Mercurial > repos > rhohensinner > galaxy_irods_interface

annotate main.py @ 0:7d8912d20007 draft

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