mirror of
https://github.com/clearml/clearml
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Limit number of _serialize requests when adding list of links with add_external_files() (#813)
This commit is contained in:
allegroai
parent
8340d4b86c
commit
b793f2dfc6
@ -116,7 +116,7 @@ class Dataset(object):
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__default_dataset_version = "1.0.0"
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__dataset_folder_template = CacheManager.set_context_folder_lookup(__cache_context, "{0}_archive_{1}")
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__preview_max_file_entries = 15000
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__preview_max_size = 5 * 1024 * 1024
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__preview_max_size = 32 * 1024
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__min_api_version = "2.20"
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__hyperparams_section = "Datasets"
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__datasets_runtime_prop = "datasets"
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@ -409,11 +409,13 @@ class Dataset(object):
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dataset_path=None, # type: Optional[str]
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recursive=True, # type: bool
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verbose=False, # type: bool
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max_workers=None # type: Optional[int]
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):
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# type: (...) -> ()
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# type: (...) -> int
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"""
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Adds an external file or a folder to the current dataset.
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External file links can be from cloud storage (s3://, gs://, azure://) or local / network storage (file://).
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Adds external files or folders to the current dataset.
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External file links can be from cloud storage (s3://, gs://, azure://), local / network storage (file://)
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or http(s)// files.
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Calculates file size for each file and compares against parent.
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A few examples:
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@ -436,92 +438,32 @@ class Dataset(object):
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'image.jpg' will be downloaded to 's3_files/image.jpg' (relative path to the dataset)
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:param recursive: If True match all wildcard files recursively
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:param verbose: If True print to console files added/modified
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:return: number of file links added
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:param max_workers: The number of threads to add the external files with. Useful when `source_url` is
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a sequence. Defaults to the number of logical cores
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:return: Number of file links added
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"""
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num_added = 0
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self._dirty = True
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if not isinstance(source_url, str):
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for source_url_ in source_url:
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num_added += self.add_external_files(
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num_added = 0
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num_modified = 0
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source_url_list = source_url if not isinstance(source_url, str) else [source_url]
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max_workers = max_workers or psutil.cpu_count()
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futures_ = []
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with ThreadPoolExecutor(max_workers=max_workers) as tp:
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for source_url_ in source_url_list:
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futures_.append(
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tp.submit(
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self._add_external_files,
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source_url_,
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wildcard=wildcard,
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dataset_path=dataset_path,
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recursive=recursive,
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verbose=verbose
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verbose=verbose,
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)
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)
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return num_added
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if dataset_path:
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dataset_path = dataset_path.lstrip("/")
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# noinspection PyBroadException
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try:
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if StorageManager.exists_file(source_url):
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links = [source_url]
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else:
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if source_url[-1] != "/":
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source_url = source_url + "/"
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links = StorageManager.list(source_url, return_full_path=True)
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except Exception:
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self._task.get_logger().report_text(
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"Could not list/find remote file(s) when adding {}".format(source_url)
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)
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return 0
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num_modified = 0
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for link in links:
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relative_path = link[len(source_url):]
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if not relative_path:
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relative_path = source_url.split("/")[-1]
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if not matches_any_wildcard(relative_path, wildcard, recursive=recursive):
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continue
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try:
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relative_path = Path(os.path.join(dataset_path or ".", relative_path)).as_posix()
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size = StorageManager.get_file_size_bytes(link, silence_errors=True)
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already_added_file = self._dataset_file_entries.get(relative_path)
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if relative_path not in self._dataset_link_entries:
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if verbose:
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self._task.get_logger().report_text(
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"External file {} added".format(link),
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print_console=False,
