diff options
Diffstat (limited to 'server.py')
| -rwxr-xr-x | server.py | 32 |
1 files changed, 31 insertions, 1 deletions
@@ -91,6 +91,32 @@ def sentences(): 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(): + topGene=request.args.get('topGene') + topGeneSentFile="gene_addiction_sentences_cnt.tab" + with open(topGeneSentFile, "r") as sents: + catCnt={} + for sent in sents: + (symb, cat0, cat1, pmid, sent)=sent.split("\t") + if (symb == topGene) : + if cat1 in catCnt.keys(): + catCnt[cat1]+=1 + else: + catCnt[cat1]=1 + nodes= "{ data: { id: '" + topGene + "', nodecolor: '" + "#2471A3" + "', fontweight:700, url:'/progress?query="+topGene+"' } },\n" + edges=str() + for key in catCnt.keys(): + if ( key in drug_d.keys()): + nc=nodecolor["drug"] + else: + nc=nodecolor["addiction"] + nodes += "{ data: { id: '" + key + "', nodecolor: '" + nc + "', nodetype: 'top150', url:'/shownode?node="+key+"' } },\n" + edgeID=topGeneSentFile+"|"+topGene+"|"+key + edges+="{ data: { id: '" + edgeID+ "', source: '" + topGene + "', target: '" + key + "', sentCnt: " + str(catCnt[key]) + ", url:'/sentences?edgeID=" + edgeID + "' } },\n" + return render_template("cytoscape.html", elements=nodes+edges) + @app.route("/shownode") def shownode(): node=request.args.get('node') @@ -139,11 +165,15 @@ def gene_gene(): edges=str() for key in hitGenes.keys(): #nodes += "{ data: { id: '" + key + "', nodecolor: '" + nodecolor['top150'] + "', nodetype: 'top150', fontcolor:'#F2D7D5', url:'/shownode?nodetype=top150&node="+key+"' } },\n" - nodes += "{ data: { id: '" + key + "', nodecolor: '" + nodecolor['top150'] + "', nodetype: 'top150', url:'/shownode?nodetype=top150&node="+key+"' } },\n" + nodes += "{ data: { id: '" + key + "', nodecolor: '" + nodecolor['top150'] + "', nodetype: 'top150', url:'/showTopGene?topGene="+key+"' } },\n" edgeID=gg_file+"|"+query+"|"+key edges+="{ data: { id: '" + edgeID+ "', source: '" + query + "', target: '" + key + "', sentCnt: " + str(hitGenes[key]) + ", url:'/sentences?edgeID=" + edgeID + "' } },\n" return render_template("cytoscape.html", elements=nodes+edges) +## 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) |