Mercurial > repos > bcclaywell > argo_navis

annotate venv/lib/python2.7/site-packages/bioblend/galaxyclient.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 Helper class for Galaxy and ToolShed Instance object
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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 A base representation of an instance
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7 """
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8 import base64
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9 import json
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10
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11 import requests
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12 from requests_toolbelt import MultipartEncoder
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13 import six
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14 from six.moves.urllib.parse import urljoin, urlparse
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15
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16 from .galaxy.client import ConnectionError
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17
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18
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19 class GalaxyClient(object):
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20
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21 def __init__(self, url, key=None, email=None, password=None):
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22 # Make sure the url scheme is defined (otherwise requests will not work)
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23 if not urlparse(url).scheme:
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24 url = "http://" + url
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25 # All of Galaxy's and ToolShed's API's are rooted at <url>/api so make that the url
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26 self.base_url = url
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27 self.url = urljoin(url, 'api')
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28 # If key has been supplied, use it; otherwise just set email and
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29 # password and grab user's key before first request.
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30 if key:
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31 self._key = key
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32 else:
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33 self._key = None
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34 self.email = email
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35 self.password = password
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36 self.json_headers = {'Content-Type': 'application/json'}
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37 self.verify = True # Should SSL verification be done
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38
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39 def _make_url(self, module, module_id=None, deleted=False, contents=False):
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40 """
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41 Compose a URL based on the provided arguments.
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42
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43 :type module: :class:`~.galaxy.Client` subclass
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44 :param module: The base module for which to make the URL. For
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45 example: an object of class LibraryClient, WorkflowClient,
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46 HistoryClient, ToolShedClient
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47
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48 :type module_id: str
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49 :param module_id: The encoded ID for a specific module (eg, library ID)
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50
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51 :type deleted: bool
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52 :param deleted: If ``True``, include ``deleted`` in the URL, after the module
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53 name (eg, ``<base_url>/api/libraries/deleted``)
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54
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55 :type contents: bool
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56 :param contents: If ``True``, include 'contents' in the URL, after the module ID:
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57 ``<base_url>/api/libraries/<encoded_library_id>/contents``
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58 """
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59 c_url = self.url
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60 c_url = '/'.join([c_url, module.module])
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61 if deleted is True:
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62 c_url = '/'.join([c_url, 'deleted'])
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63 if module_id is not None:
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64 c_url = '/'.join([c_url, module_id])
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65 if contents is True:
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66 c_url = '/'.join([c_url, 'contents'])
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67 return c_url
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68
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69 def make_get_request(self, url, **kwargs):
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70 """
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71 Make a GET request using the provided ``url``.
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72
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73 Keyword arguments are the same as in requests.request.
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74
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75 If ``verify`` is not provided, ``self.verify`` will be used.
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76
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77 If the ``params`` are not provided, use ``default_params`` class field.
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78 If params are provided and the provided dict does not have ``key`` key,
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79 the default ``self.key`` value will be included in what's passed to
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80 the server via the request.
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81 """
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82 params = kwargs.get('params')
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83 if params is not None and params.get('key', False) is False:
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84 params['key'] = self.key
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85 else:
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86 params = self.default_params
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87 kwargs['params'] = params
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88 kwargs.setdefault('verify', self.verify)
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89 r = requests.get(url, **kwargs)
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90 return r
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91
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92 def make_post_request(self, url, payload, params=None, files_attached=False):
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93 """
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94 Make a POST request using the provided ``url`` and ``payload``.
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95 The ``payload`` must be a dict that contains the request values.
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96 The payload dict may contain file handles (in which case the files_attached
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97 flag must be set to true).
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98
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99 If the ``params`` are not provided, use ``default_params`` class field.
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100 If params are provided and the provided dict does not have ``key`` key,
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101 the default ``self.key`` value will be included in what's passed to
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102 the server via the request.
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103
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104 The return value will contain the response body as a JSON object.
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105 """
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106 if params is not None and params.get('key', False) is False:
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107 params['key'] = self.key
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108 else:
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109 params = self.default_params
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110
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111 # Compute data, headers, params arguments for request.post,
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112 # leveraging the requests-toolbelt library if any files have
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113 # been attached.
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114 if files_attached:
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115 payload.update(params)
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116 payload = MultipartEncoder(fields=payload)
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117 headers = self.json_headers.copy()
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118 headers['Content-Type'] = payload.content_type
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119 post_params = {}
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120 else:
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121 payload = json.dumps(payload)
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122 headers = self.json_headers
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123 post_params = params
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124
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125 r = requests.post(url, data=payload, headers=headers,
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126 verify=self.verify, params=post_params)
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127 if r.status_code == 200:
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128 return r.json()
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129 # @see self.body for HTTP response body
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130 raise ConnectionError("Unexpected response from galaxy: %s" %
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131 r.status_code, body=r.text)
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132
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133 def make_delete_request(self, url, payload=None, params=None):
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134 """
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135 Make a DELETE request using the provided ``url`` and the optional
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136 arguments.
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137 The ``payload`` must be a dict that can be converted into a JSON
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138 object (via ``json.dumps``)
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139
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140 If the ``params`` are not provided, use ``default_params`` class field.
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141 If params are provided and the provided dict does not have ``key`` key,
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142 the default ``self.key`` value will be included in what's passed to
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143 the server via the request.
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144 """
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145 if params is not None and params.get('key', False) is False:
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146 params['key'] = self.key
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147 else:
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148 params = self.default_params
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149 r = requests.delete(url, verify=self.verify, data=payload, params=params)
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150 return r
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151
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152 def make_put_request(self, url, payload=None, params=None):
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153 """
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154 Make a PUT request using the provided ``url`` with required payload.
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155 The ``payload`` must be a dict that can be converted into a JSON
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156 object (via ``json.dumps``)
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157 """
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158 if params is not None and params.get('key', False) is False:
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159 params['key'] = self.key
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160 else:
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161 params = self.default_params
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162
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163 payload = json.dumps(payload)
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164 r = requests.put(url, verify=self.verify, data=payload, params=params)
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165 return r
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166
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167 @property
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168 def key(self):
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169 if not self._key and self.email is not None and self.password is not None:
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170 unencoded_credentials = "%s:%s" % (self.email, self.password)
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171 authorization = base64.b64encode(unencoded_credentials)
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172 headers = self.json_headers.copy()
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173 headers["Authorization"] = authorization
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174 auth_url = "%s/authenticate/baseauth" % self.url
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175 # make_post_request uses default_params, which uses this and
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176 # sets wrong headers - so using lower level method.
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177 r = requests.get(auth_url, verify=self.verify, headers=headers)
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178 if r.status_code != 200:
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179 raise Exception("Failed to authenticate user.")
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180 response = r.json()
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181 if isinstance(response, (six.string_types, six.text_type)):
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182 # bug in Tool Shed
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183 response = json.loads(response)
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184 self._key = response["api_key"]
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185 return self._key
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186
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187 @property
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188 def default_params(self):
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189 return {'key': self.key}