changeed names and added tests

verarbeitung/construct_new_graph/add_citations_rec.py

@@ -22,6 +22,22 @@ sys.path.append("../")
 from input.publication import Publication
 from verarbeitung.get_pub_from_input import get_pub
 
+def create_graph_structure_citations_test(pub, search_depth, search_depth_max, cit_type, test_var, test_nodes, test_edges):
+    '''
+        :param test_nodes:      list of publications from unit test
+        :type test_nodes:       List[Publication]
+
+        :param test_edges:      list of links from unit test
+        :type test_edges:       List[List[String,String]]
+
+        for unit test purposes only
+    '''
+    global nodes, edges
+    nodes = test_nodes
+    edges = test_edges
+    return(nodes, edges, create_graph_structure_citations(pub, search_depth, search_depth_max, cit_type, test_var))
+
+
 def get_cit_type_list(pub, cit_type):
     '''
         :param pub:                 Publication which citations will be added

verarbeitung/construct_new_graph/export_to_json.py

@@ -79,8 +79,12 @@ def output_to_json(nodes, edges, json_file = 'json_text.json', test_var = False)
     dict_of_all["nodes"] = list_of_node_dicts
     dict_of_all["links"] = list_of_edge_dicts
     if (test_var):
-        with open('test_output.json','w') as outfile:
-            json.dump(dict_of_all, outfile)
+        if json_file != 'json_text.json':
+            with open(json_file,'w') as outfile:
+                json.dump(dict_of_all, outfile)
+        else:
+            with open('test_output.json','w') as outfile:
+                json.dump(dict_of_all, outfile)
     else:
         with open(json_file,'w') as outfile:
             json.dump(dict_of_all, outfile)

verarbeitung/construct_new_graph/initialize_graph.py

@@ -27,18 +27,6 @@ from .add_citations_rec import add_citations, create_global_lists_cit
 
 def initialize_nodes_list_test(doi_input_list, search_depth_max, search_height_max, test_var):
     '''
-        :param doi_input_list:      input list of doi from UI
-        :type doi_input_list:       List[String]
-
-        :param search_depth_max:    maximum depth to search for references
-        :type search_depth_max:     int
-
-        :param search_height_max:   maximum height to search for citations
-        :type search_height_max:    int
-
-        :param test_var:            variable to differenciate between test and url call
-        :type test_var:             boolean
-
         for unit test purposes only
     '''
     global nodes, edges
@@ -51,8 +39,8 @@ def complete_inner_edges_test(test_nodes, test_edges):
         :param test_nodes:      list of publications from unit test
         :type test_nodes:       List[Publication]
 
-        :param test_nodes:      list of links from unit test
-        :type test_nodes:       List[List[String,String]]
+        :param test_edges:      list of links from unit test
+        :type test_edges:       List[List[String,String]]
 
         for unit test purposes only
         '''

