bugs fixed and added graph plan for test graphs

verarbeitung/construct_new_graph/Processing.py

@@ -86,14 +86,14 @@ def complete_inner_edges():
     for node in nodes:
         if (node.group < 0):
             for citation in node.citations:
-                for cit in nodes:
-                    if (citation == cit.doi_url and [citation, node.doi_url] not in edges):
-                        edges.append([citation, node.doi_url])
+                for pub in nodes:
+                    if ((pub.doi_url == citation.doi_url) and ([citation.doi_url, node.doi_url] not in edges)):
+                        edges.append([citation.doi_url, node.doi_url])
         if (node.group > 0):
             for reference in node.references:
-                for ref in nodes:
-                    if (reference == ref.doi_url and [node.doi_url, reference] not in edges):
-                        edges.append([node.doi_url,reference])
+                for pub in nodes:
+                    if ((pub.doi_url == reference.doi_url) and ([node.doi_url, reference.doi_url] not in edges)):
+                        edges.append([node.doi_url,reference.doi_url])
 
 
 def process_main(doi_input_list, search_height, search_depth, test_var = False):
@@ -142,6 +142,6 @@ def process_main(doi_input_list, search_height, search_depth, test_var = False):
     complete_inner_edges()
 
     # calls a skript to save nodes and edges of graph in .json file
-    output_to_json(nodes,edges, test_var)
+    output_to_json(nodes, edges, test_var)
 
     return(nodes,edges)

verarbeitung/construct_new_graph/add_citations_rec.py

@@ -95,12 +95,12 @@ def create_graph_structure_citations(pub, search_depth, search_depth_max, cit_ty
     for citation in get_cit_type_list(pub, cit_type):
         not_in_nodes = True
         for node in nodes: # checks every citation for duplication 
-            if (citation == node.doi_url):
+            if (citation.doi_url == node.doi_url):
                 not_in_nodes = False
                 break
         if (not_in_nodes):
             if (search_depth < search_depth_max): #checks if its a test and chooses input function accordingly
-                citation_pub_obj = get_pub(citation, test_var)
+                citation_pub_obj = get_pub(citation.doi_url, test_var)
                 if (type(citation_pub_obj) != Publication):
                     print(pub)
                     continue 
@@ -114,13 +114,14 @@ def create_graph_structure_citations(pub, search_depth, search_depth_max, cit_ty
                 nodes.append(citation_pub_obj)                   
                 citations_pub_obj_list.append(citation_pub_obj)
 
-        # adds only edge if citation already exists   
-        elif (cit_type == "Citation"):      
-            if ([citation,pub.doi_url] not in edges):
-                edges.append([citation,pub.doi_url])
-        elif (cit_type == "Reference"):
-            if ([pub.doi_url,citation] not in edges):
-                edges.append([pub.doi_url,citation])   
+        # adds just the edge if citation already exists   
+        else:
+            if (cit_type == "Citation"):      
+                if ([citation.doi_url,pub.doi_url] not in edges):
+                    edges.append([citation.doi_url,pub.doi_url])
+            else:
+                if ([pub.doi_url,citation.doi_url] not in edges):
+                    edges.append([pub.doi_url,citation.doi_url])   
     return citations_pub_obj_list
 
 

verarbeitung/get_pub_from_input.py

@@ -33,15 +33,14 @@ def get_pub(pub_doi, test_var):
         function to return an object of type Publication for given input doi depending on whether its a test or url doi
     '''
     #checks if it's a test and chooses appropiate function
-    # print(pub_doi)
     if(test_var): 
-            pub = input_test_func(pub_doi) 
+        pub = input_test_func(pub_doi) 
 
