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Commit 25ac97fc authored by Malte Schokolowski's avatar Malte Schokolowski
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Merge branch 'complete_graph'

parents 004d7d8a c0727d90
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1 merge request!12bug fixes and updates to code
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verarbeitung/start_script.py → start_script.py
+ 2
− 1
View file @ 25ac97fc
......@@ -8,4 +8,5 @@ doi_list = []
doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
#doi_list.append('https://doi.org/10.1021/acs.jcim.9b00249')
doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.1c00203')
Processing(doi_list, 3, 3, 'test.json')
\ No newline at end of file
doi_list.append('https://doi.org/10.1021/acs.jmedchem.0c01332')
Processing(doi_list, 3, 2, 'test.json')
verarbeitung/construct_new_graph/add_citations_rec.py
+ 4
− 2
View file @ 25ac97fc
......@@ -32,10 +32,12 @@ def get_cit_type_list(pub, cit_type):
function to create nodes and edges and call create_graph_structure_citations
'''
if (cit_type == "Citation"):
if cit_type == "Citation":
return(pub.citations)
else:
elif cit_type == "Reference":
return(pub.references)
else:
return(ValueError)
def create_global_lists_cit(input_nodes, input_edges, pub, search_depth, search_depth_max, cit_type, test_var):
'''
......
verarbeitung/construct_new_graph/export_to_json.py
+ 1
− 1
View file @ 25ac97fc
......@@ -78,7 +78,7 @@ def output_to_json(nodes, edges, json_file = 'json_text.json', test_var = False)
list_of_edge_dicts = format_edges(edges)
dict_of_all["nodes"] = list_of_node_dicts
dict_of_all["links"] = list_of_edge_dicts
if (test_var and json_file == 'json_text.json'):
if (test_var):
with open('test_output.json','w') as outfile:
json.dump(dict_of_all, outfile)
else:
......
verarbeitung/construct_new_graph/initialize_graph.py
+ 62
− 6
View file @ 25ac97fc
......@@ -15,6 +15,7 @@ __status__ = "Production"
import sys
import gc
from pathlib import Path
from os import error
sys.path.append("../")
......@@ -24,6 +25,43 @@ 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_test(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
for unit test purposes only
'''
global nodes, edges
nodes = []
edges = []
return(initialize_nodes_list(doi_input_list, search_depth_max, search_height_max, test_var))
def complete_inner_edges_test(test_nodes, test_edges):
'''
:param test_nodes: list of publications from unit test
:type test_nodes: List[Publication]
:param test_nodes: list of links from unit test
:type test_nodes: List[List[String,String]]
for unit test purposes only
'''
global nodes, edges
nodes = test_nodes
edges = test_edges
complete_inner_edges()
return(nodes, edges)
def initialize_nodes_list(doi_input_list, search_depth_max, search_height_max, test_var):
'''
......@@ -54,6 +92,7 @@ def initialize_nodes_list(doi_input_list, search_depth_max, search_height_max, t
# 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
......@@ -96,7 +135,7 @@ def complete_inner_edges():
edges.append([node.doi_url,reference.doi_url])
def init_graph_construction(doi_input_list, search_depth, search_height, test_var = False):
def init_graph_construction(doi_input_list, search_depth, search_height, test_var = False, update_var = False, input_nodes = [], input_edges = []):
'''
:param doi_input_list: input list of doi from UI
:type doi_input_list: List[String]
......@@ -110,6 +149,15 @@ def init_graph_construction(doi_input_list, search_depth, search_height, test_va
:param test_var: variable to differenciate between test and url call
:type test_var: boolean
:param test_var: variable to check if call is from update_graph with known nodes and edges or fresh construction
:type test_var: boolean
:param input_nodes: list of publications from update_graph
:type input_nodes: List[Publication]
:param input_nodes: list of links from update_graph
:type input_nodes: List[List[String,String]]
main function to start graph generation
'''
......@@ -128,8 +176,12 @@ def init_graph_construction(doi_input_list, search_depth, search_height, test_va
# creates empty lists to save nodes and edges
global nodes, edges
nodes = []
edges = []
if update_var:
nodes = input_nodes
edges = input_edges
else:
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)
......@@ -141,7 +193,11 @@ def init_graph_construction(doi_input_list, search_depth, search_height, test_va
# 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)
# garbage collection to delete nodes and edges lists. Needed because python keeps lists after function end till next function call
new_nodes = nodes.copy()
new_edges = edges.copy()
del nodes
del edges
gc.collect()
return(nodes,edges)
return(new_nodes,new_edges)
verarbeitung/json_text.json
+ 1
− 1
View file @ 25ac97fc
