import argparse
import arvados
+import arvados.collection
import base64
import datetime
import errno
import json
import os
import pwd
+import time
import signal
import socket
import sys
import tempfile
+import threading
+import copy
+import logging
from apiclient import errors as apiclient_errors
import arvados.commands._util as arv_cmd
upload_opts = argparse.ArgumentParser(add_help=False)
upload_opts.add_argument('paths', metavar='path', type=str, nargs='*',
- help="""
+ help="""
Local file or directory. Default: read from standard input.
""")
-upload_opts.add_argument('--max-manifest-depth', type=int, metavar='N',
+_group = upload_opts.add_mutually_exclusive_group()
+
+_group.add_argument('--max-manifest-depth', type=int, metavar='N',
default=-1, help="""
Maximum depth of directory tree to represent in the manifest
structure. A directory structure deeper than this will be represented
stream per filesystem directory that contains files.
""")
+_group.add_argument('--normalize', action='store_true',
+ help="""
+Normalize the manifest by re-ordering files and streams after writing
+data.
+""")
+
_group = upload_opts.add_mutually_exclusive_group()
_group.add_argument('--as-stream', action='store_true', dest='stream',
- help="""
+ help="""
Synonym for --stream.
""")
_group.add_argument('--stream', action='store_true',
- help="""
+ help="""
Store the file content and display the resulting manifest on
stdout. Do not write the manifest to Keep or save a Collection object
in Arvados.
""")
_group.add_argument('--as-manifest', action='store_true', dest='manifest',
- help="""
+ help="""
Synonym for --manifest.
""")
_group.add_argument('--in-manifest', action='store_true', dest='manifest',
- help="""
+ help="""
Synonym for --manifest.
""")
_group.add_argument('--manifest', action='store_true',
- help="""
+ help="""
Store the file data and resulting manifest in Keep, save a Collection
object in Arvados, and display the manifest locator (Collection uuid)
on stdout. This is the default behavior.
""")
_group.add_argument('--as-raw', action='store_true', dest='raw',
- help="""
+ help="""
Synonym for --raw.
""")
_group.add_argument('--raw', action='store_true',
- help="""
+ help="""
Store the file content and display the data block locators on stdout,
separated by commas, with a trailing newline. Do not store a
manifest.
""")
upload_opts.add_argument('--use-filename', type=str, default=None,
- dest='filename', help="""
+ dest='filename', help="""
Synonym for --filename.
""")
upload_opts.add_argument('--filename', type=str, default=None,
- help="""
+ help="""
Use the given filename in the manifest, instead of the name of the
local file. This is useful when "-" or "/dev/stdin" is given as an
input file. It can be used only if there is exactly one path given and
""")
upload_opts.add_argument('--portable-data-hash', action='store_true',
- help="""
+ help="""
Print the portable data hash instead of the Arvados UUID for the collection
created by the upload.
""")
+upload_opts.add_argument('--replication', type=int, metavar='N', default=None,
+ help="""
+Set the replication level for the new collection: how many different
+physical storage devices (e.g., disks) should have a copy of each data
+block. Default is to use the server-provided default (if any) or 2.
+""")
+
run_opts = argparse.ArgumentParser(add_help=False)
run_opts.add_argument('--project-uuid', metavar='UUID', help="""
_group = run_opts.add_mutually_exclusive_group()
_group.add_argument('--progress', action='store_true',
- help="""
+ help="""
Display human-readable progress on stderr (bytes and, if possible,
percentage of total data size). This is the default behavior when
stderr is a tty.
""")
_group.add_argument('--no-progress', action='store_true',
- help="""
+ help="""
Do not display human-readable progress on stderr, even if stderr is a
tty.
""")
_group.add_argument('--batch-progress', action='store_true',
- help="""
+ help="""
Display machine-readable progress on stderr (bytes and, if known,
total data size).
""")
_group = run_opts.add_mutually_exclusive_group()
_group.add_argument('--resume', action='store_true', default=True,
- help="""
+ help="""
Continue interrupted uploads from cached state (default).