     #checks that it isnt a test and chooses standart-input function
     else: 
         inter = Input()
         try:
-            pub = inter.get_publication(pub_doi.doi_url) #creates an object of class Publication
+            pub = inter.get_publication(pub_doi) #creates an object of class Publication
         except AttributeError:
             pub = inter.get_publication(pub_doi)
         except ValueError:

verarbeitung/json_text.json

-{"nodes": [{"doi": "https://doi.org/10.1021/acs.jcim.9b00249", "name": "Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis", "author": ["Emanuel S. R. Ehmki", "Robert Schmidt", "Farina Ohm", "Matthias Rarey"], "year": "May 24, 2019", "journal": "Journal of Chemical Information and Modeling", "group": "Input", "depth": 0, "citations": 5}, {"doi": "https://doi.org/10.1021/acs.chemrev.1c00107", "name": "Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems", "author": ["John A. Keith", "Valentin Vassilev-Galindo", "Bingqing Cheng", "Stefan Chmiela", "Michael Gastegger", "Klaus-Robert M\u00fcller", "Alexandre Tkatchenko"], "year": "July 7, 2021", "journal": "Chem. Rev.", "group": "Input", "depth": 0, "citations": 2}, {"doi": "https://doi.org/10.1021/acs.jcim.0c00741", "name": "Disconnected Maximum Common Substructures under Constraints", "author": ["Robert Schmidt", "Florian Krull", "Anna Lina Heinzke", "Matthias Rarey"], "year": "December 16, 2020", "journal": "Journal of Chemical Information and Modeling", "group": "Input", "depth": 0, "citations": 0}, {"doi": "https://doi.org/10.1021/acs.jmedchem.0c01332", "name": "Evolution of Novartis\u2019 Small Molecule Screening Deck Design", "author": ["Ansgar Schuffenhauer", "Nadine Schneider", "Samuel Hintermann", "Douglas Auld", "Jutta Blank", "Simona Cotesta", "Caroline Engeloch", "Nikolas Fechner", "Christoph Gaul", "Jerome Giovannoni", "Johanna Jansen", "John Joslin", "Philipp Krastel", "Eugen Lounkine", "John Manchester", "Lauren G. Monovich", "Anna Paola Pelliccioli", "Manuel Schwarze", "Michael D. Shultz", "Nikolaus Stiefl", "Daniel K. Baeschlin"], "year": "November 3, 2020", "journal": "Journal of Medicinal Chemistry", "group": "Input", "depth": 0, "citations": 8}, {"doi": "https://doi.org/10.1021/acs.jcim.9b00250", "name": "Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms", "author": ["Robert Schmidt", "Emanuel S. R. Ehmki", "Farina Ohm", "Hans-Christian Ehrlich", "Andriy Mashychev", "Matthias Rarey"], "year": "May 23, 2019", "journal": "Journal of Chemical Information and Modeling", "group": "Input", "depth": 0, "citations": 12}], "links": [{"source": "https://doi.org/10.1021/acs.chemrev.1c00107", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00741", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acs.jmedchem.0c01332", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acs.jcim.9b00250", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}]}
\ No newline at end of file
+{"nodes": [{"doi": "https://doi.org/10.1021/acs.jcim.9b00249", "name": "Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis", "author": ["Emanuel S. R. Ehmki", "Robert Schmidt", "Farina Ohm", "Matthias Rarey"], "year": "May 24, 2019", "journal": "Journal of Chemical Information and Modeling", "group": "Input", "depth": 0, "citations": 5}, {"doi": "https://doi.org/10.1021/acs.chemrev.1c00107", "name": "Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems", "author": ["John A. Keith", "Valentin Vassilev-Galindo", "Bingqing Cheng", "Stefan Chmiela", "Michael Gastegger", "Klaus-Robert M\u00fcller", "Alexandre Tkatchenko"], "year": "July 7, 2021", "journal": "Chem. Rev.", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "https://doi.org/10.1021/acs.jcim.0c00741", "name": "Disconnected Maximum Common Substructures under Constraints", "author": ["Robert Schmidt", "Florian Krull", "Anna Lina Heinzke", "Matthias Rarey"], "year": "December 16, 2020", "journal": "Journal of Chemical Information and Modeling", "group": "Citedby", "depth": 1, "citations": 0}, {"doi": "https://doi.org/10.1021/acs.jmedchem.0c01332", "name": "Evolution of Novartis\u2019 Small Molecule Screening Deck Design", "author": ["Ansgar Schuffenhauer", "Nadine Schneider", "Samuel Hintermann", "Douglas Auld", "Jutta Blank", "Simona Cotesta", "Caroline Engeloch", "Nikolas Fechner", "Christoph Gaul", "Jerome Giovannoni", "Johanna Jansen", "John Joslin", "Philipp Krastel", "Eugen Lounkine", "John Manchester", "Lauren G. Monovich", "Anna Paola Pelliccioli", "Manuel Schwarze", "Michael D. Shultz", "Nikolaus Stiefl", "Daniel K. Baeschlin"], "year": "November 3, 2020", "journal": "Journal of Medicinal Chemistry", "group": "Citedby", "depth": 1, "citations": 8}, {"doi": "https://doi.org/10.1021/acs.jcim.9b00250", "name": "Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms", "author": ["Robert Schmidt", "Emanuel S. R. Ehmki", "Farina Ohm", "Hans-Christian Ehrlich", "Andriy Mashychev", "Matthias Rarey"], "year": "May 23, 2019", "journal": "Journal of Chemical Information and Modeling", "group": "Citedby", "depth": 1, "citations": 12}], "links": [{"source": "https://doi.org/10.1021/acs.chemrev.1c00107", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00741", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acs.jmedchem.0c01332", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acs.jcim.9b00250", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acs.chemrev.1c00107", "target": "https://doi.org/10.1021/acs.jcim.9b00250"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00741", "target": "https://doi.org/10.1021/acs.jcim.9b00250"}, {"source": "https://doi.org/10.1021/acs.jmedchem.0c01332", "target": "https://doi.org/10.1021/acs.jcim.9b00250"}, {"source": "https://doi.org/10.1021/acs.jcim.9b00249", "target": "https://doi.org/10.1021/acs.jcim.9b00250"}]}
\ No newline at end of file

