From 12394774f5f71d40e023e38322e78524055d4878 Mon Sep 17 00:00:00 2001
From: Malte Schokolowski <baw8441@uni-hamburg.de>
Date: Tue, 21 Dec 2021 14:07:00 +0100
Subject: [PATCH] bug fixes
---
.../construct_new_graph/export_to_json.py | 2 +-
.../construct_new_graph/initialize_graph.py | 12 ++++++----
verarbeitung/test/construct_graph_unittest.py | 12 +++++-----
verarbeitung/test/update_graph_unittest.py | 22 +++++++++----------
verarbeitung/test_output.json | 2 +-
.../update_graph/connect_new_input.py | 5 +++--
.../update_graph/delete_nodes_edges.py | 7 +++---
verarbeitung/update_graph/update_graph.py | 2 +-
8 files changed, 35 insertions(+), 29 deletions(-)
diff --git a/verarbeitung/construct_new_graph/export_to_json.py b/verarbeitung/construct_new_graph/export_to_json.py
index c69a61b..68a25be 100644
--- a/verarbeitung/construct_new_graph/export_to_json.py
+++ b/verarbeitung/construct_new_graph/export_to_json.py
@@ -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:
diff --git a/verarbeitung/construct_new_graph/initialize_graph.py b/verarbeitung/construct_new_graph/initialize_graph.py
index 27cf455..b6bdeee 100644
--- a/verarbeitung/construct_new_graph/initialize_graph.py
+++ b/verarbeitung/construct_new_graph/initialize_graph.py
@@ -96,7 +96,7 @@ 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, input_nodes = [], input_edges = []):
+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]
@@ -128,8 +128,12 @@ 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 = input_nodes
- edges = input_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)
@@ -142,6 +146,6 @@ def init_graph_construction(doi_input_list, search_depth, search_height, test_va
complete_inner_edges()
# calls a skript to save nodes and edges of graph in .json file
- #output_to_json(nodes, edges, test_var)
+ output_to_json(nodes, edges, test_var = test_var)
return(nodes,edges)
diff --git a/verarbeitung/test/construct_graph_unittest.py b/verarbeitung/test/construct_graph_unittest.py
index 13f201c..338a612 100644
--- a/verarbeitung/test/construct_graph_unittest.py
+++ b/verarbeitung/test/construct_graph_unittest.py
@@ -51,33 +51,33 @@ class ConstructionTest(unittest.TestCase):
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)
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)
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)
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)
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)
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)
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']])
diff --git a/verarbeitung/test/update_graph_unittest.py b/verarbeitung/test/update_graph_unittest.py
index cf8261a..e7d4533 100644
--- a/verarbeitung/test/update_graph_unittest.py
+++ b/verarbeitung/test/update_graph_unittest.py
@@ -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)
diff --git a/verarbeitung/test_output.json b/verarbeitung/test_output.json
index 840e19d..f96362a 100644
--- a/verarbeitung/test_output.json
+++ b/verarbeitung/test_output.json
@@ -1 +1 @@
-{"nodes": [{"doi": "doi_lg_1_i", "name": "title_lg_1_i", "author": ["contributor_lg_1_i"], "year": "date_lg_1_i", "journal": "journal_lg_1_i", "group": "Input", "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_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_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_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}], "links": [{"source": "doi_lg_1_i", "target": "doi_lg_1_d11"}, {"source": "doi_lg_1_i", "target": "doi_lg_1_d12"}, {"source": "doi_lg_1_h11", "target": "doi_lg_1_i"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_i"}, {"source": "doi_lg_1_h21", "target": "doi_lg_1_h11"}, {"source": "doi_lg_1_h22", "target": "doi_lg_1_h11"}, {"source": "doi_lg_1_h22", "target": "doi_lg_1_h12"}, {"source": "doi_lg_1_h23", "target": "doi_lg_1_h12"}, {"source": "doi_lg_1_d11", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_d11", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d21", "target": "doi_lg_1_d22"}, {"source": "doi_lg_1_d22", "target": "doi_lg_1_d21"}, {"source": "doi_lg_1_d12", "target": "doi_lg_1_d23"}, {"source": "doi_lg_1_h12", "target": "doi_lg_1_d12"}]}
\ 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 b87b856..a7e7fda 100644
--- a/verarbeitung/update_graph/connect_new_input.py
+++ b/verarbeitung/update_graph/connect_new_input.py
@@ -48,7 +48,8 @@ def find_furthermost_citations(node, old_search_depth, cit_type):
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_citations.append(node)
+ 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
@@ -149,5 +150,5 @@ def connect_old_and_new_input(input_nodes_list, input_edges_list, inserted_nodes
#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, input_nodes = nodes, input_edges = edges)
+ 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)
diff --git a/verarbeitung/update_graph/delete_nodes_edges.py b/verarbeitung/update_graph/delete_nodes_edges.py
index 0e4571a..cf91a1b 100644
--- a/verarbeitung/update_graph/delete_nodes_edges.py
+++ b/verarbeitung/update_graph/delete_nodes_edges.py
@@ -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)
\ No newline at end of file
diff --git a/verarbeitung/update_graph/update_graph.py b/verarbeitung/update_graph/update_graph.py
index 169e17d..90114c3 100644
--- a/verarbeitung/update_graph/update_graph.py
+++ b/verarbeitung/update_graph/update_graph.py
@@ -102,7 +102,7 @@ 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)
old_search_depth, old_search_height = update_depth(processed_list, valid_edges, search_depth, search_height, test_var)
--
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