[ARVADOS] updated: 8eeb2671b0a9815345218da335731a31230ada13
git at public.curoverse.com
git at public.curoverse.com
Mon Sep 8 16:54:52 EDT 2014
Summary of changes:
sdk/python/arvados/commands/keepdocker.py | 34 ++++----
sdk/python/arvados/commands/put.py | 124 ++++++++++++++----------------
sdk/python/arvados/util.py | 7 ++
sdk/python/tests/test_arv_put.py | 91 ++++------------------
4 files changed, 95 insertions(+), 161 deletions(-)
via 8eeb2671b0a9815345218da335731a31230ada13 (commit)
from b6017f4edc19188fa26f74ff0da2bedb94841dcf (commit)
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commit 8eeb2671b0a9815345218da335731a31230ada13
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Sep 8 16:54:49 2014 -0400
3453: Refactored arv-put to remove support for name links, correctly use
ensure_name_unique to prevent name collisions. arv-keepdocker should now
correctly handle cases where the user provides a image hash instead of
repository/tag. Fixed tests.
diff --git a/sdk/python/arvados/commands/keepdocker.py b/sdk/python/arvados/commands/keepdocker.py
index df13a94..c96e2cb 100644
--- a/sdk/python/arvados/commands/keepdocker.py
+++ b/sdk/python/arvados/commands/keepdocker.py
@@ -9,7 +9,6 @@ import subprocess
import sys
import tarfile
import tempfile
-import textwrap
from collections import namedtuple
from stat import *
@@ -193,7 +192,7 @@ def list_images_in_arv():
fmt = "{:30} {:10} {:12} {:29} {:20}"
print fmt.format("REPOSITORY", "TAG", "IMAGE ID", "COLLECTION", "CREATED")
for i, j in st:
- print(fmt.format(j["repo"], j["tag"], j["dockerhash"][0:11], i, j["timestamp"].strftime("%c")))
+ print(fmt.format(j["repo"], j["tag"], j["dockerhash"][0:12], i, j["timestamp"].strftime("%c")))
def main(arguments=None):
args = arg_parser.parse_args(arguments)
@@ -213,10 +212,13 @@ def main(arguments=None):
print >>sys.stderr, "arv-keepdocker:", error.message
sys.exit(1)
- image_repo_tag = '{}:{}'.format(args.image, args.tag)
+ image_repo_tag = '{}:{}'.format(args.image, args.tag) if not image_hash.startswith(args.image.lower()) else None
if args.name is None:
- collection_name = 'Docker image {} {}'.format(image_repo_tag, image_hash[0:11])
+ if image_repo_tag:
+ collection_name = 'Docker image {} {}'.format(image_repo_tag, image_hash[0:12])
+ else:
+ collection_name = 'Docker image {}'.format(image_hash[0:12])
else:
collection_name = args.name
@@ -235,45 +237,45 @@ def main(arguments=None):
if existing_links:
# get readable collections
collections = api.collections().list(
- filters=[['uuid', 'in', [link['head_uuid'] for link in existing_links]]],
+ filters=[['uuid', 'in', [link['head_uuid'] for link in existing_links]]],
select=["uuid", "owner_uuid", "name", "manifest_text"]).execute()['items']
if collections:
# check for repo+tag links on these collections
- existing_repo_tag = api.links().list(
+ existing_repo_tag = (api.links().list(
filters=[['link_class', '=', 'docker_image_repo+tag'],
['name', '=', image_repo_tag],
- ['head_uuid', 'in', collections]]).execute()['items']
+ ['head_uuid', 'in', collections]]).execute()['items']) if image_repo_tag else []
# Filter on elements owned by the parent project
owned_col = [c for c in collections if c['owner_uuid'] == parent_project_uuid]
- owned_img = [c for c in existing_links if c['owner_uuid'] == parent_project_uuid]
- owned_rep = [c for c in existing_repo_tag if c['owner_uuid'] == parent_project_uuid]
+ owned_img = [c for c in existing_links if c['owner_uuid'] == parent_project_uuid]
+ owned_rep = [c for c in existing_repo_tag if c['owner_uuid'] == parent_project_uuid]
if owned_col:
# already have a collection owned by this project
coll_uuid = owned_col[0]['uuid']
else:
