diff --git a/.DS_Store b/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/.DS_Store differ
diff --git a/.citation_parser_ui.py.swp b/.citation_parser_ui.py.swp
deleted file mode 100644
index 38c0d61d4724d853b03e358ed4916b537560e72f..0000000000000000000000000000000000000000
Binary files a/.citation_parser_ui.py.swp and /dev/null differ
diff --git a/assets/json_text.json b/assets/json_text.json
index a69c8ec414cf10124d4279536aa32d829bb13b5a..85db8c706c7ff086b76a298bbbcdf6d2ae6e5801 100644
--- a/assets/json_text.json
+++ b/assets/json_text.json
@@ -1,3 +1,4 @@
+<<<<<<< HEAD
{
"nodes": [
{
@@ -111,4 +112,7 @@
"target": "https://doi.org/10.1021/acs.jcim.6b00709"
}
]
-}
\ No newline at end of file
+}
+=======
+{"nodes": [], "links": []}
+>>>>>>> upstream/main
diff --git a/citation_parser_ui.py b/citation_parser_main.py
similarity index 73%
rename from citation_parser_ui.py
rename to citation_parser_main.py
index 7431a912ca0f5a6d4bd31a269914aa034e083348..c2b119dce5075fb6f1e11226dbf866abccd1d4fe 100644
--- a/citation_parser_ui.py
+++ b/citation_parser_main.py
@@ -10,8 +10,13 @@ from dash.exceptions import PreventUpdate
from input.interface import InputInterface
import input.publication
from verarbeitung.process_main import Processing
+from dash.dependencies import Input, Output, State #Loading Bar
+import plotly.express as px
+import dash_bootstrap_components as dbc # pip install dash-bootstrap-components for Loading Bar
-app = dash.Dash(__name__)
+
+
+app = dash.Dash(__name__, external_stylesheets=[dbc.themes.SPACELAB]) #SPACELAB https://bootswatch.com/default/ for more themes)
# List of options when inputting data and generating the graph
additional_options = ['Update Automatically','Smart Input']
@@ -24,25 +29,47 @@ f.close()
app.layout = html.Div([
# Layer 0: For the Header and Help Function(s)
- html.Div([
- html.Button(id='show-info',children='Show Info',n_clicks=0),
- html.Div(id='info-box')
- ]),
- # Layer 1: For all mandatory Inputs
+ dbc.Button(
+ 'show Info',
+ id='collapse-button',
+ className="me-1",
+ color="primary",
+ n_clicks=0,
+ ),
+ dbc.Collapse(
+ dbc.Card(dbc.CardBody(html.Div(boxcontent, style={'whiteSpace': 'pre-line'}))),
+ id='collapse',
+ is_open=False,
+ ),
+
+ # Layer 1: For the string input
html.Div([
"Input: ",
# A simple box for inputting a string.
# Value is transmitted upon pressing return or clicking out of the box.
- dcc.Input(id='input-string', value='', type='text',debounce=True),
+ dcc.Input(id='string-input', value='', type='text',debounce=True,
+ style={ "width": "400px"},
+ ),
+
+ ]),
+ # Layer 2: For file input and recursion depths
+ html.Div([
+ "Cited-by Depth: ",
# Forward recursion. Values between 1 and 10 can be entered.
- dcc.Input(id='forward-depth',value='1',type='number',min='1',max='10'),
+ dcc.Input(id='forward-depth',value='1',type='number',min='0',max='5',
+ style={ "width": "50px"},
+ ),
+ "References Depth: ",
# Backward recursion. Values between 1 and 10 can be entered.
- dcc.Input(id='backward-depth',value='1',type='number',min='1',max='10'),
+ dcc.Input(id='backward-depth',value='1',type='number',min='0',max='5',
+ style={"width": "50px"},
+ ),
# Upload box. Can be used via drag-and-drop or byclicking on it to open a file viewer.
dcc.Upload(
- id="upload-data",
+ id="file-input",
children=html.Div(
- ["Drag and drop or click to select a file to upload."]),
+ #Drag and drop or click to select a file to upload
+ ["Drag and drop"]),
style={
"width": "30%",
"height": "60px",
@@ -54,7 +81,8 @@ app.layout = html.Div([
"margin": "10px",
})
]),
- # Layer 2: For the checklist, Remove-/Start-Buttons and input-error-message
+
+ # Layer 3: For the checklist, Remove-/Start-Buttons and error message
html.Div([
# All input DOIs are collected in this checklist.
# It is initialized to avoid error messages.
@@ -63,39 +91,39 @@ app.layout = html.Div([
# Displays error message if 'Smart Input' is active.
html.Div(id='input-err',style={'color':'red'}),
# Clears the entire list.
- html.Button(id='clear-all-button',children='Clear All'),
+ dbc.Button(id='clear-all-button',children='Clear All', color="primary", className="me-1"),
# Clear all selected elements.
- html.Button(id='clear-selected-button',children='Clear Selected'),
+ dbc.Button(id='clear-selected-button',children='Clear Selected', color="primary", className="me-1"),
# Starts the process that generates a graph.
- html.Button(id='start-button',children='Generate Graph')
+ dbc.Button(id='start-button',children='Generate Graph', color="primary", className="me-1")
]),
- # Layer 3: For additional Options (e.g. Topological Sort)
+ # Layer 4: For additional Options
html.Div([
html.H4('Additional Options'),
# A checklist of all additional options that are listed above.
dcc.Checklist(id='additional-options',
options=[{'label':k,'value':k} for k in additional_options],
value=[])
- ]),
- # Layer 4: For the Graph
- html.Div(
- [html.Iframe(
+ ]),
+ # Layer 5: For the Graph and corresponding error messages
+ html.Div([
+ html.Div(id='generate-graph-error',style={'color':'red'}),
+ html.Iframe(
src="assets/index.html",
style={"height": "600px", "width": "100%"},
),
- html.Div(id='test-output')
])
])
@app.callback(
Output('input-checklist','options'),
Output('input-checklist','value'),
- Output('input-string','value'),
+ Output('string-input','value'),
Output('input-err','children'),
- Input('input-string','value'),
+ Input('string-input','value'),
Input('clear-all-button','n_clicks'),
Input('clear-selected-button','n_clicks'),
- Input('upload-data','contents'),
+ Input('file-input','contents'),
State('input-checklist','options'),
State('input-checklist','value'),
State('additional-options','value')
@@ -105,7 +133,7 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
'''
Most important callback function. Updates the checklist that holds all inputs.
State of the checklist as input is needed so that previews entries are readded.
- input-string is required as Output to clear the input box after each input.
+ string-input is required as Output to clear the input box after each input.
Different actions are performed depending on which input triggered the callback.
The value-attribute of input-checklist must be updates so that the values
of deleted elements no longer appear in the list of selected elements.
@@ -140,7 +168,7 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
return all_inputs,list(),'',''
# when a new element is added via dcc.Input
- if 'input-string' in changed_id:
+ if 'string-input' in changed_id:
# Creates a list of previously added inputs to make sure nothing is added twice
currValues = [x['value'] for x in all_inputs]
if input_value not in currValues:
@@ -158,7 +186,10 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
# Creates a more readable string to display in the checklist
rep_str = pub.contributors[0] + ',' + pub.journal + \
',' + pub.publication_date
- all_inputs.append({'label':rep_str, 'value':input_value})
+ # Makes sure not to add the same article with different links
+ currLabels = [x['label'] for x in all_inputs]
+ if rep_str not in currLabels:
+ all_inputs.append({'label':rep_str, 'value':input_value})
# if 'Smart Input' is not selected, the input value is added as is,
# without checking for validity.
@@ -167,7 +198,7 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
return all_inputs,selected_inputs,'',''
# when a txt-file is uploaded
- if 'upload-data.contents' in changed_id:
+ if 'file-input.contents' in changed_id:
if filecontents:
# Skips the info portion that is added when a file is uploaded
found = base64.b64decode(re.search(',(.+?)$', filecontents).group(1))
@@ -187,7 +218,9 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
return all_inputs,selected_inputs,'','{}'.format(err)
rep_str = pub.contributors[0] + ',' + pub.journal + \
',' + pub.publication_date
- all_inputs.append({'label':rep_str, 'value':input_value})
+ currLabels = [x['label'] for x in all_inputs]
+ if rep_str not in currLabels:
+ all_inputs.append({'label':rep_str, 'value':input_value})
else:
all_inputs.append({'label':input_value,'value':input_value})
return all_inputs,selected_inputs,'',''
@@ -197,33 +230,33 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
if input_value == '':
return list(),list(),'',''
+
@app.callback(
- Output('info-box','children'),
- Input('show-info','n_clicks')
+ Output('collapse', 'is_open'),
+ [Input('collapse-button', 'n_clicks')],
+ [State('collapse', 'is_open')],
)
-def show_hide_info_box(n_clicks):
+def toggle_collapse(n, is_open):
'''
- This callback shows and hides the (first) info-box by, checking how often
+ This callback shows and hides the (first) info-box by, checking how# often
the button has been pressed. The text was loaded at the top.
:param n_clicks: number of times show-info has been clicked.
'type n_clicks: int
'''
- if n_clicks % 2 == 0:
- return ''
- else:
- return html.Div(boxcontent, style={'whiteSpace': 'pre-line'})
+ if n:
+ return not is_open
+ return is_open
+
@app.callback(
- Output('test-output','children'),
+ Output('generate-graph-error','children'),
Input('start-button','n_clicks'),
Input('input-checklist','options'),
- Input('input-checklist','value'),
Input('forward-depth','value'),
Input('backward-depth','value'),
State('additional-options','value')
)
-def generate_output(n_clicks,all_inputs,selected_inputs,
- forward_depth,backward_depth,additional_options):
+def generate_output(n_clicks,all_inputs,forward_depth,backward_depth,additional_options):
'''
Basic structure for a callback that generates an output. This is only a
proof of concept and has noting to do with the intended output yet.
