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saving current files on Della
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‎.gitignore‎

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@@ -5,3 +5,4 @@ template/*
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*.swp
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__pycache__/
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*.pyc
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.ipynb_checkpoints/

‎PythonSubmitDella/guiHelper.py‎

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#!/usr/bin/python
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# guiHelper has functions that help build the gui and connect to della. The functions are called by submitWorm analysis codes.
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#
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try:
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import Tkinter as tk
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import tkFileDialog
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except ImportError:
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import tkinter as tk
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import tkinter.filedialog as tkFileDialog
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import paramiko
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import socket
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import os
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import pickle
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import getpass
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#server jobs willb e submitted to
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SERVER ='della.princeton.edu'
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#location of the ssh key file shared by lefierdata
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KEYPATH='/tigress/LEIFER/.ssh/id_rsa'
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#load the pickle files for default values to put into fields. The pickle files store your previous entries in the pickles2.p file in ~.
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def pickle_load():
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# get ready for pickled variables
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pickle_path = (os.path.expanduser('~') + "/platypusTemp/")
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pickle_file = pickle_path + "pickles2.p"
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if not os.path.exists(pickle_path):
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os.makedirs(pickle_path)
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if not os.path.exists(pickle_file):
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storedUsername = { "username": getpass.getuser() }
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pickle.dump( storedUsername, open(pickle_file, "wb" ) )
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# return the dictionary with all previous values stored.
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try:
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prevUser = pickle.load( open( pickle_file, "rb" ) )
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except:
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prevUser = {'username': getpass.getuser()}
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#fill in default values
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if 'username' not in prevUser:
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prevUser['username'] = "USER"
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if 'time' not in prevUser:
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prevUser['time'] = "180"
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if 'mem' not in prevUser:
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prevUser['mem'] = "16000"
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if 'date' not in prevUser:
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prevUser['date'] = "testing_sets"
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if 'folderName' not in prevUser:
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prevUser['folderName'] = "Brain_working_dataset"
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if 'frameNumber' not in prevUser:
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prevUser['frameNumber'] = "1000"
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if 'refNumber' not in prevUser:
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prevUser['refNumber'] = "100"
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if 'neuronNumber' not in prevUser:
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prevUser['neuronNumber'] = "150"
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if 'checkNumber' not in prevUser:
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prevUser['checkNumber'] = "500"
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if 'matlab_command' not in prevUser:
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prevUser['matlab_command']='Put your code here!'
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if 'code_path' not in prevUser:
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prevUser['code_path']='Put the path to the .path file here!'
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return prevUser
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#read the submissionParameters.txt file in the data folder to get the number of frames.
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def get_nframes(client,fullPath):
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print('Getting number of frames from GUI')
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subDataFile = fullPath + '/submissionParameters.txt'
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client2 = client.open_sftp()
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sub_data={}
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# read each line, saving key-values pairs into a dictionary
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try:
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with client2.open(subDataFile) as remote_file:
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for lines in remote_file:
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lines=lines.split(" ")
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print(lines)
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sub_data[lines[0]]=lines[1]
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except Exception:
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raise NameError("Remote File not found")
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if sub_data.get('NFrames') != None:
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print('Getting number of frames from Remote')
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NFrames=sub_data['NFrames']
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return NFrames
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else:
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raise NameError("Cannot connect to get number of Frames")
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def dellaConnect(username,password=None):
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#use the username to connect to della, if password is provided, use it, otherwise, use ssh keys
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if socket.gethostname()=='tigressdata.princeton.edu':
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#if on tigressdata, use path to key file file in /tigress/LEIFEr
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key = paramiko.RSAKey.from_private_key_file(KEYPATH)
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elif socket.gethostname()=='tigressdata2.princeton.edu':
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#key = paramiko.RSAKey.from_private_key_file(KEYPATH)
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key = paramiko.RSAKey.from_private_key_file("/home/"+username+"/.ssh/id_rsa")
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else:
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key = None
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# connect and submit job via sbatch
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client = paramiko.SSHClient()
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client.load_system_host_keys()
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client.set_missing_host_key_policy(paramiko.AutoAddPolicy())
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if not password:
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client.connect(SERVER, 22, username,pkey=key)
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else:
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try:
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client.connect(SERVER, 22, username, password)
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except Exception:
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raise Exception('Cannont connect, problem with username password combo')
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return client
