From 5abc13ae06b2ce7e53480340a1b9292701dc4ab5 Mon Sep 17 00:00:00 2001
From: Hao Chen
Date: Sun, 12 May 2019 06:51:20 -0500
Subject: progress working

---
 s2.py | 112 ------------------------------------------------------------------
 1 file changed, 112 deletions(-)
 delete mode 100755 s2.py

(limited to 's2.py')

diff --git a/s2.py b/s2.py
deleted file mode 100755
index 7e2848b..0000000
--- a/s2.py
+++ /dev/null
@@ -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)
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