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)
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self._dataset_link_entries[relative_path] = LinkEntry(
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link=link, relative_path=relative_path, parent_dataset_id=self._id, size=size
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)
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num_added += 1
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elif already_added_file and already_added_file.size != size:
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if verbose:
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self._task.get_logger().report_text(
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"External file {} modified".format(link),
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print_console=False,
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)
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del self._dataset_file_entries[relative_path]
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self._dataset_link_entries[relative_path] = LinkEntry(
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link=link, relative_path=relative_path, parent_dataset_id=self._id, size=size
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)
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num_modified += 1
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elif (
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relative_path in self._dataset_link_entries
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and self._dataset_link_entries[relative_path].size != size
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):
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if verbose:
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self._task.get_logger().report_text(
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"External file {} modified".format(link),
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print_console=False,
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)
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self._dataset_link_entries[relative_path] = LinkEntry(
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link=link, relative_path=relative_path, parent_dataset_id=self._id, size=size
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)
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num_modified += 1
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else:
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if verbose:
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self._task.get_logger().report_text(
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"External file {} skipped as it was not modified".format(link),
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print_console=False,
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)
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except Exception as e:
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if verbose:
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self._task.get_logger().report_text(
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"Error '{}' encountered trying to add external file {}".format(e, link),
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print_console=False,
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)
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for future_ in futures_:
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num_added_this_call, num_modified_this_call = future_.result()
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num_added += num_added_this_call
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num_modified += num_modified_this_call
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self._task.add_tags([self.__external_files_tag])
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self._add_script_call(
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"add_external_files",
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@ -712,11 +654,21 @@ class Dataset(object):
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)
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total_size += zip_.size
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chunks_count += 1
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truncated_preview = ""
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add_truncated_message = False
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truncated_message = "...\ntruncated (too many files to preview)"
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for preview_entry in zip_.archive_preview[: Dataset.__preview_max_file_entries]:
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truncated_preview += preview_entry + "\n"
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if len(truncated_preview) > Dataset.__preview_max_size:
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add_truncated_message = True
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break
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if len(zip_.archive_preview) > Dataset.__preview_max_file_entries:
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add_truncated_message = True
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pool.submit(
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self._task.upload_artifact,
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name=artifact_name,
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artifact_object=Path(zip_path),
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preview=zip_.archive_preview,
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preview=truncated_preview + (truncated_message if add_truncated_message else ""),
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delete_after_upload=True,
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wait_on_upload=True,
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)
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@ -2972,6 +2924,110 @@ class Dataset(object):
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self._dependency_chunk_lookup = self._build_dependency_chunk_lookup()
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return self._dependency_chunk_lookup
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def _add_external_files(
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self,
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source_url, # type: str
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wildcard=None, # type: Optional[Union[str, Sequence[str]]]
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dataset_path=None, # type: Optional[str]
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recursive=True, # type: bool
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verbose=False, # type: bool
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):
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# type: (...) -> Tuple[int, int]
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"""
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Auxiliary function for `add_external_files`
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Adds an external file or a folder to the current dataset.
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External file links can be from cloud storage (s3://, gs://, azure://) or local / network storage (file://).
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Calculates file size for each file and compares against parent.
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:param source_url: Source url link (e.g. s3://bucket/folder/path)
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:param wildcard: add only specific set of files.
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Wildcard matching, can be a single string or a list of wildcards.
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:param dataset_path: The location in the dataset where the file will be downloaded into.