verarbeitung/new_height.json

+{"nodes": [{"doi": "doi_lg_1_i", "name": "title_lg_1_i", "author": ["contributor_lg_1_i"], "year": "date_lg_1_i", "journal": "journal_lg_1_i", "group": "Input", "depth": 0, "citations": 2}, {"doi": "doi_lg_1_d11", "name": "title_lg_1_d11", "author": ["contributor_lg_1_d11"], "year": "date_lg_1_d11", "journal": "journal_lg_1_d11", "group": "Reference", "depth": -1, "citations": 1}, {"doi": "doi_lg_1_d12", "name": "title_lg_1_d12", "author": ["contributor_lg_1_d12"], "year": "date_lg_1_d12", "journal": "journal_lg_1_d12", "group": "Reference", "depth": -1, "citations": 2}, {"doi": "doi_lg_1_h11", "name": "title_lg_1_h11", "author": ["contributor_lg_1_h11"], "year": "date_lg_1_h11", "journal": "journal_lg_1_h11", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "doi_lg_1_h12", "name": "title_lg_1_h12", "author": ["contributor_lg_1_h12"], "year": "date_lg_1_h12", "journal": "journal_lg_1_h12", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "doi_lg_1_h21", "name": "title_lg_1_h21", "author": ["contributor_lg_1_h21"], "year": "date_lg_1_h21", "journal": "journal_lg_1_h21", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_1_h22", "name": "title_lg_1_h22", "author": ["contributor_lg_1_h22"], "year": "date_lg_1_h22", "journal": "journal_lg_1_h22", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_1_h23", "name": "title_lg_1_h23", "author": ["contributor_lg_1_h23"], "year": "date_lg_1_h23", "journal": "journal_lg_1_h23", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_1_d21", "name": "title_lg_1_d21", "author": ["contributor_lg_1_d21"], "year": "date_lg_1_d21", "journal": "journal_lg_1_d21", "group": "Reference", "depth": -2, "citations": 2}, {"doi": "doi_lg_1_d22", "name": "title_lg_1_d22", "author": ["contributor_lg_1_d22"], "year": "date_lg_1_d22", "journal": "journal_lg_1_d22", "group": "Reference", "depth": -2, "citations": 2}, {"doi": "doi_lg_1_d23", "name": "title_lg_1_d23", "author": ["contributor_lg_1_d23"], "year": "date_lg_1_d23", "journal": "journal_lg_1_d23", "group": "Reference", "depth": -2, "citations": 2}], "links": [{"source": "doi_lg_1_i", "target": "doi_lg_1_d11"}, {"source": "doi_lg_1_i", "target": "doi_lg_1_d12"}, {"source": "doi_lg_1_h11", "target": "doi_lg_1_i"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_i"}, {"source": "doi_lg_1_h21", "target": "doi_lg_1_h11"}, {"source": "doi_lg_1_h22", "target": "doi_lg_1_h11"}, {"source": "doi_lg_1_h22", "target": "doi_lg_1_h12"}, {"source": "doi_lg_1_h23", "target": "doi_lg_1_h12"}, {"source": "doi_lg_1_d11", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_d11", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d21", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d22", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_d12", "target": "doi_lg_1_d23"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_d12"}]}
\ No newline at end of file

verarbeitung/test/construct_graph_unittest.py

@@ -6,7 +6,7 @@ import sys
 sys.path.append("../")
 
 from verarbeitung.construct_new_graph.initialize_graph import init_graph_construction, initialize_nodes_list_test, complete_inner_edges_test
-from verarbeitung.construct_new_graph.add_citations_rec import get_cit_type_list
+from verarbeitung.construct_new_graph.add_citations_rec import get_cit_type_list, create_graph_structure_citations_test
 from verarbeitung.test.input_test import input_test_func
 
 class ConstructionTest(unittest.TestCase):
@@ -138,8 +138,51 @@ class ConstructionTest(unittest.TestCase):
           self.assertCountEqual(keep_only_dois(pub_lg_1_d_12_cits), keep_only_dois(pub_lg_1_d_12.citations))
 
      def test_create_graph_structure_citations(self):
-          print("Hallo")
+          pub_lg_1_i = input_test_func('doi_lg_1_i')
+          pub_lg_1_i.group = 0
+          pub_lg_1_h_11 = input_test_func('doi_lg_1_h11')
+          pub_lg_1_h_11.group = 1
+          pub_lg_1_h_12 = input_test_func('doi_lg_1_h12')
+          pub_lg_1_h_12.group = 1
+          pub_lg_1_d_11 = input_test_func('doi_lg_1_d11')
+          pub_lg_1_d_11.group = -1
+          pub_lg_1_d_12 = input_test_func('doi_lg_1_d12')
+          pub_lg_1_d_12.group = -1
 
