diff options
| -rwxr-xr-x | s2.py | 112 | ||||
| -rw-r--r-- | templates/progress.html | 29 |
2 files changed, 141 insertions, 0 deletions
@@ -0,0 +1,112 @@ +#!/bin/env python3 +from flask import Flask, render_template, request, session, Response +import tempfile +import random +import string +from ratspub import * +import time + +app=Flask(__name__) +app.config['SECRET_KEY'] = '#DtfrL98G5t1dC*4' + +@app.route("/") +def root(): + return render_template('index.html') + +@app.route('/progress') +def progress(): + # only 1-6 terms are allowed + genes=request.args.get('query') + genes=genes.replace(",", " ") + genes=genes.replace(";", " ") + genes=genes.split() + if len(genes)>=6: + message="<span class='text-danger'>Up to five terms can be searched at a time</span>" + return render_template('index.html', message=message) + elif len(genes)==0: + message="<span class='text-danger'>Please enter a search term </span>" + return render_template('index.html', message=message) + # put the query in session cookie + session['query']=genes + # generate a unique session ID to track the results + tf_path=tempfile.gettempdir() + session['path']=tf_path+"/tmp" + ''.join(random.choice(string.ascii_letters) for x in range(6)) + return render_template('progress.html') + +@app.route("/search") +def search(): +# tf_path=tempfile.gettempdir() +# tf_name=tf_path+"/tmp"+''.join(random.choice(string.ascii_letters) for x in range(6)) + genes=session['query'] + percent=round(100/(len(genes)*3), 2) + print ("percent percent --->"+str(percent)) + cysdata=open(session['path']+"_cy","w+") + sntdata=open(session['path']+"_snt","w+") + def generate(genes): + sentences=str() + edges=str() + nodes=default_nodes + nodes=str() + progress=0 + #ft_name=session['path'] + ft_name="path" + for gene in genes: + nodes+="{ data: { id: '" + gene + "', nodecolor:'#FADBD8', fontweight:700, url:'https://www.ncbi.nlm.nih.gov/gene/?term="+gene+"'} },\n" + print ("xxxxxxxxxxxxxxxxxxxxxx") + print (genes) + sent0=gene_addiction(gene) + progress+=percent + print ("yyyyyyyyyyyyyx") + print(progress) + yield "data:"+str(progress)+"\n\n" + e0=generate_edges(sent0, "tf_name") + sent1=gene_functional(gene) + progress+=percent + yield "data:"+str(progress)+"\n\n" + e1=generate_edges(sent1, "tf_name") + sent2=gene_anatomical(gene) + progress+=percent + e2=generate_edges(sent2, "tf_name") + edges+=e0+e1+e2 + sentences+=sent0+sent1+sent2 + #save data before the last yield + if (progress>99): + progress=100 + sntdata.write(sentences) + sntdata.close() + cysdata.write(nodes) + cysdata.close() + yield "data:"+str(progress)+"\n\n" + return Response(generate(genes), mimetype='text/event-stream') + +@app.route('/cytoscape') +def cytoscape(): + with open(session['path']+"_cy","r") as f: + elements=f.read() + return render_template('cytoscape.html', elements=elements) + +@app.route("/sentences") +def sentences(): + edge=request.args.get('edgeID') + (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") + 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/progress.html b/templates/progress.html new file mode 100644 index 0000000..322604d --- /dev/null +++ b/templates/progress.html @@ -0,0 +1,29 @@ +{% extends "layout.html" %} +{% block content %} + +<script src="//ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script> + + <script> + var source = new EventSource("/search"); + source.onmessage = function(event) { + $('.progress-bar').css('width', event.data+'%').attr('aria-valuenow', event.data); + $('.progress-bar-label').text(event.data+'%'); + + if(event.data == 100){ + window.location.replace("/cytoscape") + source.close() + } + } + </script> + + <div id="progs" class="progress" style="width: 50%; margin: 50px;"> + <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 0%"> + <span class="progress-bar-label">0%</span> + </div> + </div> + + +{% endblock %} + + + |