[ARVADOS] updated: 8539a6c20fecc7bed02f1c7f81d3d2a1c0974e1f
Git user
git at public.curoverse.com
Mon Mar 21 17:06:07 EDT 2016
Summary of changes:
Makefile | 17 +
backports/python-llfuse/fpm-info.sh | 3 -
build/create-plot-data-from-log.sh | 59 ++
build/libcloud-pin | 1 +
build/package-build-dockerfiles/.gitignore | 2 +
build/package-build-dockerfiles/Makefile | 29 +
build/package-build-dockerfiles/README | 13 +
.../build-all-build-containers.sh | 16 +
build/package-build-dockerfiles/centos6/Dockerfile | 31 +
build/package-build-dockerfiles/debian7/Dockerfile | 19 +
build/package-build-dockerfiles/debian8/Dockerfile | 19 +
.../ubuntu1204/Dockerfile | 19 +
.../ubuntu1404/Dockerfile | 19 +
build/package-test-dockerfiles/centos6/Dockerfile | 20 +
.../centos6/localrepo.repo | 5 +
build/package-test-dockerfiles/debian7/Dockerfile | 14 +
build/package-test-dockerfiles/debian8/Dockerfile | 14 +
.../package-test-dockerfiles/ubuntu1204/Dockerfile | 14 +
.../package-test-dockerfiles/ubuntu1404/Dockerfile | 14 +
build/package-testing/common-test-packages.sh | 28 +
build/package-testing/deb-common-test-packages.sh | 37 +
.../test-package-arvados-api-server.sh | 20 +
.../test-package-arvados-node-manager.sh | 7 +
.../test-package-arvados-sso-server.sh | 172 +++++
.../test-package-arvados-workbench.sh | 20 +
.../test-package-python27-python-arvados-fuse.sh | 6 +
...ackage-python27-python-arvados-python-client.sh | 6 +
build/package-testing/test-packages-centos6.sh | 44 ++
build/package-testing/test-packages-debian7.sh | 1 +
build/package-testing/test-packages-debian8.sh | 1 +
build/package-testing/test-packages-ubuntu1204.sh | 1 +
build/package-testing/test-packages-ubuntu1404.sh | 1 +
build/rails-package-scripts/README.md | 14 +
build/rails-package-scripts/arvados-api-server.sh | 32 +
build/rails-package-scripts/arvados-sso-server.sh | 9 +
build/rails-package-scripts/arvados-workbench.sh | 7 +
build/rails-package-scripts/postinst.sh | 251 +++++++
build/rails-package-scripts/postrm.sh | 23 +
build/rails-package-scripts/prerm.sh | 22 +
build/rails-package-scripts/step2.sh | 28 +
build/run-build-docker-images.sh | 167 +++++
build/run-build-docker-jobs-image.sh | 164 +++++
build/run-build-packages-all-targets.sh | 98 +++
build/run-build-packages-one-target.sh | 203 ++++++
build/run-build-packages-sso.sh | 161 ++++
build/run-build-packages.sh | 567 +++++++++++++++
build/run-build-test-packages-one-target.sh | 111 +++
build/run-library.sh | 385 ++++++++++
build/run-tests.sh | 806 +++++++++++++++++++++
crunch_scripts/cwl-runner | 12 +-
docker/compute/Dockerfile | 2 +-
docker/shell/Dockerfile | 2 +-
sdk/cli/bin/crunch-job | 4 +-
sdk/cwl/arvados_cwl/__init__.py | 112 ++-
sdk/cwl/setup.py | 2 +
.../cwl/tests/__init__.py | 0
sdk/cwl/tests/test_job.py | 81 +++
sdk/go/httpserver/responsewriter.go | 6 +-
sdk/python/arvados/arvfile.py | 2 +
sdk/python/arvados/commands/run.py | 7 +-
sdk/python/tests/test_keep_client.py | 1 +
sdk/python/tests/test_stream.py | 13 +
sdk/ruby/arvados.gemspec | 5 +-
.../v1/api_client_authorizations_controller.rb | 65 +-
.../api/app/models/api_client_authorization.rb | 5 +-
.../api_client_authorizations_controller_test.rb | 92 ++-
.../arvados/v1/repositories_controller_test.rb | 14 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 300 ++++++++
.../crunch-dispatch-slurm_test.go} | 88 +--
.../crunch-dispatch-slurm/crunch-finish-slurm.sh | 20 +
services/datamanager/collection/collection.go | 14 +-
services/dockercleaner/arvados_docker/cleaner.py | 2 +-
services/dockercleaner/tests/test_cleaner.py | 16 +-
services/keepstore/azure_blob_volume.go | 6 +
services/keepstore/keepstore.go | 37 +-
services/keepstore/s3_volume.go | 7 +
services/keepstore/volume.go | 4 +
services/keepstore/volume_generic_test.go | 181 ++++-
services/keepstore/volume_test.go | 3 +
services/keepstore/volume_unix.go | 106 ++-
.../arvnodeman/computenode/dispatch/__init__.py | 8 +-
.../arvnodeman/computenode/driver/__init__.py | 11 +-