+          # checks if citations/references are found and added
+          return_nodes, return_edges, cit_list = create_graph_structure_citations_test(pub_lg_1_i, 1, 2, "Citation", True, [pub_lg_1_i, pub_lg_1_d_11, pub_lg_1_d_12],[['doi_lg_1_i','doi_lg_1_d11'],['doi_lg_1_i','doi_lg_1_d12']])
+          self.assertCountEqual(return_nodes, [pub_lg_1_i, pub_lg_1_h_11, pub_lg_1_h_12, pub_lg_1_d_11, pub_lg_1_d_12])
+          self.assertCountEqual(return_edges, [['doi_lg_1_i','doi_lg_1_d11'],['doi_lg_1_i','doi_lg_1_d12'],['doi_lg_1_h11','doi_lg_1_i'],['doi_lg_1_h12','doi_lg_1_i']])
+          self.assertCountEqual(cit_list, [pub_lg_1_h_11, pub_lg_1_h_12])
+
+          return_nodes, return_edges, cit_list = create_graph_structure_citations_test(pub_lg_1_i, 1, 2, "Reference", True, [pub_lg_1_i, pub_lg_1_h_11, pub_lg_1_h_12],[['doi_lg_1_h11','doi_lg_1_i'],['doi_lg_1_h12','doi_lg_1_i']])
+          self.assertCountEqual(return_nodes, [pub_lg_1_i, pub_lg_1_h_11, pub_lg_1_h_12, pub_lg_1_d_11, pub_lg_1_d_12])
+          self.assertCountEqual(return_edges, [['doi_lg_1_i','doi_lg_1_d11'],['doi_lg_1_i','doi_lg_1_d12'],['doi_lg_1_h11','doi_lg_1_i'],['doi_lg_1_h12','doi_lg_1_i']])
+          self.assertCountEqual(cit_list, [pub_lg_1_d_11, pub_lg_1_d_12])
+
+          # checks if max depth/height is checked before added
+          return_nodes, return_edges, cit_list = create_graph_structure_citations_test(pub_lg_1_i, 1, 1, "Citation", True, [pub_lg_1_i, pub_lg_1_d_11, pub_lg_1_d_12],[['doi_lg_1_i','doi_lg_1_d11'],['doi_lg_1_i','doi_lg_1_d12']])
+          self.assertCountEqual(return_nodes, [pub_lg_1_i, pub_lg_1_d_11, pub_lg_1_d_12])
+          self.assertCountEqual(return_edges, [['doi_lg_1_i','doi_lg_1_d11'],['doi_lg_1_i','doi_lg_1_d12']])
+          self.assertCountEqual(cit_list, [])
+
+          return_nodes, return_edges, cit_list = create_graph_structure_citations_test(pub_lg_1_i, 1, 1, "Reference", True, [pub_lg_1_i, pub_lg_1_h_11, pub_lg_1_h_12],[['doi_lg_1_h11','doi_lg_1_i'],['doi_lg_1_h12','doi_lg_1_i']])
+          self.assertCountEqual(return_nodes, [pub_lg_1_i, pub_lg_1_h_11, pub_lg_1_h_12])
+          self.assertCountEqual(return_edges, [['doi_lg_1_h11','doi_lg_1_i'],['doi_lg_1_h12','doi_lg_1_i']])
+          self.assertCountEqual(cit_list, [])
+
+          # checks if max depth/height is checked before added but citation/reference from max depth/height found and added
+          return_nodes, return_edges, cit_list = create_graph_structure_citations_test(pub_lg_1_i, 1, 1, "Citation", True, [pub_lg_1_i, pub_lg_1_d_11, pub_lg_1_d_12, pub_lg_1_h_11],[['doi_lg_1_i','doi_lg_1_d11'],['doi_lg_1_i','doi_lg_1_d12']])
+          self.assertCountEqual(return_nodes, [pub_lg_1_i, pub_lg_1_d_11, pub_lg_1_d_12, pub_lg_1_h_11])
+          self.assertCountEqual(return_edges, [['doi_lg_1_i','doi_lg_1_d11'],['doi_lg_1_i','doi_lg_1_d12'],['doi_lg_1_h11','doi_lg_1_i']])
+          self.assertCountEqual(cit_list, [])
+
+          return_nodes, return_edges, cit_list = create_graph_structure_citations_test(pub_lg_1_i, 1, 1, "Reference", True, [pub_lg_1_i, pub_lg_1_h_11, pub_lg_1_h_12, pub_lg_1_d_11],[['doi_lg_1_h11','doi_lg_1_i'],['doi_lg_1_h12','doi_lg_1_i']])
+          self.assertCountEqual(return_nodes, [pub_lg_1_i, pub_lg_1_h_11, pub_lg_1_h_12, pub_lg_1_d_11])
+          self.assertCountEqual(return_edges, [['doi_lg_1_h11','doi_lg_1_i'],['doi_lg_1_h12','doi_lg_1_i'],['doi_lg_1_i','doi_lg_1_d11']])
+          self.assertCountEqual(cit_list, [])
+
+          
 
