Merge branch 'main' of https://gitlab.rrz.uni-hamburg.de/bav1758/ci-s-projekt-verarbeitung

assets/cn.js

+/**
+* 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;
+}
+

assets/index.html

+<!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>
\ No newline at end of file

assets/json_text.json

+{"nodes": [{"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}, {"doi": "https://doi.org/10.1021/acs.jcim.0c00290", "name": "Identification of Bioisosteric Substituents by a Deep Neural Network", "author": ["Peter Ertl"], "year": "June 15, 2020", "journal": "Journal of Chemical Information and Modeling", "group": "Citedby", "depth": 2, "citations": 2}], "links": [{"source": "https://doi.org/10.1021/acs.jcim.0c00269", "target": "https://doi.org/10.1021/acs.jcim.6b00709"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00290", "target": "https://doi.org/10.1021/acs.jcim.0c00269"}]}
\ No newline at end of file

citation_parser_ui.py

+import os
 import base64
 import re
 import dash
@@ -8,6 +9,7 @@ from dash.dependencies import Input, Output, State
 from dash.exceptions import PreventUpdate
 from input.interface import InputInterface
 import input.publication
+from verarbeitung.process_main import Processing
 
 app = dash.Dash(__name__)
 
@@ -76,7 +78,11 @@ app.layout = html.Div([
             value=[])
     ]),
     # Layer 4: For the Graph
-    html.Div([
+    html.Div(
+        [html.Iframe(
+            src="assets/index.html",
+            style={"height": "600px", "width": "100%"},
+        ),
         html.Div(id='test-output')
     ])
 ])
@@ -125,6 +131,7 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
 
     # if clear-all-button was pressed:
     if 'clear-all-button' in changed_id:
+        os.remove('assets/json_text.json')
         return list(),list(),'',''
     
     # if clear-selected-button was pressed:
@@ -147,7 +154,7 @@ def update_input_checklist(input_value,btn1,btn2,filecontents,all_inputs,
                     i = InputInterface()
                     pub = i.get_pub_light(input_value)
                 except Exception as err:
-                    return options,selected_inputs,'','{}'.format(err)
+                    return all_inputs,selected_inputs,'','{}'.format(err)
                 # Creates a more readable string to display in the checklist
                 rep_str = pub.contributors[0] + ',' + pub.journal + \
                         ',' + pub.publication_date
@@ -240,16 +247,8 @@ def generate_output(n_clicks,all_inputs,selected_inputs,
         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
+        input_links = [x['value'] for x in all_inputs]
+        Processing(input_links,int(forward_depth),int(backward_depth),'assets/json_text.json')
 
 if __name__ == '__main__':
-    app.run_server(debug=True)
+    app.run_server(debug=False)

verarbeitung/start_script.py → start_script.py

 import sys
+import gc
 from pathlib import Path
 from verarbeitung.process_main import Processing
-from verarbeitung.dev_files.print_graph_test import try_known_publications, try_delete_nodes
+#from verarbeitung.dev_files.print_graph_test import try_known_publications, try_delete_nodes
 
 
 doi_list = []
-doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
+#doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249')
 #doi_list.append('https://doi.org/10.1021/acs.jcim.9b00249')
-doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.1c00203')
+#doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.1c00203')
 doi_list.append('https://doi.org/10.1021/acs.jmedchem.0c01332')
-Processing(doi_list, 2, 2, 'test.json')
+doi_list.append('https://pubs.acs.org/doi/10.1021/acs.jcim.6b00709')
+error_list = Processing(doi_list, 2, 2, 'test.json')
+print(error_list)
+
+del doi_list
+del error_list
+gc.collect()

test.json

+{"nodes": [{"doi": "https://doi.org/10.1021/acs.jmedchem.0c01332", "name": "Evolution of Novartis\u2019 Small Molecule Screening Deck Design", "author": ["Ansgar Schuffenhauer", "Nadine Schneider", "Samuel Hintermann", "Douglas Auld", "Jutta Blank", "Simona Cotesta", "Caroline Engeloch", "Nikolas Fechner", "Christoph Gaul", "Jerome Giovannoni", "Johanna Jansen", "John Joslin", "Philipp Krastel", "Eugen Lounkine", "John Manchester", "Lauren G. Monovich", "Anna Paola Pelliccioli", "Manuel Schwarze", "Michael D. Shultz", "Nikolaus Stiefl", "Daniel K. Baeschlin"], "year": "November 3, 2020", "journal": "Journal of Medicinal Chemistry", "group": "Input", "depth": 0, "citations": 8}, {"doi": "https://doi.org/10.1021/acsmedchemlett.1c00251", "name": "The Growing Importance of Chirality in 3D Chemical Space Exploration and Modern Drug Discovery Approaches for Hit-ID", "author": ["Ilaria Proietti Silvestri", "Paul J. J. Colbon"], "year": "July 16, 2021", "journal": "ACS Med. Chem. Lett.", "group": "Citedby", "depth": 1, "citations": 0}, {"doi": "https://doi.org/10.1021/acs.jmedchem.1c00416", "name": "Target-Based Evaluation of \u201cDrug-Like\u201d Properties and Ligand Efficiencies", "author": ["Paul D. Leeson", "A. Patricia Bento", "Anna Gaulton", "Anne Hersey", "Emma J. Manners", "Chris J. Radoux", "Andrew R. Leach"], "year": "May 13, 2021", "journal": "Journal of Medicinal Chemistry", "group": "Citedby", "depth": 1, "citations": 0}, {"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}, {"doi": "https://doi.org/10.1021/acs.jcim.0c00290", "name": "Identification of Bioisosteric Substituents by a Deep Neural Network", "author": ["Peter Ertl"], "year": "June 15, 2020", "journal": "Journal of Chemical Information and Modeling", "group": "Citedby", "depth": 2, "citations": 2}], "links": [{"source": "https://doi.org/10.1021/acsmedchemlett.1c00251", "target": "https://doi.org/10.1021/acs.jmedchem.0c01332"}, {"source": "https://doi.org/10.1021/acs.jmedchem.1c00416", "target": "https://doi.org/10.1021/acs.jmedchem.0c01332"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00269", "target": "https://doi.org/10.1021/acs.jcim.6b00709"}, {"source": "https://doi.org/10.1021/acs.jcim.0c00290", "target": "https://doi.org/10.1021/acs.jcim.0c00269"}]}
\ No newline at end of file

