coffee-script-source (1.12.2)
commonjs (0.2.7)
concurrent-ruby (1.1.5)
- crass (1.0.4)
+ crass (1.0.5)
deep_merge (1.2.1)
docile (1.3.1)
erubis (2.7.0)
railties (>= 4)
request_store (~> 1.0)
logstash-event (1.2.02)
- loofah (2.2.3)
+ loofah (2.3.1)
crass (~> 1.0.2)
nokogiri (>= 1.5.9)
mail (2.7.1)
net-ssh-gateway (2.0.0)
net-ssh (>= 4.0.0)
nio4r (2.3.1)
- nokogiri (1.10.4)
+ nokogiri (1.10.8)
mini_portile2 (~> 2.4.0)
npm-rails (0.2.1)
rails (>= 3.2)
method_source
rake (>= 0.8.7)
thor (>= 0.18.1, < 2.0)
- rake (12.3.2)
+ rake (13.0.1)
raphael-rails (2.1.2)
rb-fsevent (0.10.3)
rb-inotify (0.10.0)
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+# This is related to:
+# * https://github.com/advisories/GHSA-65cv-r6x7-79hv
+# * https://nvd.nist.gov/vuln/detail/CVE-2020-5267
+#
+# Until we upgrade to rails 5.2, this monkeypatch should be enough
+ActionView::Helpers::JavaScriptHelper::JS_ESCAPE_MAP.merge!(
+ {
+ "`" => "\\`",
+ "$" => "\\$"
+ }
+)
+
+module ActionView::Helpers::JavaScriptHelper
+ alias :old_ej :escape_javascript
+ alias :old_j :j
+
+ def escape_javascript(javascript)
+ javascript = javascript.to_s
+ if javascript.empty?
+ result = ""
+ else
+ result = javascript.gsub(/(\\|<\/|\r\n|\342\200\250|\342\200\251|[\n\r"']|[`]|[$])/u, JS_ESCAPE_MAP)
+ end
+ javascript.html_safe? ? result.html_safe : result
+ end
+
+ alias :j :escape_javascript
+end
\ No newline at end of file
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+require 'test_helper'
+
+# Tests XSS vulnerability monkeypatch
+# See: https://github.com/advisories/GHSA-65cv-r6x7-79hv
+class JavascriptHelperTest < ActionView::TestCase
+ def test_escape_backtick
+ assert_equal "\\`", escape_javascript("`")
+ end
+
+ def test_escape_dollar_sign
+ assert_equal "\\$", escape_javascript("$")
+ end
+end
WORKSPACE=path Path to the Arvados source tree to build packages from
CWLTOOL=path (optional) Path to cwltool git repository.
SALAD=path (optional) Path to schema_salad git repository.
-PYCMD=pythonexec (optional) Specify the python executable to use in the docker image. Defaults to "python".
+PYCMD=pythonexec (optional) Specify the python executable to use in the docker image. Defaults to "python3".
EOF
cd "$WORKSPACE"
-py=python
+py=python3
pipcmd=pip
if [[ -n "$PYCMD" ]] ; then
py="$PYCMD"
- if [[ $py = python3 ]] ; then
- pipcmd=pip3
- fi
+fi
+if [[ $py = python3 ]] ; then
+ pipcmd=pip3
fi
(cd sdk/python && python setup.py sdist)
cwl_runner_version=$(cd sdk/python && nohash_version_from_git 1.0)
fi
-docker build --build-arg sdk=$sdk --build-arg runner=$runner --build-arg salad=$salad --build-arg cwltool=$cwltool --build-arg pythoncmd=$py --build-arg pipcmd=$pipcmd -f "$WORKSPACE/sdk/dev-jobs.dockerfile" -t arvados/jobs:$cwl_runner_version "$WORKSPACE/sdk"
+set -x
+docker build --no-cache --build-arg sdk=$sdk --build-arg runner=$runner --build-arg salad=$salad --build-arg cwltool=$cwltool --build-arg pythoncmd=$py --build-arg pipcmd=$pipcmd -f "$WORKSPACE/sdk/dev-jobs.dockerfile" -t arvados/jobs:$cwl_runner_version "$WORKSPACE/sdk"
echo arv-keepdocker arvados/jobs $cwl_runner_version
arv-keepdocker arvados/jobs $cwl_runner_version
# The Python SDK - Should be built first because it's needed by others
fpm_build_virtualenv "arvados-python-client" "sdk/python"
