X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/ffb304afad93f50fd6ee43ecda6584dd0ac000c4..44c95f99098fa6c6acbfa82d4b6cbc6015eb6e39:/sdk/python/arvados/commands/put.py diff --git a/sdk/python/arvados/commands/put.py b/sdk/python/arvados/commands/put.py index 12f93298bb..cd55914614 100644 --- a/sdk/python/arvados/commands/put.py +++ b/sdk/python/arvados/commands/put.py @@ -1,3 +1,7 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + from __future__ import division from future.utils import listitems, listvalues from builtins import str @@ -10,6 +14,7 @@ import copy import datetime import errno import fcntl +import fnmatch import hashlib import json import logging @@ -39,7 +44,9 @@ upload_opts.add_argument('--version', action='version', help='Print version and exit.') upload_opts.add_argument('paths', metavar='path', type=str, nargs='*', help=""" -Local file or directory. Default: read from standard input. +Local file or directory. If path is a directory reference with a trailing +slash, then just upload the directory's contents; otherwise upload the +directory itself. Default: read from standard input. """) _group = upload_opts.add_mutually_exclusive_group() @@ -154,6 +161,16 @@ run_opts.add_argument('--name', help=""" Save the collection with the specified name. """) +run_opts.add_argument('--exclude', metavar='PATTERN', default=[], + action='append', help=""" +Exclude files and directories whose names match the given glob pattern. When +using a path-like pattern like 'subdir/*.txt', all text files inside 'subdir' +directory, relative to the provided input dirs will be excluded. +When using a filename pattern like '*.txt', any text file will be excluded +no matter where is placed. +You can specify multiple patterns by using this argument more than once. +""") + _group = run_opts.add_mutually_exclusive_group() _group.add_argument('--progress', action='store_true', help=""" @@ -242,6 +259,10 @@ def parse_arguments(arguments): if not args.filename: args.filename = 'stdin' + # Remove possible duplicated patterns + if len(args.exclude) > 0: + args.exclude = list(set(args.exclude)) + return args @@ -370,18 +391,20 @@ class ArvPutUploadJob(object): } def __init__(self, paths, resume=True, use_cache=True, reporter=None, - bytes_expected=None, name=None, owner_uuid=None, + name=None, owner_uuid=None, ensure_unique_name=False, num_retries=None, put_threads=None, replication_desired=None, filename=None, update_time=60.0, update_collection=None, logger=logging.getLogger('arvados.arv_put'), dry_run=False, - follow_links=True): + follow_links=True, exclude_paths=[], exclude_names=None): self.paths = paths self.resume = resume self.use_cache = use_cache self.update = False self.reporter = reporter - self.bytes_expected = bytes_expected + # This will set to 0 before start counting, if no special files are going + # to be read. + self.bytes_expected = None self.bytes_written = 0 self.bytes_skipped = 0 self.name = name @@ -409,6 +432,8 @@ class ArvPutUploadJob(object): self.dry_run = dry_run self._checkpoint_before_quit = True self.follow_links = follow_links + self.exclude_paths = exclude_paths + self.exclude_names = exclude_names if not self.use_cache and self.resume: raise ArvPutArgumentConflict('resume cannot be True when use_cache is False') @@ -420,47 +445,103 @@ class ArvPutUploadJob(object): # Load cached data if any and if needed self._setup_state(update_collection) + # Build the upload file list, excluding requested files and counting the + # bytes expected to be uploaded. + self._build_upload_list() + + def _build_upload_list(self): + """ + Scan the requested paths to count file sizes, excluding files & dirs if requested + and building the upload file list. + """ + # If there aren't special files to be read, reset total bytes count to zero + # to start counting. + if not any(filter(lambda p: not (os.path.isfile(p) or os.path.isdir(p)), + self.paths)): + self.bytes_expected = 0 + + for path in self.paths: + # Test for stdin first, in case some file named '-' exist + if path == '-': + if self.dry_run: + raise ArvPutUploadIsPending() + self._write_stdin(self.filename or 'stdin') + elif not os.path.exists(path): + raise PathDoesNotExistError("file or directory '{}' does not exist.".format(path)) + elif os.path.isdir(path): + # Use absolute paths on cache index so CWD doesn't interfere + # with the caching logic. + orig_path = path + path = os.path.abspath(path) + if orig_path[-1:] == os.sep: + # When passing a directory reference with a trailing slash, + # its contents should be uploaded directly to the + # collection's root. + prefixdir = path + else: + # When passing a directory reference with no trailing slash, + # upload the directory to the collection's root. + prefixdir = os.path.dirname(path) + prefixdir += os.sep + for root, dirs, files in os.walk(path, + followlinks=self.follow_links): + root_relpath = os.path.relpath(root, path) + if root_relpath == '.': + root_relpath = '' + # Exclude files/dirs by full path matching pattern + if self.exclude_paths: + dirs[:] = list(filter( + lambda d: not any( + [pathname_match(os.path.join(root_relpath, d), + pat) + for pat in self.exclude_paths]), + dirs)) + files = list(filter( + lambda f: not any( + [pathname_match(os.path.join(root_relpath, f), + pat) + for pat in self.exclude_paths]), + files)) + # Exclude files/dirs by name matching pattern + if self.exclude_names is not None: + dirs[:] = list(filter(lambda d: not self.exclude_names.match(d), dirs)) + files = list(filter(lambda f: not self.exclude_names.match(f), files)) + # Make os.walk()'s dir traversing order deterministic + dirs.sort() + files.sort() + for f in files: + filepath = os.path.join(root, f) + # Add its size to the total bytes count (if applicable) + if self.follow_links or (not os.path.islink(filepath)): + if self.bytes_expected is not None: + self.bytes_expected += os.path.getsize(filepath) + self._check_file(filepath, + os.path.join(root[len(prefixdir):], f)) + else: + filepath = os.path.abspath(path) + # Add its size to the total bytes count (if applicable) + if self.follow_links or (not os.path.islink(filepath)): + if self.bytes_expected is not None: + self.bytes_expected += os.path.getsize(filepath) + self._check_file(filepath, + self.filename or os.path.basename(path)) + # If dry-mode is on, and got up to this point, then we should notify that + # there aren't any file to upload. + if self.dry_run: + raise ArvPutUploadNotPending() + # Remove local_collection's files that don't exist locally anymore, so the + # bytes_written count is correct. + for f in self.collection_file_paths(self._local_collection, + path_prefix=""): + if f != 'stdin' and f != self.filename and not f in self._file_paths: + self._local_collection.remove(f) + def start(self, save_collection): """ Start supporting thread & file uploading """ - if not self.dry_run: - self._checkpointer.start() + self._checkpointer.start() try: - for path in self.paths: - # Test for stdin first, in case some file named '-' exist - if path == '-': - if self.dry_run: - raise ArvPutUploadIsPending() - self._write_stdin(self.filename or 'stdin') - elif not os.path.exists(path): - raise PathDoesNotExistError("file or directory '{}' does not exist.".format(path)) - elif os.path.isdir(path): - # Use absolute paths on cache index so CWD doesn't interfere - # with the caching logic. - prefixdir = path = os.path.abspath(path) - if prefixdir != '/': - prefixdir += '/' - for root, dirs, files in os.walk(path, followlinks=self.follow_links): - # Make os.walk()'s dir traversing order deterministic - dirs.sort() - files.sort() - for f in files: - self._check_file(os.path.join(root, f), - os.path.join(root[len(prefixdir):], f)) - else: - self._check_file(os.path.abspath(path), - self.filename or os.path.basename(path)) - # If dry-mode is on, and got up to this point, then we should notify that - # there aren't any file to upload. - if self.dry_run: - raise ArvPutUploadNotPending() - # Remove local_collection's files that don't exist locally anymore, so the - # bytes_written count is correct. - for f in self.collection_file_paths(self._local_collection, - path_prefix=""): - if f != 'stdin' and f != self.filename and not f in self._file_paths: - self._local_collection.remove(f) # Update bytes_written from current local collection and # report initial progress. self._update() @@ -646,7 +727,13 @@ class ArvPutUploadJob(object): should_upload = True if should_upload: - self._files_to_upload.append((source, resume_offset, filename)) + try: + self._files_to_upload.append((source, resume_offset, filename)) + except ArvPutUploadIsPending: + # This could happen when running on dry-mode, close cache file to + # avoid locking issues. + self._cache_file.close() + raise def _upload_files(self): for source, resume_offset, filename in self._files_to_upload: @@ -825,29 +912,24 @@ class ArvPutUploadJob(object): datablocks = self._datablocks_on_item(self._my_collection()) return datablocks - -def expected_bytes_for(pathlist, follow_links=True): - # Walk the given directory trees and stat files, adding up file sizes, - # so we can display progress as percent - bytesum = 0 - for path in pathlist: - if os.path.isdir(path): - for root, dirs, files