Mercurial > repos > rhohensinner > galaxy_irods_interface

annotate irods_main.py @ 4:84f685c067ad draft default tip

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"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
author rhohensinner
date Wed, 04 Aug 2021 12:01:55 +0000
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4
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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
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8 from shutil import copyfile
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9 from datetime import datetime
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10 from irods_data import registry_content
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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 python_path = []
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28
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29 with open("reg.xml", "w") as xf:
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30 xf.write(registry_content)
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31 xf.close()
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32
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33 ########################################################################################################################
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34 # Main function of the iRODS tools
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35 #
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36 # IN:
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37 # JSON Object params (argv[1])
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38 # OUT:
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39 #
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40 ########################################################################################################################
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41 def main():
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42
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43 # check input parameters
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44 if len(sys.argv) == 2:
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45 params = json.loads(sys.argv[1])
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46 else:
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47 raise Exception("Invalid Parameters submitted!")
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48
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49 tool_type = params["tool_type"]
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50
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51 try:
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52 if params["tool_type"] != "up" and params["tool_type"] != "down":
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53 raise Exception("Invalid tool-type parameter submitted!")
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54 except:
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55 raise Exception("No tool-type parameter submitted!")
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56 is_download_call = True
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57 if tool_type == "up":
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58 is_download_call = False
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59
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60 # check params for integrity
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61 result_string, params_faulty = check_params(params)
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62
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63 if params_faulty:
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64 raise Exception(result_string)
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65
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66 global iRODSCredentials, session_success, selected_file, selection_success
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67 iRODSCredentials["host"] = params["irods_host"]
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68 iRODSCredentials["port"] = params["irods_port"]
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69 iRODSCredentials["zone"] = params["irods_zone"]
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70
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71 # create login window
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72 ## make_login_window(params)
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73 iRODSCredentials["user"] = params["irods_user"]
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74 iRODSCredentials["pw"] = params["irods_password"]
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75
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76 host = iRODSCredentials["host"]
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77 port = iRODSCredentials["port"]
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78 user = iRODSCredentials["user"]
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79 password = iRODSCredentials["pw"]
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80 zone = iRODSCredentials["zone"]
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81
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82 iRODSsession = get_iRODS_connection(host=host, port=port, user=user, password=password, zone=zone)
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83 global session, session_success
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84 try:
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85 coll = iRODSsession.collections.get("/" + zone + "/" + "home" + "/" + user)
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86 except Exception:
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87 raise Exception("Invalid Login")
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88
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89 if coll:
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90 session = iRODSsession
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91 session_success = True
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92
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93
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94 # check tool settings and start tool execution
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95 if session_success:
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96 # initialize download tool
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97 if params["tool_type"] == "down":
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98
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99 selected_file = params["file_path"]
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100 params["user"] = iRODSCredentials["pw"]
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101 params["password"] = iRODSCredentials["user"]
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102 # start download routine
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103 handle_download_call(params)
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104
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105 # initialize upload tool
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106 elif params["tool_type"] == "up":
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107
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108 if session_success:
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109 params["user"] = iRODSCredentials["pw"]
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110 params["password"] = iRODSCredentials["user"]
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111 # start upload routine
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112 handle_upload_call(params)
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113 else:
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114 raise Exception("Logging into iRODS failed")
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115 else:
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116 raise Exception("Logging into iRODS failed")
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117 # -------------------------------------------------------------------------------------------------------------------- #
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118
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119
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120 ########################################################################################################################
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121 # Login Window class for Tkinter
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122 #
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123 # IN:
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124 # Tk Window win
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125 # OUT:
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126 # (sets global variables iRODSCredentials, session and session_success)
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127 #
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128 ########################################################################################################################
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129 class LoginWindow:
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130 def __init__(self, win):
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131 self.window = win
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132 self.lbl1 = Label(win, text='iRODS Username:')
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133 self.lbl2 = Label(win, text='iRODS Password:')
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134 self.t1 = Entry(bd=3)
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135 self.t2 = Entry(show="*")
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136 self.b1 = Button(win, text='Login', command=self.login)
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137
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138 self.window.grid()
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139 Grid.rowconfigure(self.window, 0, weight=1)
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140 Grid.rowconfigure(self.window, 1, weight=1)
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141 Grid.rowconfigure(self.window, 2, weight=1)
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142 Grid.rowconfigure(self.window, 3, weight=1)
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143 Grid.rowconfigure(self.window, 4, weight=1)
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144 Grid.columnconfigure(self.window, 0, weight=1)
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145
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146 self.lbl1.grid(row=0, column=0, padx="20", pady="1", sticky="w")
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147 self.t1.grid(row=1, column=0, padx="10", pady="1", sticky="nsew")
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148 self.lbl2.grid(row=2, column=0, padx="20", pady="1", sticky="w")
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149 self.t2.grid(row=3, column=0, padx="10", pady="1", sticky="nsew")
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150 self.b1.grid(row=4, column=0, padx="50", pady="10", sticky="nsew")
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151
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152 def login(self):
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153 global iRODSCredentials
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154 user = str(self.t1.get())
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155 password = str(self.t2.get())
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156 if user == "" or password == "":
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157 self.window.iconify()
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158 messagebox.showerror("Error", "Username or Password empty!")
