3 # arv-copy [--recursive] [--no-recursive] object-uuid src dst
5 # Copies an object from Arvados instance src to instance dst.
7 # By default, arv-copy recursively copies any dependent objects
8 # necessary to make the object functional in the new instance
9 # (e.g. for a pipeline instance, arv-copy copies the pipeline
10 # template, input collection, docker images, git repositories). If
11 # --no-recursive is given, arv-copy copies only the single record
12 # identified by object-uuid.
14 # The user must have files $HOME/.config/arvados/{src}.conf and
15 # $HOME/.config/arvados/{dst}.conf with valid login credentials for
16 # instances src and dst. If either of these files is not found,
17 # arv-copy will issue an error.
33 import arvados.commands._util as arv_cmd
34 import arvados.commands.keepdocker
36 from arvados.api import OrderedJsonModel
38 logger = logging.getLogger('arvados.arv-copy')
40 # local_repo_dir records which git repositories from the Arvados source
41 # instance have been checked out locally during this run, and to which
43 # e.g. if repository 'twp' from src_arv has been cloned into
44 # /tmp/gitfHkV9lu44A then local_repo_dir['twp'] = '/tmp/gitfHkV9lu44A'
48 # List of collections that have been copied in this session, and their
49 # destination collection UUIDs.
50 collections_copied = {}
52 # Set of (repository, script_version) two-tuples of commits copied in git.
53 scripts_copied = set()
55 # The owner_uuid of the object being copied
59 copy_opts = argparse.ArgumentParser(add_help=False)
61 copy_opts.add_argument(
62 '-v', '--verbose', dest='verbose', action='store_true',
63 help='Verbose output.')
64 copy_opts.add_argument(
65 '--progress', dest='progress', action='store_true',
66 help='Report progress on copying collections. (default)')
67 copy_opts.add_argument(
68 '--no-progress', dest='progress', action='store_false',
69 help='Do not report progress on copying collections.')
70 copy_opts.add_argument(
71 '-f', '--force', dest='force', action='store_true',
72 help='Perform copy even if the object appears to exist at the remote destination.')
73 copy_opts.add_argument(
74 '--src', dest='source_arvados', required=True,
75 help='The name of the source Arvados instance (required) - points at an Arvados config file. May be either a pathname to a config file, or (for example) "foo" as shorthand for $HOME/.config/arvados/foo.conf.')
76 copy_opts.add_argument(
77 '--dst', dest='destination_arvados', required=True,
78 help='The name of the destination Arvados instance (required) - points at an Arvados config file. May be either a pathname to a config file, or (for example) "foo" as shorthand for $HOME/.config/arvados/foo.conf.')
79 copy_opts.add_argument(
80 '--recursive', dest='recursive', action='store_true',
81 help='Recursively copy any dependencies for this object. (default)')
82 copy_opts.add_argument(
83 '--no-recursive', dest='recursive', action='store_false',
84 help='Do not copy any dependencies. NOTE: if this option is given, the copied object will need to be updated manually in order to be functional.')
85 copy_opts.add_argument(
86 '--dst-git-repo', dest='dst_git_repo',
87 help='The name of the destination git repository. Required when copying a pipeline recursively.')
88 copy_opts.add_argument(
89 '--project-uuid', dest='project_uuid',
90 help='The UUID of the project at the destination to which the pipeline should be copied.')
91 copy_opts.add_argument(
93 help='The UUID of the object to be copied.')
94 copy_opts.set_defaults(progress=True)
95 copy_opts.set_defaults(recursive=True)
97 parser = argparse.ArgumentParser(
98 description='Copy a pipeline instance, template or collection from one Arvados instance to another.',
99 parents=[copy_opts, arv_cmd.retry_opt])
100 args = parser.parse_args()
103 logger.setLevel(logging.DEBUG)
105 logger.setLevel(logging.INFO)
107 # Create API clients for the source and destination instances
108 src_arv = api_for_instance(args.source_arvados)
109 dst_arv = api_for_instance(args.destination_arvados)
111 if not args.project_uuid:
112 args.project_uuid = dst_arv.users().current().execute(num_retries=args.retries)["uuid"]
114 # Identify the kind of object we have been given, and begin copying.