@@ -233,8 +266,6 @@ def generate_output(n_clicks,all_inputs,selected_inputs,
:param all_inputs: all labels and values from the checklist,
regardless if they have been checked or not
:type all_inputs: list of dictionaries with 2 entries each
- :param selected_inputs: values of all checked elements
- :type selected_inputs: list of strings
:param forward_depth: forward recursion depth
:type forward_depth: unsigned int
:param backward_depth: backward recursion depth
@@ -248,7 +279,15 @@ def generate_output(n_clicks,all_inputs,selected_inputs,
elif 'Update Automatically' in additional_options \
or 'start-button' in changed_id:
input_links = [x['value'] for x in all_inputs]
- Processing(input_links,int(forward_depth),int(backward_depth),'assets/json_text.json')
+ errors = Processing(input_links,int(forward_depth),int(backward_depth),'assets/json_text.json')
+ if errors:
+ message = ['The following inputs are invalid and were not used:']
+ for error in errors:
+ message.append(html.Br())
+ message.append(error)
+ message = html.P(message)
+ #message = [html.P(error) for error in errors]
+ return message
if __name__ == '__main__':
app.run_server(debug=False)
diff --git a/input/get/__pycache__/__init__.cpython-38.pyc b/input/get/__pycache__/__init__.cpython-38.pyc
index f12fb9c33e874aa1c55d94725f867ac6503d407e..52f5d64aa3f72e25accf523fb850635617afbf5e 100644
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diff --git a/input/get/__pycache__/acs.cpython-38.pyc b/input/get/__pycache__/acs.cpython-38.pyc
index 121d1856184f02775d5bb84d081dcd91a648ea67..78c1fb0c8b885e90285224e745b09af56faf9b01 100644
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diff --git a/input/get/__pycache__/journal_fetcher.cpython-38.pyc b/input/get/__pycache__/journal_fetcher.cpython-38.pyc
index 72a774c45762b3d4cb37a7089f4d8275dab0e533..af9bd12b47a0bae4c1683adf78d92884b7e51193 100644
Binary files a/input/get/__pycache__/journal_fetcher.cpython-38.pyc and b/input/get/__pycache__/journal_fetcher.cpython-38.pyc differ
diff --git a/input/get/__pycache__/nature.cpython-38.pyc b/input/get/__pycache__/nature.cpython-38.pyc
index 3afb8454a05c8afe9b1f2aba3f534d66cbd8ae3a..ca8c9862b7234c55e49b676136ab64a62f91e58b 100644
Binary files a/input/get/__pycache__/nature.cpython-38.pyc and b/input/get/__pycache__/nature.cpython-38.pyc differ
diff --git a/input_old/README.md b/input_old/README.md
deleted file mode 100644
index 76bd11d5d70daac13e190f4d52269eb381413c69..0000000000000000000000000000000000000000
--- a/input_old/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-# Projekt CiS-Projekt 2021/22
-Input-Skripts
-
diff --git a/input_old/__pycache__/input_fj.cpython-39.pyc b/input_old/__pycache__/input_fj.cpython-39.pyc
deleted file mode 100644
index a3e6099f4ab4c56400b2698c812d4b5fc9a9a7aa..0000000000000000000000000000000000000000
Binary files a/input_old/__pycache__/input_fj.cpython-39.pyc and /dev/null differ
diff --git a/input_old/example_urls b/input_old/example_urls
deleted file mode 100644
index 96ac680c65edddcb495312000157edea1ab94884..0000000000000000000000000000000000000000
--- a/input_old/example_urls
+++ /dev/null
@@ -1,2 +0,0 @@
-https://pubs.acs.org/doi/10.1021/acs.jcim.5b00332
-https://pubs.acs.org/doi/10.1021/acs.jcim.6b00709
diff --git a/input_old/input_fj.py b/input_old/input_fj.py
deleted file mode 100644
index ecc8e68fc5a84a446ae3f09dcb5ed56e8d262766..0000000000000000000000000000000000000000
--- a/input_old/input_fj.py
+++ /dev/null
@@ -1,154 +0,0 @@
-#!/usr/bin/env python3
-"""
-Functions for information retrieval of articles from the ACS journal JCIM
-
-"""
-
-__author__ = "Florian Jochens"
-__email__ = "fj@andaco.de"
-__status__ = "Production"
-#__copyright__ = ""
-#__credits__ = ["", "", "", ""]
-#__license__ = ""
-#__version__ = ""
-#__maintainer__ = ""
-
-from bs4 import BeautifulSoup as bs
-import requests as req
-import sys
-from pathlib import Path
-
-class Publication:
- #_registry = []
- _citations = []
- _references = []
-
- def __init__(self, title, publication_date, contributors, doi_url,
- subjects = None, num_citations = None):
- #self._registry.append(self)
- self.title = title
- self.publication_date = publication_date
- self.contributors = contributors
- self.doi_url = doi_url
- self.subjects = subjects
- self.num_citations = num_citations
- #self._citations = []
- #self._references = []
-
-class Citation:
- def __init__(self, title, journal, contributors, doi_url):
- self.title = title
- self.journal = journal
- self.contributors = contributors
- self.doi_url = doi_url
-
-class References:
- def __init__(self, title, journal, contributors, doi_url):
- self.title = title
- self.journal = journal
- self.contributors = contributors
- self.doi_url = doi_url
-
-def get_article_info(soup):
- header = soup.find('div', class_ = 'article_header-left pull-left')
- article_title = header.find('span', class_ = 'hlFld-Title').text
- publication_date = header.find('span', class_ = 'pub-date-value').text
- for link in header.find('div', class_ = 'article_header-doiurl'):
- doi_url = link.get('href')
- subs = header.find('div', class_ = 'article_header-taxonomy')
- subjects = []
- for sub in subs.find_all('a'):
- subjects.append(sub.get('title'))
- cons = header.find('ul', class_ = 'loa')
- contributors = []
- for con in cons.find_all('span', class_ = 'hlFld-ContribAuthor'):
- contributors.append(con.text)
- numc = header.find('div', class_ = 'articleMetrics_count')
- if not numc.a:
- num_citations = 0
- else:
- num_citations = numc.a.text
-
- pub = Publication(article_title, publication_date, contributors, doi_url,
- subjects, num_citations)
- return pub
-
-def get_download_url():
- export = soup.find('div', class_ = 'cit-download-dropdown_content')
- url = 'https://pubs.acs.org'
- for link in export.find_all('a'):
- if link.get('title') == 'Citation and references':
- url += link.get('href')
- print(url)
- return url
-
-def download(url): # Download citation and references file
- if url.find('='):
- filename = url.rsplit('=', 1)[1]
- path = Path(('./files/' + filename))
- if path.is_file():
- print("File already exists")
- else:
- print("File does not exist")
-
-def get_citation_info(pub, num_citations, soup):
- pub._citations = []
- details = soup.find('ol', class_ = 'cited-content_cbyCitation')
- titles = []
- for title in details.find_all('span',
- class_ = 'cited-content_cbyCitation_article-title'):
- titles.append(title.text.replace('.', ''))
- journal_names = []
- for name in details.find_all('span',
- class_ = 'cited-content_cbyCitation_journal-name'):
- journal_names.append(name.text)
- doi_urls = []
- for url in details.find_all('a'):
- doi_urls.append(url.get('href'))
- contributors = []
- for contrib in details.find_all('span',
- class_ = 'cited-content_cbyCitation_article-contributors'):
- contributors.append(contrib.text)
- for i in range(0, int(num_citations)):
- pub._citations.append(Citation(titles[i], journal_names[i],
- contributors[i], doi_urls[i]))
-def print_pub_info(pub):
- print(f'''Article title: {pub.title}
-Publication date: {pub.publication_date}
-DOI-URL: {pub.doi_url}
-
-Subjects:''')
- print(*(pub.subjects), sep = ", ")
- print('\nContributors:')
- print(*(pub.contributors), sep = ", ")
-
- if int(pub.num_citations) > 0:
- if int(pub.num_citations) == 1:
- print(f'\nThis publication is cited by the following publication:\n')
- else:
- print(f'\nThis publication is cited by the following {pub.num_citations} publications:\n')
- for citation in pub._citations:
- print(f'''
- Title: {citation.title}
- Journal: {citation.journal}
- Contributors: {citation.contributors}
- DOI-URL: {citation.doi_url}
- ''')
- else:
- print('\nThis publication is not cited by any other publication.')
