From b1757d8631b649714d30d2ba8fd455ae6d59448d Mon Sep 17 00:00:00 2001
From: Merle Stahl <merle.stahl@studium.uni-hamburg.de>
Date: Mon, 17 Jan 2022 17:50:19 +0100
Subject: [PATCH] Farben angepasst
---
assets/cn.js | 2 +-
assets/cn2.js | 2 +-
assets/index.html | 2 +-
assets/json_text.json | 115 +---------------------------------------
citation_parser_main.py | 72 +++++++++++++------------
5 files changed, 43 insertions(+), 150 deletions(-)
diff --git a/assets/cn.js b/assets/cn.js
index 5b2ba32..1eb8d52 100644
--- a/assets/cn.js
+++ b/assets/cn.js
@@ -18,7 +18,7 @@ perc;
*/
var color = d3.scaleOrdinal()
.domain(["Citedby", "Input", "Reference"])
- .range(['#01d7c0', '#8b90fe', '#a15eb2']),
+ .range(['#01d7c0', '#7fa9d4', '#a15eb2']),
y_scale = d3.scaleOrdinal()
.domain(["Citedby", "Input", "Reference"])
.range([0, 200, 400]),
diff --git a/assets/cn2.js b/assets/cn2.js
index de4ab78..992356f 100644
--- a/assets/cn2.js
+++ b/assets/cn2.js
@@ -18,7 +18,7 @@ perc;
*/
var color = d3.scaleOrdinal()
.domain(["Citedby", "Input", "Reference"])
- .range(['#01d7c0', '#8b90fe', '#a15eb2']),
+ .range(['#01d7c0', '#7fa9d4', '#a15eb2']),
y_scale = d3.scaleOrdinal()
.domain(["Citedby", "Input", "Reference"])
.range([0, 200, 400]),
diff --git a/assets/index.html b/assets/index.html
index 981e9f8..ed4ed32 100644
--- a/assets/index.html
+++ b/assets/index.html
@@ -82,7 +82,7 @@
svg.graph {
position: absolute;
- top: 20px
+ top: 20px;
}
</style>
</head>
diff --git a/assets/json_text.json b/assets/json_text.json
index c023ef5..b8177a3 100644
--- a/assets/json_text.json
+++ b/assets/json_text.json
@@ -1,114 +1 @@
-{
- "nodes": [
- {
- "doi": "https://doi.org/10.1021/acs.jcim.5b00332",
- "name": "Feasibility of Active Machine Learning for Multiclass Compound Classification",
- "author": [
- "Tobias Löang",
- "Florian Flachsenberg",
- "Ulrike von Luxburg",
- "Matthias Rarey"
- ],
- "year": "January 7, 2016",
- "journal": "Journal of Chemical Information and Modeling",
- "group": "Input",
- "depth": 0,
- "citations": 5
- },
- {
- "doi": "https://doi.org/10.1021/acs.jcim.7b00729",
- "name": "Modeling Kinase Inhibition Using Highly Confident Data Sets",
- "author": [
- "Sorin Avram",
- "Alina Bora",
- "Liliana Halip",
- "Ramona Curp\u0103n"
- ],
- "year": "April 30, 2018",
- "journal": "Journal of Chemical Information and Modeling",
- "group": "Citedby",
- "depth": 1,
- "citations": 0
- },
- {
- "doi": "https://doi.org/10.1021/acs.jcim.7b00729",
- "name": "Modeling Kinase Inhibition Using Highly Confident Data Sets",
- "author": [
- "Sorin Avram",
- "Alina Bora",
- "Liliana Halip",
- "Ramona Curp\u0103n"
- ],
- "year": "April 30, 2018",
- "journal": "Journal of Chemical Information and Modeling",
- "group": "Citedby",
- "depth": 1,
- "citations": 0
- },
- {
- "doi": "https://doi.org/10.1021/acs.jcim.5b00646",
- "name": "Predictive Models for Fast and Effective Profiling of Kinase Inhibitors",
- "author": [
- "Alina Bora",
- "Sorin Avram",
