Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/bioblend/galaxyclient.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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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 import six
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13 from requests_toolbelt import MultipartEncoder
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14 from six.moves.urllib.parse import urljoin, urlparse
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15
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16 from bioblend import ConnectionError
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17 from bioblend.util import FileStream
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18
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19
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20 class GalaxyClient(object):
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21
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22 def __init__(self, url, key=None, email=None, password=None, verify=True, timeout=None):
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23 """
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24 :param verify: Whether to verify the server's TLS certificate
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25 :type verify: bool
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26 :param timeout: Timeout for requests operations, set to None for no timeout (the default).
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27 :type timeout: float
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28 """
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29 # Make sure the url scheme is defined (otherwise requests will not work)
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30 if not urlparse(url).scheme:
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31 url = "http://" + url
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32 # All of Galaxy's and ToolShed's API's are rooted at <url>/api so make that the url
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33 self.base_url = url
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34 self.url = urljoin(url, 'api')
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35 # If key has been supplied, use it; otherwise just set email and
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36 # password and grab user's key before first request.
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37 if key:
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38 self._key = key
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39 else:
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40 self._key = None
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41 self.email = email
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42 self.password = password
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43 self.json_headers = {'Content-Type': 'application/json'}
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44 self.verify = verify
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45 self.timeout = timeout
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46
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47 def _make_url(self, module, module_id=None, deleted=False, contents=False):
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48 """
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49 Compose a URL based on the provided arguments.
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50
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51 :type module: :class:`~.galaxy.Client` subclass
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52 :param module: The base module for which to make the URL. For
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53 example: an object of class LibraryClient, WorkflowClient,
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54 HistoryClient, ToolShedClient
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55
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56 :type module_id: str
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57 :param module_id: The encoded ID for a specific module (eg, library ID)
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58
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59 :type deleted: bool
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60 :param deleted: If ``True``, include ``deleted`` in the URL, after the module
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61 name (eg, ``<base_url>/api/libraries/deleted``)
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62
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63 :type contents: bool
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64 :param contents: If ``True``, include 'contents' in the URL, after the module ID:
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65 ``<base_url>/api/libraries/<encoded_library_id>/contents``
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66 """
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67 c_url = '/'.join([self.url, module.module])
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68 if deleted is True:
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69 c_url = '/'.join([c_url, 'deleted'])
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70 if module_id is not None:
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71 c_url = '/'.join([c_url, module_id])
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72 if contents is True:
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73 c_url = '/'.join([c_url, 'contents'])
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74 return c_url
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75
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76 def make_get_request(self, url, **kwargs):
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77 """
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78 Make a GET request using the provided ``url``.
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79
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80 Keyword arguments are the same as in requests.request.
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81
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82 If ``verify`` is not provided, ``self.verify`` will be used.
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83
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84 If the ``params`` are not provided, use ``default_params`` class field.
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85 If params are provided and the provided dict does not have ``key`` key,
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86 the default ``self.key`` value will be included in what's passed to
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87 the server via the request.
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88
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89 :rtype: requests.Response
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90 :return: the response object.
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91 """
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92 params = kwargs.get('params')
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93 if params is not None and params.get('key', False) is False:
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94 params['key'] = self.key
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95 else:
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96 params = self.default_params
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97 kwargs['params'] = params
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98 kwargs.setdefault('verify', self.verify)
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99 kwargs.setdefault('timeout', self.timeout)
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100 r = requests.get(url, **kwargs)
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101 return r
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102
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103 def make_post_request(self, url, payload, params=None, files_attached=False):
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104 """
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105 Make a POST request using the provided ``url`` and ``payload``.
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106 The ``payload`` must be a dict that contains the request values.
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107 The payload dict may contain file handles (in which case the files_attached
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108 flag must be set to true).
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109
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110 If the ``params`` are not provided, use ``default_params`` class field.
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111 If params are provided and the provided dict does not have ``key`` key,
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112 the default ``self.key`` value will be included in what's passed to
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113 the server via the request.
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114
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115 :return: The decoded response.
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116 """
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117
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118 def my_dumps(d):
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119 """
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120 Apply ``json.dumps()`` to the values of the dict ``d`` if they are
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121 not of type ``FileStream``.
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122 """
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123 for k, v in d.items():
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124 if not isinstance(v, FileStream):
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125 d[k] = json.dumps(v)
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126 return d
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127
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128 if params is not None and params.get('key', False) is False:
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129 params['key'] = self.key
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130 else:
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131 params = self.default_params
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132
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133 # Compute data, headers, params arguments for request.post,
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134 # leveraging the requests-toolbelt library if any files have
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135 # been attached.
