fixed bug and removed old Processing.py

verarbeitung/Processing.py

@@ -23,9 +23,10 @@ from json_demo import output_to_json
 
 # adds every publication from input list to graph structure
 # doi_input_list: list of publication dois from user
+def initialize_nodes_list(doi_input_list, search_depth_max, search_height_max, test_var):
+    references_pub_obj_list = []
+    citations_pub_obj_list = []
 
-# TO-DO: Listenelemente auf Korrektheit überprüfen
-def initialize_nodes_list(doi_input_list, test_var):
     for pub_doi in doi_input_list:
 
         #checks if its a test and chooses input function accordingly
@@ -46,60 +47,40 @@ def initialize_nodes_list(doi_input_list, test_var):
         else:
             doi_input_list.remove(pub_doi)
 
-# adds inner edges between citations and references to edges
-def complete_inner_edges(test_var):
-    for node in nodes:
-
-        # checks if its a test and chooses input function accordingly
-        if (test_var):
-            pub = input_test_func(node.doi_url)
-        else:
-            pub = input(node.doi_url)
-
-
-        if (node.group == "depth"):
-            for citation in pub.citations:
-                if (citation in nodes and [citation.doi_url, pub.doi_url] not in edges):
-                    edges.append([citation.doi_url, pub.doi_url])
-
-        if (node.group == "height"):
-            for reference in pub.references:
-                for node in nodes:
-                    if (reference.doi_url in node.doi_url and [pub.doi_url, reference.doi_url] not in edges):
-                        edges.append([pub.doi_url,reference.doi_url])
+        # inserts references as publication objects into list and 
+        # inserts first depth references into nodes/edges if maximum search depth > 0
+        for reference in create_graph_structure_references(pub, 0, search_depth_max, test_var):
+            references_pub_obj_list.append(reference)
 
+        # inserts citations as publication objects into list and 
+        # inserts first height citations into nodes if maximum search height > 0
+        for citation in create_graph_structure_citations(pub, 0, search_height_max, test_var):
+            citations_pub_obj_list.append(citation)
 
+    return(references_pub_obj_list, citations_pub_obj_list)
         
-# adds a node for every publication unknown
-# adds edges for citations between publications     
-def create_graph_structure_citations(pub, search_height, search_height_max):
-    for citation in pub.citations:
     
-        # checks if publication already exists in nodes
-        not_in_nodes = True
+# adds edges between citation and reference group
+def complete_inner_edges(test_var):
     for node in nodes:
-            # checks every citation for duplication 
-            if (citation.doi_url == node.doi_url):
-                not_in_nodes = False
-                break
-        if (not_in_nodes):
-            if (search_height <= search_height_max):
-                citation.group = "height"
-                nodes.append(citation)
-                edges.append([citation.doi_url,pub.doi_url])
-
-        # adds only an edge (citation already exists)     
-        elif [citation.doi_url,pub.doi_url] not in edges:
-            edges.append([citation.doi_url,pub.doi_url])   
+        if (node.group == "depth"):
+            for citation in node.citations:
+                for cit in nodes:
+                    if (citation.doi_url == cit.doi_url and [citation.doi_url, node.doi_url] not in edges):
+                        edges.append([citation.doi_url, node.doi_url])
+        if (node.group == "height"):
+            for reference in node.references:
+                for ref in nodes:
+                    if (reference.doi_url == ref.doi_url and [node.doi_url, reference.doi_url] not in edges):
+                        edges.append([node.doi_url,reference.doi_url])
 
 
 
 # adds a node for every publication unknown
 # adds edges for references between publications     
-def create_graph_structure_references(pub, search_depth, search_depth_max):
+def create_graph_structure_references(pub, search_depth, search_depth_max, test_var):
+    references_pub_obj_list = []
     for reference in pub.references:
-
-        # checks if publication already exists in nodes
         not_in_nodes = True
         for node in nodes:
             # checks every reference for duplication 
@@ -107,86 +88,94 @@ def create_graph_structure_references(pub, search_depth, search_depth_max):
                 not_in_nodes = False
                 break
         if (not_in_nodes):
-            if (search_depth <= search_depth_max):
-                reference.group = "depth"
-                nodes.append(reference)
-                edges.append([pub.doi_url,reference.doi_url])
-
-        # adds only an edge (citation already exists)            
-        elif [pub.doi_url,reference.doi_url] not in edges:
-            edges.append([pub.doi_url,reference.doi_url])      
-    
-
-
-# recursive function to implement height-first-search on citations
-# doi_citations: input list of citet dois
-# 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, test_var):  
-    # 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:
+            if (search_depth < search_depth_max):
 