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159 self.window.deiconify()
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160 return
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161 else:
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162 iRODSCredentials["user"] = user
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163 iRODSCredentials["pw"] = password
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164
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165 get_irods_session(self.window)
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166 if not session_success:
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167 return
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168
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169 self.window.destroy()
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170 # -------------------------------------------------------------------------------------------------------------------- #
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171
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172
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173 ########################################################################################################################
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174 # File Selection Window class for Tkinter
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175 #
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176 # IN:
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177 # Tk Window win
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178 # OUT:
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179 # (sets global variables selected_file and selection_success)
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180 #
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181 ########################################################################################################################
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182 class FileSelectWindow:
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183 def __init__(self, win):
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184 global session, iRODSCredentials
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185 self.session = session
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186 self.window = win
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187 self.b1 = Button(win, text='Select', command=self.select)
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188 self.lb1 = Listbox(win)
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189
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190 self.window.grid()
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191 Grid.rowconfigure(self.window, 0, weight=1)
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192 Grid.rowconfigure(self.window, 1, weight=1)
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193 Grid.columnconfigure(self.window, 0, weight=1)
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194
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195 self.lb1.grid(row=0, column=0, padx="20", pady="1", sticky="nswe")
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196 self.b1.grid(row=1, column=0, padx="50", pady="1", sticky="ew")
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197
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198 coll = session.collections.get("/" + iRODSCredentials["zone"] + "/" + "home" + "/" + iRODSCredentials["user"])
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199 file_list = []
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200
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201 self.get_files_from_collections(coll, file_list)
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202
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203 for counter in range(len(file_list)):
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204 self.lb1.insert(counter, file_list[counter])
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205
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206 def get_files_from_collections(self, coll, file_list):
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207 for obj in coll.data_objects:
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208 file_list.append(obj.path)
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209
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210 for col in coll.subcollections:
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211 self.get_files_from_collections(col, file_list)
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212
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213 def select(self):
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214 global session, selected_file, selection_success
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215 try:
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216 selection = self.lb1.get(self.lb1.curselection())
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217 except:
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218 self.window.iconify()
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219 messagebox.showerror("Error", "No file selected!")
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220 self.window.deiconify()
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221 return
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222
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223 selected_file = selection
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224 selection_success = True
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225 self.window.destroy()
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226 # -------------------------------------------------------------------------------------------------------------------- #
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227
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228
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229 ########################################################################################################################
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230 # Creates an iRODS session and sets the global session variable
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231 #
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232 # IN:
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233 # Tk Window window
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234 #
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235 # OUT:
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236 #
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237 ########################################################################################################################
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238 def get_irods_session(window):
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239 global iRODSCredentials
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240 host = iRODSCredentials["host"]
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241 port = iRODSCredentials["port"]
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242 user = iRODSCredentials["user"]
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243 password = iRODSCredentials["pw"]
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244 zone = iRODSCredentials["zone"]
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245
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246 iRODSsession = get_iRODS_connection(host=host, port=port, user=user, password=password, zone=zone)
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247 global session, session_success
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248 try:
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249 coll = iRODSsession.collections.get("/" + zone + "/" + "home" + "/" + user)
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250 except Exception:
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251 window.iconify()
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252 messagebox.showerror("Error", "Invalid Authentification")
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253 window.deiconify()
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254 return
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255
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256 if coll:
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257 session = iRODSsession
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258 session_success = True
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259 # -------------------------------------------------------------------------------------------------------------------- #
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260
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261
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262 ########################################################################################################################
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263 # Helper function to initialize Login Window classes and Tk windows
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264 #
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265 # IN:
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266 #
