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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/>. 

21 

22"""S3 datastore.""" 

23 

24__all__ = ("S3Datastore", ) 

25 

26import boto3 

27import logging 

28import os 

29import pathlib 

30import tempfile 

31 

32from typing import Optional, Type 

33 

34from lsst.daf.butler import ( 

35 ButlerURI, 

36 DatasetRef, 

37 Formatter, 

38 Location, 

39 StoredFileInfo, 

40) 

41 

42from .fileLikeDatastore import FileLikeDatastore 

43from lsst.daf.butler.core.s3utils import s3CheckFileExists, bucketExists 

44from lsst.daf.butler.core.utils import transactional 

45 

46log = logging.getLogger(__name__) 

47 

48 

49class S3Datastore(FileLikeDatastore): 

50 """Basic S3 Object Storage backed Datastore. 

51 

52 Parameters 

53 ---------- 

54 config : `DatastoreConfig` or `str` 

55 Configuration. A string should refer to the name of the config file. 

56 registry : `Registry` 

57 Registry to use for storing internal information about the datasets. 

58 butlerRoot : `str`, optional 

59 New datastore root to use to override the configuration value. 

60 

61 Raises 

62 ------ 

63 ValueError 

64 If root location does not exist and ``create`` is `False` in the 

65 configuration. 

66 

67 Notes 

68 ----- 

69 S3Datastore supports non-link transfer modes for file-based ingest: 

70 `"move"`, `"copy"`, and `None` (no transfer). 

71 """ 

72 

73 defaultConfigFile = "datastores/s3Datastore.yaml" 

74 """Path to configuration defaults. Relative to $DAF_BUTLER_DIR/config or 

75 absolute path. Can be None if no defaults specified. 

76 """ 

77 

78 def __init__(self, config, registry, butlerRoot=None): 

79 super().__init__(config, registry, butlerRoot) 

80 

81 self.client = boto3.client("s3") 

82 if not bucketExists(self.locationFactory.netloc): 82 ↛ 88line 82 didn't jump to line 88, because the condition on line 82 was never true

83 # PosixDatastore creates the root directory if one does not exist. 

84 # Calling s3 client.create_bucket is possible but also requires 

85 # ACL LocationConstraints, Permissions and other configuration 

86 # parameters, so for now we do not create a bucket if one is 

87 # missing. Further discussion can make this happen though. 

88 raise IOError(f"Bucket {self.locationFactory.netloc} does not exist!") 

89 

90 def exists(self, ref): 

91 """Check if the dataset exists in the datastore. 

92 

93 Parameters 

94 ---------- 

95 ref : `DatasetRef` 

96 Reference to the required dataset. 

97 

98 Returns 

99 ------- 

100 exists : `bool` 

101 `True` if the entity exists in the `Datastore`. 

102 """ 

103 location, _ = self._get_dataset_location_info(ref) 

104 if location is None: 

105 return False 

106 return s3CheckFileExists(location, client=self.client)[0] 

107 

108 def get(self, ref, parameters=None): 

109 """Load an InMemoryDataset from the store. 

110 

111 Parameters 

112 ---------- 

113 ref : `DatasetRef` 

114 Reference to the required Dataset. 

115 parameters : `dict` 

116 `StorageClass`-specific parameters that specify, for example, 

117 a slice of the Dataset to be loaded. 

118 

119 Returns 

120 ------- 

121 inMemoryDataset : `object` 

122 Requested Dataset or slice thereof as an InMemoryDataset. 

123 

124 Raises 

125 ------ 

126 FileNotFoundError 

127 Requested dataset can not be retrieved. 

128 TypeError 

129 Return value from formatter has unexpected type. 

130 ValueError 

131 Formatter failed to process the dataset. 

132 """ 

133 getInfo = self._prepare_for_get(ref, parameters) 

134 location = getInfo.location 

135 

136 # since we have to make a GET request to S3 anyhow (for download) we 

137 # might as well use the HEADER metadata for size comparison instead. 

138 # s3CheckFileExists would just duplicate GET/LIST charges in this case. 

