Mercurial > repos > rhohensinner > galaxy_irods_interface

annotate main.py @ 2:0641ea2f75b1 draft

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"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
author rhohensinner
date Fri, 02 Jul 2021 09:40:25 +0000
parents 19c1cecdfdfd
children d2be2eb8350f
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1
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1 ___author___ = "Richard Hohensinner"
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2 ___created___ = "04.02.2021"
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3 ___last_modified___ = "20.05.2021"
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4
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5 # general imports
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6 import os, sys, json
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7 import irods_upload
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8
1
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9 from shutil import copyfile
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10 from datetime import datetime
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11
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12 # irods-client imports
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13 from irods.session import iRODSSession
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14 from irods.models import Collection, DataObject
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15 from irods.query import SpecificQuery
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16
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17 # Tkinter imports
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18 from tkinter import messagebox, Label, Button, Entry, Listbox, Tk, PhotoImage, Grid
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19
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20 # global variables
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21 session = None
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22 file_path_list = []
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23 selected_file = ""
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24 session_success = False
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25 selection_success = False
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26 iRODSCredentials = {"host": "", "port": "", "user": "", "pw": "", "zone": ""}
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27
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28
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29 ########################################################################################################################
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30 # Main function of the iRODS tools
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31 #
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32 # IN:
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33 # JSON Object params (argv[1])
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34 # OUT:
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35 #
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36 ########################################################################################################################
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37 def main():
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38
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39 # check input parameters
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40 if len(sys.argv) == 2:
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41 params = json.loads(sys.argv[1])
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42 else:
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43 raise Exception("Invalid Parameters submitted!")
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44
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45 tool_type = params["tool_type"]
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46
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47 try:
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48 if params["tool_type"] != "up" and params["tool_type"] != "down":
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49 raise Exception("Invalid tool-type parameter submitted!")
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50 except:
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51 raise Exception("No tool-type parameter submitted!")
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52 is_download_call = True
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53 if tool_type == "up":
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54 is_download_call = False
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55
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56 # check params for integrity
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57 result_string, params_faulty = check_params(params)
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58
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59 if params_faulty:
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60 raise Exception(result_string)
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61
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62 global iRODSCredentials, session_success, selected_file, selection_success
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63 iRODSCredentials["host"] = params["irods_host"]
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64 iRODSCredentials["port"] = params["irods_port"]
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65 iRODSCredentials["zone"] = params["irods_zone"]
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66
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67 # create login window
2
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68 ## make_login_window(params)
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69 iRODSCredentials["user"] = params["irods_user"]
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70 iRODSCredentials["pw"] = params["irods_password"]
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71
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72 host = iRODSCredentials["host"]
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73 port = iRODSCredentials["port"]
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74 user = iRODSCredentials["user"]
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75 password = iRODSCredentials["pw"]
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76 zone = iRODSCredentials["zone"]
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77
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78 iRODSsession = get_iRODS_connection(host=host, port=port, user=user, password=password, zone=zone)
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79 global session, session_success
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80 try:
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81 coll = iRODSsession.collections.get("/" + zone + "/" + "home" + "/" + user)
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82 except Exception:
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83 raise Exception("Invalid Login")
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84
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85 if coll:
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86 session = iRODSsession
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87 session_success = True
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88
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89
1
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90 # check tool settings and start tool execution
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91 if session_success:
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92 # initialize download tool
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93 if params["tool_type"] == "down":
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94
2
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95 selected_file = params["file_path"]
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96 params["user"] = iRODSCredentials["pw"]
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97 params["password"] = iRODSCredentials["user"]
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98 # start download routine
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99 handle_download_call(params)
1
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100
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101 # initialize upload tool
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102 elif params["tool_type"] == "up":
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103
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104 if session_success:
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105 params["user"] = iRODSCredentials["pw"]
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106 params["password"] = iRODSCredentials["user"]
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107 # start upload routine
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108 handle_upload_call(params)
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109 else:
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110 raise Exception("Logging into iRODS failed")
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111 else:
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112 raise Exception("Logging into iRODS failed")
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113 # -------------------------------------------------------------------------------------------------------------------- #
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114
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115
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116 ########################################################################################################################
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117 # Login Window class for Tkinter
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118 #
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119 # IN:
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120 # Tk Window win
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121 # OUT:
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122 # (sets global variables iRODSCredentials, session and session_success)
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123 #
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124 ########################################################################################################################
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125 class LoginWindow:
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126 def __init__(self, win):
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127 self.window = win
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128 self.lbl1 = Label(win, text='iRODS Username:')
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129 self.lbl2 = Label(win, text='iRODS Password:')
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130 self.t1 = Entry(bd=3)
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131 self.t2 = Entry(show="*")
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132 self.b1 = Button(win, text='Login', command=self.login)
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133
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134 self.window.grid()
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135 Grid.rowconfigure(self.window, 0, weight=1)
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136 Grid.rowconfigure(self.window, 1, weight=1)
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137 Grid.rowconfigure(self.window, 2, weight=1)
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138 Grid.rowconfigure(self.window, 3, weight=1)
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139 Grid.rowconfigure(self.window, 4, weight=1)
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140 Grid.columnconfigure(self.window, 0, weight=1)
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141
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142 self.lbl1.grid(row=0, column=0, padx="20", pady="1", sticky="w")
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143 self.t1.grid(row=1, column=0, padx="10", pady="1", sticky="nsew")
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144 self.lbl2.grid(row=2, column=0, padx="20", pady="1", sticky="w")
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145 self.t2.grid(row=3, column=0, padx="10", pady="1", sticky="nsew")
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146 self.b1.grid(row=4, column=0, padx="50", pady="10", sticky="nsew")
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147
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148 def login(self):
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149 global iRODSCredentials
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150 user = str(self.t1.get())
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151 password = str(self.t2.get())
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152 if user == "" or password == "":
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153 self.window.iconify()
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154 messagebox.showerror("Error", "Username or Password empty!")