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267 # OUT:
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268 #
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269 ########################################################################################################################
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270 def make_login_window(params):
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271 #get login icon
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272 log_img = ""
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273 for dirpath, dirnames, filenames in os.walk(params["galaxy_root"]):
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274 for fn in filenames:
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275 if fn == "irods_galaxy_login.png":
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276 log_img = os.path.join(dirpath, fn)
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277 if log_img != "":
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278 break
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279 if log_img != "":
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280 break
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281 # print(log_img)
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282
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283 window = Tk()
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284 LoginWindow(window)
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285 window.title('iRODS Login')
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286 window.geometry("450x225+10+10")
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287 window.minsize(450, 225)
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288 window.tk.call('wm', 'iconphoto', window._w, PhotoImage(file=log_img))
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289 # alternative options:
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290 # window.iconphoto(False, PhotoImage(file='/path/to/ico/icon.png'))
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291 # window.iconbitmap("/home/richard/git/galaxy_irods_tools/login.ico")
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292 window.mainloop()
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293 # -------------------------------------------------------------------------------------------------------------------- #
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294
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295
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296 ########################################################################################################################
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297 # Helper function to initialize File Selection Window classes and Tk windows
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298 #
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299 # IN:
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300 #
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301 # OUT:
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302 #
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303 ########################################################################################################################
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304 def make_file_select_window():
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305 window = Tk()
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306 FileSelectWindow(window)
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307 window.title('iRODS File Select')
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308 window.geometry("450x225+10+10")
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309 window.minsize(450, 225)
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310 window.mainloop()
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311 # -------------------------------------------------------------------------------------------------------------------- #
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312
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313
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314 ########################################################################################################################
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315 # Checks whether arguments are valid and returns true/false depending on params
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316 #
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317 # IN:
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318 # Dict params
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319 #
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320 # OUT:
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321 # String res_string
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322 # Bool res_bool
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323 ########################################################################################################################
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324 def check_params(params):
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325 res_string = ""
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326 res_bool = False
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327
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328 try:
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329 if params["irods_host"] == "":
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330 res_string += "Host empty!\n"
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331 res_bool = True
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332 if params["irods_port"] == "":
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333 res_string += "Port empty!\n"
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334 res_bool = True
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335 if params["irods_zone"] == "":
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336 res_string += "Zone empty!\n"
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337 res_bool = True
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338 ##if params["selection_type"] == "path" and params["file_path"] == "":
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339 ## res_string += "Missing file path!\n"
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340 ## res_bool = True
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341 except:
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342 raise Exception("Invalid/Missing Parameters")
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343
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344 return res_string, res_bool
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345 # -------------------------------------------------------------------------------------------------------------------- #
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346
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347
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348 ########################################################################################################################
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349 # Function to handle iRODS download calls
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350 #
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351 # IN:
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352 # Dict params
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353 #
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354 # OUT:
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355 #
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356 ########################################################################################################################
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357 def handle_download_call(params):
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358
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359 global session, selected_file
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360
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361 # check if /ZONE/USER/...FILE... pattern is valid
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362 if len(selected_file.split("/")) < 2:
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363 raise Exception("Path to file is not valid in iRODS")
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364
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365 file_list = []
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366
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367 # check if file is a directory
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368 if "." not in selected_file:
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369 try:
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370 coll = session.collections.get(selected_file)
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371 for file in coll.data_objects:
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372 file_list.append(file.path)
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373 except:
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374 raise Exception("Invalid directory path specified!")