verarbeitung/test/Processing_unittest.py

@@ -12,16 +12,16 @@ class ProcessingTest(unittest.TestCase):
      maxDiff = None
 
 
-     # def testCycle(self):
-     #     nodes, edges = process_main(['doiz1'],1,1,True)
-     #     doi_nodes = keep_only_dois(nodes)
-     #     self.assertCountEqual(doi_nodes, ['doiz1', 'doiz2'])
-     #     self.assertCountEqual(edges, [['doiz1', 'doiz2'], ['doiz2', 'doiz1']])
+     def testCycle(self):
+         nodes, edges = process_main(['doiz1'],1,1,True)
+         doi_nodes = keep_only_dois(nodes)
+         self.assertCountEqual(doi_nodes, ['doiz1', 'doiz2'])
+         self.assertCountEqual(edges, [['doiz1', 'doiz2'], ['doiz2', 'doiz1']])
 
-     #     nodes, edges = process_main(['doiz1'],2,2,True)
-     #     doi_nodes = keep_only_dois(nodes)
-     #     self.assertCountEqual(doi_nodes, ['doiz1', 'doiz2'])
-     #     self.assertCountEqual(edges, [['doiz2', 'doiz1'], ['doiz1', 'doiz2']])
+         nodes, edges = process_main(['doiz1'],2,2,True)
+         doi_nodes = keep_only_dois(nodes)
+         self.assertCountEqual(doi_nodes, ['doiz1', 'doiz2'])
+         self.assertCountEqual(edges, [['doiz2', 'doiz1'], ['doiz1', 'doiz2']])
 
     #def testBigCycle(self):
 
@@ -29,66 +29,66 @@ class ProcessingTest(unittest.TestCase):
 
     #def testEmptyDepth(self):
 
