From a2eb55146a8a4f42795b26c475a51069f303d06d Mon Sep 17 00:00:00 2001
From: Malte Schokolowski <baw8441@uni-hamburg.de>
Date: Sat, 11 Dec 2021 14:32:52 +0100
Subject: [PATCH] Dateien und Funktionen ausgelagert
---
verarbeitung/Processing.py | 290 ------------------
verarbeitung/__init__.py | 0
.../__pycache__/Processing.cpython-36.pyc | Bin 7171 -> 0 bytes
.../__pycache__/Processing.cpython-38.pyc | Bin 4087 -> 0 bytes
.../__pycache__/Processing.cpython-39.pyc | Bin 7262 -> 0 bytes
.../Processing_pub_objs_only.cpython-39.pyc | Bin 4137 -> 0 bytes
.../__pycache__/input_fj.cpython-36.pyc | Bin 4299 -> 0 bytes
.../__pycache__/input_fj.cpython-38.pyc | Bin 4329 -> 0 bytes
.../__pycache__/input_fj.cpython-39.pyc | Bin 4337 -> 0 bytes
.../__pycache__/input_test.cpython-36.pyc | Bin 3949 -> 0 bytes
.../__pycache__/input_test.cpython-38.pyc | Bin 3865 -> 0 bytes
.../__pycache__/input_test.cpython-39.pyc | Bin 7228 -> 0 bytes
.../__pycache__/json_demo.cpython-36.pyc | Bin 1128 -> 0 bytes
.../__pycache__/json_demo.cpython-38.pyc | Bin 1153 -> 0 bytes
.../__pycache__/json_demo.cpython-39.pyc | Bin 1256 -> 0 bytes
.../__pycache__/unittest.cpython-36.pyc | Bin 646 -> 0 bytes
.../construct_new_graph/Processing.py | 151 +++++++++
verarbeitung/construct_new_graph/__init__.py | 0
.../construct_new_graph/add_citations_rec.py | 151 +++++++++
.../construct_new_graph/add_references_rec.py | 151 +++++++++
.../export_to_json.py} | 0
verarbeitung/dev_files/__init__.py | 0
.../{ => dev_files}/print_graph_test.py | 6 +-
verarbeitung/get_pub_from_input.py | 2 +-
verarbeitung/json_text.json | 1 -
verarbeitung/process_main.py | 0
.../{ => test}/Processing_unittest.py | 240 ++++++++-------
verarbeitung/test/__init__.py | 0
verarbeitung/{ => test}/input_test.py | 232 +++++++-------
verarbeitung/test_output.json | 2 +-
.../{ => update_graph}/Kanten_Vergleich.py | 0
.../{ => update_graph}/Knoten_Vergleich.py | 0
verarbeitung/update_graph/__init__.py | 0
.../{ => update_graph}/connect_new_input.py | 136 ++++----
.../{ => update_graph}/import_from_json.py | 2 +-
.../{ => update_graph}/update_graph.py | 8 +-
.../{ => update_graph}/update_graph_del.py | 5 +-
37 files changed, 772 insertions(+), 605 deletions(-)
delete mode 100644 verarbeitung/Processing.py
create mode 100644 verarbeitung/__init__.py
delete mode 100644 verarbeitung/__pycache__/Processing.cpython-36.pyc
delete mode 100644 verarbeitung/__pycache__/Processing.cpython-38.pyc
delete mode 100644 verarbeitung/__pycache__/Processing.cpython-39.pyc
delete mode 100644 verarbeitung/__pycache__/Processing_pub_objs_only.cpython-39.pyc
delete mode 100644 verarbeitung/__pycache__/input_fj.cpython-36.pyc
delete mode 100644 verarbeitung/__pycache__/input_fj.cpython-38.pyc
delete mode 100644 verarbeitung/__pycache__/input_fj.cpython-39.pyc
delete mode 100644 verarbeitung/__pycache__/input_test.cpython-36.pyc
delete mode 100644 verarbeitung/__pycache__/input_test.cpython-38.pyc
delete mode 100644 verarbeitung/__pycache__/input_test.cpython-39.pyc
delete mode 100644 verarbeitung/__pycache__/json_demo.cpython-36.pyc
delete mode 100644 verarbeitung/__pycache__/json_demo.cpython-38.pyc
delete mode 100644 verarbeitung/__pycache__/json_demo.cpython-39.pyc
delete mode 100644 verarbeitung/__pycache__/unittest.cpython-36.pyc
create mode 100644 verarbeitung/construct_new_graph/Processing.py
create mode 100644 verarbeitung/construct_new_graph/__init__.py
create mode 100644 verarbeitung/construct_new_graph/add_citations_rec.py
create mode 100644 verarbeitung/construct_new_graph/add_references_rec.py
rename verarbeitung/{json_demo.py => construct_new_graph/export_to_json.py} (100%)
create mode 100644 verarbeitung/dev_files/__init__.py
rename verarbeitung/{ => dev_files}/print_graph_test.py (94%)
delete mode 100644 verarbeitung/json_text.json
create mode 100644 verarbeitung/process_main.py
rename verarbeitung/{ => test}/Processing_unittest.py (94%)
create mode 100644 verarbeitung/test/__init__.py
rename verarbeitung/{ => test}/input_test.py (98%)
rename verarbeitung/{ => update_graph}/Kanten_Vergleich.py (100%)
rename verarbeitung/{ => update_graph}/Knoten_Vergleich.py (100%)
create mode 100644 verarbeitung/update_graph/__init__.py
rename verarbeitung/{ => update_graph}/connect_new_input.py (79%)
rename verarbeitung/{ => update_graph}/import_from_json.py (99%)
rename verarbeitung/{ => update_graph}/update_graph.py (95%)
rename verarbeitung/{ => update_graph}/update_graph_del.py (97%)
diff --git a/verarbeitung/Processing.py b/verarbeitung/Processing.py
deleted file mode 100644
index 4beb8e8..0000000
--- a/verarbeitung/Processing.py
+++ /dev/null
@@ -1,290 +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__ = ""
-
-
-import sys
-from pathlib import Path
-from os import error
-sys.path.append("../")
-
-from input.publication import Publication
-from get_pub_from_input import get_pub
-from json_demo import output_to_json
-
-
-def initialize_nodes_list(doi_input_list, search_depth_max, search_height_max, test_var):
- '''
- :param doi_input_list: input list of doi from UI
- :type doi_input_list: List[String]
-
- :param search_depth_max: maximum depth to search for references
- :type search_depth_max: int
-
- :param search_height_max: maximum height to search for citations
- :type search_height_max: int
-
- :param test_var: variable to differenciate between test and url call
- :type test_var: boolean
-
- adds input dois to nodes and retrieves citations and references for input publications
- '''
-
- # saves found citations and references in lists
- references_pub_obj_list = []
- citations_pub_obj_list = []
-
- for pub_doi in doi_input_list: #iterates over every incoming doi
- pub = get_pub(pub_doi, test_var)
- if (type(pub) != Publication):
- print(pub)
- continue
-
- # checks if publication already exists in nodes
- not_in_nodes = True #boolean value to check if a node already exists in the set of nodes
- for node in nodes: #iterates over every node in the set of nodes
- if (pub.doi_url == node.doi_url): #determines that a node with this doi already is in the set
- not_in_nodes = False #false --> node will not be created
- break
- if (not_in_nodes): #there is no node with this doi in the set
- nodes.append(pub) #appends Publication Object
- pub.group = "input"
- else:
- doi_input_list.remove(pub_doi) #deletes the doi-dublicate from input list
-
- # 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)
-
-
-
-def complete_inner_edges(test_var):
- '''
- :param test_var: variable to differenciate between test and url call
- :type test_var: boolean
-
- completes inner edges between nodes of group height and depth
- '''
-
- for node in nodes:
- if (node.group == "depth"):
- for citation in node.citations:
- for cit in nodes:
- if (citation == cit.doi_url and [citation, node.doi_url] not in edges):
- edges.append([citation, node.doi_url])
- if (node.group == "height"):
- for reference in node.references:
- for ref in nodes:
- if (reference == ref.doi_url and [node.doi_url, reference] not in edges):
- edges.append([node.doi_url,reference])
-
-
-
-def create_graph_structure_references(pub, search_depth, search_depth_max, test_var):
- '''
- :param pub: publication which references will be added
- :type pub: Publication
-
- :param search_depth: current depth to search for references
- :type search_depth: int
-
- :param search_depth_max: maximum depth to search for references
- :type search_depth_max: int
-
- :param test_var: variable to differenciate between test and url call
- :type test_var: boolean
-
- adds a node for every referenced publication unknown
- adds edges to added references
- '''
-
- references_pub_obj_list = []
- for reference in pub.references: #iterates over the references of the considered paper
- not_in_nodes = True #boolean Value to ensure that there will be no dublicates in the set of nodes
- for node in nodes: #iterates over all nodes in set of nodes #
- if (reference == node.doi_url): #determines that the node already exists
- not_in_nodes = False #boolean false --> node will not be created
- break
- if (not_in_nodes): #checks that there is no node with this doi
- if (search_depth < search_depth_max): #checks that the recursion step is smaller than the limit
- reference_pub_obj = get_pub(reference, test_var)
- if (type(reference_pub_obj) != Publication):
- print(pub)
- continue
-
- reference_pub_obj.group = "depth"
- nodes.append(reference_pub_obj) # appends the object to the set of nodes
- edges.append([pub.doi_url,reference_pub_obj.doi_url]) #appends the edge to the set of edges
- references_pub_obj_list.append(reference_pub_obj) #appends the node to the set of references