{"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", "depth": 0, "citations": 5}, {"doi": "https://doi.org/10.1021/acs.chemrev.1c00107", "name": "Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems", "author": ["John A. Keith", "Valentin Vassilev-Galindo", "Bingqing Cheng", "Stefan Chmiela", "Michael Gastegger", "Klaus-Robert M\u00fcller", "Alexandre Tkatchenko"], "year": "July 7, 2021", "journal": "Chem. Rev.", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "https://doi.org/10.1021/acs.jcim.0c00741", "name": "Disconnected Maximum Common Substructures under Constraints", "author": ["Robert Schmidt", "Florian Krull", "Anna Lina Heinzke", "Matthias Rarey"], "year": "December 16, 2020", "journal": "Journal of Chemical Information and Modeling", "group": "Citedby", "depth": 1, "citations": 0}, {"doi": "https://doi.org/10.1021/acs.jmedchem.0c01332", "name": "Evolution of Novartis\u2019 Small Molecule Screening Deck Design", "author": ["Ansgar Schuffenhauer", "Nadine Schneider", "Samuel Hintermann", "Douglas Auld", "Jutta Blank", "Simona Cotesta", "Caroline Engeloch", "Nikolas Fechner", "Christoph Gaul", "Jerome Giovannoni", "Johanna Jansen", "John Joslin", "Philipp Krastel", "Eugen Lounkine", "John Manchester", "Lauren G. Monovich", "Anna Paola Pelliccioli", "Manuel Schwarze", "Michael D. Shultz", "Nikolaus Stiefl", "Daniel K. Baeschlin"], "year": "November 3, 2020", "journal": "Journal of Medicinal Chemistry", "group": "Citedby", "depth": 1, "citations": 8}, {"doi": "https://doi.org/10.1021/acs.jcim.9b00250", "name": "Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms", "author": ["Robert Schmidt", "Emanuel S. R. Ehmki", "Farina Ohm", "Hans-Christian Ehrlich", "Andriy Mashychev", "Matthias Rarey"], "year": "May 23, 2019", "journal": "Journal of Chemical Information and Modeling", "group": "Citedby", "depth": 1, "citations": 12}, {"doi": "https://doi.org/10.1021/acs.jcim.1c00203", "name": "AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings", "author": ["Jerome Eberhardt", "Diogo Santos-Martins", "Andreas F. Tillack", "Stefano Forli"], "year": "July 19, 2021", "journal": "Journal of Chemical Information and Modeling", "group": "Input", "depth": 0, "citations": 1}, {"doi": "https://doi.org/10.1021/acs.jctc.0c01006", "name": "Accelerating AutoDock4 with GPUs and Gradient-Based Local Search", "author": ["Diogo Santos-Martins", "Leonardo Solis-Vasquez", "Andreas F Tillack", "Michel F Sanner", "Andreas Koch", "Stefano Forli"], "year": "January 6, 2021", "journal": "Journal of Chemical Theory and Computation", "group": "Reference", "depth": -1, "citations": 14}, {"doi": "https://doi.org/10.1021/acs.jctc.9b00557", "name": "Docking Flexible Cyclic Peptides with AutoDock CrankPep", "author": ["Yuqi Zhang", "Michel F. Sanner"], "year": "September 11, 2019", "journal": "Journal of Chemical Theory and Computation", "group": "Reference", "depth": -1, "citations": 9}, {"doi": "https://doi.org/10.1021/ci300604z", "name": "Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise", "author": ["David Ryan Koes", "Matthew P. Baumgartner", "Carlos J. Camacho"], "year": "February 4, 2013", "journal": "Journal of Chemical Information and Modeling", "group": "Reference", "depth": -1, "citations": 100}, {"doi": "https://doi.org/10.1021/acs.jctc.5b00834", "name": "Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking", "author": ["Anita K. Nivedha", "David F. Thieker", "Spandana Makeneni", "Huimin Hu", "Robert J. Woods"], "year": "January 8, 2016", "journal": "Journal of Chemical Theory and Computation", "group": "Reference", "depth": -1, "citations": 48}, {"doi": "https://doi.org/10.1021/ci700036j", "name": "Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems", "author": ["Stefano Forli", "Maurizio Botta"], "year": "June 22, 2007", "journal": "Journal of Chemical Information and Modeling", "group": "Reference", "depth": -1, "citations": 32}, {"doi": "https://doi.org/10.1021/ci500209e", "name": "AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins", "author": ["Diogo Santos-Martins", "Stefano Forli", "Maria Jo\u00e3o Ramos", "Arthur J. Olson"], "year": "June 15, 2014", "journal": "Journal of Chemical Information and Modeling", "group": "Reference", "depth": -1, "citations": 100}, {"doi": "https://doi.org/10.1021/jm2005145", "name": "A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking", "author": ["Stefano Forli", "Arthur J. Olson"], "year": "December 9, 2011", "journal": "Journal of Medicinal Chemistry", "group": "Reference", "depth": -1, "citations": 100}, {"doi": "https://doi.org/10.1021/ci300399w", "name": "Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context", "author": ["Douglas R. Houston", "Malcolm D. Walkinshaw"], "year": "January 27, 2013", "journal": "Journal of Chemical Information and Modeling", "group": "Reference", "depth": -1, "citations": 100}, {"doi": "https://doi.org/10.1021/jp9723574", "name": "Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory", "author": ["Themis Lazaridis"], "year": "April 14, 1998", "journal": "Journal of Physical Chemistry B", "group": "Reference", "depth": -1, "citations": 100}, {"doi": "https://doi.org/10.1021/jp972358w", "name": "Inhomogeneous Fluid Approach to Solvation Thermodynamics. 2. Applications to Simple Fluids", "author": ["Themis Lazaridis"], "year": "April 14, 1998", "journal": "Journal of Physical Chemistry B", "group": "Reference", "depth": -1, "citations": 100}, {"doi": "https://doi.org/10.1021/acs.jcim.0c00675", "name": "ZINC20\u2014A Free Ultralarge-Scale Chemical Database for Ligand Discovery", "author": ["John J. Irwin", "Khanh G. Tang", "Jennifer Young", "Chinzorig Dandarchuluun", "Benjamin R. Wong", "Munkhzul Khurelbaatar", "Yurii S. Moroz", "John Mayfield", "Roger A. Sayle"], "year": "October 29, 2020", "journal": "Journal of Chemical Information and Modeling", "group": "Reference", "depth": -1, "citations": 26}, {"doi": "https://doi.org/10.1021/acs.jmedchem.7b01243", "name": "Structural Biology-Inspired Discovery of Novel KRAS\u2013PDE\u03b4 Inhibitors", "author": ["Yan Jiang", "Chunlin Zhuang", "Long Chen", "Junjie Lu", "Guoqiang Dong", "Zhenyuan Miao", "Wannian Zhang", "Jian Li", "Chunquan Sheng"], "year": "September 20, 2017", "journal": "Journal of Medicinal Chemistry", "group": "Reference", "depth": -1, "citations": 