verarbeitung/construct_new_graph/add_citations_rec.py

@@ -120,7 +120,7 @@ def create_graph_structure_citations(pub, search_depth, search_depth_max, cit_ty
             if (search_depth < search_depth_max): #checks if its a test and chooses input function accordingly
                 citation_pub_obj = get_pub(citation.doi_url, test_var)
                 if (type(citation_pub_obj) != Publication):
-                    print(pub)
+                    #print(pub)
                     continue 
                 
                 if (cit_type == "Citation"):

verarbeitung/construct_new_graph/initialize_graph.py

@@ -75,7 +75,8 @@ def initialize_nodes_list(doi_input_list, search_depth_max, search_height_max, t
     for pub_doi in doi_input_list: #iterates over every incoming doi
         pub = get_pub(pub_doi, test_var)
         if (type(pub) != Publication):
-            print(pub)
+            #print(pub)
+            error_doi_list.append(pub_doi)
             continue       
 
         # checks if publication already exists in nodes
@@ -163,13 +164,14 @@ def init_graph_construction(doi_input_list, search_depth, search_height, test_va
 
     
     # creates empty lists to save nodes and edges
-    global nodes, edges
+    global nodes, edges, error_doi_list
     if update_var:
         nodes = input_nodes
         edges = input_edges 
     else:
         nodes = []
         edges = []
+    error_doi_list = []
 
     # 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)
@@ -188,4 +190,7 @@ def init_graph_construction(doi_input_list, search_depth, search_height, test_va
     del edges
     gc.collect()
 
-    return(new_nodes,new_edges)
+    if test_var:
+        return(new_nodes, new_edges)
+    else:
+        return(new_nodes, new_edges, error_doi_list)

verarbeitung/get_pub_from_input.py

@@ -40,9 +40,7 @@ def get_pub(pub_doi, test_var):
     else: 
         inter = Input()
         try:
-            pub = inter.get_publication(pub_doi) #creates an object of class Publication
-        except AttributeError:
-            pub = inter.get_publication(pub_doi)
+            pub = inter.get_publication(pub_doi) #creates an object of class Publication)
         except ValueError:
             return(ValueError)
         except IndexError:

verarbeitung/process_main.py

@@ -45,10 +45,12 @@ def Processing(url_list, search_depth, search_height, json_file = 'json_text.jso
     json_file = Path(json_file)
     
     if json_file.is_file():
-        nodes, edges = update_graph(url_list, json_file, search_depth, search_height)
+        nodes, edges, error_doi_list = update_graph(url_list, json_file, search_depth, search_height)
     else:
-        nodes, edges = init_graph_construction(url_list, search_depth, search_height)
+        nodes, edges, error_doi_list = init_graph_construction(url_list, search_depth, search_height)
 
     # exports graph to given json file name
     output_to_json(nodes, edges, json_file)
+
+    return error_doi_list
     
\ No newline at end of file

verarbeitung/update_graph/connect_new_input.py

@@ -149,5 +149,4 @@ def connect_old_and_new_input(input_nodes_list, input_edges_list, inserted_nodes
     #add_citations(nodes, edges, citations_obj_list, 1, new_search_height, "Citation", test_var)
     #add_citations(nodes, edges, references_obj_list, 1, new_search_depth, "Reference", test_var)
 
