1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379
|
"""
Helper class for Galaxy and ToolShed Instance object
This class is primarily a helper for the library and user code
should not use it directly.
A base representation of an instance
"""
import base64
import contextlib
import json
import logging
from typing import (
Any,
Optional,
)
import requests
import tusclient.client
import tusclient.exceptions
import tusclient.storage.filestorage
import tusclient.uploader
from requests_toolbelt import MultipartEncoder
from bioblend import ConnectionError
from bioblend.util import FileStream
log = logging.getLogger(__name__)
UPLOAD_CHUNK_SIZE = 10**7
class GalaxyClient:
def __init__(
self,
url: str,
key: Optional[str] = None,
email: Optional[str] = None,
password: Optional[str] = None,
verify: bool = True,
timeout: Optional[float] = None,
) -> None:
"""
:param verify: Whether to verify the server's TLS certificate
:type verify: bool
:param timeout: Timeout for requests operations, set to None for no timeout (the default).
:type timeout: float
"""
self.verify = verify
self.timeout = timeout
# Make sure the URL scheme is defined (otherwise requests will not work)
if not url.lower().startswith("http"):
found_scheme = None
# Try to guess the scheme, starting from the more secure
for scheme in ("https://", "http://"):
log.warning(f"Missing scheme in url, trying with {scheme}")
with contextlib.suppress(requests.RequestException):
r = requests.get(
scheme + url,
timeout=self.timeout,
verify=self.verify,
)
r.raise_for_status()
found_scheme = scheme
break
else:
raise ValueError(f"Missing scheme in url {url}")
url = found_scheme + url
self.base_url = url.rstrip("/")
# All of Galaxy's and ToolShed's API's are rooted at <url>/api so make that the url
self.url = f"{self.base_url}/api"
# If key has been supplied, use it; otherwise just set email and
# password and grab user's key before first request.
if key:
self._key: Optional[str] = key
else:
self._key = None
self.email = email
self.password = password
self.json_headers: dict = {"Content-Type": "application/json"}
# json_headers needs to be set before key can be defined, otherwise authentication with email/password causes an error
self.json_headers["x-api-key"] = self.key
# Number of attempts before giving up on a GET request.
self._max_get_attempts = 1
# Delay in seconds between subsequent retries.
self._get_retry_delay = 10.0
@property
def max_get_attempts(self) -> int:
"""
The maximum number of attempts for a GET request. Default: 1
"""
return self._max_get_attempts
@max_get_attempts.setter
def max_get_attempts(self, value: int) -> None:
"""
Set the maximum number of attempts for GET requests. A value greater
than one causes failed GET requests to be retried `value` - 1 times.
"""
if value < 1:
raise ValueError(f"Number of attempts must be >= 1 (got: {value})")
self._max_get_attempts = value
@property
def get_retry_delay(self) -> float:
"""
The delay (in seconds) to wait before retrying a failed GET request.
Default: 10.0
"""
return self._get_retry_delay
@get_retry_delay.setter
def get_retry_delay(self, value: float) -> None:
"""
Set the delay (in seconds) to wait before retrying a failed GET
request.
"""
if value < 0:
raise ValueError(f"Retry delay must be >= 0 (got: {value})")
self._get_retry_delay = value
def make_get_request(self, url: str, **kwargs: Any) -> requests.Response:
"""
Make a GET request using the provided ``url``.
Keyword arguments are the same as in requests.request.
If ``verify`` is not provided, ``self.verify`` will be used.
:rtype: requests.Response
:return: the response object.
"""
headers = self.json_headers
kwargs.setdefault("timeout", self.timeout)
kwargs.setdefault("verify", self.verify)
r = requests.get(url, headers=headers, **kwargs)
return r
def make_post_request(
self, url: str, payload: Optional[dict] = None, params: Optional[dict] = None, files_attached: bool = False
) -> Any:
"""
Make a POST request using the provided ``url`` and ``payload``.
The ``payload`` must be a dict that contains the request values.
The payload dict may contain file handles (in which case the files_attached
flag must be set to true).
:return: The decoded response.
"""
def my_dumps(d: dict) -> dict:
"""
Apply ``json.dumps()`` to the values of the dict ``d`` if they are
not of type ``FileStream``.
"""
for k, v in d.items():
if not isinstance(v, (FileStream, str, bytes)):
d[k] = json.dumps(v)
return d
# Compute data, headers, params arguments for request.post,
# leveraging the requests-toolbelt library if any files have
# been attached.
if files_attached:
payload_copy = payload.copy() if payload is not None else {}
if params:
payload_copy.update(params)
data = MultipartEncoder(fields=my_dumps(payload_copy))
headers = self.json_headers.copy()
headers["Content-Type"] = data.content_type
post_params = None
else:
data = json.dumps(payload) if payload is not None else None
headers = self.json_headers
post_params = params
r = requests.post(
url,
params=post_params,
data=data,
headers=headers,
timeout=self.timeout,
allow_redirects=False,
verify=self.verify,
)
if r.status_code == 200:
try:
return r.json()
except Exception as e:
raise ConnectionError(
f"Request was successful, but cannot decode the response content: {e}",
body=r.content,
status_code=r.status_code,
)
# @see self.body for HTTP response body
raise ConnectionError(
f"Unexpected HTTP status code: {r.status_code}",
body=r.text,
status_code=r.status_code,
)
def make_delete_request(
self, url: str, payload: Optional[dict] = None, params: Optional[dict] = None
) -> requests.Response:
"""
Make a DELETE request using the provided ``url`` and the optional
arguments.
