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Commit 20c84af6 authored by Malte Schokolowski's avatar Malte Schokolowski
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bugs fixed and added graph plan for test graphs

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1 merge request!11merge verarbeitung to main repo
This commit is part of merge request !11. Comments created here will be created in the context of that merge request.
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verarbeitung/construct_new_graph/Processing.py
+ 7
− 7
Edit View file @ 20c84af6
...@@ -86,14 +86,14 @@ def complete_inner_edges(): ...@@ -86,14 +86,14 @@ def complete_inner_edges():
for node in nodes: for node in nodes:
if (node.group < 0): if (node.group < 0):
for citation in node.citations: for citation in node.citations:
for cit in nodes: for pub in nodes:
if (citation == cit.doi_url and [citation, node.doi_url] not in edges): if ((pub.doi_url == citation.doi_url) and ([citation.doi_url, node.doi_url] not in edges)):
edges.append([citation, node.doi_url]) edges.append([citation.doi_url, node.doi_url])
if (node.group > 0): if (node.group > 0):
for reference in node.references: for reference in node.references:
for ref in nodes: for pub in nodes:
if (reference == ref.doi_url and [node.doi_url, reference] not in edges): if ((pub.doi_url == reference.doi_url) and ([node.doi_url, reference.doi_url] not in edges)):
edges.append([node.doi_url,reference]) edges.append([node.doi_url,reference.doi_url])
def process_main(doi_input_list, search_height, search_depth, test_var = False): def process_main(doi_input_list, search_height, search_depth, test_var = False):
...@@ -142,6 +142,6 @@ def process_main(doi_input_list, search_height, search_depth, test_var = False): ...@@ -142,6 +142,6 @@ def process_main(doi_input_list, search_height, search_depth, test_var = False):
complete_inner_edges() complete_inner_edges()
# calls a skript to save nodes and edges of graph in .json file # 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)
return(nodes,edges) return(nodes,edges)
verarbeitung/construct_new_graph/add_citations_rec.py
+ 10
− 9
Edit View file @ 20c84af6
...@@ -95,12 +95,12 @@ def create_graph_structure_citations(pub, search_depth, search_depth_max, cit_ty ...@@ -95,12 +95,12 @@ def create_graph_structure_citations(pub, search_depth, search_depth_max, cit_ty
for citation in get_cit_type_list(pub, cit_type): for citation in get_cit_type_list(pub, cit_type):
not_in_nodes = True not_in_nodes = True
for node in nodes: # checks every citation for duplication for node in nodes: # checks every citation for duplication
if (citation == node.doi_url): if (citation.doi_url == node.doi_url):
not_in_nodes = False not_in_nodes = False
break break
if (not_in_nodes): if (not_in_nodes):
if (search_depth < search_depth_max): #checks if its a test and chooses input function accordingly if (search_depth < search_depth_max): #checks if its a test and chooses input function accordingly
citation_pub_obj = get_pub(citation, test_var) citation_pub_obj = get_pub(citation.doi_url, test_var)
if (type(citation_pub_obj) != Publication): if (type(citation_pub_obj) != Publication):
print(pub) print(pub)
continue continue
...@@ -114,13 +114,14 @@ def create_graph_structure_citations(pub, search_depth, search_depth_max, cit_ty ...@@ -114,13 +114,14 @@ def create_graph_structure_citations(pub, search_depth, search_depth_max, cit_ty
nodes.append(citation_pub_obj) nodes.append(citation_pub_obj)
citations_pub_obj_list.append(citation_pub_obj) citations_pub_obj_list.append(citation_pub_obj)
# adds only edge if citation already exists # adds just the edge if citation already exists
elif (cit_type == "Citation"): else:
if ([citation,pub.doi_url] not in edges): if (cit_type == "Citation"):
edges.append([citation,pub.doi_url]) if ([citation.doi_url,pub.doi_url] not in edges):
elif (cit_type == "Reference"): edges.append([citation.doi_url,pub.doi_url])
if ([pub.doi_url,citation] not in edges): else:
edges.append([pub.doi_url,citation]) if ([pub.doi_url,citation.doi_url] not in edges):
edges.append([pub.doi_url,citation.doi_url])
return citations_pub_obj_list return citations_pub_obj_list
......