115 t = uuid_type(src_arv, args.object_uuid)
116 if t == 'Collection':
117 set_src_owner_uuid(src_arv.collections(), args.object_uuid, args)
118 result = copy_collection(args.object_uuid,
121 elif t == 'PipelineInstance':
122 set_src_owner_uuid(src_arv.pipeline_instances(), args.object_uuid, args)
123 result = copy_pipeline_instance(args.object_uuid,
126 elif t == 'PipelineTemplate':
127 set_src_owner_uuid(src_arv.pipeline_templates(), args.object_uuid, args)
128 result = copy_pipeline_template(args.object_uuid,
129 src_arv, dst_arv, args)
131 abort("cannot copy object {} of type {}".format(args.object_uuid, t))
133 # Clean up any outstanding temp git repositories.
134 for d in local_repo_dir.values():
135 shutil.rmtree(d, ignore_errors=True)
137 # If no exception was thrown and the response does not have an
138 # error_token field, presume success
139 if 'error_token' in result or 'uuid' not in result:
140 logger.error("API server returned an error result: {}".format(result))
144 logger.info("Success: created copy with uuid {}".format(result['uuid']))
147 def set_src_owner_uuid(resource, uuid, args):
148 global src_owner_uuid
149 c = resource.get(uuid=uuid).execute(num_retries=args.retries)
150 src_owner_uuid = c.get("owner_uuid")
152 # api_for_instance(instance_name)
154 # Creates an API client for the Arvados instance identified by
157 # If instance_name contains a slash, it is presumed to be a path
158 # (either local or absolute) to a file with Arvados configuration
161 # Otherwise, it is presumed to be the name of a file in
162 # $HOME/.config/arvados/instance_name.conf
164 def api_for_instance(instance_name):
165 if '/' in instance_name:
166 config_file = instance_name
168 config_file = os.path.join(os.environ['HOME'], '.config', 'arvados', "{}.conf".format(instance_name))
171 cfg = arvados.config.load(config_file)
172 except (IOError, OSError) as e:
173 abort(("Could not open config file {}: {}\n" +
174 "You must make sure that your configuration tokens\n" +
175 "for Arvados instance {} are in {} and that this\n" +
176 "file is readable.").format(
177 config_file, e, instance_name, config_file))
179 if 'ARVADOS_API_HOST' in cfg and 'ARVADOS_API_TOKEN' in cfg:
181 cfg.get('ARVADOS_API_HOST_INSECURE', '').lower() in set(
182 ['1', 't', 'true', 'y', 'yes']))
183 client = arvados.api('v1',
184 host=cfg['ARVADOS_API_HOST'],
185 token=cfg['ARVADOS_API_TOKEN'],
186 insecure=api_is_insecure,
187 model=OrderedJsonModel())
189 abort('need ARVADOS_API_HOST and ARVADOS_API_TOKEN for {}'.format(instance_name))
192 # Check if git is available
193 def check_git_availability():
195 arvados.util.run_command(['git', '--help'])
197 abort('git command is not available. Please ensure git is installed.')
199 # copy_pipeline_instance(pi_uuid, src, dst, args)
201 # Copies a pipeline instance identified by pi_uuid from src to dst.
203 # If the args.recursive option is set:
204 # 1. Copies all input collections
205 # * For each component in the pipeline, include all collections
206 # listed as job dependencies for that component)
207 # 2. Copy docker images
208 # 3. Copy git repositories
209 # 4. Copy the pipeline template
211 # The only changes made to the copied pipeline instance are:
212 # 1. The original pipeline instance UUID is preserved in
213 # the 'properties' hash as 'copied_from_pipeline_instance_uuid'.
214 # 2. The pipeline_template_uuid is changed to the new template uuid.
215 # 3. The owner_uuid of the instance is changed to the user who
218 def copy_pipeline_instance(pi_uuid, src, dst, args):
219 # Fetch the pipeline instance record.
