diff options
-rwxr-xr-x | ratspub.py | 27 | ||||
-rwxr-xr-x | server.py | 2 |
2 files changed, 16 insertions, 13 deletions
@@ -56,38 +56,38 @@ def generate_nodes_json(nodes_d, nodetype): return(nodes_json0) def generate_edges(data, filename): - pmid_temp=0 + pmid_list=[] json0=str() edgeCnts={} for line in data.split("\n"): if len(line.strip())!=0: (source, cat, target, pmid, sent) = line.split("\t") edgeID=filename+"|"+source+"|"+target - if (edgeID in edgeCnts) and (pmid != pmid_temp): + if (edgeID in edgeCnts) and (pmid+target not in pmid_list): edgeCnts[edgeID]+=1 - pmid_temp = pmid - elif (edgeID not in edgeCnts): + pmid_list.append(pmid+target) + elif (edgeID not in edgeCnts) and (pmid+target not in pmid_list): edgeCnts[edgeID]=1 - pmid_temp = pmid + pmid_list.append(pmid+target) for edgeID in edgeCnts: (filename, source,target)=edgeID.split("|") json0+="{ data: { id: '" + edgeID + "', source: '" + source + "', target: '" + target + "', sentCnt: " + str(edgeCnts[edgeID]) + ", url:'/sentences?edgeID=" + edgeID + "' } },\n" return(json0) def generate_edges_json(data, filename): - pmid_temp=0 + pmid_list=[] edges_json0=str() edgeCnts={} for line in data.split("\n"): if len(line.strip())!=0: (source, cat, target, pmid, sent) = line.split("\t") edgeID=filename+"|"+source+"|"+target - if (edgeID in edgeCnts) and (pmid != pmid_temp): + if (edgeID in edgeCnts) and (pmid+target not in pmid_list): edgeCnts[edgeID]+=1 - pmid_temp = pmid - elif (edgeID not in edgeCnts): + pmid_list.append(pmid+target) + elif (edgeID not in edgeCnts) and (pmid+target not in pmid_list): edgeCnts[edgeID]=1 - pmid_temp = pmid + pmid_list.append(pmid+target) for edgeID in edgeCnts: (filename, source,target)=edgeID.split("|") edges_json0+="{ \"id\": \"" + edgeID + "\", \"source\": \"" + source + "\", \"target\": \"" + target + "\", \"sentCnt\": \"" + str(edgeCnts[edgeID]) + "\", \"url\":\"/sentences?edgeID=" + edgeID + "\" },\n" @@ -160,10 +160,15 @@ nj4=generate_nodes_json(stress_d, 'stress') nj5=generate_nodes_json(psychiatric_d, 'psychiatric') nj6=generate_nodes_json(psychiatric_d, 'GWAS') + +pubmed_path="~/Dropbox/ChenLab/Hakan/RatsPub/PubMed/Archive" + +''' host= os.popen('hostname').read().strip() if host=="x1": pubmed_path="/run/media/hao/PubMed/Archive/" elif host=="hchen3": pubmed_path="/media/hao/2d554499-6c5b-462d-85f3-5c49b25f4ac8/PubMed/Archive" elif host=="penguin2": - pubmed_path="/export2/PubMed/Archive"
\ No newline at end of file + pubmed_path="/export2/PubMed/Archive" +'''
\ No newline at end of file @@ -535,7 +535,6 @@ def cytoscape(): @app.route("/sentences") def sentences(): - pmid_temp="" pmid_list=[] edge=request.args.get('edgeID') (tf_name, gene0, cat0)=edge.split("|") @@ -547,7 +546,6 @@ def sentences(): (gene,nouse,cat, pmid, text)=sent.split("\t") if (gene.upper() == gene0.upper() and cat.upper() == cat0.upper() and (pmid+cat0 not in pmid_list)) : out3+= "<li> "+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>" - pmid_temp = pmid pmid_list.append(pmid+cat0) out1="<h3>"+gene0 + " and " + cat0 + "</h3>\n" if len(pmid_list)>1: |