-     # def testEmptyDepthHeight(self):
-     #     nodes, edges = process_main(['doi1'],0,0,True)
-     #     doi_nodes = keep_only_dois(nodes)
-     #     self.assertCountEqual(doi_nodes,['doi1'])
-     #     self.assertCountEqual(edges, [])
+     def testEmptyDepthHeight(self):
+         nodes, edges = process_main(['doi1'],0,0,True)
+         doi_nodes = keep_only_dois(nodes)
+         self.assertCountEqual(doi_nodes,['doi1'])
+         self.assertCountEqual(edges, [])
 
-     #     nodes, edges = process_main(['doi1', 'doi2'],0,0,True)
-     #     doi_nodes = keep_only_dois(nodes)
-     #     self.assertCountEqual(doi_nodes, ['doi1','doi2'])
-     #     self.assertCountEqual(edges, [['doi1', 'doi2']])
+         nodes, edges = process_main(['doi1', 'doi2'],0,0,True)
+         doi_nodes = keep_only_dois(nodes)
+         self.assertCountEqual(doi_nodes, ['doi1','doi2'])
+         self.assertCountEqual(edges, [['doi1', 'doi2']])
 
-     #     nodes, edges = process_main(['doi1', 'doi2', 'doi3'],0,0,True)
-     #     doi_nodes = keep_only_dois(nodes)
-     #     self.assertCountEqual(doi_nodes, ['doi1','doi2', 'doi3'])
-     #     self.assertCountEqual(edges, [['doi3', 'doi1'], ['doi1', 'doi2']])
+         nodes, edges = process_main(['doi1', 'doi2', 'doi3'],0,0,True)
+         doi_nodes = keep_only_dois(nodes)
+         self.assertCountEqual(doi_nodes, ['doi1','doi2', 'doi3'])
+         self.assertCountEqual(edges, [['doi3', 'doi1'], ['doi1', 'doi2']])
 
 
-     # def testInnerEdges(self):
-     #    nodes, edges = process_main(['doi_ie1'],1,1,True)
-     #    doi_nodes = keep_only_dois(nodes)
-     #    self.assertCountEqual(doi_nodes,['doi_ie1','doi_ie2','doi_ie3'])
-     #    self.assertCountEqual(edges,[['doi_ie1','doi_ie2'],['doi_ie3','doi_ie1'],['doi_ie3','doi_ie2']])
+     def testInnerEdges(self):
+        nodes, edges = process_main(['doi_ie1'],1,1,True)
+        doi_nodes = keep_only_dois(nodes)
+        self.assertCountEqual(doi_nodes,['doi_ie1','doi_ie2','doi_ie3'])
+        self.assertCountEqual(edges,[['doi_ie1','doi_ie2'],['doi_ie3','doi_ie1'],['doi_ie3','doi_ie2']])
      
