Mercurial > repos > yating-l > gonramp_apollo

annotate util/subtools.py @ 0:cb8439d64ed3 draft default tip

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planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
author yating-l
date Mon, 27 Nov 2017 14:40:53 -0500
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0
cb8439d64ed3 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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1 #!/usr/bin/env python
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2
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3 """
cb8439d64ed3 planemo upload for repository https://github.com/Yating-L/suite_gonramp_apollo.git commit 9009fa8663038d2cb4a1c5130600a51f31f654a1-dirty
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4 This file include common used functions for converting file format to gff3
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5 """
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6 from collections import OrderedDict
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7 import json
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8 import subprocess
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9 import os
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10 import sys
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11 import tempfile
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12 import string
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13 import logging
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14
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15 class PopenError(Exception):
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16 def __init__(self, cmd, error, return_code):
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17 self.cmd = cmd
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18 self.error = error
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19 self.return_code = return_code
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21 def __str__(self):
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22 message = "The subprocess {0} has returned the error: {1}.".format(
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23 self.cmd, self.return_code)
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24 message = ','.join(
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25 (message, "Its error message is: {0}".format(self.error)))
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26 return repr(message)
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27
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29 def _handleExceptionAndCheckCall(array_call, **kwargs):
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30 """
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31 This class handle exceptions and call the tool.
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32 It maps the signature of subprocess.check_call:
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33 See https://docs.python.org/2/library/subprocess.html#subprocess.check_call
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34 """
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35 stdout = kwargs.get('stdout', subprocess.PIPE)
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36 stderr = kwargs.get('stderr', subprocess.PIPE)
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37 shell = kwargs.get('shell', False)
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38 stdin = kwargs.get('stdin', None)
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39
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40 cmd = array_call[0]
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41
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42 output = None
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43 error = None
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44
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45 # TODO: Check the value of array_call and <=[0]
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46 logging.debug("Calling {0}:".format(cmd))
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47 logging.debug("%s", array_call)
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48 logging.debug("---------")
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49
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50 # TODO: Use universal_newlines option from Popen?
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51 try:
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52 p = subprocess.Popen(array_call, stdout=stdout,
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53 stderr=stderr, shell=shell, stdin=stdin)
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54
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55 # TODO: Change this because of possible memory issues => https://docs.python.org/2/library/subprocess.html#subprocess.Popen.communicate
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56
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57 output, error = p.communicate()
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58
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59 if stdout == subprocess.PIPE:
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60 logging.debug("\t{0}".format(output))
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61 else:
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62 logging.debug("\tOutput in file {0}".format(stdout.name))
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63 # If we detect an error from the subprocess, then we raise an exception
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64 # TODO: Manage if we raise an exception for everything, or use CRITICAL etc... but not stop process
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65 # TODO: The responsability of returning a sys.exit() should not be there, but up in the app.
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66 if p.returncode:
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67 if stderr == subprocess.PIPE:
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68 raise PopenError(cmd, error, p.returncode)
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69 else:
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70 # TODO: To Handle properly with a design behind, if we received a option as a file for the error
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71 raise Exception("Error when calling {0}. Error as been logged in your file {1}. Error code: {2}".format(cmd, stderr.name, p.returncode))
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72
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73 except OSError as e:
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74 message = "The subprocess {0} has encountered an OSError: {1}".format(
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75 cmd, e.strerror)
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76 if e.filename:
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77 message = '\n'.join(
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78 (message, ", against this file: {0}".format(e.filename)))
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79 logging.error(message)
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80 sys.exit(-1)
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81 except PopenError as p:
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82 message = "The subprocess {0} has returned the error: {1}.".format(
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83 p.cmd, p.return_code)
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84 message = '\n'.join(
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85 (message, "Its error message is: {0}".format(p.error)))
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86
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87 logging.exception(message)
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88
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89 sys.exit(p.return_code)
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90 except Exception as e:
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91 message = "The subprocess {0} has encountered an unknown error: {1}".format(
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92 cmd, e)
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93 logging.exception(message)
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94
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95 sys.exit(-1)
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96 return output
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97
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98 def arrow_add_organism(organism_name, organism_dir, public=False):
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99 array_call = ['arrow', 'organisms', 'add_organism', organism_name, organism_dir]
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100 if public:
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101 array_call.append('--public')
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102 p = _handleExceptionAndCheckCall(array_call)
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103 #p = subprocess.check_output(array_call)
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104 return p
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105
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106 def arrow_create_user(user_email, firstname, lastname, password, admin=False):
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107 """
