#!/usr/bin/env python
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
# Implement cwl-runner interface for submitting and running work on Arvados, using
# either the Crunch jobs API or Crunch containers API.
import hashlib
import copy
import json
+import re
from functools import partial
import pkg_resources # part of setuptools
from cwltool.errors import WorkflowException
import cwltool.main
import cwltool.workflow
+import cwltool.process
import schema_salad
+from schema_salad.sourceline import SourceLine
import arvados
import arvados.config
+from arvados.keep import KeepClient
+from arvados.errors import ApiError
from .arvcontainer import ArvadosContainer, RunnerContainer
from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
-from. runner import Runner, upload_instance
+from. runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, upload_dependencies
from .arvtool import ArvadosCommandTool
from .arvworkflow import ArvadosWorkflow, upload_workflow
-from .fsaccess import CollectionFsAccess
+from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache
from .perf import Perf
-from .pathmapper import FinalOutputPathMapper
+from .pathmapper import NoFollowPathMapper
from ._version import __version__
from cwltool.pack import pack
-from cwltool.process import shortname, UnsupportedRequirement, getListing
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
+from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing
from cwltool.draft2tool import compute_checksums
from arvados.api import OrderedJsonModel
metrics = logging.getLogger('arvados.cwl-runner.metrics')
logger.setLevel(logging.INFO)
+arvados.log_handler.setFormatter(logging.Formatter(
+ '%(asctime)s %(name)s %(levelname)s: %(message)s',
+ '%Y-%m-%d %H:%M:%S'))
class ArvCwlRunner(object):
"""Execute a CWL tool or workflow, submit work (using either jobs or
"""
- def __init__(self, api_client, work_api=None, keep_client=None, output_name=None):
+ def __init__(self, api_client, work_api=None, keep_client=None, output_name=None, output_tags=None, num_retries=4):
self.api = api_client
self.processes = {}
self.lock = threading.Lock()
self.final_output = None
self.final_status = None
self.uploaded = {}
- self.num_retries = 4
+ self.num_retries = num_retries
self.uuid = None
self.stop_polling = threading.Event()
self.poll_api = None
self.pipeline = None
self.final_output_collection = None
self.output_name = output_name
+ self.output_tags = output_tags
self.project_uuid = None
+ self.intermediate_output_ttl = 0
+ self.intermediate_output_collections = []
+ self.trash_intermediate = False
if keep_client is not None:
self.keep_client = keep_client
else:
self.keep_client = arvados.keep.KeepClient(api_client=self.api, num_retries=self.num_retries)
- for api in ["jobs", "containers"]:
+ self.collection_cache = CollectionCache(self.api, self.keep_client, self.num_retries)
+
+ self.work_api = None
+ expected_api = ["jobs", "containers"]
+ for api in expected_api:
try:
methods = self.api._rootDesc.get('resources')[api]['methods']
if ('httpMethod' in methods['create'] and
break
except KeyError:
pass
+
if not self.work_api:
if work_api is None:
raise Exception("No supported APIs")
else:
- raise Exception("Unsupported API '%s'" % work_api)
+ raise Exception("Unsupported API '%s', expected one of %s" % (work_api, expected_api))
def arv_make_tool(self, toolpath_object, **kwargs):
kwargs["work_api"] = self.work_api
+ kwargs["fetcher_constructor"] = partial(CollectionFetcher,
+ api_client=self.api,
+ fs_access=CollectionFsAccess("", collection_cache=self.collection_cache),
+ num_retries=self.num_retries,
+ overrides=kwargs.get("override_tools"))
if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
return ArvadosCommandTool(self, toolpath_object, **kwargs)
elif "class" in toolpath_object and toolpath_object["class"] == "Workflow":
uuid = event["object_uuid"]
with self.lock:
j = self.processes[uuid]
- logger.info("Job %s (%s) is Running", j.name, uuid)
+ logger.info("%s %s is Running", self.label(j), uuid)
j.running = True
j.update_pipeline_component(event["properties"]["new_attributes"])
- elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled"):
+ elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled", "Final"):
uuid = event["object_uuid"]
try:
self.cond.acquire()
j = self.processes[uuid]
- txt = self.work_api[0].upper() + self.work_api[1:-1]
- logger.info("%s %s (%s) is %s", txt, j.name, uuid, event["properties"]["new_attributes"]["state"])
+ logger.info("%s %s is %s", self.label(j), uuid, event["properties"]["new_attributes"]["state"])
with Perf(metrics, "done %s" % j.name):
j.done(event["properties"]["new_attributes"])
self.cond.notify()
finally:
self.cond.release()
+ def label(self, obj):
+ return "[%s %s]" % (self.work_api[0:-1], obj.name)
+
def poll_states(self):
"""Poll status of jobs or containers listed in the processes dict.
