saving current files on Della

.gitignore

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

PythonSubmitDella/guiHelper.py

@@ -0,0 +1,236 @@
+#!/usr/bin/python
+
+# guiHelper has functions that help build the gui and connect to della. The functions are called by submitWorm  analysis codes.
+#
+
+
+try:
+    import Tkinter as tk
+    import tkFileDialog
+except ImportError:
+    import tkinter as tk
+    import tkinter.filedialog as tkFileDialog
+import paramiko
+import socket
+import os
+import pickle
+import getpass
+
+
+#server jobs willb e submitted to
+SERVER ='della.princeton.edu'
+#location of the ssh key file shared by lefierdata
+KEYPATH='/tigress/LEIFER/.ssh/id_rsa'
+
+#load the pickle files for default values to put into fields. The pickle files store your previous entries in the pickles2.p file in ~. 
+def pickle_load():
+    # get ready for pickled variables 
+    pickle_path = (os.path.expanduser('~') + "/platypusTemp/")
+    pickle_file = pickle_path + "pickles2.p"
+    if not os.path.exists(pickle_path):
+            os.makedirs(pickle_path)
+
+    if not os.path.exists(pickle_file):
+            storedUsername = { "username": getpass.getuser() }
+            pickle.dump( storedUsername, open(pickle_file, "wb" ) )
+
+    # return the dictionary with all previous values stored.
+    try:
+        prevUser = pickle.load( open( pickle_file, "rb" ) )
+    except:
+        prevUser = {'username': getpass.getuser()}
+
+
+    #fill in default values
+    if 'username' not in prevUser:
+            prevUser['username'] = "USER"
+    if 'time' not in prevUser:
+            prevUser['time'] = "180"
+    if 'mem' not in prevUser:
+            prevUser['mem'] = "16000"
+    if 'date' not in prevUser:
+            prevUser['date'] = "testing_sets"
+    if 'folderName' not in prevUser:
+            prevUser['folderName'] = "Brain_working_dataset"
+    if 'frameNumber' not in prevUser:
+            prevUser['frameNumber'] = "1000"
+    if 'refNumber' not in prevUser:
+            prevUser['refNumber'] = "100"
+    if 'neuronNumber' not in prevUser:
+            prevUser['neuronNumber'] = "150"
+    if 'checkNumber' not in prevUser:
+            prevUser['checkNumber'] = "500"
+    if 'matlab_command' not in prevUser:
+            prevUser['matlab_command']='Put your code here!'
+    if 'code_path' not in prevUser:
+            prevUser['code_path']='Put the path to the .path file here!'
+
+
+    return prevUser
+
+
+#read the submissionParameters.txt file in the data folder to get the number of frames. 
+def get_nframes(client,fullPath):
+
+    print('Getting number of frames from GUI')
+    subDataFile = fullPath + '/submissionParameters.txt'
+    client2 = client.open_sftp()
+    sub_data={}
+    # read each line, saving key-values pairs into a dictionary
+    try:
+        with client2.open(subDataFile) as remote_file:
+            for lines in remote_file:
+                lines=lines.split(" ")
+                print(lines)
+                sub_data[lines[0]]=lines[1]
+    except Exception:
+        raise NameError("Remote File not found")
+
+    if sub_data.get('NFrames') != None:
+        print('Getting number of frames from Remote')
+        NFrames=sub_data['NFrames']
+        return NFrames
+    else: 
+        raise NameError("Cannot connect to get number of Frames")
+
+
+def dellaConnect(username,password=None):
+    #use the username to connect to della, if password is provided, use it, otherwise, use ssh keys
+    if socket.gethostname()=='tigressdata.princeton.edu':
+        #if on tigressdata, use path to key file file in /tigress/LEIFEr
+        key = paramiko.RSAKey.from_private_key_file(KEYPATH)
+    elif socket.gethostname()=='tigressdata2.princeton.edu':
+        #key = paramiko.RSAKey.from_private_key_file(KEYPATH)
+        key = paramiko.RSAKey.from_private_key_file("/home/"+username+"/.ssh/id_rsa")
+    else:
+        key = None
+    # connect and submit job via sbatch
+    client = paramiko.SSHClient()
+    client.load_system_host_keys()
+    client.set_missing_host_key_policy(paramiko.AutoAddPolicy())
+    if not password:
+        client.connect(SERVER, 22, username,pkey=key)
+    else:
+        try:
+            client.connect(SERVER, 22, username, password)
+        except Exception:
+            raise Exception('Cannont connect, problem with username password combo')
+    return client
+
+def passwordReqCheck(username):
+    # check if a password is required for a given username
+    # try to see if a password is needed
+    try:
+        dellaConnect(username)
+        isNeedsPassword = False
+    except paramiko.AuthenticationException:
+        isNeedsPassword = True
+    return isNeedsPassword
+
+def selectFolder(master=None):
+    # select a folder using a popup window
+    folder=tkFileDialog.askdirectory(mustexist=False , initialdir= '/tigress/LEIFER/PanNeuronal/')
+    if folder:
+        #parse the folder path and populate the filed on the gui. 
+        path,folderName=os.path.split(folder)
+        path,date=os.path.split(path)
+        master.e['parent_path'].delete(0,tk.END)
+        master.e['parent_path'].insert(0,path)
+        master.e['date'].delete(0,tk.END)
+        master.e['date'].insert(0,date)
+        master.e['folder_name'].delete(0,tk.END)
+        master.e['folder_name'].insert(0,folderName)
+        print(folder)
+
+def selectPath(master=None):
+    filename = tkFileDialog.askopenfilename(initialdir= '/tigress/LEIFER/communalCode/ ')
+    master.e['code_path'].delete(0,tk.END)
+    master.e['code_path'].insert(0,filename)
+# 
+# #class for building the gui and populating the rows
+class submitTK(tk.Tk):
+    #build the gui with some number of max rows and cols, 
+    #submitTK is a subclass of tkinter's Tk(). 
+    def __init__(self, rows=10, cols=2):
+
+        tk.Tk.__init__(self)
+        #build rows and cols
+        for i in range(rows):
+            self.columnconfigure(i,pad=3)
+        for j in range(cols):
+            self.rowconfigure(j, pad=3)
+        # make counter for the row being populated
+        self.row_count=0
+        # self.e will have all the values of the rows stored
+        self.e=dict()
+
+        self.title("Options")
+
+    # add a text row to the field, the row will have a text label, 
+    # row is added to the next open row. 
+    # field name for using in the e, 
+    # default field entry
+    # show, for passwords, use '*'
+
+    def addGuiField(self,label,name,default="",show=None):
+        master_label = tk.Label(self, text=label)
+        master_label.grid(row=self.row_count, column=0,sticky=tk.W+tk.E)
+        self.e[name] = tk.Entry(self,show=show)
+        self.e[name].insert(0, default)
+        self.e[name].grid(row=self.row_count, column=1,sticky=tk.W+tk.E)
+        self.row_count+=1
+
+    # make checkbox, again with label and field name
+    def addGuiCheck(self,label,name,default=1):
+        master_label = tk.Label(self, text=label)
+        master_label.grid(row=self.row_count, column=0, sticky=tk.W+tk.E)
+        var1= tk.IntVar()
+        self.e[name]= tk.Checkbutton(self, text=None, variable=var1)
+        self.e[name].var = var1
+        self.e[name].grid(row=self.row_count, column=1,sticky=tk.W+tk.E)
+        self.e[name].var.set(default)
+        self.row_count+=1
+
+    # add a button with a text label and a function callback handle. 
+    def addGuiButton(self,label,b_command=None):
+        self.b = tk.Button(self, text=label, width=10, command=b_command)
+        self.b.grid(row=self.row_count,columnspan=2,sticky=tk.W+tk.E)
+        self.row_count+=1
+
+    #save values fo fields for defaults during next call
+    def pickleDump(self):
+        pickle_path = (os.path.expanduser('~') + "/platypusTemp/")
+        pickle_file = pickle_path + "pickles2.p"
+        prevUser=pickle_load()
+        #refill prevUser dict with master entries
+        if 'user_name' in self.e:
+            prevUser['username']=self.e['user_name'].get()
+        if 'time' in self.e:
+            prevUser['time']=self.e['time'].get()
+        if 'mem' in self.e:
+            prevUser['mem']=self.e['mem'].get()
+        if 'date' in self.e:
+            prevUser['date'] = self.e['date'].get()
+        if 'folder_name' in self.e:
+            prevUser['folderName']=self.e['folder_name'].get()
+        if 'nframes' in self.e:
+            prevUser['frameNumber']=self.e['nframes'].get()
+        if 'n_ref' in self.e:
+            prevUser['refNumber']=self.e['n_ref'].get()
+        if 'n_neurons' in self.e:
+            prevUser['neuronNumber']=self.e['n_neurons'].get()
+        if 'n_checks' in self.e:
+            prevUser['checkNumber']=self.e['n_checks'].get()
+        if 'matlab_command' in self.e:
+            prevUser['matlab_command']=self.e['matlab_command'].get()
+        if 'code_path' in self.e:
+            prevUser['code_path']=self.e['code_path'].get()
+
+        #save prevUser as pickle
+        pickle.dump(prevUser, open(pickle_file, "wb" ) )
+
+
+    # run the main loop. 
+    def run(self):
+        tk.mainloop()
+