verarbeitung/get_pub_from_input.py
+ 2
− 3
Edit View file @ 20c84af6
...@@ -33,15 +33,14 @@ def get_pub(pub_doi, test_var): ...@@ -33,15 +33,14 @@ def get_pub(pub_doi, test_var):
function to return an object of type Publication for given input doi depending on whether its a test or url doi function to return an object of type Publication for given input doi depending on whether its a test or url doi
''' '''
#checks if it's a test and chooses appropiate function #checks if it's a test and chooses appropiate function
# print(pub_doi)
if(test_var): if(test_var):
pub = input_test_func(pub_doi) pub = input_test_func(pub_doi)
#checks that it isnt a test and chooses standart-input function #checks that it isnt a test and chooses standart-input function
else: else:
inter = Input() inter = Input()
try: try:
pub = inter.get_publication(pub_doi.doi_url) #creates an object of class Publication pub = inter.get_publication(pub_doi) #creates an object of class Publication
except AttributeError: except AttributeError:
pub = inter.get_publication(pub_doi) pub = inter.get_publication(pub_doi)
except ValueError: except ValueError:
......
verarbeitung/json_text.json
+ 1
− 1
Edit View file @ 20c84af6
{"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": "Input", "depth": 0, "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": "Input", "depth": 0, "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": "Input", "depth": 0, "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": "Input", "depth": 0, "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"}]} {"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 \ No newline at end of file
verarbeitung/test/Processing_unittest.py
+ 64
− 64
Edit View file @ 20c84af6
...@@ -12,16 +12,16 @@ class ProcessingTest(unittest.TestCase): ...@@ -12,16 +12,16 @@ class ProcessingTest(unittest.TestCase):
maxDiff = None maxDiff = None
# def testCycle(self): def testCycle(self):
# nodes, edges = process_main(['doiz1'],1,1,True) nodes, edges = process_main(['doiz1'],1,1,True)
# doi_nodes = keep_only_dois(nodes) doi_nodes = keep_only_dois(nodes)
# self.assertCountEqual(doi_nodes, ['doiz1', 'doiz2']) self.assertCountEqual(doi_nodes, ['doiz1', 'doiz2'])
# self.assertCountEqual(edges, [['doiz1', 'doiz2'], ['doiz2', 'doiz1']]) self.assertCountEqual(edges, [['doiz1', 'doiz2'], ['doiz2', 'doiz1']])
# nodes, edges = process_main(['doiz1'],2,2,True) nodes, edges = process_main(['doiz1'],2,2,True)
# doi_nodes = keep_only_dois(nodes) doi_nodes = keep_only_dois(nodes)
# self.assertCountEqual(doi_nodes, ['doiz1', 'doiz2']) self.assertCountEqual(doi_nodes, ['doiz1', 'doiz2'])
# self.assertCountEqual(edges, [['doiz2', 'doiz1'], ['doiz1', 'doiz2']]) self.assertCountEqual(edges, [['doiz2', 'doiz1'], ['doiz1', 'doiz2']])
#def testBigCycle(self): #def testBigCycle(self):
...@@ -29,66 +29,66 @@ class ProcessingTest(unittest.TestCase): ...@@ -29,66 +29,66 @@ class ProcessingTest(unittest.TestCase):
#def testEmptyDepth(self): #def testEmptyDepth(self):
# def testEmptyDepthHeight(self): def testEmptyDepthHeight(self):
# nodes, edges = process_main(['doi1'],0,0,True) nodes, edges = process_main(['doi1'],0,0,True)
# doi_nodes = keep_only_dois(nodes) doi_nodes = keep_only_dois(nodes)
# self.assertCountEqual(doi_nodes,['doi1']) self.assertCountEqual(doi_nodes,['doi1'])
# self.assertCountEqual(edges, []) self.assertCountEqual(edges, [])
# nodes, edges = process_main(['doi1', 'doi2'],0,0,True) nodes, edges = process_main(['doi1', 'doi2'],0,0,True)
# doi_nodes = keep_only_dois(nodes) doi_nodes = keep_only_dois(nodes)
# self.assertCountEqual(doi_nodes, ['doi1','doi2']) self.assertCountEqual(doi_nodes, ['doi1','doi2'])
# self.assertCountEqual(edges, [['doi1', 'doi2']]) self.assertCountEqual(edges, [['doi1', 'doi2']])
# nodes, edges = process_main(['doi1', 'doi2', 'doi3'],0,0,True) nodes, edges = process_main(['doi1', 'doi2', 'doi3'],0,0,True)
# doi_nodes = keep_only_dois(nodes) doi_nodes = keep_only_dois(nodes)
# self.assertCountEqual(doi_nodes, ['doi1','doi2', 'doi3']) self.assertCountEqual(doi_nodes, ['doi1','doi2', 'doi3'])
# self.assertCountEqual(edges, [['doi3', 'doi1'], ['doi1', 'doi2']]) self.assertCountEqual(edges, [['doi3', 'doi1'], ['doi1', 'doi2']])
# def testInnerEdges(self): def testInnerEdges(self):
# nodes, edges = process_main(['doi_ie1'],1,1,True) nodes, edges = process_main(['doi_ie1'],1,1,True)
# doi_nodes = keep_only_dois(nodes) doi_nodes = keep_only_dois(nodes)
# self.assertCountEqual(doi_nodes,['doi_ie1','doi_ie2','doi_ie3']) 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']]) self.assertCountEqual(edges,[['doi_ie1','doi_ie2'],['doi_ie3','doi_ie1'],['doi_ie3','doi_ie2']])
# def testRightHeight(self): def testRightHeight(self):
# nodes, edges = process_main(['doi_h01'],1,0,True) nodes, edges = process_main(['doi_h01'],1,0,True)
# doi_nodes = keep_only_dois(nodes) doi_nodes = keep_only_dois(nodes)
# self.assertCountEqual(doi_nodes,['doi_h01']) self.assertCountEqual(doi_nodes,['doi_h01'])
# self.assertCountEqual(edges, []) self.assertCountEqual(edges, [])
# nodes, edges = process_main(['doi_h02'],1,0,True) nodes, edges = process_main(['doi_h02'],1,0,True)
# doi_nodes = keep_only_dois(nodes) doi_nodes = keep_only_dois(nodes)
# self.assertCountEqual(doi_nodes,['doi_h02','doi_h1']) self.assertCountEqual(doi_nodes,['doi_h02','doi_h1'])
# self.assertCountEqual(edges, [['doi_h1','doi_h02']]) self.assertCountEqual(edges, [['doi_h1','doi_h02']])
# nodes, edges = process_main(['doi_h02'],2,0,True) nodes, edges = process_main(['doi_h02'],2,0,True)
# doi_nodes = keep_only_dois(nodes) doi_nodes = keep_only_dois(nodes)
# self.assertCountEqual(doi_nodes,['doi_h02','doi_h1','doi_h2']) self.assertCountEqual(doi_nodes,['doi_h02','doi_h1','doi_h2'])
# self.assertCountEqual(edges, [['doi_h1','doi_h02'], ['doi_h2','doi_h1']]) self.assertCountEqual(edges, [['doi_h1','doi_h02'], ['doi_h2','doi_h1']])
# def testRightDepth(self): def testRightDepth(self):
# nodes, edges = process_main(['doi_d01'],0,1,True) nodes, edges = process_main(['doi_d01'],0,1,True)
# doi_nodes = keep_only_dois(nodes) doi_nodes = keep_only_dois(nodes)
# self.assertCountEqual(doi_nodes,['doi_d01']) self.assertCountEqual(doi_nodes,['doi_d01'])
# self.assertCountEqual(edges, []) self.assertCountEqual(edges, [])
# nodes, edges = process_main(['doi_d02'],0,1,True) nodes, edges = process_main(['doi_d02'],0,1,True)
# doi_nodes = keep_only_dois(nodes) doi_nodes = keep_only_dois(nodes)
# self.assertCountEqual(doi_nodes,['doi_d02','doi_d1']) self.assertCountEqual(doi_nodes,['doi_d02','doi_d1'])
# self.assertCountEqual(edges, [['doi_d02','doi_d1']]) self.assertCountEqual(edges, [['doi_d02','doi_d1']])
# nodes, edges = process_main(['doi_d02'],0,2,True) nodes, edges = process_main(['doi_d02'],0,2,True)
# doi_nodes = keep_only_dois(nodes) doi_nodes = keep_only_dois(nodes)
# self.assertCountEqual(doi_nodes,['doi_d02','doi_d1','doi_d2']) self.assertCountEqual(doi_nodes,['doi_d02','doi_d1','doi_d2'])
# self.assertCountEqual(edges, [['doi_d02','doi_d1'], ['doi_d1','doi_d2']]) self.assertCountEqual(edges, [['doi_d02','doi_d1'], ['doi_d1','doi_d2']])
# def test_import_from_json(self): def test_import_from_json(self):
# nodes_old, edges_old = process_main(['doi_lg_1_i'],2,2,True) nodes_old, edges_old = process_main(['doi_lg_1_i'],2,2,True)
# nodes_new, edges_new = input_from_json('test_output.json') nodes_new, edges_new = input_from_json('test_output.json')
# self.assertCountEqual(nodes_old,nodes_new) self.assertCountEqual(nodes_old,nodes_new)
# self.assertCountEqual(edges_old, edges_new) self.assertCountEqual(edges_old, edges_new)
def test_deleted_input_dois(self): def test_deleted_input_dois(self):
nodes_old_single, edges_old_single = process_main(['doi_lg_1_i'],2,2,True) nodes_old_single, edges_old_single = process_main(['doi_lg_1_i'],2,2,True)
......