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155 self.window.deiconify()
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156 return
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157 else:
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158 iRODSCredentials["user"] = user
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159 iRODSCredentials["pw"] = password
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160
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161 get_irods_session(self.window)
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162 if not session_success:
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163 return
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164
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165 self.window.destroy()
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166 # -------------------------------------------------------------------------------------------------------------------- #
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167
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168
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169 ########################################################################################################################
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170 # File Selection Window class for Tkinter
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171 #
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172 # IN:
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173 # Tk Window win
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174 # OUT:
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175 # (sets global variables selected_file and selection_success)
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176 #
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177 ########################################################################################################################
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178 class FileSelectWindow:
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179 def __init__(self, win):
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180 global session, iRODSCredentials
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181 self.session = session
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182 self.window = win
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183 self.b1 = Button(win, text='Select', command=self.select)
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184 self.lb1 = Listbox(win)
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185
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186 self.window.grid()
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187 Grid.rowconfigure(self.window, 0, weight=1)
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188 Grid.rowconfigure(self.window, 1, weight=1)
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189 Grid.columnconfigure(self.window, 0, weight=1)
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190
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191 self.lb1.grid(row=0, column=0, padx="20", pady="1", sticky="nswe")
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192 self.b1.grid(row=1, column=0, padx="50", pady="1", sticky="ew")
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193
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194 coll = session.collections.get("/" + iRODSCredentials["zone"] + "/" + "home" + "/" + iRODSCredentials["user"])
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195 file_list = []
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196
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197 self.get_files_from_collections(coll, file_list)
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198
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199 for counter in range(len(file_list)):
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200 self.lb1.insert(counter, file_list[counter])
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201
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202 def get_files_from_collections(self, coll, file_list):
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203 for obj in coll.data_objects:
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204 file_list.append(obj.path)
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205
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206 for col in coll.subcollections:
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207 self.get_files_from_collections(col, file_list)
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208
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209 def select(self):
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210 global session, selected_file, selection_success
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211 try:
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212 selection = self.lb1.get(self.lb1.curselection())
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213 except:
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214 self.window.iconify()
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215 messagebox.showerror("Error", "No file selected!")
