diff options
Diffstat (limited to 's2.py')
| -rwxr-xr-x | s2.py | 112 |
1 files changed, 0 insertions, 112 deletions
@@ -1,112 +0,0 @@ -#!/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) |