-# Arvados cwl runner
-fpm_build_virtualenv "arvados-cwl-runner" "sdk/cwl"
+# The Python SDK - Python3 package
+fpm_build_virtualenv "arvados-python-client" "sdk/python" "python3"
-# Arvados cwl runner - Python3 package
+# Arvados cwl runner - Only supports Python3 now
fpm_build_virtualenv "arvados-cwl-runner" "sdk/cwl" "python3"
# The PAM module
# The Arvados crunchstat-summary tool
fpm_build_virtualenv "crunchstat-summary" "tools/crunchstat-summary"
-# The Python SDK - Python3 package
-fpm_build_virtualenv "arvados-python-client" "sdk/python" "python3"
-
# The Docker image cleaner
fpm_build_virtualenv "arvados-docker-cleaner" "services/dockercleaner" "python3"
sdk/go/asyncbuf
sdk/go/stats
sdk/go/crunchrunner
-sdk/cwl
+sdk/cwl:py3
sdk/R
sdk/java-v2
tools/sync-groups
sdk/pam
sdk/python
sdk/python:py3
- sdk/cwl
sdk/cwl:py3
services/dockercleaner:py3
services/fuse
${verb}_${target}
;;
*)
- testargs["$target"]="${opts}"
+ argstarget=${target%:py3}
+ testargs["$argstarget"]="${opts}"
tt="${testfuncargs[${target}]}"
tt="${tt:-$target}"
do_$verb $tt
if svc == &cluster.Services.DispatchCloud && super.ClusterType == "test" {
continue
}
- if svc.ExternalURL.Host == "" && (svc == &cluster.Services.Controller ||
- svc == &cluster.Services.GitHTTP ||
- svc == &cluster.Services.Keepproxy ||
- svc == &cluster.Services.WebDAV ||
- svc == &cluster.Services.WebDAVDownload ||
- svc == &cluster.Services.Websocket ||
- svc == &cluster.Services.Workbench1) {
- svc.ExternalURL = arvados.URL{Scheme: "https", Host: fmt.Sprintf("%s:%s", super.ListenHost, nextPort(super.ListenHost))}
+ if svc.ExternalURL.Host == "" {
+ if svc == &cluster.Services.Controller ||
+ svc == &cluster.Services.GitHTTP ||
+ svc == &cluster.Services.Keepproxy ||
+ svc == &cluster.Services.WebDAV ||
+ svc == &cluster.Services.WebDAVDownload ||
+ svc == &cluster.Services.Workbench1 {
+ svc.ExternalURL = arvados.URL{Scheme: "https", Host: fmt.Sprintf("%s:%s", super.ListenHost, nextPort(super.ListenHost))}
+ } else if svc == &cluster.Services.Websocket {
+ svc.ExternalURL = arvados.URL{Scheme: "wss", Host: fmt.Sprintf("%s:%s", super.ListenHost, nextPort(super.ListenHost))}
+ }
}
if len(svc.InternalURLs) == 0 {
svc.InternalURLs = map[arvados.URL]arvados.ServiceInstance{
import re
import pkg_resources # part of setuptools
-### begin monkey patch ###
-# Monkey patch solution for bug #16169
-#
-# There is a bug in upstream cwltool where the version updater needs
-# to replace the document fragments in the loader index with the
-# updated ones, but actually it only does it for the root document.
-# Normally we just fix the bug in upstream but that's challenging
-# because current cwltool dropped support for Python 2.7 and we're
-# still supporting py2 in Arvados 2.0 (although py2 support will most
-# likely be dropped in Arvados 2.1). Making a bugfix fork comes with
-# its own complications (it would need to be added to PyPi) so monkey
-# patching is the least disruptive fix (and is relatively safe because
-# our cwltool dependency is pinned to a specific version). This
-# should be removed as soon as a bugfix goes into upstream cwltool and
-# we upgrade to it.