                 #checks if its a test and chooses input function accordingly
                 if (test_var):
-            pub = input_test_func(pub_doi)
+                    reference_pub_obj = input_test_func(reference.doi_url)
                 else:
-            pub = input(pub_doi)
-
-        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_height < search_height_max):
-            citations_list = []
-            for citation in pub.citations:
-
-                # currently only the references with acs are stored in the URL, because we can't 
-                # extract the info from other sources.
-                if ("acs" in citation.doi_url or test_var == True):
-                    citations_list.append(citation.doi_url)
+                    reference_pub_obj = input(reference.doi_url)
 
-            # recursive call of function.
-            process_citations_rec(citations_list, search_height, search_height_max, test_var)
+                reference_pub_obj.group = "depth"
+                nodes.append(reference_pub_obj)
+                edges.append([pub.doi_url,reference_pub_obj.doi_url])
+                references_pub_obj_list.append(reference_pub_obj)
 
+        # adds edge only if citation already exists           
+        elif [pub.doi_url,reference.doi_url] not in edges:
+            edges.append([pub.doi_url,reference.doi_url])  
+    return references_pub_obj_list 
 
 
 # recursive function to implement height-first-search on references
-# doi_references: input list of referenced dois
+# references_pub_obj_list: input list of references as publication objects
 # 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, test_var):  
-    # The depth is increased by 1 with each recursive call
-    search_depth += 1
+def process_references_rec(references_pub_obj_list, search_depth, search_depth_max, test_var):  
+    # adds next level to nodes/edges
+    for pub in references_pub_obj_list:
+        new_reference_pub_obj_list = create_graph_structure_references(pub, search_depth, search_depth_max, test_var)    
+
+        # If the maximum height has not yet been reached, calls function recursivly with increased height     
+        if (search_depth < search_depth_max):
+            process_references_rec(new_reference_pub_obj_list, search_depth+1, search_depth_max, test_var)
+
+
+
     
-    # create class object for every citation from list
-    for pub_doi in doi_references:
+# adds a node for every publication unknown
+# adds edges for citations between publications     
+def create_graph_structure_citations(pub, search_height, search_height_max, test_var):
+    citations_pub_obj_list = []
+    for citation in pub.citations:
+        not_in_nodes = True
+        for node in nodes:
+            # checks every citation for duplication 
+            if (citation.doi_url == node.doi_url):
+                not_in_nodes = False
+                break
+        if (not_in_nodes):
+            if (search_height < search_height_max):
 
                 #checks if its a test and chooses input function accordingly
                 if (test_var):
-            pub = input_test_func(pub_doi)
+                    citation_pub_obj = input_test_func(citation.doi_url)
                 else:
-            pub = input(pub_doi)
+                    citation_pub_obj = input(citation.doi_url)
 
-        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_depth < search_depth_max):
-            references_list = []
-            for reference in pub.references:
+                citation_pub_obj.group = "height"
+                nodes.append(citation_pub_obj)
+                edges.append([citation_pub_obj.doi_url,pub.doi_url])
+                citations_pub_obj_list.append(citation_pub_obj)
+
+        # adds only edge if citation already exists         
+        elif [citation.doi_url,pub.doi_url] not in edges:
+            edges.append([citation.doi_url,pub.doi_url])   
+    return citations_pub_obj_list
 
-                # currently only the references with acs are stored in the URL, because we can't 
-                # extract the info from other sources. 
-                if ("acs" in reference.doi_url or test_var == True):
-                    references_list.append(reference.doi_url)
 