""")
_group.add_argument('--no-resume', action='store_false', dest='resume',
- help="""
+ help="""
Do not continue interrupted uploads from cached state.
""")
args = arg_parser.parse_args(arguments)
if len(args.paths) == 0:
- args.paths += ['/dev/stdin']
+ args.paths = ['-']
+
+ args.paths = map(lambda x: "-" if x == "/dev/stdin" else x, args.paths)
if len(args.paths) != 1 or os.path.isdir(args.paths[0]):
if args.filename:
args.progress = True
if args.paths == ['-']:
- args.paths = ['/dev/stdin']
+ args.resume = False
if not args.filename:
- args.filename = '-'
+ args.filename = 'stdin'
return args
self.cache_file.seek(0)
return json.load(self.cache_file)
+ def check_cache(self, api_client=None, num_retries=0):
+ try:
+ state = self.load()
+ locator = None
+ try:
+ if "_finished_streams" in state and len(state["_finished_streams"]) > 0:
+ locator = state["_finished_streams"][0][1][0]
+ elif "_current_stream_locators" in state and len(state["_current_stream_locators"]) > 0:
+ locator = state["_current_stream_locators"][0]
+ if locator is not None:
+ kc = arvados.keep.KeepClient(api_client=api_client)
+ kc.head(locator, num_retries=num_retries)
+ except Exception as e:
+ self.restart()
+ except (ValueError):
+ pass
+
def save(self, data):
try:
new_cache_fd, new_cache_name = tempfile.mkstemp(
self.__init__(self.filename)
-class ArvPutCollectionWriter(arvados.ResumableCollectionWriter):
- STATE_PROPS = (arvados.ResumableCollectionWriter.STATE_PROPS +
- ['bytes_written', '_seen_inputs'])
-
- def __init__(self, cache=None, reporter=None, bytes_expected=None,
- api_client=None, num_retries=0):
- self.bytes_written = 0
- self._seen_inputs = []
- self.cache = cache
+class ArvPutUploadJob(object):
+ CACHE_DIR = '.cache/arvados/arv-put'
+ EMPTY_STATE = {
+ 'manifest' : None, # Last saved manifest checkpoint
+ 'files' : {} # Previous run file list: {path : {size, mtime}}
+ }
+
+ def __init__(self, paths, resume=True, reporter=None, bytes_expected=None,
+ name=None, owner_uuid=None, ensure_unique_name=False,
+ num_retries=None, replication_desired=None,
+ filename=None, update_time=60.0):
+ self.paths = paths
+ self.resume = resume
self.reporter = reporter
self.bytes_expected = bytes_expected
- super(ArvPutCollectionWriter, self).__init__(
- api_client, num_retries=num_retries)
-
- @classmethod
- def from_cache(cls, cache, reporter=None, bytes_expected=None,
- num_retries=0):
+ self.bytes_written = 0
+ self.bytes_skipped = 0
+ self.name = name
+ self.owner_uuid = owner_uuid
+ self.ensure_unique_name = ensure_unique_name
+ self.num_retries = num_retries
+ self.replication_desired = replication_desired
+ self.filename = filename
+ self._state_lock = threading.Lock()
+ self._state = None # Previous run state (file list & manifest)
+ self._current_files = [] # Current run file list
+ self._cache_file = None
+ self._collection = None
+ self._collection_lock = threading.Lock()
+ self._stop_checkpointer = threading.Event()
+ self._checkpointer = threading.Thread(target=self._update_task)
+ self._update_task_time = update_time # How many seconds wait between update runs
+ self.logger = logging.getLogger('arvados.arv_put')
+ # Load cached data if any and if needed
+ self._setup_state()
+
+ def start(self):
+ """
+ Start supporting thread & file uploading
+ """
+ self._checkpointer.daemon = True
+ self._checkpointer.start()
try:
- state = cache.load()
- state['_data_buffer'] = [base64.decodestring(state['_data_buffer'])]
- writer = cls.from_state(state, cache, reporter, bytes_expected,
- num_retries=num_retries)
- except (TypeError, ValueError,
- arvados.errors.StaleWriterStateError) as error:
- return cls(cache, reporter, bytes_expected, num_retries=num_retries)
- else:
- return writer
-
- def cache_state(self):
- if self.cache is None:
- return
- state = self.dump_state()
- # Transform attributes for serialization.
