From e9438ef321c47409d47bbd0c363998094726b1b9 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 22 Jun 2024 05:23:42 -0500
Subject: Bulk add version info to template renderer

---
 server.py | 94 +++++++++++++++++++++++++++++++--------------------------------
 1 file changed, 47 insertions(+), 47 deletions(-)

diff --git a/server.py b/server.py
index 331bb60..3cdb307 100755
--- a/server.py
+++ b/server.py
@@ -127,7 +127,7 @@ def root():
 
     onto_cont=open("addiction.onto","r").read()
     dict_onto=ast.literal_eval(onto_cont)
-    return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+    return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
 
 
 @app.route("/login", methods=["POST", "GET"])
@@ -154,8 +154,8 @@ def login():
             onto_list = session['onto_list']
         else:
             flash("Invalid username or password!", "inval")
-            return render_template('signup.html')
-    return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+            return render_template('signup.html',version=version())
+    return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
 
 
 @app.route("/signup", methods=["POST", "GET"])
@@ -173,7 +173,7 @@ def signup():
 
         if (found_user and (bcrypt.checkpw(password.encode('utf8'), found_user.password)==False)):
             flash("Already registered, but wrong password!", "inval")
-            return render_template('signup.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+            return render_template('signup.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
 
         session['email'] = email
         session['hashed_email'] = hashlib.md5(session['email'] .encode('utf-8')).hexdigest()
@@ -199,12 +199,12 @@ def signup():
             os.makedirs(session['user_folder']+"/ontology/")
 
         flash("Login Succesful!")
-        return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+        return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
     else:
         if 'email' in session:
             flash("Already Logged In!")
-            return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
-        return render_template('signup.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+            return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
+        return render_template('signup.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
 
 
 @app.route("/signin", methods=["POST", "GET"])
@@ -228,11 +228,11 @@ def signin():
             onto_len_dir = session['onto_len_dir']
             onto_list = session['onto_list']
             dict_onto=ast.literal_eval(onto_cont)
-            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
         else:
             flash("Invalid username or password!", "inval")
-            return render_template('signup.html')
-    return render_template('signin.html')
+            return render_template('signup.html',version=version())
+    return render_template('signin.html',version=version())
 
 # change password
 @app.route("/<nm_passwd>", methods=["POST", "GET"])
@@ -258,7 +258,7 @@ def profile(nm_passwd):
                 onto_list = ''
                 onto_cont=open("addiction.onto","r").read()
                 dict_onto=ast.literal_eval(onto_cont)
-                return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+                return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
             # remove reserved characters from the hashed passwords
             reserved = (";", "/", "?", ":", "@", "=", "&", ".")
             def replace_reserved(fullstring):
@@ -268,7 +268,7 @@ def profile(nm_passwd):
             replaced_passwd = replace_reserved(str(found_user.password))
 
             if replaced_passwd == user_passwd:
-                return render_template("/passwd_change.html", name=user_name)
+                return render_template("/passwd_change.html", name=user_name,version=version())
             else:
                 return "This url does not exist"
         else:
@@ -293,12 +293,12 @@ def logout():
     flash("You have been logged out, {user1}", "inval")
     session.pop('email', None)
     session.clear()
-    return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+    return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
 
 
 @app.route("/about")
 def about():
-    return render_template('about.html',version=version())
+    return render_template('about.html',version=version)
 
 # Ontology selection
 @app.route("/index_ontology", methods=["POST", "GET"])
@@ -319,7 +319,7 @@ def index_ontology():
     dict_onto=ast.literal_eval(onto_cont)
     onto_len_dir = session['onto_len_dir']
     onto_list = session['onto_list']
-    return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = session['namecat'], dict_onto=dict_onto )
+    return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = session['namecat'], dict_onto=dict_onto ,version=version())
 
 
 @app.route("/ontology", methods=["POST", "GET"])
@@ -567,7 +567,7 @@ def ontology():
     else:
         onto_len_dir=0
         onto_list=''
-    return render_template('ontology.html',dict_onto=dict_onto, namecat=name_to_html, onto_len_dir=onto_len_dir, onto_list=onto_list)
+    return render_template('ontology.html',dict_onto=dict_onto, namecat=name_to_html, onto_len_dir=onto_len_dir, onto_list=onto_list,version=version())
 