 def keep_only_dois(nodes):
      '''

verarbeitung/test_output.json

-{"nodes": [{"doi": "doi_h02", "name": "title_h02", "author": ["contributor_h02"], "year": "date_h02", "journal": "journal_h02", "group": "Input", "depth": 0, "citations": 1}, {"doi": "doi_h1", "name": "title_h1", "author": ["contributor_h1"], "year": "date_h1", "journal": "journal_h1", "group": "Citedby", "depth": 1, "citations": 1}, {"doi": "doi_h2", "name": "title_h2", "author": ["contributor_h2"], "year": "date_h2", "journal": "journal_h2", "group": "Citedby", "depth": 2, "citations": 1}], "links": [{"source": "doi_h1", "target": "doi_h02"}, {"source": "doi_h2", "target": "doi_h1"}]}
+{"nodes": [{"doi": "doi_lg_1_i", "name": "title_lg_1_i", "author": ["contributor_lg_1_i"], "year": "date_lg_1_i", "journal": "journal_lg_1_i", "group": "Input", "depth": 0, "citations": 2}, {"doi": "doi_lg_1_d11", "name": "title_lg_1_d11", "author": ["contributor_lg_1_d11"], "year": "date_lg_1_d11", "journal": "journal_lg_1_d11", "group": "Reference", "depth": -1, "citations": 1}, {"doi": "doi_lg_1_d12", "name": "title_lg_1_d12", "author": ["contributor_lg_1_d12"], "year": "date_lg_1_d12", "journal": "journal_lg_1_d12", "group": "Reference", "depth": -1, "citations": 2}, {"doi": "doi_lg_1_h11", "name": "title_lg_1_h11", "author": ["contributor_lg_1_h11"], "year": "date_lg_1_h11", "journal": "journal_lg_1_h11", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "doi_lg_1_h12", "name": "title_lg_1_h12", "author": ["contributor_lg_1_h12"], "year": "date_lg_1_h12", "journal": "journal_lg_1_h12", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "doi_lg_1_h21", "name": "title_lg_1_h21", "author": ["contributor_lg_1_h21"], "year": "date_lg_1_h21", "journal": "journal_lg_1_h21", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_1_h22", "name": "title_lg_1_h22", "author": ["contributor_lg_1_h22"], "year": "date_lg_1_h22", "journal": "journal_lg_1_h22", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_1_h23", "name": "title_lg_1_h23", "author": ["contributor_lg_1_h23"], "year": "date_lg_1_h23", "journal": "journal_lg_1_h23", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_1_d21", "name": "title_lg_1_d21", "author": ["contributor_lg_1_d21"], "year": "date_lg_1_d21", "journal": "journal_lg_1_d21", "group": "Reference", "depth": -2, "citations": 2}, {"doi": "doi_lg_1_d22", "name": "title_lg_1_d22", "author": ["contributor_lg_1_d22"], "year": "date_lg_1_d22", "journal": "journal_lg_1_d22", "group": "Reference", "depth": -2, "citations": 2}, {"doi": "doi_lg_1_d23", "name": "title_lg_1_d23", "author": ["contributor_lg_1_d23"], "year": "date_lg_1_d23", "journal": "journal_lg_1_d23", "group": "Reference", "depth": -2, "citations": 2}], "links": [{"source": "doi_lg_1_i", "target": "doi_lg_1_d11"}, {"source": "doi_lg_1_i", "target": "doi_lg_1_d12"}, {"source": "doi_lg_1_h11", "target": "doi_lg_1_i"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_i"}, {"source": "doi_lg_1_h21", "target": "doi_lg_1_h11"}, {"source": "doi_lg_1_h22", "target": "doi_lg_1_h11"}, {"source": "doi_lg_1_h22", "target": "doi_lg_1_h12"}, {"source": "doi_lg_1_h23", "target": "doi_lg_1_h12"}, {"source": "doi_lg_1_d11", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_d11", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d21", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d22", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_d12", "target": "doi_lg_1_d23"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_d12"}]}
\ No newline at end of file

verarbeitung/update_graph/Knoten_Vergleich.py → verarbeitung/update_graph/compare_old_and_new_node_lists.py