12}, {"doi": "https://doi.org/10.1021/jm300687e", "name": "Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking", "author": ["Michael M. Mysinger", "Michael Carchia", "John. J. Irwin", "Brian K. Shoichet"], "year": "June 20, 2012", "journal": "Journal of Medicinal Chemistry", "group": "Reference", "depth": -1, "citations": 100}, {"doi": "https://doi.org/10.1021/acs.jcim.8b00312", "name": "Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark", "author": ["Thomas Gaillard"], "year": "July 10, 2018", "journal": "Journal of Chemical Information and Modeling", "group": "Reference", "depth": -1, "citations": 74}, {"doi": "https://doi.org/10.1021/acs.jcim.9b00778", "name": "Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity", "author": ["Nguyen Thanh Nguyen", "Trung Hai Nguyen", "T. Ngoc Han Pham", "Nguyen Truong Huy", "Mai Van Bay", "Minh Quan Pham", "Pham Cam Nam", "Van V. 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Hajduk"], "year": "April 17, 2008", "journal": "Journal of Chemical Information and Modeling", "group": "Reference", "depth": -2, "citations": 100}, {"doi": "https://doi.org/10.1021/jm020155c", "name": "Do Structurally Similar Molecules Have Similar Biological Activity?", "author": ["Yvonne C. Martin", "James L. Kofron", "Linda M. Traphagen"], "year": "August 13, 2002", "journal": "Journal of Medicinal Chemistry", "group": "Reference", "depth": -2, "citations": 100}, {"doi": "https://doi.org/10.1021/jm9602928", "name": "The Properties of Known Drugs. 1. Molecular Frameworks", "author": ["Guy W. Bemis", "Mark A. Murcko"], "year": "July 19, 1996", "journal": "Journal of Medicinal Chemistry", "group": "Reference", "depth": -2, "citations": 100}, {"doi": "https://doi.org/10.1021/ci025599w", "name": "Molecular Shape Diversity of Combinatorial Libraries:\u2009 A Prerequisite for Broad Bioactivity\u2020", "author": ["Wolfgang H. B. Sauer", "Matthias K. Schwarz"], "year": "March 14, 2003", "journal": "J. Chem. Inf. Comput. 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\ No newline at end of file
verarbeitung/process_main.py
+ 7
− 7
View file @ 25ac97fc
......@@ -16,7 +16,7 @@ __status__ = "Production"
import sys
from pathlib import Path
from os import error
from os import error, path
sys.path.append("../")
......@@ -42,13 +42,13 @@ def Processing(url_list, search_depth, search_height, json_file = 'json_text.jso
'''
# updates graph if json file is known in directory otherwise starts new graph construction
try:
with open(json_file) as f:
nodes, edges = update_graph(url_list, json_file, search_depth, search_height)
except IOError:
nodes, edges = init_graph_construction(url_list, search_depth, search_height)
json_file = Path(json_file)
if json_file.is_file():
nodes, edges = update_graph(url_list, json_file, search_depth, search_height)
else:
nodes, edges = init_graph_construction(url_list, search_depth, search_height)
# exports graph to given json file name
output_to_json(nodes, edges, json_file)
\ No newline at end of file
verarbeitung/test.json
+ 1
− 1
View file @ 25ac97fc
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Ruth Julie Kavitha", "Jessie Abraham", "Micheal Arockiaraj", "Joseph Jency", "Krishnan Balasubramanian"], "year": "September 1, 2021", "journal": "J. Phys. Chem. A", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "https://doi.org/10.1021/acsmedchemlett.1c00251", "name": "The Growing Importance of Chirality in 3D Chemical Space Exploration and Modern Drug Discovery Approaches for Hit-ID", "author": ["Ilaria Proietti Silvestri", "Paul J. J. Colbon"], "year": "July 16, 2021", "journal": "ACS Med. Chem. Lett.", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "https://doi.org/10.1021/acs.jmedchem.1c00416", "name": "Target-Based Evaluation of \u201cDrug-Like\u201d Properties and Ligand Efficiencies", "author": ["Paul D. Leeson", "A. Patricia Bento", "Anna Gaulton", "Anne Hersey", "Emma J. Manners", "Chris J. Radoux", "Andrew R. Leach"], "year": "May 13, 2021", "journal": "Journal of Medicinal Chemistry", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "https://doi.org/10.1021/acs.jcim.1c00226", "name": "Automatic Identification of Lansoprazole Degradants under Stress Conditions by LC-HRMS with MassChemSite and WebChembase", "author": ["Stefano Bonciarelli", "Jenny Desantis", "Laura Goracci", "Lydia Siragusa", "Ismael Zamora", "Elisabeth Ortega-Carrasco"], "year": "June 1, 2021", "journal": "Journal of Chemical Information and Modeling", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "https://doi.org/10.1021/acs.chemrestox.0c00006", "name": "Computational Approaches to Identify Structural Alerts and Their Applications in Environmental Toxicology and Drug Discovery", "author": ["Hongbin Yang", "Chaofeng Lou", "Weihua Li", "Guixia Liu", "Yun Tang"], "year": "February 24, 2020", "journal": "Chem. Res. Toxicol.", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "https://doi.org/10.1021/acs.est.9b06379", "name": "Toward a Global Understanding of Chemical Pollution: A First Comprehensive Analysis of National and Regional Chemical Inventories", "author": ["Zhanyun Wang", "Glen W. Walker", "Derek C. G. Muir", "Kakuko Nagatani-Yoshida"], "year": "January 22, 2020", "journal": "Environ. Sci. Technol.", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "https://doi.org/10.1021/ci049714+", "name": "ZINC \u2212 A Free Database of Commercially Available Compounds for Virtual Screening", "author": ["John J. Irwin", "Brian K. Shoichet"], "year": "December 14, 2004", "journal": "Journal of Chemical Information