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216 self.window.deiconify()
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217 return
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218
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219 selected_file = selection
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220 selection_success = True
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221 self.window.destroy()
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222 # -------------------------------------------------------------------------------------------------------------------- #
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223
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224
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225 ########################################################################################################################
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226 # Creates an iRODS session and sets the global session variable
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227 #
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228 # IN:
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229 # Tk Window window
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230 #
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231 # OUT:
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232 #
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233 ########################################################################################################################
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234 def get_irods_session(window):
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235 global iRODSCredentials
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236 host = iRODSCredentials["host"]
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237 port = iRODSCredentials["port"]
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238 user = iRODSCredentials["user"]
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239 password = iRODSCredentials["pw"]
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240 zone = iRODSCredentials["zone"]
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241
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242 iRODSsession = get_iRODS_connection(host=host, port=port, user=user, password=password, zone=zone)
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243 global session, session_success
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244 try:
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245 coll = iRODSsession.collections.get("/" + zone + "/" + "home" + "/" + user)
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246 except Exception:
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247 window.iconify()
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248 messagebox.showerror("Error", "Invalid Authentification")
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249 window.deiconify()
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250 return
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251
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252 if coll:
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253 session = iRODSsession
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254 session_success = True
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255 # -------------------------------------------------------------------------------------------------------------------- #
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256
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257
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258 ########################################################################################################################
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259 # Helper function to initialize Login Window classes and Tk windows
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260 #
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261 # IN:
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262 #
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263 # OUT:
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264 #
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265 ########################################################################################################################
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266 def make_login_window(params):
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267 #get login icon
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268 log_img = ""
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269 for dirpath, dirnames, filenames in os.walk(params["galaxy_root"]):
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270 for fn in filenames:
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271 if fn == "irods_galaxy_login.png":
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272 log_img = os.path.join(dirpath, fn)
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273 if log_img != "":
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274 break
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275 if log_img != "":
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276 break
2
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277 # print(log_img)
1
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278
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279 window = Tk()
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280 LoginWindow(window)
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281 window.title('iRODS Login')
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282 window.geometry("450x225+10+10")
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283 window.minsize(450, 225)
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284 window.tk.call('wm', 'iconphoto', window._w, PhotoImage(file=log_img))
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285 # alternative options:
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286 # window.iconphoto(False, PhotoImage(file='/path/to/ico/icon.png'))
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287 # window.iconbitmap("/home/richard/git/galaxy_irods_tools/login.ico")
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288 window.mainloop()
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289 # -------------------------------------------------------------------------------------------------------------------- #
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290
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291
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292 ########################################################################################################################
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293 # Helper function to initialize File Selection Window classes and Tk windows
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294 #
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295 # IN:
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296 #
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297 # OUT:
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298 #
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299 ########################################################################################################################
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300 def make_file_select_window():
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301 window = Tk()
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302 FileSelectWindow(window)
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303 window.title('iRODS File Select')
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304 window.geometry("450x225+10+10")
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305 window.minsize(450, 225)
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306 window.mainloop()
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307 # -------------------------------------------------------------------------------------------------------------------- #
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308
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309
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310 ########################################################################################################################
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311 # Checks whether arguments are valid and returns true/false depending on params
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312 #
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313 # IN:
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314 # Dict params
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315 #
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316 # OUT:
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317 # String res_string
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318 # Bool res_bool
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319 ########################################################################################################################
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320 def check_params(params):
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321 res_string = ""
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322 res_bool = False
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323
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324 try:
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325 if params["irods_host"] == "":
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326 res_string += "Host empty!\n"
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327 res_bool = True
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328 if params["irods_port"] == "":
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329 res_string += "Port empty!\n"
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330 res_bool = True
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331 if params["irods_zone"] == "":
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332 res_string += "Zone empty!\n"
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333 res_bool = True
2
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334 ##if params["selection_type"] == "path" and params["file_path"] == "":
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335 ## res_string += "Missing file path!\n"
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336 ## res_bool = True
1
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337 except:
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338 raise Exception("Invalid/Missing Parameters")
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339
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340 return res_string, res_bool
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341 # -------------------------------------------------------------------------------------------------------------------- #
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342
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343
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344 ########################################################################################################################
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345 # Function to handle iRODS download calls
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346 #
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347 # IN:
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348 # Dict params
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349 #
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350 # OUT:
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351 #
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352 ########################################################################################################################
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353 def handle_download_call(params):
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354
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355 global session, selected_file
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356
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357 # check if /ZONE/USER/...FILE... pattern is valid
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358 if len(selected_file.split("/")) < 2:
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359 raise Exception("Path to file is not valid in iRODS")
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360
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361 file_list = []
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362
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363 # check if file is a directory
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364 if "." not in selected_file:
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365 try:
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366 coll = session.collections.get(selected_file)
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367 for file in coll.data_objects:
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368 file_list.append(file.path)
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369 except:
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370 raise Exception("Invalid directory path specified!")
