X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/16b5f7275ffa2bd4347134f7269744f4cd4baa2a..7bdffdeb9ccec113d1d9b848423be60d85a501ed:/sdk/python/arvados/commands/arv_copy.py diff --git a/sdk/python/arvados/commands/arv_copy.py b/sdk/python/arvados/commands/arv_copy.py index 5f12b62eeb..7f5245db86 100755 --- a/sdk/python/arvados/commands/arv_copy.py +++ b/sdk/python/arvados/commands/arv_copy.py @@ -2,7 +2,7 @@ # # SPDX-License-Identifier: Apache-2.0 -# arv-copy [--recursive] [--no-recursive] object-uuid src dst +# arv-copy [--recursive] [--no-recursive] object-uuid # # Copies an object from Arvados instance src to instance dst. # @@ -30,10 +30,15 @@ import getpass import os import re import shutil +import subprocess import sys import logging import tempfile import urllib.parse +import io +import json +import queue +import threading import arvados import arvados.config @@ -41,9 +46,9 @@ import arvados.keep import arvados.util import arvados.commands._util as arv_cmd import arvados.commands.keepdocker +import arvados.http_to_keep import ruamel.yaml as yaml -from arvados.api import OrderedJsonModel from arvados._version import __version__ COMMIT_HASH_RE = re.compile(r'^[0-9a-f]{1,40}$') @@ -87,20 +92,28 @@ def main(): '-f', '--force', dest='force', action='store_true', help='Perform copy even if the object appears to exist at the remote destination.') copy_opts.add_argument( - '--src', dest='source_arvados', required=True, - 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.') + '--src', dest='source_arvados', + help='The cluster id of the source Arvados instance. May be either a pathname to a config file, or (for example) "foo" as shorthand for $HOME/.config/arvados/foo.conf. If not provided, will be inferred from the UUID of the object being copied.') copy_opts.add_argument( - '--dst', dest='destination_arvados', required=True, - 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.') + '--dst', dest='destination_arvados', + help='The name of the destination Arvados instance (required). May be either a pathname to a config file, or (for example) "foo" as shorthand for $HOME/.config/arvados/foo.conf. If not provided, will use ARVADOS_API_HOST from environment.') copy_opts.add_argument( '--recursive', dest='recursive', action='store_true', - help='Recursively copy any dependencies for this object. (default)') + help='Recursively copy any dependencies for this object, and subprojects. (default)') copy_opts.add_argument( '--no-recursive', dest='recursive', action='store_false', - 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.') + help='Do not copy any dependencies or subprojects.') copy_opts.add_argument( '--project-uuid', dest='project_uuid', help='The UUID of the project at the destination to which the collection or workflow should be copied.') + copy_opts.add_argument( + '--storage-classes', dest='storage_classes', + help='Comma separated list of storage classes to be used when saving data to the destinaton Arvados instance.') + copy_opts.add_argument("--varying-url-params", type=str, default="", + help="A comma separated list of URL query parameters that should be ignored when storing HTTP URLs in Keep.") + + copy_opts.add_argument("--prefer-cached-downloads", action="store_true", default=False, + help="If a HTTP URL is found in Keep, skip upstream URL freshness check (will not notice if the upstream has changed, but also not error if upstream is unavailable).") copy_opts.add_argument( 'object_uuid', @@ -109,46 +122,71 @@ def main(): copy_opts.set_defaults(recursive=True) parser = argparse.ArgumentParser( - description='Copy a workflow or collection from one Arvados instance to another.', + description='Copy a workflow, collection or project from one Arvados instance to another. On success, the uuid of the copied object is printed to stdout.', parents=[copy_opts, arv_cmd.retry_opt]) args = parser.parse_args() + if args.storage_classes: + args.storage_classes = [x for x in args.storage_classes.strip().replace(' ', '').split(',') if x] + if args.verbose: logger.setLevel(logging.DEBUG) else: logger.setLevel(logging.INFO) + if