Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/bioblend/galaxyclient.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
parents d30785e31577
children
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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 from urllib.parse import (
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11 urljoin,
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12 urlparse,
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13 )
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14
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15 import requests
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16 from requests_toolbelt import MultipartEncoder
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17
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18 from bioblend import ConnectionError
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19 from bioblend.util import FileStream
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20
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21
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22 class GalaxyClient(object):
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23
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24 def __init__(self, url, key=None, email=None, password=None, verify=True, timeout=None):
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25 """
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26 :param verify: Whether to verify the server's TLS certificate
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27 :type verify: bool
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28 :param timeout: Timeout for requests operations, set to None for no timeout (the default).
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29 :type timeout: float
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30 """
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31 # Make sure the url scheme is defined (otherwise requests will not work)
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32 if not urlparse(url).scheme:
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33 url = "http://" + url
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34 # All of Galaxy's and ToolShed's API's are rooted at <url>/api so make that the url
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35 self.base_url = url
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36 self.url = urljoin(url, 'api')
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37 # If key has been supplied, use it; otherwise just set email and
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38 # password and grab user's key before first request.
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39 if key:
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40 self._key = key
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41 else:
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42 self._key = None
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43 self.email = email
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44 self.password = password
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45 self.json_headers = {'Content-Type': 'application/json'}
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46 self.verify = verify
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47 self.timeout = timeout
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48
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49 def make_get_request(self, url, **kwargs):
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50 """
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51 Make a GET request using the provided ``url``.
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52
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53 Keyword arguments are the same as in requests.request.
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54
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55 If ``verify`` is not provided, ``self.verify`` will be used.
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56
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57 If the ``params`` are not provided, use ``default_params`` class field.
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58 If params are provided and the provided dict does not have ``key`` key,
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59 the default ``self.key`` value will be included in what's passed to
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60 the server via the request.
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61
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62 :rtype: requests.Response
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63 :return: the response object.
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64 """
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65 params = kwargs.get('params')
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66 if params is not None and params.get('key', False) is False:
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67 params['key'] = self.key
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68 else:
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69 params = self.default_params
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70 kwargs['params'] = params
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71 kwargs.setdefault('verify', self.verify)
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72 kwargs.setdefault('timeout', self.timeout)
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73 r = requests.get(url, **kwargs)
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74 return r
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75
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76 def make_post_request(self, url, payload, params=None, files_attached=False):
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77 """
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78 Make a POST request using the provided ``url`` and ``payload``.
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79 The ``payload`` must be a dict that contains the request values.
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80 The payload dict may contain file handles (in which case the files_attached
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81 flag must be set to true).
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82
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83 If the ``params`` are not provided, use ``default_params`` class field.
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84 If params are provided and the provided dict does not have ``key`` key,
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85 the default ``self.key`` value will be included in what's passed to
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86 the server via the request.
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87
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88 :return: The decoded response.
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89 """
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90
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91 def my_dumps(d):
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92 """
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93 Apply ``json.dumps()`` to the values of the dict ``d`` if they are
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94 not of type ``FileStream``.
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95 """
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96 for k, v in d.items():
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97 if not isinstance(v, FileStream):
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98 d[k] = json.dumps(v)
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99 return d
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100
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101 if params is not None and params.get('key', False) is False:
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102 params['key'] = self.key
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103 else:
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104 params = self.default_params
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105
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106 # Compute data, headers, params arguments for request.post,
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107 # leveraging the requests-toolbelt library if any files have
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108 # been attached.
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109 if files_attached:
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110 payload = my_dumps(payload)
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111 payload.update(params)
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112 payload = MultipartEncoder(fields=payload)
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113 headers = self.json_headers.copy()
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114 headers['Content-Type'] = payload.content_type
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115 post_params = {}
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116 else:
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117 payload = json.dumps(payload)
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118 headers = self.json_headers
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119 post_params = params
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120
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121 r = requests.post(url, data=payload, headers=headers,
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122 verify=self.verify, params=post_params,
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123 timeout=self.timeout)
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124 if r.status_code == 200:
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125 try:
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126 return r.json()
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127 except Exception as e:
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128 raise ConnectionError("Request was successful, but cannot decode the response content: %s" %
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129 e, body=r.content, status_code=r.status_code)
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130 # @see self.body for HTTP response body
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131 raise ConnectionError("Unexpected HTTP status code: %s" % r.status_code,
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132 body=r.text, status_code=r.status_code)
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133
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134 def make_delete_request(self, url, payload=None, params=None):
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135 """
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136 Make a DELETE request using the provided ``url`` and the optional
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137 arguments.