220 pi = src.pipeline_instances().get(uuid=pi_uuid).execute(num_retries=args.retries)
223 check_git_availability()
225 if not args.dst_git_repo:
226 abort('--dst-git-repo is required when copying a pipeline recursively.')
227 # Copy the pipeline template and save the copied template.
228 if pi.get('pipeline_template_uuid', None):
229 pt = copy_pipeline_template(pi['pipeline_template_uuid'],
232 # Copy input collections, docker images and git repos.
233 pi = copy_collections(pi, src, dst, args)
234 copy_git_repos(pi, src, dst, args.dst_git_repo, args)
235 copy_docker_images(pi, src, dst, args)
237 # Update the fields of the pipeline instance with the copied
239 if pi.get('pipeline_template_uuid', None):
240 pi['pipeline_template_uuid'] = pt['uuid']
244 logger.info("Copying only pipeline instance %s.", pi_uuid)
245 logger.info("You are responsible for making sure all pipeline dependencies have been updated.")
247 # Update the pipeline instance properties, and create the new
249 pi['properties']['copied_from_pipeline_instance_uuid'] = pi_uuid
250 pi['description'] = "Pipeline copied from {}\n\n{}".format(
252 pi['description'] if pi.get('description', None) else '')
254 pi['owner_uuid'] = args.project_uuid
258 new_pi = dst.pipeline_instances().create(body=pi, ensure_unique_name=True).execute(num_retries=args.retries)
261 # copy_pipeline_template(pt_uuid, src, dst, args)
263 # Copies a pipeline template identified by pt_uuid from src to dst.
265 # If args.recursive is True, also copy any collections, docker
266 # images and git repositories that this template references.
268 # The owner_uuid of the new template is changed to that of the user
269 # who copied the template.
271 # Returns the copied pipeline template object.
273 def copy_pipeline_template(pt_uuid, src, dst, args):
274 # fetch the pipeline template from the source instance
275 pt = src.pipeline_templates().get(uuid=pt_uuid).execute(num_retries=args.retries)
278 check_git_availability()
280 if not args.dst_git_repo:
281 abort('--dst-git-repo is required when copying a pipeline recursively.')
282 # Copy input collections, docker images and git repos.
283 pt = copy_collections(pt, src, dst, args)
284 copy_git_repos(pt, src, dst, args.dst_git_repo, args)
285 copy_docker_images(pt, src, dst, args)
287 pt['description'] = "Pipeline template copied from {}\n\n{}".format(
289 pt['description'] if pt.get('description', None) else '')
290 pt['name'] = "{} copied from {}".format(pt.get('name', ''), pt_uuid)
293 pt['owner_uuid'] = args.project_uuid
295 return dst.pipeline_templates().create(body=pt, ensure_unique_name=True).execute(num_retries=args.retries)
297 # copy_collections(obj, src, dst, args)
299 # Recursively copies all collections referenced by 'obj' from src
300 # to dst. obj may be a dict or a list, in which case we run
301 # copy_collections on every value it contains. If it is a string,
302 # search it for any substring that matches a collection hash or uuid
303 # (this will find hidden references to collections like
304 # "input0": "$(file 3229739b505d2b878b62aed09895a55a+142/HWI-ST1027_129_D0THKACXX.1_1.fastq)")
306 # Returns a copy of obj with any old collection uuids replaced by
309 def copy_collections(obj, src, dst, args):
311 def copy_collection_fn(collection_match):
312 """Helper function for regex substitution: copies a single collection,
313 identified by the collection_match MatchObject, to the
314 destination. Returns the destination collection uuid (or the
315 portable data hash if that's what src_id is).
318 src_id = collection_match.group(0)
319 if src_id not in collections_copied:
320 dst_col = copy_collection(src_id, src, dst, args)
321 if src_id in [dst_col['uuid'], dst_col['portable_data_hash']]:
322 collections_copied[src_id] = src_id
324 collections_copied[src_id] = dst_col['uuid']
325 return collections_copied[src_id]
327 if isinstance(obj, basestring):
328 # Copy any collections identified in this string to dst, replacing
329 # them with the dst uuids as necessary.