-     # def testRightHeight(self):
-     #      nodes, edges = process_main(['doi_h01'],1,0,True)
-     #      doi_nodes = keep_only_dois(nodes)
-     #      self.assertCountEqual(doi_nodes,['doi_h01'])
-     #      self.assertCountEqual(edges, [])
-
-     #      nodes, edges = process_main(['doi_h02'],1,0,True)
-     #      doi_nodes = keep_only_dois(nodes)
-     #      self.assertCountEqual(doi_nodes,['doi_h02','doi_h1'])
-     #      self.assertCountEqual(edges, [['doi_h1','doi_h02']])
-
-     #      nodes, edges = process_main(['doi_h02'],2,0,True)
-     #      doi_nodes = keep_only_dois(nodes)
-     #      self.assertCountEqual(doi_nodes,['doi_h02','doi_h1','doi_h2'])
-     #      self.assertCountEqual(edges, [['doi_h1','doi_h02'], ['doi_h2','doi_h1']])
-
-     # def testRightDepth(self):
-     #      nodes, edges = process_main(['doi_d01'],0,1,True)
-     #      doi_nodes = keep_only_dois(nodes)
-     #      self.assertCountEqual(doi_nodes,['doi_d01'])
-     #      self.assertCountEqual(edges, [])
-
-     #      nodes, edges = process_main(['doi_d02'],0,1,True)
-     #      doi_nodes = keep_only_dois(nodes)
-     #      self.assertCountEqual(doi_nodes,['doi_d02','doi_d1'])
-     #      self.assertCountEqual(edges, [['doi_d02','doi_d1']])
-
-     #      nodes, edges = process_main(['doi_d02'],0,2,True)
-     #      doi_nodes = keep_only_dois(nodes)
-     #      self.assertCountEqual(doi_nodes,['doi_d02','doi_d1','doi_d2'])
-     #      self.assertCountEqual(edges, [['doi_d02','doi_d1'], ['doi_d1','doi_d2']])
-
-     # def test_import_from_json(self):
-     #      nodes_old, edges_old = process_main(['doi_lg_1_i'],2,2,True)
-     #      nodes_new, edges_new = input_from_json('test_output.json')
-     #      self.assertCountEqual(nodes_old,nodes_new)
-     #      self.assertCountEqual(edges_old, edges_new)
+     def testRightHeight(self):
+          nodes, edges = process_main(['doi_h01'],1,0,True)
+          doi_nodes = keep_only_dois(nodes)
+          self.assertCountEqual(doi_nodes,['doi_h01'])
+          self.assertCountEqual(edges, [])
+
+          nodes, edges = process_main(['doi_h02'],1,0,True)
+          doi_nodes = keep_only_dois(nodes)
+          self.assertCountEqual(doi_nodes,['doi_h02','doi_h1'])
+          self.assertCountEqual(edges, [['doi_h1','doi_h02']])
+
+          nodes, edges = process_main(['doi_h02'],2,0,True)
+          doi_nodes = keep_only_dois(nodes)
+          self.assertCountEqual(doi_nodes,['doi_h02','doi_h1','doi_h2'])
+          self.assertCountEqual(edges, [['doi_h1','doi_h02'], ['doi_h2','doi_h1']])
+
+     def testRightDepth(self):
+          nodes, edges = process_main(['doi_d01'],0,1,True)
+          doi_nodes = keep_only_dois(nodes)
+          self.assertCountEqual(doi_nodes,['doi_d01'])
+          self.assertCountEqual(edges, [])
+
+          nodes, edges = process_main(['doi_d02'],0,1,True)
+          doi_nodes = keep_only_dois(nodes)
+          self.assertCountEqual(doi_nodes,['doi_d02','doi_d1'])
+          self.assertCountEqual(edges, [['doi_d02','doi_d1']])
+
+          nodes, edges = process_main(['doi_d02'],0,2,True)
+          doi_nodes = keep_only_dois(nodes)
+          self.assertCountEqual(doi_nodes,['doi_d02','doi_d1','doi_d2'])
+          self.assertCountEqual(edges, [['doi_d02','doi_d1'], ['doi_d1','doi_d2']])
+
+     def test_import_from_json(self):
+          nodes_old, edges_old = process_main(['doi_lg_1_i'],2,2,True)
+          nodes_new, edges_new = input_from_json('test_output.json')
+          self.assertCountEqual(nodes_old,nodes_new)
+          self.assertCountEqual(edges_old, edges_new)
 
      def test_deleted_input_dois(self):
           nodes_old_single, edges_old_single = process_main(['doi_lg_1_i'],2,2,True)

verarbeitung/test/input_test.py

@@ -14,11 +14,13 @@ def input_test_func(pub_doi):
 
     for array in list_of_arrays:
         if pub_doi == array[0]:
-            pub = Publication(array[0], array[1], array[2], array[3], array[4], array[5], array[6], array[7])
+            pub = Publication(array[0], array[1], array[2], array[3], array[4], array[5], [], [])
+            pub.citations = cit(array[7], "Citation")
+            pub.references = cit(array[6], "Reference")
             return pub
 
