merge verarbeitung to main repo

Merge branch 'main' of https://gitlab.rrz.uni-hamburg.de/bav1758/ci-s-projekt-verarbeitung into main

verarbeitung/construct_new_graph/initialize_graph.py

+# -*- coding: utf-8 -*-
+"""
+Functions to generate a graph representing citations between multiple ACS/Nature journals
+
+"""
+
+__authors__ = "Donna Löding, Alina Molkentin, Xinyi Tang, Judith Große, Malte Schokolowski"
+__email__ = "cis-project2021@zbh.uni-hamburg.de"
+__status__ = "Production"
+#__copyright__ = ""
+#__credits__ = ["", "", "", ""]
+#__license__ = ""
+#__version__ = ""
+#__maintainer__ = ""
+
+
+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
+
+
+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 = 0
+        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_cit(nodes, edges, pub, 0, search_depth_max, "Reference", 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, "Citation", test_var):
+            citations_pub_obj_list.append(citation)
+
+    return(references_pub_obj_list, citations_pub_obj_list)
+        
+
+
+def complete_inner_edges():
+    '''
+        completes inner edges between nodes of group height and depth
+    '''
+
+    for node in nodes:
+        if (node.group < 0):
+            for citation in node.citations:
+                for pub in nodes:
+                    if ((pub.doi_url == citation.doi_url) and ([citation.doi_url, node.doi_url] not in edges)):
+                        edges.append([citation.doi_url, node.doi_url])
+        if (node.group > 0):
+            for reference in node.references:
+                for pub in nodes:
+                    if ((pub.doi_url == reference.doi_url) and ([node.doi_url, reference.doi_url] not in edges)):
+                        edges.append([node.doi_url,reference.doi_url])
+
+
+def init_graph_construction(doi_input_list, search_depth, search_height, test_var = False):
+    '''
+        :param doi_input_list:  input list of doi from UI
+        :type doi_input_list:   List[String]
+
+        :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, "Citation", test_var)
+    add_citations(nodes, edges, references_obj_list, 1, search_depth, "Reference", test_var)
+
+    # adds edges between reference group and citation group of known publications
+    complete_inner_edges()
+
+    # calls a skript to save nodes and edges of graph in .json file
+    #output_to_json(nodes, edges, test_var)
+
+    return(nodes,edges)