# create new collection owned by the project
- coll_uuid = api.collections().create(body={"manifest_text": collections[0]['manifest_text'],
- "name": collection_name,
- "owner_uuid": parent_project_uuid},
+ coll_uuid = api.collections().create(body={"manifest_text": collections[0]['manifest_text'],
+ "name": collection_name,
+ "owner_uuid": parent_project_uuid},
ensure_unique_name=True).execute()['uuid']
- link_base = {'owner_uuid': parent_project_uuid,
+ link_base = {'owner_uuid': parent_project_uuid,
'head_uuid': coll_uuid }
if not owned_img:
# create image link owned by the project
make_link('docker_image_hash', image_hash, **link_base)
- if not owned_rep:
+ if not owned_rep and image_repo_tag:
# create repo+tag link owned by the project
make_link('docker_image_repo+tag', image_repo_tag, **link_base)
print(coll_uuid)
- sys.exit(0)
+ sys.exit(0)
# Open a file for the saved image, and write it if needed.
outfile_name = '{}.tar'.format(image_hash)
@@ -305,7 +307,7 @@ def main(arguments=None):
link_base['owner_uuid'] = args.project_uuid
make_link('docker_image_hash', image_hash, **link_base)
- if not image_hash.startswith(args.image.lower()):
+ if image_repo_tag:
make_link('docker_image_repo+tag', image_repo_tag,
**link_base)
diff --git a/sdk/python/arvados/commands/put.py b/sdk/python/arvados/commands/put.py
index ed405dc..0645cb4 100644
--- a/sdk/python/arvados/commands/put.py
+++ b/sdk/python/arvados/commands/put.py
@@ -348,44 +348,18 @@ def progress_writer(progress_func, outfile=sys.stderr):
def exit_signal_handler(sigcode, frame):
sys.exit(-sigcode)
-def check_project_exists(project_uuid):
- try:
- api_client.groups().get(uuid=project_uuid).execute()
- except (apiclient.errors.Error, arvados.errors.NotFoundError) as error:
- raise ValueError("Project {} not found ({})".format(project_uuid,
- error))
+def check_project_exists(api_client, project_uuid):
+ if project_uuid:
+ if arvados.util.user_uuid_pattern.match(project_uuid):
+ api_client.users().get(uuid=project_uuid).execute()
+ return project_uuid
+ elif arvados.util.group_uuid_pattern.match(project_uuid):
+ api_client.groups().get(uuid=project_uuid).execute()
+ return project_uuid
+ else:
+ raise Exception("Not a valid project uuid: {}".format(project_uuid))
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'] = api_client.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 api_client.links().create(body=link).execute()
+ return api_client.users().current().execute()['uuid']
def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
global api_client
@@ -394,11 +368,29 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
status = 0
args = parse_arguments(arguments)
+
+ # Determine the name to use
+ if args.name:
+ if args.stream or args.raw:
+ print >>stderr, "Cannot use --name with --stream or --raw"
+ sys.exit(1)
+ collection_name = args.name
+ else:
+ collection_name = "Saved at {} by {}@{}".format(
+ datetime.datetime.utcnow().strftime("%Y-%m-%d %H:%M:%S UTC"),
+ pwd.getpwuid(os.getuid()).pw_name,
+ socket.gethostname())
+
+ if args.project_uuid and (args.stream or args.raw):
+ print >>stderr, "Cannot use --project-uuid with --stream or --raw"
+ sys.exit(1)
+
+ # Determine the parent project
try:
- project_link = prep_project_link(args, stderr)
- except ValueError as error:
- print >>stderr, "arv-put: {}.".format(error)
- sys.exit(2)
+ project_uuid = check_project_exists(api_client, args.project_uuid)
+ except Exception as error:
+ print >>stderr, "Project {} not found: {}".format(args.project_uuid, error)
+ sys.exit(1)
if args.progress:
reporter = progress_writer(human_progress)
@@ -455,33 +447,29 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr):
elif args.raw:
output = ','.join(writer.data_locators())
else:
- # Register the resulting collection in Arvados.