 
 @app.route("/ontoarchive")
@@ -581,7 +581,7 @@ def ontoarchive():
             onto_list = ''
             onto_cont=open("addiction.onto","r").read()
             dict_onto=ast.literal_eval(onto_cont)
-            return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+            return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
         else:
             session['user_folder'] = datadir+"/user/"+str(session['hashed_email'])
     else:
@@ -590,7 +590,7 @@ def ontoarchive():
         onto_list = ''
         onto_cont=open("addiction.onto","r").read()
         dict_onto=ast.literal_eval(onto_cont)
-        return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+        return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
 
     session_id=session['id']
     def sorted_alphanumeric(data):
@@ -616,7 +616,7 @@ def ontoarchive():
     session['onto_len_dir'] = onto_len_dir
     session['onto_list'] = onto_list
     message3="<ul><li> Click on the Date/Time to view archived results. <li>The Date/Time are based on US Central time zone.</ul> "
-    return render_template('ontoarchive.html', onto_len_dir=onto_len_dir, onto_list = onto_list, onto_folder_list=onto_folder_list, onto_directory_list=onto_directory_list, session_id=session_id, message3=message3)
+    return render_template('ontoarchive.html', onto_len_dir=onto_len_dir, onto_list = onto_list, onto_folder_list=onto_folder_list, onto_directory_list=onto_directory_list, session_id=session_id, message3=message3,version=version())
 
 
 # Remove an ontology folder
@@ -632,7 +632,7 @@ def removeonto():
         onto_list = ''
         onto_cont=open("addiction.onto","r").read()
         dict_onto=ast.literal_eval(onto_cont)
-        return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+        return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
 
 
 @app.route('/progress')
@@ -662,7 +662,7 @@ def progress():
         onto_cont=open("addiction.onto","r").read()
         dict_onto=ast.literal_eval(onto_cont)
         message="<span class='text-danger'>Up to 200 terms can be searched at a time</span>"
-        return render_template('index.html' ,onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto, message=message)
+        return render_template('index.html' ,onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto, message=message,version=version())
 
     if len(genes)==0:
         if ('email' in session):
@@ -674,7 +674,7 @@ def progress():
         onto_cont=open("addiction.onto","r").read()
         dict_onto=ast.literal_eval(onto_cont)
         message="<span class='text-danger'>Please enter a search term </span>"
-        return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto, message=message)
+        return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto, message=message,version=version())
 
     tf_path=tempfile.gettempdir()
     genes_for_folder_name =""
@@ -762,7 +762,7 @@ def progress():
         genes_session += str(gen) + "_"
     genes_session = genes_session[:-1]
     session['query']=genes
-    return render_template('progress.html', url_in="search", url_out="cytoscape/?rnd="+rnd+"&genequery="+genes_session)
+    return render_template('progress.html', url_in="search", url_out="cytoscape/?rnd="+rnd+"&genequery="+genes_session,version=version())
 
 
 @app.route("/search")
@@ -991,7 +991,7 @@ def tableview():
             onto_list = ''
             onto_cont=open("addiction.onto","r").read()
             dict_onto=ast.literal_eval(onto_cont)
-            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
 
         jedges =''
         file_edges = open(datadir+gene_url_tmp +'/edges.json', 'r')
@@ -1015,7 +1015,7 @@ def tableview():
             onto_list = ''
             onto_cont=open("addiction.onto","r").read()
             dict_onto=ast.literal_eval(onto_cont)
-            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
         jedges =''
         file_edges = open(gene_url_tmp +'/edges.json', 'r')
         for line in file_edges.readlines():
@@ -1039,7 +1039,7 @@ def tableview():
     num_gene = gene_name.count(',')+1
 
     message3="<ul><li> <font color=\"#E74C3C\">Click on the abstract count to read sentences linking the keyword and the gene</font>  <li> Click on a keyword to see the terms included in the search. <li>View the results in <a href='\\cytoscape/?rnd={}&genequery={}'\ ><b> a graph.</b></a> </ul> Links will be preserved when the table is copy-n-pasted into a spreadsheet.".format(rnd_url,genes_url)
-    return render_template('tableview.html', genes_session_tmp = genes_session_tmp, nodata_temp=nodata_temp, num_gene=num_gene, jedges=jedges, jnodes=jnodes,gene_name=gene_name, message3=message3, rnd_url=rnd_url, genes_url=genes_url)
+    return render_template('tableview.html', genes_session_tmp = genes_session_tmp, nodata_temp=nodata_temp, num_gene=num_gene, jedges=jedges, jnodes=jnodes,gene_name=gene_name, message3=message3, rnd_url=rnd_url, genes_url=genes_url,version=version())
 
