Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/bioblend/galaxyclient.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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: |
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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, allow_redirects=False) |
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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, allow_redirects=False) |
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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, allow_redirects=False) |
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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, allow_redirects=False) |
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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 = f"{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} |