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def passwordReqCheck(username):
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# check if a password is required for a given username
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# try to see if a password is needed
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try:
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dellaConnect(username)
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isNeedsPassword = False
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except paramiko.AuthenticationException:
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isNeedsPassword = True
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return isNeedsPassword
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def selectFolder(master=None):
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# select a folder using a popup window
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folder=tkFileDialog.askdirectory(mustexist=False , initialdir= '/tigress/LEIFER/PanNeuronal/')
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if folder:
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#parse the folder path and populate the filed on the gui.
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path,folderName=os.path.split(folder)
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path,date=os.path.split(path)
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master.e['parent_path'].delete(0,tk.END)
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master.e['parent_path'].insert(0,path)
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master.e['date'].delete(0,tk.END)
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master.e['date'].insert(0,date)
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master.e['folder_name'].delete(0,tk.END)
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master.e['folder_name'].insert(0,folderName)
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print(folder)
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def selectPath(master=None):
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filename = tkFileDialog.askopenfilename(initialdir= '/tigress/LEIFER/communalCode/ ')
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master.e['code_path'].delete(0,tk.END)
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master.e['code_path'].insert(0,filename)
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#
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# #class for building the gui and populating the rows
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class submitTK(tk.Tk):
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#build the gui with some number of max rows and cols,
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#submitTK is a subclass of tkinter's Tk().
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def __init__(self, rows=10, cols=2):
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tk.Tk.__init__(self)
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#build rows and cols
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for i in range(rows):
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self.columnconfigure(i,pad=3)
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for j in range(cols):
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self.rowconfigure(j, pad=3)
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# make counter for the row being populated
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self.row_count=0
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# self.e will have all the values of the rows stored
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self.e=dict()
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self.title("Options")
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# add a text row to the field, the row will have a text label,
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# row is added to the next open row.
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# field name for using in the e,
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# default field entry
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# show, for passwords, use '*'
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def addGuiField(self,label,name,default="",show=None):
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master_label = tk.Label(self, text=label)
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master_label.grid(row=self.row_count, column=0,sticky=tk.W+tk.E)
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self.e[name] = tk.Entry(self,show=show)
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self.e[name].insert(0, default)
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self.e[name].grid(row=self.row_count, column=1,sticky=tk.W+tk.E)
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self.row_count+=1
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# make checkbox, again with label and field name
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def addGuiCheck(self,label,name,default=1):
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master_label = tk.Label(self, text=label)
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master_label.grid(row=self.row_count, column=0, sticky=tk.W+tk.E)
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var1= tk.IntVar()
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self.e[name]= tk.Checkbutton(self, text=None, variable=var1)
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self.e[name].var = var1
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self.e[name].grid(row=self.row_count, column=1,sticky=tk.W+tk.E)
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self.e[name].var.set(default)
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self.row_count+=1
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# add a button with a text label and a function callback handle.
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def addGuiButton(self,label,b_command=None):
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self.b = tk.Button(self, text=label, width=10, command=b_command)
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self.b.grid(row=self.row_count,columnspan=2,sticky=tk.W+tk.E)
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self.row_count+=1
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#save values fo fields for defaults during next call
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def pickleDump(self):
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pickle_path = (os.path.expanduser('~') + "/platypusTemp/")
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pickle_file = pickle_path + "pickles2.p"
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prevUser=pickle_load()
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#refill prevUser dict with master entries
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if 'user_name' in self.e:
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prevUser['username']=self.e['user_name'].get()
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if 'time' in self.e:
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prevUser['time']=self.e['time'].get()
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if 'mem' in self.e:
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prevUser['mem']=self.e['mem'].get()
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if 'date' in self.e:
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prevUser['date'] = self.e['date'].get()
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if 'folder_name' in self.e:
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prevUser['folderName']=self.e['folder_name'].get()
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if 'nframes' in self.e:
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prevUser['frameNumber']=self.e['nframes'].get()
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if 'n_ref' in self.e:
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prevUser['refNumber']=self.e['n_ref'].get()
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if 'n_neurons' in self.e:
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prevUser['neuronNumber']=self.e['n_neurons'].get()
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if 'n_checks' in self.e:
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prevUser['checkNumber']=self.e['n_checks'].get()
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if 'matlab_command' in self.e:
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prevUser['matlab_command']=self.e['matlab_command'].get()
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if 'code_path' in self.e:
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prevUser['code_path']=self.e['code_path'].get()
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#save prevUser as pickle
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pickle.dump(prevUser, open(pickle_file, "wb" ) )
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# run the main loop.
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def run(self):
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tk.mainloop()
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‎PythonSubmitDella/paramiko/__init__.py‎

