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Commit 7ed27902 authored by Ehlers, Katja's avatar Ehlers, Katja
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Merge branch 'main' into 'output' 

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See merge request bax9187/projekt-cis-biochemie-2021-22!6
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# 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
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/**
* 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(["height", "input", "depth"])
.range([' #01d7c0', ' #8b90fe ', ' #a15eb2 ']),
y_scale = d3.scaleOrdinal()
.domain(["height", "input", "depth"])
.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
*/
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 100;}
else {return 65;}
}).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 1000;}
else {return 50;}
}).y(function(d) {return y_scale(d.group)}))
.alpha(0.005)
.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);
})
/**
* 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
* @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" : "#999";})
.attr('marker-end', function(o) {
return is_link_for_node(node, o) ? update_marker('#000000', o.target) : update_marker('#999', 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;
}
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<!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: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>
<!-- graph -->
<svg class="graph" width="960" height="560"></svg>
<!-- legend -->
<div class="legendbox"> <svg class="legendsvg"></svg></div>
<!-- textbox -->
<div class="textbox" id = "textbox">Click node</div>
<button id="overview" class="overview" onclick='display_abstract(false), highlight_button("overview")'>Overview</button>
<button id="abstract" class="abstract" onclick='display_abstract(true), highlight_button("abstract")'>Abstract</button>
<!-- buttons -->
<button onclick="location.reload()">Reload Graph</button>
<button class="resetZoom" onclick="reset_view()">Reset View</button>
<button class="save" onclick="save_svg()">Save</button>
<!-- D3 (version 5) -->
<script src="https://d3js.org/d3.v5.min.js"></script>
<!-- scripts to save svg element as png -->
<script src="https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js"></script>
<script src="https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js"></script>
<!-- javascript for force-directed graph -->
<script type="text/javascript" id="cn" src="cn.js"></script>
</body>
</html>
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import base64
import re
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__)
# List of options when inputting data and generating the graph
additional_options = ['Update Automatically','Smart Input']
# 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([
# 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: ",
# 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),
# Forward recursion. Values between 1 and 10 can be entered.
dcc.Input(id='forward-depth',value='1',type='number',min='1',max='10'),
# Backward recursion. Values between 1 and 10 can be entered.
dcc.Input(id='backward-depth',value='1',type='number',min='1',max='10'),
# Upload box. Can be used via drag-and-drop or byclicking on it to open a file viewer.
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",
})
]),
# Layer 2: For the checklist, Remove-/Start-Buttons and input-error-message
html.Div([
# 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.
html.Button(id='clear-all-button',children='Clear All'),
# Clear all selected elements.
html.Button(id='clear-selected-button',children='Clear Selected'),
# Starts the process that generates a graph.
html.Button(id='start-button',children='Generate Graph')
]),
# Layer 3: For additional Options (e.g. Topological Sort)
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.Div(id='test-output')
])
])
@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'),
Input('upload-data','contents'),
State('input-checklist','options'),
State('input-checklist','value'),
State('additional-options','value')
)
def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
selected_inputs,additional_options):
'''
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.
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.
:param input_value: given by dcc.Input
:type input_value: string
:param btn1: signals pressing of clear-all-button
:type btn1: int
:param btn2: signals pressing of clear-selected-button
:type btn2: int
:param filecontents: the contents of an uploaded file
:type filecontents: bit-string
: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 addtitional_options: all checked additional options
:type additional_options: list of strings
'''
# changed_id is used to determine which Input has triggered the callback
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 a new element is added via dcc.Input
if 'input-string' 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:
# 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,
# the DOI is not added and an error message is returned
i = InputInterface()
pub = i.get_pub_light(input_value)
except Exception as err:
return options,selected_inputs,'','{}'.format(err)