-#
-import cwltool.load_tool
-from cwltool.utils import visit_class
-from six.moves import urllib
-original_resolve_and_validate_document = cwltool.load_tool.resolve_and_validate_document
-def wrapped_resolve_and_validate_document(
- loadingContext, # type: LoadingContext
- workflowobj, # type: Union[CommentedMap, CommentedSeq]
- uri, # type: Text
- preprocess_only=False, # type: bool
- skip_schemas=None, # type: Optional[bool]
- ):
- loadingContext, uri = original_resolve_and_validate_document(loadingContext, workflowobj, uri, preprocess_only, skip_schemas)
- if loadingContext.do_update in (True, None):
- fileuri = urllib.parse.urldefrag(uri)[0]
- def update_index(pr):
- loadingContext.loader.idx[pr["id"]] = pr
- visit_class(loadingContext.loader.idx[fileuri], ("CommandLineTool", "Workflow", "ExpressionTool"), update_index)
- return loadingContext, uri
-cwltool.load_tool.resolve_and_validate_document = wrapped_resolve_and_validate_document
-### end monkey patch ###
-
from schema_salad.sourceline import SourceLine
import schema_salad.validate as validate
import cwltool.main
import logging
from schema_salad.sourceline import SourceLine, cmap
+import schema_salad.ref_resolver
from cwltool.pack import pack
-from cwltool.load_tool import fetch_document
+from cwltool.load_tool import fetch_document, resolve_and_validate_document
from cwltool.process import shortname
from cwltool.workflow import Workflow, WorkflowException, WorkflowStep
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
with SourceLine(self.tool, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if "id" not in self.tool:
raise WorkflowException("%s object must have 'id'" % (self.tool["class"]))
- document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
discover_secondary_files(self.arvrunner.fs_access, builder,
self.tool["inputs"], joborder)
with Perf(metrics, "subworkflow upload_deps"):
upload_dependencies(self.arvrunner,
os.path.basename(joborder.get("id", "#")),
- document_loader,
+ self.doc_loader,
joborder,
joborder.get("id", "#"),
False)
if self.wf_pdh is None:
- workflowobj["requirements"] = dedup_reqs(self.requirements)
- workflowobj["hints"] = dedup_reqs(self.hints)
+ packed = pack(self.loadingContext, self.tool["id"], loader=self.doc_loader)
- packed = pack(document_loader, workflowobj, uri, self.metadata)
+ for p in packed["$graph"]:
+ if p["id"] == "#main":
+ p["requirements"] = dedup_reqs(self.requirements)
+ p["hints"] = dedup_reqs(self.hints)
def visit(item):
+ if "requirements" in item:
+ item["requirements"] = [i for i in item["requirements"] if i["class"] != "DockerRequirement"]
for t in ("hints", "requirements"):
if t not in item:
continue
raise WorkflowException("Non-top-level ResourceRequirement in single container cannot have expressions")
if not dyn:
self.static_resource_req.append(req)
- if req["class"] == "DockerRequirement":
- if "http://arvados.org/cwl#dockerCollectionPDH" in req:
- del req["http://arvados.org/cwl#dockerCollectionPDH"]
visit_class(packed["$graph"], ("Workflow", "CommandLineTool"), visit)
upload_dependencies(self.arvrunner,
runtimeContext.name,
- document_loader,
+ self.doc_loader,
packed,
- uri,
+ self.tool["id"],
False)
# Discover files/directories referenced by the
if job_res_reqs[0].get("ramMin", 1024) < 128:
job_res_reqs[0]["ramMin"] = 128
+ arguments = ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl", "cwl.input.yml"]
+ if runtimeContext.debug:
+ arguments.insert(0, '--debug')
+
wf_runner = cmap({
"class": "CommandLineTool",
"baseCommand": "cwltool",
}]
}],
"hints": self.hints,
- "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"],
+ "arguments": arguments,
"id": "#"
})
return ArvadosCommandTool(self.arvrunner, wf_runner, self.loadingContext).job(joborder_resolved, output_callback, runtimeContext)
A "packed" workflow is one where all the components have been combined into a single document."""
rewrites = {}
- packed = pack(tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]),
- tool.tool["id"], tool.metadata, rewrite_out=rewrites)
+ packed = pack(arvrunner.loadingContext, tool.tool["id"],
+ rewrite_out=rewrites,
+ loader=tool.doc_loader)