and Modeling", "group": "Reference", "depth": -2, "citations": 3}, {"doi": "https://doi.org/10.1021/ci3001277", "name": "ZINC: A Free Tool to Discover Chemistry for Biology", "author": ["John J. Irwin", "Teague Sterling", "Michael M. Mysinger", "Erin S. Bolstad", "Ryan G. Coleman"], "year": "May 15, 2012", "journal": "Journal of Chemical Information and Modeling", "group": "Reference", "depth": -2, "citations": 2}, {"doi": "https://doi.org/10.1021/acs.jcim.5b00559", "name": "ZINC 15 \u2013 Ligand Discovery for Everyone", "author": ["Teague Sterling", "John J. Irwin"], "year": "October 19, 2015", "journal": "Journal of Chemical Information and Modeling", "group": "Reference", "depth": -2, "citations": 1}, {"doi": "https://doi.org/10.1021/ci7004498", "name": "Application of Belief Theory to Similarity Data Fusion for Use in Analog Searching and Lead Hopping", "author": ["Steven W. Muchmore", "Derek A. Debe", "James T. Metz", "Scott P. Brown", "Yvonne C. Martin", "Philip J. Hajduk"], "year": "April 17, 2008", "journal": "Journal of Chemical Information and Modeling", "group": "Reference", "depth": -2, "citations": 1}, {"doi": "https://doi.org/10.1021/jm020155c", "name": "Do Structurally Similar Molecules Have Similar Biological Activity?", "author": ["Yvonne C. Martin", "James L. Kofron", "Linda M. Traphagen"], "year": "August 13, 2002", "journal": "Journal of Medicinal Chemistry", "group": "Reference", "depth": -2, "citations": 2}, {"doi": "https://doi.org/10.1021/jm9602928", "name": "The Properties of Known Drugs. 1. Molecular Frameworks", "author": ["Guy W. Bemis", "Mark A. Murcko"], "year": "July 19, 1996", "journal": "Journal of Medicinal Chemistry", "group": "Reference", "depth": -2, "citations": 1}, {"doi": "https://doi.org/10.1021/ci025599w", "name": "Molecular Shape Diversity of Combinatorial Libraries:\u2009 A Prerequisite for Broad Bioactivity\u2020", "author": ["Wolfgang H. B. Sauer", "Matthias K. Schwarz"], "year": "March 14, 2003", "journal": "J. Chem. Inf. Comput. Sci.", "group": "Reference", "depth": -2, "citations": 3}], "links": [{"source": "https://doi.org/10.1021/acs.chemrev.1c00107", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00741", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acs.jmedchem.0c01332", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acs.jcim.9b00250", "target": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"source": "https://doi.org/10.1021/acs.jcim.1c00203", "target": "https://doi.org/10.1021/acs.jctc.0c01006"}, {"source": "https://doi.org/10.1021/acs.jcim.1c00203", "target": "https://doi.org/10.1021/acs.jctc.9b00557"}, {"source": "https://doi.org/10.1021/acs.jcim.1c00203", "target": "https://doi.org/10.1021/ci300604z"}, {"source": "https://doi.org/10.1021/acs.jcim.1c00203", "target": "https://doi.org/10.1021/acs.jctc.5b00834"}, {"source": "https://doi.org/10.1021/acs.jcim.1c00203", "target": "https://doi.org/10.1021/ci700036j"}, {"source": "https://doi.org/10.1021/acs.jcim.1c00203", "target": "https://doi.org/10.1021/ci500209e"}, {"source": "https://doi.org/10.1021/acs.jcim.1c00203", "target": "https://doi.org/10.1021/jm2005145"}, {"source": "https://doi.org/10.1021/acs.jcim.1c00203", "target": "https://doi.org/10.1021/ci300399w"}, {"source": "https://doi.org/10.1021/acs.jcim.1c00203", "target": "https://doi.org/10.1021/jp9723574"}, {"source": "https://doi.org/10.1021/acs.jcim.1c00203", "target": "https://doi.org/10.1021/jp972358w"}, {"source": "https://doi.org/10.1021/acs.jcim.1c00203", "target": "https://doi.org/10.1021/acs.jcim.0c00675"}, {"source": "https://doi.org/10.1021/acs.jcim.1c00203", "target": "https://doi.org/10.1021/acs.jmedchem.7b01243"}, {"source": "https://doi.org/10.1021/acs.jcim.1c00203", "target": "https://doi.org/10.1021/jm300687e"}, {"source": "https://doi.org/10.1021/acs.jcim.1c00203", "target": 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"https://doi.org/10.1021/acs.jcim.0c00675", "target": "https://doi.org/10.1021/ci049714+"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00675", "target": "https://doi.org/10.1021/ci3001277"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00675", "target": "https://doi.org/10.1021/acs.jcim.5b00559"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00675", "target": "https://doi.org/10.1021/ci7004498"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00675", "target": "https://doi.org/10.1021/jm020155c"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00675", "target": "https://doi.org/10.1021/jm9602928"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00675", "target": "https://doi.org/10.1021/ci025599w"}, {"source": "https://doi.org/10.1021/acs.jcim.5b00559", "target": "https://doi.org/10.1021/ci049714+"}, {"source": "https://doi.org/10.1021/acs.jcim.5b00559", "target": "https://doi.org/10.1021/ci3001277"}, {"source": "https://doi.org/10.1021/acs.jcim.5b00559", "target": 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verarbeitung/test/construct_graph_unittest.py
+ 71
− 15
View file @ 25ac97fc
import unittest
import sys
from pathlib import Path
import sys
sys.path.append("../")
from verarbeitung.construct_new_graph.initialize_graph import init_graph_construction
from verarbeitung.construct_new_graph.initialize_graph import init_graph_construction, initialize_nodes_list_test, complete_inner_edges_test
from verarbeitung.construct_new_graph.add_citations_rec import get_cit_type_list
from verarbeitung.test.input_test import input_test_func
class ConstructionTest(unittest.TestCase):
maxDiff = None
def testCycle(self):
