doc/fonts/*
doc/user/cwl/federated/*
*/docker_image
-docker/jobs/apt.arvados.org.list
+docker/jobs/apt.arvados.org*.list
+docker/jobs/1078ECD7.key
*/en.bootstrap.yml
*font-awesome.css
*.gif
function usage {
echo >&2
- echo >&2 "usage: $0 [options]"
+ echo >&2 "usage: WORKSPACE=/path/to/arvados $0 [options]"
echo >&2
echo >&2 "$0 options:"
echo >&2 " -t, --tags version tag for docker"
+ echo >&2 " -r, --repo Arvados package repot to use: dev, testing, stable (default: dev)"
echo >&2 " -u, --upload Upload the images (docker push)"
echo >&2 " --no-cache Don't use build cache"
echo >&2 " -h, --help Display this help and exit"
echo >&2
- echo >&2 " If no options are given, just builds the images."
+ echo >&2 " WORKSPACE=path Path to the Arvados source tree to build from"
+ echo >&2
}
upload=false
+REPO=dev
# NOTE: This requires GNU getopt (part of the util-linux package on Debian-based distros).
-TEMP=`getopt -o hut: \
- --long help,upload,no-cache,tags: \
+TEMP=`getopt -o hut:r: \
+ --long help,upload,no-cache,tags,repo: \
-n "$0" -- "$@"`
if [ $? != 0 ] ; then echo "Use -h for help"; exit 1 ; fi
;;
esac
;;
+ -r | --repo)
+ case "$2" in
+ "")
+ echo "ERROR: --repo needs a parameter";
+ usage;
+ exit 1
+ ;;
+ *)
+ REPO="$2";
+ shift 2
+ ;;
+ esac
+ ;;
--)
shift
break
exit $EXITCODE
}
+# Sanity check
+if ! [[ -n "$WORKSPACE" ]]; then
+ usage;
+ echo >&2 "Error: WORKSPACE environment variable not set"
+ echo >&2
+ exit 1
+fi
+
+echo $WORKSPACE
+
COLUMNS=80
. $WORKSPACE/build/run-library.sh
checkexit $ECODE "docker push $*"
}
-# Sanity check
-if ! [[ -n "$WORKSPACE" ]]; then
- echo >&2
- echo >&2 "Error: WORKSPACE environment variable not set"
- echo >&2
- exit 1
-fi
-
-echo $WORKSPACE
-
# find the docker binary
DOCKER=`which docker.io`
docker build $NOCACHE \
--build-arg python_sdk_version=${python_sdk_version} \
--build-arg cwl_runner_version=${cwl_runner_version} \
+ --build-arg repo_version=${REPO} \
-t arvados/jobs:$cwl_runner_version_orig .
ECODE=$?
# -f flag removed in Docker 1.12
FORCE=-f
fi
+
+#docker export arvados/jobs:$cwl_runner_version_orig | docker import - arvados/jobs:$cwl_runner_version_orig
+
if ! [[ -z "$version_tag" ]]; then
docker tag $FORCE arvados/jobs:$cwl_runner_version_orig arvados/jobs:"$version_tag"
else
--- /dev/null
+-----BEGIN PGP PUBLIC KEY BLOCK-----
+
+mQENBEzhgeoBCAChhoK1dqpWzNyDWqRGEvdFdkJaA9D2HRwKPfBfjAoePX6ZyrpA
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+2MTddRwz28hbmYCi+MzHYDbRv+cSyUDmvXaWhfkNKBepClBA1rTWBcldit5vvlqr
+yPet6wIKrtLGhAqZ
+=CLkG
+-----END PGP PUBLIC KEY BLOCK-----
#
# SPDX-License-Identifier: Apache-2.0
-# Based on Debian Jessie
-FROM debian:jessie
-MAINTAINER Ward Vandewege <ward@curoverse.com>
+# Based on Debian Stretch
+FROM debian:stretch
+MAINTAINER Ward Vandewege <wvandewege@veritasgenetics.com>
ENV DEBIAN_FRONTEND noninteractive
-ADD apt.arvados.org.list /etc/apt/sources.list.d/
-RUN apt-key adv --keyserver pool.sks-keyservers.net --recv 1078ECD7
-RUN gpg --keyserver pool.sks-keyservers.net --recv-keys D39DC0E3
+RUN apt-get update -q
+RUN apt-get install -yq --no-install-recommends gnupg
+
+ARG repo_version
+RUN echo repo_version $repo_version