- collection = api_client.collections().create(
- body={
- 'manifest_text': writer.manifest_text(),
- 'owner_uuid': project_link['tail_uuid']
- },
- ensure_unique_name=True
- ).execute()
-
- if args.portable_data_hash and 'portable_data_hash' in collection and collection['portable_data_hash']:
- output = collection['portable_data_hash']
- else:
- output = collection['uuid']
-
- if project_link is not None:
- # Update collection name
- try:
- if 'name' in collection:
- arvados.api().collections().update(uuid=collection['uuid'],
- body={"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
+ 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()
+
+ 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']
+ else:
+ output = collection['uuid']
+
+ except apiclient.errors.Error as error:
+ print >>stderr, (
+ "arv-put: Error adding Collection to project: {}.".format(
+ error))
+ status = 1
# Print the locator (uuid) of the new collection.
stdout.write(output)
diff --git a/sdk/python/arvados/util.py b/sdk/python/arvados/util.py
index 22a7427..47d1d5c 100644
--- a/sdk/python/arvados/util.py
+++ b/sdk/python/arvados/util.py
@@ -9,6 +9,13 @@ from arvados.collection import *
HEX_RE = re.compile(r'^[0-9a-fA-F]+$')
+portable_data_hash_pattern = re.compile(r'[0-9a-f]{32}\+\d+')
+uuid_pattern = re.compile(r'[a-z0-9]{5}-[a-z0-9]{5}-[a-z0-9]{15}')
+collection_uuid_pattern = re.compile(r'[a-z0-9]{5}-4zz18-[a-z0-9]{15}')
+group_uuid_pattern = re.compile(r'[a-z0-9]{5}-j7d0g-[a-z0-9]{15}')
+user_uuid_pattern = re.compile(r'[a-z0-9]{5}-tpzed-[a-z0-9]{15}')
+link_uuid_pattern = re.compile(r'[a-z0-9]{5}-o0j2j-[a-z0-9]{15}')
+
def clear_tmpdir(path=None):
"""
Ensure the given directory (or TASK_TMPDIR if none given)
diff --git a/sdk/python/tests/test_arv_put.py b/sdk/python/tests/test_arv_put.py
index 0ce51af..3b0ee13 100644
--- a/sdk/python/tests/test_arv_put.py
+++ b/sdk/python/tests/test_arv_put.py
@@ -326,82 +326,9 @@ class ArvadosPutReportTest(ArvadosBaseTestCase):
arv_put.human_progress(count, None)))
-class ArvadosPutProjectLinkTest(ArvadosBaseTestCase):
- Z_UUID = 'zzzzz-zzzzz-zzzzzzzzzzzzzzz'
-
- def setUp(self):
- self.stderr = StringIO()
- super(ArvadosPutProjectLinkTest, self).setUp()
-
- def tearDown(self):
- self.stderr.close()
- super(ArvadosPutProjectLinkTest, self).tearDown()
-
- def prep_link_from_arguments(self, args, uuid_found=True):
- try:
- link = arv_put.prep_project_link(arv_put.parse_arguments(args),
- self.stderr,
- lambda uuid: uuid_found)
- finally:
- self.stderr.seek(0)
- return link
-
- def check_link(self, link, project_uuid, link_name=None):
- self.assertEqual(project_uuid, link.get('tail_uuid'))
- self.assertEqual(project_uuid, link.get('owner_uuid'))
- self.assertEqual('name', link.get('link_class'))
- if link_name is None:
- self.assertNotIn('name', link)
- else:
- self.assertEqual(link_name, link.get('name'))
- self.assertNotIn('head_uuid', link)
-
- def check_stderr_empty(self):
- self.assertEqual('', self.stderr.getvalue())
-
- def test_project_link_with_name(self):
- link = self.prep_link_from_arguments(['--project-uuid', self.Z_UUID,