-
-def input(url):
- html_text = req.get(url).text
- soup = bs(html_text, 'html.parser')
-
- pub = get_article_info(soup)
- if int(pub.num_citations) > 0:
- get_citation_info(pub, int(pub.num_citations), soup)
- return pub
-
-#if len(sys.argv) != 2:
-# sys.stderr.write('Usage: {} <url>\n'.format(sys.argv[0]))
-# exit(1)
-#url = sys.argv[1]
-#pub = input(url)
-#print_pub_info(pub)
diff --git a/input_old/pub.py b/input_old/pub.py
deleted file mode 100644
index 13b90e804cd485813b731385b319b3077a017dd2..0000000000000000000000000000000000000000
--- a/input_old/pub.py
+++ /dev/null
@@ -1,32 +0,0 @@
-class Publication:
- #_registry = []
- #_citations = []
- #_references = []
-
- def __init__(self, title, publication_date, contributors, doi_url,
- subjects, num_citations):
- #self._registry.append(self)
- self.title = title
- self.publication_date = publication_date
- self.contributors = contributors
- self.doi_url = doi_url
- self.subjects = subjects
- self.num_citations = num_citations
- self.num_references = num_references
- self._citations = []
- self._references = []
-
-class Citation:
- def __init__(self, title, journal, contributors, doi_url):
- self.title = title
- self.journal = journal
- self.contributors = contributors
- self.doi_url = doi_url
-
-class References:
- def __init__(self, title, journal, contributors, doi_url):
- self.title = title
- self.journal = journal
- self.contributors = contributors
- self.doi_url = doi_url
-
diff --git a/input_old/test.py b/input_old/test.py
deleted file mode 100755
index dc623ca182691e9e06a6713a4d3d5dcf0bbf23c2..0000000000000000000000000000000000000000
--- a/input_old/test.py
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env python3
-
-from input_fj import input, print_pub_info
-import sys
-
-if len(sys.argv) != 3:
- sys.stderr.write('Usage: {} <url> <url>\n'.format(sys.argv[0]))
- exit(1)
-url = sys.argv[1]
-url2 = sys.argv[2]
-pub = input(url)
-print_pub_info(pub)
-pub2 = input(url2)
-print_pub_info(pub2)
-
diff --git a/input_old/x b/input_old/x
deleted file mode 100644
index c8ade9d56a520a3ac57e5eadce8b81bb3e63c0dd..0000000000000000000000000000000000000000
--- a/input_old/x
+++ /dev/null
@@ -1,234 +0,0 @@
-Article title: Feasibility of Active Machine Learning for Multiclass Compound Classification
-Publication date: January 7, 2016
-DOI-URL: https://doi.org/10.1021/acs.jcim.5b00332
-
-Subjects:
-Algorithms, Molecules, Drug discovery, Screening assays, Receptors
-
-Contributors:
-Tobias Lang, Florian Flachsenberg, Ulrike von Luxburg, Matthias Rarey
-
-This publication is cited by the following 30 publications:
-
-
- Title: Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery
- Journal: Chemical Reviews
- Contributors: Xin Yang, Yifei Wang, Ryan Byrne, Gisbert Schneider, Shengyong Yang.
- DOI-URL: https://doi.org/10.1021/acs.chemrev.8b00728
-
-
- Title: De Novo Molecule Design by Translating from Reduced Graphs to SMILES
- Journal: Journal of Chemical Information and Modeling
- Contributors: Peter Pogány, Navot Arad, Sam Genway, Stephen D. Pickett.
- DOI-URL: https://doi.org/10.1021/acs.jcim.8b00626
-
-
- Title: Designing Algorithms To Aid Discovery by Chemical Robots
- Journal: ACS Central Science
- Contributors: Alon B. Henson, Piotr S. Gromski, Leroy Cronin.
- DOI-URL: https://doi.org/10.1021/acscentsci.8b00176
-
-
- Title: Modeling Kinase Inhibition Using Highly Confident Data Sets
- Journal: Journal of Chemical Information and Modeling
- Contributors: Sorin Avram, Alina Bora, Liliana Halip, Ramona Curpăn.
- DOI-URL: https://doi.org/10.1021/acs.jcim.7b00729
-
-
- Title: Predictive Models for Fast and Effective Profiling of Kinase Inhibitors
- Journal: Journal of Chemical Information and Modeling
- Contributors: Alina Bora, Sorin Avram, Ionel Ciucanu, Marius Raica, and Stefana Avram .
- DOI-URL: https://doi.org/10.1021/acs.jcim.5b00646
-
-
- Title: Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery
- Journal: Bioinformatics
- Contributors: Huangqingbo Sun, Robert F Murphy, .
- DOI-URL: https://doi.org/10.1093/bioinformatics/btab322
-
-
- Title: An Artificial Intelligence Approach Based on Hybrid CNN-XGB Model to Achieve High Prediction Accuracy through Feature Extraction, Classification and Regression for Enhancing Drug Discovery in Biomedicine
- Journal: International Journal of Biology and Biomedical Engineering
- Contributors: Mukesh Madanan, Biju T. Sayed, Nurul Akhmal Mohd Zulkefli, Nitha C. Velayudhan.
- DOI-URL: https://doi.org/10.46300/91011.2021.15.22
-
-
- Title: Artificial Intelligence in Medicinal Chemistry
- Journal:
- Contributors: Edward Griffen, Alexander Dossetter, Andrew Leach, Shane Montague.
- DOI-URL: https://doi.org/10.1002/0471266949.bmc267
-
-
- Title: Practical Chemogenomic Modeling and Molecule Discovery Strategies Unveiled by Active Learning
- Journal:
- Contributors: J.B. Brown.
- DOI-URL: https://doi.org/10.1016/B978-0-12-801238-3.11533-8
-
-
- Title: Machine learning phases and criticalities without using real data for training
- Journal: Physical Review B
- Contributors: D.-R. Tan, F.-J. Jiang.
- DOI-URL: https://doi.org/10.1103/PhysRevB.102.224434
-
-
- Title: Active learning effectively identifies a minimal set of maximally informative and asymptotically performant cytotoxic structure–activity patterns in NCI-60 cell lines
- Journal: RSC Medicinal Chemistry
- Contributors: Takumi Nakano, Shunichi Takeda, J.B. Brown.
- DOI-URL: https://doi.org/10.1039/D0MD00110D
-
-
- Title: Active learning efficiently converges on rational limits of toxicity prediction and identifies patterns for molecule design
- Journal: Computational Toxicology
- Contributors: Ahsan Habib Polash, Takumi Nakano, Christin Rakers, Shunichi Takeda, J.B. Brown.
- DOI-URL: https://doi.org/10.1016/j.comtox.2020.100129
-
-
- Title: Practical considerations for active machine learning in drug discovery
- Journal: Drug Discovery Today: Technologies
- Contributors: Daniel Reker.
- DOI-URL: https://doi.org/10.1016/j.ddtec.2020.06.001
-
-
- Title: Designing compact training sets for data-driven molecular property prediction through optimal exploitation and exploration
- Journal: Molecular Systems Design & Engineering
- Contributors: Bowen Li, Srinivas Rangarajan.
- DOI-URL: https://doi.org/10.1039/C9ME00078J
-
-
- Title: Applicability Domain of Active Learning in Chemical Probe Identification: Convergence in Learning from Non-Specific Compounds and Decision Rule Clarification
- Journal: Molecules
- Contributors: Ahsan Habib Polash, Takumi Nakano, Shunichi Takeda, J.B. Brown.
- DOI-URL: https://doi.org/10.3390/molecules24152716
-
-
- Title: Capturing and applying knowledge to guide compound optimisation
- Journal: Drug Discovery Today
- Contributors: Matthew Segall, Tamsin Mansley, Peter Hunt, Edmund Champness.
- DOI-URL: https://doi.org/10.1016/j.drudis.2019.02.004
-
-
- Title: A novel graph kernel on chemical compound classification
- Journal: Journal of Bioinformatics and Computational Biology
- Contributors: Qiangrong Jiang, Jiajia Ma.
- DOI-URL: https://doi.org/10.1142/S0219720018500269
-
-
- Title: Accelerating Drug Discovery Using Convolution Neural Network Based Active Learning
- Journal:
- Contributors: Pengfei Liu, Kwong-Sak Leung.
- DOI-URL: https://doi.org/10.1109/TENCON.2018.8650298
-
-
- Title: An Adaptive Lightweight Security Framework Suited for IoT
- Journal:
- Contributors: Menachem Domb.
- DOI-URL: https://doi.org/10.5772/intechopen.73712
-
-
- Title: Adaptive mining and model building of medicinal chemistry data with a multi-metric perspective
- Journal: Future Medicinal Chemistry
- Contributors: JB Brown.
- DOI-URL: https://doi.org/10.4155/fmc-2018-0188
-
-
- Title: Chemogenomic Active Learning's Domain of Applicability on Small, Sparse qHTS Matrices: A Study Using Cytochrome P450 and Nuclear Hormone Receptor Families
- Journal: ChemMedChem
- Contributors: Christin Rakers, Rifat Ara Najnin, Ahsan Habib Polash, Shunichi Takeda, J.B. Brown.
- DOI-URL: https://doi.org/10.1002/cmdc.201700677
-
-
- Title: Automating drug discovery
- Journal: Nature Reviews Drug Discovery
- Contributors: Gisbert Schneider.
- DOI-URL: https://doi.org/10.1038/nrd.2017.232
-
-
- Title: Classifiers and their Metrics Quantified
- Journal: Molecular Informatics
- Contributors: J. B. Brown.
- DOI-URL: https://doi.org/10.1002/minf.201700127
-
-
- Title: Active Search for Computer-aided Drug Design
- Journal: Molecular Informatics
- Contributors: Dino Oglic, Steven A. Oatley, Simon J. F. Macdonald, Thomas Mcinally, Roman Garnett, Jonathan D. Hirst, Thomas Gärtner.
- DOI-URL: https://doi.org/10.1002/minf.201700130
-
-
- Title: Selection of Informative Examples in Chemogenomic Datasets
- Journal:
- Contributors: Daniel Reker, J. B. Brown.
- DOI-URL: https://doi.org/10.1007/978-1-4939-8639-2_13
-
-
- Title: The value of prior knowledge in machine learning of complex network systems
- Journal: Bioinformatics
- Contributors: Dana Ferranti, David Krane, David Craft, .
- DOI-URL: https://doi.org/10.1093/bioinformatics/btx438
-
-
- Title: Lightweight adaptive Random-Forest for IoT rule generation and execution
- Journal: Journal of Information Security and Applications
- Contributors: Menachem Domb, Elisheva Bonchek-Dokow, Guy Leshem.
- DOI-URL: https://doi.org/10.1016/j.jisa.2017.03.001
-
-
- Title: Active learning for computational chemogenomics
- Journal: Future Medicinal Chemistry
- Contributors: Daniel Reker, Petra Schneider, Gisbert Schneider, JB Brown.
- DOI-URL: https://doi.org/10.4155/fmc-2016-0197
-
-
- Title: Small Random Forest Models for Effective Chemogenomic Active Learning
- Journal: Journal of Computer Aided Chemistry
- Contributors: Christin Rakers, Daniel Reker, J.B. Brown.