+ADD apt.arvados.org-$repo_version.list /etc/apt/sources.list.d/
+
+ADD 1078ECD7.key /tmp/
+RUN cat /tmp/1078ECD7.key | apt-key add -
ARG python_sdk_version
ARG cwl_runner_version
RUN echo cwl_runner_version $cwl_runner_version python_sdk_version $python_sdk_version
RUN apt-get update -q
-RUN apt-get install -yq --no-install-recommends \
- git python-pip python-virtualenv \
- python-dev libgnutls28-dev libcurl4-gnutls-dev nodejs \
+RUN apt-get install -yq --no-install-recommends nodejs \
python-arvados-python-client=$python_sdk_version \
python-arvados-cwl-runner=$cwl_runner_version
-# use the Python executable from the python-arvados-python-client package
-RUN rm -f /usr/bin/python && ln -s /usr/share/python2.7/dist/python-arvados-python-client/bin/python /usr/bin/python
+# use the Python executable from the python-arvados-cwl-runner package
+RUN rm -f /usr/bin/python && ln -s /usr/share/python2.7/dist/python-arvados-cwl-runner/bin/python /usr/bin/python
# Install dependencies and set up system.
RUN /usr/sbin/adduser --disabled-password \
--- /dev/null
+# apt.arvados.org
+deb http://apt.arvados.org/ stretch-dev main
--- /dev/null
+# apt.arvados.org
+deb http://apt.arvados.org/ stretch main
--- /dev/null
+# apt.arvados.org
+deb http://apt.arvados.org/ stretch-testing main
+++ /dev/null
-# apt.arvados.org
-deb http://apt.arvados.org/ jessie-dev main
const tagKeyInstanceSecret = "InstanceSecret"
+type containerWrapper interface {
+ GetBlobReference(name string) *storage.Blob
+ ListBlobs(params storage.ListBlobsParameters) (storage.BlobListResponse, error)
+}
+
type virtualMachinesClientWrapper interface {
createOrUpdate(ctx context.Context,
resourceGroupName string,
}
type azureInstanceSet struct {
- azconfig azureInstanceSetConfig
- vmClient virtualMachinesClientWrapper
- netClient interfacesClientWrapper
- storageAcctClient storageacct.AccountsClient
- azureEnv azure.Environment
- interfaces map[string]network.Interface
- dispatcherID string
- namePrefix string
- ctx context.Context
- stopFunc context.CancelFunc
- stopWg sync.WaitGroup
- deleteNIC chan string
- deleteBlob chan storage.Blob
- logger logrus.FieldLogger
+ azconfig azureInstanceSetConfig
+ vmClient virtualMachinesClientWrapper
+ netClient interfacesClientWrapper
+ blobcont containerWrapper
+ azureEnv azure.Environment
+ interfaces map[string]network.Interface
+ dispatcherID string
+ namePrefix string
+ ctx context.Context
+ stopFunc context.CancelFunc
+ stopWg sync.WaitGroup
+ deleteNIC chan string
+ deleteBlob chan storage.Blob
+ logger logrus.FieldLogger
}
func newAzureInstanceSet(config json.RawMessage, dispatcherID cloud.InstanceSetID, logger logrus.FieldLogger) (prv cloud.InstanceSet, err error) {
az.vmClient = &virtualMachinesClientImpl{vmClient}
az.netClient = &interfacesClientImpl{netClient}
- az.storageAcctClient = storageAcctClient
+
+ result, err := storageAcctClient.ListKeys(az.ctx, az.azconfig.ResourceGroup, az.azconfig.StorageAccount)
+ if err != nil {
+ az.logger.WithError(err).Warn("Couldn't get account keys")
+ return err
+ }
+
+ key1 := *(*result.Keys)[0].Value
+ client, err := storage.NewBasicClientOnSovereignCloud(az.azconfig.StorageAccount, key1, az.azureEnv)
+ if err != nil {