# 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})
# if 'Smart Input' is not selected, the input value is added as is,
# without checking for validity.
else:
all_inputs.append({'label':input_value,'value':input_value})
return all_inputs,selected_inputs,'',''
# when a txt-file is uploaded
if 'upload-data.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))
# Returns the binary string into a proper text
text = found.decode('utf-8')
# Creates a list of inputs by splitting the lines
list_of_inputs = (text.strip().split('\n'))
CurrValues = [x['value'] for x in all_inputs]
# For every line the same actions as for a single input are performed
for input_value in list_of_inputs:
if input_value not in CurrValues:
if 'Smart Input' in additional_options:
try:
i = InputInterface()
pub = i.get_pub_light(input_value)
except Exception as err:
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})
else:
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
# with one element that contains an empty string
if input_value == '':
return list(),list(),'',''
@app.callback(
Output('info-box','children'),
Input('show-info','n_clicks')
)
def show_hide_info_box(n_clicks):
'''
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'})
@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):
'''
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
: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)
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English
Show Info: Can be activated and deactivated by clicking on the button.
Input: input by entering a DOI ("Digital Object Identifier")
Drag and drop or click to select a file to upload: entering multiple DOI by txt-file is only possible if every DOI has its own line.
Recursion:
Clear All: clearing all inputs
Clear Selected: clearing all selected inputs
Generate Graph: generates the graph
Update Automatically: automatically updates the graph for every new input
Smart Input: checks the correctness of the entered DOI and shows a nicer depiction: Author, Journal, publication date.
German
Show Info: Durch wiederholtes klicken kann das Fenster ein und aus geblendet werden.
Input: Die Eingabe erfolgt in Form eines DOI ("Digital Object Identifier")
Drag and drop or click to select a file to upload: Mehrere DOI in einem txt-Dokument müssen untereinander angeordnet sein.
Recursion:
Clear All: alle Eingaben werden gelöscht
Clear Selected: alle markierten Eingaben werden gelöscht
Generate Graph: generiert den zugehörigen Graphen
Update Automatically: automatische Aktualisierung des Graphen nach neuer Eingabe
Smart Input: direkte Überprüfung der Eingabe auf Richtigkeit zudem wird nicht mehr der DOI angezeigt sondern: Der Autor, Das Journal, Das Veröffentlichungsdatum.
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# Projekt CiS-Biochemie 2021-22 UI
# Benötigt:
- Dash
- Pandas
- beautifulsoup4
- requests
# Starten des Programms:
Ausführen von citation_parser_ui.py und einfügen des entstandenen Liks in einen Browser.
Danach müsste sich die Benutzeroberfläche im Browser öffnen.
# Übersicht der Benutzeroberfläche:
- Show Info: Durch wiederholtes klicken kann das Fenster ein und aus geblendet werden.
- Input: Die Eingabe erfolgt in Form eines DOI ("Digital Object Identifier")
- Drag and drop or click to select a file to upload: Mehrere DOI in einem txt-Dokument (genau ein DOI pro Zeile).
- Recursion: die beiden noch unbeschrifteten Felder rechts neben Input sind für die Rekursionstiefen in beide Richtungen
- Clear All: alle Eingaben werden gelöscht
- Clear Selected: alle markierten Eingaben werden gelöscht
- Generate Graph: generiert den zugehörigen Graphen (generiert momentan nur einen string)
- Update Automatically: automatische Aktualisierung des Graphen bei jeder neuen Eingabe
- Smart Input: direkte Überprüfung der Eingabe auf Richtigkeit zudem wird nicht mehr der DOI angezeigt sondern:
Der Autor, Das Journal, Das Veröffentlichungsdatum. (muss vor Hinzufügen aktiviert worden sein)
## Autoren
- Isabelle Siebels
- Sebastian David
ui_programm_fragmente/input_to_checklist.py 0 → 100644
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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)