 
-def cit(list_doi):
+def cit(list_doi, cit_type):
     '''
         :param list_doi list of citation dois to get their Citation Class 
         :type list_doi: List[String]
@@ -30,24 +32,9 @@ def cit(list_doi):
     for doi_url in list_doi:
         for array in list_of_arrays:
             if doi_url == array[0]:
-                cits.append(Citation(array[0], array[1], array[2], array[3], array[4]))
+                cits.append(Citation(array[0], array[1], array[2], array[3], cit_type))
     return cits
 
-def ref(list_doi):
-    '''
-        :param list_doi list of reference dois to get their Reference Class 
-        :type list_doi: List[String]
-
-        returns a list of reference objects for given doi list
-    '''
-
-    refs = []
-    for doi_url in list_doi:
-        for array in list_of_arrays:
-            if doi_url == array[0]:
-                refs.append(Citation(array[0], array[1], array[2], array[3], array[4]))
-    return refs
-
 
 
 beispiel1 = ['doi1', 'title1', ['contributor1'], 'journal1', 'date1', ['subject1'], ['doi2'], ['doi3']]
@@ -91,12 +78,13 @@ large_graph_2_h23 = ['doi_lg_2_h23', 'title_lg_2_h23', ['contributor_lg_2_h23'],
 large_graph_2_h24 = ['doi_lg_2_h24', 'title_lg_2_h24', ['contributor_lg_2_h24'], 'journal_lg_2_h24', 'date_lg_2_h24', ['subject_lg_2_h24'], ['doi_lg_2_h12','doi_lg_2_h23','doi_lg_2_d12'], ['doi_lg_2_h23']]
 large_graph_2_h11 = ['doi_lg_2_h11', 'title_lg_2_h11', ['contributor_lg_2_h11'], 'journal_lg_2_h11', 'date_lg_2_h11', ['subject_lg_2_h11'], ['doi_lg_2_i','doi_cg_i'], ['doi_lg_2_h21','doi_lg_2_h22']]
 large_graph_2_h12 = ['doi_lg_2_h12', 'title_lg_2_h12', ['contributor_lg_2_h12'], 'journal_lg_2_h12', 'date_lg_2_h12', ['subject_lg_2_h12'], ['doi_lg_2_i'], ['doi_lg_2_h23','doi_lg_2_h24']]
-large_graph_2_i =   ['doi_lg_2_i'  , 'title_lg_2_i'  , ['contributor_lg_2_i']  , 'journal_lg_2_i'  , 'date_lg_2_i'  , ['subject_lg_2_i']  , ['doi_lg_2_d11','doi_lg_2_d12'], ['doi_lg_2_h11','doi_lg_2_h12','doi_cg_i']]
-large_graph_2_d11 = ['doi_lg_2_d11', 'title_lg_2_d11', ['contributor_lg_2_d11'], 'journal_lg_2_d11', 'date_lg_2_d11', ['subject_lg_2_d11'], [], ['doi_lg_2_i']]
-large_graph_2_d12 = ['doi_lg_2_d12', 'title_lg_2_d12', ['contributor_lg_2_d12'], 'journal_lg_2_d12', 'date_lg_2_d12', ['subject_lg_2_d12'], ['doi_lg_2_d21','doi_lg_2_d22'], ['doi_lg_2_h24','doi_lg_2_i']]
-large_graph_2_d21 = ['doi_lg_2_d21', 'title_lg_2_d21', ['contributor_lg_2_d21'], 'journal_lg_2_d21', 'date_lg_2_d21', ['subject_lg_2_d21'], [], ['doi_lg_2_d12']]
+large_graph_2_i =   ['doi_lg_2_i'  , 'title_lg_2_i'  , ['contributor_lg_2_i']  , 'journal_lg_2_i'  , 'date_lg_2_i'  , ['subject_lg_2_i']  , ['doi_lg_2_d11','doi_lg_2_d12'], ['doi_lg_2_h11','doi_lg_2_h12','doi_cg_i','doi_lg_2_h11']]
+large_graph_2_d11 = ['doi_lg_2_d11', 'title_lg_2_d11', ['contributor_lg_2_d11'], 'journal_lg_2_d11', 'date_lg_2_d11', ['subject_lg_2_d11'], ['doi_lg_2_i','doi_lg_2_d21'], ['doi_lg_2_i']]
+large_graph_2_d12 = ['doi_lg_2_d12', 'title_lg_2_d12', ['contributor_lg_2_d12'], 'journal_lg_2_d12', 'date_lg_2_d12', ['subject_lg_2_d12'], ['doi_lg_2_d22','doi_lg_2_d23','doi_lg_2_d24'], ['doi_lg_2_h24','doi_lg_2_i']]
+large_graph_2_d21 = ['doi_lg_2_d21', 'title_lg_2_d21', ['contributor_lg_2_d21'], 'journal_lg_2_d21', 'date_lg_2_d21', ['subject_lg_2_d21'], [], ['doi_lg_2_d11']]
 large_graph_2_d22 = ['doi_lg_2_d22', 'title_lg_2_d22', ['contributor_lg_2_d22'], 'journal_lg_2_d22', 'date_lg_2_d22', ['subject_lg_2_d22'], [], ['doi_lg_2_d12']]
 large_graph_2_d23 = ['doi_lg_2_d23', 'title_lg_2_d23', ['contributor_lg_2_d23'], 'journal_lg_2_d23', 'date_lg_2_d23', ['subject_lg_2_d23'], [], ['doi_lg_2_d12']]
+large_graph_2_d24 = ['doi_lg_2_d24', 'title_lg_2_d24', ['contributor_lg_2_d24'], 'journal_lg_2_d24', 'date_lg_2_d24', ['subject_lg_2_d24'], [], ['doi_lg_2_d12']]
 
