load(f)
- send_to_database_component(parse_data(data, relations))
+ KnowledgeGraphMessenger.send_request(parse_data(data, relations))
 
 if __name__ == "__main__":
  main()

relation_extraction/evaluation/evaluation.py

@@ -1,13 +1,14 @@
 import sys
 import xml.etree.ElementTree as ET
+from relation_extraction.ontology_messenger import OntologyMessenger
 from relation_extraction.LessNaive.lessNaive import do_relation_extraction
 from relation_extraction.NaiveMVP.main import parse_data
 import re
-from relation_extraction.get_relations import extract_specific_relations
 import datetime
 import json
 
 
+
 def printProgressBar (iteration, total, prefix = '', suffix = '', decimals = 3, length = 100, fill = '█', printEnd = "\r"):
  percent = ("{0:." + str(decimals) + "f}").format(100 * (iteration / float(total)))
  filledLength = int(length * iteration // total)
@@ -54,7 +55,7 @@ def calculate_metrics(data):
 def main():
  input_objs = convert_testdata_to_input_format()
  print("testdata converted successfully")
- ontology_relations = extract_specific_relations()
+ ontology_relations = OntologyMessenger.send_request()
 
 
  solutions_to_test = {

relation_extraction/knowledge_graph_messenger.py

@@ -0,0 +1,24 @@
+import requests
+
+from relation_extraction.API_handler import APIHandler
+
+class KnowledgeGraphMessenger(APIHandler):
+ def API_endpoint():
+ return "http://130.225.57.13/knox-api/triples"
+
+ def send_request(output):
+ HEADERS = {"Access-Authorization":"internal_key"}
+ PARAMS={"g": "http://knox_database"}
+ FORMATTED_OUTPUT = KnowledgeGraphMessenger.format_output(output)
+ response = requests.post(url=KnowledgeGraphMessenger.API_endpoint(), json=FORMATTED_OUTPUT, params=PARAMS, headers=HEADERS)
+ print(f"db component response: {response.text}")
+ return response.text
+
+ @classmethod
+ def format_output(self, output):
+ formatted_output = {"triples": output}
+ return formatted_output
+
+
+
+

relation_extraction/meta_data_messenger.py

@@ -0,0 +1,8 @@
+from relation_extraction.API_handler import APIHandler
+
+class MetaDataMessenger(APIHandler):
+ def API_endpoint():
+ pass
+
+ def send_request(request_content):
+ pass

relation_extraction/ontology_messenger.py

@@ -0,0 +1,30 @@
+import requests
+import re
+
+from relation_extraction.API_handler import APIHandler
+
+class OntologyMessenger(APIHandler):
+ def API_endpoint():
+ return "http://130.225.57.13/knox-api/triples"
+
+ def send_request():
+ "Function to extract relations based on the specified pattern"
+ print("Getting relations from online ontology...")
+ relations = []
+ query_string_s = 'http://dbpedia.org/ontology/'
+ query_string_o = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#Property'
+ PARAMS = {"g":"http://knox_ontology", "s": query_string_s, "o": query_string_o}
+ HEADERS = {"Access-Authorization":"internal_key"}
+ r = requests.get(url=OntologyMessenger.API_endpoint(), params=PARAMS, headers=HEADERS)
+ print(f"db component response: {r.text}")
+
+ data = r.json()
+
+ for triple in data["triples"]:
+ relation = re.split("http://dbpedia.org/ontology/", triple["s"]["Value"])[1]
+ relations.append(relation)
+
+ return relations
+
+if __name__ == "__main__":
+ OntologyMessenger.send_request()

relation_extraction/relation_extractor.py

@@ -0,0 +1,7 @@
+from relation_extraction.NaiveMVP.main import handle_relation_post_request
+
+
+class RelationExtractor():
+ @classmethod
+ def begin_extraction(self, data):
+ handle_relation_post_request(data)

server/server.py

@@ -2,6 +2,7 @@
 import json
 import os
 from relation_extraction.NaiveMVP.main import handle_relation_post_request
+from relation_extraction.relation_extractor import RelationExtractor
 
 class PreProcessingHandler(BaseHTTPRequestHandler):
  def do_POST(self):
@@ -23,7 +24,7 @@ def do_POST(self):
 
  if self.path == '/tripleconstruction':
  try:
- handle_relation_post_request(post_content["post_json"])
+ RelationExtractor.begin_extraction(post_content["post_json"])
  self.send_response(200)
  self.send_header('Content-type','text/html')
  self.end_headers()

test/test_server/test_get_relations.py

@@ -1,7 +1,7 @@
 import unittest
+from relation_extraction.ontology_messenger import OntologyMessenger
 from server.server import *
 from unittest.mock import patch, Mock, MagicMock, mock_open
-from relation_extraction.get_relations import *
 
 class TestGetRelations(unittest.TestCase):
 
@@ -18,22 +18,14 @@ def test_extract_specific_relations(self, mock_get):
  mock_get.return_value.json.return_value = response
  mock_get.return_value.text.return_value = "request response"
 