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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)
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# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
# C extensions
*.so
# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
*.egg-info/
.installed.cfg
*.egg
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*,cover
# Translations
*.mo
*.pot
# Django stuff:
*.log
# Sphinx documentation
docs/_build/
# PyBuilder
target/
#CodeCounter
.VSCodeCounter/
\ No newline at end of file
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# -*- coding: utf-8 -*-
"""
Functions to generate a graph representing citations between multiple ACS/Nature journals
"""
__authors__ = "Donna Löding, Alina Molkentin, Xinyi Tang, Judith Große, Malte Schokolowski"
__email__ = "cis-project2021@zbh.uni-hamburg.de"
__status__ = "Production"
#__copyright__ = ""
#__credits__ = ["", "", "", ""]
#__license__ = ""
#__version__ = ""
#__maintainer__ = ""
from bs4 import BeautifulSoup as bs
import requests as req
import sys
from pathlib import Path
from input_fj import input
from input_test import input_test_func
from json_demo import output_to_json
# adds every publication from input list to graph structure
# doi_input_list: list of publication dois from user
def initialize_nodes_list(doi_input_list, search_depth_max, search_height_max, test_var):
references_pub_obj_list = []
citations_pub_obj_list = []
for pub_doi in doi_input_list:
#checks if its a test and chooses input function accordingly
if(test_var):
pub = input_test_func(pub_doi)
else:
pub = input(pub_doi)
# checks if publication already exists in nodes
not_in_nodes = True
for node in nodes: # checks if a pub is already in nodes
if (pub.doi_url == node.doi_url):
not_in_nodes = False
break
if (not_in_nodes):
nodes.append(pub)
pub.group = "input"
else:
doi_input_list.remove(pub_doi)
# inserts references as publication objects into list and
# inserts first depth references into nodes/edges if maximum search depth > 0
for reference in create_graph_structure_references(pub, 0, search_depth_max, test_var):
references_pub_obj_list.append(reference)
# inserts citations as publication objects into list and
# inserts first height citations into nodes if maximum search height > 0
for citation in create_graph_structure_citations(pub, 0, search_height_max, test_var):
citations_pub_obj_list.append(citation)
return(references_pub_obj_list, citations_pub_obj_list)
# adds edges between citation and reference group
def complete_inner_edges(test_var):
for node in nodes:
if (node.group == "depth"):
for citation in node.citations:
for cit in nodes:
if (citation.doi_url == cit.doi_url and [citation.doi_url, node.doi_url] not in edges):
edges.append([citation.doi_url, node.doi_url])
if (node.group == "height"):
for reference in node.references:
for ref in nodes:
if (reference.doi_url == ref.doi_url and [node.doi_url, reference.doi_url] not in edges):
edges.append([node.doi_url,reference.doi_url])
# adds a node for every publication unknown
# adds edges for references between publications
def create_graph_structure_references(pub, search_depth, search_depth_max, test_var):
references_pub_obj_list = []
for reference in pub.references:
not_in_nodes = True
for node in nodes:
# checks every reference for duplication
if (reference.doi_url == node.doi_url):
not_in_nodes = False
break
if (not_in_nodes):
if (search_depth < search_depth_max):
#checks if its a test and chooses input function accordingly
if (test_var):
reference_pub_obj = input_test_func(reference.doi_url)
else:
reference_pub_obj = input(reference.doi_url)
reference_pub_obj.group = "depth"
nodes.append(reference_pub_obj)
edges.append([pub.doi_url,reference_pub_obj.doi_url])
references_pub_obj_list.append(reference_pub_obj)
# adds edge only if citation already exists
elif [pub.doi_url,reference.doi_url] not in edges:
edges.append([pub.doi_url,reference.doi_url])
return references_pub_obj_list