Runs in a separate thread.
"""
- while True:
- self.stop_polling.wait(15)
- if self.stop_polling.is_set():
- break
- with self.lock:
- keys = self.processes.keys()
- if not keys:
- continue
+ try:
+ while True:
+ self.stop_polling.wait(15)
+ if self.stop_polling.is_set():
+ break
+ with self.lock:
+ keys = self.processes.keys()
+ if not keys:
+ continue
- if self.work_api == "containers":
- table = self.poll_api.containers()
- elif self.work_api == "jobs":
- table = self.poll_api.jobs()
+ if self.work_api == "containers":
+ table = self.poll_api.container_requests()
+ elif self.work_api == "jobs":
+ table = self.poll_api.jobs()
- try:
- proc_states = table.list(filters=[["uuid", "in", keys]]).execute(num_retries=self.num_retries)
- except Exception as e:
- logger.warn("Error checking states on API server: %s", e)
- continue
-
- for p in proc_states["items"]:
- self.on_message({
- "object_uuid": p["uuid"],
- "event_type": "update",
- "properties": {
- "new_attributes": p
- }
- })
+ try:
+ proc_states = table.list(filters=[["uuid", "in", keys]]).execute(num_retries=self.num_retries)
+ except Exception as e:
+ logger.warn("Error checking states on API server: %s", e)
+ continue
+
+ for p in proc_states["items"]:
+ self.on_message({
+ "object_uuid": p["uuid"],
+ "event_type": "update",
+ "properties": {
+ "new_attributes": p
+ }
+ })
+ except:
+ logger.error("Fatal error in state polling thread.", exc_info=(sys.exc_info()[1] if self.debug else False))
+ self.cond.acquire()
+ self.processes.clear()
+ self.cond.notify()
+ self.cond.release()
+ finally:
+ self.stop_polling.set()
def get_uploaded(self):
return self.uploaded.copy()
def add_uploaded(self, src, pair):
self.uploaded[src] = pair
- def check_writable(self, obj):
+ def add_intermediate_output(self, uuid):
+ if uuid:
+ self.intermediate_output_collections.append(uuid)
+
+ def trash_intermediate_output(self):
+ logger.info("Cleaning up intermediate output collections")
+ for i in self.intermediate_output_collections:
+ try:
+ self.api.collections().delete(uuid=i).execute(num_retries=self.num_retries)
+ except:
+ logger.warn("Failed to delete intermediate output: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
+ if sys.exc_info()[0] is KeyboardInterrupt:
+ break
+
+ def check_features(self, obj):
if isinstance(obj, dict):
if obj.get("writable"):
- raise UnsupportedRequirement("InitialWorkDir feature 'writable: true' not supported")
+ raise SourceLine(obj, "writable", UnsupportedRequirement).makeError("InitialWorkDir feature 'writable: true' not supported")
+ if obj.get("class") == "DockerRequirement":
+ if obj.get("dockerOutputDirectory"):
+ # TODO: can be supported by containers API, but not jobs API.
+ raise SourceLine(obj, "dockerOutputDirectory", UnsupportedRequirement).makeError(
+ "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
for v in obj.itervalues():
- self.check_writable(v)
- if isinstance(obj, list):
- for v in obj:
- self.check_writable(v)
+ self.check_features(v)
+ elif isinstance(obj, list):
+ for i,v in enumerate(obj):
+ with SourceLine(obj, i, UnsupportedRequirement):
+ self.check_features(v)
- def make_output_collection(self, name, outputObj):
+ def make_output_collection(self, name, tagsString, outputObj):
outputObj = copy.deepcopy(outputObj)
files = []
adjustDirObjs(outputObj, capture)
adjustFileObjs(outputObj, capture)
- generatemapper = FinalOutputPathMapper(files, "", "", separateDirs=False)
+ generatemapper = NoFollowPathMapper(files, "", "", separateDirs=False)
final = arvados.collection.Collection(api_client=self.api,
keep_client=self.keep_client,
num_retries=self.num_retries)
- srccollections = {}
for k,v in generatemapper.items():
if k.startswith("_:"):
if v.type == "Directory":
raise Exception("Output source is not in keep or a literal")
sp = k.split("/")
srccollection = sp[0][5:]
- if srccollection not in srccollections:
- try:
- srccollections[srccollection] = arvados.collection.CollectionReader(
- srccollection,
- api_client=self.api,
- keep_client=self.keep_client,
- num_retries=self.num_retries)
- except arvados.errors.ArgumentError as e:
- logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e)
- raise
- reader = srccollections[srccollection]
try:
+ reader = self.collection_cache.get(srccollection)
srcpath = "/".join(sp[1:]) if len(sp) > 1 else "."