- DOI-URL: https://doi.org/10.2751/jcac.18.124
-
-
- Title: Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing
- Journal: PLOS Computational Biology
- Contributors: Hansaim Lim, Aleksandar Poleksic, Yuan Yao, Hanghang Tong, Di He, Luke Zhuang, Patrick Meng, Lei Xie, .
- DOI-URL: https://doi.org/10.1371/journal.pcbi.1005135
-
-Article title: Matched Molecular Series: Measuring SAR Similarity
-Publication date: May 1, 2017
-DOI-URL: https://doi.org/10.1021/acs.jcim.6b00709
-
-Subjects:
-Substituents, Mathematical methods, Structure activity relationship, Biological databases
-
-Contributors:
-Emanuel S. R. Ehmki, Christian Kramer
-
-This publication is cited by the following 5 publications:
-
-
- Title: Matched Molecular Series Analysis for ADME Property Prediction
- Journal: Journal of Chemical Information and Modeling
- Contributors: Mahendra Awale, Sereina Riniker, Christian Kramer.
- DOI-URL: https://doi.org/10.1021/acs.jcim.0c00269
-
-
- Title: Approaches using AI in medicinal chemistry
- Journal:
- Contributors: Christian Tyrchan, Eva Nittinger, Dea Gogishvili, Atanas Patronov, Thierry Kogej.
- DOI-URL: https://doi.org/10.1016/B978-0-12-822249-2.00002-5
-
-
- Title: Bioactivity Prediction Based on Matched Molecular Pair and Matched Molecular Series Methods
- Journal: Current Pharmaceutical Design
- Contributors: Xiaoyu Ding, Chen Cui, Dingyan Wang, Jihui Zhao, Mingyue Zheng, Xiaomin Luo, Hualiang Jiang, Kaixian Chen.
- DOI-URL: https://doi.org/10.2174/1381612826666200427111309
-
-
- Title: BRADSHAW: a system for automated molecular design
- Journal: Journal of Computer-Aided Molecular Design
- Contributors: Darren V. S. Green, Stephen Pickett, Chris Luscombe, Stefan Senger, David Marcus, Jamel Meslamani, David Brett, Adam Powell, Jonathan Masson.
- DOI-URL: https://doi.org/10.1007/s10822-019-00234-8
-
-
- Title: The use of matched molecular series networks for cross target structure activity relationship translation and potency prediction
- Journal: MedChemComm
- Contributors: Christopher E. Keefer, George Chang.
- DOI-URL: https://doi.org/10.1039/C7MD00465F
-
diff --git a/output/README.md b/output/README.md
deleted file mode 100644
index 418fdbecc82cdc61979325e9ca7a5e87604a3a7a..0000000000000000000000000000000000000000
--- a/output/README.md
+++ /dev/null
@@ -1,46 +0,0 @@
-# Projekt CiS-Projekt 2021/22
-
-Citation network made with **d3.js**
-
-## Usage
-### Input
-Json file **json\_text.json** in directory
-```json
-{
- "nodes": [
- {
- "name": <title: string>,
- "author": [<author1: string>, <author2: string>, ...],
- "year": <date: tring>,
- "journal": <journal: string>,
- "doi": <doi: string>,
- "group": <"input"/"height"/"depth">,
- "citations": <citation: int>
- }, ...
- ],
- "links": [
- {
- "source": <doi: string>,
- "target": <doi: string>
- }, ...
- ]
-}
-```
-
-### Display the Citation Network
-Starting a python web server:
-```sh
- cd <path to file> &&python3 -m http.server <port>
-```
-Access to the server:
-[http://0.0.0.0/:\<port\>](http://0.0.0.0/:<port>)
-
-## Files in Directory
-- **index.html**: webpage
-- **cn.js**: javascript code for force-directed graph, text elements and legend
-- **json_text.json**: example data
-
-
-## Authors
-- Katja Ehlers
-- Merle Stahl
\ No newline at end of file
diff --git a/output/graph/cn.js b/output/graph/cn.js
deleted file mode 100644
index 389935df5f1469ec2f152f0adc6995a72302fde7..0000000000000000000000000000000000000000
--- a/output/graph/cn.js
+++ /dev/null
@@ -1,561 +0,0 @@
-/**
-* creates a new zoom behavior
-*/
-var zoom = d3.zoom().on("zoom", handle_zoom);
-
-/**
-* creates svg object and associated attributes
-* applies the zoom behavior to svg
-*/
-var svg = d3.select("svg.graph")
- .call(zoom),
-width = svg.attr("width"),
-height = svg.attr("height"),
-perc;
-
-/**
-* scale functions that return y coordinate/color of node depending on group
-*/
-var color = d3.scaleOrdinal()
- .domain(["Citedby", "Input", "Reference"])
- .range([' #01d7c0', ' #8b90fe ', ' #a15eb2 ']),
-y_scale = d3.scaleOrdinal()
- .domain(["Citedby", "Input", "Reference"])
- .range([0, 200, 400]),
-to_remove;
-
-/**
-* creates node object and (default) radius
-*/
-var node,
-r = 10;
-
-/**
-* creates link object
-*/
-var link;
-
-/**
-* creates a background with a click functionality
-*/
-var rect = svg.append("rect")
- .attr("x", 0)
- .attr("y", 0)
- .attr("height", height)
- .attr("width", width)
- .style("fill", 'white')
- .on('click', click_rect);
-
-/**
-* creates svg object (legend) and associated attributes
-* transform
-*/
-var svg_legend = d3.select("svg.legendsvg"),
-legend_position = [65,95,125],
-arrow_legend_position = [0,25],
-arrow_group_names = ["citation","self-citation"],
-group_names = ["cited by","input","reference"],
-line_type = d3.scaleOrdinal()
- .domain(["line","dotted"])
- .range([("8,0"),("8,8")]),
-text_info = '',
-text_abstract = '';
-
-var legend = svg_legend.selectAll(".legend")
- .data(legend_position)
- .enter()
- .append("g")
- .attr("class","legend")
- .attr("transform", function(d,i) {return "translate(0," + d + ")"; });
-
-legend.append("text")
- .attr("x", 80)
- .attr("y", 0)
- .attr("dy", ".35em")
- .style("text-anchor", "start")
- .text(function(d,i) {return group_names[i]});
-
-legend.append("circle")
- .attr("r", r)
- .attr("cx",30-r)
- .style("fill", color);
-
-var legend_arrow = svg_legend.selectAll(".legendarr")
- .data(arrow_legend_position)
- .enter()
- .append("g")
- .attr("class","legendarr")
- .attr("transform", function(d) { return "translate(0," + d + ")"; });
-
-legend_arrow.append("line")
- .attr("x1", 10)
- .attr("x2", 50)
- .attr("y1", 10)
- .attr("y2", 10)
- .style("stroke-dasharray",line_type)
- .style("stroke", '#999')
- .style("stroke-width", "1px")
- .style('pointer-events', 'none')
- .attr('marker-end',update_marker('#999',this));
-
-legend_arrow.append("text")
- .attr("x", 80)
- .attr("y", 10)
- .attr("dy", ".35em")
- .style("text-anchor", "start")
- .text(function(d,i){return arrow_group_names[i]});
-
-/**
-* creates a new simulation
-* updates the positions of the links and nodes when the
- state of the layout has changed (simulation has advanced by a tick)
-*/
-var simulation = d3.forceSimulation()
- .force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(50).strength(function(d) {
- if (d.group == "Input") {return 0;}
- else {return 5;}
- }))
- .force("collide", d3.forceCollide(function(d) {
- if (d.group == "Input") {return 70;}
- else {return 70;}
- }).strength(0.5))
- .force("charge", d3.forceManyBody().strength(0.001))
- .force("center", d3.forceCenter(width/2, height/2+20))
- .force("yscale", d3.forceY().strength(function(d) {
- if (d.group == "Input") {return 300;}
- else {return 200;}
- }).y(function(d) {return y_scale(d.group)}))
- .alpha(0.004)
- .on("end", zoom_to);
-
-/**
-* creates group element
-*/
-var g = svg.append("g")
- .attr("class", "everything")
-
-/**
-* loads JSON data and calls the update function
-*/
-d3.json("json_text.json").then(function(graph) {
- update(graph.links, graph.nodes);
-})
-
-var intervalId=window.setInterval(function(){
- d3.json("json_text.json").then(function(graph) {
- newjson_string=JSON.stringify(graph)
- var newjson = CryptoJS.MD5(newjson_string).toString();
- oldjson=localStorage.getItem("oldjson")
- if(newjson !== oldjson){
- localStorage.setItem("oldjson", newjson);
- window.location.reload()
- }
- })
-},5000);
-
-/**
-* calls update functions for links and nodes
-* adds the nodes, links and tick functionality to the simulation
-* @param {object} nodes - nodes
-* @param {object} links - links
-*/
-function update(links, nodes) {
- update_links(links);
- update_nodes(nodes);
-
- simulation
- .nodes(nodes)
- .on("tick", handle_tick);
- simulation.force("link")
- .links(links);
-
- link.attr('marker-end', function(d) {return update_marker("#999", d.target);})
- .style("stroke-dasharray",function(d){return self_citation(d.source,d.target)? ("8,8"): ("1,0")});
-}
-
-/**
-* initializes and shows links (edges)
-* @param {object} links - links
-*/
-function update_links(links) {
- link = g.append("g")
- .selectAll(".link")
- .data(links)
- .enter()
- .append("line")
- .style("stroke-width", "1px")
- .style("stroke", "#999")
- .attr("class", "link");
-}
-
-/**
-* initializes and shows nodes with circles, texts and a click functionality
-* creates a new drag behavior and applies it to the circles
-* @param {object} nodes - nodes
-*/
-function update_nodes(nodes) {
- node = g.selectAll(".node")
- .data(nodes)
- .enter()
- .append("g")
- .attr("class", "node")
- .call(d3.drag()
- .on("start", start_drag)
- .on("drag", dragged)
- );
-
- node.append("circle")
- .attr("class", "circle")
- .attr("r", function(d) {return 1.5*r+d.citations*0.05})
- .style("fill", function(d){ return color(d.group)})
- .on('click', click_node);
-
- node.append("text")