330 obj = arvados.util.portable_data_hash_pattern.sub(copy_collection_fn, obj)
331 obj = arvados.util.collection_uuid_pattern.sub(copy_collection_fn, obj)
333 elif isinstance(obj, dict):
334 return type(obj)((v, copy_collections(obj[v], src, dst, args))
336 elif isinstance(obj, list):
337 return type(obj)(copy_collections(v, src, dst, args) for v in obj)
340 def migrate_jobspec(jobspec, src, dst, dst_repo, args):
341 """Copy a job's script to the destination repository, and update its record.
343 Given a jobspec dictionary, this function finds the referenced script from
344 src and copies it to dst and dst_repo. It also updates jobspec in place to
345 refer to names on the destination.
347 repo = jobspec.get('repository')
350 # script_version is the "script_version" parameter from the source
351 # component or job. If no script_version was supplied in the
352 # component or job, it is a mistake in the pipeline, but for the
353 # purposes of copying the repository, default to "master".
354 script_version = jobspec.get('script_version') or 'master'
355 script_key = (repo, script_version)
356 if script_key not in scripts_copied:
357 copy_git_repo(repo, src, dst, dst_repo, script_version, args)
358 scripts_copied.add(script_key)
359 jobspec['repository'] = dst_repo
360 repo_dir = local_repo_dir[repo]
361 for version_key in ['script_version', 'supplied_script_version']:
362 if version_key in jobspec:
363 jobspec[version_key] = git_rev_parse(jobspec[version_key], repo_dir)
365 # copy_git_repos(p, src, dst, dst_repo, args)
367 # Copies all git repositories referenced by pipeline instance or
368 # template 'p' from src to dst.
370 # For each component c in the pipeline:
371 # * Copy git repositories named in c['repository'] and c['job']['repository'] if present
372 # * Rename script versions:
373 # * c['script_version']
374 # * c['job']['script_version']
375 # * c['job']['supplied_script_version']
376 # to the commit hashes they resolve to, since any symbolic
377 # names (tags, branches) are not preserved in the destination repo.
379 # The pipeline object is updated in place with the new repository
380 # names. The return value is undefined.
382 def copy_git_repos(p, src, dst, dst_repo, args):
383 for component in p['components'].itervalues():
384 migrate_jobspec(component, src, dst, dst_repo, args)
385 if 'job' in component:
386 migrate_jobspec(component['job'], src, dst, dst_repo, args)
388 def total_collection_size(manifest_text):
389 """Return the total number of bytes in this collection (excluding
390 duplicate blocks)."""
394 for line in manifest_text.splitlines():
396 for word in words[1:]:
398 loc = arvados.KeepLocator(word)
400 continue # this word isn't a locator, skip it
401 if loc.md5sum not in locators_seen:
402 locators_seen[loc.md5sum] = True
403 total_bytes += loc.size
407 def create_collection_from(c, src, dst, args):
408 """Create a new collection record on dst, and copy Docker metadata if
411 collection_uuid = c['uuid']
415 c['name'] = "copied from " + collection_uuid
417 if 'properties' in c:
420 c['owner_uuid'] = args.project_uuid
422 dst_collection = dst.collections().create(body=c, ensure_unique_name=True).execute(num_retries=args.retries)
424 # Create docker_image_repo+tag and docker_image_hash links
425 # at the destination.
426 for link_class in ("docker_image_repo+tag", "docker_image_hash"):
427 docker_links = src.links().list(filters=[["head_uuid", "=", collection_uuid], ["link_class", "=", link_class]]).execute(num_retries=args.retries)['items']
429 for src_link in docker_links:
430 body = {key: src_link[key]
431 for key in ['link_class', 'name', 'properties']}
432 body['head_uuid'] = dst_collection['uuid']
433 body['owner_uuid'] = args.project_uuid
435 lk = dst.links().create(body=body).execute(num_retries=args.retries)
436 logger.debug('created dst link {}'.format(lk))
438 return dst_collection
440 # copy_collection(obj_uuid, src, dst, args)
442 # Copies the collection identified by obj_uuid from src to dst.