- "Ionel Ciucanu",
- "Marius Raica",
- "Stefana Avram"
- ],
- "year": "April 11, 2016",
- "journal": "Journal of Chemical Information and Modeling",
- "group": "Citedby",
- "depth": 1,
- "citations": 2
- },
- {
- "doi": "https://doi.org/10.1021/acs.jcim.6b00709",
- "name": "Matched Molecular Series: Measuring SAR Similarity",
- "author": [
- "Emanuel S. R. Ehmki",
- "Christian Kramer"
- ],
- "year": "May 1, 2017",
- "journal": "Journal of Chemical Information and Modeling",
- "group": "Input",
- "depth": 0,
- "citations": 5
- },
- {
- "doi": "https://doi.org/10.1021/acs.jcim.0c00269",
- "name": "Matched Molecular Series Analysis for ADME Property Prediction",
- "author": [
- "Mahendra Awale",
- "Sereina Riniker",
- "Christian Kramer"
- ],
- "year": "May 5, 2020",
- "journal": "Journal of Chemical Information and Modeling",
- "group": "Citedby",
- "depth": 1,
- "citations": 6
- }
- ],
- "links": [
- {
- "source": "https://doi.org/10.1021/acs.jcim.7b00729",
- "target": "https://doi.org/10.1021/acs.jcim.5b00332"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.7b00729",
- "target": "https://doi.org/10.1021/acs.jcim.5b00332"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.5b00646",
- "target": "https://doi.org/10.1021/acs.jcim.5b00332"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.7b00729",
- "target": "https://doi.org/10.1021/acs.jcim.5b00646"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.0c00269",
- "target": "https://doi.org/10.1021/acs.jcim.6b00709"
- }
- ]
-}
+{"nodes": [], "links": []}
\ No newline at end of file
diff --git a/citation_parser_main.py b/citation_parser_main.py
index c2b119d..997a8c1 100644
--- a/citation_parser_main.py
+++ b/citation_parser_main.py
@@ -10,9 +10,9 @@ 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
+from dash.dependencies import Input, Output, State
import plotly.express as px
-import dash_bootstrap_components as dbc # pip install dash-bootstrap-components for Loading Bar
+import dash_bootstrap_components as dbc # pip install dash-bootstrap-components
@@ -21,57 +21,58 @@ app = dash.Dash(__name__, external_stylesheets=[dbc.themes.SPACELAB]) #SPACELAB
# List of options when inputting data and generating the graph
additional_options = ['Update Automatically','Smart Input']
-# Reads the contents of info_box.txt.
+# Reads the contents of info_box.txt.
# They can later be displayed by pressing the corresponding button.
f = open('info_box.txt', 'r')
boxcontent = f.read()
f.close()
app.layout = html.Div([
+html.Div(children=[
# Layer 0: For the Header and Help Function(s)
dbc.Button(
- 'show Info',
+ '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'}))),
+ dbc.Card(dbc.CardBody(html.Div(boxcontent, style={'whiteSpace': 'pre-line', 'font-size': '10px'}))),
id='collapse',
is_open=False,
),
# Layer 1: For the string input
- html.Div([
+ dbc.Spinner(html.Div([
"Input: ",
- # A simple box for inputting a string.
+ # A simple box for inputting a string.