- .attr("class", "text")
- .style("font-size", "15px")
- .style('pointer-events', 'auto')
- .text(function (d) {const first_author=d.author[0].split(" ")
- return first_author[first_author.length-1];})
- .on('click', click_node);
-}
-
-/**
-* creates arrowhead and returns its url
-* @param {string} color - color of arrowhead
-* @param {string} target - target node
-*/
-function update_marker(color, target) {
- var radius = 1.5*r+target.citations*0.05;
- svg.append('defs').append('marker')
- .attr('id',color.replace("#", "")+radius)
- .attr('viewBox','-0 -5 10 10')
- .attr('refX',radius+9.5)
- .attr('refY',0)
- .attr('orient','auto')
- .attr('markerWidth',10)
- .attr('markerHeight',15)
- .attr('xoverflow','visible')
- .append('svg:path')
- .attr('d', 'M 0,-5 L 10 ,0 L 0,5')
- .attr('fill', color)
- .style('stroke','none');
- return "url(" + color + radius + ")";
-};
-
-/**
-* sets color of circle and its links to black and removes the previous highlights
-* displays overview info of node in textbox
-* @param {object} node - node
-*/
-function click_node(node) {
- d3.select(this.parentNode).raise();
- fix_nodes(node);
- if(to_remove){
- d3.select(to_remove).selectAll(".circle").style("stroke","none")
- }
- to_remove = this.parentNode;
- d3.select(this.parentNode).selectAll(".circle").style("stroke","black")
- mark_link(node)
- textbox_content(node)
- reset_button_highlight()
- highlight_button("overview")
-}
-
-/**
-* removes the highlights of the circles and their links
-*/
-function click_rect() {
- fix_nodes(node);
- d3.selectAll(".circle").style("stroke", "none")
- d3.selectAll(".link")
- .style("stroke", "#999")
- .attr('marker-end', function(d) {return update_marker('#999', d.target);})
- text_abstract='';
- text_info='';
- reset_button_highlight()
- document.getElementById('textbox').innerHTML = "Click node";
-}
-
-/**
-* returns true if journals have a common author (self-citation)
-* @param {object} source - node
-* @param {object} target - node
-*/
-function self_citation(source,target) {
- return source.author.some(item=>target.author.includes(item))
-}
-
-/**
-* sets color of link (line and arrowhead) to black if it is directly connected to node
-* and to grey otherwise
-* @param {object} node - node
-*/
-function mark_link(node) {
- d3.selectAll(".link")
- .style("stroke", function(o) {
- return is_link_for_node(node, o) ? "black" : "#DEDEDE";})
- .attr('marker-end', function(o) {
- return is_link_for_node(node, o) ? update_marker('#000000', o.target) : update_marker('#DEDEDE', o.target);})
-}
-
-/**
-* returns true if link is directly connected to node and false if it is not
-* @param {object} node - node
-* @param {object} link - link
-*/
-function is_link_for_node(node, link) {
- return link.source.index == node.index || link.target.index == node.index;
-}
-
-/**
-* saves text for overview and abstract of node
-* outputs node info to textbox
-* @param {object} node - node
-*/
-function textbox_content(node) {
- text_info = "Title:" + '</br>' + node.name +
- '</br>' +'</br>'+"Author:"+ '</br>' +node.author+'</br>'+'</br>'+"Date:"+'</br>'
- +node.year+'</br>'+'</br>'+"Journal:"+'</br>'+node.journal+'</br>'+'</br>'+"doi:"
- +'</br>'+'<a href="'+node.doi+ '">'+node.doi+'</a>'+'</br>'+'</br>'+"Citations:"
- +'</br>'+node.citations;
- text_abstract = node.abstract;
- document.getElementById('textbox').innerHTML = text_info;
-}
-
-/**
-* sets color of btn to dark gray
-* @param {object} btn - button
-*/
-function highlight_button(btn) {
- reset_button_highlight();
- document.getElementById(btn).style.background = "#CACACA";
-}
-
-/**
-* sets color of all buttons to default light gray
-*/
-function reset_button_highlight() {
- document.getElementById("overview").style.background = '';
- document.getElementById("abstract").style.background = '';
-}
-
-/**
-* displays abstract in textbox if a is true, overview text otherwise
-* @param {bool} a- bool
-*/
-function display_abstract(a) {
- if (text_abstract == '' && text_info == '') {
- document.getElementById('textbox').innerHTML="Click node";
- }
- else {
- if (a == true) {
- document.getElementById('textbox').innerHTML = text_abstract;
- }
- else {
- document.getElementById('textbox').innerHTML = text_info;
- }
- }
-}
-
-/**
-* updates the positions of the links and nodes
-*/
-function handle_tick() {
- link.attr("x1", function (d) {return d.source.x;})
- .attr("y1", function (d) {return d.source.y;})
- .attr("x2", function (d) {return d.target.x;})
- .attr("y2", function (d) {return d.target.y;});
- node.attr("transform", function (d) {return "translate(" + d.x + ", " + d.y + ")";});
-}
-
-/**
-* initializes the dragging of the node
-* @param {object} node - node
-*/
-function start_drag(node) {
- d3.select(this).raise();
- if (!d3.event.active)
- simulation.alphaTarget(0.3).restart()
- node.fx = node.x;
- node.fy = node.y;
- fix_nodes(node);
-}
-
-/**
-* applies the dragging to the node
-* @param {object} node - node
-*/
-function dragged(node) {
- node.fx = d3.event.x;
- node.fy = d3.event.y;
- fix_nodes(node);
-}
-
-/**
-* fix positions of all nodes except for the current node
-* @param {object} this_node - node
-*/
-function fix_nodes(this_node) {
- node.each(function(d) {
- if (this_node != d) {
- d.fx = d.x;
- d.fy = d.y;
- }
- });
-}
-
-/**
-* applies the transformation (zooming or dragging) to the g element
-*/
-function handle_zoom() {
- d3.select('g').attr("transform", d3.event.transform);
-}
-
-/**
-* transforms svg so that the zoom is adapted to the size of the graph
-*/
-function zoom_to() {
- node_bounds = d3.selectAll("svg.graph").node().getBBox();
- svg_bounds = d3.select("rect").node().getBBox();
-
- perc_x = width/(node_bounds.width+100);
- perc_y = height/(node_bounds.height+100);
- perc = d3.min([perc_x, perc_y])
-
- d3.select('svg')
- .call(zoom.scaleBy, perc);
-}
-
-/**
-* transforms svg so that the zoom and drag is reset
-*/
-function reset_view() {
- d3.select('svg')
- .call(zoom.scaleTo, 1)
- d3.select('svg')
- .call(zoom.translateTo, 0.5 * width, 0.5 * height);
- d3.select('svg')
- .call(zoom.scaleBy, perc);
-}
-
-/**
-* save svg as png
-*/
-function save_svg(){
- var svgString = get_svg_string(svg.node());
- svg_string_to_image(svgString, 2*width, 2*height, 'png', save); // passes Blob and filesize String to the callback
-
- function save( dataBlob, filesize ){
- saveAs(dataBlob, 'D3 vis exported to PNG.png'); // FileSaver.js function
- }
-};
-
-/**
-* generate svgString
-* @param {object} svgNode - node
-*/
-function get_svg_string(svgNode) {
- svgNode.setAttribute('xlink', 'http://www.w3.org/1999/xlink');
- var cssStyleText = get_css_styles(svgNode);
- append_css(cssStyleText, svgNode);
-
- var serializer = new XMLSerializer();
- var svgString = serializer.serializeToString(svgNode);
- svgString = svgString.replace(/(\w+)?:?xlink=/g, 'xmlns:xlink='); // Fix root xlink without namespace
- svgString = svgString.replace(/NS\d+:href/g, 'xlink:href'); // Safari NS namespace fix
-
- return svgString;
-
- function get_css_styles(parentElement) {
- var selectorTextArr = [];
-
- // Add Parent element Id and Classes to the list
- selectorTextArr.push('#' + parentElement.id);
- for (var c = 0; c < parentElement.classList.length; c++)
- if (!contains('.'+parentElement.classList[c], selectorTextArr))
- selectorTextArr.push('.'+parentElement.classList[c]);
-
- // Add Children element Ids and Classes to the list
- var nodes = parentElement.getElementsByTagName("*");
- for (var i = 0; i < nodes.length; i++) {
- var id = nodes[i].id;
- if (!contains('#'+id, selectorTextArr))
- selectorTextArr.push('#' + id);
-
- var classes = nodes[i].classList;
- for (var c = 0; c < classes.length; c++)
- if (!contains('.'+classes[c], selectorTextArr))
- selectorTextArr.push('.'+classes[c]);
- }
-
- // Extract CSS Rules
- var extractedCSSText = "";
- for (var i = 0; i < document.styleSheets.length; i++) {
- var s = document.styleSheets[i];
-
- try {
- if(!s.cssRules) continue;
- } catch(e) {
- if(e.name !== 'SecurityError') throw e; // for Firefox
- continue;
- }
-
- var cssRules = s.cssRules;
- for (var r = 0; r < cssRules.length; r++) {
- if (contains(cssRules[r].selectorText, selectorTextArr))
- extractedCSSText += cssRules[r].cssText;
- }
- }
-
-
- return extractedCSSText;
-
- function contains(str,arr) {
- return arr.indexOf(str) === -1 ? false : true;
- }
-
- }
-
- function append_css(cssText, element) {
- var styleElement = document.createElement("style");
- styleElement.setAttribute("type","text/css");
- styleElement.innerHTML = cssText;
- var refNode = element.hasChildNodes() ? element.children[0] : null;
- element.insertBefore(styleElement, refNode);
- }
-}
-
-/**
-* convert svgString to image and export it
-* @param {object} svgString - svgString
-* @param {object} width - width of image
-* @param {object} height - height of image