 
 # Table for the zero abstract counts
@@ -1062,7 +1062,7 @@ def tableview0():
             onto_list = ''
             onto_cont=open("addiction.onto","r").read()
             dict_onto=ast.literal_eval(onto_cont)
-            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
 
         jedges =''
         file_edges = open(datadir+gene_url_tmp+'/edges.json', 'r')
@@ -1086,7 +1086,7 @@ def tableview0():
             onto_list = ''
             onto_cont=open("addiction.onto","r").read()
             dict_onto=ast.literal_eval(onto_cont)
-            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
 
         jedges =''
         file_edges = open(gene_url_tmp+'/edges.json', 'r')
@@ -1112,7 +1112,7 @@ def tableview0():
     gene_name = gene_name+added
     num_gene = gene_name.count(',')+1
     message4="<b> Notes: </b><li> These are the keywords that have <b>zero</b> abstract counts. <li>View all the results in <a href='\\cytoscape/?rnd={}&genequery={}'><b> a graph.</b></a> ".format(rnd_url,genes_url)
-    return render_template('tableview0.html',nodata_temp=nodata_temp, num_gene=num_gene, jedges=jedges, jnodes=jnodes,gene_name=gene_name, message4=message4)
+    return render_template('tableview0.html',nodata_temp=nodata_temp, num_gene=num_gene, jedges=jedges, jnodes=jnodes,gene_name=gene_name, message4=message4,version=version())
 
 
 @app.route("/userarchive")
@@ -1125,7 +1125,7 @@ def userarchive():
     if ('email' in session):
         if os.path.exists(datadir+"/user/"+str(session['hashed_email'])) == False:
             flash("Search history doesn't exist!")
-            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
         else:
             session['user_folder'] = datadir+"/user/"+str(session['hashed_email'])
     else:
@@ -1135,7 +1135,7 @@ def userarchive():
         onto_list = ''
         onto_cont=open("addiction.onto","r").read()
         dict_onto=ast.literal_eval(onto_cont)
-        return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+        return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
 
     session_id=session['id']
     def sorted_alphanumeric(data):
@@ -1165,7 +1165,7 @@ def userarchive():
             directory_list.append(filename)
     len_dir = len(directory_list)
     message3="<ul><li> Click on the Date/Time to view archived results. <li>The Date/Time are based on US Central time zone.</ul> "
-    return render_template('userarchive.html', len_dir=len_dir, gene_list = gene_list, onto_list = onto_list, folder_list=folder_list, directory_list=directory_list, session_id=session_id, message3=message3)
+    return render_template('userarchive.html', len_dir=len_dir, gene_list = gene_list, onto_list = onto_list, folder_list=folder_list, directory_list=directory_list, session_id=session_id, message3=message3,version=version())
 
 
 # Remove the search directory
@@ -1181,7 +1181,7 @@ def remove():
         onto_list = ''
         onto_cont=open("addiction.onto","r").read()
         dict_onto=ast.literal_eval(onto_cont)
-        return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+        return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
 
 
 @app.route('/date', methods=['GET', 'POST'])
@@ -1242,9 +1242,9 @@ def date():
         onto_list = ''
         onto_cont=open("addiction.onto","r").read()
         dict_onto=ast.literal_eval(onto_cont)
-        return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+        return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
     message3="<ul><li> <font color=\"#E74C3C\">Click on the abstract count to read sentences linking the keyword and the gene</font> <li> Click on a keyword to see the terms included in the search. <li>View the results in <a href='\\cytoscape/?rnd={}&genequery={}'\ ><b> a graph.</b></a> </ul> Links will be preserved when the table is copy-n-pasted into a spreadsheet.".format(select_date,genes_session)
-    return render_template('tableview.html',nodata_temp=nodata_temp, num_gene=num_gene,genes_session_tmp = genes_session_tmp, rnd_url=select_date ,jedges=jedges, jnodes=jnodes,gene_name=gene_name, genes_url=genes_session, message3=message3)
+    return render_template('tableview.html',nodata_temp=nodata_temp, num_gene=num_gene,genes_session_tmp = genes_session_tmp, rnd_url=select_date ,jedges=jedges, jnodes=jnodes,gene_name=gene_name, genes_url=genes_session, message3=message3,version=version())
 