.../arvnodeman/computenode/driver/azure.py | 6 +-
.../arvnodeman/computenode/driver/ec2.py | 4 +
.../arvnodeman/computenode/driver/gce.py | 4 +
services/nodemanager/arvnodeman/daemon.py | 6 +-
.../nodemanager/tests/test_computenode_dispatch.py | 1 +
.../tests/test_computenode_driver_azure.py | 10 +
services/nodemanager/tests/test_daemon.py | 3 +-
services/nodemanager/tests/testutil.py | 2 +-
90 files changed, 4800 insertions(+), 184 deletions(-)
create mode 100644 Makefile
create mode 100755 build/create-plot-data-from-log.sh
create mode 100644 build/libcloud-pin
create mode 100644 build/package-build-dockerfiles/.gitignore
create mode 100644 build/package-build-dockerfiles/Makefile
create mode 100644 build/package-build-dockerfiles/README
create mode 100755 build/package-build-dockerfiles/build-all-build-containers.sh
create mode 100644 build/package-build-dockerfiles/centos6/Dockerfile
create mode 100644 build/package-build-dockerfiles/debian7/Dockerfile
create mode 100644 build/package-build-dockerfiles/debian8/Dockerfile
create mode 100644 build/package-build-dockerfiles/ubuntu1204/Dockerfile
create mode 100644 build/package-build-dockerfiles/ubuntu1404/Dockerfile
create mode 100644 build/package-test-dockerfiles/centos6/Dockerfile
create mode 100644 build/package-test-dockerfiles/centos6/localrepo.repo
create mode 100644 build/package-test-dockerfiles/debian7/Dockerfile
create mode 100644 build/package-test-dockerfiles/debian8/Dockerfile
create mode 100644 build/package-test-dockerfiles/ubuntu1204/Dockerfile
create mode 100644 build/package-test-dockerfiles/ubuntu1404/Dockerfile
create mode 100755 build/package-testing/common-test-packages.sh
create mode 100755 build/package-testing/deb-common-test-packages.sh
create mode 100755 build/package-testing/test-package-arvados-api-server.sh
create mode 100755 build/package-testing/test-package-arvados-node-manager.sh
create mode 100755 build/package-testing/test-package-arvados-sso-server.sh
create mode 100755 build/package-testing/test-package-arvados-workbench.sh
create mode 100755 build/package-testing/test-package-python27-python-arvados-fuse.sh
create mode 100755 build/package-testing/test-package-python27-python-arvados-python-client.sh
create mode 100755 build/package-testing/test-packages-centos6.sh
create mode 120000 build/package-testing/test-packages-debian7.sh
create mode 120000 build/package-testing/test-packages-debian8.sh
create mode 120000 build/package-testing/test-packages-ubuntu1204.sh
create mode 120000 build/package-testing/test-packages-ubuntu1404.sh
create mode 100644 build/rails-package-scripts/README.md
create mode 100644 build/rails-package-scripts/arvados-api-server.sh
create mode 100644 build/rails-package-scripts/arvados-sso-server.sh
create mode 100644 build/rails-package-scripts/arvados-workbench.sh
create mode 100644 build/rails-package-scripts/postinst.sh
create mode 100644 build/rails-package-scripts/postrm.sh
create mode 100644 build/rails-package-scripts/prerm.sh
create mode 100644 build/rails-package-scripts/step2.sh
create mode 100755 build/run-build-docker-images.sh
create mode 100755 build/run-build-docker-jobs-image.sh
create mode 100755 build/run-build-packages-all-targets.sh
create mode 100755 build/run-build-packages-one-target.sh
create mode 100755 build/run-build-packages-sso.sh
create mode 100755 build/run-build-packages.sh
create mode 100755 build/run-build-test-packages-one-target.sh
create mode 100755 build/run-library.sh
create mode 100755 build/run-tests.sh
copy apps/workbench/app/views/application/_breadcrumb_page_name.html.erb => sdk/cwl/tests/__init__.py (100%)
create mode 100644 sdk/cwl/tests/test_job.py
create mode 100644 services/crunch-dispatch-slurm/crunch-dispatch-slurm.go
copy services/{crunch-dispatch-local/crunch-dispatch-local_test.go => crunch-dispatch-slurm/crunch-dispatch-slurm_test.go} (58%)
create mode 100755 services/crunch-dispatch-slurm/crunch-finish-slurm.sh