-* @param {object} format - format to save image in
-* @param {object} callback - callback function
-*/
-function svg_string_to_image( svgString, width, height, format, callback ) {
- var format = format ? format : 'png';
-
- var imgsrc = 'data:image/svg+xml;base64,'+ btoa(unescape(encodeURIComponent(svgString))); // Convert SVG string to data URL
-
- var canvas = document.createElement("canvas");
- var context = canvas.getContext("2d");
-
- canvas.width = width;
- canvas.height = height;
-
- var image = new Image();
- image.onload = function() {
- context.clearRect(0, 0, width, height);
- context.drawImage(image, 0, 0, width, height);
-
- canvas.toBlob(function(blob) {
- var filesize = Math.round(blob.length/1024) + ' KB';
- if (callback) callback(blob, filesize);
- });
-
- };
-
- image.src = imgsrc;
-}
-
diff --git a/output/graph/cn2.js b/output/graph/cn2.js
deleted file mode 100644
index dce918d24e11ba191318915544fd9c8179eb9414..0000000000000000000000000000000000000000
--- a/output/graph/cn2.js
+++ /dev/null
@@ -1,600 +0,0 @@
-/**
-* creates a new zoom behavior
-*/
-var zoom = d3.zoom().on("zoom", handle_zoom);
-
-/**
-* creates svg object and associated attributes
-* applies the zoom behavior to svg
-*/
-var svg = d3.select("svg.graph")
- .call(zoom),
-width = svg.attr("width"),
-height = svg.attr("height"),
-perc;
-
-/**
-* scale functions that return y coordinate/color of node depending on group
-*/
-var color = d3.scaleOrdinal()
- .domain(["Citedby", "Input", "Reference"])
- .range([' #01d7c0', ' #8b90fe ', ' #a15eb2 ']),
-y_scale = d3.scaleOrdinal()
- .domain(["Citedby", "Input", "Reference"])
- .range([0, 200, 400]),
-to_remove;
-
-/**
-* creates node object and (default) radius
-*/
-var node,
-r = 10;
-
-/**
-* creates link object
-*/
-var link;
-
-/**
-* creates a background with a click functionality
-*/
-var rect = svg.append("rect")
- .attr("x", 0)
- .attr("y", 0)
- .attr("height", height)
- .attr("width", width)
- .style("fill", 'white')
- .on('click', click_rect);
-
-/**
-* creates svg object (legend) and associated attributes
-* transform
-* mehr kommentare
-*/
-var svg_legend = d3.select("svg.legendsvg"),
-legend_position = [65,95,125],
-arrow_legend_position = [0,25],
-arrow_group_names = ["citation","self-citation"],
-group_names = ["cited by","input","reference"],
-line_type = d3.scaleOrdinal()
- .domain(["line","dotted"])
- .range([("8,0"),("8,8")]),
-text_info = '',
-text_abstract = '';
-
-var legend = svg_legend.selectAll(".legend")
- .data(legend_position)
- .enter()
- .append("g")
- .attr("class","legend")
- .attr("transform", function(d,i) {return "translate(0," + d + ")"; });
-
-legend.append("text")
- .attr("x", 80)
- .attr("y", 0)
- .attr("dy", ".35em")
- .style("text-anchor", "start")
- .text(function(d,i) {return group_names[i]});
-
-legend.append("circle")
- .attr("r", r)
- .attr("cx",30-r)
- .style("fill", color);
-
-var legend_arrow = svg_legend.selectAll(".legendarr")
- .data(arrow_legend_position)
- .enter()
- .append("g")
- .attr("class","legendarr")
- .attr("transform", function(d) { return "translate(0," + d + ")"; });
-
-legend_arrow.append("line")
- .attr("x1", 10)
- .attr("x2", 50)
- .attr("y1", 10)
- .attr("y2", 10)
- .style("stroke-dasharray",line_type)
- .style("stroke", '#999')
- .style("stroke-width", "1px")
- .style('pointer-events', 'none')
- .attr('marker-end',update_marker('#999',this));
-
-legend_arrow.append("text")
- .attr("x", 80)
- .attr("y", 10)
- .attr("dy", ".35em")
- .style("text-anchor", "start")
- .text(function(d,i){return arrow_group_names[i]});
-
-/**
-* creates a new simulation
-* updates the positions of the links and nodes when the
- state of the layout has changed (simulation has advanced by a tick)
-*/
-
-var simulation = d3.forceSimulation()
- .force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(50).strength(function(d) {
- if (d.group == "Input") {return 0;}
- else {return 5;}
- }))
- .force("collide", d3.forceCollide(function(d) {
- if (d.group == "Input") {return 70;}
- else {return 75;}
- }).strength(1))
- .force("charge", d3.forceManyBody().strength(0.001))
- .force("center", d3.forceCenter(width/2, height/2+20))
- .alpha(0.004)
- .on("end", zoom_to);
-
-/**
-* creates group element
-*/
-var g = svg.append("g")
- .attr("class", "everything")
-
-/**
-* creates xAxis element
-*/
-var xAxis = d3.axisBottom()
- .tickFormat(function(d) {return d;})
- .ticks(10);;
-
-/**
-* draw xAxis
-*/
-var gX = svg.append("g")
- .attr("class", "axis axis--x")
- .attr("transform", "translate(0,25)")
- gX.append("text")
- .attr("y", 0)
- .attr("x", 80)
- .attr("text-anchor", "end")
- .attr("stroke", "black")
- .text("year");
-
-/**
-* loads JSON data and calls the update function
-*/
-d3.json("json_text.json").then(function(graph) {
- update(graph.links, graph.nodes);
-})
-
-var intervalId=window.setInterval(function(){
- d3.json("json_text.json").then(function(graph) {
- newjson_string=JSON.stringify(graph)
- var newjson = CryptoJS.MD5(newjson_string).toString();
- oldjson=localStorage.getItem("oldjson")
- if(newjson !== oldjson){
- localStorage.setItem("oldjson", newjson);
- window.location.reload()
- }
- })
-},5000);
-
-/**
-* calls update functions for links and nodes
-* adds the nodes, links and tick functionality to the simulation
-* @param {object} nodes - nodes
-* @param {object} links - links
-*/
-function update(links, nodes) {
- updateXAxis(nodes);
- update_links(links);
- update_nodes(nodes);
-
- simulation
- .nodes(nodes)
- .on("tick", handle_tick);
- simulation.force("link")
- .links(links);
-
- link.attr('marker-end', function(d) {return update_marker("#999", d.target);})
- .style("stroke-dasharray",function(d){return self_citation(d.source,d.target)? ("8,8"): ("1,0")});
-}
-
-/**
-* initializes and shows xAxis
-* @param {object} nodes - nodes
-*/
-function updateXAxis(nodes) {
- years = [];
- for (i = 0; i < nodes.length; i++) {
- years.push(parseInt((nodes[i]["year"]).split(" ")[2]));
- }
-
- xscale = d3.scaleLinear()
- .domain([d3.min(years)-1, d3.max(years)+1])
- .range([50, width-50])
-
- xAxis.scale(xscale);
- gX.call(xAxis);
-}
-
-/**
-* initializes and shows links (edges)
-* @param {object} links - links
-*/
-function update_links(links) {
- link = g.append("g")
- .selectAll(".link")
- .data(links)
- .enter()
- .append("line")
- .style("stroke-width", "1px")
- .style("stroke", "#999")
- .attr("class", "link");
-}
-
-/**
-* initializes and shows nodes with circles, texts and a click functionality
-* creates a new drag behavior and applies it to the circles
-* @param {object} nodes - nodes
-*/
-function update_nodes(nodes) {
- node = g.selectAll(".node")
- .data(nodes)
- .enter()
- .append("g")
- .attr("class", "node")
- .call(d3.drag()
- .on("start", start_drag)
- .on("drag", dragged)
- );
-
- node.append("circle")
- .attr("class", "circle")
- .attr("r", function(d) {return 1.5*r+d.citations*0.05})
- .style("fill", function(d){ return color(d.group)})
- .on('click', click_node);
-
- node.append("text")
- .attr("class", "text")
- .style("font-size", "15px")
- .style('pointer-events', 'auto')
- .text(function (d) {const first_author=d.author[0].split(" ")
- return first_author[first_author.length-1];})
- .on('click', click_node);
-}
-
-/**
-* creates arrowhead and returns its url
-* @param {string} color - color of arrowhead
-* @param {string} target - target node
-*/
-function update_marker(color, target) {
- var radius = 1.5*r+target.citations*0.05;
- svg.append('defs').append('marker')
- .attr('id',color.replace("#", "")+radius)
- .attr('viewBox','-0 -5 10 10')
- .attr('refX',radius+9.5)
- .attr('refY',0)
- .attr('orient','auto')
- .attr('markerWidth',10)
- .attr('markerHeight',15)
- .attr('xoverflow','visible')
- .append('svg:path')
- .attr('d', 'M 0,-5 L 10 ,0 L 0,5')
- .attr('fill', color)
- .style('stroke','none');
- return "url(" + color + radius + ")";
-};
-
-/**
-* sets color of circle and its links to black and removes the previous highlights
-* displays overview info of node in textbox
-* @param {object} node - node
-*/
-function click_node(node) {
- d3.select(this.parentNode).raise();
- fix_nodes(node);
- if(to_remove){
- d3.select(to_remove).selectAll(".circle").style("stroke","none")
- }
- to_remove = this.parentNode;
- d3.select(this.parentNode).selectAll(".circle").style("stroke","black")
- mark_link(node)
- textbox_content(node)
- reset_button_highlight()
- highlight_button("overview")
-}
-
-/**
-* removes the highlights of the circles and their links
-*/
-function click_rect() {
- fix_nodes(node);
- d3.selectAll(".circle").style("stroke", "none")
- d3.selectAll(".link")
- .style("stroke", "#999")
- .attr('marker-end', function(d) {return update_marker('#999', d.target);})
- text_abstract='';
- text_info='';
- reset_button_highlight()
- document.getElementById('textbox').innerHTML = "Click node";