139 try: 

140 response = self.client.get_object(Bucket=location.netloc, 

141 Key=location.relativeToPathRoot) 

142 except self.client.exceptions.ClientError as err: 

143 errorcode = err.response["ResponseMetadata"]["HTTPStatusCode"] 

144 # head_object returns 404 when object does not exist only when user 

145 # has s3:ListBucket permission. If list permission does not exist a 

146 # 403 is returned. In practical terms this usually means that the 

147 # file does not exist, but it could also mean user lacks GetObject 

148 # permission. It's hard to tell which case is it. 

149 # docs.aws.amazon.com/AmazonS3/latest/API/RESTObjectHEAD.html 

150 # Unit tests right now demand FileExistsError is raised, but this 

151 # should be updated to PermissionError like in s3CheckFileExists. 

152 if errorcode == 403: 

153 raise FileNotFoundError(f"Dataset with Id {ref.id} not accessible at " 

154 f"expected location {location}. Forbidden HEAD " 

155 "operation error occured. Verify s3:ListBucket " 

156 "and s3:GetObject permissions are granted for " 

157 "your IAM user and that file exists. ") from err 

158 if errorcode == 404: 

159 errmsg = f"Dataset with Id {ref.id} does not exists at expected location {location}." 

160 raise FileNotFoundError(errmsg) from err 

161 # other errors are reraised also, but less descriptively 

162 raise err 

163 

164 storedFileInfo = getInfo.info 

165 if response["ContentLength"] != storedFileInfo.file_size: 165 ↛ 166line 165 didn't jump to line 166, because the condition on line 165 was never true

166 raise RuntimeError("Integrity failure in Datastore. Size of file {} ({}) does not" 

167 " match recorded size of {}".format(location.path, response["ContentLength"], 

168 storedFileInfo.file_size)) 

169 

170 # download the data as bytes 

171 serializedDataset = response["Body"].read() 

172 

173 # format the downloaded bytes into appropriate object directly, or via 

174 # tempfile (when formatter does not support to/from/Bytes). This is S3 

175 # equivalent of PosixDatastore formatter.read try-except block. 

176 formatter = getInfo.formatter 

177 try: 

178 result = formatter.fromBytes(serializedDataset, component=getInfo.component) 

179 except NotImplementedError: 179 ↛ 184line 179 didn't jump to line 184

180 with tempfile.NamedTemporaryFile(suffix=formatter.extension) as tmpFile: 

181 tmpFile.file.write(serializedDataset) 

182 formatter._fileDescriptor.location = Location(*os.path.split(tmpFile.name)) 

183 result = formatter.read(component=getInfo.component) 

184 except Exception as e: 

185 raise ValueError(f"Failure from formatter for Dataset {ref.id}: {e}") from e 

186 

187 return self._post_process_get(result, getInfo.readStorageClass, getInfo.assemblerParams) 

188 

189 @transactional 

190 def put(self, inMemoryDataset, ref): 

191 """Write a InMemoryDataset with a given `DatasetRef` to the store. 

192 

193 Parameters 

194 ---------- 

195 inMemoryDataset : `object` 

196 The Dataset to store. 

197 ref : `DatasetRef` 

198 Reference to the associated Dataset. 

199 

200 Raises 

201 ------ 

202 TypeError 

203 Supplied object and storage class are inconsistent. 

204 DatasetTypeNotSupportedError 

205 The associated `DatasetType` is not handled by this datastore. 

206 

207 Notes 

208 ----- 

209 If the datastore is configured to reject certain dataset types it 

210 is possible that the put will fail and raise a 

211 `DatasetTypeNotSupportedError`. The main use case for this is to 

212 allow `ChainedDatastore` to put to multiple datastores without 

213 requiring that every datastore accepts the dataset. 

214 """ 

215 location, formatter = self._prepare_for_put(inMemoryDataset, ref) 

216 

217 # in PosixDatastore a directory can be created by `safeMakeDir`. In S3 

218 # `Keys` instead only look like directories, but are not. We check if 

219 # an *exact* full key already exists before writing instead. The insert 

220 # key operation is equivalent to creating the dir and the file. 