final.copy(srcpath, v.target, source_collection=reader, overwrite=False)
+ except arvados.errors.ArgumentError as e:
+ logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e)
+ raise
except IOError as e:
logger.warn("While preparing output collection: %s", e)
final.api_response()["name"],
final.manifest_locator())
+ final_uuid = final.manifest_locator()
+ tags = tagsString.split(',')
+ for tag in tags:
+ self.api.links().create(body={
+ "head_uuid": final_uuid, "link_class": "tag", "name": tag
+ }).execute(num_retries=self.num_retries)
+
def finalcollection(fileobj):
fileobj["location"] = "keep:%s/%s" % (final.portable_data_hash(), fileobj["location"])
if self.work_api == "containers":
try:
current = self.api.containers().current().execute(num_retries=self.num_retries)
+ except ApiError as e:
+ # Status code 404 just means we're not running in a container.
+ if e.resp.status != 404:
+ logger.info("Getting current container: %s", e)
+ return
+ try:
self.api.containers().update(uuid=current['uuid'],
body={
'output': self.final_output_collection.portable_data_hash(),
}).execute(num_retries=self.num_retries)
+ self.api.collections().update(uuid=self.final_output_collection.manifest_locator(),
+ body={
+ 'is_trashed': True
+ }).execute(num_retries=self.num_retries)
except Exception as e:
logger.info("Setting container output: %s", e)
elif self.work_api == "jobs" and "TASK_UUID" in os.environ:
def arv_executor(self, tool, job_order, **kwargs):
self.debug = kwargs.get("debug")
- tool.visit(self.check_writable)
+ tool.visit(self.check_features)
- useruuid = self.api.users().current().execute()["uuid"]
- self.project_uuid = kwargs.get("project_uuid") if kwargs.get("project_uuid") else useruuid
+ self.project_uuid = kwargs.get("project_uuid")
self.pipeline = None
make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess,
- api_client=self.api,
- keep_client=self.keep_client)
+ collection_cache=self.collection_cache)
self.fs_access = make_fs_access(kwargs["basedir"])
- if kwargs.get("create_template"):
- tmpl = RunnerTemplate(self, tool, job_order, kwargs.get("enable_reuse"))
- tmpl.save()
- # cwltool.main will write our return value to stdout.
- return tmpl.uuid
- if kwargs.get("create_workflow") or kwargs.get("update_workflow"):
- return upload_workflow(self, tool, job_order, self.project_uuid, kwargs.get("update_workflow"))
+ self.trash_intermediate = kwargs["trash_intermediate"]
+ if self.trash_intermediate and self.work_api != "containers":
+ raise Exception("--trash-intermediate is only supported with --api=containers.")
+
+ self.intermediate_output_ttl = kwargs["intermediate_output_ttl"]
+ if self.intermediate_output_ttl and self.work_api != "containers":
+ raise Exception("--intermediate-output-ttl is only supported with --api=containers.")
+ if self.intermediate_output_ttl < 0:
+ raise Exception("Invalid value %d for --intermediate-output-ttl, cannot be less than zero" % self.intermediate_output_ttl)
+
+ if not kwargs.get("name"):
+ kwargs["name"] = self.name = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
+
+ # Upload direct dependencies of workflow steps, get back mapping of files to keep references.
+ # Also uploads docker images.
+ override_tools = {}
+ upload_workflow_deps(self, tool, override_tools)
+
+ # Reload tool object which may have been updated by
+ # upload_workflow_deps
+ tool = self.arv_make_tool(tool.doc_loader.idx[tool.tool["id"]],
+ makeTool=self.arv_make_tool,
+ loader=tool.doc_loader,
+ avsc_names=tool.doc_schema,
+ metadata=tool.metadata,
+ override_tools=override_tools)
+
+ # Upload local file references in the job order.
