# TODO:
# --md5sum - display md5 of each file as read from disk
+import apiclient.errors
import argparse
import arvados
import base64
+import datetime
import errno
import fcntl
import hashlib
import json
import os
+import pwd
import signal
+import socket
import sys
import tempfile
stream per filesystem directory that contains files.
""")
+upload_opts.add_argument('--project-uuid', metavar='UUID', help="""
+Store the collection in the specified project, instead of your Home
+project.
+""")
+
+upload_opts.add_argument('--name', help="""
+Save the collection with the specified name, rather than the default
+generic name "Saved at {time} by {username}@{host}".
+""")
+
_group = upload_opts.add_mutually_exclusive_group()
_group.add_argument('--as-stream', action='store_true', dest='stream',
class ResumeCache(object):
CACHE_DIR = '.cache/arvados/arv-put'
- @classmethod
- def setup_user_cache(cls):
- return arv_cmd.make_home_conf_dir(cls.CACHE_DIR, 0o700)
-
def __init__(self, file_spec):
self.cache_file = open(file_spec, 'a+')
self._lock_file(self.cache_file)
md5.update(str(max(args.max_manifest_depth, -1)))
elif args.filename:
md5.update(args.filename)
- return os.path.join(cls.CACHE_DIR, md5.hexdigest())
+ return os.path.join(
+ arv_cmd.make_home_conf_dir(cls.CACHE_DIR, 0o700, 'raise'),
+ md5.hexdigest())
def _lock_file(self, fileobj):
try:
def exit_signal_handler(sigcode, frame):
sys.exit(-sigcode)
-def main(arguments=None, output_to=sys.stdout):
+def check_project_exists(project_uuid):
+ try:
+ arvados.api('v1').groups().get(uuid=project_uuid).execute()
+ except (apiclient.errors.Error, arvados.errors.NotFoundError) as error:
+ raise ValueError("Project {} not found ({})".format(project_uuid,
+ error))
+ else:
+ return True
+
+def prep_project_link(args, stderr, project_exists=check_project_exists):
+ # Given the user's command line arguments, return a dictionary with data
+ # to create the desired project link for this Collection, or None.
+ # Raises ValueError if the arguments request something impossible.
+ making_collection = not (args.raw or args.stream)
+ if not making_collection:
+ if args.name or args.project_uuid:
+ raise ValueError("Requested a Link without creating a Collection")
+ return None
+ link = {'tail_uuid': args.project_uuid,
+ 'link_class': 'name',
+ 'name': args.name}
+ if not link['tail_uuid']:
+ link['tail_uuid'] = arvados.api('v1').users().current().execute()['uuid']
+ elif not project_exists(link['tail_uuid']):
+ raise ValueError("Project {} not found".format(args.project_uuid))
+ if not link['name']:
+ link['name'] = "Saved at {} by {}@{}".format(
+ datetime.datetime.utcnow().strftime("%Y-%m-%d %H:%M:%S UTC"),
+ pwd.getpwuid(os.getuid()).pw_name,
+ socket.gethostname())
+ stderr.write(
+ "arv-put: No --name specified. Saving as \"%s\"\n" % link['name'])
+ link['owner_uuid'] = link['tail_uuid']
+ return link
+
+def create_project_link(locator, link):
+ link['head_uuid'] = locator
+ return arvados.api('v1').links().create(body=link).execute()
+
+def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
+ status = 0
+
args = parse_arguments(arguments)
+ try:
+ project_link = prep_project_link(args, stderr)
+ except ValueError as error:
+ print >>stderr, "arv-put: {}.".format(error)
+ sys.exit(2)
if args.progress:
reporter = progress_writer(human_progress)
bytes_expected = expected_bytes_for(args.paths)
resume_cache = None
- try:
- if ResumeCache.setup_user_cache() is not None:
+ if args.resume:
+ try:
resume_cache = ResumeCache(ResumeCache.make_path(args))
- except (IOError, OSError):
- pass # Couldn't open cache directory/file. Continue without it.
- except ResumeCacheConflict:
- output_to.write(
- "arv-put: Another process is already uploading this data.\n")
- sys.exit(1)
+ 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)
else:
- if not args.resume:
- resume_cache.restart()
writer = ArvPutCollectionWriter.from_cache(
resume_cache, reporter, bytes_expected)
for sigcode in CAUGHT_SIGNALS}
if writer.bytes_written > 0: # We're resuming a previous upload.
- print >>sys.stderr, "\n".join([
+ print >>stderr, "\n".join([
"arv-put: Resuming previous upload from last checkpoint.",
" Use the --no-resume option to start over."])
- writer.report_progress()
+ 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.finish_current_stream()
if args.progress: # Print newline to split stderr from stdout for humans.
- print >>sys.stderr
+ print >>stderr
if args.stream:
output = writer.manifest_text()
# Register the resulting collection in Arvados.
collection = arvados.api().collections().create(
body={
- 'uuid': writer.finish(),
'manifest_text': writer.manifest_text(),
},
).execute()
# Print the locator (uuid) of the new collection.
output = collection['uuid']
-
- output_to.write(output)
+ if project_link is not None:
+ try:
+ if 'name' in collection:
+ arvados.api().collections().update(uuid=output,
+ body={"owner_uuid": project_link["tail_uuid"],
+ "name": project_link["name"]}).execute()
+ else:
+ create_project_link(output, project_link)
+ except apiclient.errors.Error as error:
+ print >>stderr, (
+ "arv-put: Error adding Collection to project: {}.".format(
+ error))
+ status = 1
+
+ stdout.write(output)
if not output.endswith('\n'):
- output_to.write('\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()
projects / arvados.git / blobdiff