Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/bioblend/galaxy/client.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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0
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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 time
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9
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10 import requests
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11 from requests.packages.urllib3.exceptions import ProtocolError
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12
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13 import bioblend
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14 # The following import must be preserved for compatibility because
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15 # ConnectionError class was originally defined here
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16 from bioblend import ConnectionError # noqa: I202
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17
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18
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19 class Client(object):
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20
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21 # Class variables that configure GET request retries. Note that since these
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22 # are class variables their values are shared by all Client instances --
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23 # i.e., HistoryClient, WorkflowClient, etc.
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24 #
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25 # Number of attempts before giving up on a GET request.
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26 _max_get_retries = 1
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27 # Delay in seconds between subsequent retries.
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28 _get_retry_delay = 10
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29
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30 @classmethod
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31 def max_get_retries(cls):
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32 """
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33 The maximum number of attempts for a GET request.
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34 """
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35 return cls._max_get_retries
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36
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37 @classmethod
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38 def set_max_get_retries(cls, value):
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39 """
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40 Set the maximum number of attempts for GET requests. A value greater
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41 than one causes failed GET requests to be retried `value` - 1 times.
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42
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43 Default: 1
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44 """
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45 if value < 1:
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46 raise ValueError("Number of retries must be >= 1 (got: %s)" % value)
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47 cls._max_get_retries = value
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48 return cls
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49
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50 @classmethod
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51 def get_retry_delay(cls):
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52 """
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53 The delay (in seconds) to wait before retrying a failed GET
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54 request.
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55 """
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56 return cls._get_retry_delay
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57
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58 @classmethod
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59 def set_get_retry_delay(cls, value):
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60 """
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61 Set the delay (in seconds) to wait before retrying a failed GET
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62 request. Default: 10
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63 """
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64 if value < 0:
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65 raise ValueError("Retry delay must be >= 0 (got: %s)" % value)
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66 cls._get_retry_delay = value
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67 return cls
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68
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69 def __init__(self, galaxy_instance):
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70 """
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71 A generic Client interface defining the common fields.
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72
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73 All clients *must* define the following field (which will be
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74 used as part of the URL composition (e.g.,
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75 ``http://<galaxy_instance>/api/libraries``): ``self.module =
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76 'workflows' | 'libraries' | 'histories' | ...``
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77 """
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78 self.gi = galaxy_instance
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79 self.url = '/'.join([self.gi.url, self.module])
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80
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81 def _get(self, id=None, deleted=False, contents=None, url=None,
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82 params=None, json=True):
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83 """
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84 Do a GET request, composing the URL from ``id``, ``deleted`` and
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85 ``contents``. Alternatively, an explicit ``url`` can be provided.
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86 If ``json`` is set to ``True``, return a decoded JSON object
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87 (and treat an empty or undecodable response as an error).
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88
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89 The request will optionally be retried as configured by
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90 ``max_get_retries`` and ``get_retry_delay``: this offers some
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91 resilience in the presence of temporary failures.
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92
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93 :return: The decoded response if ``json`` is set to ``True``, otherwise
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94 the response object
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95 """
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96 if not url:
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97 url = self.gi._make_url(self, module_id=id, deleted=deleted,
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98 contents=contents)
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99 attempts_left = self.max_get_retries()
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100 retry_delay = self.get_retry_delay()
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101 bioblend.log.debug("GET - attempts left: %s; retry delay: %s",
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102 attempts_left, retry_delay)
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103 msg = ''
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104 while attempts_left > 0:
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105 attempts_left -= 1
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106 try:
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107 r = self.gi.make_get_request(url, params=params)
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108 except (requests.exceptions.ConnectionError, ProtocolError) as e:
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109 msg = str(e)
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110 r = requests.Response() # empty Response object used when raising ConnectionError
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111 else:
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112 if r.status_code == 200:
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113 if not json:
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114 return r
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115 elif not r.content:
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116 msg = "GET: empty response"
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117 else:
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118 try:
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119 return r.json()
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120 except ValueError:
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121 msg = "GET: invalid JSON : %r" % (r.content,)
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122 else:
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123 msg = "GET: error %s: %r" % (r.status_code, r.content)
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124 msg = "%s, %d attempts left" % (msg, attempts_left)
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125 if attempts_left <= 0:
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126 bioblend.log.error(msg)
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127 raise ConnectionError(msg, body=r.text,
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128 status_code=r.status_code)
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129 else:
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130 bioblend.log.warning(msg)
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131 time.sleep(retry_delay)
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132
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133 def _post(self, payload, id=None, deleted=False, contents=None, url=None,
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134 files_attached=False):
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135 """
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136 Do a generic POST request, composing the url from the contents of the
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137 arguments. Alternatively, an explicit ``url`` can be provided to use
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138 for the request. ``payload`` must be a dict that contains additional
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139 request arguments which will be sent along with the request body.
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140 The payload dict may contain file handles (in which case the
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141 ``files_attached`` flag must be set to true).
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142
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143 If ``files_attached`` is set to ``False``, the request body will be
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144 JSON-encoded; otherwise, it will be encoded as multipart/form-data.
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145
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146 :return: The decoded response.
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147 """
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148 if not url:
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149 url = self.gi._make_url(self, module_id=id, deleted=deleted,
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150 contents=contents)
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151 return self.gi.make_post_request(url, payload=payload,
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152 files_attached=files_attached)
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153
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154 def _put(self, payload, id=None, url=None, params=None):
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155 """
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156 Do a generic PUT request, composing the url from the contents of the
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157 arguments. Alternatively, an explicit ``url`` can be provided to use
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158 for the request. ``payload`` must be a dict that contains additional
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159 request arguments which will be sent along with the request body.
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160
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161 :return: The decoded response.
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162 """
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163 if not url:
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164 url = self.gi._make_url(self, module_id=id)
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165 return self.gi.make_put_request(url, payload=payload, params=params)
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166
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167 def _patch(self, payload, id=None, url=None, params=None):
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168 """
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169 Do a generic PATCH request, composing the url from the contents of the
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170 arguments. Alternatively, an explicit ``url`` can be provided to use
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171 for the request. ``payload`` must be a dict that contains additional
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172 request arguments which will be sent along with the request body.
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173
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174 :return: The decoded response.
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175 """
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176 if not url:
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177 url = self.gi._make_url(self, module_id=id)
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178 return self.gi.make_patch_request(url, payload=payload, params=params)
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179
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180 def _delete(self, payload=None, id=None, deleted=False, contents=None, url=None, params=None):
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181 """
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182 Do a generic DELETE request, composing the url from the contents of the
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183 arguments. Alternatively, an explicit ``url`` can be provided to use
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184 for the request. ``payload`` must be a dict that contains additional
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185 request arguments which will be sent along with the request body.
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186
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187 :return: The decoded response.
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188 """
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189 if not url:
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190 url = self.gi._make_url(self, module_id=id, deleted=deleted,
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191 contents=contents)
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192 r = self.gi.make_delete_request(url, payload=payload, params=params)
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193 if r.status_code == 200:
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194 return r.json()
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195 # @see self.body for HTTP response body
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196 raise ConnectionError("Unexpected HTTP status code: %s" % r.status_code,
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197 body=r.text, status_code=r.status_code)