links from nodes

6 files changed, 61 insertions, 42 deletions

diff --git a/ratspub.py b/ratspub.py
index 345146e..ea78d85 100755
--- a/ratspub.py
+++ b/ratspub.py
@@ -3,6 +3,8 @@ from nltk.tokenize import sent_tokenize
 import os
 import re
 
+global function_d, brain_d, drug_d, addiction_d
+
 ## turn dictionary (synonyms) to regular expression
 def undic(dic):
     return "|".join(dic.values())
@@ -67,27 +69,28 @@ def gene_functional(gene):
                 out+=gene+"\t"+"function\t"+bio0+"\t"+sent+"\n"
     return(out)
 
-def generate_nodes(nodes_d, nodecolor):
+def generate_nodes(nodes_d, nodetype):
+    nodecolor={'function':"#A9CCE3", 'addiction': "#D7BDE2", 'drug': "#F9E79F", 'brain':"#A3E4D7"}
     # include all search terms even if there are no edges, just to show negative result 
-    json0 =str() #"{ data: { id: '" + gene +  "'} },\n"
+    json0 =str()
     for node in nodes_d:
-        json0 += "{ data: { id: '" + node +  "', nodecolor: '" + nodecolor + "' } },\n"
+        json0 += "{ data: { id: '" + node +  "', nodecolor: '" + nodecolor[nodetype] + "', nodetype: '"+nodetype + "', url:'/shownode?nodetype=" + nodetype + "&node="+node+"' } },\n"
     return(json0)
 
-def generate_edges(data):
+def generate_edges(data, filename):
     json0=str()
     edgeCnts={}
     for line in  data.split("\n"):
         if len(line.strip())!=0:
             (source, cat, target, pmid, sent) = line.split("\t")
-            edgeID=source+"|"+target
+            edgeID=filename+"|"+source+"|"+target
             if edgeID in edgeCnts:
                 edgeCnts[edgeID]+=1
             else:
                 edgeCnts[edgeID]=1
     for edgeID in edgeCnts:
-        (source,target)=edgeID.split("|")
-        json0+="{ data: { id: \'" + edgeID + "\', source: \'" + source + "\', target: '" + target + "\', sentCnt: '" + str(edgeCnts[edgeID]) + "',  url:'/sentences?edgeID=" + edgeID + "' } },\n"
+        (filename, source,target)=edgeID.split("|")
+        json0+="{ data: { id: '" + edgeID + "', source: '" + source + "', target: '" + target + "', sentCnt: '" + str(edgeCnts[edgeID]) + "',  url:'/sentences?edgeID=" + edgeID + "' } },\n"
     return(json0)
 
 addiction_d = {"reward":"reward|hedonic|incentive|intracranial self stimulation|ICSS|reinforcement|conditioned place preference|CPP|self administration|self administered|drug reinforced|operant|instrumental response",
@@ -126,9 +129,11 @@ function_d={"neuroplasticity":"neuroplasticity|plasticity|long term potentiation
             }
 function=undic(function_d)
 
+
+
 #https://htmlcolorcodes.com/
-n0=generate_nodes(function_d, "#D7BDE2")
-n1=generate_nodes(addiction_d,"#A9CCE3")
-n2=generate_nodes(drug_d, "#A3E4D7")
-n3=generate_nodes(brain_d, "#F9E79F")
+n0=generate_nodes(function_d, 'function')
+n1=generate_nodes(addiction_d, 'addiction')
+n2=generate_nodes(drug_d, 'drug')
+n3=generate_nodes(brain_d, 'brain')
 default_nodes=n0+n1+n2+n3
diff --git a/server.py b/server.py
index 0f3d94b..804e0fc 100755
--- a/server.py
+++ b/server.py
@@ -1,5 +1,8 @@
 #!/bin/env  python3
 from flask import Flask, render_template, request, redirect
+import tempfile
+import random
+import string
 from ratspub import *
 
 app=Flask(__name__)
@@ -11,43 +14,55 @@ def root():
 