-            # recursive call of function.
-            process_references_rec(references_list, search_depth, search_depth_max, test_var)
+
+# recursive function to implement height-first-search on citations
+# citations_pub_obj_list: input list of citations as publication objects
+# search_height: current search_height of height-first-search
+# search_height_max: maximal search_height for dfs
+def process_citations_rec(citations_pub_obj_list, search_height, search_height_max, test_var):  
+    # adds next level to nodes/edges
+    for pub in citations_pub_obj_list:
+        new_citation_pub_obj_list = create_graph_structure_citations(pub, search_height, search_height_max, test_var)   
+
+        # If the maximum height has not yet been reached, calls function recursivly with increased height 
+        if (search_height < search_height_max):
+            process_citations_rec(new_citation_pub_obj_list, search_height+1, search_height_max, test_var)
 
 
 
 
+# main function to call. Needs as input:
+# doi_input_list:   input list of dois
+# search_height:    max search height to process to
+# search_depth:     max search depth to process to
+# test_var:         only needed for unit test as True, default is False
 def process_main(doi_input_list, search_height, search_depth, test_var = False):
     # ERROR-Handling doi_array = NULL
     if (len(doi_input_list) == 0):
@@ -206,24 +195,30 @@ def process_main(doi_input_list, search_height, search_depth, test_var = False):
     nodes = []
     edges = []
 
+    # initializes nodes/edges from input and gets a list with publication objects for citations and references returned
+    references_obj_list, citations_obj_list = initialize_nodes_list(doi_input_list,search_depth, search_height, test_var)
 
-    initialize_nodes_list(doi_input_list,test_var)
-    process_citations_rec(doi_input_list, 0, search_height, test_var)
-    process_references_rec(doi_input_list, 0, search_depth, test_var)
+    # function calls to begin recursive processing up to max depth/height
+    process_citations_rec(citations_obj_list, 1, search_height, test_var)
+    process_references_rec(references_obj_list, 1, search_depth, test_var)
+
+    # adds edges between reference group and citation group of known publications
     complete_inner_edges(test_var)
 
+    # calls a skript to save nodes and edges of graph in .json file
     output_to_json(nodes,edges)
 
-    # only for internal testing
-    doi_nodes = []
+    # only for unit tests
+    if (test_var == True):
+        doi_nodes_list = []
         for node in nodes:
-        doi_nodes.append(node.doi_url)
-    return(doi_nodes,edges)
-
+            doi_nodes_list.append(node.doi_url)
+        return(doi_nodes_list, edges)
 
 
 
     
+# a function to print nodes and edges from a graph
 def print_graph(nodes, edges):
     print("Knoten:\n")
     for node in nodes:
@@ -233,24 +228,12 @@ def print_graph(nodes, edges):
         print(edge,"\n")
    
     
-# function to test cycles
-def test_cycle():
-    arr = []
-    arr.append('doiz1')
-    #arr.append('doiz2')
-
-    nodes,edges = process_main(arr,1,1,True)
-
-    print(nodes, edges)
-
-    print_graph(nodes, edges)
-    
-# program test, because there is no connection to the input yet.
-def test_print():
-    arr = []
-    #arr.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
+# program test, because there is no connection to UI yet.
+def try_known_publications():
+    doi_list = []
+    doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
     #arr.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
-    #arr.append('https://doi.org/10.1021/acs.jmedchem.0c01332')
+    doi_list.append('https://doi.org/10.1021/acs.jmedchem.0c01332')
     #arr.append('https://doi.org/10.1021/acs.jcim.0c00741')
 
     #arr.append('https://doi.org/10.1021/ci700007b')
@@ -259,13 +242,6 @@ def test_print():
     #arr.append[url]
 
 
-    nodes,edges = process_main(arr,2,2,True)
+    nodes,edges = process_main(doi_list,2,2)
 
     print_graph(nodes, edges)    
\ No newline at end of file
-
-#test_print()
-#test_cycle()
-#print(process_main(['doiz1'],1,1,True))
-#print(process_main(['doi1'],0,0,True))
-
-        
\ No newline at end of file

