def update(self, plugin: RepositoryPlugin) -> None:
require(self.replica is None or self.replica == 'gcp')
assert self.drs_path is not None
drs_uri = plugin.drs_uri(self.drs_path)
drs_client = plugin.drs_client()
access = drs_client.get_object(drs_uri, access_method=AccessMethod.gs)
assert access.headers is None
url = furl(access.url)
blob_name = '/'.join(url.path.segments)
# https://github.com/databiosphere/azul/issues/2479#issuecomment-733410253
if url.fragmentstr:
blob_name += '#' + unquote(url.fragmentstr)
else:
# furl does not differentiate between no fragment and empty
# fragment
if access.url.endswith('#'):
blob_name += '#'
blob = self._get_blob(bucket_name=url.netloc, blob_name=blob_name)
expiration = int(time.time() + 3600)
file_name = self.file_name.replace('"', r'\"')
assert all(0x1f < ord(c) < 0x80 for c in file_name)
disposition = f"attachment; filename={file_name}"
signed_url = blob.generate_signed_url(expiration=expiration,
response_disposition=disposition)
self._location = signed_url
def update(self, plugin: RepositoryPlugin,
authentication: Optional[Authentication]) -> None:
require(self.replica is None or self.replica == 'gcp')
assert self.drs_path is not None
drs_uri = plugin.drs_uri(self.drs_path)
drs_client = plugin.drs_client(authentication)
access = drs_client.get_object(drs_uri, access_method=AccessMethod.gs)
require(access.method is AccessMethod.https, access.method)
require(access.headers is None, access.headers)
signed_url = access.url
args = furl(signed_url).args
require('X-Goog-Signature' in args, args)
self._location = signed_url
def update(self,
plugin: RepositoryPlugin,
authentication: Optional[Authentication]
) -> None:
assert isinstance(plugin, Plugin)
url = plugin.direct_file_url(file_uuid=self.file_uuid,
file_version=self.file_version,
replica=None)
self._location = url
def _create_db(self) -> Tuple[JSONs, str]:
"""
Write hardcoded portal integrations DB to S3.
:return: Newly created DB and accompanying version.
"""
catalog = config.default_catalog
plugin = RepositoryPlugin.load(catalog).create(catalog)
db = self.demultiplex(plugin.portal_db())
version = self._write_db(db, None)
return db, version
def update(self, plugin: RepositoryPlugin,
authentication: Optional[Authentication]) -> None:
self.drs_path = None # to shorten the retry URLs
if self.replica is None:
self.replica = 'aws'
assert isinstance(plugin, Plugin)
dss_url = plugin.direct_file_url(file_uuid=self.file_uuid,
file_version=self.file_version,
replica=self.replica,
token=self.token)
dss_response = requests.get(dss_url, allow_redirects=False)
if dss_response.status_code == 301:
retry_after = int(dss_response.headers.get('Retry-After'))
location = dss_response.headers['Location']
location = urllib.parse.urlparse(location)
query = urllib.parse.parse_qs(location.query, strict_parsing=True)
self.token = one(query['token'])
self.replica = one(query['replica'])
self.file_version = one(query['version'])
self._retry_after = retry_after
elif dss_response.status_code == 302:
location = dss_response.headers['Location']
# Remove once https://github.com/HumanCellAtlas/data-store/issues/1837 is resolved
if True:
location = urllib.parse.urlparse(location)
query = urllib.parse.parse_qs(location.query,
strict_parsing=True)
expires = int(one(query['Expires']))
bucket = location.netloc.partition('.')[0]
dss_endpoint = one(plugin.sources).name
assert bucket == aws.dss_checkout_bucket(dss_endpoint), bucket
with aws.direct_access_credentials(dss_endpoint,
lambda_name='service'):
# FIXME: make region configurable (https://github.com/DataBiosphere/azul/issues/1560)
s3 = aws.client('s3', region_name='us-east-1')
params = {
'Bucket':
bucket,
'Key':
location.path[1:],
'ResponseContentDisposition':
'attachment;filename=' + self.file_name,
}
location = s3.generate_presigned_url(
ClientMethod=s3.get_object.__name__,
ExpiresIn=round(expires - time.time()),
Params=params)
self._location = location
else:
dss_response.raise_for_status()
assert False
def verify_sources():
tdr_catalogs = {
catalog.name
for catalog in config.catalogs.values()
if catalog.plugins[RepositoryPlugin.type_name()].name == 'tdr'
}
assert tdr_catalogs, tdr_catalogs
futures = []
with ThreadPoolExecutor(max_workers=16) as tpe:
for source in set(chain.from_iterable(map(config.sources, tdr_catalogs))):
source = TDRSourceSpec.parse(source)
for check in (tdr.check_api_access, tdr.check_bigquery_access, verify_source):
futures.append(tpe.submit(check, source))
for completed_future in as_completed(futures):
futures.remove(completed_future)
e = completed_future.exception()
if e is not None:
for running_future in futures:
running_future.cancel()
raise e
def main(argv):
configure_script_logging(logger)
import argparse
parser = argparse.ArgumentParser(
description='Subscribe indexer lambda to bundle events from DSS')
parser.add_argument('--unsubscribe',
'-U',
dest='subscribe',
action='store_false',
default=True)
parser.add_argument(
'--personal',
'-p',
dest='shared',
action='store_false',
default=True,
help=
"Do not use the shared credentials of the Google service account that represents the "
"current deployment, but instead use personal credentials for authenticating to the DSS. "
"When specifying this option you will need to a) run `hca dss login` prior to running "
"this script or b) set GOOGLE_APPLICATION_CREDENTIALS to point to another service "
"account's credentials. Note that this implies that the resulting DSS subscription will "
"be owned by a) you or b) the other service account and that only a) you or b) someone "
"in possession of those credentials can modify the subscription in the future. This is "
"typically not what you'd want.")
options = parser.parse_args(argv)
dss_client = azul.dss.client()
for catalog in config.catalogs:
plugin = RepositoryPlugin.load(catalog)
if isinstance(plugin, dss.Plugin):
if options.shared:
with aws.service_account_credentials(
config.ServiceAccount.indexer):
subscription.manage_subscriptions(
plugin, dss_client, subscribe=options.subscribe)
else:
subscription.manage_subscriptions(plugin,
dss_client,
subscribe=options.subscribe)
def main(argv):
parser = argparse.ArgumentParser(description=__doc__, formatter_class=AzulArgumentHelpFormatter)
default_catalog = config.default_catalog
plugin_cls = RepositoryPlugin.load(default_catalog)
plugin = plugin_cls.create(default_catalog)
if len(plugin.sources) == 1:
source_arg = {'default': str(one(plugin.sources))}
else:
source_arg = {'required': True}
parser.add_argument('--source', '-s',
**source_arg,
help='The repository source containing the bundle')
parser.add_argument('--uuid', '-b',
required=True,
help='The UUID of the bundle to can.')
parser.add_argument('--version', '-v',
help='The version of the bundle to can (default: the latest version).')
parser.add_argument('--output-dir', '-O',
default=os.path.join(config.project_root, 'test', 'indexer', 'data'),
help='The path to the output directory (default: %(default)s).')
args = parser.parse_args(argv)
bundle = fetch_bundle(args.source, args.uuid, args.version)
save_bundle(bundle, args.output_dir)
def repository_plugin(self, catalog: CatalogName) -> RepositoryPlugin:
return RepositoryPlugin.load(catalog).create(catalog)
def plugin_for(catalog):
return RepositoryPlugin.load(catalog).create(catalog)
def plugin_db(self) -> JSONs:
# Must be lazy so the mock catalog's repository plugin is used
catalog = config.default_catalog
plugin = RepositoryPlugin.load(catalog).create(catalog)
return plugin.portal_db()
def default_db(self) -> JSONs:
# FIXME: Parameterize PortalService instances with current catalog
# https://github.com/DataBiosphere/azul/issues/2716
catalog = config.default_catalog
plugin = RepositoryPlugin.load(catalog).create(catalog)
return self.demultiplex(plugin.portal_db())
def repository_plugin(self) -> RepositoryPlugin:
catalog = self.catalog
return RepositoryPlugin.load(catalog).create(catalog)
