Mercurial > repos > bcclaywell > argo_navis

annotate venv/lib/python2.7/site-packages/bioblend/galaxy/client.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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1 """
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2 An interface the clients should implement.
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3
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4 This class is primarily a helper for the library and user code
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5 should not use it directly.
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6 """
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7
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8 import json
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9 import time
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10
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11 import requests
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12 try:
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13 # The following import will work only for Requests >= 2.4.0 and is
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14 # needed to workaround its "urllib3.exceptions.ProtocolError not
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15 # wrapped" bug: https://github.com/kennethreitz/requests/issues/2192
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16 # pylint: disable=E0611,F0401
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17 from requests.packages.urllib3.exceptions import ProtocolError
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18 # pylint: enable=E0611,F0401
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19 except ImportError:
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20 ProtocolError = None # pylint: disable=C0103
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21
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22 import bioblend as bb
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23
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24
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25 class ConnectionError(Exception):
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26 """
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27 An exception class that is raised when unexpected HTTP responses come back.
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28
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29 Should make it easier to debug when strange HTTP things happen such as a
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30 proxy server getting in the way of the request etc.
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31 @see: body attribute to see the content of the http response
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32 """
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33 def __init__(self, message, body=None):
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34 super(ConnectionError, self).__init__(message)
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35 self.body = body
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36
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37 def __str__(self):
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38 return "{0}: {1}".format(self.args[0], self.body)
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39
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40
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41 class Client(object):
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42
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43 # Class variables that configure GET request retries. Note that since these
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44 # are class variables their values are shared by all Client instances --
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45 # i.e., HistoryClient, WorkflowClient, etc.
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46 #
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47 # Number of attempts before giving up on a GET request.
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48 _max_get_retries = 1
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49 # Delay in seconds between subsequent retries.
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50 _get_retry_delay = 10
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51
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52 @classmethod
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53 def max_get_retries(cls):
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54 """
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55 The maximum number of attempts for a GET request.
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56 """
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57 return cls._max_get_retries
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58
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59 @classmethod
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60 def set_max_get_retries(cls, value):
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61 """
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62 Set the maximum number of attempts for GET requests. A value greater
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63 than one causes failed GET requests to be retried `value` - 1 times.
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64
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65 Default: 1
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66 """
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67 if value < 1:
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68 raise ValueError("Number of retries must be >= 1 (got: %s)" % value)
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69 cls._max_get_retries = value
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70 return cls
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71
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72 @classmethod
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73 def get_retry_delay(cls):
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74 """
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75 The delay (in seconds) to wait before retrying a failed GET
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76 request.
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77 """
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78 return cls._get_retry_delay
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79
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80 @classmethod
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81 def set_get_retry_delay(cls, value):
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82 """
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83 Set the delay (in seconds) to wait before retrying a failed GET
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84 request. Default: 1
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85 """
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86 if value < 0:
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87 raise ValueError("Retry delay must be >= 0 (got: %s)" % value)
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88 cls._get_retry_delay = value
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89 return cls
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90
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91 def __init__(self, galaxy_instance):
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92 """
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93 A generic Client interface defining the common fields.
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94
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95 All clients *must* define the following field (which will be
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96 used as part of the URL composition (e.g.,
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97 ``http://<galaxy_instance>/api/libraries``): ``self.module =
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98 'workflows' | 'libraries' | 'histories' | ...``
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99 """
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100 self.gi = galaxy_instance
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101 self.url = '/'.join([self.gi.url, self.module])
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102
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103 def _get(self, id=None, deleted=False, contents=None, url=None,
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104 params=None, json=True):
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105 """
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106 Do a GET request, composing the URL from ``id``, ``deleted`` and
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107 ``contents``. Alternatively, an explicit ``url`` can be provided.
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108 If ``json`` is set to ``True``, return a decoded JSON object
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109 (and treat an empty or undecodable response as an error).
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110
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111 The request will optionally be retried as configured by
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112 ``max_get_retries`` and ``get_retry_delay``: this offers some
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113 resilience in the presence of temporary failures.
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114 """
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115 if not url:
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116 url = self.gi._make_url(self, module_id=id, deleted=deleted,
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117 contents=contents)
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118 attempts_left = self.max_get_retries()
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119 retry_delay = self.get_retry_delay()
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120 bb.log.debug("GET - attempts left: %s; retry delay: %s",
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121 attempts_left, retry_delay)
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122 msg = ''
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123 while attempts_left > 0:
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124 attempts_left -= 1
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125 try:
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126 r = self.gi.make_get_request(url, params=params)
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127 except (requests.exceptions.ConnectionError, ProtocolError) as e:
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128 msg = str(e)
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129 else:
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130 if r is None:
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131 msg = "GET: no response"
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132 if r.status_code == 200:
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133 if not json:
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134 return r
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135 elif not r.content:
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136 msg = "GET: empty response"
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137 else:
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138 try:
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139 return r.json()
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140 except ValueError:
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141 msg = "GET: invalid JSON : %r" % (r.content,)
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142 else:
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143 msg = "GET: error %s: %r" % (r.status_code, r.content)
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144 msg = "%s, %d attempts left" % (msg, attempts_left)
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145 if attempts_left <= 0:
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146 bb.log.error(msg)
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147 raise ConnectionError(msg)
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148 else:
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149 bb.log.warn(msg)
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150 time.sleep(retry_delay)
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151
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152 def _post(self, payload, id=None, deleted=False, contents=None, url=None,
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153 files_attached=False):
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154 """
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155 Do a generic POST request, composing the url from the contents of the
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156 arguments. Alternatively, an explicit ``url`` can be provided to use
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157 for the request. ``payload`` must be a dict that contains additional
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158 request arguments which will be sent along with the request body.
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159 The payload dict may contain file handles (in which case the
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160 ``files_attached`` flag must be set to true).
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161
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162 If ``files_attached`` is set to ``False``, the request body will be
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163 JSON-encoded; otherwise, it will be encoded as multipart/form-data.
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164
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165 The return value will contain the response body as a JSON object.
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166 """
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167 if not url:
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168 url = self.gi._make_url(self, module_id=id, deleted=deleted,
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169 contents=contents)
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170 return self.gi.make_post_request(url, payload=payload,
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171 files_attached=files_attached)
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172
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173 def _put(self, payload, id=None, url=None, params=None):
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174 """
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175 Do a generic PUT request, composing the url from the contents of the
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176 arguments. Alternatively, an explicit ``url`` can be provided to use
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177 for the request. ``payload`` must be a dict that contains additional
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178 request arguments which will be sent along with the request body.
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179
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180 This method returns the HTTP request object.
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181 """
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182 if not url:
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183 url = self.gi._make_url(self, module_id=id)
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184 return self.gi.make_put_request(url, payload=payload, params=params)
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185
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186 def _delete(self, payload, id=None, deleted=False, contents=None, url=None):
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187 """
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188 Do a generic DELETE request, composing the url from the contents of the
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189 arguments. Alternatively, an explicit ``url`` can be provided to use
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190 for the request. ``payload`` must be a dict that can be converted
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191 into a JSON object (which will be done within this method)
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192 """
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193 if not url:
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194 url = self.gi._make_url(self, module_id=id, deleted=deleted,
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195 contents=contents)
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196 payload = json.dumps(payload)
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197 r = self.gi.make_delete_request(url, payload=payload)
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198 if r.status_code == 200:
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199 return r.json()
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200 # @see self.body for HTTP response body
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201 raise ConnectionError(
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202 "Unexpected HTTP status code: %s" % r.status_code, body=r.text
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203 )