-
- # adds edge only if citation already exists
- elif [pub.doi_url,reference] not in edges:
- edges.append([pub.doi_url,reference])
- return references_pub_obj_list
-
-
-def process_references_rec(references_pub_obj_list, search_depth, search_depth_max, test_var):
- '''
- :param references_pub_obj_list: list of publications which references will be added
- :type references_pub_obj_list: List[Publication]
-
- :param search_depth: current depth to search for references
- :type search_depth: int
-
- :param search_depth_max: maximum depth to search for references
- :type search_depth_max: int
-
- :param test_var: variable to differenciate between test and url call
- :type test_var: boolean
-
- recursive function to implement height-first-search on references
- '''
-
- # 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)
-
-
-
-def create_graph_structure_citations(pub, search_height, search_height_max, test_var):
- '''
- :param pub: publication which citations will be added
- :type pub: Publication
-
- :param search_height: current height to search for citations
- :type search_height_max: int
-
- :param search_height_max: maximum height to search for citations
- :type search_height_max: int
-
- :param test_var: variable to differenciate between test and url call
- :type test_var: boolean
-
- adds a node for every citing publication unknown
- adds edges to added citations
- '''
-
- citations_pub_obj_list = []
- for citation in pub.citations:
- not_in_nodes = True
- for node in nodes: # checks every citation for duplication
- if (citation == 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
- citation_pub_obj = get_pub(citation, test_var)
- if (type(citation_pub_obj) != Publication):
- print(pub)
- continue
-
- 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,pub.doi_url] not in edges:
- edges.append([citation,pub.doi_url])
- return citations_pub_obj_list
-
-
-def process_citations_rec(citations_pub_obj_list, search_height, search_height_max, test_var):
- '''
- :param citations_pub_obj_list: list of publications which citations will be added
- :type citations_pub_obj_list: List[Publication]
-
- :param search_height: current height to search for citations
- :type search_height_max: int
-
- :param search_height_max: maximum height to search for citations
- :type search_height_max: int
-
- :param test_var: variable to differenciate between test and url call
- :type test_var: boolean
-
- recursive function to implement depth-first-search on citations
- '''
-
- # 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):
- '''
- :param doi_input_list: input list of doi from UI
- :type doi_input_list: list of strings
-
- :param search_height: maximum height to search for citations
- :type search_height: int
-
- :param search_depth: maximum depth to search for references
- :type search_depth: int
-
- :param test_var: variable to differenciate between test and url call
- :type test_var: boolean
-
- main function to start graph generation
- '''
-
- # 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")
-
-
- # creates empty lists to save nodes and 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)
-
- # 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, test_var)
-
- return(nodes,edges)
diff --git a/verarbeitung/__init__.py b/verarbeitung/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/verarbeitung/__pycache__/Processing.cpython-36.pyc b/verarbeitung/__pycache__/Processing.cpython-36.pyc
deleted file mode 100644
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diff --git a/verarbeitung/construct_new_graph/Processing.py b/verarbeitung/construct_new_graph/Processing.py
new file mode 100644
index 0000000..a9a85f9
--- /dev/null
+++ b/verarbeitung/construct_new_graph/Processing.py
@@ -0,0 +1,151 @@
+# -*- 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__ = ""
+
+
+import sys
+from pathlib import Path
+from os import error
+sys.path.append("../")
+
+from input.publication import Publication
+from verarbeitung.get_pub_from_input import get_pub
+from .export_to_json import output_to_json
+from .add_citations_rec import add_citations, create_global_lists_cit
+from .add_references_rec import add_references, create_global_lists_ref
+
+
+def initialize_nodes_list(doi_input_list, search_depth_max, search_height_max, test_var):
+ '''
+ :param doi_input_list: input list of doi from UI
+ :type doi_input_list: List[String]
+
+ :param search_depth_max: maximum depth to search for references
+ :type search_depth_max: int
+
+ :param search_height_max: maximum height to search for citations
+ :type search_height_max: int
+
+ :param test_var: variable to differenciate between test and url call
+ :type test_var: boolean
+
+ adds input dois to nodes and retrieves citations and references for input publications
+ '''
+
+ # saves found citations and references in lists
+ references_pub_obj_list = []
+ citations_pub_obj_list = []
+
+ for pub_doi in doi_input_list: #iterates over every incoming doi
+ pub = get_pub(pub_doi, test_var)
+ if (type(pub) != Publication):
+ print(pub)
+ continue
+
+ # checks if publication already exists in nodes
+ not_in_nodes = True #boolean value to check if a node already exists in the set of nodes
+ for node in nodes: #iterates over every node in the set of nodes
+ if (pub.doi_url == node.doi_url): #determines that a node with this doi already is in the set
+ not_in_nodes = False #false --> node will not be created
+ break
+ if (not_in_nodes): #there is no node with this doi in the set
+ nodes.append(pub) #appends Publication Object
+ pub.group = "input"
+ else:
+ doi_input_list.remove(pub_doi) #deletes the doi-dublicate from input list
+
+ # inserts references as publication objects into list and
+ # inserts first depth references into nodes/edges if maximum search depth > 0
+ for reference in create_global_lists_ref(nodes, edges, 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_global_lists_cit(nodes, edges, pub, 0, search_height_max, test_var):
+ citations_pub_obj_list.append(citation)
+
+ return(references_pub_obj_list, citations_pub_obj_list)
+
+
+
+def complete_inner_edges(test_var):
+ '''
+ :param test_var: variable to differenciate between test and url call
+ :type test_var: boolean
+
+ completes inner edges between nodes of group height and depth
+ '''
+
+ for node in nodes:
+ if (node.group == "depth"):
+ for citation in node.citations:
+ for cit in nodes:
+ if (citation == cit.doi_url and [citation, node.doi_url] not in edges):
+ edges.append([citation, node.doi_url])
+ if (node.group == "height"):
+ for reference in node.references:
+ for ref in nodes:
+ if (reference == ref.doi_url and [node.doi_url, reference] not in edges):
+ edges.append([node.doi_url,reference])
+
+
+def process_main(doi_input_list, search_height, search_depth, test_var = False):
+ '''
+ :param doi_input_list: input list of doi from UI
+ :type doi_input_list: list of strings
+
+ :param search_height: maximum height to search for citations
+ :type search_height: int
+
+ :param search_depth: maximum depth to search for references
+ :type search_depth: int
+
+ :param test_var: variable to differenciate between test and url call
+ :type test_var: boolean
+
+ main function to start graph generation
+ '''
+
+ # 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")
+
+
+ # creates empty lists to save nodes and 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)
+
+ # function calls to begin recursive processing up to max depth/height
+ add_citations(nodes, edges, citations_obj_list, 1, search_height, test_var)
+ add_references(nodes, edges, 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, test_var)
+
+ return(nodes,edges)
diff --git a/verarbeitung/construct_new_graph/__init__.py b/verarbeitung/construct_new_graph/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/verarbeitung/construct_new_graph/add_citations_rec.py b/verarbeitung/construct_new_graph/add_citations_rec.py
new file mode 100644
index 0000000..6dd815f
--- /dev/null
+++ b/verarbeitung/construct_new_graph/add_citations_rec.py
@@ -0,0 +1,151 @@
+# -*- coding: utf-8 -*-
+"""
+Functions to add citations recursivly for 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__ = ""
+
+
+import sys
+from pathlib import Path
+from os import error
+sys.path.append("../../")
+
+from input.publication import Publication
+from verarbeitung.get_pub_from_input import get_pub
+
+def create_global_lists_cit(input_nodes, input_edges, pub, search_height, search_height_max, test_var):
+ '''
+ :param input_nodes: list of nodes from Processing
+ :type input_nodes: List[Publication]
+
