diff options
| -rwxr-xr-x | server.py | 28 |
1 files changed, 21 insertions, 7 deletions
@@ -25,7 +25,7 @@ def progress(): genes=genes.replace(",", " ") genes=genes.replace(";", " ") genes=genes.split() - if len(genes)>=60: + if len(genes)>=160: 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: @@ -45,15 +45,16 @@ def search(): 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("-"," ") - nodes+="{ data: { id: '" + gene + "', nodecolor:'#E74C3C', fontweight:700, url:'/gene_gene?gene="+gene+"'} },\n" # report progress immediately progress+=percent yield "data:"+str(progress)+"\n\n" @@ -77,7 +78,12 @@ def search(): sent3=gene_category(gene, brain_d, brain_query_term, "brain") progress+=percent e3=generate_edges(sent3, tf_name) - edges+=e0+e1+e2+e3 + geneEdges=e0+e1+e2+e3 + if len(geneEdges) >1: + edges+=geneEdges + nodes+="{ data: { id: '" + gene + "', nodecolor:'#E74C3C', fontweight:700, url:'/gene_gene?gene="+gene+"'} },\n" + else: + nodesToHide+=gene + " " sentences+=sent0+sent1+sent2+sent3 #save data before the last yield searchCnt+=1 @@ -87,14 +93,21 @@ def search(): 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="This graph is interactive: <li>Click on a line to see the sentences <i>in a new window</i><li> Click on a gene to search its relations with top 150 addiction genes<li>Click on a keyword to see the terms included in the search <i> in a new window</i><p>" with open(session['path']+"_cy","r") as f: elements=f.read() - return render_template('cytoscape.html', elements=elements) + 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, message="Gene vs Keywords", message2=message2) @app.route("/sentences") def sentences(): @@ -134,7 +147,8 @@ def showTopGene(): 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) + message2="<li><strong>"+topGene + "</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=nodes+edges, message="Top addiction genes", message2=message2) @app.route("/shownode") def shownode(): @@ -180,14 +194,14 @@ def gene_gene(): gg.write(out) gg.close() nodecolor={'query':"#E74C3C", 'top150': "#ccd1d1"} - nodes= "{ data: { id: '" + query + "', nodecolor: '" + nodecolor['query'] + "', nodetype: 'ggquery', fontweight:700, url:'/shownode?nodetype=ggquery&node="+query+"' } },\n" + nodes= "{ data: { id: '" + query + "', nodecolor: '" + nodecolor['query'] + "', nodetype: 'ggquery', fontweight:700} },\n" 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:'/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) + return render_template("cytoscape.html", elements=nodes+edges, message="Gene vs top addiction genes", message2="<li>Top addiction genes are shown in grey. <li>Click on a grey gene will show an archived search. <li>Click on the lines will show gene-gene relations <i>in a new window</i>") ## generate a page that lists all the top 150 addiction genes with links to cytoscape graph. @app.route("/allTopGenes") |