From 396593b91d358c5a2640db392d002b220573a7c2 Mon Sep 17 00:00:00 2001
From: Malte Schokolowski <baw8441@uni-hamburg.de>
Date: Sun, 14 Nov 2021 17:22:05 +0100
Subject: [PATCH] updated processing_test_doi_ueberarbeitet
---
.../Processing_test_doi_ueberarbeitet.py | 37 +++++++++-----
.../__pycache__/input_fj.cpython-38.pyc | Bin 0 -> 4341 bytes
.../__pycache__/json_demo.cpython-38.pyc | Bin 0 -> 750 bytes
{input => verarbeitung}/input_fj.py | 0
verarbeitung/json_demo.py | 46 ++++++++++--------
verarbeitung/json_text.txt | 1 +
verarbeitung/json_text_json.txt | 0
7 files changed, 52 insertions(+), 32 deletions(-)
create mode 100644 verarbeitung/__pycache__/input_fj.cpython-38.pyc
create mode 100644 verarbeitung/__pycache__/json_demo.cpython-38.pyc
rename {input => verarbeitung}/input_fj.py (100%)
mode change 100755 => 100644
create mode 100644 verarbeitung/json_text.txt
create mode 100644 verarbeitung/json_text_json.txt
diff --git a/verarbeitung/Processing_test_doi_ueberarbeitet.py b/verarbeitung/Processing_test_doi_ueberarbeitet.py
index ac6ce63..bfa533a 100644
--- a/verarbeitung/Processing_test_doi_ueberarbeitet.py
+++ b/verarbeitung/Processing_test_doi_ueberarbeitet.py
@@ -10,12 +10,13 @@ import requests as req
import sys
from pathlib import Path
from input_fj import input
+from json_demo import output_to_json
-def process_main(array, depth):
+def process_main(doi_input_array, depth):
# ERROR-Handling doi_array = NULL
- if (len(array) == 0):
+ if (len(doi_input_array) == 0):
print("Error, no input data")
# ERROR- wenn für die Tiefe eine negative Zahl eingegeben wird
@@ -30,14 +31,21 @@ def process_main(array, depth):
edges = []
# Jede Publikation aus dem Input-Array wird in den Knoten-Array(nodes) eingefügt.
- for pub in array:
- if (pub not in nodes):
+ for pub_doi in doi_input_array:
+ pub = input(pub_doi)
+ not_in_nodes = True
+ for node in nodes:
+ if (pub.doi_url == node.doi_url):
+ not_in_nodes = False
+ break
+ if (not_in_nodes):
nodes.append(pub)
else:
- array.remove(pub)
+ doi_input_array.remove(pub_doi)
- process_rec_depth(array, 0, depth)
+ process_rec_depth(doi_input_array, 0, depth)
+ output_to_json(nodes,edges)
return(nodes,edges)
@@ -56,9 +64,14 @@ def process_rec_depth(array, depth, depth_max):
# Wenn die citation noch nicht im Knoten-Array(nodes) existiert UND die maximale Tiefe
# noch nicht erreicht wurde, wird diese als Knoten im Knoten-Array gespeichert. Zusätzlich
# wird die Verbindung zur Publikation als Tupel im Kanten-Array(edges) gespeichert.
- if (citation.doi_url not in nodes):
+ not_in_nodes = True
+ for node in nodes:
+ if (citation.doi_url == node.doi_url):
+ not_in_nodes = False
+ break
+ if (not_in_nodes):
if (depth <= depth_max):
- nodes.append(citation.doi_url)
+ nodes.append(citation)
edges.append([pub.doi_url,citation.doi_url])
# Wenn die citaion bereits im Knoten-Array existiert, wird nur die Verbindung zur Publikation
@@ -85,8 +98,8 @@ def process_rec_depth(array, depth, depth_max):