 crossed_graph_h21 = ['doi_cg_h21', 'title_cg_h21', ['contributor_cg_h21'], 'journal_cg_h21', 'date_cg_h21', ['subject_cg_h21'], ['doi_cg_h11'], []]
 crossed_graph_h22 = ['doi_cg_h22', 'title_cg_h22', ['contributor_cg_h22'], 'journal_cg_h22', 'date_cg_h22', ['subject_cg_h22'], ['doi_cg_h11'], []]

verarbeitung/test_output.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_2_i", "name": "title_lg_2_i", "author": ["contributor_lg_2_i"], "year": "date_lg_2_i", "journal": "journal_lg_2_i", "group": "Input", "depth": 0, "citations": 3}, {"doi": "doi_lg_2_d11", "name": "title_lg_2_d11", "author": ["contributor_lg_2_d11"], "year": "date_lg_2_d11", "journal": "journal_lg_2_d11", "group": "Reference", "depth": -1, "citations": 1}, {"doi": "doi_lg_2_d12", "name": "title_lg_2_d12", "author": ["contributor_lg_2_d12"], "year": "date_lg_2_d12", "journal": "journal_lg_2_d12", "group": "Reference", "depth": -1, "citations": 2}, {"doi": "doi_lg_2_h11", "name": "title_lg_2_h11", "author": ["contributor_lg_2_h11"], "year": "date_lg_2_h11", "journal": "journal_lg_2_h11", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "doi_lg_2_h12", "name": "title_lg_2_h12", "author": ["contributor_lg_2_h12"], "year": "date_lg_2_h12", "journal": "journal_lg_2_h12", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "doi_cg_i", "name": "title_cg_i", "author": ["contributor_cg_i"], "year": "date_cg_i", "journal": "journal_cg_i", "group": "Citedby", "depth": 1, "citations": 3}, {"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_2_h21", "name": "title_lg_2_h21", "author": ["contributor_lg_2_h21"], "year": "date_lg_2_h21", "journal": "journal_lg_2_h21", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_2_h22", "name": "title_lg_2_h22", "author": ["contributor_lg_2_h22"], "year": "date_lg_2_h22", "journal": "journal_lg_2_h22", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_2_h23", "name": "title_lg_2_h23", "author": ["contributor_lg_2_h23"], "year": "date_lg_2_h23", "journal": "journal_lg_2_h23", "group": "Citedby", "depth": 2, "citations": 1}, {"doi": "doi_lg_2_h24", "name": "title_lg_2_h24", "author": ["contributor_lg_2_h24"], "year": "date_lg_2_h24", "journal": "journal_lg_2_h24", "group": "Citedby", "depth": 2, "citations": 1}, {"doi": "doi_cg_h11", "name": "title_cg_h11", "author": ["contributor_cg_h11"], "year": "date_cg_h11", "journal": "journal_cg_h11", "group": "Citedby", "depth": 2, "citations": 2}, {"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}, {"doi": "doi_lg_2_d21", "name": "title_lg_2_d21", "author": ["contributor_lg_2_d21"], "year": "date_lg_2_d21", "journal": "journal_lg_2_d21", "group": "Reference", "depth": -2, "citations": 1}, {"doi": "doi_lg_2_d22", "name": "title_lg_2_d22", "author": ["contributor_lg_2_d22"], "year": "date_lg_2_d22", "journal": "journal_lg_2_d22", "group": "Reference", "depth": -2, "citations": 