From 45b197458fac038869f7a18ae0d1c03e4710bcdc Mon Sep 17 00:00:00 2001
From: Malte Schokolowski <baw8441@uni-hamburg.de>
Date: Thu, 2 Dec 2021 22:27:41 +0100
Subject: [PATCH] added Processing_pub_objs_only.py, which adds only objects of
type publication to nodes. Has the same functions as Processing.py
---
verarbeitung/Processing_pub_objs_only.py | 255 +++++++++++++++++++++++
1 file changed, 255 insertions(+)
create mode 100644 verarbeitung/Processing_pub_objs_only.py
diff --git a/verarbeitung/Processing_pub_objs_only.py b/verarbeitung/Processing_pub_objs_only.py
new file mode 100644
index 0000000..a6c1ed3
--- /dev/null
+++ b/verarbeitung/Processing_pub_objs_only.py
@@ -0,0 +1,255 @@
+# -*- 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
--
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