-}
-
-/**
-* returns true if journals have a common author (self-citation)
-* @param {object} source - node
-* @param {object} target - node
-*/
-function self_citation(source,target) {
- return source.author.some(item=>target.author.includes(item))
-}
-
-/**
-* sets color of link (line and arrowhead) to black if it is directly connected to node
-* and to grey otherwise
-* @param {object} node - node
-*/
-function mark_link(node) {
- d3.selectAll(".link")
- .style("stroke", function(o) {
- return is_link_for_node(node, o) ? "black" : "#DEDEDE";})
- .attr('marker-end', function(o) {
- return is_link_for_node(node, o) ? update_marker('#000000', o.target) : update_marker("#DEDEDE", o.target);})
-}
-
-/**
-* returns true if link is directly connected to node and false if it is not
-* @param {object} node - node
-* @param {object} link - link
-*/
-function is_link_for_node(node, link) {
- return link.source.index == node.index || link.target.index == node.index;
-}
-
-/**
-* saves text for overview and abstract of node
-* outputs node info to textbox
-* @param {object} node - node
-*/
-function textbox_content(node) {
- text_info = "Title:" + '</br>' + node.name +
- '</br>' +'</br>'+"Author:"+ '</br>' +node.author+'</br>'+'</br>'+"Date:"+'</br>'
- +node.year+'</br>'+'</br>'+"Journal:"+'</br>'+node.journal+'</br>'+'</br>'+"doi:"
- +'</br>'+'<a href="'+node.doi+ '">'+node.doi+'</a>'+'</br>'+'</br>'+"Citations:"
- +'</br>'+node.citations;
- text_abstract = node.abstract;
- document.getElementById('textbox').innerHTML = text_info;
-}
-
-/**
-* sets color of btn to dark gray
-* @param {object} btn - button
-*/
-function highlight_button(btn) {
- reset_button_highlight();
- document.getElementById(btn).style.background = "#CACACA";
-}
-
-/**
-* sets color of all buttons to default light gray
-*/
-function reset_button_highlight() {
- document.getElementById("overview").style.background = '';
- document.getElementById("abstract").style.background = '';
-}
-
-/**
-* displays abstract in textbox if a is true, overview text otherwise
-* @param {bool} a- bool
-*/
-function display_abstract(a) {
- if (text_abstract == '' && text_info == '') {
- document.getElementById('textbox').innerHTML="Click node";
- }
- else {
- if (a == true) {
- document.getElementById('textbox').innerHTML = text_abstract;
- }
- else {
- document.getElementById('textbox').innerHTML = text_info;
- }
- }
-}
-
-/**
-* updates the positions of the links and nodes
-*/
-function handle_tick() {
- link.attr("x1", function (d) {return xscale(parseInt((d.source.year).split(" ")[2]));})
- .attr("y1", function (d) {return d.source.y;})
- .attr("x2", function (d) {return xscale(parseInt((d.target.year).split(" ")[2]));})
- .attr("y2", function (d) {return d.target.y;});
- node.attr("transform", function (d) {return "translate(" + xscale(parseInt((d.year).split(" ")[2])) + ", " + d.y + ")";});
-}
-
-/**
-* initializes the dragging of the node
-* @param {object} node - node
-*/
-function start_drag(node) {
- d3.select(this).raise();
- if (!d3.event.active)
- simulation.alphaTarget(0.3).restart()
- //node.fx = node.x;
- node.fy = node.y;
- fix_nodes(node);
-}
-
-/**
-* applies the dragging to the node
-* @param {object} node - node
-*/
-function dragged(node) {
- //node.fx = d3.event.x;
- node.fy = d3.event.y;
- fix_nodes(node);
-}
-
-/**
-* fix positions of all nodes except for the current node
-* @param {object} this_node - node
-*/
-function fix_nodes(this_node) {
- node.each(function(d) {
- if (this_node != d) {
- d.fx = d.x;
- d.fy = d.y;
- }
- });
-}
-
-/**
-* applies the transformation (zooming or dragging) to the g element
-*/
-function handle_zoom() {
- d3.select('g').attr("transform", d3.event.transform);
- var new_xScale = d3.event.transform.rescaleX(xscale)
- gX.call(xAxis.scale(new_xScale));
-}
-
-/**
-* transforms svg so that the zoom is adapted to the size of the graph
-*/
-function zoom_to() {
- node_bounds = d3.selectAll("svg.graph").node().getBBox();
- svg_bounds = d3.select("rect").node().getBBox();
-
- perc_x = width/(node_bounds.width+100);
- perc_y = height/(node_bounds.height+100);
- perc = d3.min([perc_x, perc_y])
-
- d3.select('svg')
- .call(zoom.scaleBy, perc);
-}
-
-/**
-* transforms svg so that the zoom and drag is reset
-*/
-function reset_view() {
- d3.select('svg')
- .call(zoom.scaleTo, 1)
- d3.select('svg')
- .call(zoom.translateTo, 0.5 * width, 0.5 * height);
- d3.select('svg')
- .call(zoom.scaleBy, perc);
-}
-
-/**
-* save svg as png
-*/
-function save_svg(){
- var svgString = get_svg_string(svg.node());
- svg_string_to_image(svgString, 2*width, 2*height, 'png', save); // passes Blob and filesize String to the callback
-
- function save( dataBlob, filesize ){
- saveAs(dataBlob, 'D3 vis exported to PNG.png'); // FileSaver.js function
- }
-};
-
-/**
-* generate svgString
-* @param {object} svgNode - node
-*/
-function get_svg_string(svgNode) {
- svgNode.setAttribute('xlink', 'http://www.w3.org/1999/xlink');
- var cssStyleText = get_css_styles(svgNode);
- append_css(cssStyleText, svgNode);
-
- var serializer = new XMLSerializer();
- var svgString = serializer.serializeToString(svgNode);
- svgString = svgString.replace(/(\w+)?:?xlink=/g, 'xmlns:xlink='); // Fix root xlink without namespace
- svgString = svgString.replace(/NS\d+:href/g, 'xlink:href'); // Safari NS namespace fix
-
- return svgString;
-
- function get_css_styles(parentElement) {
- var selectorTextArr = [];
-
- // Add Parent element Id and Classes to the list
- selectorTextArr.push('#' + parentElement.id);
- for (var c = 0; c < parentElement.classList.length; c++)
- if (!contains('.'+parentElement.classList[c], selectorTextArr))
- selectorTextArr.push('.'+parentElement.classList[c]);
-
- // Add Children element Ids and Classes to the list
- var nodes = parentElement.getElementsByTagName("*");
- for (var i = 0; i < nodes.length; i++) {
- var id = nodes[i].id;
- if (!contains('#'+id, selectorTextArr))
- selectorTextArr.push('#' + id);
-
- var classes = nodes[i].classList;
- for (var c = 0; c < classes.length; c++)
- if (!contains('.'+classes[c], selectorTextArr))
- selectorTextArr.push('.'+classes[c]);
- }
-
- // Extract CSS Rules
- var extractedCSSText = "";
- for (var i = 0; i < document.styleSheets.length; i++) {
- var s = document.styleSheets[i];
-
- try {
- if(!s.cssRules) continue;
- } catch(e) {
- if(e.name !== 'SecurityError') throw e; // for Firefox
- continue;
- }
-
- var cssRules = s.cssRules;
- for (var r = 0; r < cssRules.length; r++) {
- if (contains(cssRules[r].selectorText, selectorTextArr))
- extractedCSSText += cssRules[r].cssText;
- }
- }
-
-
- return extractedCSSText;
-
- function contains(str,arr) {
- return arr.indexOf(str) === -1 ? false : true;
- }
-
- }
-
- function append_css(cssText, element) {
- var styleElement = document.createElement("style");
- styleElement.setAttribute("type","text/css");
- styleElement.innerHTML = cssText;
- var refNode = element.hasChildNodes() ? element.children[0] : null;
- element.insertBefore(styleElement, refNode);
- }
-}
-
-/**
-* convert svgString to image and export it
-* @param {object} svgString - svgString
-* @param {object} width - width of image
-* @param {object} height - height of image
-* @param {object} format - format to save image in
-* @param {object} callback - callback function
-*/
-function svg_string_to_image( svgString, width, height, format, callback ) {
- var format = format ? format : 'png';
-
- var imgsrc = 'data:image/svg+xml;base64,'+ btoa(unescape(encodeURIComponent(svgString))); // Convert SVG string to data URL
-
- var canvas = document.createElement("canvas");
- var context = canvas.getContext("2d");
-
- canvas.width = width;
- canvas.height = height;
-
- var image = new Image();
- image.onload = function() {
- context.clearRect(0, 0, width, height);
- context.drawImage(image, 0, 0, width, height);
-
- canvas.toBlob(function(blob) {
- var filesize = Math.round(blob.length/1024) + ' KB';
- if (callback) callback(blob, filesize);
- });
-
- };
-
- image.src = imgsrc;
-}
-
diff --git a/output/graph/index.html b/output/graph/index.html
deleted file mode 100644
index 374abe283271574e67bd8d73e3691ef35b9e782d..0000000000000000000000000000000000000000
--- a/output/graph/index.html
+++ /dev/null
@@ -1,172 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-<head>
- <meta charset="utf-8">
-
- <!-- style specifications for button and div elements -->
- <style type="text/css">
- button {
- width: 100px;
- height:20px;
- display: flex;
- justify-content: center;
- position: absolute;
- left: 455px;
- top: 575px;
- transition-duration: 0.4s;
- border-radius:3px;
- border:1px solid #909090;
- }
-
- button.display{
- width: 120px;
- top: 0px;
- margin-left: 100px;
- }
-
- .button:hover {
- background-color: #CACACA;
- }
-
- button.resetZoom {
- margin-left: 110px;
- }
-