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108 Create a new user of Apollo, the default user_role is "user"
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109 """
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110 array_call = ['arrow', 'users', 'create_user', user_email, firstname, lastname, password]
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111 if admin:
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112 array_call += ['--role', 'admin']
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113 p = _handleExceptionAndCheckCall(array_call)
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114 j = json.loads(p)
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115 if "userId" in j:
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116 return j['userId']
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117 elif "error" in j:
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118 logging.error("User %s already exist", user_email)
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119 raise Exception(j['error'])
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120
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121
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122 def arrow_delete_user(user_email):
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123 array_call = ['arrow', 'users', 'delete_user', user_email]
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124 p = _handleExceptionAndCheckCall(array_call)
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125 j = json.loads(p)
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126 if "error" in j:
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127 raise Exception(j['error'])
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128
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129 def arrow_add_to_group(groupname, user_email):
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130 if not arrow_get_groups(groupname):
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131 arrow_create_group(groupname)
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132 array_call = ['arrow', 'users', 'add_to_group', groupname, user_email]
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133 p = _handleExceptionAndCheckCall(array_call)
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134 j = json.loads(p)
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135 if j != dict():
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136 raise Exception("Error add user %s to group %s", user_email, groupname)
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137
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138
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139 def arrow_remove_from_group(groupname, user_email):
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140 if arrow_get_groups(groupname):
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141 array_call = ['arrow', 'users', 'remove_from_group', groupname, user_email]
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142 p = _handleExceptionAndCheckCall(array_call)
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143 else:
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144 raise Exception("Group %s doesn't exist. Check if you spell the name correctly", groupname)
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145
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146 def arrow_create_group(groupname):
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147 if arrow_get_groups(groupname):
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148 raise Exception("Group %s already exist. Create a group with another name.", groupname)
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149 array_call = ['arrow', 'groups', 'create_group', groupname]
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150 p = _handleExceptionAndCheckCall(array_call)
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151
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152 def arrow_get_groups(groupname):
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153 array_call = ['arrow', 'groups', 'get_groups']
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154 p = _handleExceptionAndCheckCall(array_call)
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155 all_groups = json.loads(p)
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156 for g in all_groups:
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157 if g['name'] == groupname:
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158 return True
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159 return False
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160
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161 def arrow_update_organism_permissions(user_id, organism, **user_permissions):
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162 array_call = ['arrow', 'users', 'update_organism_permissions', str(user_id), str(organism)]
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163 admin = user_permissions.get("admin", False)
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164 write = user_permissions.get("write", False)
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165 read = user_permissions.get("read", False)
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166 export = user_permissions.get("export", False)
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167 if admin:
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168 array_call.append('--administrate')
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169 if write:
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170 array_call.append('--write')
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171 if read:
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172 array_call.append('--read')
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173 if export:
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174 array_call.append('--export')
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175 p = _handleExceptionAndCheckCall(array_call)
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176 return p
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177
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178 def arrow_get_users(user_email):
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179 array_call = ['arrow', 'users', 'get_users']
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180 p = _handleExceptionAndCheckCall(array_call)
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181 all_users = json.loads(p)
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182 for d in all_users:
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183 if d['username'] == user_email:
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184 return d['userId']
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185 logging.error("Cannot find user %s", user_email)
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186
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187 def arrow_get_organism(organism_name):
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188 array_call= ['arrow', 'organisms', 'get_organisms']
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189 p = _handleExceptionAndCheckCall(array_call)
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190 all_organisms = json.loads(p)
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191 for org in all_organisms:
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192 if org['commonName'] == organism_name:
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193 return org['id']
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194
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195
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196 def arrow_delete_organism(organism_id):
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197 array_call = ['arrow', 'organisms', 'delete_organism', organism_id]
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198 p = _handleExceptionAndCheckCall(array_call)
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199 return p
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200
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201 def verify_user_login(username, password, apollo_host):
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202 user_info = {'username': username, 'password': password}
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203 array_call = ['curl',
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204 '-b', 'cookies.txt',
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205 '-c', 'cookies.txt',
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206 '-H', 'Content-Type:application/json',
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207 '-d', json.dumps(user_info),
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208 apollo_host + '/Login?operation=login'
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209 ]
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210 p = _handleExceptionAndCheckCall(array_call)
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211 msg = json.loads(p)
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212 if 'error' in msg:
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213 logging.error("The Authentication for user %s failed. Get error message %s", username, msg['error'])
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214 exit(-1)
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215
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216