+ :param input_edges: list of edges from Processing
+ :type input_edges: List[String, String]
+
+ :param pub: Publication which citations will be added
+ :type pub: Publication
+
+ :param search_height: current height to search for citations
+ :type search_height_max: int
+
+ :param search_height_max: maximum height to search for citations
+ :type search_height_max: int
+
+ :param test_var: variable to differenciate between test and url call
+ :type test_var: boolean
+
+ function to create nodes and edges and call create_graph_structure_citations
+ '''
+
+ global nodes, edges
+ nodes = input_nodes
+ edges = input_edges
+
+ return create_graph_structure_citations(pub, search_height, search_height_max, test_var)
+
+
+def create_graph_structure_citations(pub, search_height, search_height_max, test_var):
+ '''
+ :param pub: publication which citations will be added
+ :type pub: Publication
+
+ :param search_height: current height to search for citations
+ :type search_height_max: int
+
+ :param search_height_max: maximum height to search for citations
+ :type search_height_max: int
+
+ :param test_var: variable to differenciate between test and url call
+ :type test_var: boolean
+
+ adds a node for every citing publication unknown
+ adds edges to added citations
+ '''
+
+ citations_pub_obj_list = []
+ for citation in pub.citations:
+ not_in_nodes = True
+ for node in nodes: # checks every citation for duplication
+ if (citation == 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
+ citation_pub_obj = get_pub(citation, test_var)
+ if (type(citation_pub_obj) != Publication):
+ print(pub)
+ continue
+
+ 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,pub.doi_url] not in edges:
+ edges.append([citation,pub.doi_url])
+ return citations_pub_obj_list
+
+
+def process_citations_rec(citations_pub_obj_list, search_height, search_height_max, test_var):
+ '''
+ :param citations_pub_obj_list: list of publications which citations will be added
+ :type citations_pub_obj_list: List[Publication]
+
+ :param search_height: current height to search for citations
+ :type search_height_max: int
+
+ :param search_height_max: maximum height to search for citations
+ :type search_height_max: int
+
+ :param test_var: variable to differenciate between test and url call
+ :type test_var: boolean
+
+ recursive function to implement depth-first-search on citations
+ '''
+
+ # 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 add_citations(input_nodes, input_edges, citations_pub_obj_list, search_height, search_height_max, test_var):
+ '''
+ :param input_nodes: list of nodes from Processing
+ :type input_nodes: List[Publication]
+
+ :param input_edges: list of edges from Processing
+ :type input_edges: List[String, String]
+
+ :param citations_pub_obj_list: list of publications which citations will be added
+ :type citations_pub_obj_list: List[Publication]
+
+ :param search_height: current height to search for citations
+ :type search_height_max: int
+
+ :param search_height_max: maximum height to search for citations
+ :type search_height_max: int
+
+ :param test_var: variable to differenciate between test and url call
+ :type test_var: boolean
+
+ function to call recursive depth-first-search of citations
+ '''
+ global nodes, edges
+ nodes = input_nodes
+ edges = input_edges
+
+ process_citations_rec(citations_pub_obj_list, search_height, search_height_max, test_var)
+ return(nodes, edges)
\ No newline at end of file
diff --git a/verarbeitung/construct_new_graph/add_references_rec.py b/verarbeitung/construct_new_graph/add_references_rec.py
new file mode 100644
index 0000000..320bc21
--- /dev/null
+++ b/verarbeitung/construct_new_graph/add_references_rec.py
@@ -0,0 +1,151 @@
+# -*- coding: utf-8 -*-
+"""
+Functions to add references recursivly for 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__ = ""
+
+
+import sys
+from pathlib import Path
+from os import error
+sys.path.append("../../")
+
+from input.publication import Publication
+from verarbeitung.get_pub_from_input import get_pub
+
+def create_global_lists_ref(input_nodes, input_edges, pub, search_depth, search_depth_max, test_var):
+ '''
+ :param input_nodes: list of nodes from Processing
+ :type input_nodes: List[Publication]
+
+ :param input_edges: list of edges from Processing
+ :type input_edges: List[String, String]
+
+ :param pub: Publication which references will be added
+ :type pub: Publication
+
+ :param search_height: current height to search for references
+ :type search_height_max: int
+
+ :param search_height_max: maximum height to search for references
+ :type search_height_max: int
+
+ :param test_var: variable to differenciate between test and url call
+ :type test_var: boolean
+
+ function to create nodes and edges and call create_graph_structure_references
+ '''
+
+ global nodes, edges
+ nodes = input_nodes
+ edges = input_edges
+
+ return create_graph_structure_references(pub, search_depth, search_depth_max, test_var)
+
+
+def create_graph_structure_references(pub, search_depth, search_depth_max, test_var):
+ '''
+ :param pub: publication which references will be added
+ :type pub: Publication
+
+ :param search_depth: current depth to search for references
+ :type search_depth: int
+
+ :param search_depth_max: maximum depth to search for references
+ :type search_depth_max: int
+
+ :param test_var: variable to differenciate between test and url call
+ :type test_var: boolean
+
+ adds a node for every referenced publication unknown
+ adds edges to added references
+ '''
+
+ references_pub_obj_list = []
+ for reference in pub.references: #iterates over the references of the considered paper
+ not_in_nodes = True #boolean Value to ensure that there will be no dublicates in the set of nodes
+ for node in nodes: #iterates over all nodes in set of nodes #
+ if (reference == node.doi_url): #determines that the node already exists
+ not_in_nodes = False #boolean false --> node will not be created
+ break
+ if (not_in_nodes): #checks that there is no node with this doi
+ if (search_depth < search_depth_max): #checks that the recursion step is smaller than the limit
+ reference_pub_obj = get_pub(reference, test_var)
+ if (type(reference_pub_obj) != Publication):
+ print(pub)
+ continue
+
+ reference_pub_obj.group = "depth"
+ nodes.append(reference_pub_obj) # appends the object to the set of nodes
+ edges.append([pub.doi_url,reference_pub_obj.doi_url]) #appends the edge to the set of edges
+ references_pub_obj_list.append(reference_pub_obj) #appends the node to the set of references
+
+ # adds edge only if citation already exists
+ elif [pub.doi_url,reference] not in edges:
+ edges.append([pub.doi_url,reference])
+ return references_pub_obj_list
+
+
+def process_references_rec(references_pub_obj_list, search_depth, search_depth_max, test_var):
+ '''
+ :param references_pub_obj_list: list of publications which references will be added
+ :type references_pub_obj_list: List[Publication]
+
+ :param search_depth: current depth to search for references
+ :type search_depth: int
+
+ :param search_depth_max: maximum depth to search for references
+ :type search_depth_max: int
+
+ :param test_var: variable to differenciate between test and url call
+ :type test_var: boolean
+
+ recursive function to implement height-first-search on references
+ '''
+
+ # 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)
+
+
+def add_references(input_nodes, input_edges, references_pub_obj_list, search_height, search_height_max, test_var):
+ '''
+ :param input_nodes: list of nodes from Processing
+ :type input_nodes: List[Publication]
+
+ :param input_edges: list of edges from Processing
+ :type input_edges: List[String, String]
+
+ :param references_pub_obj_list: list of publications which references will be added
+ :type references_pub_obj_list: List[Publication]
+
+ :param search_height: current height to search for references
+ :type search_height_max: int
+
+ :param search_height_max: maximum height to search for references
+ :type search_height_max: int
+
+ :param test_var: variable to differenciate between test and url call
+ :type test_var: boolean
+
+ function to call recursive depth-first-search of references
+ '''
+ global nodes, edges
+ nodes = input_nodes
+ edges = input_edges
+
+ process_references_rec(references_pub_obj_list, search_height, search_height_max, test_var)
+ return(nodes, edges)
\ No newline at end of file
diff --git a/verarbeitung/json_demo.py b/verarbeitung/construct_new_graph/export_to_json.py
similarity index 100%
rename from verarbeitung/json_demo.py
rename to verarbeitung/construct_new_graph/export_to_json.py