1}], "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_2_i", "target": "doi_lg_2_d11"}, {"source": "doi_lg_2_i", "target": "doi_lg_2_d12"}, {"source": "doi_lg_2_h11", "target": "doi_lg_2_i"}, {"source": "doi_lg_2_h12", "target": "doi_lg_2_i"}, {"source": "doi_cg_i", "target": "doi_lg_2_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_2_h21", "target": "doi_lg_2_h11"}, {"source": "doi_lg_2_h22", "target": "doi_lg_2_h11"}, {"source": "doi_lg_2_h23", "target": "doi_lg_2_h12"}, {"source": "doi_lg_2_h24", "target": "doi_lg_2_h12"}, {"source": "doi_lg_2_h24", "target": "doi_lg_2_h23"}, {"source": "doi_lg_2_h23", "target": "doi_lg_2_h24"}, {"source": "doi_lg_1_h23", "target": "doi_cg_i"}, {"source": "doi_cg_h11", "target": "doi_cg_i"}, {"source": "doi_lg_2_h11", "target": "doi_cg_i"}, {"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_2_d12", "target": "doi_lg_2_d21"}, {"source": "doi_lg_2_d12", "target": "doi_lg_2_d22"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_d12"}, {"source": "doi_lg_1_h11", "target": "doi_lg_1_h12"}, {"source": "doi_lg_2_h24", "target": "doi_lg_2_d12"}]}
\ No newline at end of file
+{"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"}, {"source": "doi_lg_1_h11", "target": "doi_lg_1_h12"}]}
\ No newline at end of file

verarbeitung/update_graph/update_graph_del.py

@@ -29,10 +29,15 @@ def delete_ref_nodes_rec(pub):
     '''
     for reference in pub.references:
         for ref_pub in processed_list:
-            if (ref_pub.doi_url == reference):
+            if (ref_pub.doi_url == reference.doi_url):
                 
                 # to find a cyclus and avoid recursion error
-                if (reference not in pub.citations):
+                not_in_citations = True
+                for citation in pub.citations:
+                    if (reference.doi_url == citation.doi_url):
+                        not_in_citations = False
+                        break
+                if (not_in_citations):  
                     delete_ref_nodes_rec(ref_pub)
 
     # removes publication from list after recursion and if it's not of group input
@@ -49,10 +54,15 @@ def delete_cit_nodes_rec(pub):
     '''
     for citation in pub.citations:
         for cit_pub in processed_list:
-            if (cit_pub.doi_url == citation):
+            if (cit_pub.doi_url == citation.doi_url):
 
                 # to find a cyclus and avoid recursion error
-                if (citation not in pub.references):
+                not_in_references = True
+                for reference in pub.references:
+                    if (citation.doi_url == reference.doi_url):
+                        not_in_references = False
+                        break
+                if (not_in_references):  
                     delete_cit_nodes_rec(cit_pub)
 
     # removes publication from list after recursion and if it's not of group input