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371 else:
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372 file_list.append(selected_file)
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373
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374 # get registry file
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375 reg_file = ""
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376 for dirpath, dirnames, filenames in os.walk(params["galaxy_root"]):
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377 for fn in filenames:
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378 if fn == "irods_galaxy_registry.xml":
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379 reg_file = os.path.join(dirpath, fn)
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380 if reg_file != "":
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381 break
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382 if reg_file != "":
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383 break
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384
2
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385 # print(file_list)
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386 # print(os.getcwd())
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387
1
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388 # handle download for all files in file_list
2
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389 for f in file_list:
1
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390
2
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391 file_to_get = f
1
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392
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393 # handle path and file name
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394 name_file_to_get = file_to_get.split("/")[-1]
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395 path_file_to_get = "/".join(file_to_get.split("/")[0:len(file_to_get.split("/")) - 1])
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396
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397 # check iRODS filesystem
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398 check_iRODS_destination(session, path_file_to_get, name_file_to_get)
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399
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400 # get file object from iRODS
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401 iRODS_file_object = session.data_objects.get(path_file_to_get + "/" + name_file_to_get)
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402 input_file = iRODS_file_object.open("r+")
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403 output_file = open(name_file_to_get, "wb")
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404 output_file.write(input_file.read())
2
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405 #input_file.seek(0,0)
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406 #print(input_file.read().decode("utf-8"))
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407 #temp = open("/home/richard/test.txt", "w")
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408 #input_file.seek(0,0)
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409 #temp.write(input_file.read().decode("utf-8"))
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410
1
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411 input_file.close()
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412 output_file.close()
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413
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414 abs_file_path = os.path.abspath(name_file_to_get)
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415
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416 file_type = str(name_file_to_get.split(".")[-1])
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417
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418 file_content = {"uuid": None,
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419 "file_type": "auto",
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420 "space_to_tab": False,
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421 "dbkey": "?",
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422 "to_posix_lines": True,
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423 "ext": file_type,
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424 "path": abs_file_path,
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425 "in_place": True,
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426 "dataset_id": params["job_id"],
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427 "type": "file",
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428 "is_binary": False,
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429 "link_data_only": "copy_files",
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430 "name": name_file_to_get
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431 }
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432
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433 with open("temporal.json", "w") as fileParams:
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434 fileParams.write(json.dumps(file_content))
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435 fileParams.close()
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436
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437 # load file into Galaxy by using the integrated upload tool - Preparation
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438 python_command = params["galaxy_root"] + "/tools/data_source/upload.py"
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439 arg1 = params["galaxy_root"]
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440 arg2 = params["galaxy_datatypes"]
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441 arg3 = os.path.abspath(fileParams.name)
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442 arg4 = params["job_id"] + ":" + params["out_dir"] + ":" + params["out_file"]
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443
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444 # copy sample registry.xml to working directory
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445 copyfile(reg_file, params["galaxy_datatypes"])
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446
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447 # activate environment for new process call and call the python upload command either both with
2
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448 #sys.path.append(params["galaxy_root"] + "/lib")
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449 #os.system("python -c \'import sys;sys.path.append(\"" + params["galaxy_root"] + "/lib\")\'" + "&& python3 " +
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450 # python_command + " " + arg1 + " " + arg2 + " " + arg3 + " " + arg4)
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451
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452 # get upload file
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453 upload_file = ""
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454 for dirpath, dirnames, filenames in os.walk(params["galaxy_root"]):
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455 for fn in filenames:
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456 if fn == "irods_upload.py":
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457 upload_file = os.path.join(dirpath, fn)
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458 if upload_file != "":
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459 break
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460 if upload_file != "":
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461 break
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462
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463 os.system("python " + upload_file + " " + arg1 + " " + arg2 + " " + arg3 + " " + arg4)
1
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464 # close connection
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465 session.cleanup()
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466 # -------------------------------------------------------------------------------------------------------------------- #
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467
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468
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469 ########################################################################################################################
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diff changeset
470 # Function to handle iRODS upload calls
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diff changeset
471 #
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diff changeset
472 # IN:
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diff changeset
473 # Dict params
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diff changeset
474 #
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diff changeset
475 # OUT:
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diff changeset
476 #
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diff changeset
477 ########################################################################################################################
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diff changeset
478 def handle_upload_call(params):
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diff changeset
479
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diff changeset
480 global session, iRODSCredentials
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diff changeset
481
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diff changeset
482 path_to_file = params["up_file_path"]
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diff changeset
483 name_of_file = params["up_file"]
2
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diff changeset
484 #print(path_to_file)
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diff changeset
485 #print(name_of_file)
1
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diff changeset
486
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diff changeset
487 coll_path = "/" + iRODSCredentials["zone"] + "/home/" + iRODSCredentials["user"] + "/galaxyupload"
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diff changeset
488 try:
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diff changeset
489 coll = session.collections.get(coll_path)
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diff changeset
490 except:
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diff changeset
491 coll = session.collections.create(coll_path)
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diff changeset
492
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diff changeset
493 now = datetime.now()
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diff changeset
494
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diff changeset
495 # dd/mm/YY
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496 day = now.strftime("%d%m%Y")
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diff changeset
497 time = now.strftime("%H%M%S")
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diff changeset
498
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499 coll_path = coll_path + "/" + day
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diff changeset
500
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501 try:
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502 coll = session.collections.get(coll_path)
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diff changeset
503 except:
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diff changeset
504 coll = session.collections.create(coll_path)
2
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diff changeset
505
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506 if "/" in name_of_file:
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507 name_of_file = name_of_file.split("/")[-1]
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diff changeset
508
1
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diff changeset
509 irods_file_name = time + "_" + name_of_file
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diff changeset
510 iRODS_file_object = session.data_objects.create(coll_path + "/" + irods_file_name)
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511 iRODS_file_object = session.data_objects.get(coll_path + "/" + irods_file_name)
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512
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513 irods_file = iRODS_file_object.open("w")
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514 galaxy_file = open(path_to_file, "rb")
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diff changeset
515 content = galaxy_file.read()
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diff changeset
516 irods_file.write(content)
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diff changeset
517
2
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diff changeset
518 print("Successfully uploaded: " + name_of_file + "\n as: " + irods_file_name)
1
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diff changeset
519 # TODO can't close session without writing process finished - but reading/writing happens async.