221 location.updateExtension(formatter.extension) 

222 if s3CheckFileExists(location, client=self.client,)[0]: 

223 raise FileExistsError(f"Cannot write file for ref {ref} as " 

224 f"output file {location.uri} exists.") 

225 

226 # upload the file directly from bytes or by using a temporary file if 

227 # _toBytes is not implemented 

228 try: 

229 serializedDataset = formatter.toBytes(inMemoryDataset) 

230 self.client.put_object(Bucket=location.netloc, Key=location.relativeToPathRoot, 

231 Body=serializedDataset) 

232 log.debug("Wrote file directly to %s", location.uri) 

233 except NotImplementedError: 

234 with tempfile.NamedTemporaryFile(suffix=formatter.extension) as tmpFile: 

235 formatter._fileDescriptor.location = Location(*os.path.split(tmpFile.name)) 

236 formatter.write(inMemoryDataset) 

237 self.client.upload_file(Bucket=location.netloc, Key=location.relativeToPathRoot, 

238 Filename=tmpFile.name) 

239 log.debug("Wrote file to %s via a temporary directory.", location.uri) 

240 

241 # Register a callback to try to delete the uploaded data if 

242 # the ingest fails below 

243 self._transaction.registerUndo("write", self.client.delete_object, 

244 Bucket=location.netloc, Key=location.relativeToPathRoot) 

245 

246 # URI is needed to resolve what ingest case are we dealing with 

247 info = self._extractIngestInfo(location.uri, ref, formatter=formatter) 

248 self._register_datasets([(ref, info)]) 

249 

250 def _standardizeIngestPath(self, path: str, *, transfer: Optional[str] = None) -> str: 

251 # Docstring inherited from FileLikeDatastore._standardizeIngestPath. 

252 if transfer not in (None, "move", "copy"): 252 ↛ 253line 252 didn't jump to line 253, because the condition on line 252 was never true

253 raise NotImplementedError(f"Transfer mode {transfer} not supported.") 

254 # ingest can occur from file->s3 and s3->s3 (source can be file or s3, 

255 # target will always be s3). File has to exist at target location. Two 

256 # Schemeless URIs are assumed to obey os.path rules. Equivalent to 

257 # os.path.exists(fullPath) check in PosixDatastore. 

258 srcUri = ButlerURI(path) 

259 if srcUri.scheme == 'file' or not srcUri.scheme: 259 ↛ 262line 259 didn't jump to line 262, because the condition on line 259 was never false

260 if not os.path.exists(srcUri.ospath): 260 ↛ 261line 260 didn't jump to line 261, because the condition on line 260 was never true

261 raise FileNotFoundError(f"File at '{srcUri}' does not exist.") 

262 elif srcUri.scheme == 's3': 

263 if not s3CheckFileExists(srcUri, client=self.client)[0]: 

264 raise FileNotFoundError(f"File at '{srcUri}' does not exist.") 

265 else: 

266 raise NotImplementedError(f"Scheme type {srcUri.scheme} not supported.") 

267 

268 if transfer is None: 268 ↛ 269line 268 didn't jump to line 269, because the condition on line 268 was never true

269 rootUri = ButlerURI(self.root) 

270 if srcUri.scheme == "file": 

271 raise RuntimeError(f"'{srcUri}' is not inside repository root '{rootUri}'. " 

272 "Ingesting local data to S3Datastore without upload " 

273 "to S3 is not allowed.") 

274 elif srcUri.scheme == "s3": 

275 if not srcUri.path.startswith(rootUri.path): 

276 raise RuntimeError(f"'{srcUri}' is not inside repository root '{rootUri}'.") 

277 return path 

278 

279 def _extractIngestInfo(self, path: str, ref: DatasetRef, *, formatter: Type[Formatter], 

280 transfer: Optional[str] = None) -> StoredFileInfo: 

281 # Docstring inherited from FileLikeDatastore._extractIngestInfo. 