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diff changeset
375 else:
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376 file_list.append(selected_file)
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377
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378 ## get registry file
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379 #reg_file = ""
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diff changeset
380 #for dirpath, dirnames, filenames in os.walk(params["galaxy_root"]):
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381 # for fn in filenames:
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382 # if fn == "irods_galaxy_registry.xml":
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383 # reg_file = os.path.join(dirpath, fn)
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384 # if reg_file != "":
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385 # break
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386 # if reg_file != "":
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387 # break
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388 reg_file = "reg.xml"
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389
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390 # print(file_list)
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391 # print(os.getcwd())
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392
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393 # handle download for all files in file_list
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394 for f in file_list:
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395
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396 file_to_get = f
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397
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398 # handle path and file name
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399 name_file_to_get = file_to_get.split("/")[-1]
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400 path_file_to_get = "/".join(file_to_get.split("/")[0:len(file_to_get.split("/")) - 1])
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401
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402 # check iRODS filesystem
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403 check_iRODS_destination(session, path_file_to_get, name_file_to_get)
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404
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405 # get file object from iRODS
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406 iRODS_file_object = session.data_objects.get(path_file_to_get + "/" + name_file_to_get)
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407 input_file = iRODS_file_object.open("r+")
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408 output_file = open(name_file_to_get, "wb")
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409 output_file.write(input_file.read())
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410 #input_file.seek(0,0)
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411 #print(input_file.read().decode("utf-8"))
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412 #temp = open("/home/richard/test.txt", "w")
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413 #input_file.seek(0,0)
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414 #temp.write(input_file.read().decode("utf-8"))
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415
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416 input_file.close()
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417 output_file.close()
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418
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419 abs_file_path = os.path.abspath(name_file_to_get)
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420
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421 file_type = str(name_file_to_get.split(".")[-1])
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422
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423 file_content = {"uuid": None,
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424 "file_type": "auto",
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425 "space_to_tab": False,
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426 "dbkey": "?",
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427 "to_posix_lines": True,
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428 "ext": file_type,
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429 "path": abs_file_path,
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430 "in_place": True,
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431 "dataset_id": params["job_id"],
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432 "type": "file",
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433 "is_binary": False,
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434 "link_data_only": "copy_files",
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435 "name": name_file_to_get
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436 }
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437
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438 with open("temporal.json", "w") as fileParams:
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439 fileParams.write(json.dumps(file_content))
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440 fileParams.close()
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441
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442 # load file into Galaxy by using the integrated upload tool - Preparation
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443 python_command = params["galaxy_root"] + "/tools/data_source/upload.py"
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444 arg1 = params["galaxy_root"]
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445 arg2 = params["galaxy_datatypes"]
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446 arg3 = os.path.abspath(fileParams.name)
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447 arg4 = params["job_id"] + ":" + params["out_dir"] + ":" + params["out_file"]
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448 arg5 = params["galaxy_root"] + "/lib/galaxy"
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449
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450 # copy sample registry.xml to working directory
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451 copyfile(reg_file, params["galaxy_datatypes"])
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452
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453 # activate environment for new process call and call the python upload command either both with
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454 #sys.path.append(params["galaxy_root"] + "/lib")
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455 #os.system("python -c \'import sys;sys.path.append(\"" + params["galaxy_root"] + "/lib\")\'" + "&& python3 " +
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456 # python_command + " " + arg1 + " " + arg2 + " " + arg3 + " " + arg4)
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457
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458 # get upload file
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459 upload_file = ""
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460 for dirpath, dirnames, filenames in os.walk(params["galaxy_root"]):
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461 for fn in filenames:
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462 if fn == "irods_upload.py":
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463 upload_file = os.path.join(dirpath, fn)
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464 if upload_file != "":
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465 break
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466 if upload_file != "":
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467 break
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468 sys.path.append(params["galaxy_root"] + "/lib")
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469 #sys.path.append(params["galaxy_root"] + "/tools/data_source")
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470 #sys.path.append(params["galaxy_root"] + "/.venv/lib/python3.8/site-packages")
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471 with open("python__path.txt", "w") as pp:
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472 pp.truncate(0)
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473 for item in sys.path:
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474 pp.write(item + ",")
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475
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476 os.system(params["galaxy_root"] + "/.venv/bin/python " + upload_file + " " + arg1 + " " + arg2 + " " + arg3 + " " + arg4)
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477 # close connection
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478 session.cleanup()
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479 # -------------------------------------------------------------------------------------------------------------------- #
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480
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481
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482 ########################################################################################################################
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483 # Function to handle iRODS upload calls
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484 #
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485 # IN:
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486 # Dict params
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487 #
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488 # OUT:
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489 #
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490 ########################################################################################################################
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491 def handle_upload_call(params):
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rhohensinner
parents:
diff changeset
492
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
493 global session, iRODSCredentials
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
494
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
495 path_to_file = params["up_file_path"]
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
496 name_of_file = params["up_file"]
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
497 #print(path_to_file)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
498 #print(name_of_file)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
499
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
500 coll_path = "/" + iRODSCredentials["zone"] + "/home/" + iRODSCredentials["user"] + "/galaxyupload"
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
501 try:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
502 coll = session.collections.get(coll_path)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
503 except:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
504 coll = session.collections.create(coll_path)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
505
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
506 now = datetime.now()
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
507
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
508 # dd/mm/YY
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
509 day = now.strftime("%d%m%Y")
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
510 time = now.strftime("%H%M%S")
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
511
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
512 coll_path = coll_path + "/" + day
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
513
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
514 try:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
515 coll = session.collections.get(coll_path)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
516 except:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
517 coll = session.collections.create(coll_path)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
518
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
519 if "/" in name_of_file:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
520 name_of_file = name_of_file.split("/")[-1]
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
521
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
522 irods_file_name = time + "_" + name_of_file
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
523 iRODS_file_object = session.data_objects.create(coll_path + "/" + irods_file_name)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
524 iRODS_file_object = session.data_objects.get(coll_path + "/" + irods_file_name)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
525
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
526 irods_file = iRODS_file_object.open("w")
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
527 galaxy_file = open(path_to_file, "rb")
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
528 content = galaxy_file.read()
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
529 irods_file.write(content)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
530
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
531 print("Successfully uploaded: " + name_of_file + "\n as: " + irods_file_name)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
532 # TODO can't close session without writing process finished - but reading/writing happens async.