+ job_order = upload_job_order(self, "%s input" % kwargs["name"],
+ tool, job_order)
+
+ existing_uuid = kwargs.get("update_workflow")
+ if existing_uuid or kwargs.get("create_workflow"):
+ # Create a pipeline template or workflow record and exit.
+ if self.work_api == "jobs":
+ tmpl = RunnerTemplate(self, tool, job_order,
+ kwargs.get("enable_reuse"),
+ uuid=existing_uuid,
+ submit_runner_ram=kwargs.get("submit_runner_ram"),
+ name=kwargs["name"])
+ tmpl.save()
+ # cwltool.main will write our return value to stdout.
+ return (tmpl.uuid, "success")
+ elif self.work_api == "containers":
+ return (upload_workflow(self, tool, job_order,
+ self.project_uuid,
+ uuid=existing_uuid,
+ submit_runner_ram=kwargs.get("submit_runner_ram"),
+ name=kwargs["name"]),
+ "success")
self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
kwargs["enable_reuse"] = kwargs.get("enable_reuse")
kwargs["use_container"] = True
kwargs["tmpdir_prefix"] = "tmp"
- kwargs["on_error"] = "continue"
kwargs["compute_checksum"] = kwargs.get("compute_checksum")
if self.work_api == "containers":
kwargs["docker_outdir"] = "$(task.outdir)"
kwargs["tmpdir"] = "$(task.tmpdir)"
- upload_instance(self, shortname(tool.tool["id"]), tool, job_order)
-
runnerjob = None
if kwargs.get("submit"):
+ # Submit a runner job to run the workflow for us.
if self.work_api == "containers":
- if tool.tool["class"] == "CommandLineTool":
+ if tool.tool["class"] == "CommandLineTool" and kwargs.get("wait"):
+ kwargs["runnerjob"] = tool.tool["id"]
+ upload_dependencies(self,
+ kwargs["name"],
+ tool.doc_loader,
+ tool.tool,
+ tool.tool["id"],
+ False)
runnerjob = tool.job(job_order,
self.output_callback,
**kwargs).next()
else:
- runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name)
- else:
- runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name)
-
- if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and not self.work_api == "containers":
+ runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"),
+ self.output_name,
+ self.output_tags,
+ submit_runner_ram=kwargs.get("submit_runner_ram"),
+ name=kwargs.get("name"),
+ on_error=kwargs.get("on_error"),
+ submit_runner_image=kwargs.get("submit_runner_image"),
+ intermediate_output_ttl=kwargs.get("intermediate_output_ttl"))
+ elif self.work_api == "jobs":
+ runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"),
+ self.output_name,
+ self.output_tags,
+ submit_runner_ram=kwargs.get("submit_runner_ram"),
+ name=kwargs.get("name"),
+ on_error=kwargs.get("on_error"),
+ submit_runner_image=kwargs.get("submit_runner_image"))
+ elif "cwl_runner_job" not in kwargs and self.work_api == "jobs":
# Create pipeline for local run
self.pipeline = self.api.pipeline_instances().create(
body={
"owner_uuid": self.project_uuid,
- "name": shortname(tool.tool["id"]),
+ "name": kwargs["name"] if kwargs.get("name") else shortname(tool.tool["id"]),
"components": {},
"state": "RunningOnClient"}).execute(num_retries=self.num_retries)
logger.info("Pipeline instance %s", self.pipeline["uuid"])
if runnerjob and not kwargs.get("wait"):
runnerjob.run(wait=kwargs.get("wait"))
- return runnerjob.uuid
+ return (runnerjob.uuid, "success")
self.poll_api = arvados.api('v1')
self.polling_thread = threading.Thread(target=self.poll_states)
loopperf.__enter__()
for runnable in jobiter:
loopperf.__exit__()
+
+ if self.stop_polling.is_set():
+ break
+
if runnable:
with Perf(metrics, "run"):
runnable.run(**kwargs)
if sys.exc_info()[0] is KeyboardInterrupt:
logger.error("Interrupted, marking pipeline as failed")
else:
- logger.error("Caught unhandled exception, marking pipeline as failed. Error was: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
+ logger.error("Execution failed: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
if self.pipeline:
self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
body={"state": "Failed"}).execute(num_retries=self.num_retries)
else:
if self.output_name is None:
self.output_name = "Output of %s" % (shortname(tool.tool["id"]))
- self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, self.final_output)
+ if self.output_tags is None:
+ self.output_tags = ""
+ self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, self.output_tags, self.final_output)
self.set_crunch_output()
- if self.final_status != "success":
- raise WorkflowException("Workflow failed.")