# recursive function to implement height-first-search on references
# references_pub_obj_list: input list of references as publication objects
# search_depth: current search_depth of height-first-search
# search_depth_max: maximal search_depth for dfs
def process_references_rec(references_pub_obj_list, search_depth, search_depth_max, test_var):
# adds next level to nodes/edges
for pub in references_pub_obj_list:
new_reference_pub_obj_list = create_graph_structure_references(pub, search_depth, search_depth_max, test_var)
# If the maximum height has not yet been reached, calls function recursivly with increased height
if (search_depth < search_depth_max):
process_references_rec(new_reference_pub_obj_list, search_depth+1, search_depth_max, test_var)
# adds a node for every publication unknown
# adds edges for citations between publications
def create_graph_structure_citations(pub, search_height, search_height_max, test_var):
citations_pub_obj_list = []
for citation in pub.citations:
not_in_nodes = True
for node in nodes:
# checks every citation for duplication
if (citation.doi_url == node.doi_url):
not_in_nodes = False
break
if (not_in_nodes):
if (search_height < search_height_max):
#checks if its a test and chooses input function accordingly
if (test_var):
citation_pub_obj = input_test_func(citation.doi_url)
else:
citation_pub_obj = input(citation.doi_url)
citation_pub_obj.group = "height"
nodes.append(citation_pub_obj)
edges.append([citation_pub_obj.doi_url,pub.doi_url])
citations_pub_obj_list.append(citation_pub_obj)
# adds only edge if citation already exists
elif [citation.doi_url,pub.doi_url] not in edges:
edges.append([citation.doi_url,pub.doi_url])
return citations_pub_obj_list
# recursive function to implement height-first-search on citations
# citations_pub_obj_list: input list of citations as publication objects
# search_height: current search_height of height-first-search
# search_height_max: maximal search_height for dfs
def process_citations_rec(citations_pub_obj_list, search_height, search_height_max, test_var):
# adds next level to nodes/edges
for pub in citations_pub_obj_list:
new_citation_pub_obj_list = create_graph_structure_citations(pub, search_height, search_height_max, test_var)
# If the maximum height has not yet been reached, calls function recursivly with increased height
if (search_height < search_height_max):
process_citations_rec(new_citation_pub_obj_list, search_height+1, search_height_max, test_var)
# main function to call. Needs as input:
# doi_input_list: input list of dois
# search_height: max search height to process to
# search_depth: max search depth to process to
# test_var: only needed for unit test as True, default is False
def process_main(doi_input_list, search_height, search_depth, test_var = False):
# ERROR-Handling doi_array = NULL
if (len(doi_input_list) == 0):
print("Error, no input data")
# ERROR- if a negative number is entered for height
if (search_height < 0):
print("Error, search_height of search must be positive")
# ERROR- if a negative number is entered for depth
if (search_depth < 0):
print("Error, search_depth of search must be positive")
# create empty array for the nodes
# create empty array for the edges
global nodes, edges
nodes = []
edges = []
# initializes nodes/edges from input and gets a list with publication objects for citations and references returned
references_obj_list, citations_obj_list = initialize_nodes_list(doi_input_list,search_depth, search_height, test_var)
# function calls to begin recursive processing up to max depth/height
process_citations_rec(citations_obj_list, 1, search_height, test_var)
process_references_rec(references_obj_list, 1, search_depth, test_var)
# adds edges between reference group and citation group of known publications
complete_inner_edges(test_var)
# calls a skript to save nodes and edges of graph in .json file
output_to_json(nodes,edges)
# only for unit tests
if (test_var == True):
doi_nodes_list = []
for node in nodes:
doi_nodes_list.append(node.doi_url)
return(doi_nodes_list, edges)
# a function to print nodes and edges from a graph
def print_graph(nodes, edges):
print("Knoten:\n")
for node in nodes:
print(node.title, "\n")
print("\nKanten:\n")
for edge in edges:
print(edge,"\n")