not args.source_arvados and arvados.util.uuid_pattern.match(args.object_uuid): + args.source_arvados = args.object_uuid[:5] + # Create API clients for the source and destination instances - src_arv = api_for_instance(args.source_arvados) - dst_arv = api_for_instance(args.destination_arvados) + src_arv = api_for_instance(args.source_arvados, args.retries) + dst_arv = api_for_instance(args.destination_arvados, args.retries) if not args.project_uuid: args.project_uuid = dst_arv.users().current().execute(num_retries=args.retries)["uuid"] # Identify the kind of object we have been given, and begin copying. t = uuid_type(src_arv, args.object_uuid) - if t == 'Collection': - set_src_owner_uuid(src_arv.collections(), args.object_uuid, args) - result = copy_collection(args.object_uuid, - src_arv, dst_arv, - args) - elif t == 'Workflow': - set_src_owner_uuid(src_arv.workflows(), args.object_uuid, args) - result = copy_workflow(args.object_uuid, src_arv, dst_arv, args) - else: - abort("cannot copy object {} of type {}".format(args.object_uuid, t)) + + try: + if t == 'Collection': + set_src_owner_uuid(src_arv.collections(), args.object_uuid, args) + result = copy_collection(args.object_uuid, + src_arv, dst_arv, + args) + elif t == 'Workflow': + set_src_owner_uuid(src_arv.workflows(), args.object_uuid, args) + result = copy_workflow(args.object_uuid, src_arv, dst_arv, args) + elif t == 'Group': + set_src_owner_uuid(src_arv.groups(), args.object_uuid, args) + result = copy_project(args.object_uuid, src_arv, dst_arv, args.project_uuid, args) + elif t == 'httpURL': + result = copy_from_http(args.object_uuid, src_arv, dst_arv, args) + else: + abort("cannot copy object {} of type {}".format(args.object_uuid, t)) + except Exception as e: + logger.error("%s", e, exc_info=args.verbose) + exit(1) # Clean up any outstanding temp git repositories. for d in listvalues(local_repo_dir): shutil.rmtree(d, ignore_errors=True) + if not result: + exit(1) + # If no exception was thrown and the response does not have an # error_token field, presume success - if 'error_token' in result or 'uuid' not in result: - logger.error("API server returned an error result: {}".format(result)) + if result is None or 'error_token' in result or 'uuid' not in result: + if result: + logger.error("API server returned an error result: {}".format(result)) + exit(1) + + print(result['uuid']) + + if result.get('partial_error'): + logger.warning("Warning: created copy with uuid {} but failed to copy some items: {}".format(result['uuid'], result['partial_error'])) exit(1) - logger.info("") logger.info("Success: created copy with uuid {}".format(result['uuid'])) exit(0) @@ -169,7 +207,11 @@ def set_src_owner_uuid(resource, uuid, args): # Otherwise, it is presumed to be the name of a file in # $HOME/.config/arvados/instance_name.conf # -def api_for_instance(instance_name): +def api_for_instance(instance_name, num_retries): + if not instance_name: + # Use environment + return arvados.api('v1') + if '/' in instance_name: config_file = instance_name else: @@ -192,7 +234,8 @@ def api_for_instance(instance_name): host=cfg['ARVADOS_API_HOST'], token=cfg['ARVADOS_API_TOKEN'], insecure=api_is_insecure, - model=OrderedJsonModel()) + num_retries=num_retries, + ) else: abort('need ARVADOS_API_HOST and ARVADOS_API_TOKEN for {}'.format(instance_name)) return client @@ -200,8 +243,12 @@ def api_for_instance(instance_name): # Check if git is available def check_git_availability(): try: - arvados.util.run_command(['git', '--help']) - except Exception: + subprocess.run( + ['git', '--version'], + check=True, + stdout=subprocess.DEVNULL, + ) + except FileNotFoundError: abort('git command is not available. Please ensure git is installed.') @@ -275,28 +322,43 @@ def copy_workflow(wf_uuid, src, dst, args): # fetch the workflow from the source instance wf = src.workflows().get(uuid=wf_uuid).execute(num_retries=args.retries) + if not wf["definition"]: + logger.warning("Workflow object {} has an empty or null definition, it won't do anything.".format(wf_uuid)) + # copy collections and docker images - if args.recursive: - wf_def = yaml.safe_load(wf["definition"]) - if wf_def is not None: - locations = [] - docker_images = {} - graph = wf_def.get('$graph', None) - if graph is not None: - workflow_collections(graph, locations, docker_images) - else: - workflow_collections(wf_def, locations, docker_images) + if args.recursive and wf["definition"]: + env = {"ARVADOS_API_HOST": urllib.parse.urlparse(src._rootDesc["rootUrl"]).netloc, + "ARVADOS_API_TOKEN": src.api_token, + "PATH": os.environ["PATH"]} + try: + result = subprocess.run(["arvados-cwl-runner", "--quiet", "--print-keep-deps", "arvwf:"+wf_uuid], + capture_output=True, env=env) + except FileNotFoundError: + no_arv_copy = True + else: + no_arv_copy = result.returncode == 2 - if locations: - copy_collections(locations, src, dst, args) + if no_arv_copy: + raise Exception('Copying workflows requires arvados-cwl-runner 2.7.1 or later to be installed in PATH.') + elif result.returncode != 0: + raise Exception('There was an error getting Keep dependencies from workflow using arvados-cwl-runner --print-keep-deps') - for image in docker_images: - copy_docker_image(image, docker_images[image], src, dst, args) + locations = json.loads(result.stdout) + + if locations: + copy_collections(locations, src, dst, args) # copy the workflow itself del wf['uuid'] wf['owner_uuid'] = args.project_uuid - return dst.workflows().create(body=wf).execute(num_retries=args.retries) + + existing = dst.workflows().list(filters=[["owner_uuid", "=", args.project_uuid], + ["name", "=", wf["name"]]]).execute() + if len(existing["items"]) == 0: + return dst.workflows().create(body=wf).execute(num_retries=args.retries) + else: + return dst.workflows().update(uuid=existing["items"][0]["uuid"], body=wf).execute(num_retries=args.retries) + def workflow_collections(obj, locations, docker_images): if isinstance(obj, dict): @@ -305,7 +367,7 @@ def workflow_collections(obj, locations, docker_images): if loc.startswith("keep:"): locations.append(loc[5:]) - docker_image = obj.get('dockerImageId', None) or obj.get('dockerPull', None) + docker_image = obj.get('dockerImageId', None) or obj.get('dockerPull', None) or obj.get('acrContainerImage', None) if docker_image is not None: ds = docker_image.split(":", 1) tag = ds[1] if len(ds)==2 else 'latest' @@ -392,6 +454,9 @@ def create_collection_from(c, src, dst, args): if not body["name"]: body['name'] = "copied from " + collection_uuid + if args.storage_classes: + body['storage_classes_desired'] = args.storage_classes + body['owner_uuid'] = args.project_uuid dst_collection = dst.collections().create(body=body, ensure_unique_name=True).execute(num_retries=args.retries) @@ -516,7 +581,7 @@ def copy_collection(obj_uuid, src, dst, args): # a new manifest as we go. src_keep = arvados.keep.KeepClient(api_client=src, num_retries=args.retries) dst_keep = arvados.keep.KeepClient(api_client=dst, num_retries=args.retries) - dst_manifest = "" + dst_manifest = io.StringIO() dst_locators = {} bytes_written = 0 bytes_expected = total_collection_size(manifest) @@ -525,39 +590,150 @@ def copy_collection(obj_uuid, src, dst, args): else: progress_writer = None + # go through the words + # put each block loc into 'get' queue + # 'get' threads get block and put it into 'put' queue + # 'put' threads put block and then update dst_locators + # + # after going through the whole manifest we go back through it + # again and build dst_manifest + + lock = threading.Lock() + + # the get queue should be unbounded because we'll add all the + # block hashes we want to get, but these are small + get_queue = queue.Queue() + + threadcount = 4 + + # the put queue contains full data blocks + # and if 'get' is faster than 'put' we could end up consuming + # a great deal of RAM if it isn't bounded. + put_queue = queue.Queue(threadcount) + transfer_error = [] + + def get_thread(): + while True: + word = get_queue.get() + if word is None: + put_queue.put(None) + get_queue.task_done() + return + + blockhash = arvados.KeepLocator(word).md5sum + with lock: + if blockhash in dst_locators: + # Already uploaded + get_queue.task_done() + continue + + try: + logger.debug("Getting block %s", word) + data = src_keep.get(word) + put_queue.put((word, data)) + except e: + logger.error("Error getting block %s: %s", word, e) + transfer_error.append(e) + try: + # Drain the 'get' queue so we end early + while True: + get_queue.get(False) + get_queue.task_done() + except queue.Empty: + pass + finally: + get_queue.task_done() + + def put_thread(): + nonlocal bytes_written + while True: + item = put_queue.get() + if item is None: + put_queue.task_done() + return + + word, data = item + loc = arvados.KeepLocator(word) + blockhash = loc.md5sum + with lock: + if blockhash in dst_locators: + # Already uploaded + put_queue.task_done() + continue + + try: + logger.debug("Putting block %s (%s bytes)", blockhash, loc.size) + dst_locator = dst_keep.put(data, classes=(args.storage_classes or [])) + with lock: + dst_locators[blockhash] = dst_locator + bytes_written += loc.size + if progress_writer: + progress_writer.report(obj_uuid, bytes_written, bytes_expected) + except e: + logger.error("Error putting block %s (%s bytes): %s", blockhash, loc.size, e) + try: + # Drain the 'get' queue so we end early + while True: + get_queue.get(False) + get_queue.task_done() + except queue.Empty: + pass + transfer_error.append(e) + finally: + put_queue.task_done() + + for line in manifest.splitlines(): + words = line.split() + for word in words[1:]: + try: + loc = arvados.KeepLocator(word) + except ValueError: + # If 'word' can't be parsed as a locator, + # presume it's a filename. + continue + + get_queue.put(word) + + for i in range(0, threadcount): + get_queue.put(None) + + for i in range(0, threadcount): + threading.Thread(target=get_thread, daemon=True).start() + + for i in range(0, threadcount): + threading.Thread(target=put_thread, daemon=True).start() + + get_queue.join() + put_queue.join() + + if len(transfer_error) > 0: + return {"error_token": "Failed to transfer blocks"} + for line in manifest.splitlines(): words = line.split() - dst_manifest += words[0] + dst_manifest.write(words[0]) for word in words[1:]: try: loc = arvados.KeepLocator(word) except ValueError: # If 'word' can't be parsed as a locator, # presume it's a filename. - dst_manifest += ' ' + word + dst_manifest.write(' ') + dst_manifest.write(word) continue blockhash = loc.md5sum - # copy this block if we haven't seen it before - # (otherwise, just reuse the existing dst_locator) - if blockhash not in dst_locators: - logger.debug("Copying block %s (%s bytes)", blockhash, loc.size) - if progress_writer: - progress_writer.report(obj_uuid, bytes_written, bytes_expected) - data = src_keep.get(word) - dst_locator = dst_keep.put(data) - dst_locators[blockhash] = dst_locator - bytes_written += loc.size - dst_manifest += ' ' + dst_locators[blockhash] - dst_manifest += "\n" + dst_manifest.write(' ') + dst_manifest.write(dst_locators[blockhash]) + dst_manifest.write("\n") if progress_writer: progress_writer.report(obj_uuid, bytes_written, bytes_expected) progress_writer.finish() # Copy the manifest and save the collection. - logger.debug('saving %s with manifest: <%s>', obj_uuid, dst_manifest) + logger.debug('saving %s with manifest: <%s>', obj_uuid, dst_manifest.getvalue()) - c['manifest_text'] = dst_manifest + c['manifest_text'] = dst_manifest.getvalue() return create_collection_from(c, src, dst, args) def select_git_url(api, repo_name, retries, allow_insecure_http, allow_insecure_http_opt): @@ -573,8 +749,6 @@ def select_git_url(api, repo_name, retries, allow_insecure_http, allow_insecure_ priority = https_url + other_url + http_url - git_config = [] - git_url = None for url in priority: if url.startswith("http"): u = urllib.parse.urlsplit(url) @@ -586,17 +760,22 @@ def select_git_url(api, repo_name, retries, allow_insecure_http, allow_insecure_ try: logger.debug("trying %s", url) - arvados.util.run_command(["git"] + git_config + ["ls-remote", url], - env={"HOME": os.environ["HOME"], - "ARVADOS_API_TOKEN": api.api_token, - "GIT_ASKPASS": "/bin/false"}) - except arvados.errors.CommandFailedError: + subprocess.run( + ['git', *git_config, 'ls-remote', url], + check=True, + env={ + 'ARVADOS_API_TOKEN': api.api_token, + 'GIT_ASKPASS': '/bin/false', + 'HOME': os.environ['HOME'], + }, + stdout=subprocess.DEVNULL, + ) + except subprocess.CalledProcessError: pass else: git_url = url break - - if not git_url: + else: raise Exception('Cannot access git repository, tried {}' .format(priority)) @@ -632,6 +811,56 @@ def copy_docker_image(docker_image, docker_image_tag, src, dst, args): else: logger.warning('Could not find docker image {}:{}'.format(docker_image, docker_image_tag)) +def copy_project(obj_uuid, src, dst, owner_uuid, args): + + src_project_record = src.groups().get(uuid=obj_uuid).execute(num_retries=args.retries) + + # Create/update the destination project + existing = dst.groups().list(filters=[["owner_uuid", "=", owner_uuid], + ["name", "=", src_project_record["name"]]]).execute(num_retries=args.retries) + if len(existing["items"]) == 0: + project_record = dst.groups().create(body={"group": {"group_class": "project", + "owner_uuid": owner_uuid, + "name": src_project_record["name"]}}).execute(num_retries=args.retries) + else: + project_record = existing["items"][0] + + dst.groups().update(uuid=project_record["uuid"], + body={"group": { + "description": src_project_record["description"]}}).execute(num_retries=args.retries) + + args.project_uuid = project_record["uuid"] + + logger.debug('Copying %s to %s', obj_uuid, project_record["uuid"]) + + + partial_error = "" + + # Copy collections + try: + copy_collections([col["uuid"] for col in arvados.util.keyset_list_all(src.collections().list, filters=[["owner_uuid", "=", obj_uuid]])], + src, dst, args) + except Exception as e: + partial_error += "\n" + str(e) + + # Copy workflows + for w in arvados.util.keyset_list_all(src.workflows().list, filters=[["owner_uuid", "=", obj_uuid]]): + try: + copy_workflow(w["uuid"], src, dst, args) + except Exception as e: + partial_error += "\n" + "Error while copying %s: %s" % (w["uuid"], e) + + if args.recursive: + for g in arvados.util.keyset_list_all(src.groups().list, filters=[["owner_uuid", "=", obj_uuid]]): + try: + copy_project(g["uuid"], src, dst, project_record["uuid"], args) + except Exception as e: + partial_error += "\n" + "Error while copying %s: %s" % (g["uuid"], e) + + project_record["partial_error"] = partial_error + + return project_record + # git_rev_parse(rev, repo) # # Returns the 40-character commit hash corresponding to 'rev' in @@ -639,9 +868,14 @@ def copy_docker_image(docker_image, docker_image_tag, src, dst, args): # repository) # def git_rev_parse(rev, repo): - gitout, giterr = arvados.util.run_command( - ['git', 'rev-parse', rev], cwd=repo) - return gitout.strip() + proc = subprocess.run( + ['git', 'rev-parse', rev], + check=True, + cwd=repo, + stdout=subprocess.PIPE, + text=True, + ) + return proc.stdout.read().strip() # uuid_type(api, object_uuid) # @@ -654,8 +888,12 @@ def git_rev_parse(rev, repo): # Special case: if handed a Keep locator hash, return 'Collection'. # def uuid_type(api, object_uuid): - if re.match(r'^[a-f0-9]{32}\+[0-9]+(\+[A-Za-z0-9+-]+)?$', object_uuid): + if re.match(arvados.util.keep_locator_pattern, object_uuid): return 'Collection' + + if object_uuid.startswith("http:") or object_uuid.startswith("https:"): + return 'httpURL' + p = object_uuid.split('-') if len(p) == 3: type_prefix = p[1] @@ -665,6 +903,27 @@ def uuid_type(api, object_uuid): return k return None + +def copy_from_http(url, src, dst, args): + + project_uuid = args.project_uuid + varying_url_params = args.varying_url_params + prefer_cached_downloads = args.prefer_cached_downloads + + cached = arvados.http_to_keep.check_cached_url(src, project_uuid, url, {}, + varying_url_params=varying_url_params, + prefer_cached_downloads=prefer_cached_downloads) + if cached[2] is not None: + return copy_collection(cached[2], src, dst, args) + + cached = arvados.http_to_keep.http_to_keep(dst, project_uuid, url, + varying_url_params=varying_url_params, + prefer_cached_downloads=prefer_cached_downloads) + + if cached is not None: + return {"uuid": cached[2]} + + def abort(msg, code=1): logger.info("arv-copy: %s", msg) exit(code)