Coverage for python/lsst/daf/butler/core/_butlerUri/s3.py : 79%

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1# This file is part of daf_butler.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (http://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <http://www.gnu.org/licenses/>.
22from __future__ import annotations
24import logging
25import re
26import tempfile
28__all__ = ('ButlerS3URI',)
30from typing import (
31 TYPE_CHECKING,
32 Optional,
33 Any,
34 Callable,
35 Iterator,
36 List,
37 Tuple,
38 Union,
39)
41from ..utils import time_this
42from .utils import NoTransaction
43from ._butlerUri import ButlerURI
44from .s3utils import getS3Client, s3CheckFileExists, bucketExists
46from botocore.exceptions import ClientError
47from http.client import ImproperConnectionState, HTTPException
48from urllib3.exceptions import RequestError, HTTPError
50if TYPE_CHECKING: 50 ↛ 51line 50 didn't jump to line 51, because the condition on line 50 was never true
51 try:
52 import boto3
53 except ImportError:
54 pass
55 from ..datastore import DatastoreTransaction
57# https://pypi.org/project/backoff/
58try:
59 import backoff
60except ImportError:
61 class Backoff():
62 @staticmethod
63 def expo(func: Callable, *args: Any, **kwargs: Any) -> Callable:
64 return func
66 @staticmethod
67 def on_exception(func: Callable, *args: Any, **kwargs: Any) -> Callable:
68 return func
70 backoff = Backoff
72# settings for "backoff" retry decorators. these retries are belt-and-
73# suspenders along with the retries built into Boto3, to account for
74# semantic differences in errors between S3-like providers.
75retryable_io_errors = (
76 # http.client
77 ImproperConnectionState, HTTPException,
78 # urllib3.exceptions
79 RequestError, HTTPError,
80 # built-ins
81 TimeoutError, ConnectionError)
82retryable_client_errors = (
83 # botocore.exceptions
84 ClientError,
85 # built-ins
86 PermissionError)
87all_retryable_errors = retryable_client_errors + retryable_io_errors
88max_retry_time = 60
91log = logging.getLogger(__name__)
94class ButlerS3URI(ButlerURI):
95 """S3 URI implementation class."""
97 @property
98 def client(self) -> boto3.client:
99 """Client object to address remote resource."""
100 # Defer import for circular dependencies
101 return getS3Client()
103 @backoff.on_exception(backoff.expo, retryable_client_errors, max_time=max_retry_time)
104 def exists(self) -> bool:
105 """Check that the S3 resource exists."""
106 if self.is_root: 106 ↛ 108line 106 didn't jump to line 108, because the condition on line 106 was never true
107 # Only check for the bucket since the path is irrelevant
108 return bucketExists(self.netloc)
109 exists, _ = s3CheckFileExists(self, client=self.client)
110 return exists
112 @backoff.on_exception(backoff.expo, retryable_client_errors, max_time=max_retry_time)
113 def size(self) -> int:
114 """Return the size of the resource in bytes."""
115 if self.dirLike: 115 ↛ 116line 115 didn't jump to line 116, because the condition on line 115 was never true
116 return 0
117 exists, sz = s3CheckFileExists(self, client=self.client)
118 if not exists:
119 raise FileNotFoundError(f"Resource {self} does not exist")
120 return sz
122 @backoff.on_exception(backoff.expo, retryable_client_errors, max_time=max_retry_time)
123 def remove(self) -> None:
124 """Remove the resource."""
125 # https://github.com/boto/boto3/issues/507 - there is no
126 # way of knowing if the file was actually deleted except
127 # for checking all the keys again, reponse is HTTP 204 OK
128 # response all the time
129 self.client.delete_object(Bucket=self.netloc, Key=self.relativeToPathRoot)
131 @backoff.on_exception(backoff.expo, all_retryable_errors, max_time=max_retry_time)
132 def read(self, size: int = -1) -> bytes:
133 """Read the contents of the resource."""