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136 if files_attached:
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137 payload = my_dumps(payload)
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138 payload.update(params)
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139 payload = MultipartEncoder(fields=payload)
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140 headers = self.json_headers.copy()
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141 headers['Content-Type'] = payload.content_type
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142 post_params = {}
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143 else:
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144 payload = json.dumps(payload)
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145 headers = self.json_headers
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146 post_params = params
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147
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148 r = requests.post(url, data=payload, headers=headers,
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149 verify=self.verify, params=post_params,
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150 timeout=self.timeout)
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151 if r.status_code == 200:
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152 try:
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153 return r.json()
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154 except Exception as e:
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155 raise ConnectionError("Request was successful, but cannot decode the response content: %s" %
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156 e, body=r.content, status_code=r.status_code)
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157 # @see self.body for HTTP response body
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158 raise ConnectionError("Unexpected HTTP status code: %s" % r.status_code,
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159 body=r.text, status_code=r.status_code)
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160
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161 def make_delete_request(self, url, payload=None, params=None):
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162 """
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163 Make a DELETE request using the provided ``url`` and the optional
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164 arguments.
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165
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166 If the ``params`` are not provided, use ``default_params`` class field.
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167 If params are provided and the provided dict does not have ``key`` key,
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168 the default ``self.key`` value will be included in what's passed to
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169 the server via the request.
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170
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171 :type payload: dict
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172 :param payload: a JSON-serializable dictionary
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173
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174 :rtype: requests.Response
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175 :return: the response object.
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176 """
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177 if params is not None and params.get('key', False) is False:
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178 params['key'] = self.key
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179 else:
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180 params = self.default_params
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181 if payload is not None:
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182 payload = json.dumps(payload)
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183 headers = self.json_headers
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184 r = requests.delete(url, verify=self.verify, data=payload, params=params,
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185 headers=headers, timeout=self.timeout)
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186 return r
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187
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188 def make_put_request(self, url, payload=None, params=None):
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189 """
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190 Make a PUT request using the provided ``url`` with required payload.
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191
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192 :type payload: dict
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193 :param payload: a JSON-serializable dictionary
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194
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195 :return: The decoded response.
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196 """
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197 if params is not None and params.get('key', False) is False:
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198 params['key'] = self.key
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199 else:
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200 params = self.default_params
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201
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202 payload = json.dumps(payload)
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203 headers = self.json_headers
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204 r = requests.put(url, data=payload, params=params, headers=headers,
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205 verify=self.verify, timeout=self.timeout)
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206 if r.status_code == 200:
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207 try:
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208 return r.json()
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209 except Exception as e:
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210 raise ConnectionError("Request was successful, but cannot decode the response content: %s" %
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211 e, body=r.content, status_code=r.status_code)
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212 # @see self.body for HTTP response body
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213 raise ConnectionError("Unexpected HTTP status code: %s" % r.status_code,
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214 body=r.text, status_code=r.status_code)
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215
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216 def make_patch_request(self, url, payload=None, params=None):
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217 """
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218 Make a PATCH request using the provided ``url`` with required payload.
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219
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220 :type payload: dict
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221 :param payload: a JSON-serializable dictionary
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222
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223 :return: The decoded response.
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224 """
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225 if params is not None and params.get('key', False) is False:
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226 params['key'] = self.key
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227 else:
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228 params = self.default_params
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229
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230 payload = json.dumps(payload)
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231 headers = self.json_headers
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232 r = requests.patch(url, data=payload, params=params, headers=headers,
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233 verify=self.verify, timeout=self.timeout)
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234 if r.status_code == 200:
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235 try:
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236 return r.json()
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237 except Exception as e:
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238 raise ConnectionError("Request was successful, but cannot decode the response content: %s" %
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239 e, body=r.content, status_code=r.status_code)
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240 # @see self.body for HTTP response body
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241 raise ConnectionError("Unexpected HTTP status code: %s" % r.status_code,
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242 body=r.text, status_code=r.status_code)
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243
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244 @property
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245 def key(self):
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246 if not self._key and self.email is not None and self.password is not None:
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247 unencoded_credentials = "%s:%s" % (self.email, self.password)
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248 authorization = base64.b64encode(unencoded_credentials.encode())
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249 headers = self.json_headers.copy()
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250 headers["Authorization"] = authorization
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251 auth_url = "%s/authenticate/baseauth" % self.url
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252 # make_post_request uses default_params, which uses this and
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253 # sets wrong headers - so using lower level method.
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254 r = requests.get(auth_url, verify=self.verify, headers=headers)
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255 if r.status_code != 200:
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256 raise Exception("Failed to authenticate user.")
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257 response = r.json()
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258 if isinstance(response, (six.string_types, six.text_type)):
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259 # bug in Tool Shed
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260 response = json.loads(response)
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261 self._key = response["api_key"]
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262 return self._key
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263
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264 @property
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265 def default_params(self):
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266 return {'key': self.key}