-
if kwargs.get("compute_checksum"):
- adjustDirObjs(self.final_output, partial(getListing, self.fs_access))
+ adjustDirObjs(self.final_output, partial(get_listing, self.fs_access))
adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
- return self.final_output
+ if self.trash_intermediate and self.final_status == "success":
+ self.trash_intermediate_output()
+
+ return (self.final_output, self.final_status)
def versionstring():
help="Time to wait for a Javascript expression to evaluate before giving an error, default 20s.",
type=float,
default=20)
- parser.add_argument("--version", action="store_true", help="Print version and exit")
+
+ exgroup = parser.add_mutually_exclusive_group()
+ exgroup.add_argument("--print-dot", action="store_true",
+ help="Print workflow visualization in graphviz format and exit")
+ exgroup.add_argument("--version", action="store_true", help="Print version and exit")
+ exgroup.add_argument("--validate", action="store_true", help="Validate CWL document only.")
exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--verbose", action="store_true", help="Default logging")
exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--enable-reuse", action="store_true",
default=True, dest="enable_reuse",
- help="")
+ help="Enable job or container reuse (default)")
exgroup.add_argument("--disable-reuse", action="store_false",
default=True, dest="enable_reuse",
- help="")
+ help="Disable job or container reuse")
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("--output-name", type=str, help="Name to use for collection that stores the final output.", default=None)
+ parser.add_argument("--output-tags", type=str, help="Tags for the final output collection separated by commas, e.g., '--output-tags tag0,tag1,tag2'.", default=None)
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("--local", action="store_false", help="Run workflow on local host (submits jobs to Arvados).",
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, metavar="UUID", help="Update existing Arvados workflow with uuid.")
+ exgroup.add_argument("--create-template", action="store_true", help="(Deprecated) synonym for --create-workflow.",
+ dest="create_workflow")
+ exgroup.add_argument("--create-workflow", action="store_true", help="Create an Arvados workflow (if using the 'containers' API) or pipeline template (if using the 'jobs' API). See --api.")
+ exgroup.add_argument("--update-workflow", type=str, metavar="UUID", help="Update an existing Arvados workflow or pipeline template with the given UUID.")
exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",
exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner job and exit.",
default=True, dest="wait")
+ exgroup = parser.add_mutually_exclusive_group()
+ exgroup.add_argument("--log-timestamps", action="store_true", help="Prefix logging lines with timestamp",
+ default=True, dest="log_timestamps")
+ exgroup.add_argument("--no-log-timestamps", action="store_false", help="No timestamp on logging lines",
+ default=True, dest="log_timestamps")
+
parser.add_argument("--api", type=str,
default=None, dest="work_api",
- help="Select work submission API, one of 'jobs' or 'containers'. Default is 'jobs' if that API is available, otherwise 'containers'.")
+ choices=("jobs", "containers"),
+ help="Select work submission API. Default is 'jobs' if that API is available, otherwise 'containers'.")
parser.add_argument("--compute-checksum", action="store_true", default=False,
help="Compute checksum of contents while collecting outputs",
dest="compute_checksum")
+ parser.add_argument("--submit-runner-ram", type=int,
+ help="RAM (in MiB) required for the workflow runner job (default 1024)",
+ default=1024)
+
+ parser.add_argument("--submit-runner-image", type=str,
+ help="Docker image for workflow runner job, default arvados/jobs:%s" % __version__,
+ default=None)
+
+ parser.add_argument("--name", type=str,
+ help="Name to use for workflow execution instance.",
+ default=None)
+
+ parser.add_argument("--on-error", type=str,
+ help="Desired workflow behavior when a step fails. One of 'stop' or 'continue'. "
+ "Default is 'continue'.", default="continue", choices=("stop", "continue"))
+
+ parser.add_argument("--enable-dev", action="store_true",
+ help="Enable loading and running development versions "
+ "of CWL spec.", default=False)
+
+ parser.add_argument("--intermediate-output-ttl", type=int, metavar="N",
+ help="If N > 0, intermediate output collections will be trashed N seconds after creation. Default is 0 (don't trash).",
+ default=0)
+
+ exgroup = parser.add_mutually_exclusive_group()
+ exgroup.add_argument("--trash-intermediate", action="store_true",
+ default=False, dest="trash_intermediate",
+ help="Immediately trash intermediate outputs on workflow success.")
