From e570bd7271713f7dd5e5a0b99087d07f73854385 Mon Sep 17 00:00:00 2001
From: Malte Schokolowski <baw8441@uni-hamburg.de>
Date: Fri, 3 Dec 2021 18:28:30 +0100
Subject: [PATCH] fixed bug and removed old Processing.py
---
verarbeitung/Processing.py | 262 ++++++++----------
verarbeitung/Processing_pub_objs_only.py | 255 -----------------
verarbeitung/Processing_unittest.py | 2 +-
.../__pycache__/Processing.cpython-39.pyc | Bin 4021 -> 4045 bytes
.../Processing_pub_objs_only.cpython-39.pyc | Bin 0 -> 4137 bytes
5 files changed, 120 insertions(+), 399 deletions(-)
delete mode 100644 verarbeitung/Processing_pub_objs_only.py
create mode 100644 verarbeitung/__pycache__/Processing_pub_objs_only.cpython-39.pyc
diff --git a/verarbeitung/Processing.py b/verarbeitung/Processing.py
index ab7db1d..0dcc739 100644
--- a/verarbeitung/Processing.py
+++ b/verarbeitung/Processing.py
@@ -23,12 +23,13 @@ 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
+ #checks if its a test and chooses input function accordingly
if(test_var):
pub = input_test_func(pub_doi)
else:
@@ -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)
+ # 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 pub.citations:
- if (citation in nodes and [citation.doi_url, pub.doi_url] not in edges):
- edges.append([citation.doi_url, pub.doi_url])
-
+ 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 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])
-
-
-
-# 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
- 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])
+ 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])
+ if (search_depth < search_depth_max):
- # 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])
-
+ #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)
-# 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
+ # 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
- # create class object for every citation from list
- for pub_doi in doi_citations:
- # checks if its a test and chooses input function accordingly
- if (test_var):
- pub = input_test_func(pub_doi)
- else:
- pub = input(pub_doi)
+# 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)
- 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:
+ # 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)
- # 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)
- # recursive call of function.
- process_citations_rec(citations_list, search_height, search_height_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)
-# recursive function to implement height-first-search on references
-# doi_references: input list of referenced dois
-# 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
+ 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)
- # create class object for every citation from list
- for pub_doi in doi_references:
+ # 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
- #checks if its a test and chooses input function accordingly
- if (test_var):
- pub = input_test_func(pub_doi)
- else:
- pub = input(pub_doi)
- 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:
- # 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 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)
- # recursive call of function.
- process_references_rec(references_list, search_depth, search_depth_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)
+
+ # 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)
- 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)
+ # 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 = []
- for node in nodes:
- doi_nodes.append(node.doi_url)
- return(doi_nodes,edges)
+ # only for unit tests
+ if (test_var == True):
+ doi_nodes_list = []
+ for node in nodes:
+ 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:
@@ -232,25 +227,13 @@ def print_graph(nodes, edges):
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')
+# 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)
-
- print_graph(nodes, edges)
-
-#test_print()
-#test_cycle()
-#print(process_main(['doiz1'],1,1,True))
-#print(process_main(['doi1'],0,0,True))
+ nodes,edges = process_main(doi_list,2,2)
-
\ No newline at end of file
+ print_graph(nodes, edges)
\ No newline at end of file
diff --git a/verarbeitung/Processing_pub_objs_only.py b/verarbeitung/Processing_pub_objs_only.py
deleted file mode 100644
index a6c1ed3..0000000
--- a/verarbeitung/Processing_pub_objs_only.py
+++ /dev/null
@@ -1,255 +0,0 @@
-# -*- 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
diff --git a/verarbeitung/Processing_unittest.py b/verarbeitung/Processing_unittest.py
index 772d572..fd11131 100644
--- a/verarbeitung/Processing_unittest.py
+++ b/verarbeitung/Processing_unittest.py
@@ -1,5 +1,5 @@
import unittest
-from Processing import process_main
+from Processing_pub_objs_only import process_main
class ProcessingTest(unittest.TestCase):
def testCycle(self):
diff --git a/verarbeitung/__pycache__/Processing.cpython-39.pyc b/verarbeitung/__pycache__/Processing.cpython-39.pyc
index e08ca682bcdfcff17580d1e2c0923b6aac9ce00d..54c63251bbf3affbdd176d3d55f4956c2fc08406 100644
GIT binary patch
delta 400
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delta 346
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zc{$7&8EYp`<5Jw5%4xvJIDhjruIr49`zGh{JZF47IgGc6@z&&%yndo@L0$z110xF~
z7qbu(7gLe`WF5X}M!m@$d~$+6LGo;1TUmI7n2HQ1Z|B>`rq95@P-Hl{n%|jUl0$++
PibIJ*o=cU3i-QLMj-5@$
diff --git a/verarbeitung/__pycache__/Processing_pub_objs_only.cpython-39.pyc b/verarbeitung/__pycache__/Processing_pub_objs_only.cpython-39.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..9ce1023e6ea54e1b04b37ad5a1fd08115d5f52a4
GIT binary patch
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C633hX
literal 0
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--
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