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e.g: for source_url='s3://bucket/remote_folder/image.jpg' and dataset_path='s3_files',
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'image.jpg' will be downloaded to 's3_files/image.jpg' (relative path to the dataset)
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:param recursive: If True match all wildcard files recursively
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:param verbose: If True print to console files added/modified
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:return: Number of file links added and modified
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"""
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if dataset_path:
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dataset_path = dataset_path.lstrip("/")
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remote_objects = None
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# noinspection PyBroadException
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try:
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if StorageManager.exists_file(source_url):
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remote_objects = [StorageManager.get_metadata(source_url)]
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elif not source_url.startswith(("http://", "https://")):
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if source_url[-1] != "/":
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source_url = source_url + "/"
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remote_objects = StorageManager.list(source_url, with_metadata=True, return_full_path=True)
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except Exception:
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pass
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if not remote_objects:
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self._task.get_logger().report_text(
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"Could not list/find remote file(s) when adding {}".format(source_url)
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)
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return 0, 0
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num_added = 0
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num_modified = 0
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for remote_object in remote_objects:
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link = remote_object.get("name")
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relative_path = link[len(source_url):]
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if not relative_path:
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relative_path = source_url.split("/")[-1]
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if not matches_any_wildcard(relative_path, wildcard, recursive=recursive):
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continue
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try:
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relative_path = Path(os.path.join(dataset_path or ".", relative_path)).as_posix()
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size = remote_object.get("size")
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already_added_file = self._dataset_file_entries.get(relative_path)
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if relative_path not in self._dataset_link_entries:
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if verbose:
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self._task.get_logger().report_text(
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"External file {} added".format(link),
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print_console=False,
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)
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self._dataset_link_entries[relative_path] = LinkEntry(
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link=link, relative_path=relative_path, parent_dataset_id=self._id, size=size
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)
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num_added += 1
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elif already_added_file and already_added_file.size != size:
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if verbose:
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self._task.get_logger().report_text(
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"External file {} modified".format(link),
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print_console=False,
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)
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del self._dataset_file_entries[relative_path]
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self._dataset_link_entries[relative_path] = LinkEntry(
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link=link, relative_path=relative_path, parent_dataset_id=self._id, size=size
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)
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num_modified += 1
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elif (
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relative_path in self._dataset_link_entries
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and self._dataset_link_entries[relative_path].size != size
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):
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if verbose:
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self._task.get_logger().report_text(
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"External file {} modified".format(link),
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print_console=False,
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)
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self._dataset_link_entries[relative_path] = LinkEntry(
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link=link, relative_path=relative_path, parent_dataset_id=self._id, size=size
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)
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num_modified += 1
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else:
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if verbose:
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self._task.get_logger().report_text(
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"External file {} skipped as it was not modified".format(link),
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print_console=False,
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)
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except Exception as e:
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if verbose:
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self._task.get_logger().report_text(
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"Error '{}' encountered trying to add external file {}".format(e, link),
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print_console=False,
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)
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return num_added, num_modified
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def _build_chunk_selection(self, part, num_parts):
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# type: (int, int) -> Dict[str, int]
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"""
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@ -595,8 +595,20 @@ class StorageHelper(object):
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:return: The size of the file in bytes.
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None if the file could not be found or an error occurred.
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"""
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size = None
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obj = self.get_object(remote_url, silence_errors=silence_errors)
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return self._get_object_size_bytes(obj)
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def _get_object_size_bytes(self, obj):
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# type: (object, bool) -> [int, None]
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"""
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Auxiliary function for `get_object_size_bytes`.
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Get size of the remote object in bytes.
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:param object obj: The remote object
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:return: The size of the object in bytes.
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None if an error occurred.
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"""
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if not obj:
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return None
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try:
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@ -615,6 +627,21 @@ class StorageHelper(object):
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pass
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return size
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def get_object_metadata(self, obj):
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# type: (object) -> dict
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"""
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Get the metadata of the a remote object.
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The metadata is a dict containing the following keys: `name`, `size`.
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:param object obj: The remote object
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:return: A dict containing the metadata of the remote object
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"""
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return {
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"name": obj.name if hasattr(obj, "name") else obj.url if hasattr(obj, "url") else None,
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"size": self._get_object_size_bytes(obj),
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}
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def verify_upload(self, folder_uri='', raise_on_error=True, log_on_error=True):
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"""
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Verify that this helper can upload files to a folder.
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@ -716,12 +743,13 @@ class StorageHelper(object):
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res = quote_url(res)
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return res
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def list(self, prefix=None):
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def list(self, prefix=None, with_metadata=False):
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"""
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List entries in the helper base path.
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Return a list of names inside this helper base path. The base path is
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determined at creation time and is specific for each storage medium.
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Return a list of names inside this helper base path or a list of dictionaries containing
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the objects' metadata. The base path is determined at creation time and is specific
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for each storage medium.