- for attr, value in state.items():
- if attr == '_data_buffer':
- state[attr] = base64.encodestring(''.join(value))
- elif hasattr(value, 'popleft'):
- state[attr] = list(value)
- self.cache.save(state)
+ for path in self.paths:
+ # Test for stdin first, in case some file named '-' exist
+ if path == '-':
+ self._write_stdin(self.filename or 'stdin')
+ elif os.path.isdir(path):
+ self._write_directory_tree(path)
+ else:
+ self._write_file(path, self.filename or os.path.basename(path))
+ finally:
+ # Stop the thread before doing anything else
+ self._stop_checkpointer.set()
+ self._checkpointer.join()
+ # Commit all & one last _update()
+ self.manifest_text()
+ self._update()
+ if self.resume:
+ self._cache_file.close()
+ # Correct the final written bytes count
+ self.bytes_written -= self.bytes_skipped
+
+ def save_collection(self):
+ with self._collection_lock:
+ self._my_collection().save_new(
+ name=self.name, owner_uuid=self.owner_uuid,
+ ensure_unique_name=self.ensure_unique_name,
+ num_retries=self.num_retries)
+
+ def destroy_cache(self):
+ if self.resume:
+ try:
+ os.unlink(self._cache_filename)
+ except OSError as error:
+ # That's what we wanted anyway.
+ if error.errno != errno.ENOENT:
+ raise
+ self._cache_file.close()
+
+ def _collection_size(self, collection):
+ """
+ Recursively get the total size of the collection
+ """
+ size = 0
+ for item in collection.values():
+ if isinstance(item, arvados.collection.Collection) or isinstance(item, arvados.collection.Subcollection):
+ size += self._collection_size(item)
+ else:
+ size += item.size()
+ return size
+
+ def _update_task(self):
+ """
+ Periodically called support task. File uploading is
+ asynchronous so we poll status from the collection.
+ """
+ while not self._stop_checkpointer.wait(self._update_task_time):
+ self._update()
+
+ def _update(self):
+ """
+ Update cached manifest text and report progress.
+ """
+ with self._collection_lock:
+ self.bytes_written = self._collection_size(self._my_collection())
+ # Update cache, if resume enabled
+ if self.resume:
+ with self._state_lock:
+ # Get the manifest text without comitting pending blocks
+ self._state['manifest'] = self._my_collection()._get_manifest_text(".", strip=False, normalize=False, only_committed=True)
+ if self.resume:
+ self._save_state()
+ # Call the reporter, if any
+ self.report_progress()
def report_progress(self):
if self.reporter is not None:
self.reporter(self.bytes_written, self.bytes_expected)
- def flush_data(self):
- start_buffer_len = self._data_buffer_len
- start_block_count = self.bytes_written / self.KEEP_BLOCK_SIZE
- super(ArvPutCollectionWriter, self).flush_data()
- if self._data_buffer_len < start_buffer_len: # We actually PUT data.
- self.bytes_written += (start_buffer_len - self._data_buffer_len)
- self.report_progress()
- if (self.bytes_written / self.KEEP_BLOCK_SIZE) > start_block_count:
- self.cache_state()
-
- def _record_new_input(self, input_type, source_name, dest_name):
- # The key needs to be a list because that's what we'll get back
- # from JSON deserialization.
- key = [input_type, source_name, dest_name]
- if key in self._seen_inputs:
- return False
- self._seen_inputs.append(key)
- return True
-
- def write_file(self, source, filename=None):
- if self._record_new_input('file', source, filename):
- super(ArvPutCollectionWriter, self).write_file(source, filename)
-
- def write_directory_tree(self,
- path, stream_name='.', max_manifest_depth=-1):
- if self._record_new_input('directory', path, stream_name):
- super(ArvPutCollectionWriter, self).write_directory_tree(
- path, stream_name, max_manifest_depth)
+ def _write_directory_tree(self, path, stream_name="."):
+ # TODO: Check what happens when multiple directories are passed as
+ # arguments.