134 args = {}
135 if size > 0:
136 args["Range"] = f"bytes=0-{size-1}"
137 try:
138 response = self.client.get_object(Bucket=self.netloc,
139 Key=self.relativeToPathRoot,
140 **args)
141 except (self.client.exceptions.NoSuchKey, self.client.exceptions.NoSuchBucket) as err:
142 raise FileNotFoundError(f"No such resource: {self}") from err
143 with time_this(log, msg="Read from %s", args=(self,)):
144 body = response["Body"].read()
145 response["Body"].close()
146 return body
148 @backoff.on_exception(backoff.expo, all_retryable_errors, max_time=max_retry_time)
149 def write(self, data: bytes, overwrite: bool = True) -> None:
150 """Write the supplied data to the resource."""
151 if not overwrite:
152 if self.exists(): 152 ↛ 153line 152 didn't jump to line 153, because the condition on line 152 was never true
153 raise FileExistsError(f"Remote resource {self} exists and overwrite has been disabled")
154 with time_this(log, msg="Write to %s", args=(self,)):
155 self.client.put_object(Bucket=self.netloc, Key=self.relativeToPathRoot,
156 Body=data)
158 @backoff.on_exception(backoff.expo, all_retryable_errors, max_time=max_retry_time)
159 def mkdir(self) -> None:
160 """Write a directory key to S3."""
161 if not bucketExists(self.netloc): 161 ↛ 162line 161 didn't jump to line 162, because the condition on line 161 was never true
162 raise ValueError(f"Bucket {self.netloc} does not exist for {self}!")
164 if not self.dirLike: 164 ↛ 165line 164 didn't jump to line 165, because the condition on line 164 was never true
165 raise ValueError(f"Can not create a 'directory' for file-like URI {self}")
167 # don't create S3 key when root is at the top-level of an Bucket
168 if not self.path == "/": 168 ↛ exitline 168 didn't return from function 'mkdir', because the condition on line 168 was never false
169 self.client.put_object(Bucket=self.netloc, Key=self.relativeToPathRoot)
171 @backoff.on_exception(backoff.expo, all_retryable_errors, max_time=max_retry_time)
172 def _as_local(self) -> Tuple[str, bool]:
173 """Download object from S3 and place in temporary directory.
175 Returns
176 -------
177 path : `str`
178 Path to local temporary file.
179 temporary : `bool`
180 Always returns `True`. This is always a temporary file.
181 """
182 with tempfile.NamedTemporaryFile(suffix=self.getExtension(), delete=False) as tmpFile:
183 with time_this(log, msg="Downloading %s to local file", args=(self,)):
184 self.client.download_fileobj(self.netloc, self.relativeToPathRoot, tmpFile)
185 return tmpFile.name, True
187 @backoff.on_exception(backoff.expo, all_retryable_errors, max_time=max_retry_time)
188 def transfer_from(self, src: ButlerURI, transfer: str = "copy",
189 overwrite: bool = False,
190 transaction: Optional[Union[DatastoreTransaction, NoTransaction]] = None) -> None:
191 """Transfer the current resource to an S3 bucket.
193 Parameters
194 ----------
195 src : `ButlerURI`
196 Source URI.
197 transfer : `str`
198 Mode to use for transferring the resource. Supports the following
199 options: copy.
200 overwrite : `bool`, optional
201 Allow an existing file to be overwritten. Defaults to `False`.
202 transaction : `DatastoreTransaction`, optional
203 Currently unused.
204 """
205 # Fail early to prevent delays if remote resources are requested
206 if transfer not in self.transferModes:
207 raise ValueError(f"Transfer mode '{transfer}' not supported by URI scheme {self.scheme}")
209 # Existence checks cost time so do not call this unless we know
210 # that debugging is enabled.
211 if log.isEnabledFor(logging.DEBUG): 211 ↛ 212line 211 didn't jump to line 212, because the condition on line 211 was never true
212 log.debug("Transferring %s [exists: %s] -> %s [exists: %s] (transfer=%s)",
213 src, src.exists(), self, self.exists(), transfer)
215 if not overwrite and self.exists():
216 raise FileExistsError(f"Destination path '{self}' already exists.")