rewrite_to_orig = {v: k for k,v in viewitems(rewrites)}
# file to determine what version of cwltool and schema-salad to
# build.
install_requires=[
- 'cwltool==1.0.20190831161204',
- 'schema-salad==4.5.20190815125611',
- 'typing >= 3.6.4',
- 'ruamel.yaml >=0.15.54, <=0.15.77',
+ 'cwltool==3.0.20200317203547',
+ 'schema-salad==5.0.20200302192450',
'arvados-python-client{}'.format(pysdk_dep),
'setuptools',
- 'ciso8601 >= 2.0.0',
- 'networkx < 2.3'
+ 'ciso8601 >= 2.0.0'
],
extras_require={
':os.name=="posix" and python_version<"3"': ['subprocess32 >= 3.5.1'],
data_files=[
('share/doc/arvados-cwl-runner', ['LICENSE-2.0.txt', 'README.rst']),
],
+ python_requires=">=3.5, <4",
classifiers=[
- 'Programming Language :: Python :: 2',
'Programming Language :: Python :: 3',
],
test_suite='tests',
reset_container=1
leave_running=0
config=dev
+devcwl=0
tag="latest"
-pythoncmd=python
+pythoncmd=python3
suite=conformance
runapi=containers
build=1
shift
;;
+ --devcwl)
+ devcwl=1
+ shift
+ ;;
--pythoncmd)
pythoncmd=$2
shift ; shift
shift ; shift
;;
-h|--help)
- echo "$0 [--no-reset-container] [--leave-running] [--config dev|localdemo] [--tag docker_tag] [--build] [--pythoncmd python(2|3)] [--suite (integration|conformance-v1.0|conformance-v1.1)]"
+ echo "$0 [--no-reset-container] [--leave-running] [--config dev|localdemo] [--tag docker_tag] [--build] [--pythoncmd python(2|3)] [--suite (integration|conformance-v1.0|conformance-*)]"
exit
;;
*)
git clone https://github.com/common-workflow-language/common-workflow-language.git
fi
cd common-workflow-language
-elif [[ "$suite" = "conformance-v1.1" ]] ; then
- if ! test -d cwl-v1.1 ; then
- git clone https://github.com/common-workflow-language/cwl-v1.1.git
+elif [[ "$suite" =~ conformance-(.*) ]] ; then
+ version=\${BASH_REMATCH[1]}
+ if ! test -d cwl-\${version} ; then
+ git clone https://github.com/common-workflow-language/cwl-\${version}.git
fi
- cd cwl-v1.1
+ cd cwl-\${version}
fi
if [[ "$suite" != "integration" ]] ; then
EOF2
chmod +x /tmp/cwltest/arv-cwl-containers
+EXTRA=--compute-checksum
+
+if [[ $devcwl == 1 ]] ; then
+ EXTRA="\$EXTRA --enable-dev"
+fi
+
env
if [[ "$suite" = "integration" ]] ; then
cd /usr/src/arvados/sdk/cwl/tests
exec ./arvados-tests.sh $@
else
- exec ./run_test.sh RUNNER=/tmp/cwltest/arv-cwl-${runapi} EXTRA=--compute-checksum $@
+ exec ./run_test.sh RUNNER=/tmp/cwltest/arv-cwl-${runapi} EXTRA="\$EXTRA" $@
fi
EOF
import functools
import cwltool.process
import cwltool.secrets
+from cwltool.update import INTERNAL_VERSION
from schema_salad.ref_resolver import Loader
from schema_salad.sourceline import cmap
cwltool.process._names = set()
def helper(self, runner, enable_reuse=True):
- document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1")
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(INTERNAL_VERSION)
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
"basedir": "",
"make_fs_access": make_fs_access,
"loader": Loader({}),
- "metadata": {"cwlVersion": "v1.1", "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"}})
+ "metadata": {"cwlVersion": INTERNAL_VERSION, "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"}})
runtimeContext = arvados_cwl.context.ArvRuntimeContext(
{"work_api": "containers",
"basedir": "",
runner.api.collections().get().execute.return_value = {
"portable_data_hash": "99999999999999999999999999999993+99"}
- document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1")
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema(INTERNAL_VERSION)
tool = cmap({
"inputs": [],
cwltool.process._names = set()
def helper(self, runner, enable_reuse=True):
- document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.1")
+ document_loader, avsc_names, schema_metadata, metaschema_loader = cwltool.process.get_schema("v1.0")
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
"basedir": "",
"make_fs_access": make_fs_access,
"loader": document_loader,
- "metadata": {"cwlVersion": "v1.1", "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"},
+ "metadata": {"cwlVersion": INTERNAL_VERSION, "http://commonwl.org/cwltool#original_cwlVersion": "v1.0"},
"construct_tool_object": runner.arv_make_tool})
runtimeContext = arvados_cwl.context.ArvRuntimeContext(
{"work_api": "containers",
"--no-container",
"--move-outputs",
"--preserve-entire-environment",
- "workflow.cwl#main",
+ "workflow.cwl",
"cwl.input.yml"
],
"container_image": "99999999999999999999999999999993+99",
u'--no-container',
u'--move-outputs',
u'--preserve-entire-environment',
- u'workflow.cwl#main',
+ u'workflow.cwl',
u'cwl.input.yml'
],
'use_existing': True,
import sys
import unittest
import cwltool.process
+import re
from io import BytesIO
self.assertEqual(exited, 1)
self.assertRegexpMatches(
- capture_stderr.getvalue(),
+ re.sub(r'[ \n]+', ' ', capture_stderr.getvalue()),
r"Expected collection uuid zzzzz-4zz18-zzzzzzzzzzzzzzz to be 99999999999999999999999999999998\+99 but API server reported 99999999999999999999999999999997\+99")
finally:
cwltool_logger.removeHandler(stderr_logger)
{
"$graph": [