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Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 8539a6c20fecc7bed02f1c7f81d3d2a1c0974e1f
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Mar 21 17:05:08 2016 -0400
8654: Job has uuid and state fields
diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 05be46a..80995f3 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -37,7 +37,7 @@ try:
np.enable_reuse = True
np.submit = False
np.debug = True
- outputObj = runner.arvExecutor(t, job_order_object, "", np, cwl_runner_job=arvados.current_job())
+ outputObj = runner.arvExecutor(t, job_order_object, "", np, cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]})
files = {}
def capture(path):
commit cb6d05e27e37f29ea99cf6e474ee09a1479252e1
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Mar 21 17:02:51 2016 -0400
8654: Add args.debug = True to get backtraces on errors
diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index fbcb873..05be46a 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -36,6 +36,7 @@ try:
np.project_uuid = arvados.current_job()["owner_uuid"]
np.enable_reuse = True
np.submit = False
+ np.debug = True
outputObj = runner.arvExecutor(t, job_order_object, "", np, cwl_runner_job=arvados.current_job())
files = {}
commit 46f5721a767f8e012b3e3183412bb8f9c5ff0ac6
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Mar 21 17:01:15 2016 -0400
8654: Set args.submit = False
diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 7fb14ab..fbcb873 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -35,6 +35,7 @@ try:
np = argparse.Namespace()
np.project_uuid = arvados.current_job()["owner_uuid"]
np.enable_reuse = True
+ np.submit = False
outputObj = runner.arvExecutor(t, job_order_object, "", np, cwl_runner_job=arvados.current_job())
files = {}
commit 8f46e1564dd7c4f42fdccc6e5c8222ce8955405e
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Mar 21 16:55:12 2016 -0400
8654: Add runner job to pipeline instance.
diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 2b52557..7fb14ab 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -35,7 +35,7 @@ try:
np = argparse.Namespace()
np.project_uuid = arvados.current_job()["owner_uuid"]
np.enable_reuse = True
- outputObj = runner.arvExecutor(t, job_order_object, "", np)
+ outputObj = runner.arvExecutor(t, job_order_object, "", np, cwl_runner_job=arvados.current_job())
files = {}
def capture(path):
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index d4c0b64..e170648 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -460,11 +460,15 @@ class ArvCwlRunner(object):
if kwargs.get("conformance_test"):
return cwltool.main.single_job_executor(tool, job_order, input_basedir, args, **kwargs)
else:
+ components = {}
+ if "cwl_runner_job" in kwargs:
+ components[os.path.basename(tool.tool["id"])] = {"job": kwargs["cwl_runner_job"]}
+
self.pipeline = self.api.pipeline_instances().create(
body={
"owner_uuid": self.project_uuid,
"name": shortname(tool.tool["id"]),
- "components": {},
+ "components": components,
"state": "RunningOnClient"}).execute(num_retries=self.num_retries)
logger.info("Pipeline instance %s", self.pipeline["uuid"])
commit 76c7406f60319da7011ac9797ae32eb22f574d4c
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Mar 21 16:46:26 2016 -0400
8654: Update cwl:tool entry
diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 003e418..2b52557 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -24,6 +24,8 @@ try:
if arvados.util.keep_locator_pattern.match(v):
return "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
+ job_order_object["cwl:tool"] = keeppath(job_order_object["cwl:tool"])
+
adjustFiles(job_order_object, keeppath)
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
commit 785a877a46f0c6580d46dac179ea2d4c4a6e7de3
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Mar 21 16:44:31 2016 -0400
8654: Fix keeppath and add ensure_unique_name to upload.
diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 81755b8..003e418 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -22,7 +22,7 @@ try:
def keeppath(v):
if arvados.util.keep_locator_pattern.match(v):
- job_order_object[k] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
+ return "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
adjustFiles(job_order_object, keeppath)
diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py
index 046f706..643d3f5 100644
--- a/sdk/python/arvados/commands/run.py
+++ b/sdk/python/arvados/commands/run.py
@@ -151,7 +151,7 @@ def uploadfiles(files, api, dry_run=False, num_retries=0, project=None, fnPatter
body = {"owner_uuid": project, "manifest_text": collection.manifest_text()}
if name is not None:
body["name"] = name
- item = api.collections().create(body=body).execute()
+ item = api.collections().create(body=body, ensure_unique_name=True).execute()
pdh = item["portable_data_hash"]
logger.info("Uploaded to %s", item["uuid"])
commit 4fecea55bd6dd5befd82bf7ec5dd4fe93bd93cea
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Mar 21 16:24:06 2016 -0400
8654: Scanning for and uploading dependencies for submit works. Add test for
--submit. Fix cwl-runner to handle CWL File objects in script_parameters.
diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index d042426..81755b8 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -20,10 +20,12 @@ try:
print job_order_object
- for k,v in job_order_object.items():
+ def keeppath(v):
if arvados.util.keep_locator_pattern.match(v):
job_order_object[k] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
+ adjustFiles(job_order_object, keeppath)
+
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
t = cwltool.main.load_tool(job_order_object, False, True, runner.arvMakeTool, True)
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index c0adb33..d4c0b64 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -19,8 +19,9 @@ import logging
import re
import os
import sys
+import functools
-from cwltool.process import get_feature
+from cwltool.process import get_feature, adjustFiles, scandeps
from arvados.api import OrderedJsonModel
logger = logging.getLogger('arvados.cwl-runner')
@@ -249,7 +250,7 @@ class ArvadosJob(object):
class ArvPathMapper(cwltool.pathmapper.PathMapper):
def __init__(self, arvrunner, referenced_files, basedir,
- collection_pattern, file_pattern, **kwargs):
+ collection_pattern, file_pattern, name=None, **kwargs):
self._pathmap = arvrunner.get_uploaded()
uploadfiles = []
@@ -276,6 +277,7 @@ class ArvPathMapper(cwltool.pathmapper.PathMapper):
dry_run=kwargs.get("dry_run"),
num_retries=3,
fnPattern=file_pattern,
+ name=name,
project=arvrunner.project_uuid)
for src, ab, st in uploadfiles:
@@ -368,22 +370,43 @@ class ArvCwlRunner(object):
pass
def submit(self, tool, job_order, input_basedir, args, **kwargs):
- files = set()
- def visitFiles(self, path):
+ workflowfiles = set()
+ jobfiles = set()
+ workflowfiles.add(tool.tool["id"])
+
+ def visitFiles(files, path):
files.add(path)
+ return path
- adjustFiles(process.scandeps("", tool.tool,
- set(("run")),
- set(("$schemas", "path"))),
- visitFiles)
- adjustFiles(job_order, visitFiles)
+ document_loader, _, _ = cwltool.process.get_schema()
+ def loadref(b, u):
+ return document_loader.resolve_ref(u, base_url=b)[0]
- mapper = ArvPathMapper(self, files, "",
- "$(task.keep)/%s",
- "$(task.keep)/%s/%s",
- **kwargs)
+ adjustFiles(scandeps("", tool.tool,
+ set(("run",)),
+ set(("$schemas", "path")),
+ loadref),
+ functools.partial(visitFiles, workflowfiles))
+ adjustFiles(job_order, functools.partial(visitFiles, jobfiles))
+
+ workflowmapper = ArvPathMapper(self, workflowfiles, "",
+ "%s",
+ "%s/%s",
+ name=os.path.basename(tool.tool["id"]),
+ **kwargs)
+
+ jobmapper = ArvPathMapper(self, jobfiles, "",
+ "%s",
+ "%s/%s",
+ name=os.path.basename(job_order.get("id", "#")),
+ **kwargs)
- job_order = adjustFiles(job_order, lambda p: mapper.mapper(p))
+ adjustFiles(job_order, lambda p: jobmapper.mapper(p)[1])
+
+ if "id" in job_order:
+ del job_order["id"]
+
+ job_order["cwl:tool"] = workflowmapper.mapper(tool.tool["id"])[1]
response = self.api.jobs().create(body={
"script": "cwl-runner",
@@ -394,14 +417,18 @@ class ArvCwlRunner(object):
"docker_image": "arvados/jobs"
}
}, find_or_create=args.enable_reuse).execute(num_retries=self.num_retries)
- print response["uuid"]
- return None
+
+ logger.info("Submitted job %s", response["uuid"])
+
+ return
def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
+ useruuid = self.api.users().current().execute()["uuid"]
+ self.project_uuid = args.project_uuid if args.project_uuid else useruuid
+
if args.submit:
- self.submit(tool, job_order, input_basedir, args, **kwargs)
- return
+ return self.submit(tool, job_order, input_basedir, args, **kwargs)
events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
@@ -430,9 +457,6 @@ class ArvCwlRunner(object):
kwargs["outdir"] = "$(task.outdir)"
kwargs["tmpdir"] = "$(task.tmpdir)"
- useruuid = self.api.users().current().execute()["uuid"]
- self.project_uuid = args.project_uuid if args.project_uuid else useruuid
-
if kwargs.get("conformance_test"):
return cwltool.main.single_job_executor(tool, job_order, input_basedir, args, **kwargs)
else:
@@ -500,12 +524,20 @@ def main(args, stdout, stderr, api_client=None):
default=True, dest="enable_reuse",
help="")
parser.add_argument("--project-uuid", type=str, help="Project that will own the workflow jobs")
- parser.add_argument("--submit", type=str, help="Submit job and print job uuid.")