nodes, edges = init_graph_construction(['doiz1'],1,1,True)
nodes, edges = init_graph_construction(['doiz1'],1,1,True,False)
doi_nodes = keep_only_dois(nodes)
self.assertCountEqual(doi_nodes, ['doiz1', 'doiz2'])
self.assertCountEqual(edges, [['doiz1', 'doiz2'], ['doiz2', 'doiz1']])
nodes, edges = init_graph_construction(['doiz1'],2,2,True)
nodes, edges = init_graph_construction(['doiz1'],2,2,True,False)
doi_nodes = keep_only_dois(nodes)
self.assertCountEqual(doi_nodes, ['doiz1', 'doiz2'])
self.assertCountEqual(edges, [['doiz2', 'doiz1'], ['doiz1', 'doiz2']])
......@@ -28,61 +31,114 @@ class ConstructionTest(unittest.TestCase):
#def testEmptyDepth(self):
def testEmptyDepthHeight(self):
nodes, edges = init_graph_construction(['doi1'],0,0,True)
nodes, edges = init_graph_construction(['doi1'],0,0,True,False)
doi_nodes = keep_only_dois(nodes)
self.assertCountEqual(doi_nodes,['doi1'])
self.assertCountEqual(edges, [])
nodes, edges = init_graph_construction(['doi1', 'doi2'],0,0,True)
nodes, edges = init_graph_construction(['doi1', 'doi2'],0,0,True,False)
doi_nodes = keep_only_dois(nodes)
self.assertCountEqual(doi_nodes, ['doi1','doi2'])
self.assertCountEqual(edges, [['doi1', 'doi2']])
nodes, edges = init_graph_construction(['doi1', 'doi2', 'doi3'],0,0,True)
nodes, edges = init_graph_construction(['doi1', 'doi2', 'doi3'],0,0,True,False)
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 = init_graph_construction(['doi_ie1'],1,1,True)
nodes, edges = init_graph_construction(['doi_ie1'],1,1,True,False)
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 = init_graph_construction(['doi_h01'],1,0,True)
nodes, edges = init_graph_construction(['doi_h01'],0,1,True,False)
doi_nodes = keep_only_dois(nodes)
self.assertCountEqual(doi_nodes,['doi_h01'])
self.assertCountEqual(edges, [])
nodes, edges = init_graph_construction(['doi_h02'],1,0,True)
nodes, edges = init_graph_construction(['doi_h02'],0,1,True,False)
doi_nodes = keep_only_dois(nodes)
self.assertCountEqual(doi_nodes,['doi_h02','doi_h1'])
self.assertCountEqual(edges, [['doi_h1','doi_h02']])
nodes, edges = init_graph_construction(['doi_h02'],2,0,True)
nodes, edges = init_graph_construction(['doi_h02'],0,2,True,False)
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 = init_graph_construction(['doi_d01'],0,1,True)
nodes, edges = init_graph_construction(['doi_d01'],1,0,True,False)
doi_nodes = keep_only_dois(nodes)
self.assertCountEqual(doi_nodes,['doi_d01'])
self.assertCountEqual(edges, [])
nodes, edges = init_graph_construction(['doi_d02'],0,1,True)
nodes, edges = init_graph_construction(['doi_d02'],1,0,True,False)
doi_nodes = keep_only_dois(nodes)
self.assertCountEqual(doi_nodes,['doi_d02','doi_d1'])
self.assertCountEqual(edges, [['doi_d02','doi_d1']])
nodes, edges = init_graph_construction(['doi_d02'],0,2,True)
nodes, edges = init_graph_construction(['doi_d02'],2,0,True,False)
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']])
## Ab hier die Tests für die einzelnen Funktionen ##
# initialize_graph.py:
def test_initialize_nodes_list(self):
references_pub_obj_list, citations_pub_obj_list = initialize_nodes_list_test(['doi_lg_1_i','doi_lg_2_i'], 0, 0, True)
doi_references = keep_only_dois(references_pub_obj_list)
doi_citations = keep_only_dois(citations_pub_obj_list)
self.assertCountEqual(doi_references, [])
self.assertCountEqual(doi_citations, [])
references_pub_obj_list, citations_pub_obj_list = initialize_nodes_list_test(['doi_lg_1_i','doi_lg_2_i'], 1, 1, True)
doi_references = keep_only_dois(references_pub_obj_list)
doi_citations = keep_only_dois(citations_pub_obj_list)
self.assertCountEqual(doi_references, ['doi_lg_1_d11','doi_lg_1_d12','doi_lg_2_d11','doi_lg_2_d12'])
self.assertCountEqual(doi_citations, ['doi_lg_1_h11','doi_lg_1_h12','doi_cg_i','doi_lg_2_h11','doi_lg_2_h12'])
def test_complete_inner_edges(self):
pub_lg_1_i = input_test_func('doi_lg_1_i')
pub_lg_1_i.group = 0
pub_lg_1_h_12 = input_test_func('doi_lg_1_h12')
pub_lg_1_h_12.group = 1
pub_lg_1_d_12 = input_test_func('doi_lg_1_d12')
pub_lg_1_d_12.group = -1
nodes = [pub_lg_1_i, pub_lg_1_h_12, pub_lg_1_d_12]
edges = [['doi_lg_1_i','doi_lg_1_d12'],['doi_lg_1_h12','doi_lg_1_i']]
processed_nodes, processed_edges = complete_inner_edges_test(nodes, edges)
self.assertCountEqual(processed_nodes, [pub_lg_1_i, pub_lg_1_h_12, pub_lg_1_d_12])
self.assertCountEqual(processed_edges, [['doi_lg_1_i','doi_lg_1_d12'],['doi_lg_1_h12','doi_lg_1_i'],['doi_lg_1_h12','doi_lg_1_d12']])
# add_citations_rec.py:
def test_get_type_list(self):
pub_lg_1_i = input_test_func('doi_lg_1_i')
pub_lg_1_i.group = 0
self.assertEqual(get_cit_type_list(pub_lg_1_i, "Hallo"), ValueError)
pub_lg_1_h_12 = input_test_func('doi_lg_1_h12')
pub_lg_1_h_12.group = 1
pub_lg_1_h_12_refs = get_cit_type_list(pub_lg_1_h_12, "Reference")
pub_lg_1_h_12_cits = get_cit_type_list(pub_lg_1_h_12, "Citation")
self.assertCountEqual(keep_only_dois(pub_lg_1_h_12_refs), keep_only_dois(pub_lg_1_h_12.references))
self.assertCountEqual(keep_only_dois(pub_lg_1_h_12_cits), keep_only_dois(pub_lg_1_h_12.citations))
pub_lg_1_d_12 = input_test_func('doi_lg_1_d12')
pub_lg_1_d_12.group = -1
pub_lg_1_d_12_refs = get_cit_type_list(pub_lg_1_d_12, "Reference")
pub_lg_1_d_12_cits = get_cit_type_list(pub_lg_1_d_12, "Citation")
self.assertCountEqual(keep_only_dois(pub_lg_1_d_12_refs), keep_only_dois(pub_lg_1_d_12.references))
self.assertCountEqual(keep_only_dois(pub_lg_1_d_12_cits), keep_only_dois(pub_lg_1_d_12.citations))
def test_create_graph_structure_citations(self):
print("Hallo")
def keep_only_dois(nodes):
......