 @app.route("/search")
 def search():
-    global all_sentences 
+    tf_path=tempfile.gettempdir()
+    tf_name=tf_path+"/tmp"+''.join(random.choice(string.ascii_letters) for x in range(6))
     all_sentences=str()
     genes=request.args.get('query')
     genes=genes.replace(",", " ")
     genes=genes.replace(";", " ")
     genes=genes.split()
-    if len(genes)>=6: 
+    if len(genes)>=6:
         return render_template('index.html')
     nodes=default_nodes
     edges=str()
     for  gene in genes:
-        nodes+="{ data: { id: '" + gene +  "', nodecolor:'#FADBD8', fontweight:700} },\n"
+        nodes+="{ data: { id: '" + gene +  "', nodecolor:'#FADBD8', fontweight:700, url:'https://www.ncbi.nlm.nih.gov/gene/?term="+gene+"'} },\n"
         sent0=gene_addiction(gene)
-        e0=generate_edges(sent0)
+        e0=generate_edges(sent0, tf_name)
         sent1=gene_functional(gene)
-        e1=generate_edges(sent1)
+        e1=generate_edges(sent1, tf_name)
         sent2=gene_anatomical(gene)
-        e2=generate_edges(sent2)
+        e2=generate_edges(sent2, tf_name)
         edges+=e0+e1+e2
         all_sentences+=sent0+sent1+sent2
-    #f=open("all_sentences.tab","w")
-    #f.write(all_sentences)
-    #f.close()
+    #session['tmpfile']={'filename':tf_name}
+    with open(tf_name,"w") as f:
+        f.write(all_sentences)
+        f.close()
     return render_template('cytoscape.html', elements=nodes+edges)
 
 @app.route("/sentences")
 def sentences():
     edge=request.args.get('edgeID')
-    (gene0, cat0)=edge.split("|")
-    print (gene0 + cat0)
-    out="<h3>"+gene0 + " and " + cat0  + "</h3>\n"
-    for sent in all_sentences.split("\n"):
+    (tf_name, gene0, cat0)=edge.split("|")
+    out="<h3>"+gene0 + " and " + cat0  + "</h3><hr>\n"
+    print(tf_name)
+    with open(tf_name, "r") as df:
+        all_sents=df.read()
+    for sent in all_sents.split("\n"):
         if len(sent.strip())!=0:
-           (gene,nouse,cat, pmid, text)=sent.split("\t") 
+           (gene,nouse,cat, pmid, text)=sent.split("\t")
            if (gene == gene0 and cat == cat0) :
                out+= "<li> "+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>"
     return render_template('sentences.html', sentences="<ol>"+out+"</ol><p>")
 
+@app.route("/shownode")
+def shownode():
+    node=request.args.get('node')
+    allnodes={**brain_d, **drug_d, **function_d, **addiction_d}
+    out="<p>"+node.upper()+"<hr><li>"+ allnodes[node].replace("|", "<li>")
+    return render_template('sentences.html', sentences=out+"<p>")
+
+
 if __name__ == '__main__':
     app.run(debug=True)
diff --git a/templates/cytoscape.html b/templates/cytoscape.html
index fd2000e..c0c6bf6 100644
--- a/templates/cytoscape.html
+++ b/templates/cytoscape.html
@@ -22,7 +22,7 @@
 					css: {
 						'content': 'data(sentCnt)',
 						'curve-style': 'bezier',
-			            'opacity': '0.3' 
+			            'opacity': 'mapData(sentCnt, 1, 50, 0.2, 0.3)', 
 					}
 				},
 			{ selector: 'node.highlight',
@@ -50,6 +50,7 @@
 				name: 'circle'
 			}
 		});
+
 		cy.on('tap', 'edge', function(){
 			try { // your browser may block popups
 				window.open( this.data('url') );
@@ -57,6 +58,13 @@
 				window.location.href = this.data('url');
 			}
 	  	});
+		cy.on('tap', 'node', function(){
+			try { // your browser may block popups
+				window.open( this.data('url') );
+			} catch(e){ // fall back on url change
+				window.location.href = this.data('url');
+			}
+	  	});
 		cy.on('mouseover', 'node', function(e){
 			var sel = e.target;
 			cy.elements().difference(sel.outgoers()).not(sel).addClass('semitransp');
diff --git a/templates/index.html b/templates/index.html
index ba18e0c..011aa6f 100644
--- a/templates/index.html
+++ b/templates/index.html
@@ -3,22 +3,14 @@
 <p>
 
