Mercurial > repos > shellac > guppy_basecaller
annotate env/lib/python3.7/site-packages/bioblend/galaxy/client.py @ 0:26e78fe6e8c4 draft
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author | shellac |
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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) |