+ # If the code below is uncommented, integration test
+ # test_ArvPutSignedManifest (tests.test_arv_put.ArvPutIntegrationTest)
+ # fails, I suppose it is because the manifest_uuid changes because
+ # of the dir addition to stream_name.
+
+ # if stream_name == '.':
+ # stream_name = os.path.join('.', os.path.basename(path))
+ for item in os.listdir(path):
+ if os.path.isdir(os.path.join(path, item)):
+ self._write_directory_tree(os.path.join(path, item),
+ os.path.join(stream_name, item))
+ else:
+ self._write_file(os.path.join(path, item),
+ os.path.join(stream_name, item))
+
+ def _write_stdin(self, filename):
+ with self._collection_lock:
+ output = self._my_collection().open(filename, 'w')
+ self._write(sys.stdin, output)
+ output.close()
+
+ def _write_file(self, source, filename):
+ resume_offset = 0
+ if self.resume:
+ # Check if file was already uploaded (at least partially)
+ with self._collection_lock:
+ try:
+ file_in_collection = self._my_collection().find(filename)
+ except IOError:
+ # Not found
+ file_in_collection = None
+ # If no previous cached data on this file, store it for an eventual
+ # repeated run.
+ if source not in self._state['files']:
+ with self._state_lock:
+ self._state['files'][source] = {
+ 'mtime': os.path.getmtime(source),
+ 'size' : os.path.getsize(source)
+ }
+ with self._state_lock:
+ cached_file_data = self._state['files'][source]
+ # See if this file was already uploaded at least partially
+ if file_in_collection:
+ if cached_file_data['mtime'] == os.path.getmtime(source) and cached_file_data['size'] == os.path.getsize(source):
+ if cached_file_data['size'] == file_in_collection.size():
+ # File already there, skip it.
+ self.bytes_skipped += cached_file_data['size']
+ return
+ elif cached_file_data['size'] > file_in_collection.size():
+ # File partially uploaded, resume!
+ resume_offset = file_in_collection.size()
+ else:
+ # Inconsistent cache, re-upload the file
+ self.logger.warning("Uploaded version of file '{}' is bigger than local version, will re-upload it from scratch.".format(source))
+ else:
+ # Local file differs from cached data, re-upload it
+ pass
+ with open(source, 'r') as source_fd:
+ if resume_offset > 0:
+ # Start upload where we left off
+ with self._collection_lock:
+ output = self._my_collection().open(filename, 'a')
+ source_fd.seek(resume_offset)
+ self.bytes_skipped += resume_offset
+ else:
+ # Start from scratch
+ with self._collection_lock:
+ output = self._my_collection().open(filename, 'w')
+ self._write(source_fd, output)
+ output.close()
+
+ def _write(self, source_fd, output):
+ first_read = True
+ while True:
+ data = source_fd.read(arvados.config.KEEP_BLOCK_SIZE)
+ # Allow an empty file to be written
+ if not data and not first_read:
+ break
+ if first_read:
+ first_read = False
+ output.write(data)
+
+ def _my_collection(self):
+ """
+ Create a new collection if none cached. Load it from cache otherwise.
+ """
+ if self._collection is None:
+ with self._state_lock:
+ manifest = self._state['manifest']
+ if self.resume and manifest is not None:
+ # Create collection from saved state
+ self._collection = arvados.collection.Collection(
+ manifest,
+ replication_desired=self.replication_desired)
+ else:
+ # Create new collection
+ self._collection = arvados.collection.Collection(
+ replication_desired=self.replication_desired)
+ return self._collection
+
+ def _setup_state(self):
+ """
+ Create a new cache file or load a previously existing one.
