From f1a12544d77f35064063288571524d8f1382cdf1 Mon Sep 17 00:00:00 2001
From: Malte Schokolowski <baw8441@uni-hamburg.de>
Date: Thu, 20 Jan 2022 19:50:06 +0100
Subject: [PATCH] verarbeitung: performance boost for update graph and bug
fixing
---
.../construct_new_graph/export_to_json.py | 3 +-
.../construct_new_graph/initialize_graph.py | 25 +++++--
verarbeitung/json_text.json | 2 +-
verarbeitung/new_height.json | 2 +-
verarbeitung/process_main.py | 2 +-
verarbeitung/start_script.py | 9 +--
verarbeitung/test/update_graph_unittest.py | 28 ++++----
verarbeitung/test_output.json | 2 +-
.../update_graph/connect_new_input.py | 15 ++--
.../update_graph/delete_nodes_edges.py | 68 +++++++++++++------
verarbeitung/update_graph/import_from_json.py | 5 +-
verarbeitung/update_graph/update_depth.py | 20 +-----
verarbeitung/update_graph/update_graph.py | 10 ++-
13 files changed, 111 insertions(+), 80 deletions(-)
diff --git a/verarbeitung/construct_new_graph/export_to_json.py b/verarbeitung/construct_new_graph/export_to_json.py
index 0aaf996..d093f63 100644
--- a/verarbeitung/construct_new_graph/export_to_json.py
+++ b/verarbeitung/construct_new_graph/export_to_json.py
@@ -61,7 +61,7 @@ def format_edges(edges):
return list_of_edge_dicts
-def output_to_json(nodes, edges, json_file = 'json_text.json', test_var = False):
+def output_to_json(nodes, edges, search_depth, search_height, json_file = 'json_text.json', test_var = False):
'''
:param nodes: list of publications to export to json
:type nodes: List[Publication]
@@ -79,6 +79,7 @@ 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
+ dict_of_all["depth_height"] = [search_depth, search_height]
if (test_var):
if json_file != 'json_text.json':
with open(json_file,'w') as outfile:
diff --git a/verarbeitung/construct_new_graph/initialize_graph.py b/verarbeitung/construct_new_graph/initialize_graph.py
index 1368f6e..4615d5e 100644
--- a/verarbeitung/construct_new_graph/initialize_graph.py
+++ b/verarbeitung/construct_new_graph/initialize_graph.py
@@ -85,6 +85,7 @@ def initialize_nodes_list(doi_input_list, search_depth_max, search_height_max, t
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
+ node.group = 0
break
if (not_in_nodes): #there is no node with this doi in the set
nodes.append(pub) #appends Publication Object
@@ -106,10 +107,24 @@ def initialize_nodes_list(doi_input_list, search_depth_max, search_height_max, t
-def complete_inner_edges():
+def complete_inner_edges(update_var = False, input_nodes = [], input_edges = []):
'''
+ :param update_var: variable to check if call is from update_graph with known nodes and edges or fresh construction
+ :type update_var: boolean
+
+ :param input_nodes: list of publications from update_graph
+ :type input_nodes: List[Publication]
+
+ :param input_edges: list of links from update_graph
+ :type input_edges: List[List[String,String]]
+
completes inner edges between nodes of group height and depth
'''
+ if update_var:
+ global nodes, edges
+
+ nodes = input_nodes
+ edges = input_edges
for node in nodes:
if (node.group < 0):
@@ -138,14 +153,14 @@ 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 update_var: variable to check if call is from update_graph with known nodes and edges or fresh construction
+ :type update_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]]
+ :param input_edges: list of links from update_graph
+ :type input_edges: List[List[String,String]]
main function to start graph generation
'''
diff --git a/verarbeitung/json_text.json b/verarbeitung/json_text.json
index 183e764..f77fc38 100644
--- a/verarbeitung/json_text.json
+++ b/verarbeitung/json_text.json
@@ -1 +1 @@