verarbeitung/Processing_pub_objs_only.py

-# -*- coding: utf-8 -*-
-"""
-Functions to generate a graph representing citations between multiple ACS/Nature journals
-
-"""
-
-__authors__ = "Donna Löding, Alina Molkentin, Xinyi Tang, Judith Große, Malte Schokolowski"
-__email__ = "cis-project2021@zbh.uni-hamburg.de"
-__status__ = "Production"
-#__copyright__ = ""
-#__credits__ = ["", "", "", ""]
-#__license__ = ""
-#__version__ = ""
-#__maintainer__ = ""
-
-from bs4 import BeautifulSoup as bs
-import requests as req
-import sys  
-from pathlib import Path
-from input_fj import input
-from input_test import input_test_func
-from json_demo import output_to_json
-
-# adds every publication from input list to graph structure
-# doi_input_list: list of publication dois from user
-def initialize_nodes_list(doi_input_list, search_depth_max, search_height_max, test_var):
-    references_pub_obj_list = []
-    citations_pub_obj_list = []
-
-    for pub_doi in doi_input_list:
-
-        #checks if its a test and chooses input function accordingly
-        if(test_var):
-            pub = input_test_func(pub_doi)
-        else:
-            pub = input(pub_doi)
-
-        # checks if publication already exists in nodes
-        not_in_nodes = True
-        for node in nodes:                                              # checks if a pub is already in nodes
-            if (pub.doi_url == node.doi_url):
-                not_in_nodes = False
-                break
-        if (not_in_nodes):
-            nodes.append(pub)
-            pub.group = "input"
-        else:
-            doi_input_list.remove(pub_doi)
-
-        # inserts references as publication objects into list and 
-        # inserts first depth references into nodes/edges if maximum search depth > 0
-        for reference in create_graph_structure_references(pub, 0, search_depth_max, test_var):
-            references_pub_obj_list.append(reference)
-
-        # inserts citations as publication objects into list and 
-        # inserts first height citations into nodes if maximum search height > 0
-        for citation in create_graph_structure_citations(pub, 0, search_height_max, test_var):
-            citations_pub_obj_list.append(citation)
-
-    return(references_pub_obj_list, citations_pub_obj_list)
-        
-    
-# adds edges between citation and reference group
-def complete_inner_edges(test_var):
-    for node in nodes:
-        if (node.group == "depth"):
-            for citation in node.citations:
-                if (citation in nodes and [citation.doi_url, node.doi_url] not in edges):
-                    edges.append([citation.doi_url, node.doi_url])
-        if (node.group == "height"):
-            for reference in node.references:
-                if (reference in nodes and [node.doi_url, reference.doi_url] not in edges):
-                    edges.append([node.doi_url,reference.doi_url])
-
-
-
-
-# adds a node for every publication unknown
-# adds edges for references between publications     
-def create_graph_structure_references(pub, search_depth, search_depth_max, test_var):
-    references_pub_obj_list = []
-    for reference in pub.references:
-        not_in_nodes = True
-        for node in nodes:
-            # checks every reference for duplication 
-            if (reference.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
-                if (test_var):
-                    reference_pub_obj = input_test_func(reference.doi_url)
-                else:
-                    reference_pub_obj = input(reference.doi_url)
-
-                reference_pub_obj.group = "depth"
-                nodes.append(reference_pub_obj)
-                edges.append([pub.doi_url,reference_pub_obj.doi_url])
-                references_pub_obj_list.append(reference_pub_obj)
-
-        # adds edge only if citation already exists           
-        elif [pub.doi_url,reference.doi_url] not in edges:
-            edges.append([pub.doi_url,reference.doi_url])  
-    return references_pub_obj_list 
-
-
-# recursive function to implement height-first-search on references
-# references_pub_obj_list: input list of references as publication objects
-# search_depth: current search_depth of height-first-search
-# search_depth_max: maximal search_depth for dfs
-def process_references_rec(references_pub_obj_list, search_depth, search_depth_max, test_var):  
-    # adds next level to nodes/edges
-    for pub in references_pub_obj_list:
-        new_reference_pub_obj_list = create_graph_structure_references(pub, search_depth, search_depth_max, test_var)    
-
-        # If the maximum height has not yet been reached, calls function recursivly with increased height     
-        if (search_depth < search_depth_max):