PythonSubmitDella/paramiko/__init__.py

@@ -0,0 +1,143 @@
+# Copyright (C) 2003-2011  Robey Pointer <[email protected]>
+#
+# This file is part of paramiko.
+#
+# Paramiko is free software; you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 2.1 of the License, or (at your option)
+# any later version.
+#
+# Paramiko is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with Paramiko; if not, write to the Free Software Foundation, Inc.,
+# 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA.
+
+# flake8: noqa
+import sys
+from paramiko._version import __version__, __version_info__
+from paramiko.transport import SecurityOptions, Transport
+from paramiko.client import (
+    SSHClient,
+    MissingHostKeyPolicy,
+    AutoAddPolicy,
+    RejectPolicy,
+    WarningPolicy,
+)
+from paramiko.auth_handler import AuthHandler
+from paramiko.ssh_gss import GSSAuth, GSS_AUTH_AVAILABLE, GSS_EXCEPTIONS
+from paramiko.channel import (
+    Channel,
+    ChannelFile,
+    ChannelStderrFile,
+    ChannelStdinFile,
+)
+from paramiko.ssh_exception import (
+    AuthenticationException,
+    BadAuthenticationType,
+    BadHostKeyException,
+    ChannelException,
+    ConfigParseError,
+    CouldNotCanonicalize,
+    IncompatiblePeer,
+    PasswordRequiredException,
+    ProxyCommandFailure,
+    SSHException,
+)
+from paramiko.server import ServerInterface, SubsystemHandler, InteractiveQuery
+from paramiko.rsakey import RSAKey
+from paramiko.dsskey import DSSKey
+from paramiko.ecdsakey import ECDSAKey
+from paramiko.ed25519key import Ed25519Key
+from paramiko.sftp import SFTPError, BaseSFTP
+from paramiko.sftp_client import SFTP, SFTPClient
+from paramiko.sftp_server import SFTPServer
+from paramiko.sftp_attr import SFTPAttributes
+from paramiko.sftp_handle import SFTPHandle
+from paramiko.sftp_si import SFTPServerInterface
+from paramiko.sftp_file import SFTPFile
+from paramiko.message import Message
+from paramiko.packet import Packetizer
+from paramiko.file import BufferedFile
+from paramiko.agent import Agent, AgentKey
+from paramiko.pkey import PKey, PublicBlob
+from paramiko.hostkeys import HostKeys
+from paramiko.config import SSHConfig, SSHConfigDict
+from paramiko.proxy import ProxyCommand
+
+from paramiko.common import (
+    AUTH_SUCCESSFUL,
+    AUTH_PARTIALLY_SUCCESSFUL,
+    AUTH_FAILED,
+    OPEN_SUCCEEDED,
+    OPEN_FAILED_ADMINISTRATIVELY_PROHIBITED,
+    OPEN_FAILED_CONNECT_FAILED,
+    OPEN_FAILED_UNKNOWN_CHANNEL_TYPE,
+    OPEN_FAILED_RESOURCE_SHORTAGE,
+)
+
+from paramiko.sftp import (
+    SFTP_OK,
+    SFTP_EOF,
+    SFTP_NO_SUCH_FILE,
+    SFTP_PERMISSION_DENIED,
+    SFTP_FAILURE,
+    SFTP_BAD_MESSAGE,
+    SFTP_NO_CONNECTION,
+    SFTP_CONNECTION_LOST,
+    SFTP_OP_UNSUPPORTED,
+)
+
+from paramiko.common import io_sleep
+
+
+__author__ = "Jeff Forcier <[email protected]>"
+__license__ = "GNU Lesser General Public License (LGPL)"
+
+__all__ = [
+    "Agent",
+    "AgentKey",
+    "AuthenticationException",
+    "AutoAddPolicy",
+    "BadAuthenticationType",
+    "BadHostKeyException",
+    "BufferedFile",
+    "Channel",
+    "ChannelException",
+    "ConfigParseError",
+    "CouldNotCanonicalize",
+    "DSSKey",
+    "ECDSAKey",
+    "Ed25519Key",
+    "HostKeys",
+    "Message",
+    "MissingHostKeyPolicy",
+    "PKey",
+    "PasswordRequiredException",
+    "ProxyCommand",
+    "ProxyCommandFailure",
+    "RSAKey",
+    "RejectPolicy",
+    "SFTP",
+    "SFTPAttributes",
+    "SFTPClient",
+    "SFTPError",
+    "SFTPFile",
+    "SFTPHandle",
+    "SFTPServer",
+    "SFTPServerInterface",
+    "SSHClient",
+    "SSHConfig",
+    "SSHConfigDict",
+    "SSHException",
+    "SecurityOptions",
+    "ServerInterface",
+    "SubsystemHandler",
+    "Transport",
+    "WarningPolicy",
+    "io_sleep",
+    "util",
+]

PythonSubmitDella/paramiko/_version.py

@@ -0,0 +1,2 @@
+__version_info__ = (2, 9, 2)
+__version__ = ".".join(map(str, __version_info__))