diff options
| -rwxr-xr-x | server.py | 94 |
1 files changed, 47 insertions, 47 deletions
@@ -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__': |