-    init_graph_construction(not_handled_inserted_nodes, new_search_depth, new_search_height, test_var = test_var, update_var = True, input_nodes = nodes, input_edges = edges)
-
+    nodes, edges, error_doi_list = init_graph_construction(not_handled_inserted_nodes, new_search_depth, new_search_height, test_var = test_var, update_var = True, input_nodes = nodes, input_edges = edges)

verarbeitung/update_graph/update_depth.py

@@ -18,7 +18,9 @@ sys.path.append("../../")
 
 from verarbeitung.construct_new_graph.add_citations_rec import add_citations
 from verarbeitung.construct_new_graph.initialize_graph import complete_inner_edges
+from verarbeitung.get_pub_from_input import get_pub
 from .update_edges import back_to_valid_edges
+from input.publication import Publication
 
 
 def reduce_max_height(max_height):
@@ -62,7 +64,7 @@ def get_old_height_depth():
             max_height = max(max_height, pub.group)
     return(max_height, max_depth)
 
-def get_old_max_references(old_depth):
+def get_old_max_references(old_depth, test_var):
     '''
         :param old_depth:       old maximum depth to search for citations
         :type old_depth:        int
@@ -72,13 +74,14 @@ def get_old_max_references(old_depth):
     old_max_references = []
     for pub in processed_input_list:
         if (abs(pub.group) == old_depth):
-            for reference in pub.references:
-                for ref_pub in processed_input_list:
-                    if reference.doi_url == ref_pub.doi_url:
-                        old_max_references.append(ref_pub)
+            pub = get_pub(pub.doi_url, test_var)
+            if (type(pub) != Publication):
+                #print(pub)
+                continue
+            old_max_references.append(pub)
     return(old_max_references)
 
-def get_old_max_citations(old_height):
+def get_old_max_citations(old_height, test_var):
     '''
         :param old_height:      old maximum height to search for citations
         :type old_height:       int
@@ -88,10 +91,11 @@ def get_old_max_citations(old_height):
     old_max_citations = []
     for pub in processed_input_list:
         if (abs(pub.group) == old_height):
-            for citation in pub.citations:
-                for cit_pub in processed_input_list:
-                    if citation.doi_url == cit_pub.doi_url:
-                        old_max_citations.append(cit_pub)
+            pub = get_pub(pub.doi_url, test_var)
+            if (type(pub) != Publication):
+                #print(pub)
+                continue
+            old_max_citations.append(pub)
     return(old_max_citations)
 
 def update_depth(obj_input_list, input_edges, new_depth, new_height, test_var):
@@ -120,20 +124,22 @@ def update_depth(obj_input_list, input_edges, new_depth, new_height, test_var):
 
     old_height, old_depth = get_old_height_depth()
 
-    # removes publications and links from recursion levels which aren't needed anymore
+    # removes publications and links from recursion levels which aren't needed anymore or adds new ones
     if (old_depth > new_depth):
         reduce_max_depth(new_depth)
-    elif (old_height > new_height):
+    elif (old_depth < new_depth):
+        old_max_references = get_old_max_references(old_depth, test_var)
+        add_citations(processed_input_list, valid_edges, old_max_references, old_depth, new_depth, "Reference", test_var)
+    
+    if (old_height > new_height):
         reduce_max_height(new_height)
+    elif (old_height < new_height):
+        old_max_citations = get_old_max_citations(old_height, test_var)
+        add_citations(processed_input_list, valid_edges, old_max_citations, old_height, new_height, "Citation", test_var)
+    
+   
     
     
-    # adds publications and links for new recursion levels
-    elif (old_depth < new_depth):
-        old_max_references = get_old_max_references(old_depth)
-        add_citations(processed_input_list, valid_edges, old_max_references, old_depth+1, new_depth, "Reference", test_var)
-    elif (old_height < new_height):
-        old_max_citations = get_old_max_citations(old_height)
-        add_citations(processed_input_list, valid_edges, old_max_citations, old_height+1, new_height, "Citation", test_var)
     back_to_valid_edges(valid_edges, processed_input_list)
 
     # adds edges between reference group and citation group of known publications

verarbeitung/update_graph/update_graph.py

@@ -59,7 +59,8 @@ def get_new_input_dois(new_input, test_var):
         # retrieves information and adds to new list if successful 
         pub = get_pub(new_node, test_var)
         if (type(pub) != Publication):
-            print(pub)
+            #print(pub)
+            error_doi_list.append(new_node)
             continue
 
         new_input_dois.append(pub.doi_url)
@@ -87,9 +88,10 @@ def update_graph(new_doi_input_list, json_file, search_depth, search_height, tes
     old_obj_input_list , old_edges_list = input_from_json(json_file)
 
     # one global list to save the process of removing unneeded publications and one to save valid edges
-    global processed_list, valid_edges
+    global processed_list, valid_edges, error_doi_list
     processed_list = old_obj_input_list
     valid_edges = old_edges_list
+    error_doi_list = []
 
 
     # get dois from lists to compare for differences
@@ -108,4 +110,7 @@ def update_graph(new_doi_input_list, json_file, search_depth, search_height, tes
     if (len(inserted_nodes) > 0):
         connect_old_and_new_input(processed_list, valid_edges, inserted_nodes, old_search_depth, old_search_height, search_depth, search_height, test_var)
 
-    return(processed_list, valid_edges) 
+    if test_var:
+        return(processed_list, valid_edges)
+    else:
+        return(processed_list, valid_edges, error_doi_list)