-{"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}], "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.chemrev.1c00107", "target": "https://doi.org/10.1021/acs.jcim.9b00250"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00741", "target": "https://doi.org/10.1021/acs.jcim.9b00250"}, {"source": "https://doi.org/10.1021/acs.jmedchem.0c01332", "target": "https://doi.org/10.1021/acs.jcim.9b00250"}, {"source": "https://doi.org/10.1021/acs.jcim.9b00249", "target": "https://doi.org/10.1021/acs.jcim.9b00250"}]}
\ 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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Citedby", "depth": 1, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Citedby", "depth": 2, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Reference", "depth": -2, "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_d12", "target": "doi_lg_1_d23"}, {"source": "doi_lg_1_d21", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d22", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_d12"}], "depth_height": ["new_height.json", true]}
\ No newline at end of file
diff --git a/verarbeitung/new_height.json b/verarbeitung/new_height.json
index 6d4d75d..0cc5940 100644
--- a/verarbeitung/new_height.json
+++ b/verarbeitung/new_height.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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Citedby", "depth": 1, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Citedby", "depth": 2, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Reference", "depth": -2, "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_d12", "target": "doi_lg_1_d23"}, {"source": "doi_lg_1_d21", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d22", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_d12"}]}
\ 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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Citedby", "depth": 1, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Citedby", "depth": 2, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Reference", "depth": -2, "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_d12", "target": "doi_lg_1_d23"}, {"source": "doi_lg_1_d21", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d22", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_d12"}], "depth_height": [2, 2]}
\ No newline at end of file
diff --git a/verarbeitung/process_main.py b/verarbeitung/process_main.py
index 78df2db..581c426 100644
--- a/verarbeitung/process_main.py
+++ b/verarbeitung/process_main.py
@@ -50,7 +50,7 @@ def Processing(url_list, search_depth, search_height, json_file = 'json_text.jso
nodes, edges, error_doi_list = init_graph_construction(url_list, search_depth, search_height)
# exports graph to given json file name
- output_to_json(nodes, edges, json_file)
+ output_to_json(nodes, edges, search_depth, search_height, json_file)
return error_doi_list
\ No newline at end of file
diff --git a/verarbeitung/start_script.py b/verarbeitung/start_script.py
index 43e9bcc..92295ee 100644
--- a/verarbeitung/start_script.py
+++ b/verarbeitung/start_script.py
@@ -6,16 +6,17 @@ from verarbeitung.process_main import Processing
doi_list = []
-#doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
+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')
#doi_list.append('https://doi.org/10.1021/acs.jmedchem.0c01332')
#doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.6b00709')
#doi_list.append('https://doi.org/10.1021/acs.chemrev.8b00728')
#doi_list.append('https://pubs.acs.org/doi/10.1021/acs.chemrestox.0c00006')#
-doi_list.append('https://doi.org/10.1021/acs.chemrev.8b00728')
-doi_list.append('https://doi.org/10.1021/acs.jpclett.1c03335 ')
-error_list = Processing(doi_list, 2, 2, 'test728.json')
+#doi_list.append('https://doi.org/10.1021/acs.chemrev.8b00728')