diff --git a/verarbeitung/dev_files/__init__.py b/verarbeitung/dev_files/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/verarbeitung/print_graph_test.py b/verarbeitung/dev_files/print_graph_test.py
similarity index 94%
rename from verarbeitung/print_graph_test.py
rename to verarbeitung/dev_files/print_graph_test.py
index efb62ec..f5e3a03 100644
--- a/verarbeitung/print_graph_test.py
+++ b/verarbeitung/dev_files/print_graph_test.py
@@ -19,9 +19,9 @@ 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
-from Processing import process_main
-from import_from_json import input_from_json
-from update_graph import check_graph_updates
+from verarbeitung.construct_new_graph.Processing import process_main
+from verarbeitung.update_graph.import_from_json import input_from_json
+from update_graph.update_graph import check_graph_updates
# a function to print nodes and edges from a graph
def print_graph(nodes, edges):
diff --git a/verarbeitung/get_pub_from_input.py b/verarbeitung/get_pub_from_input.py
index a8636a4..9cf4b9c 100644
--- a/verarbeitung/get_pub_from_input.py
+++ b/verarbeitung/get_pub_from_input.py
@@ -19,7 +19,7 @@ from pathlib import Path
sys.path.append("../")
from input.interface import InputInterface as Input
-from input_test import input_test_func
+from verarbeitung.test.input_test import input_test_func
def get_pub(pub_doi, test_var):
diff --git a/verarbeitung/json_text.json b/verarbeitung/json_text.json
deleted file mode 100644
index de3ddf5..0000000
--- a/verarbeitung/json_text.json
+++ /dev/null
@@ -1 +0,0 @@
-{"nodes": [{"doi": "https://doi.org/10.1021/acs.jcim.9b00249", "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", "group": "input", "citations": 5}], "links": []}
\ No newline at end of file
diff --git a/verarbeitung/process_main.py b/verarbeitung/process_main.py
new file mode 100644
index 0000000..e69de29
diff --git a/verarbeitung/Processing_unittest.py b/verarbeitung/test/Processing_unittest.py
similarity index 94%
rename from verarbeitung/Processing_unittest.py
rename to verarbeitung/test/Processing_unittest.py
index def1442..47dd268 100644
--- a/verarbeitung/Processing_unittest.py
+++ b/verarbeitung/test/Processing_unittest.py
@@ -1,119 +1,123 @@
-import unittest
-
-from Processing import process_main
-from import_from_json import input_from_json
-from update_graph import check_graph_updates
-
-class ProcessingTest(unittest.TestCase):
- maxDiff = None
-
-
- def testCycle(self):
- nodes, edges = process_main(['doiz1'],1,1,True)
- doi_nodes = keep_only_dois(nodes)
- self.assertCountEqual(doi_nodes, ['doiz1', 'doiz2'])
- self.assertCountEqual(edges, [['doiz1', 'doiz2'], ['doiz2', 'doiz1']])
-
- nodes, edges = process_main(['doiz1'],2,2,True)
- doi_nodes = keep_only_dois(nodes)
- self.assertCountEqual(doi_nodes, ['doiz1', 'doiz2'])
- self.assertCountEqual(edges, [['doiz2', 'doiz1'], ['doiz1', 'doiz2']])
-
- #def testBigCycle(self):
-
- #def testEmptyHeight(self):
-
- #def testEmptyDepth(self):
-
- def testEmptyDepthHeight(self):
- nodes, edges = process_main(['doi1'],0,0,True)
- doi_nodes = keep_only_dois(nodes)
- self.assertCountEqual(doi_nodes,['doi1'])
- self.assertCountEqual(edges, [])
-
- nodes, edges = process_main(['doi1', 'doi2'],0,0,True)
- doi_nodes = keep_only_dois(nodes)
- self.assertCountEqual(doi_nodes, ['doi1','doi2'])
- self.assertCountEqual(edges, [['doi1', 'doi2']])
-
- nodes, edges = process_main(['doi1', 'doi2', 'doi3'],0,0,True)
- doi_nodes = keep_only_dois(nodes)
- self.assertCountEqual(doi_nodes, ['doi1','doi2', 'doi3'])
- self.assertCountEqual(edges, [['doi3', 'doi1'], ['doi1', 'doi2']])
-
-
- def testInnerEdges(self):
- nodes, edges = process_main(['doi_ie1'],1,1,True)
- doi_nodes = keep_only_dois(nodes)
- self.assertCountEqual(doi_nodes,['doi_ie1','doi_ie2','doi_ie3'])
- self.assertCountEqual(edges,[['doi_ie1','doi_ie2'],['doi_ie3','doi_ie1'],['doi_ie3','doi_ie2']])
-
- def testRightHeight(self):
- nodes, edges = process_main(['doi_h01'],1,0,True)
- doi_nodes = keep_only_dois(nodes)
- self.assertCountEqual(doi_nodes,['doi_h01'])
- self.assertCountEqual(edges, [])
-
- nodes, edges = process_main(['doi_h02'],1,0,True)
- doi_nodes = keep_only_dois(nodes)
- self.assertCountEqual(doi_nodes,['doi_h02','doi_h1'])
- self.assertCountEqual(edges, [['doi_h1','doi_h02']])
-
- nodes, edges = process_main(['doi_h02'],2,0,True)
- doi_nodes = keep_only_dois(nodes)
- self.assertCountEqual(doi_nodes,['doi_h02','doi_h1','doi_h2'])
- self.assertCountEqual(edges, [['doi_h1','doi_h02'], ['doi_h2','doi_h1']])
-
- def testRightDepth(self):
- nodes, edges = process_main(['doi_d01'],0,1,True)
- doi_nodes = keep_only_dois(nodes)
- self.assertCountEqual(doi_nodes,['doi_d01'])
- self.assertCountEqual(edges, [])
-
- nodes, edges = process_main(['doi_d02'],0,1,True)
- doi_nodes = keep_only_dois(nodes)
- self.assertCountEqual(doi_nodes,['doi_d02','doi_d1'])
- self.assertCountEqual(edges, [['doi_d02','doi_d1']])
-
- nodes, edges = process_main(['doi_d02'],0,2,True)
- doi_nodes = keep_only_dois(nodes)
- self.assertCountEqual(doi_nodes,['doi_d02','doi_d1','doi_d2'])
- self.assertCountEqual(edges, [['doi_d02','doi_d1'], ['doi_d1','doi_d2']])
-
- def test_import_from_json(self):
- nodes_old, edges_old = process_main(['doi_lg_1_i'],2,2,True)
- nodes_new, edges_new = input_from_json('test_output.json')
- self.assertCountEqual(nodes_old,nodes_new)
- self.assertCountEqual(edges_old, edges_new)
-
- def test_deleted_input_dois(self):
- nodes_old_single, edges_old_single = process_main(['doi_lg_1_i'],2,2,True)
- nodes_old_both, edges_old_both = process_main(['doi_lg_1_i','doi_lg_2_i'],2,2,True)
- nodes_new_both, edges_new_both = input_from_json('test_output.json')
- nodes_new_single, edges_new_single = check_graph_updates(['doi_lg_1_i'], nodes_old_both, edges_old_both, True)
- self.assertCountEqual(nodes_old_single,nodes_new_single)
- self.assertCountEqual(edges_old_single, edges_new_single)
-
- nodes_old_single, edges_old_single = process_main(['doi_cg_i'],3,3,True)
- nodes_old_two, edges_old_two = process_main(['doi_lg_1_i','doi_cg_i'],3,3,True)
- nodes_old_three, edges_old_three = process_main(['doi_lg_1_i','doi_lg_2_i','doi_cg_i'],3,3,True)
-
-
-
-
-
-def keep_only_dois(nodes):
- '''
- :param nodes: input list of nodes of type Publication
- :type nodes: List[Publication]
-
- gets nodes of type pub and return only their doi
- '''
- doi_list = []
- for node in nodes:
- doi_list.append(node.doi_url)
- return doi_list
-
-
-if __name__ == "__main__":
+import unittest
+
+import sys
+from pathlib import Path
+sys.path.append("../")
+
+from verarbeitung.construct_new_graph.Processing import process_main
+from verarbeitung.update_graph.import_from_json import input_from_json
+from verarbeitung.update_graph.update_graph import check_graph_updates
+
+class ProcessingTest(unittest.TestCase):
+ maxDiff = None
+
+
+ def testCycle(self):
+ nodes, edges = process_main(['doiz1'],1,1,True)
+ doi_nodes = keep_only_dois(nodes)
+ self.assertCountEqual(doi_nodes, ['doiz1', 'doiz2'])
+ self.assertCountEqual(edges, [['doiz1', 'doiz2'], ['doiz2', 'doiz1']])
+
+ nodes, edges = process_main(['doiz1'],2,2,True)
+ doi_nodes = keep_only_dois(nodes)
+ self.assertCountEqual(doi_nodes, ['doiz1', 'doiz2'])
+ self.assertCountEqual(edges, [['doiz2', 'doiz1'], ['doiz1', 'doiz2']])
+
+ #def testBigCycle(self):
+
+ #def testEmptyHeight(self):
+
+ #def testEmptyDepth(self):
+
+ def testEmptyDepthHeight(self):
+ nodes, edges = process_main(['doi1'],0,0,True)
+ doi_nodes = keep_only_dois(nodes)
+ self.assertCountEqual(doi_nodes,['doi1'])
+ self.assertCountEqual(edges, [])
+
+ nodes, edges = process_main(['doi1', 'doi2'],0,0,True)
+ doi_nodes = keep_only_dois(nodes)
+ self.assertCountEqual(doi_nodes, ['doi1','doi2'])
+ self.assertCountEqual(edges, [['doi1', 'doi2']])
+
+ nodes, edges = process_main(['doi1', 'doi2', 'doi3'],0,0,True)
+ doi_nodes = keep_only_dois(nodes)
+ self.assertCountEqual(doi_nodes, ['doi1','doi2', 'doi3'])
+ self.assertCountEqual(edges, [['doi3', 'doi1'], ['doi1', 'doi2']])
+
+
+ def testInnerEdges(self):
+ nodes, edges = process_main(['doi_ie1'],1,1,True)
+ doi_nodes = keep_only_dois(nodes)
+ self.assertCountEqual(doi_nodes,['doi_ie1','doi_ie2','doi_ie3'])
+ self.assertCountEqual(edges,[['doi_ie1','doi_ie2'],['doi_ie3','doi_ie1'],['doi_ie3','doi_ie2']])
+
+ def testRightHeight(self):
+ nodes, edges = process_main(['doi_h01'],1,0,True)
+ doi_nodes = keep_only_dois(nodes)
+ self.assertCountEqual(doi_nodes,['doi_h01'])
+ self.assertCountEqual(edges, [])
+
+ nodes, edges = process_main(['doi_h02'],1,0,True)
+ doi_nodes = keep_only_dois(nodes)
+ self.assertCountEqual(doi_nodes,['doi_h02','doi_h1'])