+ """
+ if self.resume:
+ md5 = hashlib.md5()
+ md5.update(arvados.config.get('ARVADOS_API_HOST', '!nohost'))
+ realpaths = sorted(os.path.realpath(path) for path in self.paths)
+ md5.update('\0'.join(realpaths))
+ if self.filename:
+ md5.update(self.filename)
+ cache_filename = md5.hexdigest()
+ self._cache_file = open(os.path.join(
+ arv_cmd.make_home_conf_dir(self.CACHE_DIR, 0o700, 'raise'),
+ cache_filename), 'a+')
+ self._cache_filename = self._cache_file.name
+ self._lock_file(self._cache_file)
+ self._cache_file.seek(0)
+ with self._state_lock:
+ try:
+ self._state = json.load(self._cache_file)
+ if not set(['manifest', 'files']).issubset(set(self._state.keys())):
+ # Cache at least partially incomplete, set up new cache
+ self._state = copy.deepcopy(self.EMPTY_STATE)
+ except ValueError:
+ # Cache file empty, set up new cache
+ self._state = copy.deepcopy(self.EMPTY_STATE)
+ # Load how many bytes were uploaded on previous run
+ with self._collection_lock:
+ self.bytes_written = self._collection_size(self._my_collection())
+ # No resume required
+ else:
+ with self._state_lock:
+ self._state = copy.deepcopy(self.EMPTY_STATE)
+
+ def _lock_file(self, fileobj):
+ try:
+ fcntl.flock(fileobj, fcntl.LOCK_EX | fcntl.LOCK_NB)
+ except IOError:
+ raise ResumeCacheConflict("{} locked".format(fileobj.name))
+
+ def _save_state(self):
+ """
+ Atomically save current state into cache.
+ """
+ try:
+ with self._state_lock:
+ state = self._state
+ new_cache_fd, new_cache_name = tempfile.mkstemp(
+ dir=os.path.dirname(self._cache_filename))
+ self._lock_file(new_cache_fd)
+ new_cache = os.fdopen(new_cache_fd, 'r+')
+ json.dump(state, new_cache)
+ new_cache.flush()
+ os.fsync(new_cache)
+ os.rename(new_cache_name, self._cache_filename)
+ except (IOError, OSError, ResumeCacheConflict) as error:
+ self.logger.error("There was a problem while saving the cache file: {}".format(error))
+ try:
+ os.unlink(new_cache_name)
+ except NameError: # mkstemp failed.
+ pass
+ else:
+ self._cache_file.close()
+ self._cache_file = new_cache
+
+ def collection_name(self):
+ with self._collection_lock:
+ name = self._my_collection().api_response()['name'] if self._my_collection().api_response() else None
+ return name
+
+ def manifest_locator(self):
+ with self._collection_lock:
+ locator = self._my_collection().manifest_locator()
+ return locator
+
+ def portable_data_hash(self):
+ with self._collection_lock:
+ datahash = self._my_collection().portable_data_hash()
+ return datahash
+
+ def manifest_text(self, stream_name=".", strip=False, normalize=False):
+ with self._collection_lock:
+ manifest = self._my_collection().manifest_text(stream_name, strip, normalize)
+ return manifest
+
+ def _datablocks_on_item(self, item):
+ """
+ Return a list of datablock locators, recursively navigating
+ through subcollections
+ """
+ if isinstance(item, arvados.arvfile.ArvadosFile):
+ if item.size() == 0:
+ # Empty file locator
+ return ["d41d8cd98f00b204e9800998ecf8427e+0"]
+ else:
+ locators = []
+ for segment in item.segments():
+ loc = segment.locator
+ locators.append(loc)
+ return locators
+ elif isinstance(item, arvados.collection.Collection):
+ l = [self._datablocks_on_item(x) for x in item.values()]
+ # Fast list flattener method taken from:
+ # http://stackoverflow.com/questions/952914/making-a-flat-list-out-of-list-of-lists-in-python
+ return [loc for sublist in l for loc in sublist]
+ else:
+ return None
+
+ def data_locators(self):
+ with self._collection_lock:
+ # Make sure all datablocks are flushed before getting the locators
+ self._my_collection().manifest_text()
+ datablocks = self._datablocks_on_item(self._my_collection())
+ return datablocks
def expected_bytes_for(pathlist):
reporter = progress_writer(machine_progress)
else:
reporter = None
- bytes_expected = expected_bytes_for(args.paths)
-
- resume_cache = None
- if args.resume:
- try:
- resume_cache = ResumeCache(ResumeCache.make_path(args))
- except (IOError, OSError, ValueError):
- pass # Couldn't open cache directory/file. Continue without it.