+#doi_list.append('https://doi.org/10.1021/acs.jpclett.1c03335 ')
+doi_list.append('https://doi.org/10.1021/acs.chemrestox.5b00481')
+error_list = Processing(doi_list, 2, 2, 'test481.json')
print(error_list)
del doi_list
diff --git a/verarbeitung/test/update_graph_unittest.py b/verarbeitung/test/update_graph_unittest.py
index 77746ff..62504e5 100644
--- a/verarbeitung/test/update_graph_unittest.py
+++ b/verarbeitung/test/update_graph_unittest.py
@@ -23,7 +23,7 @@ class UpdatingTest(unittest.TestCase):
def test_deleted_input_dois(self):
nodes_old_single, edges_old_single, err_list = init_graph_construction(['doi_lg_1_i'],2,2,True)
nodes_old_both, edges_old_both, err_list = 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)
+ output_to_json(nodes_old_both, edges_old_both, 2, 2, test_var=True)
nodes_new_single, edges_new_single, err_list = 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)
@@ -37,13 +37,13 @@ class UpdatingTest(unittest.TestCase):
nodes_height_1, edges_height_1, err_list = init_graph_construction(['doi_lg_1_i'],2,1,True)
nodes_height_2, edges_height_2, err_list = init_graph_construction(['doi_lg_1_i'],2,2,True)
- output_to_json(nodes_height_2, edges_height_2, 'new_height.json', True)
+ output_to_json(nodes_height_2, edges_height_2, 2, 2, 'new_height.json', True)
nodes_new_height_1, edges_new_height_1, err_list = update_graph(['doi_lg_1_i'], 'new_height.json', 2, 1, True)
self.assertCountEqual(nodes_height_1, nodes_new_height_1)
self.assertCountEqual(edges_height_1, edges_new_height_1)
nodes_height_2, edges_height_2, err_list = init_graph_construction(['doi_lg_1_i'],2,2,True)
- output_to_json(nodes_height_2, edges_height_2, 'new_height.json', True)
+ output_to_json(nodes_height_2, edges_height_2, 2, 2, 'new_height.json', True)
nodes_new_height_0, edges_new_height_0, err_list = update_graph(['doi_lg_1_i'], 'new_height.json', 2, 0, True)
self.assertCountEqual(nodes_height_0, nodes_new_height_0)
self.assertCountEqual(edges_height_0, edges_new_height_0)
@@ -51,7 +51,7 @@ class UpdatingTest(unittest.TestCase):
def test_ref_to_input(self):
nodes, edges, err_list = init_graph_construction(['doi_cg_i'], 2, 2, True)
nodes_2, edges_2, err_list_2 = init_graph_construction(['doi_cg_d11'], 2, 2, True)
- output_to_json(nodes, edges, 'ref_to_input.json')
+ output_to_json(nodes, edges, 2, 2, 'ref_to_input.json')
new_nodes, new_edges, new_err_list = update_graph(['doi_cg_d11'], 'ref_to_input.json', 2, 2, True)
self.assertCountEqual(new_nodes, nodes_2)
self.assertCountEqual(new_edges, edges_2)
@@ -59,12 +59,12 @@ class UpdatingTest(unittest.TestCase):
nodes, edges, err_list = init_graph_construction(['doi_cg_i','doi_lg_2_i'], 2, 2, True)
nodes_2, edges_2, err_list_2 = init_graph_construction(['doi_cg_d11','doi_lg_2_i'], 2, 2, True)
- output_to_json(nodes, edges, 'ref_to_input.json')
+ output_to_json(nodes, edges, 2, 2, 'ref_to_input.json')
new_nodes, new_edges, new_err_list = update_graph(['doi_cg_d11','doi_lg_2_i'], 'ref_to_input.json', 2, 2, True)
self.assertCountEqual(new_nodes, nodes_2)
self.assertCountEqual(new_edges, edges_2)
- output_to_json(nodes_2, edges_2, 'ref_to_input.json')
+ output_to_json(nodes_2, edges_2, 2, 2, 'ref_to_input.json')
new_nodes, new_edges, new_err_list = update_graph(['doi_cg_d11','doi_lg_2_i'], 'ref_to_input.json', 2, 2, True)
self.assertCountEqual(new_nodes, nodes_2)
self.assertCountEqual(new_edges, edges_2)
@@ -72,7 +72,7 @@ class UpdatingTest(unittest.TestCase):
nodes, edges, err_list = init_graph_construction(['doi_cg_i','doi_lg_2_i'], 2, 2, True)
nodes_2, edges_2, err_list_2 = init_graph_construction(['doi_cg_i','doi_lg_2_h11','doi_lg_1_i'], 3, 3, True)
- output_to_json(nodes_2, edges_2, 'ref_to_input.json')
+ output_to_json(nodes_2, edges_2, 2, 2, 'ref_to_input.json')