:type payload: dict
:param payload: a JSON-serializable dictionary
:rtype: requests.Response
:return: the response object.
"""
data = json.dumps(payload) if payload is not None else None
headers = self.json_headers
r = requests.delete(
url,
params=params,
data=data,
headers=headers,
timeout=self.timeout,
allow_redirects=False,
verify=self.verify,
)
return r
def make_put_request(self, url: str, payload: Optional[dict] = None, params: Optional[dict] = None) -> Any:
"""
Make a PUT request using the provided ``url`` with required payload.
:type payload: dict
:param payload: a JSON-serializable dictionary
:return: The decoded response.
"""
data = json.dumps(payload) if payload is not None else None
headers = self.json_headers
r = requests.put(
url,
params=params,
data=data,
headers=headers,
timeout=self.timeout,
allow_redirects=False,
verify=self.verify,
)
if r.status_code == 200:
try:
return r.json()
except Exception as e:
raise ConnectionError(
f"Request was successful, but cannot decode the response content: {e}",
body=r.content,
status_code=r.status_code,
)
# @see self.body for HTTP response body
raise ConnectionError(
f"Unexpected HTTP status code: {r.status_code}",
body=r.text,
status_code=r.status_code,
)
def make_patch_request(self, url: str, payload: Optional[dict] = None, params: Optional[dict] = None) -> Any:
"""
Make a PATCH request using the provided ``url`` with required payload.
:type payload: dict
:param payload: a JSON-serializable dictionary
:return: The decoded response.
"""
data = json.dumps(payload) if payload is not None else None
headers = self.json_headers
r = requests.patch(
url,
params=params,
data=data,
headers=headers,
timeout=self.timeout,
allow_redirects=False,
verify=self.verify,
)
if r.status_code == 200:
try:
return r.json()
except Exception as e:
raise ConnectionError(
f"Request was successful, but cannot decode the response content: {e}",
body=r.content,
status_code=r.status_code,
)
# @see self.body for HTTP response body
raise ConnectionError(
f"Unexpected HTTP status code: {r.status_code}",
body=r.text,
status_code=r.status_code,
)
def get_tus_uploader(
self,
path: str,
url: str = "/upload/resumable_upload",
storage: Optional[str] = None,
metadata: Optional[dict] = None,
chunk_size: Optional[int] = UPLOAD_CHUNK_SIZE,
) -> tusclient.uploader.Uploader:
"""
Return the tus client uploader object for uploading to the Galaxy tus endpoint
:type path: str
:param path: path of the file to upload
:type url: str
:param url: URL (relative to base URL) of the upload endpoint
:type storage: str
:param storage: Local path to store URLs resuming uploads
:type metadata: dict
:param metadata: Metadata to send with upload request
:type chunk_size: int
:param chunk_size: Number of bytes to send in each chunk
:rtype: tusclient.uploader.Uploader
:return: tus uploader object
"""
headers = {"x-api-key": self.key}
client = tusclient.client.TusClient(self.url + url, headers=headers)
if storage:
storage = tusclient.storage.filestorage.FileStorage(storage)
try:
return client.uploader(
file_path=path,
chunk_size=chunk_size,
metadata=metadata,
store_url=storage is not None,
url_storage=storage,
)
except tusclient.exceptions.TusCommunicationError as exc:
raise ConnectionError(
f"Unexpected HTTP status code: {exc.status_code}",
body=str(exc),
status_code=exc.status_code,
)
@property
def key(self) -> Optional[str]:
if not self._key and self.email is not None and self.password is not None:
unencoded_credentials = f"{self.email}:{self.password}"
authorization = base64.b64encode(unencoded_credentials.encode())
headers = self.json_headers.copy()
headers["Authorization"] = authorization
auth_url = f"{self.url}/authenticate/baseauth"
# Use lower level method instead of make_get_request() because we
# need the additional Authorization header.
r = requests.get(
auth_url,
headers=headers,
timeout=self.timeout,
verify=self.verify,
)
if r.status_code != 200:
raise Exception("Failed to authenticate user.")
response = r.json()
if isinstance(response, str):
# bug in Tool Shed
response = json.loads(response)
self._key = response["api_key"]
return self._key
def _tus_uploader_session_id(self: tusclient.uploader.Uploader) -> str:
return self.url.rsplit("/", 1)[1]
# monkeypatch a session_id property on to uploader
tusclient.uploader.Uploader.session_id = property(_tus_uploader_session_id)
|