+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
import logging
import re
import copy
import json
import time
-from cwltool.process import get_feature, shortname
+from cwltool.process import get_feature, shortname, UnsupportedRequirement
from cwltool.errors import WorkflowException
from cwltool.draft2tool import revmap_file, CommandLineTool
from cwltool.load_tool import fetch_document
from cwltool.builder import Builder
-from cwltool.pathmapper import adjustDirObjs
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
+
+from schema_salad.sourceline import SourceLine
import ruamel.yaml as yaml
import arvados.collection
+from arvados.errors import ApiError
from .arvdocker import arv_docker_get_image
-from .runner import Runner, arvados_jobs_image, packed_workflow, trim_listing
-from .pathmapper import InitialWorkDirPathMapper
+from .runner import Runner, arvados_jobs_image, packed_workflow, upload_workflow_collection, trim_anonymous_location
+from .pathmapper import VwdPathMapper, trim_listing
from .perf import Perf
from . import done
from ._version import __version__
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
script_parameters["task.vwd"] = {}
- generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
- separateDirs=False)
+ generatemapper = VwdPathMapper([self.generatefiles], "", "",
+ separateDirs=False)
with Perf(metrics, "createfiles %s" % self.name):
for f, p in generatemapper.items():
with vwd.open(p.target, "w") as n:
n.write(p.resolved.encode("utf-8"))
- with Perf(metrics, "generatefiles.save_new %s" % self.name):
- vwd.save_new()
+ if vwd:
+ with Perf(metrics, "generatefiles.save_new %s" % self.name):
+ vwd.save_new()
for f, p in generatemapper.items():
if p.type == "File":
if runtime_req:
if "keep_cache" in runtime_req:
runtime_constraints["keep_cache_mb_per_task"] = runtime_req["keep_cache"]
+ runtime_constraints["min_ram_mb_per_node"] += runtime_req["keep_cache"]
if "outputDirType" in runtime_req:
if runtime_req["outputDirType"] == "local_output_dir":
script_parameters["task.keepTmpOutput"] = False
if not self.arvrunner.ignore_docker_for_reuse:
filters.append(["docker_image_locator", "in docker", runtime_constraints["docker_image"]])
+ enable_reuse = kwargs.get("enable_reuse", True)
+ if enable_reuse:
+ reuse_req, _ = get_feature(self, "http://arvados.org/cwl#ReuseRequirement")
+ if reuse_req:
+ enable_reuse = reuse_req["enableReuse"]
+
try:
with Perf(metrics, "create %s" % self.name):
response = self.arvrunner.api.jobs().create(
"runtime_constraints": runtime_constraints
},
filters=filters,
- find_or_create=kwargs.get("enable_reuse", True)
+ find_or_create=enable_reuse
).execute(num_retries=self.arvrunner.num_retries)
self.arvrunner.processes[response["uuid"]] = self
self.update_pipeline_component(response)
- logger.info("%s %s is %s", self.arvrunner.label(self), response["uuid"], response["state"])
+ if response["state"] == "Complete":
+ logger.info("%s reused job %s", self.arvrunner.label(self), response["uuid"])
+ # Give read permission to the desired project on reused jobs
+ if response["owner_uuid"] != self.arvrunner.project_uuid:
+ try:
+ self.arvrunner.api.links().create(body={
+ 'link_class': 'permission',
+ 'name': 'can_read',
+ 'tail_uuid': self.arvrunner.project_uuid,
+ 'head_uuid': response["uuid"],
+ }).execute(num_retries=self.arvrunner.num_retries)
+ except ApiError as e:
+ # The user might not have "manage" access on the job: log
+ # a message and continue.
+ logger.info("Creating read permission on job %s: %s",
+ response["uuid"],
+ e)
- if response["state"] in ("Complete", "Failed", "Cancelled"):
with Perf(metrics, "done %s" % self.name):
self.done(response)
+ else:
+ logger.info("%s %s is %s", self.arvrunner.label(self), response["uuid"], response["state"])
except Exception as e:
logger.exception("%s error" % (self.arvrunner.label(self)))
self.output_callback({}, "permanentFail")
class RunnerJob(Runner):
"""Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
- def upload_workflow_collection(self, packed):
- collection = arvados.collection.Collection(api_client=self.arvrunner.api,
- keep_client=self.arvrunner.keep_client,
- num_retries=self.arvrunner.num_retries)
- with collection.open("workflow.cwl", "w") as f:
- f.write(yaml.round_trip_dump(packed))
-
- exists = self.arvrunner.api.collections().list(filters=[["owner_uuid", "=", self.arvrunner.project_uuid],
- ["portable_data_hash", "=", collection.portable_data_hash()],
- ["name", "like", self.name+"%"]]).execute(num_retries=self.arvrunner.num_retries)
-
- if exists["items"]:
- logger.info("Using collection %s", exists["items"][0]["uuid"])
- else:
- collection.save_new(name=self.name,
- owner_uuid=self.arvrunner.project_uuid,
- ensure_unique_name=True,
- num_retries=self.arvrunner.num_retries)
- logger.info("Uploaded to %s", collection.manifest_locator())
-
- return collection.portable_data_hash()
-
def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs):
"""Create an Arvados job specification for this workflow.
"""
if self.tool.tool["id"].startswith("keep:"):
- pass
+ self.job_order["cwl:tool"] = self.tool.tool["id"][5:]
else:
packed = packed_workflow(self.arvrunner, self.tool)
- wf_pdh = self.upload_workflow_collection(packed)
- self.job_order["cwl:tool"] = "%s/workflow.cwl" % wf_pdh
+ wf_pdh = upload_workflow_collection(self.arvrunner, self.name, packed)
+ self.job_order["cwl:tool"] = "%s/workflow.cwl#main" % wf_pdh
adjustDirObjs(self.job_order, trim_listing)
+ adjustFileObjs(self.job_order, trim_anonymous_location)
+ adjustDirObjs(self.job_order, trim_anonymous_location)
if self.output_name:
self.job_order["arv:output_name"] = self.output_name
if not isinstance(types, list):
types = [types]
param['required'] = 'null' not in types
- non_null_types = set(types) - set(['null'])
+ non_null_types = [t for t in types if t != "null"]
if len(non_null_types) == 1:
the_type = [c for c in non_null_types][0]
- dataclass = self.type_to_dataclass.get(the_type)
+ dataclass = None
+ if isinstance(the_type, basestring):
+ dataclass = self.type_to_dataclass.get(the_type)
if dataclass:
param['dataclass'] = dataclass
# Note: If we didn't figure out a single appropriate
projects / arvados.git / blobdiff