 @app.route('/cytoscape/')
 def cytoscape():
@@ -1267,7 +1267,7 @@ def cytoscape():
             onto_list = ''
             onto_cont=open("addiction.onto","r").read()
             dict_onto=ast.literal_eval(onto_cont)
-            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
 
         with open(rnd_url_tmp+"_0link","r") as z:
             zeroLink=z.read()
@@ -1285,13 +1285,13 @@ def cytoscape():
             onto_list = ''
             onto_cont=open("addiction.onto","r").read()
             dict_onto=ast.literal_eval(onto_cont)
-            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto)
+            return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto,version=version())
 
         with open(rnd_url_tmp+"_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, message2=message2)
+    return render_template('cytoscape.html', elements=elements, message2=message2,version=version())
 
 
 @app.route("/sentences")
@@ -1359,7 +1359,7 @@ def sentences():
     elif(out_neg != "" and out_pos == ""):
         out = out1 +out2+stress_cellular+out_neg
     K.clear_session()
-    return render_template('sentences.html', sentences="<ol>"+out+"</ol><p>")
+    return render_template('sentences.html', sentences="<ol>"+out+"</ol><p>",version=version())
 
 
 # Show the cytoscape graph for one gene from the top gene list
@@ -1368,7 +1368,7 @@ def showTopGene():
     query=request.args.get('topGene')
     nodesEdges=searchArchived('topGene',query, 'cys','','')[0]
     message2="<li><strong>"+query + "</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=nodesEdges, message="Top addiction genes", message2=message2)
+    return render_template("cytoscape.html", elements=nodesEdges, message="Top addiction genes", message2=message2,version=version())
 
 
 @app.route("/shownode")
@@ -1385,7 +1385,7 @@ def shownode():
         for ky in dictionary.keys():
             if node in dictionary[ky].keys():
                 out="<p>"+node.upper()+"<hr><li>"+ next(iter(dictionary[ky][node])).replace("|", "<li>")
-    return render_template('sentences.html', sentences=out+"<p>")
+    return render_template('sentences.html', sentences=out+"<p>",version=version())
 
 
 @app.route("/synonyms")
@@ -1401,23 +1401,23 @@ def synonyms():
         synonym_list_str = ';'.join([str(syn) for syn in synonym_list])
         synonym_list_str +=';' + node
         case = 1
-        return render_template('genenames.html', case = case, gene = node.upper(), synonym_list = synonym_list, synonym_list_str=synonym_list_str)
+        return render_template('genenames.html', case = case, gene = node.upper(,version=version()), synonym_list = synonym_list, synonym_list_str=synonym_list_str)
     except:
         try:
             synonym_list = session['synonym_list']
             synonym_list_str = ';'.join([str(syn) for syn in synonym_list])
             synonym_list_str +=';' + node
             case = 1
-            return render_template('genenames.html', case=case, gene = session['main_gene'] , synonym_list = synonym_list, synonym_list_str=synonym_list_str)
+            return render_template('genenames.html', case=case, gene = session['main_gene'] , synonym_list = synonym_list, synonym_list_str=synonym_list_str,version=version())
         except:
             case = 2
-            return render_template('genenames.html', gene = node, case = case)
+            return render_template('genenames.html', gene = node, case = case,version=version())
 
 
 @app.route("/startGeneGene")
 def startGeneGene():
     session['forTopGene']=request.args.get('forTopGene')
-    return render_template('progress.html', url_in="searchGeneGene", url_out="showGeneTopGene")
+    return render_template('progress.html', url_in="searchGeneGene", url_out="showGeneTopGene",version=version())
 
 
 @app.route("/searchGeneGene")
@@ -1501,13 +1501,13 @@ def gene_gene():
 def showGeneTopGene ():
     with open(session['path']+"_ggResult", "r") as result_f:
         results=result_f.read()
-    return render_template('sentences.html', sentences=results+"<p><br>")
+    return render_template('sentences.html', sentences=results+"<p><br>",version=version())
 
 
 # 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")
+    return render_template("topAddictionGene.html",version=version())
 
 
 if __name__ == '__main__':
-- 
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