{
+ "$namespaces": {
+ "arv": "http://arvados.org/cwl#"
+ },
"class": "Workflow",
- "cwlVersion": "v1.1",
+ "cwlVersion": "v1.0",
"hints": [],
"id": "#main",
"inputs": [
"run": {
"baseCommand": "sleep",
"class": "CommandLineTool",
- "id": "#main/sleep1/run/subtool",
+ "id": "#main/sleep1/subtool",
"inputs": [
{
- "id": "#main/sleep1/run/subtool/sleeptime",
+ "id": "#main/sleep1/subtool/sleeptime",
"inputBinding": {
"position": 1
},
],
"outputs": [
{
- "id": "#main/sleep1/run/subtool/out",
+ "id": "#main/sleep1/subtool/out",
"outputBinding": {
"outputEval": "out"
},
]
}
],
- "cwlVersion": "v1.1"
-}
+ "cwlVersion": "v1.0"
+}
\ No newline at end of file
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import org.arvados.client.api.model.Link;
+import org.arvados.client.api.model.LinkList;
+import org.arvados.client.config.ConfigProvider;
+
+public class LinksApiClient extends BaseStandardApiClient<Link, LinkList> {
+
+ private static final String RESOURCE = "links";
+
+ public LinksApiClient(ConfigProvider config) {
+ super(config);
+ }
+
+ @Override
+ String getResource() {
+ return RESOURCE;
+ }
+
+ @Override
+ Class<Link> getType() {
+ return Link.class;
+ }
+
+ @Override
+ Class<LinkList> getListType() {
+ return LinkList.class;
+ }
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonPropertyOrder({ "name", "head_kind", "head_uuid", "link_class" })
+public class Link extends Item {
+
+ @JsonProperty("name")
+ private String name;
+ @JsonProperty("head_kind")
+ private String headKind;
+ @JsonProperty("head_uuid")
+ private String headUuid;
+ @JsonProperty("link_class")
+ private String linkClass;
+
+ public String getName() {
+ return name;
+ }
+
+ public String getHeadKind() {
+ return headKind;
+ }
+
+ public String getHeadUuid() {
+ return headUuid;
+ }
+
+ public String getLinkClass() {
+ return linkClass;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public void setHeadKind(String headKind) {
+ this.headKind = headKind;
+ }
+
+ public void setHeadUuid(String headUuid) {
+ this.headUuid = headUuid;
+ }
+
+ public void setLinkClass(String linkClass) {
+ this.linkClass = linkClass;
+ }
+
+}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.model;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+import java.util.List;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonPropertyOrder({ "items" })
+public class LinkList extends ItemList {
+
+ @JsonProperty("items")
+ private List<Link> items;
+
+ public List<Link> getItems() {
+ return this.items;
+ }
+
+ public void setItems(List<Link> items) {
+ this.items = items;
+ }
+}
#
# By default, arv-copy recursively copies any dependent objects
# necessary to make the object functional in the new instance
-# (e.g. for a pipeline instance, arv-copy copies the pipeline
-# template, input collection, docker images, git repositories). If
+# (e.g. for a workflow, arv-copy copies the workflow,
+# input collections, and docker images). If
# --no-recursive is given, arv-copy copies only the single record
# identified by object-uuid.
#
copy_opts.add_argument(
'-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(
- '--force-filters', action='store_true', default=False,
- help="Copy pipeline template filters verbatim, even if they act differently on the destination cluster.")
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.')
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.')
- copy_opts.add_argument(
- '--dst-git-repo', dest='dst_git_repo',
- help='The name of the destination git repository. Required when copying a pipeline recursively.')
copy_opts.add_argument(
'--project-uuid', dest='project_uuid',
- help='The UUID of the project at the destination to which the pipeline should be copied.')
- copy_opts.add_argument(
- '--allow-git-http-src', action="store_true",
- help='Allow cloning git repositories over insecure http')
- copy_opts.add_argument(
- '--allow-git-http-dst', action="store_true",
- help='Allow pushing git repositories over insecure http')
+ help='The UUID of the project at the destination to which the collection or workflow should be copied.')
copy_opts.add_argument(
'object_uuid',
copy_opts.set_defaults(recursive=True)
parser = argparse.ArgumentParser(
- description='Copy a pipeline instance, template, workflow, or collection from one Arvados instance to another.',
+ description='Copy a workflow or collection from one Arvados instance to another.',
parents=[copy_opts, arv_cmd.retry_opt])
args = parser.parse_args()
result = copy_collection(args.object_uuid,
src_arv, dst_arv,
args)
- elif t == 'PipelineInstance':
- set_src_owner_uuid(src_arv.pipeline_instances(), args.object_uuid, args)
- result = copy_pipeline_instance(args.object_uuid,
- src_arv, dst_arv,
- args)
- elif t == 'PipelineTemplate':
- set_src_owner_uuid(src_arv.pipeline_templates(), args.object_uuid, args)
- result = copy_pipeline_template(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)
except Exception:
abort('git command is not available. Please ensure git is installed.')