new_nodes, new_edges, new_err_list = update_graph(['doi_cg_i','doi_lg_2_i'], 'ref_to_input.json', 2, 2, True)
self.assertCountEqual(new_nodes, nodes)
self.assertCountEqual(new_edges, edges)
@@ -172,8 +172,8 @@ class UpdatingTest(unittest.TestCase):
def test_input_from_json(self):
nodes_old, edges_old, err_list = init_graph_construction(['doi_lg_1_i'],2,2,True)
- output_to_json(nodes_old, edges_old, test_var = True)
- nodes_new, edges_new = input_from_json('test_output.json')
+ output_to_json(nodes_old, edges_old, 2, 2, test_var = True)
+ nodes_new, edges_new, old_depth, old_height = input_from_json('test_output.json')
self.assertCountEqual(nodes_old,nodes_new)
self.assertCountEqual(edges_old, edges_new)
@@ -220,7 +220,7 @@ class UpdatingTest(unittest.TestCase):
pub_cg_d11 = input_test_func('doi_cg_d12')
pub_cg_d11.group = -1
pubs = [pub_lg_2_i, pub_lg_2_h11, pub_lg_2_h12, pub_lg_2_d11, pub_lg_2_d12, pub_lg_2_h21, pub_lg_2_h22, pub_lg_2_d21, pub_cg_i, pub_cg_d11, pub_cg_d12, pub_cg_h11]
- usable_nodes = search_ref_cit_graph_rec_test(pubs, [pub_cg_i], "Citation")
+ usable_nodes = search_ref_cit_graph_rec_test(pubs, [pub_cg_i], 2, "Citation")
self.assertCountEqual(usable_nodes, [pub_cg_h11, pub_lg_2_h11, pub_lg_2_h21, pub_lg_2_h22])
# compare_old_and_new_node_lists.py:
@@ -257,11 +257,11 @@ class UpdatingTest(unittest.TestCase):
pub_lg_2_d22.group = -2
pubs = [pub_lg_2_i, pub_lg_2_h11, pub_lg_2_h12, pub_lg_2_d11, pub_lg_2_d12, pub_lg_2_h21, pub_lg_2_h22, pub_lg_2_d21, pub_lg_2_d22]
- self.assertCountEqual(find_furthermost_citations_test(pubs, [], pub_lg_2_h11, 2, "Citation"),[pub_lg_2_h21, pub_lg_2_h22])
- self.assertCountEqual(find_furthermost_citations_test(pubs, [], pub_lg_2_h11, 1, "Citation"),[pub_lg_2_h11])
+ self.assertCountEqual(find_furthermost_citations_test(pubs, [], pub_lg_2_h11, 2, 2, "Citation"),[pub_lg_2_h21, pub_lg_2_h22])
+ self.assertCountEqual(find_furthermost_citations_test(pubs, [], pub_lg_2_h11, 2, 1, "Citation"),[pub_lg_2_h21, pub_lg_2_h22])
- self.assertCountEqual(find_furthermost_citations_test(pubs, [], pub_lg_2_d11, 2, "Reference"),[pub_lg_2_d21, pub_lg_2_i])
- self.assertCountEqual(find_furthermost_citations_test(pubs, [], pub_lg_2_d11, 1, "Reference"),[pub_lg_2_d11])
+ self.assertCountEqual(find_furthermost_citations_test(pubs, [], pub_lg_2_d11, 2, 2, "Reference"),[pub_lg_2_d21, pub_lg_2_i])
+ self.assertCountEqual(find_furthermost_citations_test(pubs, [], pub_lg_2_d11, 2, 1, "Reference"),[pub_lg_2_d21, pub_lg_2_i])
def test_complete_changed_group_nodes(self):
diff --git a/verarbeitung/test_output.json b/verarbeitung/test_output.json
index 6d4d75d..0cc5940 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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Citedby", "depth": 1, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Citedby", "depth": 2, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Reference", "depth": -2, "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_d12", "target": "doi_lg_1_d23"}, {"source": "doi_lg_1_d21", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d22", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_d12"}]}
\ 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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Citedby", "depth": 1, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Citedby", "depth": 2, "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", "abstract": null, "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", "abstract": null, "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", "abstract": null, "group": "Reference", "depth": -2, "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_d12", "target": "doi_lg_1_d23"}, {"source": "doi_lg_1_d21", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d22", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_d12"}], "depth_height": [2, 2]}