# Programmtest, weil noch keine Verbindung zum Input besteht.
arr = []
arr.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
-#arr.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
-#arr.append('https://doi.org/10.1021/acs.jmedchem.0c01332')
+arr.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
+arr.append('https://doi.org/10.1021/acs.jmedchem.0c01332')
#arr.append('https://doi.org/10.1021/acs.jcim.0c00741')
#arr.append('https://doi.org/10.1021/ci700007b')
@@ -97,8 +110,8 @@ arr.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
nodes,edges = process_main(arr,1)
print("Knoten:\n")
-for vortex in nodes:
- print(vortex, "\n")
+for node in nodes:
+ print(node.title, "\n")
print("\nKanten:\n")
for edge in edges:
print(edge,"\n")
\ No newline at end of file
diff --git a/verarbeitung/__pycache__/input_fj.cpython-38.pyc b/verarbeitung/__pycache__/input_fj.cpython-38.pyc
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diff --git a/input/input_fj.py b/verarbeitung/input_fj.py
old mode 100755
new mode 100644
similarity index 100%
rename from input/input_fj.py
rename to verarbeitung/input_fj.py
diff --git a/verarbeitung/json_demo.py b/verarbeitung/json_demo.py
index e6cd618..77ce148 100644
--- a/verarbeitung/json_demo.py
+++ b/verarbeitung/json_demo.py
@@ -1,27 +1,33 @@
#!/usr/bin/env python3
import json
+from input_fj import input
def output_to_json(V,E):
- list_of_node_dicts = list()
- list_of_edge_dicts = list()
- dict_of_all = dict()
- for node in V:
- new_dict = dict()
- new_dict["doi"] = node
- list_of_node_dicts.append(new_dict)
- for edge in E:
- new_dict_2 = dict()
- new_dict_2["source"] = edge[0]
- new_dict_2["target"] = edge[1]
- list_of_edge_dicts.append(new_dict_2)
- dict_of_all["nodes"] = list_of_node_dicts
- dict_of_all["links"] = list_of_edge_dicts
- return(dict_of_all)
- with open('json_text_json','w') as outfile:
- json_dump(dict_of_all, outfile)
+ list_of_node_dicts = list()
+ list_of_edge_dicts = list()
+ dict_of_all = dict()
+ for node in V:
+ new_dict = dict()
+ new_dict["name"] = node.title
+ new_dict["author"] = node.contributors
+ new_dict["year"] = node.publication_date
+ new_dict["doi"] = node.doi_url
+
+
+ list_of_node_dicts.append(new_dict)
+ for edge in E:
+ new_dict_2 = dict()
+ new_dict_2["source"] = edge[0]
+ new_dict_2["target"] = edge[1]
+ list_of_edge_dicts.append(new_dict_2)
+ dict_of_all["nodes"] = list_of_node_dicts
+ dict_of_all["links"] = list_of_edge_dicts
+ #return(dict_of_all)
+ with open('json_text.txt','w') as outfile:
+ json.dump(dict_of_all, outfile)
-knoten = ["doi1", "doi2", "doi3"]
-kanten = [[1,2],[3,4],[5,6]]
-output_to_json(knoten,kanten)
+#knoten = ["doi1", "doi2", "doi3"]
+#kanten = [[1,2],[3,4],[5,6]]
+#output_to_json(knoten,kanten)
diff --git a/verarbeitung/json_text.txt b/verarbeitung/json_text.txt
new file mode 100644
index 0000000..b5e7fa9
--- /dev/null
+++ b/verarbeitung/json_text.txt
@@ -0,0 +1 @@
+{"nodes": [{"name": "Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis", "doi": "https://doi.org/10.1021/acs.jcim.9b00249"}, {"name": "Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems ", "doi": "https://doi.org/10.1021/acs.chemrev.1c00107"}, {"name": "Disconnected Maximum Common Substructures under Constraints ", "doi": "https://doi.org/10.1021/acs.jcim.0c00741"}, {"name": "Evolution of Novartis\u2019 Small Molecule Screening Deck Design ", "doi": "https://doi.org/10.1021/acs.jmedchem.0c01332"}, {"name": "Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms ", "doi": "https://doi.org/10.1021/acs.jcim.9b00250"}, {"name": "Machine learning accelerates quantum mechanics predictions of molecular crystals ", "doi": "https://doi.org/10.1016/j.physrep.2021.08.002"}, {"name": "The Growing Importance of Chirality in 3D Chemical Space Exploration and Modern Drug Discovery Approaches for Hit-ID ", "doi": "https://doi.org/10.1021/acsmedchemlett.1c00251"}, {"name": "Target-Based Evaluation of \u201cDrug-Like\u201d Properties and Ligand Efficiencies ", "doi": "https://doi.org/10.1021/acs.jmedchem.1c00416"}, {"name": "BonMOLi\u00e8re: Small-Sized Libraries of Readily Purchasable Compounds, Optimized to Produce Genuine Hits in Biological Screens across the Protein Space ", "doi": "https://doi.org/10.3390/ijms22157773"}, {"name": "Accelerating high-throughput virtual screening through molecular pool-based active learning ", "doi": "https://doi.org/10.1039/D0SC06805E"}, {"name": "Compound Screening ", "doi": "https://doi.org/10.1016/B978-0-12-820472-6.00078-5"}], "links": [{"source": "https://doi.org/10.1021/acs.jcim.9b00249", "target": "https://doi.org/10.1021/acs.chemrev.1c00107"}, {"source": "https://doi.org/10.1021/acs.jcim.9b00249", "target": "https://doi.org/10.1021/acs.jcim.0c00741"}, {"source": "https://doi.org/10.1021/acs.jcim.9b00249", "target": "https://doi.org/10.1021/acs.jmedchem.0c01332"}, {"source": "https://doi.org/10.1021/acs.jcim.9b00249", "target": "https://doi.org/10.1021/acs.jcim.9b00250"}, {"source": "https://doi.org/10.1021/acs.jcim.9b00249", "target": "https://doi.org/10.1016/j.physrep.2021.08.002"}, {"source": "https://doi.org/10.1021/acs.jmedchem.0c01332", "target": "https://doi.org/10.1021/acsmedchemlett.1c00251"}, {"source": "https://doi.org/10.1021/acs.jmedchem.0c01332", "target": "https://doi.org/10.1021/acs.jmedchem.1c00416"}, {"source": "https://doi.org/10.1021/acs.jmedchem.0c01332", "target": "https://doi.org/10.3390/ijms22157773"}, {"source": "https://doi.org/10.1021/acs.jmedchem.0c01332", "target": "https://doi.org/10.1039/D0SC06805E"}, {"source": "https://doi.org/10.1021/acs.jmedchem.0c01332", "target": "https://doi.org/10.1016/B978-0-12-820472-6.00078-5"}]}
\ No newline at end of file
diff --git a/verarbeitung/json_text_json.txt b/verarbeitung/json_text_json.txt
new file mode 100644
index 0000000..e69de29
--
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