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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
import os
app=Flask(__name__)
app.config['SECRET_KEY'] = '#DtfrL98G5t1dC*4'
@app.route("/")
def root():
return render_template('index.html')
@app.route("/about")
def about():
return render_template('about.html')
@app.route('/progress')
def progress():
# only 1-6 terms are allowed
genes=request.args.get('query')
genes=genes.replace(",", " ")
genes=genes.replace(";", " ")
genes=re.sub(r'\bLOC\d*?\b', "", genes, flags=re.I)
genes=genes.split()
if len(genes)>=100:
message="<span class='text-danger'>Up to 100 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', url_in="search", url_out="cytoscape")
@app.route("/search")
def search():
genes=session['query']
percent=round(100/(len(genes)*4),1)
snt_file=session['path']+"_snt"
cysdata=open(session['path']+"_cy","w+")
sntdata=open(snt_file,"w+")
zeroLinkNode=open(session['path']+"_0link","w+")
def generate(genes, tf_name):
sentences=str()
edges=str()
nodes=default_nodes
progress=0
searchCnt=0
nodesToHide=str()
for gene in genes:
gene=gene.replace("-"," ")
# report progress immediately
progress+=percent
yield "data:"+str(progress)+"\n\n"
#addiction terms must present with at least one drug
addiction=undic(addiction_d) +") AND ("+undic(drug_d)
sent0=gene_category(gene, addiction_d, addiction, "addiction")
e0=generate_edges(sent0, tf_name)
#
drug=undic(drug_d)
sent1=gene_category(gene, drug_d, drug, "drug")
progress+=percent
yield "data:"+str(progress)+"\n\n"
e1=generate_edges(sent1, tf_name)
#
function=undic(function_d)
sent2=gene_category(gene, function_d, function, "function")
progress+=percent
yield "data:"+str(progress)+"\n\n"
e2=generate_edges(sent2, tf_name)
# brain has its own query terms that does not include the many short acronyms
sent3=gene_category(gene, brain_d, brain_query_term, "brain")
progress+=percent
e3=generate_edges(sent3, tf_name)
# gwas
e4=searchArchived('gwas', gene)
geneEdges=e0+e1+e2+e3+e4
## there is a bug here. zero link notes are not excluded anymore
if len(geneEdges) >1:
edges+=geneEdges
nodes+="{ data: { id: '" + gene + "', nodecolor:'#E74C3C', fontweight:700, url:'/startGeneGene?forTopGene="+gene+"'} },\n"
else:
nodesToHide+=gene + " "
sentences+=sent0+sent1+sent2+sent3
#save data before the last yield
searchCnt+=1
if (searchCnt==len(genes)):
progress=100
sntdata.write(sentences)
sntdata.close()
cysdata.write(nodes+edges)
cysdata.close()
zeroLinkNode.write(nodesToHide)
zeroLinkNode.close()
yield "data:"+str(progress)+"\n\n"
return Response(generate(genes, snt_file), mimetype='text/event-stream')
@app.route('/cytoscape')
def cytoscape():
message2="<b> This <i>Genes vs Keywords</i> graph is interactive: </b><li>Click on a line to see the indicated number of sentences <li> Click on a gene to search its relations with top 200 addiction genes<li>Click on a keyword to see the terms included in the search<li>Hover your pointer over a node will hide other links <li>Nodes can be moved around for better visibility, reload the page will restore the original layout<p>"
with open(session['path']+"_cy","r") as f:
elements=f.read()
with open(session['path']+"_0link","r") as z:
zeroLink=z.read()
if (len(zeroLink)>0):
message2+="<span style=\"color:darkred;\">No result was found for these genes: " + zeroLink + "</span>"
return render_template('cytoscape.html', elements=elements, message2=message2)
@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.upper() == gene0.upper() and cat.upper() == cat0.upper()) :
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>")
## show the cytoscape graph for one gene from the top gene list
@app.route("/showTopGene")
def showTopGene():
query=request.args.get('topGene')
nodesEdges=searchArchived('topGene',query)