verarbeitung/test/input_test.py
+ 10
− 22
Edit View file @ 20c84af6
...@@ -14,11 +14,13 @@ def input_test_func(pub_doi): ...@@ -14,11 +14,13 @@ def input_test_func(pub_doi):
for array in list_of_arrays: for array in list_of_arrays:
if pub_doi == array[0]: if pub_doi == array[0]:
pub = Publication(array[0], array[1], array[2], array[3], array[4], array[5], array[6], array[7]) pub = Publication(array[0], array[1], array[2], array[3], array[4], array[5], [], [])
pub.citations = cit(array[7], "Citation")
pub.references = cit(array[6], "Reference")
return pub return pub
def cit(list_doi): def cit(list_doi, cit_type):
''' '''
:param list_doi list of citation dois to get their Citation Class :param list_doi list of citation dois to get their Citation Class
:type list_doi: List[String] :type list_doi: List[String]
...@@ -30,24 +32,9 @@ def cit(list_doi): ...@@ -30,24 +32,9 @@ def cit(list_doi):
for doi_url in list_doi: for doi_url in list_doi:
for array in list_of_arrays: for array in list_of_arrays:
if doi_url == array[0]: if doi_url == array[0]:
cits.append(Citation(array[0], array[1], array[2], array[3], array[4])) cits.append(Citation(array[0], array[1], array[2], array[3], cit_type))
return cits return cits
def ref(list_doi):
'''
:param list_doi list of reference dois to get their Reference Class
:type list_doi: List[String]
returns a list of reference objects for given doi list
'''
refs = []
for doi_url in list_doi:
for array in list_of_arrays:
if doi_url == array[0]:
refs.append(Citation(array[0], array[1], array[2], array[3], array[4]))
return refs
beispiel1 = ['doi1', 'title1', ['contributor1'], 'journal1', 'date1', ['subject1'], ['doi2'], ['doi3']] beispiel1 = ['doi1', 'title1', ['contributor1'], 'journal1', 'date1', ['subject1'], ['doi2'], ['doi3']]
...@@ -91,12 +78,13 @@ large_graph_2_h23 = ['doi_lg_2_h23', 'title_lg_2_h23', ['contributor_lg_2_h23'], ...@@ -91,12 +78,13 @@ large_graph_2_h23 = ['doi_lg_2_h23', 'title_lg_2_h23', ['contributor_lg_2_h23'],
large_graph_2_h24 = ['doi_lg_2_h24', 'title_lg_2_h24', ['contributor_lg_2_h24'], 'journal_lg_2_h24', 'date_lg_2_h24', ['subject_lg_2_h24'], ['doi_lg_2_h12','doi_lg_2_h23','doi_lg_2_d12'], ['doi_lg_2_h23']] large_graph_2_h24 = ['doi_lg_2_h24', 'title_lg_2_h24', ['contributor_lg_2_h24'], 'journal_lg_2_h24', 'date_lg_2_h24', ['subject_lg_2_h24'], ['doi_lg_2_h12','doi_lg_2_h23','doi_lg_2_d12'], ['doi_lg_2_h23']]
large_graph_2_h11 = ['doi_lg_2_h11', 'title_lg_2_h11', ['contributor_lg_2_h11'], 'journal_lg_2_h11', 'date_lg_2_h11', ['subject_lg_2_h11'], ['doi_lg_2_i','doi_cg_i'], ['doi_lg_2_h21','doi_lg_2_h22']] large_graph_2_h11 = ['doi_lg_2_h11', 'title_lg_2_h11', ['contributor_lg_2_h11'], 'journal_lg_2_h11', 'date_lg_2_h11', ['subject_lg_2_h11'], ['doi_lg_2_i','doi_cg_i'], ['doi_lg_2_h21','doi_lg_2_h22']]