+ exgroup.add_argument("--no-trash-intermediate", action="store_false",
+ default=False, dest="trash_intermediate",
+ help="Do not trash intermediate outputs (default).")
+
parser.add_argument("workflow", type=str, nargs="?", default=None, help="The workflow to execute")
parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
return parser
def add_arv_hints():
- cache = {}
+ cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
+ cwltool.draft2tool.ACCEPTLIST_RE = cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE
res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
- cache["http://arvados.org/cwl"] = res.read()
+ use_custom_schema("v1.0", "http://arvados.org/cwl", res.read())
res.close()
- document_loader, cwlnames, _, _ = cwltool.process.get_schema("v1.0")
- _, extnames, _, _ = schema_salad.schema.load_schema("http://arvados.org/cwl", 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, ""))
- document_loader.idx["http://arvados.org/cwl#"+n] = {}
+ cwltool.process.supportedProcessRequirements.extend([
+ "http://arvados.org/cwl#RunInSingleContainer",
+ "http://arvados.org/cwl#OutputDirType",
+ "http://arvados.org/cwl#RuntimeConstraints",
+ "http://arvados.org/cwl#PartitionRequirement",
+ "http://arvados.org/cwl#APIRequirement",
+ "http://commonwl.org/cwltool#LoadListingRequirement",
+ "http://arvados.org/cwl#IntermediateOutput",
+ "http://arvados.org/cwl#ReuseRequirement"
+ ])
def main(args, stdout, stderr, api_client=None, keep_client=None):
parser = arg_parser()
job_order_object = None
arvargs = parser.parse_args(args)
- if (arvargs.create_template or arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
+
+ if arvargs.version:
+ print versionstring()
+ return
+
+ if arvargs.update_workflow:
+ if arvargs.update_workflow.find('-7fd4e-') == 5:
+ want_api = 'containers'
+ elif arvargs.update_workflow.find('-p5p6p-') == 5:
+ want_api = 'jobs'
+ else:
+ want_api = None
+ if want_api and arvargs.work_api and want_api != arvargs.work_api:
+ logger.error('--update-workflow arg {!r} uses {!r} API, but --api={!r} specified'.format(
+ arvargs.update_workflow, want_api, arvargs.work_api))
+ return 1
+ arvargs.work_api = want_api
+
+ if (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())
- runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, keep_client=keep_client, output_name=arvargs.output_name)
+ if keep_client is None:
+ keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4)
+ runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, keep_client=keep_client,
+ num_retries=4, output_name=arvargs.output_name,
+ output_tags=arvargs.output_tags)
except Exception as e:
logger.error(e)
return 1
if arvargs.debug:
logger.setLevel(logging.DEBUG)
+ logging.getLogger('arvados').setLevel(logging.DEBUG)
if arvargs.quiet:
logger.setLevel(logging.WARN)
+ logging.getLogger('arvados').setLevel(logging.WARN)
logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
if arvargs.metrics:
metrics.setLevel(logging.DEBUG)
logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG)
+ if arvargs.log_timestamps:
+ arvados.log_handler.setFormatter(logging.Formatter(
+ '%(asctime)s %(name)s %(levelname)s: %(message)s',
+ '%Y-%m-%d %H:%M:%S'))
+ else:
+ arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
+
arvargs.conformance_test = None
arvargs.use_container = True
+ arvargs.relax_path_checks = True
+ arvargs.validate = None
+
+ make_fs_access = partial(CollectionFsAccess,
+ collection_cache=runner.collection_cache)
return cwltool.main.main(args=arvargs,
stdout=stdout,
makeTool=runner.arv_make_tool,
versionfunc=versionstring,
job_order_object=job_order_object,
- make_fs_access=partial(CollectionFsAccess, api_client=api_client))
+ make_fs_access=make_fs_access,
+ fetcher_constructor=partial(CollectionFetcher,
+ api_client=api_client,
+ fs_access=make_fs_access(""),
+ num_retries=runner.num_retries),
+ resolver=partial(collectionResolver, api_client, num_retries=runner.num_retries),
+ logger_handler=arvados.log_handler,
+ custom_schema_callback=add_arv_hints)
projects / arvados.git / blobdiff