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For Google Storage and S3 it is the bucket of the path.
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For local files it is the root directory.
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@ -731,11 +759,14 @@ class StorageHelper(object):
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must be a string - the path of a sub directory under the base path.
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the returned list will include only objects under that subdir.
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:return: The paths of all the objects in the storage base
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path under prefix. Listed relative to the base path.
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:param with_metadata: Instead of returning just the names of the objects, return a list of dictionaries
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containing the name and metadata of the remote file. Thus, each dictionary will contain the following
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keys: `name`, `size`.
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:return: The paths of all the objects in the storage base path under prefix or
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a list of dictionaries containing the objects' metadata.
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Listed relative to the base path.
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"""
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if prefix:
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if prefix.startswith(self._base_url):
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prefix = prefix[len(self.base_url):].lstrip("/")
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@ -746,15 +777,22 @@ class StorageHelper(object):
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res = self._driver.list_container_objects(self._container)
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result = [
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obj.name
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obj.name if not with_metadata else self.get_object_metadata(obj)
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for obj in res
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if (obj.name.startswith(prefix) or self._base_url == "file://") and obj.name != prefix
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]
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if self._base_url == "file://":
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result = [Path(f).as_posix() for f in result]
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if not with_metadata:
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result = [Path(f).as_posix() for f in result]
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else:
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for metadata_entry in result:
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metadata_entry["name"] = Path(metadata_entry["name"]).as_posix()
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return result
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else:
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return [obj.name for obj in self._driver.list_container_objects(self._container)]
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return [
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obj.name if not with_metadata else self.get_object_metadata(obj)
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for obj in self._driver.list_container_objects(self._container)
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]
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def download_to_file(
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self,
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@ -314,15 +314,21 @@ class StorageManager(object):
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:return: True is the remote_url stores a file and False otherwise
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"""
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if remote_url.startswith("file://"):
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return os.path.isfile(remote_url[len("file://"):])
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if remote_url.startswith("http://") or remote_url.startswith("https://"):
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return requests.head(remote_url).status_code == requests.codes.ok
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helper = StorageHelper.get(remote_url)
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obj = helper.get_object(remote_url)
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if not obj:
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# noinspection PyBroadException
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try:
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if remote_url.endswith("/"):
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return False
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if remote_url.startswith("file://"):
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return os.path.isfile(remote_url[len("file://"):])
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if remote_url.startswith(("http://", "https://")):
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return requests.head(remote_url).ok
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helper = StorageHelper.get(remote_url)
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obj = helper.get_object(remote_url)
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if not obj:
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return False
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return True
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except Exception:
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return False
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return len(StorageManager.list(remote_url)) == 0
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@classmethod
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def get_file_size_bytes(cls, remote_url, silence_errors=False):
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@ -419,10 +425,11 @@ class StorageManager(object):
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return local_folder
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@classmethod
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def list(cls, remote_url, return_full_path=False):
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# type: (str, bool) -> Optional[List[str]]
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def list(cls, remote_url, return_full_path=False, with_metadata=False):
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# type: (str, bool) -> Optional[List[Union[str, dict]]]
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"""
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Return a list of object names inside the base path
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Return a list of object names inside the base path or dictionaries containing the corresponding
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objects' metadata (in case `with_metadata` is True)
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:param str remote_url: The base path.
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For Google Storage, Azure and S3 it is the bucket of the path, for local files it is the root directory.
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@ -431,17 +438,49 @@ class StorageManager(object):
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Azure blob storage: `azure://bucket/folder_` and also file system listing: `/mnt/share/folder_`
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:param bool return_full_path: If True, return a list of full object paths, otherwise return a list of
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relative object paths (default False).
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:param with_metadata: Instead of returning just the names of the objects, return a list of dictionaries
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containing the name and metadata of the remote file. Thus, each dictionary will contain the following
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keys: `name`, `size`.
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`return_full_path` will modify the name of each dictionary entry to the full path.
