links from nodes

1 files changed, 29 insertions, 14 deletions

diff --git a/server.py b/server.py
index 0f3d94b..804e0fc 100755
--- a/server.py
+++ b/server.py
@@ -1,5 +1,8 @@
 #!/bin/env  python3
 from flask import Flask, render_template, request, redirect
+import tempfile
+import random
+import string
 from ratspub import *
 
 app=Flask(__name__)
@@ -11,43 +14,55 @@ def root():
 
 @app.route("/search")
 def search():
-    global all_sentences 
+    tf_path=tempfile.gettempdir()
+    tf_name=tf_path+"/tmp"+''.join(random.choice(string.ascii_letters) for x in range(6))
     all_sentences=str()
     genes=request.args.get('query')
     genes=genes.replace(",", " ")
     genes=genes.replace(";", " ")
     genes=genes.split()
-    if len(genes)>=6: 
+    if len(genes)>=6:
         return render_template('index.html')
     nodes=default_nodes
     edges=str()
     for  gene in genes:
-        nodes+="{ data: { id: '" + gene +  "', nodecolor:'#FADBD8', fontweight:700} },\n"
+        nodes+="{ data: { id: '" + gene +  "', nodecolor:'#FADBD8', fontweight:700, url:'https://www.ncbi.nlm.nih.gov/gene/?term="+gene+"'} },\n"
         sent0=gene_addiction(gene)
-        e0=generate_edges(sent0)
+        e0=generate_edges(sent0, tf_name)
         sent1=gene_functional(gene)
-        e1=generate_edges(sent1)
+        e1=generate_edges(sent1, tf_name)
         sent2=gene_anatomical(gene)
-        e2=generate_edges(sent2)
+        e2=generate_edges(sent2, tf_name)
         edges+=e0+e1+e2
         all_sentences+=sent0+sent1+sent2
-    #f=open("all_sentences.tab","w")
-    #f.write(all_sentences)
-    #f.close()
+    #session['tmpfile']={'filename':tf_name}
+    with open(tf_name,"w") as f:
+        f.write(all_sentences)
+        f.close()
     return render_template('cytoscape.html', elements=nodes+edges)
 
 @app.route("/sentences")
 def sentences():
     edge=request.args.get('edgeID')
-    (gene0, cat0)=edge.split("|")
-    print (gene0 + cat0)
-    out="<h3>"+gene0 + " and " + cat0  + "</h3>\n"
-    for sent in all_sentences.split("\n"):
+    (tf_name, gene0, cat0)=edge.split("|")
+    out="<h3>"+gene0 + " and " + cat0  + "</h3><hr>\n"
+    print(tf_name)
+    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") 
+           (gene,nouse,cat, pmid, text)=sent.split("\t")
            if (gene == gene0 and cat == cat0) :
                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>")
 
+@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>")
+
+
 if __name__ == '__main__':
     app.run(debug=True)