-# copy_pipeline_instance(pi_uuid, src, dst, args)
-#
-# Copies a pipeline instance identified by pi_uuid from src to dst.
-#
-# If the args.recursive option is set:
-# 1. Copies all input collections
-# * For each component in the pipeline, include all collections
-# listed as job dependencies for that component)
-# 2. Copy docker images
-# 3. Copy git repositories
-# 4. Copy the pipeline template
-#
-# The only changes made to the copied pipeline instance are:
-# 1. The original pipeline instance UUID is preserved in
-# the 'properties' hash as 'copied_from_pipeline_instance_uuid'.
-# 2. The pipeline_template_uuid is changed to the new template uuid.
-# 3. The owner_uuid of the instance is changed to the user who
-# copied it.
-#
-def copy_pipeline_instance(pi_uuid, src, dst, args):
- # Fetch the pipeline instance record.
- pi = src.pipeline_instances().get(uuid=pi_uuid).execute(num_retries=args.retries)
-
- if args.recursive:
- check_git_availability()
-
- if not args.dst_git_repo:
- abort('--dst-git-repo is required when copying a pipeline recursively.')
- # Copy the pipeline template and save the copied template.
- if pi.get('pipeline_template_uuid', None):
- pt = copy_pipeline_template(pi['pipeline_template_uuid'],
- src, dst, args)
-
- # Copy input collections, docker images and git repos.
- pi = copy_collections(pi, src, dst, args)
- copy_git_repos(pi, src, dst, args.dst_git_repo, args)
- copy_docker_images(pi, src, dst, args)
-
- # Update the fields of the pipeline instance with the copied
- # pipeline template.
- if pi.get('pipeline_template_uuid', None):
- pi['pipeline_template_uuid'] = pt['uuid']
-
- else:
- # not recursive
- logger.info("Copying only pipeline instance %s.", pi_uuid)
- logger.info("You are responsible for making sure all pipeline dependencies have been updated.")
-
- # Update the pipeline instance properties, and create the new
- # instance at dst.
- pi['properties']['copied_from_pipeline_instance_uuid'] = pi_uuid
- pi['description'] = "Pipeline copied from {}\n\n{}".format(
- pi_uuid,
- pi['description'] if pi.get('description', None) else '')
-
- pi['owner_uuid'] = args.project_uuid
-
- del pi['uuid']
-
- new_pi = dst.pipeline_instances().create(body=pi, ensure_unique_name=True).execute(num_retries=args.retries)
- return new_pi
def filter_iter(arg):
"""Iterate a filter string-or-list.
except exc_types as error:
handler(error)
-def migrate_components_filters(template_components, dst_git_repo):
- """Update template component filters in-place for the destination.
-
- template_components is a dictionary of components in a pipeline template.
- This method walks over each component's filters, and updates them to have
- identical semantics on the destination cluster. It returns a list of
- error strings that describe what filters could not be updated safely.
-
- dst_git_repo is the name of the destination Git repository, which can
- be None if that is not known.
- """
- errors = []
- for cname, cspec in template_components.items():
- def add_error(errmsg):
- errors.append("{}: {}".format(cname, errmsg))
- if not isinstance(cspec, dict):
- add_error("value is not a component definition")
- continue
- src_repository = cspec.get('repository')
- filters = cspec.get('filters', [])
- if not isinstance(filters, list):
- add_error("filters are not a list")
- continue
- for cfilter in filters:
- if not (isinstance(cfilter, list) and (len(cfilter) == 3)):
- add_error("malformed filter {!r}".format(cfilter))
- continue
- if attr_filtered(cfilter, 'repository'):
- with exception_handler(add_error, ValueError):
- migrate_repository_filter(cfilter, src_repository, dst_git_repo)
- if attr_filtered(cfilter, 'script_version'):
- with exception_handler(add_error, ValueError):
- migrate_script_version_filter(cfilter)
- return errors
-
-# copy_pipeline_template(pt_uuid, src, dst, args)
-#
-# Copies a pipeline template identified by pt_uuid from src to dst.
-#
-# If args.recursive is True, also copy any collections, docker
-# images and git repositories that this template references.
