[ARVADOS] updated: fd42d69ffa558918ec40f9aeaceb2cbf93de1e8a
Git user
git at public.curoverse.com
Mon Mar 20 09:40:45 EDT 2017
Summary of changes:
sdk/python/arvados/commands/migrate19.py | 204 +++++++++++++++++++++++++++++++
1 file changed, 204 insertions(+)
create mode 100644 sdk/python/arvados/commands/migrate19.py
via fd42d69ffa558918ec40f9aeaceb2cbf93de1e8a (commit)
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commit fd42d69ffa558918ec40f9aeaceb2cbf93de1e8a
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Mar 20 09:36:17 2017 -0400
8567: Add migrate19
diff --git a/sdk/python/arvados/commands/migrate19.py b/sdk/python/arvados/commands/migrate19.py
new file mode 100644
index 0000000..e75095b
--- /dev/null
+++ b/sdk/python/arvados/commands/migrate19.py
@@ -0,0 +1,204 @@
+import argparse
+import time
+import sys
+import logging
+import shutil
+import tempfile
+import os
+import subprocess
+import re
+
+import arvados
+import arvados.commands.keepdocker
+from arvados._version import __version__
+from arvados.collection import CollectionReader
+
+logger = logging.getLogger('arvados.migrate-docker19')
+logger.setLevel(logging.DEBUG if arvados.config.get('ARVADOS_DEBUG')
+ else logging.INFO)
+
+_migration_link_class = 'docker_image_migration'
+_migration_link_name = 'migrate_1.9_1.10'
+
+class MigrationFailed(Exception):
+ pass
+
+def main(arguments=None):
+ """Docker image format migration tool for Arvados.
+
+ This converts Docker images stored in Arvados from image format v1
+ (Docker <= 1.9) to image format v2 (Docker >= 1.10).
+
+ Requires Docker running on the local host.
+
+ Usage:
+
+ 1) Run arvados/docker/migrate-docker19/build.sh to create
+ arvados/migrate-docker19 Docker image.
+
+ 2) Set ARVADOS_API_HOST and ARVADOS_API_TOKEN to the cluster you want to migrate.
+
+ 3) Run arv-migrate-docker19 from the Arvados Python SDK on the host (not in a container).
+
+ This will query Arvados for v1 format Docker images. For each image that
+ does not already have a corresponding v2 format image (as indicated by a
+ docker_image_migration tag) it will perform the following process:
+
+ i) download the image from Arvados
+ ii) load it into Docker
+ iii) update the Docker version, which updates the image
+ iv) save the v2 format image and upload to Arvados
+ v) create a migration link
+
+ """
+
+ migrate19_parser = argparse.ArgumentParser()
+ migrate19_parser.add_argument(
+ '--version', action='version', version="%s %s" % (sys.argv[0], __version__),
+ help='Print version and exit.')
+
+ exgroup = migrate19_parser.add_mutually_exclusive_group()
+ exgroup.add_argument(
+ '--dry-run', action='store_true', help="Print number of pending migrations.")
+ exgroup.add_argument(
+ '--print-unmigrated', action='store_true',
+ default=False, help="Print list of images needing migration.")