\ No newline at end of file
diff --git a/verarbeitung/update_graph/connect_new_input.py b/verarbeitung/update_graph/connect_new_input.py
index f4d2ef9..7dcad9b 100644
--- a/verarbeitung/update_graph/connect_new_input.py
+++ b/verarbeitung/update_graph/connect_new_input.py
@@ -88,7 +88,7 @@ def find_furthermost_citations(new_nodes, new_edges, node, old_search_depth, new
new_citations.append(new_cit_node)
# change height accordingly and add link to edge
- new_cit_node.group = node.group + depth + 1
+ new_cit_node.group = node.group + depth
if [cit_node.doi_url,cit_node.doi_url] not in new_edges:
new_edges.append([new_cit_node.doi_url,cit_node.doi_url])
@@ -104,7 +104,7 @@ def find_furthermost_citations(new_nodes, new_edges, node, old_search_depth, new
new_citations.append(new_cit_node)
# change height accordingly and add link to edge
- new_cit_node.group = node.group - depth - 1
+ new_cit_node.group = node.group + depth
if [cit_node.doi_url, new_cit_node.doi_url] not in new_edges:
new_edges.append([cit_node.doi_url, new_cit_node.doi_url])
@@ -241,9 +241,10 @@ def connect_old_and_new_input(input_nodes_list, input_edges_list, inserted_nodes
# function call to begin recursive processing up to max depth/height for unhandled nodes
- nodes, edges, error_doi_list_new = init_graph_construction(not_handled_inserted_nodes, new_search_depth, new_search_height, test_var = test_var, update_var = True, input_nodes = new_nodes, input_edges = new_edges)
- for err_node in error_doi_list_new:
- if err_node not in error_doi_list:
- error_doi_list.append(err_node)
+ if len(not_handled_inserted_nodes) > 0:
+ new_nodes, new_edges, error_doi_list_new = init_graph_construction(not_handled_inserted_nodes, new_search_depth, new_search_height, test_var = test_var, update_var = True, input_nodes = new_nodes, input_edges = new_edges)
+ for err_node in error_doi_list_new:
+ if err_node not in error_doi_list:
+ error_doi_list.append(err_node)
- return(nodes, edges, error_doi_list)
\ No newline at end of file
+ return(new_nodes, new_edges, error_doi_list)
\ No newline at end of file
diff --git a/verarbeitung/update_graph/delete_nodes_edges.py b/verarbeitung/update_graph/delete_nodes_edges.py
index 205c82e..08d0dbb 100644
--- a/verarbeitung/update_graph/delete_nodes_edges.py
+++ b/verarbeitung/update_graph/delete_nodes_edges.py
@@ -20,76 +20,100 @@ sys.path.append("../../")
from .update_edges import back_to_valid_edges
-def search_ref_cit_graph_rec_test(pubs, new_test_input, cit_var):
+def search_ref_cit_graph_rec_test(pubs, new_test_input, old_max_depth, cit_var):
global usable_nodes, input_obj_list
usable_nodes = []
input_obj_list = pubs
if cit_var == "Reference":
for pub in new_test_input:
- search_ref_graph_rec(pub)
+ search_ref_graph_rec(pub, 1, old_max_depth)
elif cit_var == "Citation":
for pub in new_test_input:
- search_cit_graph_rec(pub)
+ search_cit_graph_rec(pub, 1, old_max_depth)
return usable_nodes
-def search_ref_graph_rec(pub):
+def search_ref_graph_rec(pub, curr_depth, old_max_depth):
'''
:param pub: pub go get appended to usable_nodes
:type pub: Publication
+
+ :param curr_depth: current recursion depth
+ :type curr_depth: int
+
+ :param old_max_depth: old max search depth
+ :type old_max_depth: int
function that appends nodes of group "reference" to list usable_nodes, if they are reachable from input nodes
'''
+ usable_doi_nodes = []
for reference in pub.references:
for ref_pub in input_obj_list:
if ((reference.doi_url == ref_pub.doi_url) and (ref_pub not in usable_nodes)):
usable_nodes.append(ref_pub)
+ usable_doi_nodes.append(ref_pub.doi_url)
# to find a cyclus and avoid recursion error
not_in_citations = True
