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authorhakangunturkun2020-03-17 20:33:55 -0500
committerhakangunturkun2020-03-17 20:33:55 -0500
commit3231b70c2c815d1d87908b09c71551c665857edd (patch)
tree4c46ee0840b39380632f571139d846fa71721430
parent6680945184dbe82176236cbdf58124fbcac6a934 (diff)
downloadgenecup-3231b70c2c815d1d87908b09c71551c665857edd.tar.gz
move writable files to datadir
-rwxr-xr-xserver.py54
1 files changed, 27 insertions, 27 deletions
diff --git a/server.py b/server.py
index 15699ac..9f68e22 100755
--- a/server.py
+++ b/server.py
@@ -16,10 +16,10 @@ import re
import pytz
app=Flask(__name__)
+datadir="/export/ratspub/"
app.config['SECRET_KEY'] = '#DtfrL98G5t1dC*4'
-app.config['SQLALCHEMY_DATABASE_URI'] = 'sqlite:///userspub.sqlite'
+app.config['SQLALCHEMY_DATABASE_URI'] = 'sqlite:///'+datadir+'userspub.sqlite'
db = SQLAlchemy(app)
-datadir="/export/ratspub/"
# the sqlite database
class users(db.Model):
@@ -209,10 +209,10 @@ def search():
#create a folder for the search
if ('email' in session):
user_login=1
- os.makedirs("./user/"+str(session['email']+"/"+timeextension+"_0_"+genes_for_folder_name+marker),exist_ok=True)
- session['user_folder'] = "./user/"+str(session['email'])
+ os.makedirs(datadir+"user/"+str(session['email']+"/"+timeextension+"_0_"+genes_for_folder_name+marker),exist_ok=True)
+ session['user_folder'] = datadir+"user/"+str(session['email'])
user_folder=session['user_folder']
- session['path'] = "./user/"+str(session['email'])+"/"+timeextension+"_0_"+genes_for_folder_name+marker+"/"+timeextension
+ session['path'] = datadir+"user/"+str(session['email'])+"/"+timeextension+"_0_"+genes_for_folder_name+marker+"/"+timeextension
percent=round(100/(len(genes)*6),1) # 6 categories
snt_file=session['path']+"_snt"
cysdata=open(session['path']+"_cy","w+")
@@ -351,34 +351,34 @@ def search():
json_edges = json_edges[:-2]
json_edges =json_edges+"]}"
#write edges to txt file in json format
- with open("json_edges.txt", 'w') as edgesjson:
+ with open(datadir+"edges.json", 'w') as edgesjson:
edgesjson.write(json_edges)
#write edges to txt file in json format also in user folder
if (user_login == 1):
- with open(user_folder+"/"+timeextension+"_0_"+genes_for_folder_name+marker+"/json_edges.txt", "w") as temp_file_edges:
+ with open(user_folder+"/"+timeextension+"_0_"+genes_for_folder_name+marker+"/edges.json", "w") as temp_file_edges:
temp_file_edges.write(json_edges)
#write nodes to txt file in json format
- with open("json_nodes.txt", 'w') as nodesjson:
+ with open(datadir+"nodes.json", 'w') as nodesjson:
#if (userlogin) == 1:
nodesjson.write(json_nodes)
#write nodes to txt file in json format also in user folder
if ('email' in session):
- with open("./user/"+str(session['email'])+"/"+timeextension+"_0_"+genes_for_folder_name+marker+"/json_nodes.txt", "w") as temp_file_nodes:
+ with open(datadir+"user/"+str(session['email'])+"/"+timeextension+"_0_"+genes_for_folder_name+marker+"/nodes.json", "w") as temp_file_nodes:
temp_file_nodes.write(json_nodes)
return Response(generate(genes, snt_file), mimetype='text/event-stream')
@app.route("/tableview")
def tableview():
- with open("json_nodes.txt") as jsonfile:
+ with open(datadir+"nodes.json") as jsonfile:
jnodes = json.load(jsonfile)
jedges =''
- file_edges = open('json_edges.txt', 'r')
+ file_edges = open(datadir+'edges.json', 'r')
for line in file_edges.readlines():
if ':' not in line:
nodata_temp = 1
else:
nodata_temp = 0