- button.save {
- margin-left: 220px;
- }
-
- button.abstract {
- width:146px;
- position:absolute;
- top: 181px;
- left: 1114px;
- border-radius:0;
- border:1px solid #909090;
- }
-
- button.overview {
- width:147px;
- position:absolute;
- display:inline-block;
- top: 181px;
- left: 968px;
- border-radius:0;
- border:1px solid #909090;
- }
-
- div.legendbox {
- width:270px;
- height:170px;
- padding: 10px;
- /*border: 1px solid #999;*/
- position: absolute;
- top: 10px;
- left: 968px;
- display: inline-block;
- margin: 0;
- }
-
- div.textbox {
- width:270px;
- min-height:200px;
- max-height:370px;
- padding: 10px;
- border: 1px solid #999;
- position: absolute;
- top: 200px;
- left: 968px;
- display: inline-block;
- overflow-y: scroll;
- margin: 0;
- }
- </style>
-</head>
-
-<body>
- <button id="change_graph" class="display" onclick="display()">display timeline</button>
-
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- }
- ]
-}
\ No newline at end of file
diff --git a/ui_programm_fragmente/input_to_checklist.py b/ui_programm_fragmente/input_to_checklist.py
deleted file mode 100644
index 3c00ed4c23c7acf914c02af576fec41d8ba2efc7..0000000000000000000000000000000000000000
--- a/ui_programm_fragmente/input_to_checklist.py
+++ /dev/null
@@ -1,160 +0,0 @@
-import dash
-from dash import dcc
-from dash import html
-from dash import callback_context
-from dash.dependencies import Input, Output, State
-from dash.exceptions import PreventUpdate
-from input.interface import InputInterface
-import input.publication
-
-app = dash.Dash(__name__)
-
-additional_options = ['Update Automatically']
-
-app.layout = html.Div([
- # Layer 0: For the Header and Help Function(s)
- html.Div([
- html.Button(id='show-info',children='Show Info',n_clicks=0),
- html.Div(id='info-box')
- ]),
- # Layer 1: For all mandatory Inputs
- html.Div([
- "Input: ",
- dcc.Input(id='input-string', value='', type='text',debounce=True),
- dcc.Input(id='forward-depth',value='1',type='number',min='1',max='10'),
- dcc.Input(id='backward-depth',value='1',type='number',min='1',max='10')
- ]),
- # Layer 2: For the checklist, Remove-/Start-Buttons and input-error-message
- html.Div([
- dcc.Checklist(id='input-checklist',options=[],labelStyle = dict(display='block'),value=[]),
- html.Div(id='input-err',style={'color':'red'}),
- html.Button(id='clear-all-button',children='Clear All'),
- html.Button(id='clear-selected-button',children='Clear Selected'),
- html.Button(id='start-button',children='Generate Graph')
- ]),
- # Layer 3: For additional Options (e.g. Topological Sort)
- html.Div([
- html.H4('Additional Options'),
- dcc.Checklist(id='additional-options',
- options=[{'label':k,'value':k} for k in additional_options],
- value=[])
- ]),
- # Layer 4: For the Graph
- html.Div([
- html.Div(id='test-output')
- ])
-])
-
-'''
-Most important callback function. Updates the checklist that holds all inputs.
-input-string is required as Output to clear the input box after each input
-'''
-@app.callback(
- Output('input-checklist','options'),
- Output('input-checklist','value'),
- Output('input-string','value'),
- Output('input-err','children'),
- Input('input-string','value'),
- Input('clear-all-button','n_clicks'),
- Input('clear-selected-button','n_clicks'),
- State('input-checklist','options'),
- State('input-checklist','value')
-)
-def update_input_checklist(input_value,btn1,btn2,all_inputs,selected_inputs):
- '''
- :param input_value: given by dcc.Input
- :type input_value: string
- :param btn1: signals pressing of clear-all-button
- :param btn2: signals pressing of clear-selected-button
- :param all_inputs: all labels and values from the checklist,
- regardless if they have been checked or not
- :type all_inputs: list of dictionaries with 2 entries each
- :param selected_inputs: values of all checked elements
- :type selected_inputs: list of strings
- '''
- changed_id = [p['prop_id'] for p in callback_context.triggered][0]
- # if clear-all-button was pressed:
- if 'clear-all-button' in changed_id:
- return list(),list(),'',''
- # if clear-selected-button was pressed:
- if 'clear-selected-button' in changed_id:
- all_inputs = [i for i in all_inputs if i['value'] not in selected_inputs]
- return all_inputs,list(),'',''
- # when the programm is first started:
- if input_value == '':
- app.layout['input-checklist'].options.clear()
- return list(),list(),'',''
- # when a new element is added via dcc.Input
- if 'input-string' in changed_id:
- options = all_inputs
- currValues = [x['value'] for x in options]
- if input_value not in currValues:
- try:
- i = InputInterface()
- pub = i.get_pub_light(input_value)
- except Exception as err:
- return options,selected_inputs,'','{}'.format(err)
- rep_str = pub.contributors[0] + ',' + pub.journal + ',' + pub.publication_date
- options.append({'label':rep_str, 'value':input_value})
- return options,selected_inputs,'',''
-
-'''
-This callback shows and hides the (first) help-box
-'''
-@app.callback(
- Output('info-box','children'),
- Input('show-info','n_clicks')
-)
-def show_hide_info_box(n_clicks):
- if n_clicks % 2 == 0:
- return ''
- else:
- return 'Hier koennte Ihre Werbung stehen'
-
-'''
-Basic structure for a callback that generates an output
-'''
-@app.callback(
- Output('test-output','children'),
- Input('start-button','n_clicks'),
- Input('input-checklist','options'),
- Input('input-checklist','value'),
- Input('forward-depth','value'),
- Input('backward-depth','value'),
- State('additional-options','value')
-)
-def generate_output(n_clicks,all_inputs,selected_inputs,
- forward_depth,backward_depth,additional_options):
- '''
- :param n_clicks: how often has Generate Graph been clicked
- :type n_clicks: int
- :param all_inputs: all labels and values from the checklist,
- regardless if they have been checked or not
- :type all_inputs: list of dictionaries with 2 entries each
- :param selected_inputs: values of all checked elements
- :type selected_inputs: list of strings
- :param forward_depth: forward recursion depth
- :type forward_depth: unsigned int
- :param backward_depth: backward recursion depth
- :type backward_depth: unsigned int
- :param additional_options: value of all selected additional options
- :type additional_options: list of strings
- '''
- changed_id = [p['prop_id'] for p in callback_context.triggered][0]
- if n_clicks is None:
- raise PreventUpdate
- elif 'Update Automatically' in additional_options \
- or 'start-button' in changed_id:
- s = ''
- for i in range(len(all_inputs)):
- x = all_inputs[i]['value']
- if x in selected_inputs:
- s += x*(abs(int(forward_depth)-int(backward_depth)))
- else:
- s += x*(int(forward_depth)+int(backward_depth))
- return s
- else:
- raise PreventUpdate
-
-if __name__ == '__main__':
- app.run_server(debug=True)
diff --git a/ui_programm_fragmente/upload_to_checklist.py b/ui_programm_fragmente/upload_to_checklist.py
deleted file mode 100644
index 9a094f213901a808ad924f4b1ffa87fb87f2f75d..0000000000000000000000000000000000000000
--- a/ui_programm_fragmente/upload_to_checklist.py
+++ /dev/null
@@ -1,78 +0,0 @@
-import dash
-from dash import dcc
-from dash import html
-from dash.dependencies import Input, Output, State
-import base64
-import re
-
-app = dash.Dash(__name__)
-
-list_of_inputs = dict()
-
-app.layout = html.Div([
- html.H4("Add all lines in a file to a list"),
- html.Div([
- dcc.Upload(
- id="upload-data",
- children=html.Div(
- ["Drag and drop or click to select a file to upload."]
- ),
-
- style={
- "width": "30%",
- "height": "60px",
- "lineHeight": "60px",
- "borderWidth": "1px",
- "borderStyle": "dashed",
- "borderRadius": "5px",
- "textAlign": "center",
- "margin": "10px",
- }),
-
- ]),
- dcc.Checklist(id='input-checklist',options=list(),labelStyle = dict(display='block'),value=[]),
-
-])
-
-@app.callback(
- Output('input-checklist','options'),
- Input('upload-data','filename'),
- Input('upload-data','contents'),
- State('input-checklist','options')
-)
-def update_input_list(uploaded_filenames,uploaded_file_contents,all_inputs):
- if uploaded_file_contents is not None:
-
-
- string = uploaded_file_contents
-
- #cutting the first part of the String away to decode
- found = base64.b64decode(re.search(',(.+?)$', string).group(1))
- print(found.decode('utf-8'))
-
- uploaded_file_contents = found.decode('utf-8')
-
-
- list_of_inputs = (uploaded_file_contents.split())
- #das hier sollte es untereinander anzeigen, bekomme ich allerdings nicht auf die Seite...
- #return (*list_of_inputs, sep="\n")
-
- options = all_inputs
- if not options:
- options = list()
- CurrValues = [x['value'] for x in options]
-
-
- # würde auch funktionieren
- # return (found.decode('utf-8'))
- for i in list_of_inputs:
- if i not in CurrValues:
- options.append({'label':i, 'value':i})
-
-
- return options
-
-if __name__ == '__main__':
- app.run_server(debug=True)
-
-