+ self.assertCountEqual(edges, [['doi_h1','doi_h02']])
+
+ nodes, edges = process_main(['doi_h02'],2,0,True)
+ doi_nodes = keep_only_dois(nodes)
+ self.assertCountEqual(doi_nodes,['doi_h02','doi_h1','doi_h2'])
+ self.assertCountEqual(edges, [['doi_h1','doi_h02'], ['doi_h2','doi_h1']])
+
+ def testRightDepth(self):
+ nodes, edges = process_main(['doi_d01'],0,1,True)
+ doi_nodes = keep_only_dois(nodes)
+ self.assertCountEqual(doi_nodes,['doi_d01'])
+ self.assertCountEqual(edges, [])
+
+ nodes, edges = process_main(['doi_d02'],0,1,True)
+ doi_nodes = keep_only_dois(nodes)
+ self.assertCountEqual(doi_nodes,['doi_d02','doi_d1'])
+ self.assertCountEqual(edges, [['doi_d02','doi_d1']])
+
+ nodes, edges = process_main(['doi_d02'],0,2,True)
+ doi_nodes = keep_only_dois(nodes)
+ self.assertCountEqual(doi_nodes,['doi_d02','doi_d1','doi_d2'])
+ self.assertCountEqual(edges, [['doi_d02','doi_d1'], ['doi_d1','doi_d2']])
+
+ def test_import_from_json(self):
+ nodes_old, edges_old = process_main(['doi_lg_1_i'],2,2,True)
+ nodes_new, edges_new = input_from_json('test_output.json')
+ self.assertCountEqual(nodes_old,nodes_new)
+ self.assertCountEqual(edges_old, edges_new)
+
+ def test_deleted_input_dois(self):
+ nodes_old_single, edges_old_single = process_main(['doi_lg_1_i'],2,2,True)
+ nodes_old_both, edges_old_both = process_main(['doi_lg_1_i','doi_lg_2_i'],2,2,True)
+ nodes_new_both, edges_new_both = input_from_json('test_output.json')
+ nodes_new_single, edges_new_single = check_graph_updates(['doi_lg_1_i'], nodes_old_both, edges_old_both, True)
+ self.assertCountEqual(nodes_old_single,nodes_new_single)
+ self.assertCountEqual(edges_old_single, edges_new_single)
+
+ nodes_old_single, edges_old_single = process_main(['doi_cg_i'],3,3,True)
+ nodes_old_two, edges_old_two = process_main(['doi_lg_1_i','doi_cg_i'],3,3,True)
+ nodes_old_three, edges_old_three = process_main(['doi_lg_1_i','doi_lg_2_i','doi_cg_i'],3,3,True)
+
+
+
+
+
+def keep_only_dois(nodes):
+ '''
+ :param nodes: input list of nodes of type Publication
+ :type nodes: List[Publication]
+
+ gets nodes of type pub and return only their doi
+ '''
+ doi_list = []
+ for node in nodes:
+ doi_list.append(node.doi_url)
+ return doi_list
+
+
+if __name__ == "__main__":
unittest.main()
\ No newline at end of file
diff --git a/verarbeitung/test/__init__.py b/verarbeitung/test/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/verarbeitung/input_test.py b/verarbeitung/test/input_test.py
similarity index 98%
rename from verarbeitung/input_test.py
rename to verarbeitung/test/input_test.py
index 4c9bf31..928c8b4 100644
--- a/verarbeitung/input_test.py
+++ b/verarbeitung/test/input_test.py
@@ -1,116 +1,116 @@
-import sys
-sys.path.append("../")
-
-from input.publication import Publication, Citation
-
-
-def input_test_func(pub_doi):
- '''
- :param pub_doi: pub doi to find publication in list_of_arrays
- :type pub_doi: String
-
- returns the publication class for given doi
- '''
-
- for array in list_of_arrays:
- if pub_doi == array[0]:
- pub = Publication(array[0], array[1], array[2], array[3], array[4], array[5], array[6], array[7])
- return pub
-
-
-def cit(list_doi):
- '''
- :param list_doi list of citation dois to get their Citation Class
- :type list_doi: List[String]
-
- returns a list of citations objects for given doi list
- '''
-
- cits = []
- for doi_url in list_doi:
- for array in list_of_arrays:
- if doi_url == array[0]:
- cits.append(Citation(array[0], array[1], array[2], array[3], array[4]))
- return cits
-
-def ref(list_doi):
- '''
- :param list_doi list of reference dois to get their Reference Class
- :type list_doi: List[String]
-
- returns a list of reference objects for given doi list
- '''
-
- refs = []
- for doi_url in list_doi:
- for array in list_of_arrays:
- if doi_url == array[0]:
- refs.append(Citation(array[0], array[1], array[2], array[3], array[4]))
- return refs
-
-
-
-beispiel1 = ['doi1', 'title1', ['contributor1'], 'journal1', 'date1', ['subject1'], ['doi2'], ['doi3']]
-beispiel2 = ['doi2', 'title2', ['contributor2'], 'journal2', 'date2', ['subject2'], [], ['doi1']]
-beispiel3 = ['doi3', 'title3', ['contributor3'], 'journal3', 'date3', ['subject3'], ['doi1'], []]
-
-zyklus1 = ['doiz1', 'titlez1', ['contributorz1.1', 'contributorz1.2'], 'journalz1', 'datez1', ['subjectz1'], ['doiz2'], ['doiz2']]
-zyklus2 = ['doiz2', 'titlez2', ['contributorz2.1', 'contributorz2.2'], 'journalz2', 'datez2', ['subjectz1'], ['doiz1'], ['doiz1']]
-
-inner_edge1 = ['doi_ie1', 'title_ie1', ['contributor_ie1.1', 'contributor_ie1.2'], 'journal_ie1', 'date_ie1', ['subject_ie1'], ['doi_ie2'], ['doi_ie3']]
-inner_edge2 = ['doi_ie2', 'title_ie2', ['contributor_ie2.1', 'contributor_ie2.2'], 'journal_ie2', 'date_ie2', ['subject_ie2'], [], ['doi_ie1','doi_ie3']]
-inner_edge3 = ['doi_ie3', 'titlez_ie3', ['contributor_ie3.1', 'contributor_ie3.2'], 'journal_ie3', 'date_ie3', ['subject_ie3'], ['doi_ie1','doi_ie2'], []]
-
-right_height01 = ['doi_h01', 'title_h01', ['contributor_h01'], 'journal_h01', 'date_h01', ['subject_h01'], [], []]
-right_height02 = ['doi_h02', 'title_h02', ['contributor_h02'], 'journal_h02', 'date_h02', ['subject_h02'], [], ['doi_h1']]
-right_height1 = ['doi_h1', 'title_h1', ['contributor_h1'], 'journal_h1', 'date_h1', ['subject_h1'], [], ['doi_h2']]
-right_height2 = ['doi_h2', 'title_h2', ['contributor_h2'], 'journal_h2', 'date_h2', ['subject_h2'], [], ['doi_h3']]
-right_height3 = ['doi_h3', 'title_h3', ['contributor_h3'], 'journal_h3', 'date_h3', ['subject_h3'], [], []]
-
-right_depth01 = ['doi_d01', 'title_d01', ['contributor_d01'], 'journal_d01', 'date_d01', ['subject_d01'], [], []]
-right_depth02 = ['doi_d02', 'title_d02', ['contributor_d02'], 'journal_d02', 'date_d02', ['subject_d01'], ['doi_d1'], []]
-right_depth1 = ['doi_d1', 'title_d1', ['contributor_d1'], 'journal_d1', 'date_d1', ['subject_d1'], ['doi_d2'], []]
-right_depth2 = ['doi_d2', 'title_d2', ['contributor_d2'], 'journal_d2', 'date_d2', ['subject_d2'], ['doi_d3'], []]
-right_depth3 = ['doi_d3', 'title_d3', ['contributor_d3'], 'journal_d3', 'date_d3', ['subject_d3'], [], []]
-
-large_graph_1_h21 = ['doi_lg_1_h21', 'title_lg_1_h21', ['contributor_lg_1_h21'], 'journal_lg_1_h21', 'date_lg_1_h21', ['subject_lg_1_h21'], ['doi_lg_1_h11'], []]
-large_graph_1_h22 = ['doi_lg_1_h22', 'title_lg_1_h22', ['contributor_lg_1_h22'], 'journal_lg_1_h22', 'date_lg_1_h22', ['subject_lg_1_h22'], ['doi_lg_1_h11','doi_lg_1_h12'], []]
-large_graph_1_h23 = ['doi_lg_1_h23', 'title_lg_1_h23', ['contributor_lg_1_h23'], 'journal_lg_1_h23', 'date_lg_1_h23', ['subject_lg_1_h23'], ['doi_lg_1_h12','doi_cg_i'], []]
-large_graph_1_h11 = ['doi_lg_1_h11', 'title_lg_1_h11', ['contributor_lg_1_h11'], 'journal_lg_1_h11', 'date_lg_1_h11', ['subject_lg_1_h11'], ['doi_lg_1_h12','doi_lg_1_i'], ['doi_lg_1_h21','doi_lg_1_h22']]
-large_graph_1_h12 = ['doi_lg_1_h12', 'title_lg_1_h12', ['contributor_lg_1_h12'], 'journal_lg_1_h12', 'date_lg_1_h12', ['subject_lg_1_h12'], ['doi_lg_1_i','doi_lg_1_d12'], ['doi_lg_1_h22','doi_lg_1_h23']]
-large_graph_1_i = ['doi_lg_1_i' , 'title_lg_1_i' , ['contributor_lg_1_i'] , 'journal_lg_1_i' , 'date_lg_1_i' , ['subject_lg_1_i'] , ['doi_lg_1_d11','doi_lg_1_d12'], ['doi_lg_1_h11','doi_lg_1_h12']]
-large_graph_1_d11 = ['doi_lg_1_d11', 'title_lg_1_d11', ['contributor_lg_1_d11'], 'journal_lg_1_d11', 'date_lg_1_d11', ['subject_lg_1_d11'], ['doi_lg_1_d21','doi_lg_1_d22'], ['doi_lg_1_i']]
-large_graph_1_d12 = ['doi_lg_1_d12', 'title_lg_1_d12', ['contributor_lg_1_d12'], 'journal_lg_1_d12', 'date_lg_1_d12', ['subject_lg_1_d12'], ['doi_lg_1_d23'], ['doi_lg_1_h12','doi_lg_1_i']]
-large_graph_1_d21 = ['doi_lg_1_d21', 'title_lg_1_d21', ['contributor_lg_1_d21'], 'journal_lg_1_d21', 'date_lg_1_d21', ['subject_lg_1_d21'], ['doi_lg_1_d22'], ['doi_lg_1_d11','doi_lg_1_d22']]
-large_graph_1_d22 = ['doi_lg_1_d22', 'title_lg_1_d22', ['contributor_lg_1_d22'], 'journal_lg_1_d22', 'date_lg_1_d22', ['subject_lg_1_d22'], ['doi_lg_1_d21'], ['doi_lg_1_d11','doi_lg_1_d21']]
-large_graph_1_d23 = ['doi_lg_1_d23', 'title_lg_1_d23', ['contributor_lg_1_d23'], 'journal_lg_1_d23', 'date_lg_1_d23', ['subject_lg_1_d23'], [], ['doi_lg_1_d12','doi_cg_d11']]
-
-large_graph_2_h21 = ['doi_lg_2_h21', 'title_lg_2_h21', ['contributor_lg_2_h21'], 'journal_lg_2_h21', 'date_lg_2_h21', ['subject_lg_2_h21'], ['doi_lg_2_h11'], []]
-large_graph_2_h22 = ['doi_lg_2_h22', 'title_lg_2_h22', ['contributor_lg_2_h22'], 'journal_lg_2_h22', 'date_lg_2_h22', ['subject_lg_2_h22'], ['doi_lg_2_h11'], []]
-large_graph_2_h23 = ['doi_lg_2_h23', 'title_lg_2_h23', ['contributor_lg_2_h23'], 'journal_lg_2_h23', 'date_lg_2_h23', ['subject_lg_2_h23'], ['doi_lg_2_h12','doi_lg_2_h24'], ['doi_lg_2_h24']]