# Value is transmitted upon pressing return or clicking out of the box.
dcc.Input(id='string-input', value='', type='text',debounce=True,
- style={ "width": "400px"},
+ style={ "width": "362px", 'margin-top': "10px"},
),
- ]),
+ ]),size="lg", color="primary", type="border", fullscreen=True,),
# Layer 2: For file input and recursion depths
- html.Div([
- "Cited-by Depth: ",
+ html.Div([
+ "References Depth: ",
# Forward recursion. Values between 1 and 10 can be entered.
dcc.Input(id='forward-depth',value='1',type='number',min='0',max='5',
- style={ "width": "50px"},
+ style={ "width": "50px", 'margin-top': "10px"},
),
- "References Depth: ",
+ " Cited-by Depth: ",
# Backward recursion. Values between 1 and 10 can be entered.
dcc.Input(id='backward-depth',value='1',type='number',min='0',max='5',
- style={"width": "50px"},
+ style={"width": "50px", 'margin-top': "10px"},
),
# Upload box. Can be used via drag-and-drop or byclicking on it to open a file viewer.
- dcc.Upload(
+ dbc.Spinner(dcc.Upload(
id="file-input",
children=html.Div(
#Drag and drop or click to select a file to upload
["Drag and drop"]),
style={
- "width": "30%",
+ "width": "400px",
"height": "60px",
"lineHeight": "60px",
"borderWidth": "1px",
@@ -79,23 +80,23 @@ app.layout = html.Div([
"borderRadius": "5px",
"textAlign": "center",
"margin": "10px",
- })
+ }),size="lg", color="primary", type="border", fullscreen=True,),
]),
# Layer 3: For the checklist, Remove-/Start-Buttons and error message
html.Div([
- # All input DOIs are collected in this checklist.
+ # All input DOIs are collected in this checklist.
# It is initialized to avoid error messages.
dcc.Checklist(id='input-checklist',options=[],
labelStyle = dict(display='block'),value=[]),
# Displays error message if 'Smart Input' is active.
html.Div(id='input-err',style={'color':'red'}),
# Clears the entire list.
- dbc.Button(id='clear-all-button',children='Clear All', color="primary", className="me-1"),
+ dbc.Button(id='clear-all-button',children='Clear All', color="primary", className="me-1",style={'display': 'inline-block'}),
# Clear all selected elements.
- dbc.Button(id='clear-selected-button',children='Clear Selected', color="primary", className="me-1"),
+ dbc.Button(id='clear-selected-button',children='Clear Selected', color="primary", className="me-1",style={'display': 'inline-block'}),
# Starts the process that generates a graph.
- dbc.Button(id='start-button',children='Generate Graph', color="primary", className="me-1")
+ dbc.Button(id='start-button',children='Generate Graph', color="primary", className="me-1",style={'display': 'inline-block'})
]),
# Layer 4: For additional Options
html.Div([
@@ -103,17 +104,22 @@ app.layout = html.Div([
# 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=[])
- ]),
+ value=[],labelStyle = dict(display= 'block'))
+ ],style={'margin-top': "50px"}),
+
+ ], style={'padding': 10, 'flex': 0.8}),
+
+ html.Div(children=[
# Layer 5: For the Graph and corresponding error messages
- html.Div([
+ dbc.Spinner(html.Div([
html.Div(id='generate-graph-error',style={'color':'red'}),
html.Iframe(
src="assets/index.html",
- style={"height": "600px", "width": "100%"},
+ style={"height": "650px", "width": "980px"},
),
- ])
-])
+ ]),size="lg", color="primary", type="border", fullscreen=True,),
+ ], style={'padding': 10, 'flex': 1.2})
+], style={'display': 'flex', 'flex-direction': 'row'})
@app.callback(
Output('input-checklist','options'),
@@ -170,14 +176,14 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
# when a new element is added via dcc.Input
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]
+ currValues = [x['value'] for x in all_inputs]
if input_value not in currValues:
- # if 'Smart Input' is selected, the input will be checked for validity
+ # if 'Smart Input' is selected, the input will be checked for validity
# and a more readable string will be returned
if 'Smart Input' in additional_options:
try:
- # Attempts to call get_publication. If unsuccesful,
+ # Attempts to call get_publication. If unsuccesful,
# the DOI is not added and an error message is returned
i = InputInterface()
pub = i.get_pub_light(input_value)
@@ -225,7 +231,7 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
all_inputs.append({'label':input_value,'value':input_value})
return all_inputs,selected_inputs,'',''
# when the programm is first started:
- # if this is not done, the input_checklist will be generated
+ # if this is not done, the input_checklist will be generated
# with one element that contains an empty string
if input_value == '':
return list(),list(),'',''
@@ -258,7 +264,7 @@ def toggle_collapse(n, is_open):
)
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
+ 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.
:param n_clicks: how often has Generate Graph been clicked
@@ -277,7 +283,7 @@ def generate_output(n_clicks,all_inputs,forward_depth,backward_depth,additional_
if n_clicks is None:
raise PreventUpdate
elif 'Update Automatically' in additional_options \
- or 'start-button' in changed_id:
+ or 'start-button' in changed_id:
input_links = [x['value'] for x in all_inputs]
errors = Processing(input_links,int(forward_depth),int(backward_depth),'assets/json_text.json')
if errors:
--
GitLab