verarbeitung/test/update_graph_unittest.py
+ 11
− 11
View file @ 25ac97fc
......@@ -20,17 +20,17 @@ class UpdatingTest(unittest.TestCase):
# self.assertCountEqual(nodes_old,nodes_new)
# self.assertCountEqual(edges_old, edges_new)
# def test_deleted_input_dois(self):
# nodes_old_single, edges_old_single = init_graph_construction(['doi_lg_1_i'],2,2,True)
# nodes_old_both, edges_old_both = init_graph_construction(['doi_lg_1_i','doi_lg_2_i'],2,2,True)
# output_to_json(nodes_old_both, edges_old_both, test_var=True)
# nodes_new_single, edges_new_single = update_graph(['doi_lg_1_i'], 'test_output.json', 2, 2, True)
# self.assertCountEqual(nodes_old_single,nodes_new_single)
# self.assertCountEqual(edges_old_single, edges_new_single)
# nodes_old_single, edges_old_single = init_graph_construction(['doi_cg_i'],3,3,True)
# nodes_old_two, edges_old_two = init_graph_construction(['doi_lg_1_i','doi_cg_i'],3,3,True)
# nodes_old_three, edges_old_three = init_graph_construction(['doi_lg_1_i','doi_lg_2_i','doi_cg_i'],3,3,True)
def test_deleted_input_dois(self):
nodes_old_single, edges_old_single = init_graph_construction(['doi_lg_1_i'],2,2,True)
nodes_old_both, edges_old_both = init_graph_construction(['doi_lg_1_i','doi_lg_2_i'],2,2,True)
output_to_json(nodes_old_both, edges_old_both, test_var=True)
nodes_new_single, edges_new_single = update_graph(['doi_lg_1_i'], 'test_output.json', 2, 2, True)
self.assertCountEqual(nodes_old_single,nodes_new_single)
self.assertCountEqual(edges_old_single, edges_new_single)
nodes_old_single, edges_old_single = init_graph_construction(['doi_cg_i'],3,3,True)
nodes_old_two, edges_old_two = init_graph_construction(['doi_lg_1_i','doi_cg_i'],3,3,True)
nodes_old_three, edges_old_three = init_graph_construction(['doi_lg_1_i','doi_lg_2_i','doi_cg_i'],3,3,True)
def test_new_height(self):
nodes_height_0, edges_height_0 = init_graph_construction(['doi_lg_1_i'],2,0,True)
......
verarbeitung/test_output.json
+ 1
− 1
View file @ 25ac97fc
{"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", "depth": 0, "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": "Reference", "depth": -1, "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": "Reference", "depth": -1, "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": "Citedby", "depth": 1, "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": "Citedby", "depth": 1, "citations": 2}, {"doi": "doi_lg_2_i", "name": "title_lg_2_i", "author": ["contributor_lg_2_i"], "year": "date_lg_2_i", "journal": "journal_lg_2_i", "group": "Input", "depth": 0, "citations": 4}, {"doi": "doi_lg_2_d11", "name": "title_lg_2_d11", "author": ["contributor_lg_2_d11"], "year": "date_lg_2_d11", "journal": "journal_lg_2_d11", "group": "Reference", "depth": -1, "citations": 1}, {"doi": "doi_lg_2_d12", "name": "title_lg_2_d12", "author": ["contributor_lg_2_d12"], "year": "date_lg_2_d12", "journal": "journal_lg_2_d12", "group": "Reference", "depth": -1, "citations": 2}, {"doi": "doi_lg_2_h11", "name": "title_lg_2_h11", "author": ["contributor_lg_2_h11"], "year": "date_lg_2_h11", "journal": "journal_lg_2_h11", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "doi_lg_2_h12", "name": "title_lg_2_h12", "author": ["contributor_lg_2_h12"], "year": "date_lg_2_h12", "journal": "journal_lg_2_h12", "group": "Citedby", "depth": 1, "citations": 2}, {"doi": "doi_cg_i", "name": "title_cg_i", "author": ["contributor_cg_i"], "year": "date_cg_i", "journal": "journal_cg_i", "group": "Citedby", "depth": 1, "citations": 3}, {"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": "Citedby", "depth": 2, "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": "Citedby", "depth": 2, "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": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_2_h21", "name": "title_lg_2_h21", "author": ["contributor_lg_2_h21"], "year": "date_lg_2_h21", "journal": "journal_lg_2_h21", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_2_h22", "name": "title_lg_2_h22", "author": ["contributor_lg_2_h22"], "year": "date_lg_2_h22", "journal": "journal_lg_2_h22", "group": "Citedby", "depth": 2, "citations": 0}, {"doi": "doi_lg_2_h23", "name": "title_lg_2_h23", "author": ["contributor_lg_2_h23"], "year": "date_lg_2_h23", "journal": "journal_lg_2_h23", "group": "Citedby", "depth": 2, "citations": 1}, {"doi": "doi_lg_2_h24", "name": "title_lg_2_h24", "author": ["contributor_lg_2_h24"], "year": "date_lg_2_h24", "journal": "journal_lg_2_h24", "group": "Citedby", "depth": 2, "citations": 1}, {"doi": "doi_cg_h11", "name": "title_cg_h11", "author": ["contributor_cg_h11"], "year": "date_cg_h11", "journal": "journal_cg_h11", "group": "Citedby", "depth": 2, "citations": 2}, {"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": "Reference", "depth": -2, "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": "Reference", "depth": -2, "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": "Reference", "depth": -2, "citations": 2}, {"doi": "doi_lg_2_d21", "name": "title_lg_2_d21", "author": ["contributor_lg_2_d21"], "year": "date_lg_2_d21", "journal": "journal_lg_2_d21", "group": "Reference", "depth": -2, "citations": 1}, {"doi": "doi_lg_2_d22", "name": "title_lg_2_d22", "author": ["contributor_lg_2_d22"], "year": "date_lg_2_d22", "journal": "journal_lg_2_d22", "group": "Reference", "depth": -2, "citations": 1}, {"doi": "doi_lg_2_d23", "name": "title_lg_2_d23", "author": ["contributor_lg_2_d23"], "year": "date_lg_2_d23", "journal": "journal_lg_2_d23", "group": "Reference", "depth": -2, "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_2_i", "target": "doi_lg_2_d11"}, {"source": "doi_lg_2_i", "target": "doi_lg_2_d12"}, {"source": "doi_lg_2_h11", "target": "doi_lg_2_i"}, {"source": "doi_lg_2_h12", "target": "doi_lg_2_i"}, {"source": "doi_cg_i", "target": "doi_lg_2_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_2_h21", "target": "doi_lg_2_h11"}, {"source": "doi_lg_2_h22", "target": "doi_lg_2_h11"}, {"source": "doi_lg_2_h23", "target": "doi_lg_2_h12"}, {"source": "doi_lg_2_h24", "target": "doi_lg_2_h12"}, {"source": "doi_lg_2_h24", "target": "doi_lg_2_h23"}, {"source": "doi_lg_2_h23", "target": "doi_lg_2_h24"}, {"source": "doi_lg_1_h23", "target": "doi_cg_i"}, {"source": "doi_cg_h11", "target": "doi_cg_i"}, {"source": "doi_lg_2_h11", "target": "doi_cg_i"}, {"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_2_d11", "target": "doi_lg_2_i"}, {"source": "doi_lg_2_d11", "target": "doi_lg_2_d21"}, {"source": "doi_lg_2_d12", "target": "doi_lg_2_d22"}, {"source": "doi_lg_2_d12", "target": "doi_lg_2_d23"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_d12"}, {"source": "doi_lg_1_h11", "target": "doi_lg_1_h12"}, {"source": "doi_lg_2_h24", "target": "doi_lg_2_d12"}]}