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138
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139 If the ``params`` are not provided, use ``default_params`` class field.
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140 If params are provided and the provided dict does not have ``key`` key,
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141 the default ``self.key`` value will be included in what's passed to
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142 the server via the request.
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143
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144 :type payload: dict
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145 :param payload: a JSON-serializable dictionary
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146
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147 :rtype: requests.Response
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148 :return: the response object.
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149 """
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150 if params is not None and params.get('key', False) is False:
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151 params['key'] = self.key
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152 else:
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153 params = self.default_params
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154 if payload is not None:
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155 payload = json.dumps(payload)
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156 headers = self.json_headers
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157 r = requests.delete(url, verify=self.verify, data=payload, params=params,
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158 headers=headers, timeout=self.timeout)
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159 return r
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160
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161 def make_put_request(self, url, payload=None, params=None):
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162 """
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163 Make a PUT request using the provided ``url`` with required payload.
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164
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165 :type payload: dict
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166 :param payload: a JSON-serializable dictionary
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167
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168 :return: The decoded response.
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169 """
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170 if params is not None and params.get('key', False) is False:
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171 params['key'] = self.key
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172 else:
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173 params = self.default_params
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174
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175 payload = json.dumps(payload)
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176 headers = self.json_headers
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177 r = requests.put(url, data=payload, params=params, headers=headers,
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178 verify=self.verify, timeout=self.timeout)
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179 if r.status_code == 200:
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180 try:
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181 return r.json()
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182 except Exception as e:
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183 raise ConnectionError("Request was successful, but cannot decode the response content: %s" %
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184 e, body=r.content, status_code=r.status_code)
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185 # @see self.body for HTTP response body
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186 raise ConnectionError("Unexpected HTTP status code: %s" % r.status_code,
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187 body=r.text, status_code=r.status_code)
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188
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189 def make_patch_request(self, url, payload=None, params=None):
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190 """
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191 Make a PATCH request using the provided ``url`` with required payload.
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192
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193 :type payload: dict
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194 :param payload: a JSON-serializable dictionary
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195
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196 :return: The decoded response.
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197 """
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198 if params is not None and params.get('key', False) is False:
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199 params['key'] = self.key
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200 else:
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201 params = self.default_params
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202
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203 payload = json.dumps(payload)
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204 headers = self.json_headers
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205 r = requests.patch(url, data=payload, params=params, headers=headers,
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206 verify=self.verify, timeout=self.timeout)
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207 if r.status_code == 200:
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208 try:
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209 return r.json()
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210 except Exception as e:
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211 raise ConnectionError("Request was successful, but cannot decode the response content: %s" %
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212 e, body=r.content, status_code=r.status_code)
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213 # @see self.body for HTTP response body
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214 raise ConnectionError("Unexpected HTTP status code: %s" % r.status_code,
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215 body=r.text, status_code=r.status_code)
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216
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217 @property
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218 def key(self):
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219 if not self._key and self.email is not None and self.password is not None:
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220 unencoded_credentials = "%s:%s" % (self.email, self.password)
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221 authorization = base64.b64encode(unencoded_credentials.encode())
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222 headers = self.json_headers.copy()
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223 headers["Authorization"] = authorization
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224 auth_url = "%s/authenticate/baseauth" % self.url
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225 # make_post_request uses default_params, which uses this and
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226 # sets wrong headers - so using lower level method.
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227 r = requests.get(auth_url, verify=self.verify, headers=headers)
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228 if r.status_code != 200:
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229 raise Exception("Failed to authenticate user.")
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230 response = r.json()
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231 if isinstance(response, str):
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232 # bug in Tool Shed
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233 response = json.loads(response)
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234 self._key = response["api_key"]
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235 return self._key
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236
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237 @property
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238 def default_params(self):
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239 return {'key': self.key}