- with open("json_edges.txt") as edgesjsonfile:
+ with open(datadir+"edges.json") as edgesjsonfile:
jedges = json.load(edgesjsonfile)
break
genename=session['query']
@@ -397,16 +397,16 @@ def tableview():
@app.route("/tableview0")
def tableview0():
- with open("json_nodes.txt") as jsonfile:
+ with open(datadir+"nodes.json") as jsonfile:
jnodes = json.load(jsonfile)
jedges =''
- file_edges = open('json_edges.txt', 'r')
+ file_edges = open(datadir+'edges.json', 'r')
for line in file_edges.readlines():
if ':' not in line:
nodata_temp = 1
else:
nodata_temp = 0
- with open("json_edges.txt") as edgesjsonfile:
+ with open(datadir+"edges.json") as edgesjsonfile:
jedges = json.load(edgesjsonfile)
break
genename=session['query']
@@ -425,11 +425,11 @@ def tableview0():
@app.route("/userarchive")
def userarchive():
- if os.path.exists("./user/"+str(session['email'])) == False:
+ if os.path.exists(datadir+"user/"+str(session['email'])) == False:
flash("Search history doesn't exist!")
return render_template('index.html')
if ('email' in session):
- session['user_folder'] = "./user/"+str(session['email'])
+ session['user_folder'] = datadir+"user/"+str(session['email'])
session_id=session['id']
def sorted_alphanumeric(data):
convert = lambda text: int(text) if text.isdigit() else text.lower()
@@ -458,14 +458,14 @@ def userarchive():
@app.route('/remove', methods=['GET', 'POST'])
def remove():
remove_folder = request.args.get('remove_folder')
- shutil.rmtree("./user/"+str(session['email']+"/"+remove_folder), ignore_errors=True)
+ shutil.rmtree(datadir+"user/"+str(session['email']+"/"+remove_folder), ignore_errors=True)
return redirect(url_for('userarchive'))
@app.route('/date', methods=['GET', 'POST'])
def date():
select_date = request.args.get('selected_date')
#open the cache folder for the user
- tf_path="./user"
+ tf_path=datadir+"user"
if ('email' in session):
time_extension = str(select_date)
time_extension = time_extension.split('_0_')[0]
@@ -477,25 +477,25 @@ def date():
else:
tf_path=tempfile.gettempdir()
session['path']=tf_path+"/tmp" + ''.join(random.choice(string.ascii_letters) for x in range(6))
- with open(tf_path+"/"+str(session['email'])+"/"+select_date+"/json_edges.txt", "r") as archive_file:
- with open("json_edges.txt", "w") as temp_file:
+ with open(tf_path+"/"+str(session['email'])+"/"+select_date+"/edges.json", "r") as archive_file:
+ with open(datadir+"edges.json", "w") as temp_file:
for line in archive_file:
temp_file.write(line)
- with open(tf_path+"/"+str(session['email'])+"/"+select_date+"/json_nodes.txt", "r") as archive_file:
- with open("json_nodes.txt", "w") as temp_file:
+ with open(tf_path+"/"+str(session['email'])+"/"+select_date+"/nodes.json", "r") as archive_file:
+ with open(datadir+"nodes.json", "w") as temp_file:
for line in archive_file:
temp_file.write(line)
- with open("json_nodes.txt", "r") as jsonfile:
+ with open(datadir+"nodes.json", "r") as jsonfile:
jnodes = json.load(jsonfile)
jedges =''
- file_edges = open('json_edges.txt', 'r')
+ file_edges = open(datadir+'edges.json', 'r')
for line in file_edges.readlines():
if ':' not in line:
nodata_temp = 1
else:
nodata_temp = 0
- with open("json_edges.txt") as edgesjsonfile:
+ with open(datadir+"edges.json") as edgesjsonfile:
jedges = json.load(edgesjsonfile)
break
gene_list=[]
@@ -665,4 +665,4 @@ def top150genes():
if __name__ == '__main__':
db.create_all()
- app.run(debug=True, port=4206)
+ app.run(debug=True, port=4200)