\ No newline at end of file
{"nodes": [{"doi": "doi_h02", "name": "title_h02", "author": ["contributor_h02"], "year": "date_h02", "journal": "journal_h02", "group": "Input", "depth": 0, "citations": 1}, {"doi": "doi_h1", "name": "title_h1", "author": ["contributor_h1"], "year": "date_h1", "journal": "journal_h1", "group": "Citedby", "depth": 1, "citations": 1}, {"doi": "doi_h2", "name": "title_h2", "author": ["contributor_h2"], "year": "date_h2", "journal": "journal_h2", "group": "Citedby", "depth": 2, "citations": 1}], "links": [{"source": "doi_h1", "target": "doi_h02"}, {"source": "doi_h2", "target": "doi_h1"}]}
\ No newline at end of file
verarbeitung/update_graph/connect_new_input.py
+ 112
− 43
View file @ 25ac97fc
......@@ -16,69 +16,138 @@ __status__ = "Production"
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.initialize_graph import initialize_nodes_list, complete_inner_edges
from verarbeitung.construct_new_graph.add_citations_rec import add_citations
from verarbeitung.construct_new_graph.export_to_json import output_to_json
from verarbeitung.construct_new_graph.initialize_graph import init_graph_construction
from verarbeitung.construct_new_graph.add_citations_rec import add_citations, get_cit_type_list, create_global_lists_cit
def connect_old_and_new_input(json_file, new_doi_list, search_depth, search_height, test_var = False):
def find_furthermost_citations(node, old_search_depth, cit_type):
'''
:param json_file: json file with old graph
:type json_file: json file
:param node: node which is known but not from input group
:type node: Publication
:param new_doi_list: additional dois which has to be connected to the old graph
:type new_doi_list: list of strings
:param old_search_depth: depth to search for references from old construction call
:type old_search_depth: int
:param search_depth: depth to search for references
:type search_depth: int
:param cit_type: determines whether the function call is for a reference or citation
:type cit_type: String
:param search_height: height to search for citations
:type search_height: int
function to find the furthermost citation/reference for given node which is from the same group
'''
citations_saved = get_cit_type_list(node, cit_type)
# group of node and old search depth/height determines how often the loop needs to be repeated
for depth in range(old_search_depth - abs(node.group)):
new_citations = []
for citation in citations_saved:
for cit_node in nodes:
if citation.doi_url == cit_node.doi_url:
for new_cit in get_cit_type_list(cit_node, cit_type):
for new_cit_node in nodes:
if new_cit.doi_url == new_cit_node.doi_url:
new_cit_node.group -= node.group
new_citations.append(new_cit_node)
citations_saved = new_citations
# returns the references/citations which needs to be processed to complete contruction
return(citations_saved)
def complete_changed_group_nodes(inserted_nodes, old_search_depth, old_search_height, new_search_depth, new_search_height, test_var):
'''
:param inserted_nodes: list of nodes which are inserted to new input array
:type inserted_nodes: List[String]
:param test_var: variable to differenciate between test and url call
:type test_var: boolean
:param old_search_depth: depth to search for references from old construction call
:type old_search_depth: int
connetcs the old graph and the new input dois to a complete new graph
'''
global nodes, edges
nodes = []
edges = []
:param old_search_height: height to search for citations from old construction call
:type old_search_height: int
nodes, edges = input_from_json(json_file)
:param new_search_depth: depth to search for references from new construction call
:type new_search_depth: int
complete_changed_group_nodes(new_doi_list, search_depth, search_height, 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)
:param new_search_height: height to search for citations from new construction call
:type new_search_height: int
# 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)
:param test_var: variable to differenciate between test and url call
:type test_var: boolean
# adds edges between reference group and citation group of known publications
complete_inner_edges(test_var)
completes the references and citations for nodes which were known in non input group
'''
#changed_group_node_citations = []
#changed_group_node_references = []
# calls a skript to save nodes and edges of graph in .json file
output_to_json(nodes,edges, test_var)
# saves which nodes were handled because they were known before
handled_inserted_nodes = []
for node in nodes:
return(nodes, edges)
# moves known reference node to input and completes citations and references for this node
if (node.group < 0) and (node.doi_url in inserted_nodes):
node_citations = create_global_lists_cit(nodes, edges, node, 1, new_search_height, "Citation", test_var)
add_citations(nodes, edges, node_citations, 1, new_search_height, "Citation", test_var)
old_max_references = find_furthermost_citations(node, old_search_depth, "Reference")
add_citations(nodes, edges, old_max_references, old_search_depth, new_search_depth, "Reference", test_var)
node.group = 0
handled_inserted_nodes.append(node)
# moves known citation node to input and completes citations and references for this node
elif (node.group > 0) and (node.doi_url in inserted_nodes):
node_references = create_global_lists_cit(nodes, edges, node, 1, new_search_depth, "Reference", test_var)
add_citations(nodes, edges, node_references, 1, new_search_depth, "Reference", test_var)
old_max_citations = find_furthermost_citations(node, old_search_height, "Citation")
add_citations(nodes, edges, old_max_citations, old_search_height, new_search_height, "Citation", test_var)
node.group = 0
handled_inserted_nodes.append(node)
def complete_changed_group_nodes(new_doi_list, search_depth_max, search_height_max, test_var):
return(handled_inserted_nodes)
def connect_old_and_new_input(input_nodes_list, input_edges_list, inserted_nodes, old_search_depth, old_search_height, new_search_depth, new_search_height, test_var = False):
'''
work in progress
:param input_nodes_list: list of nodes which are processed for new construction call
:type input_nodes_list: List[Publication]
:param input_edges_list: list of links between nodes from input_nodes_list.