- except ResumeCacheConflict:
- print >>stderr, "\n".join([
- "arv-put: Another process is already uploading this data.",
- " Use --no-resume if this is really what you want."])
- sys.exit(1)
- if resume_cache is None:
- writer = ArvPutCollectionWriter(resume_cache, reporter, bytes_expected,
- num_retries=args.retries)
- else:
- writer = ArvPutCollectionWriter.from_cache(
- resume_cache, reporter, bytes_expected, num_retries=args.retries)
+ bytes_expected = expected_bytes_for(args.paths)
+ try:
+ writer = ArvPutUploadJob(paths = args.paths,
+ resume = args.resume,
+ filename = args.filename,
+ reporter = reporter,
+ bytes_expected = bytes_expected,
+ num_retries = args.retries,
+ replication_desired = args.replication,
+ name = collection_name,
+ owner_uuid = project_uuid,
+ ensure_unique_name = True)
+ except ResumeCacheConflict:
+ print >>stderr, "\n".join([
+ "arv-put: Another process is already uploading this data.",
+ " Use --no-resume if this is really what you want."])
+ sys.exit(1)
# Install our signal handler for each code in CAUGHT_SIGNALS, and save
# the originals.
orig_signal_handlers = {sigcode: signal.signal(sigcode, exit_signal_handler)
for sigcode in CAUGHT_SIGNALS}
- if writer.bytes_written > 0: # We're resuming a previous upload.
+ if args.resume and writer.bytes_written > 0:
print >>stderr, "\n".join([
"arv-put: Resuming previous upload from last checkpoint.",
" Use the --no-resume option to start over."])
writer.report_progress()
- writer.do_queued_work() # Do work resumed from cache.
- for path in args.paths: # Copy file data to Keep.
- if os.path.isdir(path):
- writer.write_directory_tree(
- path, max_manifest_depth=args.max_manifest_depth)
- else:
- writer.start_new_stream()
- writer.write_file(path, args.filename or os.path.basename(path))
- writer.finish_current_stream()
-
+ output = None
+ writer.start()
if args.progress: # Print newline to split stderr from stdout for humans.
print >>stderr
if args.stream:
- output = writer.manifest_text()
+ if args.normalize:
+ output = writer.manifest_text(normalize=True)
+ else:
+ output = writer.manifest_text()
elif args.raw:
output = ','.join(writer.data_locators())
else:
try:
- # Register the resulting collection in Arvados.
- collection = api_client.collections().create(
- body={
- 'owner_uuid': project_uuid,
- 'name': collection_name,
- 'manifest_text': writer.manifest_text()
- },
- ensure_unique_name=True
- ).execute(num_retries=args.retries)
-
- print >>stderr, "Collection saved as '%s'" % collection['name']
-
- if args.portable_data_hash and 'portable_data_hash' in collection and collection['portable_data_hash']:
- output = collection['portable_data_hash']
+ writer.save_collection()
+ print >>stderr, "Collection saved as '%s'" % writer.collection_name()
+ if args.portable_data_hash:
+ output = writer.portable_data_hash()
else:
- output = collection['uuid']
-
+ output = writer.manifest_locator()
except apiclient_errors.Error as error:
print >>stderr, (
"arv-put: Error creating Collection on project: {}.".format(
status = 1
# Print the locator (uuid) of the new collection.
- stdout.write(output)
- if not output.endswith('\n'):
- stdout.write('\n')
+ if output is None:
+ status = status or 1
+ else:
+ stdout.write(output)
+ if not output.endswith('\n'):
+ stdout.write('\n')
for sigcode, orig_handler in orig_signal_handlers.items():
signal.signal(sigcode, orig_handler)
if status != 0:
sys.exit(status)
- if resume_cache is not None:
- resume_cache.destroy()
-
+ # Success!
+ writer.destroy_cache()
return output
+
if __name__ == '__main__':
main()