282 srcUri = ButlerURI(path) 

283 if transfer is None: 

284 rootUri = ButlerURI(self.root) 

285 p = pathlib.PurePosixPath(srcUri.relativeToPathRoot) 

286 pathInStore = str(p.relative_to(rootUri.relativeToPathRoot)) 

287 tgtLocation = self.locationFactory.fromPath(pathInStore) 

288 else: 

289 assert transfer == "move" or transfer == "copy", "Should be guaranteed by _standardizeIngestPath" 

290 if srcUri.scheme == "file": 290 ↛ 300line 290 didn't jump to line 300, because the condition on line 290 was never false

291 # source is on local disk. 

292 template = self.templates.getTemplate(ref) 

293 location = self.locationFactory.fromPath(template.format(ref)) 

294 tgtPathInStore = formatter.predictPathFromLocation(location) 

295 tgtLocation = self.locationFactory.fromPath(tgtPathInStore) 

296 self.client.upload_file(Bucket=tgtLocation.netloc, Key=tgtLocation.relativeToPathRoot, 

297 Filename=srcUri.ospath) 

298 if transfer == "move": 298 ↛ 299line 298 didn't jump to line 299, because the condition on line 298 was never true

299 os.remove(srcUri.ospath) 

300 elif srcUri.scheme == "s3": 

301 # source is another S3 Bucket 

302 relpath = srcUri.relativeToPathRoot 

303 copySrc = {"Bucket": srcUri.netloc, "Key": relpath} 

304 self.client.copy(copySrc, self.locationFactory.netloc, relpath) 

305 if transfer == "move": 

306 # https://github.com/boto/boto3/issues/507 - there is no 

307 # way of knowing if the file was actually deleted except 

308 # for checking all the keys again, reponse is HTTP 204 OK 

309 # response all the time 

310 self.client.delete(Bucket=srcUri.netloc, Key=relpath) 

311 p = pathlib.PurePosixPath(srcUri.relativeToPathRoot) 

312 relativeToDatastoreRoot = str(p.relative_to(rootUri.relativeToPathRoot)) 

313 tgtLocation = self.locationFactory.fromPath(relativeToDatastoreRoot) 

314 

315 # the file should exist on the bucket by now 

316 exists, size = s3CheckFileExists(path=tgtLocation.relativeToPathRoot, 

317 bucket=tgtLocation.netloc, 

318 client=self.client) 

319 

320 return StoredFileInfo(formatter=formatter, path=tgtLocation.pathInStore, 

321 storageClass=ref.datasetType.storageClass, 

322 file_size=size, checksum=None) 

323 

324 def remove(self, ref): 

325 """Indicate to the Datastore that a Dataset can be removed. 

326 

327 .. warning:: 

328 

329 This method does not support transactions; removals are 

330 immediate, cannot be undone, and are not guaranteed to 

331 be atomic if deleting either the file or the internal 

332 database records fails. 

333 

334 Parameters 

335 ---------- 

336 ref : `DatasetRef` 

337 Reference to the required Dataset. 

338 

339 Raises 

340 ------ 

341 FileNotFoundError 

342 Attempt to remove a dataset that does not exist. 

343 """ 

344 location, _ = self._get_dataset_location_info(ref) 

345 if location is None: 345 ↛ 346line 345 didn't jump to line 346, because the condition on line 345 was never true

346 raise FileNotFoundError(f"Requested dataset ({ref}) does not exist") 

347 

348 if not s3CheckFileExists(location, client=self.client): 348 ↛ 349line 348 didn't jump to line 349, because the condition on line 348 was never true

349 raise FileNotFoundError(f"No such file: {location.uri}") 

350 

351 if self._can_remove_dataset_artifact(ref): 

352 # https://github.com/boto/boto3/issues/507 - there is no way of 

353 # knowing if the file was actually deleted 

354 self.client.delete_object(Bucket=location.netloc, Key=location.relativeToPathRoot) 

355 

356 # Remove rows from registries 

357 self._remove_from_registry(ref)