443 # Returns the collection object created at dst.
445 # If args.progress is True, produce a human-friendly progress
448 # If a collection with the desired portable_data_hash already
449 # exists at dst, and args.force is False, copy_collection returns
450 # the existing collection without copying any blocks. Otherwise
451 # (if no collection exists or if args.force is True)
452 # copy_collection copies all of the collection data blocks from src
455 # For this application, it is critical to preserve the
456 # collection's manifest hash, which is not guaranteed with the
457 # arvados.CollectionReader and arvados.CollectionWriter classes.
458 # Copying each block in the collection manually, followed by
459 # the manifest block, ensures that the collection's manifest
460 # hash will not change.
462 def copy_collection(obj_uuid, src, dst, args):
463 if arvados.util.keep_locator_pattern.match(obj_uuid):
464 # If the obj_uuid is a portable data hash, it might not be uniquely
465 # identified with a particular collection. As a result, it is
466 # ambigious as to what name to use for the copy. Apply some heuristics
467 # to pick which collection to get the name from.
468 srccol = src.collections().list(
469 filters=[['portable_data_hash', '=', obj_uuid]],
470 order="created_at asc"
471 ).execute(num_retries=args.retries)
473 items = srccol.get("items")
476 logger.warning("Could not find collection with portable data hash %s", obj_uuid)
482 # There's only one collection with the PDH, so use that.
485 # See if there is a collection that's in the same project
486 # as the root item (usually a pipeline) being copied.
488 if i.get("owner_uuid") == src_owner_uuid and i.get("name"):
492 # Didn't find any collections located in the same project, so
493 # pick the oldest collection that has a name assigned to it.
499 # None of the collections have names (?!), so just pick the
503 # list() doesn't return manifest text (and we don't want it to,
504 # because we don't need the same maninfest text sent to us 50
505 # times) so go and retrieve the collection object directly
506 # which will include the manifest text.
507 c = src.collections().get(uuid=c["uuid"]).execute(num_retries=args.retries)
509 # Assume this is an actual collection uuid, so fetch it directly.
510 c = src.collections().get(uuid=obj_uuid).execute(num_retries=args.retries)
512 # If a collection with this hash already exists at the
513 # destination, and 'force' is not true, just return that
516 if 'portable_data_hash' in c:
517 colhash = c['portable_data_hash']
520 dstcol = dst.collections().list(
521 filters=[['portable_data_hash', '=', colhash]]
522 ).execute(num_retries=args.retries)
523 if dstcol['items_available'] > 0:
524 for d in dstcol['items']:
525 if ((args.project_uuid == d['owner_uuid']) and
526 (c.get('name') == d['name']) and
527 (c['portable_data_hash'] == d['portable_data_hash'])):
529 c['manifest_text'] = dst.collections().get(
530 uuid=dstcol['items'][0]['uuid']
531 ).execute(num_retries=args.retries)['manifest_text']
532 return create_collection_from(c, src, dst, args)
534 # Fetch the collection's manifest.
535 manifest = c['manifest_text']
536 logger.debug("Copying collection %s with manifest: <%s>", obj_uuid, manifest)
538 # Copy each block from src_keep to dst_keep.
539 # Use the newly signed locators returned from dst_keep to build
540 # a new manifest as we go.
541 src_keep = arvados.keep.KeepClient(api_client=src, num_retries=args.retries)
542 dst_keep = arvados.keep.KeepClient(api_client=dst, num_retries=args.retries)
546 bytes_expected = total_collection_size(manifest)
548 progress_writer = ProgressWriter(human_progress)
550 progress_writer = None
552 for line in manifest.splitlines():
554 dst_manifest += words[0]
555 for word in words[1:]:
557 loc = arvados.KeepLocator(word)
559 # If 'word' can't be parsed as a locator,
560 # presume it's a filename.
