added groups to Processing and json

verarbeitung/Processing.py

 # -*- coding: utf-8 -*-
 """
-Functions to generate a graph representing citations between multiple JCIM ACS journals
+Functions to generate a graph representing citations between multiple ACS/Nature journals
 
 """
 
@@ -41,7 +41,7 @@ def initialize_nodes_list(doi_input_list):
 
 # adds a node for every publication unknown
 # adds edges for citations between publications     
-def create_graph_structure_citations(pub, search_depth, search_depth_max):
+def create_graph_structure_citations(pub, search_height, search_height_max):
     for citation in pub._citations:
         not_in_nodes = True
         for node in nodes:
@@ -50,7 +50,8 @@ def create_graph_structure_citations(pub, search_depth, search_depth_max):
                 not_in_nodes = False
                 break
         if (not_in_nodes):
-            if (search_depth <= search_depth_max):
+            if (search_height <= search_height_max):
+                #citation.group = "citation"
                 nodes.append(citation)
                 edges.append([pub.doi_url,citation.doi_url])
 
@@ -62,7 +63,7 @@ def create_graph_structure_citations(pub, search_depth, search_depth_max):
 
 # adds a node for every publication unknown
 # adds edges for references between publications     
-def create_graph_structure_references(pub, search_height, search_height_max):
+def create_graph_structure_references(pub, search_depth, search_depth_max):
     for reference in pub._references:
         not_in_nodes = True
         for node in nodes:
@@ -71,7 +72,8 @@ def create_graph_structure_references(pub, search_height, search_height_max):
                 not_in_nodes = False
                 break
         if (not_in_nodes):
-            if (search_height <= search_height_max):
+            if (search_depth <= search_depth_max):
+                #reference.group = "reference"
                 nodes.append(reference)
                 edges.append([reference.doi_url,pub.doi_url])
 
@@ -81,21 +83,21 @@ def create_graph_structure_references(pub, search_height, search_height_max):
     
 
 
-# recursive function to implement depth-first-search on citations
+# recursive function to implement height-first-search on citations
 # doi_citations: input list of citet dois
-# search_depth: current search_depth of depth-first-search
-# search_depth_max: maximal search_depth for dfs
-def process_citations_rec(doi_citations, search_depth, search_depth_max):  
-    # depth of search is increased by 1 with each recursive call
-    search_depth += 1
+# search_height: current search_height of height-first-search
+# search_height_max: maximal search_height for dfs
+def process_citations_rec(doi_citations, search_height, search_height_max):  
+    # height of search is increased by 1 with each recursive call
+    search_height += 1
 
     # create class object for every citation from list
     for pub_doi in doi_citations:
         pub = input(pub_doi)
-        create_graph_structure_citations(pub, search_depth, search_depth_max)    
-        # If the maximum depth has not yet been reached, all references from the publication 
+        create_graph_structure_citations(pub, search_height, search_height_max)    
+        # If the maximum height has not yet been reached, all references from the publication 
         # are written to an array and the function is called again with this array.       
-        if (search_depth < search_depth_max):
+        if (search_height < search_height_max):
             citations_list = []
             for citation in pub._citations:
 
@@ -105,25 +107,25 @@ def process_citations_rec(doi_citations, search_depth, search_depth_max):
                     citations_list.append(citation.doi_url)
 
             # recursive call of function.
-            process_citations_rec(citations_list, search_depth, search_depth_max)
+            process_citations_rec(citations_list, search_height, search_height_max)
 
 
 
-# recursive function to implement depth-first-search on references
+# recursive function to implement height-first-search on references
 # doi_references: input list of referenced dois
-# search_height: current search_height of depth-first-search
-# search_height_max: maximal search_height for dfs
-def process_references_rec(doi_references, search_height, search_height_max):  
-    # The height is increased by 1 with each recursive call
-    search_height += 1
+# search_depth: current search_depth of height-first-search
+# search_depth_max: maximal search_depth for dfs
+def process_references_rec(doi_references, search_depth, search_depth_max):  
+    # The depth is increased by 1 with each recursive call
+    search_depth += 1
 
     # create class object for every citation from list
     for pub_doi in doi_references:
         pub = input(pub_doi)
-        create_graph_structure_references(pub, search_height, search_height_max)    
-        # If the maximum height has not yet been reached, all references from the publication 
+        create_graph_structure_references(pub, search_depth, search_depth_max)    
+        # If the maximum depth has not yet been reached, all references from the publication 
         # are written to an array and the function is called again with this array.       
-        if (search_height < search_height_max):
+        if (search_depth < search_depth_max):
             references_list = []
             for reference in pub._references:
 
@@ -133,23 +135,23 @@ def process_references_rec(doi_references, search_height, search_height_max):
                     references_list.append(reference.doi_url)
 
             # recursive call of function.
-            process_references_rec(references_list, search_height, search_height_max)
+            process_references_rec(references_list, search_depth, search_depth_max)
 
 
 
            
-def process_main(doi_input_list, search_depth, search_height):
+def process_main(doi_input_list, search_height, search_depth):
     # ERROR-Handling doi_array = NULL
     if (len(doi_input_list) == 0):
         print("Error, no input data")
 
-    # ERROR- if a negative number is entered for depth
-    if (search_depth < 0):
-        print("Error, search_depth of search must be positive")
-
     # ERROR- if a negative number is entered for height
     if (search_height < 0):
-        print("Error, search_height of search must be positive")       
+        print("Error, search_height of search must be positive")
+
+    # ERROR- if a negative number is entered for depth
+    if (search_depth < 0):
+        print("Error, search_depth of search must be positive")       
 
     # create empty array for the nodes
     # create empty array for the edges
@@ -158,8 +160,8 @@ def process_main(doi_input_list, search_depth, search_height):
     edges = []
 
     initialize_nodes_list(doi_input_list)
-    process_citations_rec(doi_input_list, 0, search_depth)
-    process_references_rec(doi_input_list, 0, search_height)
+    process_citations_rec(doi_input_list, 0, search_height)
+    process_references_rec(doi_input_list, 0, search_depth)
 
     output_to_json(nodes,edges)
 

verarbeitung/json_demo.py

@@ -11,7 +11,9 @@ def output_to_json(V,E):
         new_dict["name"] = node.title
         new_dict["author"] = node.contributors
         #new_dict["year"] = node.publication_date
+        #new_dict["journal"] = node.journal
         new_dict["doi"] = node.doi_url
+        #new_dict["group"] = node.group
         list_of_node_dicts.append(new_dict)
     for edge in E:
         new_dict_2 = dict()