for citation in pub.citations:
- if (reference.doi_url == citation.doi_url):
+ if (reference.doi_url == citation.doi_url and citation.doi_url not in usable_doi_nodes):
not_in_citations = False
break
- if (not_in_citations):
- search_ref_graph_rec(ref_pub)
+ if not_in_citations and curr_depth < old_max_depth:
+ search_ref_graph_rec(ref_pub, curr_depth + 1, old_max_depth)
-def search_cit_graph_rec(pub):
+def search_cit_graph_rec(pub, curr_height, old_max_height):
'''
- :param pub: pub go get appended to usable_nodes
- :type pub: Publication
+ :param pub: pub go get appended to usable_nodes
+ :type pub: Publication
+
+ :param curr_height: current recursion height
+ :type curr_height: int
+
+ :param old_max_height: old max search height
+ :type old_max_height: int
function that appends nodes of group "citation" to list usable_nodes, if they are reachable from input nodes
'''
+
+ usable_doi_nodes = []
for citation in pub.citations:
for cit_pub in input_obj_list:
- if ((citation.doi_url == cit_pub.doi_url) and (cit_pub not in usable_nodes)):
- usable_nodes.append(cit_pub)
+ if ((citation.doi_url == cit_pub.doi_url)):
+ if cit_pub not in usable_nodes:
+ usable_nodes.append(cit_pub)
+ usable_doi_nodes.append(cit_pub.doi_url)
# to find a cyclus and avoid recursion error
not_in_references = True
for reference in pub.references:
- if (citation.doi_url == reference.doi_url):
+ if (citation.doi_url == reference.doi_url and reference.doi_url not in usable_doi_nodes):
not_in_references = False
break
- if (not_in_references):
- search_cit_graph_rec(cit_pub)
+ if not_in_references and curr_height < old_max_height:
+ search_cit_graph_rec(cit_pub,curr_height + 1, old_max_height)
-def delete_nodes_and_edges(input_list, common_nodes, old_edges_list):
+def delete_nodes_and_edges(input_list, common_nodes, old_edges_list, old_depth, old_height):
'''
:param input_list: list of publications to get reduced
:type input_list: List[Publication]
- :param common_nodes: list of input dois which are in old and new input call
- :type common_nodes: List[String]
+ :param common_nodes: list of input dois which are in old and new input call
+ :type common_nodes: List[String]
+
+ :param old_edges_list: list of links between publications from old call
+ :type old_edges_list: List[List[String,String]]
+
+ :param old_depth: old max search depth
+ :type old_depth: int
- :param old_edges_list: list of links between publications from old call
- :type old_edges_list: List[List[String,String]]
+ :param old_height: old max search height
+ :type old_height: int
function to start recursive node removal for references and citations and to change edge list to valid state
'''
@@ -102,8 +126,8 @@ def delete_nodes_and_edges(input_list, common_nodes, old_edges_list):
for pub in input_obj_list:
if (common == pub.doi_url):
usable_nodes.append(pub)
- search_ref_graph_rec(pub)
- search_cit_graph_rec(pub)
+ search_ref_graph_rec(pub, 1, old_depth)
+ search_cit_graph_rec(pub, 1, old_height)
back_to_valid_edges(old_edges_list, usable_nodes)
diff --git a/verarbeitung/update_graph/import_from_json.py b/verarbeitung/update_graph/import_from_json.py
index 92d9b02..72217d5 100644
--- a/verarbeitung/update_graph/import_from_json.py
+++ b/verarbeitung/update_graph/import_from_json.py
@@ -86,6 +86,9 @@ def input_from_json(json_file):
# adds references and citations to publications and creates edges
add_ref_and_cit_to_pubs(input_dict)
+ old_depth_height = input_dict["depth_height"]
+ old_depth = old_depth_height[0]
+ old_height = old_depth_height[1]
- return(list_of_nodes_py, list_of_edges_py)
\ No newline at end of file
+ return(list_of_nodes_py, list_of_edges_py, old_depth, old_height)
\ No newline at end of file