561 dst_manifest += ' ' + word
563 blockhash = loc.md5sum
564 # copy this block if we haven't seen it before
565 # (otherwise, just reuse the existing dst_locator)
566 if blockhash not in dst_locators:
567 logger.debug("Copying block %s (%s bytes)", blockhash, loc.size)
569 progress_writer.report(obj_uuid, bytes_written, bytes_expected)
570 data = src_keep.get(word)
571 dst_locator = dst_keep.put(data)
572 dst_locators[blockhash] = dst_locator
573 bytes_written += loc.size
574 dst_manifest += ' ' + dst_locators[blockhash]
578 progress_writer.report(obj_uuid, bytes_written, bytes_expected)
579 progress_writer.finish()
581 # Copy the manifest and save the collection.
582 logger.debug('saving %s with manifest: <%s>', obj_uuid, dst_manifest)
584 c['manifest_text'] = dst_manifest
585 return create_collection_from(c, src, dst, args)
587 def setup_git_http(url):
588 u = urlparse.urlsplit(url)
589 url = urlparse.urlunsplit((u.scheme, u.netloc, "", "", ""))
590 arvados.util.run_command(["git",
593 "credential.%s/.username" % url,
595 arvados.util.run_command(["git",
598 "credential.%s/.helper" % url,
599 """!cred(){ cat >/dev/null; if [ "$1" = get ]; then echo password=$ARVADOS_API_TOKEN; fi; };cred"""])
601 # copy_git_repo(src_git_repo, src, dst, dst_git_repo, script_version, args)
603 # Copies commits from git repository 'src_git_repo' on Arvados
604 # instance 'src' to 'dst_git_repo' on 'dst'. Both src_git_repo
605 # and dst_git_repo are repository names, not UUIDs (i.e. "arvados"
608 # All commits will be copied to a destination branch named for the
609 # source repository URL.
611 # The destination repository must already exist.
613 # The user running this command must be authenticated
614 # to both repositories.
616 def copy_git_repo(src_git_repo, src, dst, dst_git_repo, script_version, args):
617 # Identify the fetch and push URLs for the git repositories.
618 r = src.repositories().list(
619 filters=[['name', '=', src_git_repo]]).execute(num_retries=args.retries)
620 if r['items_available'] != 1:
621 raise Exception('cannot identify source repo {}; {} repos found'
622 .format(src_git_repo, r['items_available']))
624 http_url = [c for c in r['items'][0]['clone_urls'] if c.startswith("http")]
626 src_git_url = http_url[0]
627 setup_git_http(src_git_url)
629 src_git_url = r['items'][0]['fetch_url']
630 logger.debug('src_git_url: {}'.format(src_git_url))
632 r = dst.repositories().list(
633 filters=[['name', '=', dst_git_repo]]).execute(num_retries=args.retries)
634 if r['items_available'] != 1:
635 raise Exception('cannot identify destination repo {}; {} repos found'
636 .format(dst_git_repo, r['items_available']))
638 http_url = [c for c in r['items'][0]['clone_urls'] if c.startswith("http")]
640 dst_git_push_url = http_url[0]
641 setup_git_http(dst_git_push_url)
643 dst_git_push_url = r['items'][0]['push_url']
645 logger.debug('dst_git_push_url: {}'.format(dst_git_push_url))
647 dst_branch = re.sub(r'\W+', '_', "{}_{}".format(src_git_url, script_version))
649 # Copy git commits from src repo to dst repo.
650 if src_git_repo not in local_repo_dir:
651 local_repo_dir[src_git_repo] = tempfile.mkdtemp()
652 arvados.util.run_command(
653 ["git", "clone", "--bare", src_git_url,
654 local_repo_dir[src_git_repo]],
655 cwd=os.path.dirname(local_repo_dir[src_git_repo]),
656 env={"HOME": os.environ["HOME"],
657 "ARVADOS_API_TOKEN": src.api_token})
658 arvados.util.run_command(
659 ["git", "remote", "add", "dst", dst_git_push_url],
660 cwd=local_repo_dir[src_git_repo])
661 arvados.util.run_command(
662 ["git", "branch", dst_branch, script_version],
663 cwd=local_repo_dir[src_git_repo])
664 arvados.util.run_command(["git", "push", "dst", dst_branch],
665 cwd=local_repo_dir[src_git_repo],
666 env={"HOME": os.environ["HOME"],
667 "ARVADOS_API_TOKEN": dst.api_token})
669 def copy_docker_images(pipeline, src, dst, args):
670 """Copy any docker images named in the pipeline components'
671 runtime_constraints field from src to dst."""