-#
-# The owner_uuid of the new template is changed to that of the user
-# who copied the template.
-#
-# Returns the copied pipeline template object.
-#
-def copy_pipeline_template(pt_uuid, src, dst, args):
- # fetch the pipeline template from the source instance
- pt = src.pipeline_templates().get(uuid=pt_uuid).execute(num_retries=args.retries)
-
- if not args.force_filters:
- filter_errors = migrate_components_filters(pt['components'], args.dst_git_repo)
- if filter_errors:
- abort("Template filters cannot be copied safely. Use --force-filters to copy anyway.\n" +
- "\n".join(filter_errors))
-
- if args.recursive:
- check_git_availability()
-
- if not args.dst_git_repo:
- abort('--dst-git-repo is required when copying a pipeline recursively.')
- # Copy input collections, docker images and git repos.
- pt = copy_collections(pt, src, dst, args)
- copy_git_repos(pt, src, dst, args.dst_git_repo, args)
- copy_docker_images(pt, src, dst, args)
-
- pt['description'] = "Pipeline template copied from {}\n\n{}".format(
- pt_uuid,
- pt['description'] if pt.get('description', None) else '')
- pt['name'] = "{} copied from {}".format(pt.get('name', ''), pt_uuid)
- del pt['uuid']
-
- pt['owner_uuid'] = args.project_uuid
-
- return dst.pipeline_templates().create(body=pt, ensure_unique_name=True).execute(num_retries=args.retries)
# copy_workflow(wf_uuid, src, dst, args)
#
return type(obj)(copy_collections(v, src, dst, args) for v in obj)
return obj
-def migrate_jobspec(jobspec, src, dst, dst_repo, args):
- """Copy a job's script to the destination repository, and update its record.
-
- Given a jobspec dictionary, this function finds the referenced script from
- src and copies it to dst and dst_repo. It also updates jobspec in place to
- refer to names on the destination.
- """
- repo = jobspec.get('repository')
- if repo is None:
- return
- # script_version is the "script_version" parameter from the source
- # component or job. If no script_version was supplied in the
- # component or job, it is a mistake in the pipeline, but for the
- # purposes of copying the repository, default to "master".
- script_version = jobspec.get('script_version') or 'master'
- script_key = (repo, script_version)
- if script_key not in scripts_copied:
- copy_git_repo(repo, src, dst, dst_repo, script_version, args)
- scripts_copied.add(script_key)
- jobspec['repository'] = dst_repo
- repo_dir = local_repo_dir[repo]
- for version_key in ['script_version', 'supplied_script_version']:
- if version_key in jobspec:
- jobspec[version_key] = git_rev_parse(jobspec[version_key], repo_dir)
-
-# copy_git_repos(p, src, dst, dst_repo, args)
-#
-# Copies all git repositories referenced by pipeline instance or
-# template 'p' from src to dst.
-#
-# For each component c in the pipeline:
-# * Copy git repositories named in c['repository'] and c['job']['repository'] if present
-# * Rename script versions:
-# * c['script_version']
-# * c['job']['script_version']
-# * c['job']['supplied_script_version']
-# to the commit hashes they resolve to, since any symbolic
-# names (tags, branches) are not preserved in the destination repo.
-#
-# The pipeline object is updated in place with the new repository
-# names. The return value is undefined.
-#
-def copy_git_repos(p, src, dst, dst_repo, args):
- for component in p['components'].values():
- migrate_jobspec(component, src, dst, dst_repo, args)
- if 'job' in component:
- migrate_jobspec(component['job'], src, dst, dst_repo, args)
def total_collection_size(manifest_text):
"""Return the total number of bytes in this collection (excluding
available."""
collection_uuid = c['uuid']
- del c['uuid']
-
- if not c["name"]:
- c['name'] = "copied from " + collection_uuid
+ body = {}
+ for d in ('description', 'manifest_text', 'name', 'portable_data_hash', 'properties'):
+ body[d] = c[d]
- if 'properties' in c:
- del c['properties']
+ if not body["name"]:
+ body['name'] = "copied from " + collection_uuid
- c['owner_uuid'] = args.project_uuid
+ body['owner_uuid'] = args.project_uuid
- dst_collection = dst.collections().create(body=c, ensure_unique_name=True).execute(num_retries=args.retries)
+ dst_collection = dst.collections().create(body=body, ensure_unique_name=True).execute(num_retries=args.retries)
# Create docker_image_repo+tag and docker_image_hash links
# at the destination.
c = items[0]
if not c:
# See if there is a collection that's in the same project
- # as the root item (usually a pipeline) being copied.
