added comments in Processing

verarbeitung/Processing.py

@@ -43,7 +43,7 @@ def initialize_nodes_list(doi_input_list, search_depth_max, search_height_max, t
             except ValueError:
                 continue
             except IndexError:
-                        print(pub_doi)
+                continue
             
 
         # checks if publication already exists in nodes
@@ -113,7 +113,6 @@ def create_graph_structure_references(pub, search_depth, search_depth_max, test_
                         continue
                     # nur aus Testzwecken, da noch was bei Input falsch ist
                     except IndexError:
-                        print(reference.doi_url)
                         continue
 
                 reference_pub_obj.group = "depth"
@@ -168,7 +167,6 @@ def create_graph_structure_citations(pub, search_height, search_height_max, test
                     except ValueError:
                         continue
                     except IndexError:
-                        print(citation.doi_url)
                         continue
 
                 citation_pub_obj.group = "height"
@@ -236,7 +234,6 @@ def process_main(doi_input_list, search_height, search_depth, test_var = False):
     # calls a skript to save nodes and edges of graph in .json file
     output_to_json(nodes,edges)
 
-    return(nodes,edges)
 
     # only for unit tests
     if (test_var == True):
@@ -244,4 +241,5 @@ def process_main(doi_input_list, search_height, search_depth, test_var = False):
         for node in nodes:
             doi_nodes_list.append(node.doi_url)
         return(doi_nodes_list, edges)
-   
\ No newline at end of file
+
+    return(nodes,edges)
\ No newline at end of file

verarbeitung/import_from_json.py

 # -*- coding: utf-8 -*-
 """
-Functions to read old json files to recreate old grpah structure
+Functions to read old json files to recreate old graph structure
 
 """
 
@@ -71,14 +71,20 @@ def add_ref_and_cit_to_pubs(input_dict):
     '''
 
     # iterates over the list of edges
-    for edge in input_dict["links"]: #iterates over the list of edges
+    for edge in input_dict["links"]:
         for node in list_of_nodes_py:
+
+            # adds reference to current node
             if (node.doi_url == edge["source"]):
                 new_reference = Reference(node.doi_url, node.title, node.contributors, node.journal, node.publication_date)
                 node.references.append(new_reference)
+            
+            # adds citation to current node
             if (node.doi_url == edge["target"]):
                 new_citation = Citation(node.doi_url, node.title, node.contributors, node.journal, node.publication_date)
                 node.citations.append(new_citation)
+        
+        # adds edge to list
         list_of_edges_py.append([edge["source"],edge["target"]])
 
 
@@ -88,21 +94,20 @@ def input_from_json(json_file):
     :type json_file: Json File
     '''
 
+    # creates global sets for nodes and edges
     global list_of_nodes_py, list_of_edges_py
     list_of_nodes_py = []
     list_of_edges_py = []
-    with open(json_file,'r') as file: #opens the json file with reading permission
-        input_dict = json.load(file) #saves the information in a dictionary
 
-    create_pubs_from_json(input_dict)
+    #opens the json file and saves content in dictionary
+    with open(json_file,'r') as file: 
+        input_dict = json.load(file)
 
+    # creates nodes of Class Publication from input Json file
+    create_pubs_from_json(input_dict)
 
+    # adds references and citations to publications and creates edges 
     add_ref_and_cit_to_pubs(input_dict)
-    
-
-
-    # Iteriert über die Liste der Kanten_dictionaries  speichert sie als Liste
-    
-            
+              
 
     return(list_of_nodes_py, list_of_edges_py)

verarbeitung/json_demo.py

@@ -18,7 +18,7 @@ def format_nodes(V):
         new_dict["journal"] = node.journal
         new_dict["doi"] = node.doi_url
         new_dict["group"] = node.group
-        new_dict["citation count"] = len(node.citations)
+        new_dict["citations"] = len(node.citations)
         list_of_node_dicts.append(new_dict)
     return list_of_node_dicts
     

verarbeitung/json_text.json

-{"nodes": [{"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", "doi": "https://doi.org/10.1021/acs.jcim.9b00249", "group": "input", "citation count": 5}, {"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.", "doi": "https://doi.org/10.1021/acs.chemrev.1c00107", "group": "height", "citation count": 1}, {"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", "doi": "https://doi.org/10.1021/acs.jcim.0c00741", "group": "height", "citation count": 0}, {"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", "doi": "https://doi.org/10.1021/acs.jmedchem.0c01332", "group": "height", "citation count": 8}, {"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", "doi": "https://doi.org/10.1021/acs.jcim.9b00250", "group": "height", "citation count": 12}, {"name": "The Growing Importance of Chirality in 3D Chemical Space Exploration and Modern Drug Discovery Approaches for Hit-ID", "author": ["Ilaria Proietti Silvestri", "Paul J. J. Colbon"], "year": "July 16, 2021", "journal": "ACS Med. Chem. Lett.", "doi": "https://doi.org/10.1021/acsmedchemlett.1c00251", "group": "height", "citation count": 0}, {"name": "Target-Based Evaluation of \u201cDrug-Like\u201d Properties and Ligand Efficiencies", "author": ["Paul D. Leeson", "A. Patricia Bento", "Anna Gaulton", "Anne Hersey", "Emma J. Manners", "Chris J. Radoux", "Andrew R. Leach"], "year": "May 13, 2021", "journal": "Journal of Medicinal Chemistry", "doi": "https://doi.org/10.1021/acs.jmedchem.1c00416", "group": "height", "citation count": 0}], "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/acsmedchemlett.1c00251", "target": "https://doi.org/10.1021/acs.jmedchem.0c01332"}, {"source": "https://doi.org/10.1021/acs.jmedchem.1c00416", "target": "https://doi.org/10.1021/acs.jmedchem.0c01332"}, {"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/print_graph_test.py

@@ -15,11 +15,13 @@ __status__ = "Production"
 
 
 import sys
+
 #sys.path.insert(1, 'C:\Users\Malte\Git\CiS-Projekt\ci-s-projekt-verarbeitung\input')
 sys.path.append(".")
 from input.interface import InputInterface as Input
 #import input
 from Processing import process_main
+from import_from_json import input_from_json
 
 # a function to print nodes and edges from a graph
 def print_graph(nodes, edges):
@@ -33,12 +35,12 @@ def print_graph(nodes, edges):
     print(len(edges))
 
 
-# program test, because there is no connection to UI yet.
+# program test with some random dois
 def try_known_publications():
     doi_list = []
     doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
     #doi_list.append('https://doi.org/10.1021/acs.jcim.9b00249')
-    #doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.1c00203')
+    doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.1c00203')
     #arr.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
     doi_list.append('https://doi.org/10.1021/acs.jmedchem.0c01332')
     #arr.append('https://doi.org/10.1021/acs.jcim.0c00741')
@@ -51,8 +53,12 @@ def try_known_publications():
     #arr.append[url]
 
 
-    nodes, edges = process_main(doi_list,1,1)
+    nodes, edges = process_main(doi_list,2,2)
 
     print_graph(nodes, edges) 
 
-try_known_publications()
\ No newline at end of file
+    return(nodes, edges)
+
+nodes, edges = try_known_publications()
+#nodes_new, edges_new = input_from_json("json_text.json")
+#print_graph(nodes_new, edges_new)
\ No newline at end of file