-            process_references_rec(new_reference_pub_obj_list, search_depth+1, search_depth_max, test_var)
-
-
-
-    
-# adds a node for every publication unknown
-# adds edges for citations between publications     
-def create_graph_structure_citations(pub, search_height, search_height_max, test_var):
-    citations_pub_obj_list = []
-    for citation in pub.citations:
-        not_in_nodes = True
-        for node in nodes:
-            # checks every citation for duplication 
-            if (citation.doi_url == node.doi_url):
-                not_in_nodes = False
-                break
-        if (not_in_nodes):
-            if (search_height < search_height_max):
-
-                #checks if its a test and chooses input function accordingly
-                if (test_var):
-                    citation_pub_obj = input_test_func(citation.doi_url)
-                else:
-                    citation_pub_obj = input(citation.doi_url)
-
-                citation_pub_obj.group = "height"
-                nodes.append(citation_pub_obj)
-                edges.append([citation_pub_obj.doi_url,pub.doi_url])
-                citations_pub_obj_list.append(citation_pub_obj)
-
-        # adds only edge if citation already exists         
-        elif [citation.doi_url,pub.doi_url] not in edges:
-            edges.append([citation.doi_url,pub.doi_url])   
-    return citations_pub_obj_list
-
-
-
-# recursive function to implement height-first-search on citations
-# citations_pub_obj_list: input list of citations as publication objects
-# search_height: current search_height of height-first-search
-# search_height_max: maximal search_height for dfs
-def process_citations_rec(citations_pub_obj_list, search_height, search_height_max, test_var):  
-    # adds next level to nodes/edges
-    for pub in citations_pub_obj_list:
-        new_citation_pub_obj_list = create_graph_structure_citations(pub, search_height, search_height_max, test_var)   
-
-        # If the maximum height has not yet been reached, calls function recursivly with increased height 
-        if (search_height < search_height_max):
-            process_citations_rec(new_citation_pub_obj_list, search_height+1, search_height_max, test_var)
-
-
-
-
-           
-def process_main(doi_input_list, search_height, search_depth, test_var = False):
-    # ERROR-Handling doi_array = NULL
-    if (len(doi_input_list) == 0):
-        print("Error, no input data")
-
-    # ERROR- if a negative number is entered for height
-    if (search_height < 0):
-        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
-    global nodes, edges
-    nodes = []
-    edges = []
-
-    # initializes nodes/edges from input and gets a list with publication objects for citations and references returned
-    references_obj_list, citations_obj_list = initialize_nodes_list(doi_input_list,search_depth, search_height, test_var)
-    process_citations_rec(citations_obj_list, 1, search_height, test_var)
-    process_references_rec(references_obj_list, 1, search_depth, test_var)
-    complete_inner_edges(test_var)
-
-    output_to_json(nodes,edges)
-
-    # only for internal testing
-    doi_nodes = []
-    for node in nodes:
-        doi_nodes.append(node.doi_url)
-    return(doi_nodes,edges)
-
-
-
-    
-# a function to print nodes and edges from a graph
-def print_graph(nodes, edges):
-    print("Knoten:\n")
-    for node in nodes:
-        print(node.title, "\n")
-    print("\nKanten:\n")
-    for edge in edges:
-        print(edge,"\n")
-   
-
-# function to test cycles
-def test_cycle():
-    arr = []
-    arr.append('doiz1')
-    #arr.append('doiz2')
-
-    nodes,edges = process_main(arr,1,1,True)
-
-    print(nodes, edges)
-
-    print_graph(nodes, edges)
-    
-# program test, because there is no connection to the input yet.
-def test_print():
-    arr = []
-    #arr.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
-    #arr.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
-    #arr.append('https://doi.org/10.1021/acs.jmedchem.0c01332')
-    #arr.append('https://doi.org/10.1021/acs.jcim.0c00741')
-
-    #arr.append('https://doi.org/10.1021/ci700007b')
-    #arr.append('https://doi.org/10.1021/acs.jcim.5b00292')
-    #url = sys.argv[1]
-    #arr.append[url]
-
-
-    nodes,edges = process_main(arr,2,2,True)
-
-    print_graph(nodes, edges)
-
-#test_print()
-#test_cycle()
-#print(process_main(['doiz1'],1,1,True))
-#print(process_main(['doi1'],0,0,True))
-
-        
\ No newline at end of file

verarbeitung/Processing_unittest.py

 import unittest
-from Processing import process_main
+from Processing_pub_objs_only import process_main
 
 class ProcessingTest(unittest.TestCase):
      def testCycle(self):