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diff changeset
520 # session.cleanup()
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diff changeset
521
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522 pass
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diff changeset
523 # -------------------------------------------------------------------------------------------------------------------- #
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diff changeset
524
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diff changeset
525
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526 ########################################################################################################################
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diff changeset
527 # Function to initialize an iRODS Session - will raise an Exception if timeout is longer than 2 seconds
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528 #
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529 # IN:
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diff changeset
530 # String host
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diff changeset
531 # String port
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532 # String user
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533 # String password
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534 # String zone
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diff changeset
535 #
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536 # OUT:
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diff changeset
537 # iRODSSession-object session
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diff changeset
538 ########################################################################################################################
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diff changeset
539 def get_iRODS_connection(host, port, user, password, zone):
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diff changeset
540
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diff changeset
541 # initialize timeout checker - fires after 2 secs
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542 import signal
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543 signal.signal(signal.SIGALRM, timeout_checker)
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544 signal.alarm(2)
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diff changeset
545
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546 try:
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547 session = iRODSSession(host=host, port=port, user=user, password=password, zone=zone)
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548 except Exception:
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549 raise Exception("There was a timeout creating the iRODS session")
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diff changeset
550
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diff changeset
551 # void/reset alarm
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diff changeset
552 signal.alarm(0)
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diff changeset
553
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554 return session
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diff changeset
555 # -------------------------------------------------------------------------------------------------------------------- #
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diff changeset
556
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diff changeset
557
19c1cecdfdfd "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
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558 ########################################################################################################################
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diff changeset
559 # Helper function to raise timeout exception when SIGALRM fires
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diff changeset
560 #
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diff changeset
561 # IN:
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diff changeset
562 #
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diff changeset
563 # OUT:
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564 #
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diff changeset
565 ########################################################################################################################
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diff changeset
566 def timeout_checker():
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diff changeset
567
19c1cecdfdfd "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
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568 raise Exception("iRODS session timeout")
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diff changeset
569 # -------------------------------------------------------------------------------------------------------------------- #
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diff changeset
570
19c1cecdfdfd "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
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parents: 0
diff changeset
571
19c1cecdfdfd "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
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diff changeset
572 ########################################################################################################################
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diff changeset
573 # Function to check if file exists in iRODS
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diff changeset
574 #
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diff changeset
575 # IN:
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576 # String path
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577 #
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578 # OUT:
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diff changeset
579 # Bool ret_bool
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580 #
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581 ########################################################################################################################
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diff changeset
582 def check_if_file_exists(path):
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583
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584 if os.path.isfile(path):
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585 ret_bool = True
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586 else:
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587 ret_bool = False
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588
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diff changeset
589 return ret_bool
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diff changeset
590 # -------------------------------------------------------------------------------------------------------------------- #
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591
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592
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593 ########################################################################################################################
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594 # Function to check iRODS destination
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595 #
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596 # IN:
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597 # iRODSSession-object session
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598 # String path
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599 # String name
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600 #
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601 # OUT:
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602 # Bool ret_bool
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603 #
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604 ########################################################################################################################
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605 def check_iRODS_destination(session, path, name):
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606
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607 try:
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608 session.collections.get(path.rstrip("/"))
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609 except Exception:
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610 raise Exception("Collection doesn't exist in iRODS file system")
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611
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612 try:
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613 session.data_objects.get(path.rstrip("/") + "/" + name)
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614 except Exception:
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615 raise Exception("File doesn't exist in iRODS file system")
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616 # -------------------------------------------------------------------------------------------------------------------- #
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617
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618
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619 if __name__ == "__main__":
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620 main()