diff --git a/verarbeitung/update_graph/update_depth.py b/verarbeitung/update_graph/update_depth.py
index 1d99d5a..f843bb5 100644
--- a/verarbeitung/update_graph/update_depth.py
+++ b/verarbeitung/update_graph/update_depth.py
@@ -93,20 +93,6 @@ def reduce_max_depth(max_depth):
processed_input_list.remove(pub)
-
-def get_old_height_depth():
- '''
- function to get old max height and max depth from previous construction call
- '''
- max_height = 0
- max_depth = 0
- for pub in processed_input_list:
- if (pub.group < 0):
- max_depth = max(max_depth, abs(pub.group))
- if (pub.group > 0):
- max_height = max(max_height, pub.group)
- return(max_height, max_depth)
-
def get_old_max_references(old_depth, test_var):
'''
:param old_depth: old maximum depth to search for citations
@@ -141,7 +127,7 @@ def get_old_max_citations(old_height, test_var):
old_max_citations.append(pub)
return(old_max_citations)
-def update_depth(obj_input_list, input_edges, new_depth, new_height, test_var):
+def update_depth(obj_input_list, input_edges, new_depth, new_height, old_depth, old_height, test_var):
'''
:param obj_input_list: input list of publications of type Publication from update_graph
:type obj_input_list: List[Publication]
@@ -165,8 +151,6 @@ def update_depth(obj_input_list, input_edges, new_depth, new_height, test_var):
processed_input_list = obj_input_list
valid_edges = input_edges
- old_height, old_depth = get_old_height_depth()
-
# removes publications and links from recursion levels which aren't needed anymore or adds new ones
if (old_depth > new_depth):
reduce_max_depth(new_depth)
@@ -187,8 +171,6 @@ def update_depth(obj_input_list, input_edges, new_depth, new_height, test_var):
# adds edges between reference group and citation group of known publications
- return(old_depth, old_height)
-
diff --git a/verarbeitung/update_graph/update_graph.py b/verarbeitung/update_graph/update_graph.py
index 1e74773..8143ab4 100644
--- a/verarbeitung/update_graph/update_graph.py
+++ b/verarbeitung/update_graph/update_graph.py
@@ -16,9 +16,11 @@ __status__ = "Production"
import sys
+
sys.path.append("../../")
from input.publication import Publication
+from verarbeitung.construct_new_graph.initialize_graph import complete_inner_edges
from verarbeitung.get_pub_from_input import get_pub
from .compare_old_and_new_node_lists import compare_old_and_new_node_lists
from .delete_nodes_edges import delete_nodes_and_edges
@@ -85,7 +87,7 @@ 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)
+ old_obj_input_list , old_edges_list, old_search_depth, old_search_height = input_from_json(json_file)
# one global list to save the process of removing unneeded publications and one to save valid edges
global processed_list, valid_edges, error_doi_list
@@ -106,11 +108,11 @@ def update_graph(new_doi_input_list, json_file, search_depth, search_height, tes
processed_list_copy = processed_list.copy()
valid_edges_copy = valid_edges.copy()
- old_search_depth, old_search_height = update_depth(processed_list, valid_edges, search_depth, search_height, test_var)
+ update_depth(processed_list, valid_edges, search_depth, search_height, old_search_depth, old_search_height, test_var)
# 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, valid_edges)
+ processed_list, valid_edges = delete_nodes_and_edges(processed_list, common_nodes, valid_edges, old_search_depth, old_search_height)
if (len(inserted_nodes) > 0):
@@ -134,4 +136,6 @@ def update_graph(new_doi_input_list, json_file, search_depth, search_height, tes
if inserted_edge not in valid_edges:
valid_edges.append(inserted_edge)
+ complete_inner_edges(True, processed_list, valid_edges)
+
return(processed_list, valid_edges, error_doi_list)
--
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