# program test, because there is no connection to UI yet.
def try_known_publications():
doi_list = []
doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
#arr.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
doi_list.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')
#arr.append('https://doi.org/10.1021/acs.jcim.5b00292')
#url = sys.argv[1]
#arr.append[url]
nodes,edges = process_main(doi_list,2,2)
print_graph(nodes, edges)
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import unittest
from Processing import process_main
class ProcessingTest(unittest.TestCase):
def testCycle(self):
nodes, edges = process_main(['doiz1'],1,1,True)
self.assertCountEqual(nodes, ['doiz1', 'doiz2'])
self.assertCountEqual(edges, [['doiz1', 'doiz2'], ['doiz2', 'doiz1']])
nodes, edges = process_main(['doiz1'],2,2,True)
self.assertCountEqual(nodes, ['doiz1', 'doiz2'])
self.assertCountEqual(edges, [['doiz2', 'doiz1'], ['doiz1', 'doiz2']])
#def testBigCycle(self):
#def testEmptyHeight(self):
#def testEmptyDepth(self):
def testEmptyDepthHeight(self):
nodes, edges = process_main(['doi1'],0,0,True)
self.assertCountEqual(nodes,['doi1'])
self.assertCountEqual(edges, [])
nodes, edges = process_main(['doi1', 'doi2'],0,0,True)
self.assertCountEqual(nodes, ['doi1','doi2'])
self.assertCountEqual(edges, [['doi1', 'doi2']])
nodes, edges = process_main(['doi1', 'doi2', 'doi3'],0,0,True)
self.assertCountEqual(nodes, ['doi1','doi2', 'doi3'])
self.assertCountEqual(edges, [['doi3', 'doi1'], ['doi1', 'doi2']])
def testInnerEdges(self):
nodes, edges = process_main(['doi_ie1'],1,1,True)
self.assertCountEqual(nodes,['doi_ie1','doi_ie2','doi_ie3'])
self.assertCountEqual(edges,[['doi_ie1','doi_ie2'],['doi_ie3','doi_ie1'],['doi_ie3','doi_ie2']])
def testRightHeight(self):
nodes, edges = process_main(['doi_h01'],1,0,True)
self.assertCountEqual(nodes,['doi_h01'])
self.assertCountEqual(edges, [])
nodes, edges = process_main(['doi_h02'],1,0,True)
self.assertCountEqual(nodes,['doi_h02','doi_h1'])
self.assertCountEqual(edges, [['doi_h1','doi_h02']])
nodes, edges = process_main(['doi_h02'],2,0,True)
self.assertCountEqual(nodes,['doi_h02','doi_h1','doi_h2'])
self.assertCountEqual(edges, [['doi_h1','doi_h02'], ['doi_h2','doi_h1']])
def testRightDepth(self):
nodes, edges = process_main(['doi_d01'],0,1,True)
self.assertCountEqual(nodes,['doi_d01'])
self.assertCountEqual(edges, [])
nodes, edges = process_main(['doi_d02'],0,1,True)
self.assertCountEqual(nodes,['doi_d02','doi_d1'])
self.assertCountEqual(edges, [['doi_d02','doi_d1']])
nodes, edges = process_main(['doi_d02'],0,2,True)
self.assertCountEqual(nodes,['doi_d02','doi_d1','doi_d2'])
self.assertCountEqual(edges, [['doi_d02','doi_d1'], ['doi_d1','doi_d2']])
if __name__ == "__main__":
unittest.main()
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# Projekt CiS-Projekt 2021/22
Processing-Package to generate theoretical graph for citations and references of given input publications.
## Usage/Examples
```python
from verarbeitung.process_main import Processing
def main(url_list):
Processing(url_list)
```
Grundlegender Prozess:
Es wird von der UI eine Liste an DOIs an die Verarbeitung übergeben und
diese wird dann umgewandelt in eine Knoten-und Kantenmenge, welche die Zitierungen darstellen.
Die Informationen über die Paper und die Zitierungen kommen von der Input Gruppe über den Aufruf
von der Funktion Publication. Die Knoten- und Kantenmengen werden in Form einer
Json Datei an den Output übergeben.
## Files and functions in directory
get_pub_from_input.py:
```python
def get_pub(pub_doi, test_var)
```
- Gibt für eine DOI ein Klassenobjekt zurück, in dem alle nötigen Informationen gespeichert sind.
process_main.py:
```python
def Processing(url_list)
```
- Überprüft, ob bereits eine Json Datei existiert und ruft dann entweder die Funktion auf, um
einen neuen Graphen zu erstellen oder die Funktion um einen Vorhandenen zu updaten.
start.script.py:
- Wird benötigt, um die Dateien ordnerübergreifend aufzurufen. Nur fürs interne Testen der
Funktionalität
<name>.json:
- sind momentan Beispiele, die an den Output übergeben werden könnten.
## Testing
python -m unittest discover verarbeitung/test -v
## Authors
- Donna Löding
- Alina Molkentin
- Xinyi Tang
- Judith Große
- Malte Schokolowski
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