-large_graph_2_h24 = ['doi_lg_2_h24', 'title_lg_2_h24', ['contributor_lg_2_h24'], 'journal_lg_2_h24', 'date_lg_2_h24', ['subject_lg_2_h24'], ['doi_lg_2_h12','doi_lg_2_h23','doi_lg_2_d12'], ['doi_lg_2_h23']]
-large_graph_2_h11 = ['doi_lg_2_h11', 'title_lg_2_h11', ['contributor_lg_2_h11'], 'journal_lg_2_h11', 'date_lg_2_h11', ['subject_lg_2_h11'], ['doi_lg_2_i','doi_cg_i'], ['doi_lg_2_h21','doi_lg_2_h22']]
-large_graph_2_h12 = ['doi_lg_2_h12', 'title_lg_2_h12', ['contributor_lg_2_h12'], 'journal_lg_2_h12', 'date_lg_2_h12', ['subject_lg_2_h12'], ['doi_lg_2_i'], ['doi_lg_2_h23','doi_lg_2_h24']]
-large_graph_2_i = ['doi_lg_2_i' , 'title_lg_2_i' , ['contributor_lg_2_i'] , 'journal_lg_2_i' , 'date_lg_2_i' , ['subject_lg_2_i'] , ['doi_lg_2_d11','doi_lg_2_d12'], ['doi_lg_2_h11','doi_lg_2_h12','doi_cg_i']]
-large_graph_2_d11 = ['doi_lg_2_d11', 'title_lg_2_d11', ['contributor_lg_2_d11'], 'journal_lg_2_d11', 'date_lg_2_d11', ['subject_lg_2_d11'], [], ['doi_lg_2_i']]
-large_graph_2_d12 = ['doi_lg_2_d12', 'title_lg_2_d12', ['contributor_lg_2_d12'], 'journal_lg_2_d12', 'date_lg_2_d12', ['subject_lg_2_d12'], ['doi_lg_2_d21','doi_lg_2_d22'], ['doi_lg_2_h24','doi_lg_2_i']]
-large_graph_2_d21 = ['doi_lg_2_d21', 'title_lg_2_d21', ['contributor_lg_2_d21'], 'journal_lg_2_d21', 'date_lg_2_d21', ['subject_lg_2_d21'], [], ['doi_lg_2_d12']]
-large_graph_2_d22 = ['doi_lg_2_d22', 'title_lg_2_d22', ['contributor_lg_2_d22'], 'journal_lg_2_d22', 'date_lg_2_d22', ['subject_lg_2_d22'], [], ['doi_lg_2_d12']]
-large_graph_2_d23 = ['doi_lg_2_d23', 'title_lg_2_d23', ['contributor_lg_2_d23'], 'journal_lg_2_d23', 'date_lg_2_d23', ['subject_lg_2_d23'], [], ['doi_lg_2_d12']]
-
-crossed_graph_h21 = ['doi_cg_h21', 'title_cg_h21', ['contributor_cg_h21'], 'journal_cg_h21', 'date_cg_h21', ['subject_cg_h21'], ['doi_cg_h11'], []]
-crossed_graph_h22 = ['doi_cg_h22', 'title_cg_h22', ['contributor_cg_h22'], 'journal_cg_h22', 'date_cg_h22', ['subject_cg_h22'], ['doi_cg_h11'], []]
-crossed_graph_h11 = ['doi_cg_h11', 'title_cg_h11', ['contributor_cg_h11'], 'journal_cg_h11', 'date_cg_h11', ['subject_cg_h11'], ['doi_cg_i'], ['doi_cg_h21','doi_cg_h22']]
-crossed_graph_i = ['doi_cg_i', 'title_cg_i', ['contributor_cg_i'], 'journal_cg_i', 'date_cg_i', ['subject_cg_i'], ['doi_lg_2_i','doi_cg_d11','doi_cg_d12'], ['doi_lg_1_h23','doi_cg_h11','doi_lg_2_h11']]
-crossed_graph_d11 = ['doi_cg_d11', 'title_cg_d11', ['contributor_cg_d11'], 'journal_cg_d11', 'date_cg_d11', ['subject_cg_d11'], ['doi_lg_1_d23','doi_cg_d21'], ['doi_cg_i']]
-crossed_graph_d12 = ['doi_cg_d12', 'title_cg_d12', ['contributor_cg_d12'], 'journal_cg_d12', 'date_cg_d12', ['subject_cg_d12'], ['doi_cg_d22'], ['doi_cg_i']]
-crossed_graph_d21 = ['doi_cg_d21', 'title_cg_d21', ['contributor_cg_d21'], 'journal_cg_d21', 'date_cg_d21', ['subject_cg_d21'], [], ['doi_cg_d11']]
-crossed_graph_d22 = ['doi_cg_d22', 'title_cg_d22', ['contributor_cg_d22'], 'journal_cg_d22', 'date_cg_d22', ['subject_cg_d22'], [], ['doi_cg_d12']]
-
-
-list_of_arrays = [beispiel1, beispiel2, beispiel3, zyklus1, zyklus2, inner_edge1, inner_edge2, inner_edge3,
- right_height01, right_height02, right_height1, right_height2, right_height3, right_depth01, right_depth02, right_depth1, right_depth2, right_depth3,
- large_graph_1_h21, large_graph_1_h22, large_graph_1_h23, large_graph_1_h11, large_graph_1_h12, large_graph_1_i, large_graph_1_d11, large_graph_1_d12,
- large_graph_1_d21, large_graph_1_d22, large_graph_1_d23, large_graph_2_h21, large_graph_2_h22, large_graph_2_h23, large_graph_2_h24, large_graph_2_h11, large_graph_2_h12,
- large_graph_2_i, large_graph_2_d11, large_graph_2_d12, large_graph_2_d21, large_graph_2_d22, large_graph_2_d23, crossed_graph_h21, crossed_graph_h22, crossed_graph_h11,
- crossed_graph_i, crossed_graph_d11, crossed_graph_d12, crossed_graph_d21, crossed_graph_d22]
+import sys
+sys.path.append("../")
+
+from input.publication import Publication, Citation
+
+
+def input_test_func(pub_doi):
+ '''
+ :param pub_doi: pub doi to find publication in list_of_arrays
+ :type pub_doi: String
+
+ returns the publication class for given doi
+ '''
+
+ for array in list_of_arrays:
+ if pub_doi == array[0]:
+ pub = Publication(array[0], array[1], array[2], array[3], array[4], array[5], array[6], array[7])
+ return pub
+
+
+def cit(list_doi):
+ '''
+ :param list_doi list of citation dois to get their Citation Class
+ :type list_doi: List[String]
+
+ returns a list of citations objects for given doi list
+ '''
+
+ cits = []
+ for doi_url in list_doi:
+ for array in list_of_arrays:
+ if doi_url == array[0]:
+ cits.append(Citation(array[0], array[1], array[2], array[3], array[4]))
+ return cits
+
+def ref(list_doi):
+ '''
+ :param list_doi list of reference dois to get their Reference Class
+ :type list_doi: List[String]
+
+ returns a list of reference objects for given doi list
+ '''
+
+ refs = []
+ for doi_url in list_doi:
+ for array in list_of_arrays:
+ if doi_url == array[0]:
+ refs.append(Citation(array[0], array[1], array[2], array[3], array[4]))
+ return refs
+
+
+
+beispiel1 = ['doi1', 'title1', ['contributor1'], 'journal1', 'date1', ['subject1'], ['doi2'], ['doi3']]
+beispiel2 = ['doi2', 'title2', ['contributor2'], 'journal2', 'date2', ['subject2'], [], ['doi1']]
+beispiel3 = ['doi3', 'title3', ['contributor3'], 'journal3', 'date3', ['subject3'], ['doi1'], []]
+
+zyklus1 = ['doiz1', 'titlez1', ['contributorz1.1', 'contributorz1.2'], 'journalz1', 'datez1', ['subjectz1'], ['doiz2'], ['doiz2']]
+zyklus2 = ['doiz2', 'titlez2', ['contributorz2.1', 'contributorz2.2'], 'journalz2', 'datez2', ['subjectz1'], ['doiz1'], ['doiz1']]
+
+inner_edge1 = ['doi_ie1', 'title_ie1', ['contributor_ie1.1', 'contributor_ie1.2'], 'journal_ie1', 'date_ie1', ['subject_ie1'], ['doi_ie2'], ['doi_ie3']]
+inner_edge2 = ['doi_ie2', 'title_ie2', ['contributor_ie2.1', 'contributor_ie2.2'], 'journal_ie2', 'date_ie2', ['subject_ie2'], [], ['doi_ie1','doi_ie3']]
+inner_edge3 = ['doi_ie3', 'titlez_ie3', ['contributor_ie3.1', 'contributor_ie3.2'], 'journal_ie3', 'date_ie3', ['subject_ie3'], ['doi_ie1','doi_ie2'], []]
+
+right_height01 = ['doi_h01', 'title_h01', ['contributor_h01'], 'journal_h01', 'date_h01', ['subject_h01'], [], []]
+right_height02 = ['doi_h02', 'title_h02', ['contributor_h02'], 'journal_h02', 'date_h02', ['subject_h02'], [], ['doi_h1']]
+right_height1 = ['doi_h1', 'title_h1', ['contributor_h1'], 'journal_h1', 'date_h1', ['subject_h1'], [], ['doi_h2']]
+right_height2 = ['doi_h2', 'title_h2', ['contributor_h2'], 'journal_h2', 'date_h2', ['subject_h2'], [], ['doi_h3']]
+right_height3 = ['doi_h3', 'title_h3', ['contributor_h3'], 'journal_h3', 'date_h3', ['subject_h3'], [], []]
+
+right_depth01 = ['doi_d01', 'title_d01', ['contributor_d01'], 'journal_d01', 'date_d01', ['subject_d01'], [], []]
+right_depth02 = ['doi_d02', 'title_d02', ['contributor_d02'], 'journal_d02', 'date_d02', ['subject_d01'], ['doi_d1'], []]
+right_depth1 = ['doi_d1', 'title_d1', ['contributor_d1'], 'journal_d1', 'date_d1', ['subject_d1'], ['doi_d2'], []]
+right_depth2 = ['doi_d2', 'title_d2', ['contributor_d2'], 'journal_d2', 'date_d2', ['subject_d2'], ['doi_d3'], []]
+right_depth3 = ['doi_d3', 'title_d3', ['contributor_d3'], 'journal_d3', 'date_d3', ['subject_d3'], [], []]
+
+large_graph_1_h21 = ['doi_lg_1_h21', 'title_lg_1_h21', ['contributor_lg_1_h21'], 'journal_lg_1_h21', 'date_lg_1_h21', ['subject_lg_1_h21'], ['doi_lg_1_h11'], []]
+large_graph_1_h22 = ['doi_lg_1_h22', 'title_lg_1_h22', ['contributor_lg_1_h22'], 'journal_lg_1_h22', 'date_lg_1_h22', ['subject_lg_1_h22'], ['doi_lg_1_h11','doi_lg_1_h12'], []]
+large_graph_1_h23 = ['doi_lg_1_h23', 'title_lg_1_h23', ['contributor_lg_1_h23'], 'journal_lg_1_h23', 'date_lg_1_h23', ['subject_lg_1_h23'], ['doi_lg_1_h12','doi_cg_i'], []]
+large_graph_1_h11 = ['doi_lg_1_h11', 'title_lg_1_h11', ['contributor_lg_1_h11'], 'journal_lg_1_h11', 'date_lg_1_h11', ['subject_lg_1_h11'], ['doi_lg_1_h12','doi_lg_1_i'], ['doi_lg_1_h21','doi_lg_1_h22']]
+large_graph_1_h12 = ['doi_lg_1_h12', 'title_lg_1_h12', ['contributor_lg_1_h12'], 'journal_lg_1_h12', 'date_lg_1_h12', ['subject_lg_1_h12'], ['doi_lg_1_i','doi_lg_1_d12'], ['doi_lg_1_h22','doi_lg_1_h23']]
+large_graph_1_i = ['doi_lg_1_i' , 'title_lg_1_i' , ['contributor_lg_1_i'] , 'journal_lg_1_i' , 'date_lg_1_i' , ['subject_lg_1_i'] , ['doi_lg_1_d11','doi_lg_1_d12'], ['doi_lg_1_h11','doi_lg_1_h12']]
+large_graph_1_d11 = ['doi_lg_1_d11', 'title_lg_1_d11', ['contributor_lg_1_d11'], 'journal_lg_1_d11', 'date_lg_1_d11', ['subject_lg_1_d11'], ['doi_lg_1_d21','doi_lg_1_d22'], ['doi_lg_1_i']]