large_graph_2_h12 = ['doi_lg_2_h12', 'title_lg_2_h12', ['contributor_lg_2_h12'], 'journal_lg_2_h12', 'date_lg_2_h12', ['subject_lg_2_h12'], ['doi_lg_2_i'], ['doi_lg_2_h23','doi_lg_2_h24']] large_graph_2_h12 = ['doi_lg_2_h12', 'title_lg_2_h12', ['contributor_lg_2_h12'], 'journal_lg_2_h12', 'date_lg_2_h12', ['subject_lg_2_h12'], ['doi_lg_2_i'], ['doi_lg_2_h23','doi_lg_2_h24']]
large_graph_2_i = ['doi_lg_2_i' , 'title_lg_2_i' , ['contributor_lg_2_i'] , 'journal_lg_2_i' , 'date_lg_2_i' , ['subject_lg_2_i'] , ['doi_lg_2_d11','doi_lg_2_d12'], ['doi_lg_2_h11','doi_lg_2_h12','doi_cg_i']] large_graph_2_i = ['doi_lg_2_i' , 'title_lg_2_i' , ['contributor_lg_2_i'] , 'journal_lg_2_i' , 'date_lg_2_i' , ['subject_lg_2_i'] , ['doi_lg_2_d11','doi_lg_2_d12'], ['doi_lg_2_h11','doi_lg_2_h12','doi_cg_i','doi_lg_2_h11']]
large_graph_2_d11 = ['doi_lg_2_d11', 'title_lg_2_d11', ['contributor_lg_2_d11'], 'journal_lg_2_d11', 'date_lg_2_d11', ['subject_lg_2_d11'], [], ['doi_lg_2_i']] large_graph_2_d11 = ['doi_lg_2_d11', 'title_lg_2_d11', ['contributor_lg_2_d11'], 'journal_lg_2_d11', 'date_lg_2_d11', ['subject_lg_2_d11'], ['doi_lg_2_i','doi_lg_2_d21'], ['doi_lg_2_i']]
large_graph_2_d12 = ['doi_lg_2_d12', 'title_lg_2_d12', ['contributor_lg_2_d12'], 'journal_lg_2_d12', 'date_lg_2_d12', ['subject_lg_2_d12'], ['doi_lg_2_d21','doi_lg_2_d22'], ['doi_lg_2_h24','doi_lg_2_i']] large_graph_2_d12 = ['doi_lg_2_d12', 'title_lg_2_d12', ['contributor_lg_2_d12'], 'journal_lg_2_d12', 'date_lg_2_d12', ['subject_lg_2_d12'], ['doi_lg_2_d22','doi_lg_2_d23','doi_lg_2_d24'], ['doi_lg_2_h24','doi_lg_2_i']]
large_graph_2_d21 = ['doi_lg_2_d21', 'title_lg_2_d21', ['contributor_lg_2_d21'], 'journal_lg_2_d21', 'date_lg_2_d21', ['subject_lg_2_d21'], [], ['doi_lg_2_d12']] large_graph_2_d21 = ['doi_lg_2_d21', 'title_lg_2_d21', ['contributor_lg_2_d21'], 'journal_lg_2_d21', 'date_lg_2_d21', ['subject_lg_2_d21'], [], ['doi_lg_2_d11']]
large_graph_2_d22 = ['doi_lg_2_d22', 'title_lg_2_d22', ['contributor_lg_2_d22'], 'journal_lg_2_d22', 'date_lg_2_d22', ['subject_lg_2_d22'], [], ['doi_lg_2_d12']] large_graph_2_d22 = ['doi_lg_2_d22', 'title_lg_2_d22', ['contributor_lg_2_d22'], 'journal_lg_2_d22', 'date_lg_2_d22', ['subject_lg_2_d22'], [], ['doi_lg_2_d12']]
large_graph_2_d23 = ['doi_lg_2_d23', 'title_lg_2_d23', ['contributor_lg_2_d23'], 'journal_lg_2_d23', 'date_lg_2_d23', ['subject_lg_2_d23'], [], ['doi_lg_2_d12']] large_graph_2_d23 = ['doi_lg_2_d23', 'title_lg_2_d23', ['contributor_lg_2_d23'], 'journal_lg_2_d23', 'date_lg_2_d23', ['subject_lg_2_d23'], [], ['doi_lg_2_d12']]
large_graph_2_d24 = ['doi_lg_2_d24', 'title_lg_2_d24', ['contributor_lg_2_d24'], 'journal_lg_2_d24', 'date_lg_2_d24', ['subject_lg_2_d24'], [], ['doi_lg_2_d12']]
crossed_graph_h21 = ['doi_cg_h21', 'title_cg_h21', ['contributor_cg_h21'], 'journal_cg_h21', 'date_cg_h21', ['subject_cg_h21'], ['doi_cg_h11'], []] crossed_graph_h21 = ['doi_cg_h21', 'title_cg_h21', ['contributor_cg_h21'], 'journal_cg_h21', 'date_cg_h21', ['subject_cg_h21'], ['doi_cg_h11'], []]