218 if transfer == "auto": 218 ↛ 219line 218 didn't jump to line 219, because the condition on line 218 was never true
219 transfer = self.transferDefault
221 timer_msg = "Transfer from %s to %s"
222 timer_args = (src, self)
224 if isinstance(src, type(self)):
225 # Looks like an S3 remote uri so we can use direct copy
226 # note that boto3.resource.meta.copy is cleverer than the low
227 # level copy_object
228 copy_source = {
229 "Bucket": src.netloc,
230 "Key": src.relativeToPathRoot,
231 }
232 with time_this(log, msg=timer_msg, args=timer_args):
233 self.client.copy_object(CopySource=copy_source, Bucket=self.netloc,
234 Key=self.relativeToPathRoot)
235 else:
236 # Use local file and upload it
237 with src.as_local() as local_uri:
239 # resource.meta.upload_file seems like the right thing
240 # but we have a low level client
241 with time_this(log, msg=timer_msg, args=timer_args):
242 with open(local_uri.ospath, "rb") as fh:
243 self.client.put_object(Bucket=self.netloc,
244 Key=self.relativeToPathRoot, Body=fh)
246 # This was an explicit move requested from a remote resource
247 # try to remove that resource
248 if transfer == "move": 248 ↛ 250line 248 didn't jump to line 250, because the condition on line 248 was never true
249 # Transactions do not work here
250 src.remove()
252 @backoff.on_exception(backoff.expo, all_retryable_errors, max_time=max_retry_time)
253 def walk(self, file_filter: Optional[Union[str, re.Pattern]] = None) -> Iterator[Union[List,
254 Tuple[ButlerURI,
255 List[str],
256 List[str]]]]:
257 """Walk the directory tree returning matching files and directories.
259 Parameters
260 ----------
261 file_filter : `str` or `re.Pattern`, optional
262 Regex to filter out files from the list before it is returned.
264 Yields
265 ------
266 dirpath : `ButlerURI`
267 Current directory being examined.
268 dirnames : `list` of `str`
269 Names of subdirectories within dirpath.
270 filenames : `list` of `str`
271 Names of all the files within dirpath.
272 """
273 # We pretend that S3 uses directories and files and not simply keys
274 if not (self.isdir() or self.is_root): 274 ↛ 275line 274 didn't jump to line 275, because the condition on line 274 was never true
275 raise ValueError(f"Can not walk a non-directory URI: {self}")
277 if isinstance(file_filter, str): 277 ↛ 278line 277 didn't jump to line 278, because the condition on line 277 was never true
278 file_filter = re.compile(file_filter)
280 s3_paginator = self.client.get_paginator('list_objects_v2')
282 # Limit each query to a single "directory" to match os.walk
283 # We could download all keys at once with no delimiter and work
284 # it out locally but this could potentially lead to large memory
285 # usage for millions of keys. It will also make the initial call
286 # to this method potentially very slow. If making this method look
287 # like os.walk was not required, we could query all keys with
288 # pagination and return them in groups of 1000, but that would
289 # be a different interface since we can't guarantee we would get
290 # them all grouped properly across the 1000 limit boundary.
291 prefix = self.relativeToPathRoot if not self.is_root else ""
292 prefix_len = len(prefix)
293 dirnames = []
294 filenames = []
295 files_there = False
297 for page in s3_paginator.paginate(Bucket=self.netloc, Prefix=prefix, Delimiter="/"):
298 # All results are returned as full key names and we must
299 # convert them back to the root form. The prefix is fixed
300 # and delimited so that is a simple trim
302 # Directories are reported in the CommonPrefixes result
303 # which reports the entire key and must be stripped.
304 found_dirs = [dir["Prefix"][prefix_len:] for dir in page.get("CommonPrefixes", ())]
305 dirnames.extend(found_dirs)
307 found_files = [file["Key"][prefix_len:] for file in page.get("Contents", ())]
308 if found_files:
309 files_there = True
310 if file_filter is not None:
311 found_files = [f for f in found_files if file_filter.search(f)]
313 filenames.extend(found_files)
315 # Directories do not exist so we can't test for them. If no files
316 # or directories were found though, this means that it effectively
317 # does not exist and we should match os.walk() behavior and return
318 # [].
319 if not dirnames and not files_there: 319 ↛ 320line 319 didn't jump to line 320, because the condition on line 319 was never true
320 yield []
321 else:
322 yield self, dirnames, filenames
324 for dir in dirnames:
325 new_uri = self.join(dir)
326 yield from new_uri.walk(file_filter)