+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
import logging
import re
import copy
from cwltool.process import get_feature, shortname, UnsupportedRequirement
from cwltool.errors import WorkflowException
-from cwltool.draft2tool import revmap_file, CommandLineTool
+from cwltool.command_line_tool import revmap_file, CommandLineTool
from cwltool.load_tool import fetch_document
from cwltool.builder import Builder
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
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, upload_workflow_collection, trim_anonymous_location
+from .runner import Runner, arvados_jobs_image, packed_workflow, upload_workflow_collection, trim_anonymous_location, remove_redundant_fields
from .pathmapper import VwdPathMapper, trim_listing
from .perf import Perf
from . import done
logger = logging.getLogger('arvados.cwl-runner')
metrics = logging.getLogger('arvados.cwl-runner.metrics')
-crunchrunner_re = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.(tmpdir|outdir|keep)\)=(.*)")
+crunchrunner_re = re.compile(r"^.*crunchrunner: \$\(task\.(tmpdir|outdir|keep)\)=(.*)$")
crunchrunner_git_commit = 'a3f2cb186e437bfce0031b024b2157b73ed2717d'
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"]
+
+ self.output_callback = self.arvrunner.get_wrapped_callback(self.output_callback)
+
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.uuid = response["uuid"]
+ self.arvrunner.process_submitted(self)
self.update_pipeline_component(response)
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)
+
with Perf(metrics, "done %s" % self.name):
self.done(response)
else:
if self.arvrunner.pipeline:
self.arvrunner.pipeline["components"][self.name] = {"job": record}
with Perf(metrics, "update_pipeline_component %s" % self.name):
- self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(uuid=self.arvrunner.pipeline["uuid"],
- body={
- "components": self.arvrunner.pipeline["components"]
- }).execute(num_retries=self.arvrunner.num_retries)
+ self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(
+ uuid=self.arvrunner.pipeline["uuid"],
+ body={
+ "components": self.arvrunner.pipeline["components"]
+ }).execute(num_retries=self.arvrunner.num_retries)
if self.arvrunner.uuid:
try:
job = self.arvrunner.api.jobs().get(uuid=self.arvrunner.uuid).execute()
if job:
components = job["components"]
components[self.name] = record["uuid"]
- self.arvrunner.api.jobs().update(uuid=self.arvrunner.uuid,
+ self.arvrunner.api.jobs().update(
+ uuid=self.arvrunner.uuid,
body={
"components": components
}).execute(num_retries=self.arvrunner.num_retries)
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
log = logc.open(logc.keys()[0])
- dirs = {}
- tmpdir = None
- outdir = None
- keepdir = None
+ dirs = {
+ "tmpdir": "/tmpdir",
+ "outdir": "/outdir",
+ "keep": "/keep"
+ }
for l in log:
- # Determine the tmpdir, outdir and keepdir paths from
+ # Determine the tmpdir, outdir and keep paths from
# the job run. Unfortunately, we can't take the first
# values we find (which are expected to be near the
# top) and stop scanning because if the node fails and
processStatus = "permanentFail"
finally:
self.output_callback(outputs, processStatus)
- if record["uuid"] in self.arvrunner.processes:
- del self.arvrunner.processes[record["uuid"]]
+ self.arvrunner.process_done(record["uuid"])
+
class RunnerJob(Runner):
"""Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
if self.tool.tool["id"].startswith("keep:"):
self.job_order["cwl:tool"] = self.tool.tool["id"][5:]
else:
- packed = packed_workflow(self.arvrunner, self.tool)
+ packed = packed_workflow(self.arvrunner, self.tool, self.merged_map)
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)
+ visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
+ visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
if self.output_name:
self.job_order["arv:output_name"] = self.output_name
if self.on_error:
self.job_order["arv:on_error"] = self.on_error
+ if kwargs.get("debug"):
+ self.job_order["arv:debug"] = True
+
return {
"script": "cwl-runner",
"script_version": "master",
}
}
- def run(self, *args, **kwargs):
- job_spec = self.arvados_job_spec(*args, **kwargs)
+ def run(self, **kwargs):
+ job_spec = self.arvados_job_spec(**kwargs)
job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid)
find_or_create=self.enable_reuse
).execute(num_retries=self.arvrunner.num_retries)
- if self.enable_reuse:
- reused_collections = [('Output', job['output']), ('Log', job['log'])]
- for col_type, pdh in [(n, p) for n, p in reused_collections if p]:
- # When reusing jobs, copy its output/log collection to the desired project
- c = arvados.collection.Collection(pdh,
- api_client=self.arvrunner.api,
- keep_client=self.arvrunner.keep_client,
- num_retries=self.arvrunner.num_retries)
- c.save_new(name="{} of {}".format(col_type, self.name),
- owner_uuid=self.arvrunner.project_uuid,
- ensure_unique_name=True,
- num_retries=self.arvrunner.num_retries)
- logger.info("Copied reused job's %s to collection %s",
- col_type.lower(),
- c.manifest_locator())
-
for k,v in job_spec["script_parameters"].items():
if v is False or v is None or isinstance(v, dict):
job_spec["script_parameters"][k] = {"value": v}
del job_spec["owner_uuid"]
job_spec["job"] = job
+
+ instance_spec = {
+ "owner_uuid": self.arvrunner.project_uuid,
+ "name": self.name,
+ "components": {
+ "cwl-runner": job_spec,
+ },
+ "state": "RunningOnServer",
+ }
+ if not self.enable_reuse:
+ instance_spec["properties"] = {"run_options": {"enable_job_reuse": False}}
+
self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().create(
- body={
- "owner_uuid": self.arvrunner.project_uuid,
- "name": self.name,
- "components": {"cwl-runner": job_spec },
- "state": "RunningOnServer"}).execute(num_retries=self.arvrunner.num_retries)
+ body=instance_spec).execute(num_retries=self.arvrunner.num_retries)
logger.info("Created pipeline %s", self.arvrunner.pipeline["uuid"])
if kwargs.get("wait") is False:
return
self.uuid = job["uuid"]
- self.arvrunner.processes[self.uuid] = self
+ self.arvrunner.process_submitted(self)
if job["state"] in ("Complete", "Failed", "Cancelled"):
self.done(job)
}
def __init__(self, runner, tool, job_order, enable_reuse, uuid,
- submit_runner_ram=0, name=None):
+ submit_runner_ram=0, name=None, merged_map=None):
self.runner = runner
self.tool = tool
self.job = RunnerJob(
output_name=None,
output_tags=None,
submit_runner_ram=submit_runner_ram,
- name=name)
+ name=name,
+ merged_map=merged_map)
self.uuid = uuid
def pipeline_component_spec(self):
projects / arvados.git / blobdiff