#!/usr/bin/env python
+# Implement cwl-runner interface for submitting and running jobs on Arvados.
+
import argparse
import arvados
import arvados.events
import re
import os
import sys
+import functools
+import json
+import pkg_resources # part of setuptools
-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')
def arv_docker_get_image(api_client, dockerRequirement, pull_image, project_uuid):
+ """Check if a Docker image is available in Keep, if not, upload it using arv-keepdocker."""
+
if "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"]
if image_tag:
args.append(image_tag)
logger.info("Uploading Docker image %s", ":".join(args[1:]))
- arvados.commands.keepdocker.main(args)
+ arvados.commands.keepdocker.main(args, stdout=sys.stderr)
return dockerRequirement["dockerImageId"]
class CollectionFsAccess(cwltool.process.StdFsAccess):
+ """Implement the cwltool FsAccess interface for Arvados Collections."""
+
def __init__(self, basedir):
self.collections = {}
self.basedir = basedir
return os.path.exists(self._abs(fn))
class ArvadosJob(object):
+ """Submit and manage a Crunch job for executing a CWL CommandLineTool."""
+
def __init__(self, runner):
self.arvrunner = runner
self.running = False
del self.arvrunner.jobs[record["uuid"]]
+class RunnerJob(object):
+ """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
+
+ def __init__(self, runner, tool, job_order, enable_reuse):
+ self.arvrunner = runner
+ self.tool = tool
+ self.job_order = job_order
+ self.running = False
+ self.enable_reuse = enable_reuse
+
+ def update_pipeline_component(self, record):
+ pass
+
+ def upload_docker(self, tool):
+ if isinstance(tool, cwltool.draft2tool.CommandLineTool):
+ (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement")
+ if docker_req:
+ arv_docker_get_image(self.arvrunner.api, docker_req, True, self.arvrunner.project_uuid)
+ elif isinstance(tool, cwltool.workflow.Workflow):
+ for s in tool.steps:
+ self.upload_docker(s.embedded_tool)
+
+ def run(self, dry_run=False, pull_image=True, **kwargs):
+ self.upload_docker(self.tool)
+
+ workflowfiles = set()
+ jobfiles = set()
+ workflowfiles.add(self.tool.tool["id"])
+
+ self.name = os.path.basename(self.tool.tool["id"])
+
+ def visitFiles(files, path):
+ files.add(path)
+ return path
+
+ document_loader, _, _ = cwltool.process.get_schema()
+ def loadref(b, u):
+ return document_loader.resolve_ref(u, base_url=b)[0]
+
+ sc = scandeps("", self.tool.tool,
+ set(("$import", "run")),
+ set(("$include", "$schemas", "path")),
+ loadref)
+ adjustFiles(sc, functools.partial(visitFiles, workflowfiles))
+ adjustFiles(self.job_order, functools.partial(visitFiles, jobfiles))
+
+ workflowmapper = ArvPathMapper(self.arvrunner, workflowfiles, "",
+ "%s",
+ "%s/%s",
+ name=self.name,
+ **kwargs)
+
+ jobmapper = ArvPathMapper(self.arvrunner, jobfiles, "",
+ "%s",
+ "%s/%s",
+ name=os.path.basename(self.job_order.get("id", "#")),
+ **kwargs)
+
+ adjustFiles(self.job_order, lambda p: jobmapper.mapper(p)[1])
+
+ if "id" in self.job_order:
+ del self.job_order["id"]
+
+ self.job_order["cwl:tool"] = workflowmapper.mapper(self.tool.tool["id"])[1]
+
+ response = self.arvrunner.api.jobs().create(body={
+ "script": "cwl-runner",
+ "script_version": "master",
+ "repository": "arvados",
+ "script_parameters": self.job_order,
+ "runtime_constraints": {
+ "docker_image": "arvados/jobs"
+ }
+ }, find_or_create=self.enable_reuse).execute(num_retries=self.arvrunner.num_retries)
+
+ self.arvrunner.jobs[response["uuid"]] = self
+
+ logger.info("Submitted job %s", response["uuid"])
+
+ if response["state"] in ("Complete", "Failed", "Cancelled"):
+ self.done(response)
+
+ def done(self, record):
+ if record["state"] == "Complete":
+ processStatus = "success"
+ else:
+ processStatus = "permanentFail"
+
+ outputs = None
+ try:
+ try:
+ outc = arvados.collection.Collection(record["output"])
+ with outc.open("cwl.output.json") as f:
+ outputs = json.load(f)
+ except Exception as e:
+ logger.error("While getting final output object: %s", e)
+ self.arvrunner.output_callback(outputs, processStatus)
+ finally:
+ del self.arvrunner.jobs[record["uuid"]]
+
class ArvPathMapper(cwltool.pathmapper.PathMapper):
- def __init__(self, arvrunner, referenced_files, basedir, **kwargs):
+ """Convert container-local paths to and from Keep collection ids."""