+large_graph_1_d12 = ['doi_lg_1_d12', 'title_lg_1_d12', ['contributor_lg_1_d12'], 'journal_lg_1_d12', 'date_lg_1_d12', ['subject_lg_1_d12'], ['doi_lg_1_d23'], ['doi_lg_1_h12','doi_lg_1_i']]
+large_graph_1_d21 = ['doi_lg_1_d21', 'title_lg_1_d21', ['contributor_lg_1_d21'], 'journal_lg_1_d21', 'date_lg_1_d21', ['subject_lg_1_d21'], ['doi_lg_1_d22'], ['doi_lg_1_d11','doi_lg_1_d22']]
+large_graph_1_d22 = ['doi_lg_1_d22', 'title_lg_1_d22', ['contributor_lg_1_d22'], 'journal_lg_1_d22', 'date_lg_1_d22', ['subject_lg_1_d22'], ['doi_lg_1_d21'], ['doi_lg_1_d11','doi_lg_1_d21']]
+large_graph_1_d23 = ['doi_lg_1_d23', 'title_lg_1_d23', ['contributor_lg_1_d23'], 'journal_lg_1_d23', 'date_lg_1_d23', ['subject_lg_1_d23'], [], ['doi_lg_1_d12','doi_cg_d11']]
+
+large_graph_2_h21 = ['doi_lg_2_h21', 'title_lg_2_h21', ['contributor_lg_2_h21'], 'journal_lg_2_h21', 'date_lg_2_h21', ['subject_lg_2_h21'], ['doi_lg_2_h11'], []]
+large_graph_2_h22 = ['doi_lg_2_h22', 'title_lg_2_h22', ['contributor_lg_2_h22'], 'journal_lg_2_h22', 'date_lg_2_h22', ['subject_lg_2_h22'], ['doi_lg_2_h11'], []]
+large_graph_2_h23 = ['doi_lg_2_h23', 'title_lg_2_h23', ['contributor_lg_2_h23'], 'journal_lg_2_h23', 'date_lg_2_h23', ['subject_lg_2_h23'], ['doi_lg_2_h12','doi_lg_2_h24'], ['doi_lg_2_h24']]
+large_graph_2_h24 = ['doi_lg_2_h24', 'title_lg_2_h24', ['contributor_lg_2_h24'], 'journal_lg_2_h24', 'date_lg_2_h24', ['subject_lg_2_h24'], ['doi_lg_2_h12','doi_lg_2_h23','doi_lg_2_d12'], ['doi_lg_2_h23']]
+large_graph_2_h11 = ['doi_lg_2_h11', 'title_lg_2_h11', ['contributor_lg_2_h11'], 'journal_lg_2_h11', 'date_lg_2_h11', ['subject_lg_2_h11'], ['doi_lg_2_i','doi_cg_i'], ['doi_lg_2_h21','doi_lg_2_h22']]
+large_graph_2_h12 = ['doi_lg_2_h12', 'title_lg_2_h12', ['contributor_lg_2_h12'], 'journal_lg_2_h12', 'date_lg_2_h12', ['subject_lg_2_h12'], ['doi_lg_2_i'], ['doi_lg_2_h23','doi_lg_2_h24']]
+large_graph_2_i = ['doi_lg_2_i' , 'title_lg_2_i' , ['contributor_lg_2_i'] , 'journal_lg_2_i' , 'date_lg_2_i' , ['subject_lg_2_i'] , ['doi_lg_2_d11','doi_lg_2_d12'], ['doi_lg_2_h11','doi_lg_2_h12','doi_cg_i']]
+large_graph_2_d11 = ['doi_lg_2_d11', 'title_lg_2_d11', ['contributor_lg_2_d11'], 'journal_lg_2_d11', 'date_lg_2_d11', ['subject_lg_2_d11'], [], ['doi_lg_2_i']]
+large_graph_2_d12 = ['doi_lg_2_d12', 'title_lg_2_d12', ['contributor_lg_2_d12'], 'journal_lg_2_d12', 'date_lg_2_d12', ['subject_lg_2_d12'], ['doi_lg_2_d21','doi_lg_2_d22'], ['doi_lg_2_h24','doi_lg_2_i']]
+large_graph_2_d21 = ['doi_lg_2_d21', 'title_lg_2_d21', ['contributor_lg_2_d21'], 'journal_lg_2_d21', 'date_lg_2_d21', ['subject_lg_2_d21'], [], ['doi_lg_2_d12']]
+large_graph_2_d22 = ['doi_lg_2_d22', 'title_lg_2_d22', ['contributor_lg_2_d22'], 'journal_lg_2_d22', 'date_lg_2_d22', ['subject_lg_2_d22'], [], ['doi_lg_2_d12']]
+large_graph_2_d23 = ['doi_lg_2_d23', 'title_lg_2_d23', ['contributor_lg_2_d23'], 'journal_lg_2_d23', 'date_lg_2_d23', ['subject_lg_2_d23'], [], ['doi_lg_2_d12']]
+
+crossed_graph_h21 = ['doi_cg_h21', 'title_cg_h21', ['contributor_cg_h21'], 'journal_cg_h21', 'date_cg_h21', ['subject_cg_h21'], ['doi_cg_h11'], []]
+crossed_graph_h22 = ['doi_cg_h22', 'title_cg_h22', ['contributor_cg_h22'], 'journal_cg_h22', 'date_cg_h22', ['subject_cg_h22'], ['doi_cg_h11'], []]
+crossed_graph_h11 = ['doi_cg_h11', 'title_cg_h11', ['contributor_cg_h11'], 'journal_cg_h11', 'date_cg_h11', ['subject_cg_h11'], ['doi_cg_i'], ['doi_cg_h21','doi_cg_h22']]
+crossed_graph_i = ['doi_cg_i', 'title_cg_i', ['contributor_cg_i'], 'journal_cg_i', 'date_cg_i', ['subject_cg_i'], ['doi_lg_2_i','doi_cg_d11','doi_cg_d12'], ['doi_lg_1_h23','doi_cg_h11','doi_lg_2_h11']]
+crossed_graph_d11 = ['doi_cg_d11', 'title_cg_d11', ['contributor_cg_d11'], 'journal_cg_d11', 'date_cg_d11', ['subject_cg_d11'], ['doi_lg_1_d23','doi_cg_d21'], ['doi_cg_i']]
+crossed_graph_d12 = ['doi_cg_d12', 'title_cg_d12', ['contributor_cg_d12'], 'journal_cg_d12', 'date_cg_d12', ['subject_cg_d12'], ['doi_cg_d22'], ['doi_cg_i']]
+crossed_graph_d21 = ['doi_cg_d21', 'title_cg_d21', ['contributor_cg_d21'], 'journal_cg_d21', 'date_cg_d21', ['subject_cg_d21'], [], ['doi_cg_d11']]
+crossed_graph_d22 = ['doi_cg_d22', 'title_cg_d22', ['contributor_cg_d22'], 'journal_cg_d22', 'date_cg_d22', ['subject_cg_d22'], [], ['doi_cg_d12']]
+
+
+list_of_arrays = [beispiel1, beispiel2, beispiel3, zyklus1, zyklus2, inner_edge1, inner_edge2, inner_edge3,
+ right_height01, right_height02, right_height1, right_height2, right_height3, right_depth01, right_depth02, right_depth1, right_depth2, right_depth3,
+ large_graph_1_h21, large_graph_1_h22, large_graph_1_h23, large_graph_1_h11, large_graph_1_h12, large_graph_1_i, large_graph_1_d11, large_graph_1_d12,
+ large_graph_1_d21, large_graph_1_d22, large_graph_1_d23, large_graph_2_h21, large_graph_2_h22, large_graph_2_h23, large_graph_2_h24, large_graph_2_h11, large_graph_2_h12,
+ large_graph_2_i, large_graph_2_d11, large_graph_2_d12, large_graph_2_d21, large_graph_2_d22, large_graph_2_d23, crossed_graph_h21, crossed_graph_h22, crossed_graph_h11,
+ crossed_graph_i, crossed_graph_d11, crossed_graph_d12, crossed_graph_d21, crossed_graph_d22]
diff --git a/verarbeitung/test_output.json b/verarbeitung/test_output.json
index b013fbf..8a15eeb 100644
--- a/verarbeitung/test_output.json
+++ b/verarbeitung/test_output.json
@@ -1 +1 @@
-{"nodes": [{"doi": "doi_lg_1_i", "name": "title_lg_1_i", "author": ["contributor_lg_1_i"], "year": "date_lg_1_i", "journal": "journal_lg_1_i", "group": "input", "citations": 2}, {"doi": "doi_lg_1_d11", "name": "title_lg_1_d11", "author": ["contributor_lg_1_d11"], "year": "date_lg_1_d11", "journal": "journal_lg_1_d11", "group": "depth", "citations": 1}, {"doi": "doi_lg_1_d12", "name": "title_lg_1_d12", "author": ["contributor_lg_1_d12"], "year": "date_lg_1_d12", "journal": "journal_lg_1_d12", "group": "depth", "citations": 2}, {"doi": "doi_lg_1_h11", "name": "title_lg_1_h11", "author": ["contributor_lg_1_h11"], "year": "date_lg_1_h11", "journal": "journal_lg_1_h11", "group": "height", "citations": 2}, {"doi": "doi_lg_1_h12", "name": "title_lg_1_h12", "author": ["contributor_lg_1_h12"], "year": "date_lg_1_h12", "journal": "journal_lg_1_h12", "group": "height", "citations": 2}, {"doi": "doi_lg_1_h21", "name": "title_lg_1_h21", "author": ["contributor_lg_1_h21"], "year": "date_lg_1_h21", "journal": "journal_lg_1_h21", "group": "height", "citations": 0}, {"doi": "doi_lg_1_h22", "name": "title_lg_1_h22", "author": ["contributor_lg_1_h22"], "year": "date_lg_1_h22", "journal": "journal_lg_1_h22", "group": "height", "citations": 0}, {"doi": "doi_lg_1_h23", "name": "title_lg_1_h23", "author": ["contributor_lg_1_h23"], "year": "date_lg_1_h23", "journal": "journal_lg_1_h23", "group": "height", "citations": 0}, {"doi": "doi_lg_1_d21", "name": "title_lg_1_d21", "author": ["contributor_lg_1_d21"], "year": "date_lg_1_d21", "journal": "journal_lg_1_d21", "group": "depth", "citations": 2}, {"doi": "doi_lg_1_d22", "name": "title_lg_1_d22", "author": ["contributor_lg_1_d22"], "year": "date_lg_1_d22", "journal": "journal_lg_1_d22", "group": "depth", "citations": 2}, {"doi": "doi_lg_1_d23", "name": "title_lg_1_d23", "author": ["contributor_lg_1_d23"], "year": "date_lg_1_d23", "journal": "journal_lg_1_d23", "group": "depth", "citations": 1}], "links": [{"source": "doi_lg_1_i", "target": "doi_lg_1_d11"}, {"source": "doi_lg_1_i", "target": "doi_lg_1_d12"}, {"source": "doi_lg_1_h11", "target": "doi_lg_1_i"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_i"}, {"source": "doi_lg_1_h21", "target": "doi_lg_1_h11"}, {"source": "doi_lg_1_h22", "target": "doi_lg_1_h11"}, {"source": "doi_lg_1_h22", "target": "doi_lg_1_h12"}, {"source": "doi_lg_1_h23", "target": "doi_lg_1_h12"}, {"source": "doi_lg_1_d11", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_d11", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d21", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d22", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_d12", "target": "doi_lg_1_d23"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_d12"}, {"source": "doi_lg_1_h11", "target": "doi_lg_1_h12"}]}
\ No newline at end of file