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:return: The paths of all the objects in the storage base path under prefix, relative to the base path.
|
||||
:return: The paths of all the objects the storage base path under prefix or the dictionaries containing the objects' metadata, relative to the base path.
|
||||
None in case of list operation is not supported (http and https protocols for example)
|
||||
"""
|
||||
helper = StorageHelper.get(remote_url)
|
||||
try:
|
||||
names_list = helper.list(prefix=remote_url)
|
||||
helper_list_result = helper.list(prefix=remote_url, with_metadata=with_metadata)
|
||||
except Exception as ex:
|
||||
LoggerRoot.get_base_logger().warning("Can not list files for '{}' - {}".format(remote_url, ex))
|
||||
names_list = None
|
||||
return None
|
||||
|
||||
if helper.base_url == 'file://':
|
||||
return ["{}/{}".format(remote_url.rstrip('/'), name) for name in names_list] if return_full_path else names_list
|
||||
return ["{}/{}".format(helper.base_url, name) for name in names_list] if return_full_path else names_list
|
||||
prefix = remote_url.rstrip("/") if helper.base_url == "file://" else helper.base_url
|
||||
if not with_metadata:
|
||||
return (
|
||||
["{}/{}".format(prefix, name) for name in helper_list_result]
|
||||
if return_full_path
|
||||
else helper_list_result
|
||||
)
|
||||
else:
|
||||
if return_full_path:
|
||||
for obj in helper_list_result:
|
||||
obj["name"] = "{}/{}".format(prefix, obj.get("name"))
|
||||
return helper_list_result
|
||||
|
||||
@classmethod
|
||||
def get_metadata(cls, remote_url):
|
||||
# type: (str) -> Optional[dict]
|
||||
"""
|
||||
Get the metadata of the a remote object.
|
||||
The metadata is a dict containing the following keys: `name`, `size`.
|
||||
|
||||
:param str remote_url: Source remote storage location, tree structure of `remote_url` will
|
||||
be created under the target local_folder. Supports S3/GS/Azure, shared filesystem and http(s).
|
||||
Example: 's3://bucket/data/'
|
||||
|
||||
:return: A dict containing the metadata of the remote object. In case of an error, `None` is returned
|
||||
"""
|
||||
helper = StorageHelper.get(remote_url)
|
||||
obj = helper.get_object(remote_url)
|
||||
if not obj:
|
||||
return None
|
||||
return helper.get_object_metadata(obj)
|
||||
|
||||
@ -238,7 +238,7 @@ class ParallelZipper(object):
|
||||
self.fd, self.zip_path = mkstemp(prefix=zip_prefix, suffix=zip_suffix)
|
||||
self.zip_path = Path(self.zip_path)
|
||||
self.zip_file = ZipFile(self.zip_path.as_posix(), "w", allowZip64=allow_zip_64, compression=compression)
|
||||
self.archive_preview = ""
|
||||
self.archive_preview = []
|
||||
self.count = 0
|
||||
self.files_zipped = set()
|
||||
|
||||
@ -259,7 +259,7 @@ class ParallelZipper(object):
|
||||
preview_path = arcname
|
||||
if not preview_path:
|
||||
preview_path = file_path
|
||||
self.archive_preview += "{} - {}\n".format(preview_path, format_size(self.size))
|
||||
self.archive_preview.append("{} - {}".format(preview_path, format_size(self.size)))
|
||||
self.files_zipped.add(Path(file_path).as_posix())
|
||||
if self._chunk_size <= 0 or self.size < self._chunk_size:
|
||||
self._zipper_queue.put(self)
|
||||
@ -294,7 +294,7 @@ class ParallelZipper(object):
|
||||
parent_zip.writestr(child_name, child_zip.open(child_name).read())
|
||||
self.files_zipped |= other.files_zipped
|
||||
self.count += other.count
|
||||
self.archive_preview += other.archive_preview
|
||||
self.archive_preview.extend(other.archive_preview)
|
||||
|
||||
def close(self):
|
||||
# type: () -> ()
|
||||
|
||||
Loading…
Reference in New Issue
Block a user