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
533 # session.cleanup()
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
534
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
535 pass
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
536 # -------------------------------------------------------------------------------------------------------------------- #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
537
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
538
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
539 ########################################################################################################################
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
540 # Function to initialize an iRODS Session - will raise an Exception if timeout is longer than 2 seconds
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
541 #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
542 # IN:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
543 # String host
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
544 # String port
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
545 # String user
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
546 # String password
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
547 # String zone
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
548 #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
549 # OUT:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
550 # iRODSSession-object session
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
551 ########################################################################################################################
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
552 def get_iRODS_connection(host, port, user, password, zone):
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
553
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
554 # initialize timeout checker - fires after 2 secs
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
555 import signal
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
556 signal.signal(signal.SIGALRM, timeout_checker)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
557 signal.alarm(2)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
558
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
559 try:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
560 session = iRODSSession(host=host, port=port, user=user, password=password, zone=zone)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
561 except Exception:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
562 raise Exception("There was a timeout creating the iRODS session")
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
563
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
564 # void/reset alarm
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
565 signal.alarm(0)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
566
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
567 return session
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
568 # -------------------------------------------------------------------------------------------------------------------- #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
569
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
570
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
571 ########################################################################################################################
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
572 # Helper function to raise timeout exception when SIGALRM fires
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
573 #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
574 # IN:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
575 #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
576 # OUT:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
577 #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
578 ########################################################################################################################
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
579 def timeout_checker():
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
580
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
581 raise Exception("iRODS session timeout")
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
582 # -------------------------------------------------------------------------------------------------------------------- #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
583
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
584
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
585 ########################################################################################################################
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
586 # Function to check if file exists in iRODS
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
587 #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
588 # IN:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
589 # String path
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
590 #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
591 # OUT:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
592 # Bool ret_bool
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
593 #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
594 ########################################################################################################################
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
595 def check_if_file_exists(path):
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
596
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
597 if os.path.isfile(path):
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
598 ret_bool = True
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
599 else:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
600 ret_bool = False
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
601
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
602 return ret_bool
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
603 # -------------------------------------------------------------------------------------------------------------------- #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
604
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
605
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
606 ########################################################################################################################
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
607 # Function to check iRODS destination
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
608 #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
609 # IN:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
610 # iRODSSession-object session
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
611 # String path
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
612 # String name
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
613 #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
614 # OUT:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
615 # Bool ret_bool
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
616 #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
617 ########################################################################################################################
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
618 def check_iRODS_destination(session, path, name):
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
619
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
620 try:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
621 session.collections.get(path.rstrip("/"))
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
622 except Exception:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
623 raise Exception("Collection doesn't exist in iRODS file system")
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
624
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
625 try:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
626 session.data_objects.get(path.rstrip("/") + "/" + name)
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
627 except Exception:
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
628 raise Exception("File doesn't exist in iRODS file system")
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
629 # -------------------------------------------------------------------------------------------------------------------- #
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
630
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
631
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
632 if __name__ == "__main__":
84f685c067ad "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
rhohensinner
parents:
diff changeset
633 main()