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# Copyright (C) 2003-2011 Robey Pointer <robeypointer@gmail.com>
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#
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# This file is part of paramiko.
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#
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# Paramiko is free software; you can redistribute it and/or modify it under the
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# terms of the GNU Lesser General Public License as published by the Free
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# Software Foundation; either version 2.1 of the License, or (at your option)
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# any later version.
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#
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# Paramiko is distributed in the hope that it will be useful, but WITHOUT ANY
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# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
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# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
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# details.
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#
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# You should have received a copy of the GNU Lesser General Public License
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# along with Paramiko; if not, write to the Free Software Foundation, Inc.,
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# 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
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# flake8: noqa
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import sys
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from paramiko._version import __version__, __version_info__
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from paramiko.transport import SecurityOptions, Transport
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from paramiko.client import (
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SSHClient,
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MissingHostKeyPolicy,
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AutoAddPolicy,
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RejectPolicy,
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WarningPolicy,
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)
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from paramiko.auth_handler import AuthHandler
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from paramiko.ssh_gss import GSSAuth, GSS_AUTH_AVAILABLE, GSS_EXCEPTIONS
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from paramiko.channel import (
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Channel,
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ChannelFile,
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ChannelStderrFile,
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ChannelStdinFile,
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)
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from paramiko.ssh_exception import (
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AuthenticationException,
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BadAuthenticationType,
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BadHostKeyException,
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ChannelException,
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ConfigParseError,
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CouldNotCanonicalize,
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IncompatiblePeer,
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PasswordRequiredException,
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ProxyCommandFailure,
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SSHException,
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)
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from paramiko.server import ServerInterface, SubsystemHandler, InteractiveQuery
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from paramiko.rsakey import RSAKey
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from paramiko.dsskey import DSSKey
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from paramiko.ecdsakey import ECDSAKey
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from paramiko.ed25519key import Ed25519Key
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from paramiko.sftp import SFTPError, BaseSFTP
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from paramiko.sftp_client import SFTP, SFTPClient
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from paramiko.sftp_server import SFTPServer
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from paramiko.sftp_attr import SFTPAttributes
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from paramiko.sftp_handle import SFTPHandle
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from paramiko.sftp_si import SFTPServerInterface
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from paramiko.sftp_file import SFTPFile
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from paramiko.message import Message
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from paramiko.packet import Packetizer
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from paramiko.file import BufferedFile
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from paramiko.agent import Agent, AgentKey
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from paramiko.pkey import PKey, PublicBlob
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from paramiko.hostkeys import HostKeys
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from paramiko.config import SSHConfig, SSHConfigDict
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from paramiko.proxy import ProxyCommand
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from paramiko.common import (
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AUTH_SUCCESSFUL,
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AUTH_PARTIALLY_SUCCESSFUL,
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AUTH_FAILED,
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OPEN_SUCCEEDED,
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OPEN_FAILED_ADMINISTRATIVELY_PROHIBITED,
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OPEN_FAILED_CONNECT_FAILED,
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OPEN_FAILED_UNKNOWN_CHANNEL_TYPE,
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OPEN_FAILED_RESOURCE_SHORTAGE,
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)
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from paramiko.sftp import (
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SFTP_OK,
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SFTP_EOF,
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SFTP_NO_SUCH_FILE,
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SFTP_PERMISSION_DENIED,
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SFTP_FAILURE,
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SFTP_BAD_MESSAGE,
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SFTP_NO_CONNECTION,
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SFTP_CONNECTION_LOST,
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SFTP_OP_UNSUPPORTED,
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)
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from paramiko.common import io_sleep
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__author__ = "Jeff Forcier <jeff@bitprophet.org>"
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__license__ = "GNU Lesser General Public License (LGPL)"
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__all__ = [
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"Agent",
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"AgentKey",
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"AuthenticationException",
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"AutoAddPolicy",
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"BadAuthenticationType",
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"BadHostKeyException",
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"BufferedFile",
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"Channel",
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"ChannelException",
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"ConfigParseError",
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"CouldNotCanonicalize",
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"DSSKey",
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"ECDSAKey",
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"Ed25519Key",
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"HostKeys",
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"Message",
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"MissingHostKeyPolicy",
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"PKey",
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"PasswordRequiredException",
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"ProxyCommand",
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"ProxyCommandFailure",
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"RSAKey",
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"RejectPolicy",
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"SFTP",
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"SFTPAttributes",
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"SFTPClient",
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"SFTPError",
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"SFTPFile",
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"SFTPHandle",
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"SFTPServer",
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"SFTPServerInterface",
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"SSHClient",
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"SSHConfig",
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"SSHConfigDict",
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"SSHException",
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"SecurityOptions",
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"ServerInterface",
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"SubsystemHandler",
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"Transport",
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"WarningPolicy",
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"io_sleep",
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"util",
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]

‎PythonSubmitDella/paramiko/_version.py‎

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__version_info__ = (2, 9, 2)
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__version__ = ".".join(map(str, __version_info__))

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