673 logger.debug('copy_docker_images: {}'.format(pipeline['uuid']))
674 for c_name, c_info in pipeline['components'].iteritems():
675 if ('runtime_constraints' in c_info and
676 'docker_image' in c_info['runtime_constraints']):
678 c_info['runtime_constraints']['docker_image'],
679 c_info['runtime_constraints'].get('docker_image_tag', 'latest'),
683 def copy_docker_image(docker_image, docker_image_tag, src, dst, args):
684 """Copy the docker image identified by docker_image and
685 docker_image_tag from src to dst. Create appropriate
686 docker_image_repo+tag and docker_image_hash links at dst.
690 logger.debug('copying docker image {}:{}'.format(docker_image, docker_image_tag))
692 # Find the link identifying this docker image.
693 docker_image_list = arvados.commands.keepdocker.list_images_in_arv(
694 src, args.retries, docker_image, docker_image_tag)
695 if docker_image_list:
696 image_uuid, image_info = docker_image_list[0]
697 logger.debug('copying collection {} {}'.format(image_uuid, image_info))
699 # Copy the collection it refers to.
700 dst_image_col = copy_collection(image_uuid, src, dst, args)
701 elif arvados.util.keep_locator_pattern.match(docker_image):
702 dst_image_col = copy_collection(docker_image, src, dst, args)
704 logger.warning('Could not find docker image {}:{}'.format(docker_image, docker_image_tag))
706 # git_rev_parse(rev, repo)
708 # Returns the 40-character commit hash corresponding to 'rev' in
709 # git repository 'repo' (which must be the path of a local git
712 def git_rev_parse(rev, repo):
713 gitout, giterr = arvados.util.run_command(
714 ['git', 'rev-parse', rev], cwd=repo)
715 return gitout.strip()
717 # uuid_type(api, object_uuid)
719 # Returns the name of the class that object_uuid belongs to, based on
720 # the second field of the uuid. This function consults the api's
721 # schema to identify the object class.
723 # It returns a string such as 'Collection', 'PipelineInstance', etc.
725 # Special case: if handed a Keep locator hash, return 'Collection'.
727 def uuid_type(api, object_uuid):
728 if re.match(r'^[a-f0-9]{32}\+[0-9]+(\+[A-Za-z0-9+-]+)?$', object_uuid):
730 p = object_uuid.split('-')
733 for k in api._schema.schemas:
734 obj_class = api._schema.schemas[k].get('uuidPrefix', None)
735 if type_prefix == obj_class:
739 def abort(msg, code=1):
740 logger.info("arv-copy: %s", msg)
744 # Code for reporting on the progress of a collection upload.
745 # Stolen from arvados.commands.put.ArvPutCollectionWriter
746 # TODO(twp): figure out how to refactor into a shared library
747 # (may involve refactoring some arvados.commands.arv_copy.copy_collection
750 def machine_progress(obj_uuid, bytes_written, bytes_expected):
751 return "{} {}: {} {} written {} total\n".format(
756 -1 if (bytes_expected is None) else bytes_expected)
758 def human_progress(obj_uuid, bytes_written, bytes_expected):
760 return "\r{}: {}M / {}M {:.1%} ".format(
762 bytes_written >> 20, bytes_expected >> 20,
763 float(bytes_written) / bytes_expected)
765 return "\r{}: {} ".format(obj_uuid, bytes_written)
767 class ProgressWriter(object):
768 _progress_func = None
771 def __init__(self, progress_func):
772 self._progress_func = progress_func
774 def report(self, obj_uuid, bytes_written, bytes_expected):
775 if self._progress_func is not None:
777 self._progress_func(obj_uuid, bytes_written, bytes_expected))
780 self.outfile.write("\n")
782 if __name__ == '__main__':