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#!/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():
genes=session['query']
percent=round(100/(len(genes)*3),1)
snt_file=session['path']+"_snt"
cysdata=open(session['path']+"_cy","w+")
sntdata=open(snt_file,"w+")
def generate(genes, tf_name):
sentences=str()
edges=str()
nodes=default_nodes
progress=0
for gene in genes:
nodes+="{ data: { id: '" + gene + "', nodecolor:'#FADBD8', fontweight:700, url:'https://www.ncbi.nlm.nih.gov/gene/?term="+gene+"'} },\n"
progress+=percent
yield "data:"+str(progress)+"\n\n"
sent0=gene_addiction(gene)
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+edges)
cysdata.close()
yield "data:"+str(progress)+"\n\n"
return Response(generate(genes, snt_file), 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"
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)
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