- relations = extract_specific_relations()
+ relations = OntologyMessenger.send_request()
 
  self.assertEqual(len(relations), 2)
  self.assertEqual(relations[0], "test")
  self.assertEqual(relations[1], "another_test")
  mock_get.assert_called_once_with(url='http://130.225.57.13/knox-api/triples', params={'g': 'http://knox_ontology', 's': 'http://dbpedia.org/ontology/', 'o': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#Property'}, headers={'Access-Authorization': 'internal_key'})
 
 
- @patch("builtins.open", new_callable=mock_open, read_data=":testline\na rdf:Property, owl:ObjectProperty ;")
- def test_extract_specific_relations_offline(self, mock_open):
- res = extract_specific_relations_offline()
- mock_open.assert_called_once()
-
- self.assertEqual(res, ["testline"])
-
-
 
 if __name__ == "__main__":
  unittest.main()

test/test_server/test_output.py

@@ -1,12 +1,12 @@
 import unittest
-from relation_extraction.output import *
+from relation_extraction.knowledge_graph_messenger import KnowledgeGraphMessenger
 from unittest.mock import patch, Mock, MagicMock
 
 class TestOutput(unittest.TestCase):
 
  def test_format_output(self):
  input = [["this", "is", "triples"]]
- res = format_output(input)
+ res = KnowledgeGraphMessenger.format_output(input)
  self.assertTrue("triples" in res.keys())
  self.assertEqual(res["triples"], input)
 
@@ -15,7 +15,7 @@ def test_send_to_database(self, mock_request):
  mock_response = MagicMock()
  mock_response.text = "response"
  mock_request.return_value = mock_response
- res = send_to_database_component("test_output")
+ res = KnowledgeGraphMessenger.send_request("test_output")
 
  mock_request.assert_called_once_with(url='http://130.225.57.13/knox-api/triples', json={'triples': 'test_output'}, params={'g': 'http://knox_database'}, headers={'Access-Authorization': 'internal_key'})
  self.assertEqual(res, "response")

test/test_server/test_pre_processing_handler.py

@@ -5,7 +5,7 @@
 
 class TestPreProcessingHandler(unittest.TestCase):
  @patch("os.getenv")
- @patch('server.server.handle_relation_post_request', return_value=Mock()) 
+ @patch('relation_extraction.relation_extractor.RelationExtractor.begin_extraction', return_value=Mock()) 
  @patch.object(PreProcessingHandler, 'wrongly_formatted_request_response')
  @patch.object(PreProcessingHandler, 'handled_request_body', return_value=True)
  @patch.object(PreProcessingHandler, '__init__', return_value=None)
@@ -57,7 +57,7 @@ def test_do_post_invalid_endpoint(self, mock_init, mock_handled_body, mock_wrong
  handler.end_headers.assert_called_once()
 
  @patch("os.getenv")
- @patch('server.server.handle_relation_post_request', return_value=Mock()) 
+ @patch('relation_extraction.relation_extractor.RelationExtractor.begin_extraction', return_value=Mock()) 
  @patch.object(PreProcessingHandler, 'wrongly_formatted_request_response')
  @patch.object(PreProcessingHandler, 'handled_request_body', return_value=True)
  @patch.object(PreProcessingHandler, '__init__', return_value=None)

test/test_server/test_relation_extraction.py

@@ -4,7 +4,7 @@
 
 
 class TestHandleRelationPostRequest(unittest.TestCase):
- @mock.patch('relation_extraction.NaiveMVP.main.extract_specific_relations')
+ @mock.patch('relation_extraction.ontology_messenger.OntologyMessenger.send_request')
  def test_handle_post_request_raises_exception_if_relations_fail(self, mock_extract_specific_relations):
  mock_extract_specific_relations.side_effect = Exception()
  data = dict()
@@ -15,7 +15,7 @@ def test_handle_post_request_raises_exception_if_relations_fail(self, mock_extra
 
 
  @mock.patch('relation_extraction.NaiveMVP.main.parse_data')
- @mock.patch('relation_extraction.NaiveMVP.main.extract_specific_relations')
+ @mock.patch('relation_extraction.ontology_messenger.OntologyMessenger.send_request')
  def test_handle_post_request_raises_exception_if_parse_fail(self, mock_extract_specific_relations, mock_parse_data):
  mock_extract_specific_relations.return_value = []
  mock_parse_data.side_effect = Exception()
@@ -28,9 +28,9 @@ def test_handle_post_request_raises_exception_if_parse_fail(self, mock_extract_s
  mock_parse_data.assert_called_once()
 
 
- @mock.patch('relation_extraction.NaiveMVP.main.send_to_database_component')
+ @mock.patch('relation_extraction.knowledge_graph_messenger.KnowledgeGraphMessenger.send_request')
  @mock.patch('relation_extraction.NaiveMVP.main.parse_data')
- @mock.patch('relation_extraction.NaiveMVP.main.extract_specific_relations')
+ @mock.patch('relation_extraction.ontology_messenger.OntologyMessenger.send_request')
  def test_handle_post_request_raises_exception_if_db_component_fail(self, mock_extract_specific_relations, mock_parse_data, mock_send_to_db):
  mock_extract_specific_relations.return_value = []
  mock_parse_data.return_value = dict()