 #!/usr/bin/env python3
 from collections import Counter
 
-def doi_listen_vergleichen(alte,neue):
+def compare_old_and_new_node_lists(old_doi_node_list,new_doi_node_list):
     '''
-    :param alte: list of dois from old graph
-    :type alte: list
-    :param neue: list of dois from new graph
-    :type neue: list
+    :param old_doi_node_list:   list of dois from old graph
+    :type old_doi_node_list:    List[String]
+    
+    :param new_doi_node_list:   list of dois from new graph
+    :type new_doi_node_list:    List[String]
     
     function to calculate, which nodes from the old graph are deleted and which are added
     '''
-    dois_from_old_graph = alte #WICHTIG: Keine doppelten DOIs
-    dois_from_new_graph = neue
+    dois_from_old_graph = old_doi_node_list #WICHTIG: Keine doppelten DOIs
+    dois_from_new_graph = new_doi_node_list
     deleted_nodes = []
     common_nodes = []
     inserted_nodes = []

verarbeitung/update_graph/delete_nodes_edges.py

@@ -17,7 +17,7 @@ import sys
 from pathlib import Path
 sys.path.append("../../")
 
-from .Kanten_Vergleich import back_to_valid_edges
+from .update_edges import back_to_valid_edges
 
 
 def search_ref_graph_rec(pub):
@@ -91,6 +91,5 @@ def delete_nodes_and_edges(input_list, common_nodes, old_edges_list):
                 search_cit_graph_rec(pub)
 
     back_to_valid_edges(old_edges_list, usable_nodes)
-    input_list = usable_nodes.copy()
-    print(input_list)
-    #return(usable_nodes, valid_edges)
+
+    return(usable_nodes, old_edges_list)

verarbeitung/update_graph/update_depth.py

@@ -18,7 +18,7 @@ sys.path.append("../../")
 
 from verarbeitung.construct_new_graph.add_citations_rec import add_citations
 from verarbeitung.construct_new_graph.initialize_graph import complete_inner_edges
-from .Kanten_Vergleich import back_to_valid_edges
+from .update_edges import back_to_valid_edges
 
 
 def reduce_max_height(max_height):

verarbeitung/update_graph/update_graph.py

@@ -20,7 +20,7 @@ sys.path.append("../../")
 
 from input.publication import Publication
 from verarbeitung.get_pub_from_input import get_pub
-from .Knoten_Vergleich import doi_listen_vergleichen
+from .compare_old_and_new_node_lists import compare_old_and_new_node_lists
 from .delete_nodes_edges import delete_nodes_and_edges
 from .connect_new_input import connect_old_and_new_input
 from .update_depth import update_depth
@@ -97,11 +97,11 @@ def update_graph(new_doi_input_list, json_file, search_depth, search_height, tes
     new_doi_input_list = get_new_input_dois(new_doi_input_list, test_var)
 
     # retrieve which publications are already known, removed, inserted
-    common_nodes, inserted_nodes, deleted_nodes = doi_listen_vergleichen(old_doi_input_list, new_doi_input_list)
+    common_nodes, inserted_nodes, deleted_nodes = compare_old_and_new_node_lists(old_doi_input_list, new_doi_input_list)
 
     # deletes publications and edges from node_list if publications can no longer be reached
     if (len(deleted_nodes) > 0):
-        delete_nodes_and_edges(processed_list, common_nodes, valid_edges)
+        processed_list, valid_edges = delete_nodes_and_edges(processed_list, common_nodes, valid_edges)
     
     old_search_depth, old_search_height = update_depth(processed_list, valid_edges, search_depth, search_height, test_var)