+{"nodes": [{"doi": "doi_lg_1_i", "name": "title_lg_1_i", "author": ["contributor_lg_1_i"], "year": "date_lg_1_i", "journal": "journal_lg_1_i", "group": "input", "citations": 2}, {"doi": "doi_lg_1_d11", "name": "title_lg_1_d11", "author": ["contributor_lg_1_d11"], "year": "date_lg_1_d11", "journal": "journal_lg_1_d11", "group": "depth", "citations": 1}, {"doi": "doi_lg_1_d12", "name": "title_lg_1_d12", "author": ["contributor_lg_1_d12"], "year": "date_lg_1_d12", "journal": "journal_lg_1_d12", "group": "depth", "citations": 2}, {"doi": "doi_lg_1_h11", "name": "title_lg_1_h11", "author": ["contributor_lg_1_h11"], "year": "date_lg_1_h11", "journal": "journal_lg_1_h11", "group": "height", "citations": 2}, {"doi": "doi_lg_1_h12", "name": "title_lg_1_h12", "author": ["contributor_lg_1_h12"], "year": "date_lg_1_h12", "journal": "journal_lg_1_h12", "group": "height", "citations": 2}, {"doi": "doi_lg_1_h21", "name": "title_lg_1_h21", "author": ["contributor_lg_1_h21"], "year": "date_lg_1_h21", "journal": "journal_lg_1_h21", "group": "height", "citations": 0}, {"doi": "doi_lg_1_h22", "name": "title_lg_1_h22", "author": ["contributor_lg_1_h22"], "year": "date_lg_1_h22", "journal": "journal_lg_1_h22", "group": "height", "citations": 0}, {"doi": "doi_lg_1_h23", "name": "title_lg_1_h23", "author": ["contributor_lg_1_h23"], "year": "date_lg_1_h23", "journal": "journal_lg_1_h23", "group": "height", "citations": 0}, {"doi": "doi_lg_1_d21", "name": "title_lg_1_d21", "author": ["contributor_lg_1_d21"], "year": "date_lg_1_d21", "journal": "journal_lg_1_d21", "group": "depth", "citations": 2}, {"doi": "doi_lg_1_d22", "name": "title_lg_1_d22", "author": ["contributor_lg_1_d22"], "year": "date_lg_1_d22", "journal": "journal_lg_1_d22", "group": "depth", "citations": 2}, {"doi": "doi_lg_1_d23", "name": "title_lg_1_d23", "author": ["contributor_lg_1_d23"], "year": "date_lg_1_d23", "journal": "journal_lg_1_d23", "group": "depth", "citations": 2}], "links": [{"source": "doi_lg_1_i", "target": "doi_lg_1_d11"}, {"source": "doi_lg_1_i", "target": "doi_lg_1_d12"}, {"source": "doi_lg_1_h11", "target": "doi_lg_1_i"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_i"}, {"source": "doi_lg_1_h21", "target": "doi_lg_1_h11"}, {"source": "doi_lg_1_h22", "target": "doi_lg_1_h11"}, {"source": "doi_lg_1_h22", "target": "doi_lg_1_h12"}, {"source": "doi_lg_1_h23", "target": "doi_lg_1_h12"}, {"source": "doi_lg_1_d11", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_d11", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d21", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d22", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_d12", "target": "doi_lg_1_d23"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_d12"}, {"source": "doi_lg_1_h11", "target": "doi_lg_1_h12"}]}
\ No newline at end of file
diff --git a/verarbeitung/Kanten_Vergleich.py b/verarbeitung/update_graph/Kanten_Vergleich.py
similarity index 100%
rename from verarbeitung/Kanten_Vergleich.py
rename to verarbeitung/update_graph/Kanten_Vergleich.py
diff --git a/verarbeitung/Knoten_Vergleich.py b/verarbeitung/update_graph/Knoten_Vergleich.py
similarity index 100%
rename from verarbeitung/Knoten_Vergleich.py
rename to verarbeitung/update_graph/Knoten_Vergleich.py
diff --git a/verarbeitung/update_graph/__init__.py b/verarbeitung/update_graph/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/verarbeitung/connect_new_input.py b/verarbeitung/update_graph/connect_new_input.py
similarity index 79%
rename from verarbeitung/connect_new_input.py
rename to verarbeitung/update_graph/connect_new_input.py
index b9167dc..c61b00a 100644
--- a/verarbeitung/connect_new_input.py
+++ b/verarbeitung/update_graph/connect_new_input.py
@@ -1,67 +1,69 @@
-# -*- coding: utf-8 -*-
-"""
-Functions to update 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__ = ""
-
-import sys
-from pathlib import Path
-from os import error
-sys.path.append("../")
-
-from import_form_json import input_from_json
-from Processing import initialize_nodes_list, process_citations_rec, process_references_rec, complete_inner_edges, create_graph_structure_references, create_graph_structure_citations
-from json_demo import output_to_json
-
-def connect_old_and_new_input(json_file, new_doi_list, search_height, search_depth, test_var = False):
- global nodes, edges
- nodes = []
- edges = []
-
- nodes, edges = input_from_json(json_file)
-
- complete_changed_group_nodes(new_doi_list, search_height, search_depth, test_var)
-
- # 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(new_doi_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)
-
- # 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, test_var)
-
- return(nodes, edges)
-
-
-def complete_changed_group_nodes(new_doi_list, search_height_max, search_depth_max, test_var):
- changed_group_node_citations = []
- changed_group_node_references = []
-
- for node in nodes:
- if (node.group != "input") and (node.doi in new_doi_list):
- node.group = "input"
-
- # 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(node, 0, search_depth_max, test_var):
- changed_group_node_references.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(node, 0, search_height_max, test_var):
- changed_group_node_citations.append(citation)
-
+# -*- coding: utf-8 -*-
+"""
+Functions to update 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__ = ""
+
+import sys
+from pathlib import Path
+from os import error
+sys.path.append("../")
+
+from import_from_json import input_from_json
+from verarbeitung.construct_new_graph.Processing import initialize_nodes_list, complete_inner_edges, create_graph_structure_references, create_graph_structure_citations
+from verarbeitung.construct_new_graph.add_citations_rec import add_citations
+from verarbeitung.construct_new_graph.add_references_rec import add_references
+from verarbeitung.construct_new_graph.export_to_json import output_to_json
+
+def connect_old_and_new_input(json_file, new_doi_list, search_height, search_depth, test_var = False):
+ global nodes, edges
+ nodes = []
+ edges = []
+
+ nodes, edges = input_from_json(json_file)
+
+ complete_changed_group_nodes(new_doi_list, search_height, search_depth, test_var)
+
+ # 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(new_doi_list,search_depth, search_height, test_var)
+
+ # function calls to begin recursive processing up to max depth/height
+ add_citations(nodes, edges, citations_obj_list, 1, search_height, test_var)
+ add_references(nodes, edges, 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, test_var)
+
+ return(nodes, edges)
+
+
+def complete_changed_group_nodes(new_doi_list, search_height_max, search_depth_max, test_var):
+ changed_group_node_citations = []
+ changed_group_node_references = []
+
+ for node in nodes:
+ if (node.group != "input") and (node.doi in new_doi_list):
+ node.group = "input"
+
+ # 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(node, 0, search_depth_max, test_var):
+ changed_group_node_references.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(node, 0, search_height_max, test_var):
+ changed_group_node_citations.append(citation)
+
diff --git a/verarbeitung/import_from_json.py b/verarbeitung/update_graph/import_from_json.py
similarity index 99%
rename from verarbeitung/import_from_json.py
rename to verarbeitung/update_graph/import_from_json.py
index 11e5d82..748e541 100644
--- a/verarbeitung/import_from_json.py
+++ b/verarbeitung/update_graph/import_from_json.py
@@ -16,7 +16,7 @@ __status__ = "Production"
import json
import sys
-sys.path.append("../")
+sys.path.append("../../")
from input.publication import Publication, Citation
diff --git a/verarbeitung/update_graph.py b/verarbeitung/update_graph/update_graph.py
similarity index 95%
rename from verarbeitung/update_graph.py
rename to verarbeitung/update_graph/update_graph.py
index 9853456..0e4f52a 100644
--- a/verarbeitung/update_graph.py
+++ b/verarbeitung/update_graph/update_graph.py
@@ -17,12 +17,12 @@ __status__ = "Production"
import sys
from pathlib import Path
from os import error
-sys.path.append("../")
+sys.path.append("../../")
from input.publication import Publication
-from get_pub_from_input import get_pub
-from Knoten_Vergleich import doi_listen_vergleichen
-from update_graph_del import delete_nodes_and_edges
+from verarbeitung.get_pub_from_input import get_pub
+from .Knoten_Vergleich import doi_listen_vergleichen
+from .update_graph_del import delete_nodes_and_edges
def get_old_input_dois(old_obj_input_list):
diff --git a/verarbeitung/update_graph_del.py b/verarbeitung/update_graph/update_graph_del.py
similarity index 97%
rename from verarbeitung/update_graph_del.py
rename to verarbeitung/update_graph/update_graph_del.py
index 10ca42b..df958d1 100644
--- a/verarbeitung/update_graph_del.py
+++ b/verarbeitung/update_graph/update_graph_del.py
@@ -15,10 +15,9 @@ __status__ = "Production"
import sys
from pathlib import Path
-sys.path.append("../")
+sys.path.append("../../")
-from input.interface import InputInterface as Input
-from Kanten_Vergleich import back_to_valid_edges
+from .Kanten_Vergleich import back_to_valid_edges
def delete_ref_nodes_rec(pub):
--
GitLab