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authorHao Chen2019-05-12 05:40:39 -0500
committerHao Chen2019-05-12 05:40:39 -0500
commitbc6a6e1d5974cb1c9f8a181728d93dafc531da01 (patch)
treed09256b29d323a95f44d2fa4aec6928522c665ba
parent08503676ea318ade7a72fcd999a32bc6e5433e0c (diff)
downloadgenecup-bc6a6e1d5974cb1c9f8a181728d93dafc531da01.tar.gz
prog bar showing
-rwxr-xr-xs2.py112
-rw-r--r--templates/progress.html29
2 files changed, 141 insertions, 0 deletions
diff --git a/s2.py b/s2.py
new file mode 100755
index 0000000..7e2848b
--- /dev/null
+++ b/s2.py
@@ -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 %}
+
+
+