+ # as the root item (usually a workflow) being copied.
for i in items:
if i.get("owner_uuid") == src_owner_uuid and i.get("name"):
c = i
return (git_url, git_config)
-# copy_git_repo(src_git_repo, src, dst, dst_git_repo, script_version, args)
-#
-# Copies commits from git repository 'src_git_repo' on Arvados
-# instance 'src' to 'dst_git_repo' on 'dst'. Both src_git_repo
-# and dst_git_repo are repository names, not UUIDs (i.e. "arvados"
-# or "jsmith")
-#
-# All commits will be copied to a destination branch named for the
-# source repository URL.
-#
-# The destination repository must already exist.
-#
-# The user running this command must be authenticated
-# to both repositories.
-#
-def copy_git_repo(src_git_repo, src, dst, dst_git_repo, script_version, args):
- # Identify the fetch and push URLs for the git repositories.
-
- (src_git_url, src_git_config) = select_git_url(src, src_git_repo, args.retries, args.allow_git_http_src, "--allow-git-http-src")
- (dst_git_url, dst_git_config) = select_git_url(dst, dst_git_repo, args.retries, args.allow_git_http_dst, "--allow-git-http-dst")
-
- logger.debug('src_git_url: {}'.format(src_git_url))
- logger.debug('dst_git_url: {}'.format(dst_git_url))
-
- dst_branch = re.sub(r'\W+', '_', "{}_{}".format(src_git_url, script_version))
-
- # Copy git commits from src repo to dst repo.
- if src_git_repo not in local_repo_dir:
- local_repo_dir[src_git_repo] = tempfile.mkdtemp()
- arvados.util.run_command(
- ["git"] + src_git_config + ["clone", "--bare", src_git_url,
- local_repo_dir[src_git_repo]],
- cwd=os.path.dirname(local_repo_dir[src_git_repo]),
- env={"HOME": os.environ["HOME"],
- "ARVADOS_API_TOKEN": src.api_token,
- "GIT_ASKPASS": "/bin/false"})
- arvados.util.run_command(
- ["git", "remote", "add", "dst", dst_git_url],
- cwd=local_repo_dir[src_git_repo])
- arvados.util.run_command(
- ["git", "branch", dst_branch, script_version],
- cwd=local_repo_dir[src_git_repo])
- arvados.util.run_command(["git"] + dst_git_config + ["push", "dst", dst_branch],
- cwd=local_repo_dir[src_git_repo],
- env={"HOME": os.environ["HOME"],
- "ARVADOS_API_TOKEN": dst.api_token,
- "GIT_ASKPASS": "/bin/false"})
-
-def copy_docker_images(pipeline, src, dst, args):
- """Copy any docker images named in the pipeline components'
- runtime_constraints field from src to dst."""
-
- logger.debug('copy_docker_images: {}'.format(pipeline['uuid']))
- for c_name, c_info in pipeline['components'].items():
- if ('runtime_constraints' in c_info and
- 'docker_image' in c_info['runtime_constraints']):
- copy_docker_image(
- c_info['runtime_constraints']['docker_image'],
- c_info['runtime_constraints'].get('docker_image_tag', 'latest'),
- src, dst, args)
-
-
def copy_docker_image(docker_image, docker_image_tag, src, dst, args):
"""Copy the docker image identified by docker_image and
docker_image_tag from src to dst. Create appropriate
# the second field of the uuid. This function consults the api's
# schema to identify the object class.
#
-# It returns a string such as 'Collection', 'PipelineInstance', etc.
+# It returns a string such as 'Collection', 'Workflow', etc.
#
# Special case: if handed a Keep locator hash, return 'Collection'.
#
'google-api-python-client >=1.6.2, <1.7',
'httplib2 >=0.9.2',
'pycurl >=7.19.5.1',
- 'ruamel.yaml >=0.15.54, <=0.15.77',
+ 'ruamel.yaml >=0.15.54, <=0.16.5',
'setuptools',
'ws4py >=0.4.2',
],
net-ssh-gateway (2.0.0)
net-ssh (>= 4.0.0)
nio4r (2.3.1)
- nokogiri (1.10.2)
+ nokogiri (1.10.8)
mini_portile2 (~> 2.4.0)
oauth2 (1.4.1)
faraday (>= 0.8, < 0.16.0)
method_source
rake (>= 0.8.7)
thor (>= 0.18.1, < 2.0)
- rake (12.3.2)
+ rake (13.0.1)
rb-fsevent (0.10.3)
rb-inotify (0.9.10)
ffi (>= 0.5.0, < 2)
projects / arvados.git / commitdiff