+ parser.add_argument("--submit", action="store_true", help="Submit job and print job uuid.",
+ default=False)
try:
- runner = ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
+ if api_client is None:
+ api_client=arvados.api('v1', model=OrderedJsonModel())
+ runner = ArvCwlRunner(api_client)
except Exception as e:
logger.error(e)
return 1
- return cwltool.main.main(args, executor=runner.arvExecutor, makeTool=runner.arvMakeTool, parser=parser)
+ return cwltool.main.main(args,
+ stdout=stdout,
+ stderr=stderr,
+ executor=runner.arvExecutor,
+ makeTool=runner.arvMakeTool,
+ parser=parser)
diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py
index ef39be8..046f706 100644
--- a/sdk/python/arvados/commands/run.py
+++ b/sdk/python/arvados/commands/run.py
@@ -101,7 +101,7 @@ def statfile(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)"):
return prefix+fn
-def uploadfiles(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)"):
+def uploadfiles(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)", name=None):
# Find the smallest path prefix that includes all the files that need to be uploaded.
# This starts at the root and iteratively removes common parent directory prefixes
# until all file pathes no longer have a common parent.
@@ -148,7 +148,10 @@ def uploadfiles(files, api, dry_run=False, num_retries=0, project=None, fnPatter
stream = sp[0]
collection.start_new_stream(stream)
collection.write_file(f.fn, sp[1])
- item = api.collections().create(body={"owner_uuid": project, "manifest_text": collection.manifest_text()}).execute()
+ body = {"owner_uuid": project, "manifest_text": collection.manifest_text()}
+ if name is not None:
+ body["name"] = name
+ item = api.collections().create(body=body).execute()
pdh = item["portable_data_hash"]
logger.info("Uploaded to %s", item["uuid"])
commit f04cfcce18c6e4bd1faf3140ccbc835328580024
Merge: 8e6e328 9c65985
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Mar 21 12:37:38 2016 -0400
Merge branch 'master' into 8654-arv-jobs-cwl-runner
diff --cc sdk/cwl/arvados_cwl/__init__.py
index 480d18e,5ed83ab..c0adb33
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@@ -348,47 -360,11 +364,49 @@@ class ArvCwlRunner(object)
def add_uploaded(self, src, pair):
self.uploaded[src] = pair
+ def upload_docker(self, tool):
+ pass
+
+ def submit(self, tool, job_order, input_basedir, args, **kwargs):
+ files = set()
+ def visitFiles(self, path):
+ files.add(path)
+
+ adjustFiles(process.scandeps("", tool.tool,
+ set(("run")),
+ set(("$schemas", "path"))),
+ visitFiles)
+ adjustFiles(job_order, visitFiles)
+
+ mapper = ArvPathMapper(self, files, "",
+ "$(task.keep)/%s",
+ "$(task.keep)/%s/%s",
+ **kwargs)
+
+ job_order = adjustFiles(job_order, lambda p: mapper.mapper(p))
+
+ response = self.api.jobs().create(body={
+ "script": "cwl-runner",
+ "script_version": "8654-arv-jobs-cwl-runner",
+ "repository": "arvados",
+ "script_parameters": job_order,
+ "runtime_constraints": {
+ "docker_image": "arvados/jobs"
+ }
+ }, find_or_create=args.enable_reuse).execute(num_retries=self.num_retries)
+ print response["uuid"]
+ return None
+
+
def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
+ if args.submit:
+ self.submit(tool, job_order, input_basedir, args, **kwargs)
+ return
+
events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
+ self.debug = args.debug
+
try:
self.api.collections().get(uuid=crunchrunner_pdh).execute()
except arvados.errors.ApiError as e:
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