- '--name', 'test link AAA'])
- self.check_link(link, self.Z_UUID, 'test link AAA')
- self.check_stderr_empty()
-
- def test_project_link_without_name(self):
- username = pwd.getpwuid(os.getuid()).pw_name
- link = self.prep_link_from_arguments(['--project-uuid', self.Z_UUID])
- self.assertIsNotNone(link.get('name', None))
- self.assertRegexpMatches(
- link['name'],
- r'^Saved at .* by {}@'.format(re.escape(username)))
- self.check_link(link, self.Z_UUID, link.get('name', None))
- for line in self.stderr:
- if "No --name specified" in line:
- break
- else:
- self.fail("no warning emitted about the lack of collection name")
-
- @unittest.skip("prep_project_link needs an API lookup for this case")
- def test_collection_without_project_defaults_to_home(self):
- link = self.prep_link_from_arguments(['--name', 'test link BBB'])
- self.check_link(link, self.Z_UUID)
- self.check_stderr_empty()
-
- def test_no_link_or_warning_with_no_collection(self):
- self.assertIsNone(self.prep_link_from_arguments(['--raw']))
- self.check_stderr_empty()
-
- def test_error_when_project_not_found(self):
- self.assertRaises(ValueError,
- self.prep_link_from_arguments,
- ['--project-uuid', self.Z_UUID], False)
-
- def test_link_without_collection_is_error(self):
- self.assertRaises(ValueError,
- self.prep_link_from_arguments,
- ['--project-uuid', self.Z_UUID, '--stream'])
-
-
class ArvadosPutTest(run_test_server.TestCaseWithServers, ArvadosBaseTestCase):
MAIN_SERVER = {}
+ Z_UUID = 'zzzzz-zzzzz-zzzzzzzzzzzzzzz'
def call_main_with_args(self, args):
self.main_stdout = StringIO()
@@ -454,11 +381,21 @@ class ArvadosPutTest(run_test_server.TestCaseWithServers, ArvadosBaseTestCase):
arv_put.ResumeCache.CACHE_DIR = orig_cachedir
os.chmod(cachedir, 0o700)
- def test_link_without_collection_aborts(self):
+ def test_error_name_without_collection(self):
self.assertRaises(SystemExit, self.call_main_with_args,
['--name', 'test without Collection',
'--stream', '/dev/null'])
+ def test_error_when_project_not_found(self):
+ self.assertRaises(SystemExit,
+ self.call_main_with_args,
+ ['--project-uuid', self.Z_UUID])
+
+ def test_error_bad_project_uuid(self):
+ self.assertRaises(SystemExit,
+ self.call_main_with_args,
+ ['--project-uuid', self.Z_UUID, '--stream'])
+
class ArvPutIntegrationTest(run_test_server.TestCaseWithServers,
ArvadosBaseTestCase):
def _getKeepServerConfig():
@@ -503,14 +440,14 @@ class ArvPutIntegrationTest(run_test_server.TestCaseWithServers,
def test_check_real_project_found(self):
self.authorize_with('active')
- self.assertTrue(arv_put.check_project_exists(self.PROJECT_UUID),
+ self.assertTrue(arv_put.check_project_exists(arv_put.api_client, self.PROJECT_UUID),
"did not correctly find test fixture project")
def test_check_error_finding_nonexistent_project(self):
BAD_UUID = 'zzzzz-zzzzz-zzzzzzzzzzzzzzz'
self.authorize_with('active')
try:
- result = arv_put.check_project_exists(BAD_UUID)
+ result = arv_put.check_project_exists(arv_put.api_client, BAD_UUID)
except ValueError as error:
self.assertIn(BAD_UUID, error.message)
else:
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