     <form action="/search">
-      <input name="query" class="form-control form-control-lg" type="search" placeholder="e.g., Rgma Nrxn3, up to 5 terms are allowed" aria-label="search" value="">
+      <input name="query" class="form-control form-control-lg" type="search" placeholder="Rgma Nrxn3" aria-label="search" value="">
       <button class="btn btn-outline-success my-2 my-sm-0" type="submit">Search</button>
     </form>
 	<br>
-	This app searches PubMed to find <u>sentences</u> that contain the query terms (e.g., gene symbols) and  a drug addiction related keyword.  <a href="https://github.com/chen42/RatsPub/blob/master/ratspub.py#L95-L129">These keywords</a> belong to the following categories:  
-<ul>
-<li> names of abused drugs, e.g., opioids</li>
-<li> terms describing addiction, e.g., relapse </li>
-<li> key brain regions implicated in addiction, e.g., ventral striatum </li>
-<li> neurotrasmission, e.g., dopaminergic </li>
-<li> synaptic plasticity, e.g., long term potentiation </li> 
-<li> intracellular signaling, e.g., phosphorylation </li>
-</ul>
-
+	This app searches PubMed to find <i>sentences</i> that contain the query terms (e.g., gene symbols, <b>up to five are allowed per search</b>) and  <a href="https://github.com/chen42/RatsPub/blob/master/ratspub.py#L95-L129">keywords</a> related to drug addiction.
+	<p>
 <br> 
-Live searches are conducted through PubMed to get relevant PMIDs, which are then used to retrieve the abstracts from a <a href="https://dataguide.nlm.nih.gov/edirect/archive.html">local archive</a>. The relationships are presented as an interactive <a href="https://js.cytoscape.org" >cytoscape</a> graph. The nodes can be moved around to better reveal the connections.  Clicking on the links will bring up the corresponding sentences in a new browser window. 
+Searches are conducted through PubMed to get relevant PMIDs, which are then used to retrieve the abstracts from a <a href="https://dataguide.nlm.nih.gov/edirect/archive.html">local archive</a>. The relationships are presented as an interactive <a href="https://js.cytoscape.org" >cytoscape</a> graph. The nodes can be moved around to better reveal the connections.  Clicking on the links will bring up the corresponding sentences in a new browser window. 
 <p>
 <hr>
 <a href="https://github.com/chen42/ratspub"> Source code </a>
diff --git a/templates/layout.html b/templates/layout.html
index d64b331..cf8e8ed 100644
--- a/templates/layout.html
+++ b/templates/layout.html
@@ -13,7 +13,7 @@
 </head>
 <body>
 
-	<nav class="navbar navbar-expand-lg navbar-light bg-light">
+	<nav class="navbar navbar-expand-lg navbar-dark bg-dark">
 	<a class="navbar-brand" href="/">RatsPub:</br> <span style="font-size:small"> <u>R</u>elationship  with <u>A</u>ddiction <u>T</u>hrough <u>S</u>earches of <u>Pub</u>Med </span></a>
   	<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
     <span class="navbar-toggler-icon"></span>
@@ -24,8 +24,6 @@
 	{% block content %}{% endblock %}
 	</div>
 
-<script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous"></script>
-<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js" integrity="sha384-JjSmVgyd0p3pXB1rRibZUAYoIIy6OrQ6VrjIEaFf/nJGzIxFDsf4x0xIM+B07jRM" crossorigin="anonymous"></script>
 <script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.6.0/cytoscape.min.js" integrity="sha256-uZV2wRlscgr52q3Wb3Oew0rKCPsM3g4aBTv46sF4qzg=" crossorigin="anonymous"></script>
 </body>
 
diff --git a/templates/sentences.html b/templates/sentences.html
index c481817..f8da871 100644
--- a/templates/sentences.html
+++ b/templates/sentences.html
@@ -1,8 +1,9 @@
 {% extends "layout.html" %}
 {% block content %}
+<br>
 
 {{ sentences | safe }}
-    
+ 
 {% endblock %}