in os.walk(path, followlinks=follow_links): - # Sum file sizes - for f in files: - filepath = os.path.join(root, f) - # Ignore symlinked files when requested - if (not follow_links) and os.path.islink(filepath): - continue - bytesum += os.path.getsize(filepath) - elif not os.path.isfile(path): - return None - else: - bytesum += os.path.getsize(path) - return bytesum - _machine_format = "{} {}: {{}} written {{}} total\n".format(sys.argv[0], os.getpid()) + +# Simulate glob.glob() matching behavior without the need to scan the filesystem +# Note: fnmatch() doesn't work correctly when used with pathnames. For example the +# pattern 'tests/*.py' will match 'tests/run_test.py' and also 'tests/subdir/run_test.py', +# so instead we're using it on every path component. +def pathname_match(pathname, pattern): + name = pathname.split(os.sep) + # Fix patterns like 'some/subdir/' or 'some//subdir' + pat = [x for x in pattern.split(os.sep) if x != ''] + if len(name) != len(pat): + return False + for i in range(len(name)): + if not fnmatch.fnmatch(name[i], pat[i]): + return False + return True + def machine_progress(bytes_written, bytes_expected): return _machine_format.format( bytes_written, -1 if (bytes_expected is None) else bytes_expected) @@ -923,19 +1005,53 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): else: reporter = None + # Setup exclude regex from all the --exclude arguments provided + name_patterns = [] + exclude_paths = [] + exclude_names = None + if len(args.exclude) > 0: + # We're supporting 2 kinds of exclusion patterns: + # 1) --exclude '*.jpg' (file/dir name patterns, will only match + # the name) + # 2) --exclude 'foo/bar' (file/dir path patterns, will match the + # entire path, and should be relative to + # any input dir argument) + for p in args.exclude: + # Only relative paths patterns allowed + if p.startswith(os.sep): + logger.error("Cannot use absolute paths with --exclude") + sys.exit(1) + if os.path.dirname(p): + # We don't support of path patterns with '.' or '..' + p_parts = p.split(os.sep) + if '.' in p_parts or '..' in p_parts: + logger.error( + "Cannot use path patterns that include '.' or '..'") + sys.exit(1) + # Path search pattern + exclude_paths.append(p) + else: + # Name-only search pattern + name_patterns.append(p) + # For name only matching, we can combine all patterns into a single regexp, + # for better performance. + exclude_names = re.compile('|'.join( + [fnmatch.translate(p) for p in name_patterns] + )) if len(name_patterns) > 0 else None + # Show the user the patterns to be used, just in case they weren't specified inside + # quotes and got changed by the shell expansion. + logger.info("Exclude patterns: {}".format(args.exclude)) + # If this is used by a human, and there's at least one directory to be # uploaded, the expected bytes calculation can take a moment. if args.progress and any([os.path.isdir(f) for f in args.paths]): logger.info("Calculating upload size, this could take some time...") - bytes_expected = expected_bytes_for(args.paths, follow_links=args.follow_links) - try: writer = ArvPutUploadJob(paths = args.paths, resume = args.resume, use_cache = args.use_cache, filename = args.filename, reporter = reporter, - bytes_expected = bytes_expected, num_retries = args.retries, replication_desired = args.replication, put_threads = args.threads, @@ -945,7 +1061,9 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): update_collection = args.update_collection, logger=logger, dry_run=args.dry_run, - follow_links=args.follow_links) + follow_links=args.follow_links, + exclude_paths=exclude_paths, + exclude_names=exclude_names) except ResumeCacheConflict: logger.error("\n".join([ "arv-put: Another process is already uploading this data.", @@ -961,6 +1079,10 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): except ArvPutUploadNotPending: # No files pending for upload sys.exit(0) + except PathDoesNotExistError as error: + logger.error("\n".join([ + "arv-put: %s" % str(error)])) + sys.exit(1) # Install our signal handler for each code in CAUGHT_SIGNALS, and save # the originals. @@ -981,16 +1103,6 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr): logger.error("\n".join([ "arv-put: %s" % str(error)])) sys.exit(1) - except ArvPutUploadIsPending: - # Dry run check successful, return proper exit code. - sys.exit(2) - except ArvPutUploadNotPending: - # No files pending for upload - sys.exit(0) - except PathDoesNotExistError as error: - logger.error("\n".join([ - "arv-put: %s" % str(error)])) - sys.exit(1) if args.progress: # Print newline to split stderr from stdout for humans. logger.info("\n")