+
+ migrate19_parser.add_argument('infile', nargs='?', type=argparse.FileType('r'),
+ default=None, help="List of images to be migrated")
+
+ args = migrate19_parser.parse_args(arguments)
+
+ only_migrate = None
+ if args.infile:
+ only_migrate = set()
+ for l in args.infile:
+ only_migrate.add(l.strip())
+
+ api_client = arvados.api()
+
+ user = api_client.users().current().execute()
+ if not user['is_admin']:
+ raise Exception("This command requires an admin token")
+ sys_uuid = user['uuid'][:12] + '000000000000000'
+
+ images = arvados.commands.keepdocker.list_images_in_arv(api_client, 3)
+
+ is_new = lambda img: img['dockerhash'].startswith('sha256:')
+
+ count_new = 0
+ old_images = []
+ for uuid, img in images:
+ if img["dockerhash"].startswith("sha256:"):
+ continue
+ key = (img["repo"], img["tag"], img["timestamp"])
+ old_images.append(img)
+
+ migration_links = arvados.util.list_all(api_client.links().list, filters=[
+ ['link_class', '=', _migration_link_class],
+ ['name', '=', _migration_link_name],
+ ])
+
+ already_migrated = set()
+ for m in migration_links:
+ already_migrated.add(m["tail_uuid"])
+
+ items = arvados.util.list_all(api_client.collections().list,
+ filters=[["uuid", "in", [img["collection"] for img in old_images]]],
+ select=["uuid", "portable_data_hash"])
+ uuid_to_pdh = {i["uuid"]: i["portable_data_hash"] for i in items}
+
+ need_migrate = {}
+ for img in old_images:
+ pdh = uuid_to_pdh[img["collection"]]
+ if pdh not in already_migrated and (only_migrate is None or pdh in only_migrate):
+ need_migrate[pdh] = img
+
+ if args.print_unmigrated:
+ only_migrate = set()
+ for pdh in need_migrate:
+ print pdh
+ return
+
+ logger.info("Already migrated %i images", len(already_migrated))
+ logger.info("Need to migrate %i images", len(need_migrate))
+
+ if args.dry_run:
+ return
+
+ success = []
+ failures = []
+ count = 1
+ for old_image in need_migrate.values():
+ if uuid_to_pdh[old_image["collection"]] in already_migrated:
+ continue
+
+ logger.info("[%i/%i] Migrating %s:%s (%s)", count, len(need_migrate), old_image["repo"], old_image["tag"], old_image["collection"])
+ count += 1
+ start = time.time()
+
+ oldcol = CollectionReader(old_image["collection"])
+ tarfile = oldcol.keys()[0]
+
+ varlibdocker = tempfile.mkdtemp()
+ try:
+ with tempfile.NamedTemporaryFile() as envfile:
+ envfile.write("ARVADOS_API_HOST=%s\n" % (os.environ["ARVADOS_API_HOST"]))
+ envfile.write("ARVADOS_API_TOKEN=%s\n" % (os.environ["ARVADOS_API_TOKEN"]))
+ if "ARVADOS_API_HOST_INSECURE" in os.environ:
+ envfile.write("ARVADOS_API_HOST_INSECURE=%s\n" % (os.environ["ARVADOS_API_HOST_INSECURE"]))
+ envfile.flush()
+
+ dockercmd = ["docker", "run",
+ "--privileged",
+ "--rm",
+ "--env-file", envfile.name,
+ "--volume", "%s:/var/lib/docker" % varlibdocker,
+ "arvados/migrate-docker19",
+ "/root/migrate.sh",
+ "%s/%s" % (old_image["collection"], tarfile),
+ tarfile[0:40],
+ old_image["repo"],
+ old_image["tag"],
+ oldcol.api_response()["owner_uuid"]]
+
+ proc = subprocess.Popen(dockercmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ out, err = proc.communicate()
+
+ if proc.returncode != 0:
+ logger.error("Failed with return code %i", proc.returncode)
+ logger.error("--- Stdout ---\n%s", out)
+ logger.error("--- Stderr ---\n%s", err)
+ raise MigrationFailed()
+
+ migrated = re.search(r"Migrated uuid is ([a-z0-9]{5}-[a-z0-9]{5}-[a-z0-9]{15})", out)
+ if migrated:
+ newcol = CollectionReader(migrated.group(1))
+
+ api_client.links().create(body={"link": {
+ 'owner_uuid': sys_uuid,
+ 'link_class': _migration_link_class,
+ 'name': _migration_link_name,
+ 'tail_uuid': oldcol.portable_data_hash(),
+ 'head_uuid': newcol.portable_data_hash()
+ }}).execute(num_retries=3)
+
+ logger.info("Migrated '%s' (%s) to '%s' (%s) in %is",
+ oldcol.portable_data_hash(), old_image["collection"],
+ newcol.portable_data_hash(), migrated.group(1),
+ time.time() - start)
+ already_migrated.add(oldcol.portable_data_hash())
+ success.append(old_image["collection"])
+ else:
+ logger.error("Error migrating '%s'", old_image["collection"])
+ failures.append(old_image["collection"])
+ except Exception as e:
+ logger.error("Failed to migrate %s in %is", old_image["collection"], time.time() - start,
+ exc_info=(not isinstance(e, MigrationFailed)))
+ failures.append(old_image["collection"])
+ finally:
+ shutil.rmtree(varlibdocker)
+
+ logger.info("Successfully migrated %i images", len(success))
+ if failures:
+ logger.error("Failed to migrate %i images", len(failures))
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