From ff5c5d3aff13f4f81c9b3e9a39a63e7794cb609e Mon Sep 17 00:00:00 2001
From: Hao Chen
Date: Sat, 7 Mar 2020 22:34:27 -0600
Subject: Hakan fixing the count bug

---
 ratspub.py | 27 ++++++++++++++++-----------
 server.py  |  2 --
 2 files changed, 16 insertions(+), 13 deletions(-)

diff --git a/ratspub.py b/ratspub.py
index 355bc1f..f3effad 100755
--- a/ratspub.py
+++ b/ratspub.py
@@ -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
diff --git a/server.py b/server.py
index 90e783e..b0ba670 100755
--- a/server.py
+++ b/server.py
@@ -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:
-- 
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