+
+ def __init__(self, arvrunner, referenced_files, basedir,
+ collection_pattern, file_pattern, name=None, **kwargs):
self._pathmap = arvrunner.get_uploaded()
- uploadfiles = []
+ uploadfiles = set()
pdh_path = re.compile(r'^keep:[0-9a-f]{32}\+\d+/.+')
for src in referenced_files:
if isinstance(src, basestring) and pdh_path.match(src):
- self._pathmap[src] = (src, "$(task.keep)/%s" % src[5:])
+ self._pathmap[src] = (src, collection_pattern % src[5:])
+ if "#" in src:
+ src = src[:src.index("#")]
if src not in self._pathmap:
ab = cwltool.pathmapper.abspath(src, basedir)
- st = arvados.commands.run.statfile("", ab, fnPattern="$(task.keep)/%s/%s")
+ st = arvados.commands.run.statfile("", ab, fnPattern=file_pattern)
if kwargs.get("conformance_test"):
self._pathmap[src] = (src, ab)
elif isinstance(st, arvados.commands.run.UploadFile):
- uploadfiles.append((src, ab, st))
+ uploadfiles.add((src, ab, st))
elif isinstance(st, arvados.commands.run.ArvFile):
self._pathmap[src] = (ab, st.fn)
else:
arvrunner.api,
dry_run=kwargs.get("dry_run"),
num_retries=3,
- fnPattern="$(task.keep)/%s/%s",
+ fnPattern=file_pattern,
+ name=name,
project=arvrunner.project_uuid)
for src, ab, st in uploadfiles:
class ArvadosCommandTool(cwltool.draft2tool.CommandLineTool):
+ """Wrap cwltool CommandLineTool to override selected methods."""
+
def __init__(self, arvrunner, toolpath_object, **kwargs):
super(ArvadosCommandTool, self).__init__(toolpath_object, **kwargs)
self.arvrunner = arvrunner
return ArvadosJob(self.arvrunner)
def makePathMapper(self, reffiles, input_basedir, **kwargs):
- return ArvPathMapper(self.arvrunner, reffiles, input_basedir, **kwargs)
+ return ArvPathMapper(self.arvrunner, reffiles, input_basedir,
+ "$(task.keep)/%s",
+ "$(task.keep)/%s/%s",
+ **kwargs)
class ArvCwlRunner(object):
+ """Execute a CWL tool or workflow, submit crunch jobs, wait for them to
+ complete, and report output."""