:type input_edges_list: List[List[String,String]]
:param inserted_nodes: list of nodes which are inserted to new input array
:type inserted_nodes: List[String]
:param old_search_depth: depth to search for references from old construction call
:type old_search_depth: int
:param old_search_height: height to search for citations from old construction call
:type old_search_height: int
:param new_search_depth: depth to search for references from new construction call
:type new_search_depth: int
:param new_search_height: height to search for citations from new construction call
:type new_search_height: int
:param test_var: variable to differenciate between test and url call
:type test_var: boolean
completes the references and citations for nodes which were known in non input group
'''
changed_group_node_citations = []
changed_group_node_references = []
global nodes, edges
nodes = input_nodes_list
edges = input_edges_list
for node in nodes:
if (node.group < 0) and (node.doi in new_doi_list):
node.group = "input"
handled_inserted_nodes = complete_changed_group_nodes(inserted_nodes, old_search_depth, old_search_height, new_search_depth, new_search_height, test_var)
elif (node.group > 0) and (node.doi in new_doi_list):
node.group = "input"
# copy all nodes from inserted_nodes to new node, if node is not in handled_inserted_nodes
not_handled_inserted_nodes = [node for node in inserted_nodes if node not in handled_inserted_nodes]
# 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(not_handled_inserted_nodes, new_search_depth, new_search_height, test_var)
# function calls to begin recursive processing up to max depth/height
#add_citations(nodes, edges, citations_obj_list, 1, new_search_height, "Citation", test_var)
#add_citations(nodes, edges, references_obj_list, 1, new_search_depth, "Reference", test_var)
init_graph_construction(not_handled_inserted_nodes, new_search_depth, new_search_height, test_var = test_var, update_var = True, input_nodes = nodes, input_edges = edges)
verarbeitung/update_graph/delete_nodes_edges.py
+ 4
− 3
View file @ 25ac97fc
......@@ -90,6 +90,7 @@ def delete_nodes_and_edges(input_list, common_nodes, old_edges_list):
search_ref_graph_rec(pub)
search_cit_graph_rec(pub)
valid_edges = back_to_valid_edges(old_edges_list, usable_nodes)
return(usable_nodes, valid_edges)
\ No newline at end of file
back_to_valid_edges(old_edges_list, usable_nodes)
input_list = usable_nodes.copy()
print(input_list)
#return(usable_nodes, valid_edges)
verarbeitung/update_graph/update_depth.py
+ 11
− 4
View file @ 25ac97fc
......@@ -13,7 +13,7 @@ __status__ = "Production"
#__version__ = ""
#__maintainer__ = ""
import sys
import sys
sys.path.append("../../")
from verarbeitung.construct_new_graph.add_citations_rec import add_citations
......@@ -72,7 +72,10 @@ def get_old_max_references(old_depth):
old_max_references = []
for pub in processed_input_list:
if (abs(pub.group) == old_depth):
old_max_references.append(pub.references)
for reference in pub.references:
for ref_pub in processed_input_list:
if reference.doi_url == ref_pub.doi_url:
old_max_references.append(ref_pub)
return(old_max_references)
def get_old_max_citations(old_height):
......@@ -85,7 +88,10 @@ def get_old_max_citations(old_height):
old_max_citations = []
for pub in processed_input_list:
if (abs(pub.group) == old_height):
old_max_citations.append(pub.citations)
for citation in pub.citations:
for cit_pub in processed_input_list:
if citation.doi_url == cit_pub.doi_url:
old_max_citations.append(cit_pub)
return(old_max_citations)
def update_depth(obj_input_list, input_edges, new_depth, new_height, test_var):
......@@ -131,7 +137,8 @@ def update_depth(obj_input_list, input_edges, new_depth, new_height, test_var):
back_to_valid_edges(valid_edges, processed_input_list)
# adds edges between reference group and citation group of known publications
complete_inner_edges()
return(old_depth, old_height)
......
verarbeitung/update_graph/update_graph.py
+ 4
− 5
View file @ 25ac97fc
# -*- coding: utf-8 -*-
1# -*- coding: utf-8 -*-
"""
Functions to update a graph representing citations between multiple ACS/Nature journals
......@@ -85,7 +85,6 @@ def update_graph(new_doi_input_list, json_file, search_depth, search_height, tes
# gets information from previous cunstruction call
old_obj_input_list , old_edges_list = input_from_json(json_file)
print(type(old_edges_list[1]))
# one global list to save the process of removing unneeded publications and one to save valid edges
global processed_list, valid_edges
......@@ -102,11 +101,11 @@ def update_graph(new_doi_input_list, json_file, search_depth, search_height, tes
# deletes publications and edges from node_list if publications can no longer be reached
if (len(deleted_nodes) > 0):
processed_list, valid_edges = delete_nodes_and_edges(processed_list, common_nodes, old_edges_list)
delete_nodes_and_edges(processed_list, common_nodes, valid_edges)
update_depth(processed_list, valid_edges, search_depth, search_height, test_var)
old_search_depth, old_search_height = update_depth(processed_list, valid_edges, search_depth, search_height, test_var)
if (len(inserted_nodes) > 0):
connect_old_and_new_input(json_file, inserted_nodes, search_depth, search_height, test_var)
connect_old_and_new_input(processed_list, valid_edges, inserted_nodes, old_search_depth, old_search_height, search_depth, search_height, test_var)
return(processed_list, valid_edges)
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