") - -@app.route("/shownode") -def shownode(): - node=request.args.get('node') - allnodes={**brain_d, **drug_d, **function_d, **addiction_d} - out="
"+node.upper()+"
") - - -if __name__ == '__main__': - app.run(debug=True) diff --git a/server.py b/server.py index 457a8cd..b171c1e 100755 --- a/server.py +++ b/server.py @@ -1,9 +1,10 @@ #!/bin/env python3 -from flask import Flask, render_template, request, redirect +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' @@ -12,11 +13,9 @@ app.config['SECRET_KEY'] = '#DtfrL98G5t1dC*4' def root(): return render_template('index.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)) - all_sentences=str() +@app.route('/progress') +def progress(): + # only 1-6 terms are allowed genes=request.args.get('query') genes=genes.replace(",", " ") genes=genes.replace(";", " ") @@ -24,30 +23,64 @@ def search(): if len(genes)>=6: message="Up to five terms can be searched at a time" return render_template('index.html', message=message) - nodes=default_nodes - edges=str() - for gene in genes: - 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, tf_name) - sent1=gene_functional(gene) - e1=generate_edges(sent1, tf_name) - sent2=gene_anatomical(gene) - e2=generate_edges(sent2, tf_name) - edges+=e0+e1+e2 - all_sentences+=sent0+sent1+sent2 - #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) + elif len(genes)==0: + message="Please enter a search term " + 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" + sent0=gene_addiction(gene) + progress+=percent + 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+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="
{{ message | safe }}
-
+ +
+