+
def __init__(self, api_client):
self.api = api_client
self.jobs = {}
def output_callback(self, out, processStatus):
if processStatus == "success":
logger.info("Overall job status is %s", processStatus)
- self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
- body={"state": "Complete"}).execute(num_retries=self.num_retries)
+ if self.pipeline:
+ self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
+ body={"state": "Complete"}).execute(num_retries=self.num_retries)
else:
logger.warn("Overall job status is %s", processStatus)
- self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
- body={"state": "Failed"}).execute(num_retries=self.num_retries)
+ if self.pipeline:
+ self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
+ body={"state": "Failed"}).execute(num_retries=self.num_retries)
self.final_output = out
self.uploaded[src] = pair
def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
+ self.debug = args.debug
+
+ if args.quiet:
+ logger.setLevel(logging.WARN)
+ logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
+
+ useruuid = self.api.users().current().execute()["uuid"]
+ self.project_uuid = args.project_uuid if args.project_uuid else useruuid
+ self.pipeline = None
+
+ if args.submit:
+ runnerjob = RunnerJob(self, tool, job_order, args.enable_reuse)
+ if not args.wait:
+ runnerjob.run()
+ return
+
events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
- self.debug = args.debug
self.fs_access = CollectionFsAccess(input_basedir)
kwargs["fs_access"] = self.fs_access
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:
- self.pipeline = self.api.pipeline_instances().create(
- body={
- "owner_uuid": self.project_uuid,
- "name": shortname(tool.tool["id"]),
- "components": {},
- "state": "RunningOnClient"}).execute(num_retries=self.num_retries)
+ if args.submit:
+ jobiter = iter((runnerjob,))
+ 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,
+ "state": "RunningOnClient"}).execute(num_retries=self.num_retries)
- logger.info("Pipeline instance %s", self.pipeline["uuid"])
+ logger.info("Pipeline instance %s", self.pipeline["uuid"])
- jobiter = tool.job(job_order,
- input_basedir,
- self.output_callback,
- docker_outdir="$(task.outdir)",
- **kwargs)
+ jobiter = tool.job(job_order,
+ input_basedir,
+ self.output_callback,
+ docker_outdir="$(task.outdir)",
+ **kwargs)
try:
self.cond.acquire()
logger.error("Interrupted, marking pipeline as failed")
else:
logger.error("Caught unhandled exception, marking pipeline as failed. Error was: %s", sys.exc_info()[0], exc_info=(sys.exc_info()[1] if self.debug else False))
- self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
- body={"state": "Failed"}).execute(num_retries=self.num_retries)
+ if self.pipeline:
+ self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
+ body={"state": "Failed"}).execute(num_retries=self.num_retries)
finally:
self.cond.release()
return self.final_output
+def versionstring():
+ """Print version string of key packages for provenance and debugging."""
+
+ cwlpkg = pkg_resources.require("cwltool")
+ arvpkg = pkg_resources.require("arvados-python-client")
+ arvcwlpkg = pkg_resources.require("arvados-cwl-runner")
+
+ return "%s %s, %s %s, %s %s" % (sys.argv[0],
+ arvcwlpkg[0].version,
+ "arvados-python-client", cwlpkg[0].version,
+ "cwltool", arvpkg[0].version)
def main(args, stdout, stderr, api_client=None):
args.insert(0, "--leave-outputs")
parser = cwltool.main.arg_parser()
+
exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--enable-reuse", action="store_true",
default=True, dest="enable_reuse",
exgroup.add_argument("--disable-reuse", action="store_false",
default=True, dest="enable_reuse",
help="")
+
parser.add_argument("--project-uuid", type=str, help="Project that will own the workflow jobs")
+ exgroup = parser.add_mutually_exclusive_group()
+ exgroup.add_argument("--submit", action="store_true", help="Submit runner job so workflow can run unattended.",
+ default=True, dest="submit")
+ exgroup.add_argument("--local", action="store_false", help="Workflow runner runs on local host and submits jobs.",
+ default=True, dest="submit")
+
+ exgroup = parser.add_mutually_exclusive_group()
+ exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",
+ default=True, dest="wait")
+ exgroup.add_argument("--no-wait", action="store_false", help="Exit after submitting workflow runner job.",
+ default=True, dest="wait")
+
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,
+ versionfunc=versionstring)
projects / arvados.git / commitdiff