message2="<li><strong>"+query + "</strong> is one of the top addiction genes. <li> An archived search is shown. Click on the blue circle to update the results and include keywords for brain region and gene function. <strong> The update may take a long time to finish.</strong> "
return render_template("cytoscape.html", elements=nodesEdges, message="Top addiction genes", message2=message2)
@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>")
@app.route("/startGeneGene")
def startGeneGene():
session['forTopGene']=request.args.get('forTopGene')
return render_template('progress.html', url_in="searchGeneGene", url_out="showGeneTopGene")
@app.route("/searchGeneGene")
def gene_gene():
tmp_ggPMID=session['path']+"_ggPMID"
gg_file=session['path']+"_ggSent" #gene_gene
result_file=session['path']+"_ggResult"
def generate(query):
progress=1
yield "data:"+str(progress)+"\n\n"
os.system("esearch -db pubmed -query \"" + query + "\" | efetch -format uid |sort >" + tmp_ggPMID)
abstracts=os.popen("comm -1 -2 topGene_uniq.pmid " + tmp_ggPMID + " |fetch-pubmed -path "+pubmed_path+ " | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText|sed \"s/-/ /g\"").read()
os.system("rm "+tmp_ggPMID)
progress=10
yield "data:"+str(progress)+"\n\n"
topGenes=dict()
out=str()
hitGenes=dict()
with open("topGene_symb_alias.txt", "r") as top_f:
for line in top_f:
(symb, alias)=line.strip().split("\t")
topGenes[symb]=alias.replace("; ","|")
allAbstracts= abstracts.split("\n")
abstractCnt=len(allAbstracts)
rowCnt=0
for row in allAbstracts:
rowCnt+=1
if rowCnt/10==int(rowCnt/10):
progress=10+round(rowCnt/abstractCnt,2)*80
yield "data:"+str(progress)+"\n\n"
tiab=row.split("\t")
pmid = tiab.pop(0)
tiab= " ".join(tiab)
sentences = sent_tokenize(tiab)
## keep the sentence only if it contains the gene
for sent in sentences:
if findWholeWord(query)(sent):
sent=re.sub(r'\b(%s)\b' % query, r'<strong>\1</strong>', sent, flags=re.I)
for symb in topGenes:
allNames=symb+"|"+topGenes[symb]
if findWholeWord(allNames)(sent) :
sent=sent.replace("<b>","").replace("</b>","")
sent=re.sub(r'\b(%s)\b' % allNames, r'<b>\1</b>', sent, flags=re.I)
out+=query+"\t"+"gene\t" + symb+"\t"+pmid+"\t"+sent+"\n"
if symb in hitGenes.keys():
hitGenes[symb]+=1
else:
hitGenes[symb]=1
progress=95
yield "data:"+str(progress)+"\n\n"
with open(gg_file, "w+") as gg:
gg.write(out)
gg.close()
results="<h4>"+query+" vs top addiction genes</h4> Click on the number of sentences will show those sentences. Click on the <span style=\"background-color:#FcF3cf\">top addiction genes</span> will show an archived search for that gene.<hr>"
topGeneHits={}
for key in hitGenes.keys():
url=gg_file+"|"+query+"|"+key
if hitGenes[key]==1:
sentword="sentence"
else:
sentword="sentences"
topGeneHits[ "<li> <a href=/sentences?edgeID=" + url+ " target=_new>" + "Show " + str(hitGenes[key]) + " " + sentword +" </a> about "+query+" and <a href=/showTopGene?topGene="+key+" target=_gene><span style=\"background-color:#FcF3cf\">"+key+"</span></a>" ]=hitGenes[key]
topSorted = [(k, topGeneHits[k]) for k in sorted(topGeneHits, key=topGeneHits.get, reverse=True)]
for k,v in topSorted:
results+=k
saveResult=open(result_file, "w+")
saveResult.write(results)
saveResult.close()
progress=100
yield "data:"+str(progress)+"\n\n"
## start the run
query=session['forTopGene']
return Response(generate(query), mimetype='text/event-stream')
@app.route('/showGeneTopGene')
def showGeneTopGene ():
with open(session['path']+"_ggResult", "r") as result_f:
results=result_f.read()
return render_template('sentences.html', sentences=results+"<p><br>")
## generate a page that lists all the top 150 addiction genes with links to cytoscape graph.
@app.route("/allTopGenes")
def top150genes():
return render_template("topAddictionGene.html")
if __name__ == '__main__':
app.run(debug=True, port=4200)
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