crossed_graph_h22 = ['doi_cg_h22', 'title_cg_h22', ['contributor_cg_h22'], 'journal_cg_h22', 'date_cg_h22', ['subject_cg_h22'], ['doi_cg_h11'], []] crossed_graph_h22 = ['doi_cg_h22', 'title_cg_h22', ['contributor_cg_h22'], 'journal_cg_h22', 'date_cg_h22', ['subject_cg_h22'], ['doi_cg_h11'], []]
......
verarbeitung/test/test_graphs_plan.pdf 0 → 100644
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verarbeitung/test_output.json
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{"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": 3}, {"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}], "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_d12", "target": "doi_lg_2_d21"}, {"source": "doi_lg_2_d12", "target": "doi_lg_2_d22"}, {"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"}]} {"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"}, {"source": "doi_lg_1_h11", "target": "doi_lg_1_h12"}]}
\ No newline at end of file \ No newline at end of file
verarbeitung/update_graph/update_graph_del.py
+ 14
− 4
Edit View file @ 20c84af6
...@@ -29,10 +29,15 @@ def delete_ref_nodes_rec(pub): ...@@ -29,10 +29,15 @@ def delete_ref_nodes_rec(pub):
''' '''
for reference in pub.references: for reference in pub.references:
for ref_pub in processed_list: for ref_pub in processed_list:
if (ref_pub.doi_url == reference): if (ref_pub.doi_url == reference.doi_url):
# to find a cyclus and avoid recursion error # to find a cyclus and avoid recursion error
if (reference not in pub.citations): not_in_citations = True
for citation in pub.citations:
if (reference.doi_url == citation.doi_url):
not_in_citations = False
break
if (not_in_citations):
delete_ref_nodes_rec(ref_pub) delete_ref_nodes_rec(ref_pub)
# removes publication from list after recursion and if it's not of group input # removes publication from list after recursion and if it's not of group input
...@@ -49,10 +54,15 @@ def delete_cit_nodes_rec(pub): ...@@ -49,10 +54,15 @@ def delete_cit_nodes_rec(pub):
''' '''
for citation in pub.citations: for citation in pub.citations:
for cit_pub in processed_list: for cit_pub in processed_list:
if (cit_pub.doi_url == citation): if (cit_pub.doi_url == citation.doi_url):
# to find a cyclus and avoid recursion error # to find a cyclus and avoid recursion error
if (citation not in pub.references): not_in_references = True
for reference in pub.references:
if (citation.doi_url == reference.doi_url):
not_in_references = False
break
if (not_in_references):
delete_cit_nodes_rec(cit_pub) delete_cit_nodes_rec(cit_pub)
# removes publication from list after recursion and if it's not of group input # removes publication from list after recursion and if it's not of group input
......
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