+ az.logger.WithError(err).Warn("Couldn't make client")
+ return err
+ }
+
+ blobsvc := client.GetBlobService()
+ az.blobcont = blobsvc.GetContainerReference(az.azconfig.BlobContainer)
az.dispatcherID = dispatcherID
az.namePrefix = fmt.Sprintf("compute-%s-", az.dispatcherID)
return nil, wrapAzureError(err)
}
- instanceVhd := fmt.Sprintf("https://%s.blob.%s/%s/%s-os.vhd",
+ blobname := fmt.Sprintf("%s-os.vhd", name)
+ instanceVhd := fmt.Sprintf("https://%s.blob.%s/%s/%s",
az.azconfig.StorageAccount,
az.azureEnv.StorageEndpointSuffix,
az.azconfig.BlobContainer,
- name)
+ blobname)
customData := base64.StdEncoding.EncodeToString([]byte("#!/bin/sh\n" + initCommand + "\n"))
vm, err := az.vmClient.createOrUpdate(az.ctx, az.azconfig.ResourceGroup, name, vmParameters)
if err != nil {
+ _, delerr := az.blobcont.GetBlobReference(blobname).DeleteIfExists(nil)
+ if delerr != nil {
+ az.logger.WithError(delerr).Warnf("Error cleaning up vhd blob after failed create")
+ }
+
+ _, delerr = az.netClient.delete(context.Background(), az.azconfig.ResourceGroup, *nic.Name)
+ if delerr != nil {
+ az.logger.WithError(delerr).Warnf("Error cleaning up NIC after failed create")
+ }
+
return nil, wrapAzureError(err)
}
// leased to a VM) and haven't been modified for
// DeleteDanglingResourcesAfter seconds.
func (az *azureInstanceSet) manageBlobs() {
- result, err := az.storageAcctClient.ListKeys(az.ctx, az.azconfig.ResourceGroup, az.azconfig.StorageAccount)
- if err != nil {
- az.logger.WithError(err).Warn("Couldn't get account keys")
- return
- }
-
- key1 := *(*result.Keys)[0].Value
- client, err := storage.NewBasicClientOnSovereignCloud(az.azconfig.StorageAccount, key1, az.azureEnv)
- if err != nil {
- az.logger.WithError(err).Warn("Couldn't make client")
- return
- }
-
- blobsvc := client.GetBlobService()
- blobcont := blobsvc.GetContainerReference(az.azconfig.BlobContainer)
page := storage.ListBlobsParameters{Prefix: az.namePrefix}
timestamp := time.Now()
for {
- response, err := blobcont.ListBlobs(page)
+ response, err := az.blobcont.ListBlobs(page)
if err != nil {
az.logger.WithError(err).Warn("Error listing blobs")
return
}
func (ai *azureInstance) Address() string {
- return *(*ai.nic.IPConfigurations)[0].PrivateIPAddress
+ if ai.nic.IPConfigurations != nil &&
+ len(*ai.nic.IPConfigurations) > 0 &&
+ (*ai.nic.IPConfigurations)[0].PrivateIPAddress != nil {
+
+ return *(*ai.nic.IPConfigurations)[0].PrivateIPAddress
+ }
+ return ""
}
func (ai *azureInstance) RemoteUser() string {
return network.InterfaceListResultIterator{}, nil
}
+type BlobContainerStub struct{}
+
+func (*BlobContainerStub) GetBlobReference(name string) *storage.Blob {
+ return nil
+}
+
+func (*BlobContainerStub) ListBlobs(params storage.ListBlobsParameters) (storage.BlobListResponse, error) {
+ return storage.BlobListResponse{}, nil
+}
+
type testConfig struct {
ImageIDForTestSuite string
DriverParameters json.RawMessage
ap.ctx, ap.stopFunc = context.WithCancel(context.Background())
ap.vmClient = &VirtualMachinesClientStub{}
ap.netClient = &InterfacesClientStub{}
+ ap.blobcont = &BlobContainerStub{}
return &ap, cloud.ImageID("blob"), cluster, nil
}
if record["output_uuid"]:
if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
# Compute the trash time to avoid requesting the collection record.
- trash_at = ciso8601.parse_datetime_unaware(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
+ trash_at = ciso8601.parse_datetime(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
'ruamel.yaml >=0.15.54, <=0.15.77',
'arvados-python-client>=1.3.0.20190205182514',
'setuptools',
- 'ciso8601 >=1.0.6, <2.0.0',
+ 'ciso8601 >= 2.0.0',
],
extras_require={
':os.name=="posix" and python_version<"3"': ['subprocess32 >= 3.5.1'],
+ ':python_version<"3"': ['pytz'],
},
data_files=[
('share/doc/arvados-cwl-runner', ['LICENSE-2.0.txt', 'README.rst']),
def get_trash_at(self):
if self._api_response and self._api_response["trash_at"]:
- return ciso8601.parse_datetime(self._api_response["trash_at"])
+ try:
+ return ciso8601.parse_datetime(self._api_response["trash_at"])
+ except ValueError:
+ return None
else:
return None
Docker metadata links to sort them from least to most preferred.
"""
try:
- image_timestamp = ciso8601.parse_datetime_unaware(
+ image_timestamp = ciso8601.parse_datetime(
link['properties']['image_timestamp'])
except (KeyError, ValueError):
image_timestamp = EARLIEST_DATETIME
- return (image_timestamp,
- ciso8601.parse_datetime_unaware(link['created_at']))
+ try:
+ created_timestamp = ciso8601.parse_datetime(link['created_at'])
+ except ValueError:
+ created_timestamp = None
+ return (image_timestamp, created_timestamp)
def _get_docker_links(api_client, num_retries, **kwargs):
links = arvados.util.list_all(api_client.links().list,
('share/doc/arvados-python-client', ['LICENSE-2.0.txt', 'README.rst']),
],
install_requires=[
- 'ciso8601 >=1.0.6, <2.0.0',
+ 'ciso8601 >=2.0.0',
'future',
'google-api-python-client >=1.6.2, <1.7',
'httplib2 >=0.9.2',
],
extras_require={
':os.name=="posix" and python_version<"3"': ['subprocess32 >= 3.5.1'],
+ ':python_version<"3"': ['pytz'],
},
classifiers=[
'Programming Language :: Python :: 2',
end
def add_copy(src_item, key)
- self[key] = src_item.copy_named("#{path}/#{key}")
+ if key == "."
+ self[key] = src_item.copy_named("#{path}")
+ else
+ self[key] = src_item.copy_named("#{path}/#{key}")
+ end
end
def merge(src_item, key)
items["."] = CollectionStream.new(".")
end
+ def add_copy(src_item, key)
+ items["."].add_copy(src_item, key)
+ end
+
def raise_root_write_error(key)
raise ArgumentError.new("can't write to %p at collection root" % key)
end
dst_coll.manifest_text)
end
+ def test_copy_root_into_empty_collection
+ block = random_block(8)
+ src_coll = Arv::Collection.new(". #{block} 0:8:f1\n")
+ dst_coll = Arv::Collection.new()
+ dst_coll.cp_r("./", ".", src_coll)
+ assert_equal(". %s 0:8:f1\n" %
+ [block],
+ dst_coll.manifest_text)
+ end
+
def test_copy_empty_source_path_raises_ArgumentError(src="", dst="./s1")
coll = Arv::Collection.new(SIMPLEST_MANIFEST)
assert_raises(ArgumentError) do
if not t:
return 0
try:
- return calendar.timegm(ciso8601.parse_datetime_unaware(t).timetuple())
+ return calendar.timegm(ciso8601.parse_datetime(t).timetuple())
except (TypeError, ValueError):
return 0
# llfuse 1.3.4 fails to install via pip
'llfuse >=1.2, <1.3.4',
'python-daemon',
- 'ciso8601 >=1.0.6, <2.0.0',
+ 'ciso8601 >= 2.0.0',
'setuptools'
],
+ extras_require={
+ ':python_version<"3"': ['pytz'],
+ },
test_suite='tests',
tests_require=['pbr<1.7.0', 'mock>=1.0', 'PyYAML'],
zip_safe=False
projects / arvados.git / commitdiff