from cwltool.errors import WorkflowException
import cwltool.main
import cwltool.workflow
+import schema_salad
import arvados
import arvados.config
from .arvcontainer import ArvadosContainer, RunnerContainer
from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
from .arvtool import ArvadosCommandTool
+from .arvworkflow import ArvadosWorkflow, upload_workflow
from .fsaccess import CollectionFsAccess
-from .arvworkflow import make_workflow
+from .perf import Perf
+from cwltool.pack import pack
from cwltool.process import shortname, UnsupportedRequirement
from cwltool.pathmapper import adjustFileObjs
self.work_api = work_api
self.stop_polling = threading.Event()
self.poll_api = None
+ self.pipeline = None
if self.work_api is None:
# todo: autodetect API to use.
if self.work_api not in ("containers", "jobs"):
raise Exception("Unsupported API '%s'" % self.work_api)
- def arvMakeTool(self, toolpath_object, **kwargs):
+ def arv_make_tool(self, toolpath_object, **kwargs):
+ kwargs["work_api"] = self.work_api
if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
- kwargs["work_api"] = self.work_api
return ArvadosCommandTool(self, toolpath_object, **kwargs)
+ elif "class" in toolpath_object and toolpath_object["class"] == "Workflow":
+ return ArvadosWorkflow(self, toolpath_object, **kwargs)
else:
return cwltool.workflow.defaultMakeTool(toolpath_object, **kwargs)
self.cond.acquire()
j = self.processes[uuid]
logger.info("Job %s (%s) is %s", j.name, uuid, event["properties"]["new_attributes"]["state"])
- j.done(event["properties"]["new_attributes"])
+ with Perf(logger, "done %s" % j.name):
+ j.done(event["properties"]["new_attributes"])
self.cond.notify()
finally:
self.cond.release()
for v in obj:
self.check_writable(v)
- def arvExecutor(self, tool, job_order, **kwargs):
+ def arv_executor(self, tool, job_order, **kwargs):
self.debug = kwargs.get("debug")
tool.visit(self.check_writable)
- if kwargs.get("quiet"):
- logger.setLevel(logging.WARN)
- logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
-
useruuid = self.api.users().current().execute()["uuid"]
self.project_uuid = kwargs.get("project_uuid") if kwargs.get("project_uuid") else useruuid
self.pipeline = None
return tmpl.uuid
if kwargs.get("create_workflow") or kwargs.get("update_workflow"):
- return make_workflow(self, tool, job_order, self.project_uuid, kwargs.get("update_workflow"))
+ return upload_workflow(self, tool, job_order, self.project_uuid, kwargs.get("update_workflow"))
- self.debug = kwargs.get("debug")
self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
kwargs["make_fs_access"] = make_fs_access
for runnable in jobiter:
if runnable:
- runnable.run(**kwargs)
+ with Perf(logger, "run"):
+ runnable.run(**kwargs)
else:
if self.processes:
self.cond.wait(1)
default=True, dest="enable_reuse",
help="")
- parser.add_argument("--project-uuid", type=str, help="Project that will own the workflow jobs, if not provided, will go to home project.")
+ parser.add_argument("--project-uuid", type=str, metavar="UUID", help="Project that will own the workflow jobs, if not provided, will go to home project.")
parser.add_argument("--ignore-docker-for-reuse", action="store_true",
help="Ignore Docker image version when deciding whether to reuse past jobs.",
default=False)
default=True, dest="submit")
exgroup.add_argument("--create-template", action="store_true", help="Create an Arvados pipeline template.")
exgroup.add_argument("--create-workflow", action="store_true", help="Create an Arvados workflow.")
- exgroup.add_argument("--update-workflow", type=str, help="Update Arvados workflow.")
+ exgroup.add_argument("--update-workflow", type=str, metavar="UUID", help="Update existing Arvados workflow with uuid.")
exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",
return parser
+def add_arv_hints():
+ cache = {}
+ res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
+ cache["https://w3id.org/cwl/arv-cwl-schema.yml"] = res.read()
+ res.close()
+ _, cwlnames, _, _ = cwltool.process.get_schema("v1.0")
+ _, extnames, _, _ = schema_salad.schema.load_schema("https://w3id.org/cwl/arv-cwl-schema.yml", cache=cache)
+ for n in extnames.names:
+ if not cwlnames.has_name("http://arvados.org/cwl#"+n, ""):
+ cwlnames.add_name("http://arvados.org/cwl#"+n, "", extnames.get_name(n, ""))
def main(args, stdout, stderr, api_client=None):
parser = arg_parser()
if (arvargs.create_template or arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
job_order_object = ({}, "")
+ add_arv_hints()
+
try:
if api_client is None:
api_client=arvados.api('v1', model=OrderedJsonModel())
logger.error(e)
return 1
+ if arvargs.debug:
+ logger.setLevel(logging.DEBUG)
+
+ if arvargs.quiet:
+ logger.setLevel(logging.WARN)
+ logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
+
arvargs.conformance_test = None
arvargs.use_container = True
return cwltool.main.main(args=arvargs,
stdout=stdout,
stderr=stderr,
- executor=runner.arvExecutor,
- makeTool=runner.arvMakeTool,
+ executor=runner.arv_executor,
+ makeTool=runner.arv_make_tool,
versionfunc=versionstring,
job_order_object=job_order_object,
make_fs_access=partial(CollectionFsAccess, api_client=api_client))
projects / arvados.git / blobdiff