#!/usr/bin/env python
+# Implement cwl-runner interface for submitting and running jobs on Arvados.
+
import argparse
import arvados
import arvados.events
import cwltool.workflow
import cwltool.main
from cwltool.process import shortname
+from cwltool.errors import WorkflowException
import threading
import cwltool.docker
import fnmatch
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')
logger.setLevel(logging.INFO)
-crunchrunner_pdh = "83db29f08544e1c319572a6bd971088a+140"
-crunchrunner_download = "https://cloud.curoverse.com/collections/download/qr1hi-4zz18-n3m1yxd0vx78jic/1i1u2qtq66k1atziv4ocfgsg5nu5tj11n4r6e0bhvjg03rix4m/crunchrunner"
-certs_download = "https://cloud.curoverse.com/collections/download/qr1hi-4zz18-n3m1yxd0vx78jic/1i1u2qtq66k1atziv4ocfgsg5nu5tj11n4r6e0bhvjg03rix4m/ca-certificates.crt"
-
tmpdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.tmpdir\)=(.*)")
outdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.outdir\)=(.*)")
keepre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.keep\)=(.*)")
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
(docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
if docker_req and kwargs.get("use_container") is not False:
runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvrunner.project_uuid)
+ else:
+ runtime_constraints["docker_image"] = "arvados/jobs"
+
+ resources = self.builder.resources
+ if resources is not None:
+ runtime_constraints["min_cores_per_node"] = resources.get("cores", 1)
+ runtime_constraints["min_ram_mb_per_node"] = resources.get("ram")
+ runtime_constraints["min_scratch_mb_per_node"] = resources.get("tmpdirSize", 0) + resources.get("outdirSize", 0)
+
+ filters = [["repository", "=", "arvados"],
+ ["script", "=", "crunchrunner"],
+ ["script_version", "in git", "9e5b98e8f5f4727856b53447191f9c06e3da2ba6"]]
+ if not self.arvrunner.ignore_docker_for_reuse:
+ filters.append(["docker_image_locator", "in docker", runtime_constraints["docker_image"]])
try:
- response = self.arvrunner.api.jobs().create(body={
- "owner_uuid": self.arvrunner.project_uuid,
- "script": "crunchrunner",
- "repository": "arvados",
- "script_version": "master",
- "minimum_script_version": "9e5b98e8f5f4727856b53447191f9c06e3da2ba6",
- "script_parameters": {"tasks": [script_parameters], "crunchrunner": crunchrunner_pdh+"/crunchrunner"},
- "runtime_constraints": runtime_constraints
- }, find_or_create=kwargs.get("enable_reuse", True)).execute(num_retries=self.arvrunner.num_retries)
+ response = self.arvrunner.api.jobs().create(
+ body={
+ "owner_uuid": self.arvrunner.project_uuid,
+ "script": "crunchrunner",
+ "repository": "arvados",
+ "script_version": "master",
+ "minimum_script_version": "9e5b98e8f5f4727856b53447191f9c06e3da2ba6",
+ "script_parameters": {"tasks": [script_parameters]},
+ "runtime_constraints": runtime_constraints
+ },
+ filters=filters,
+ find_or_create=kwargs.get("enable_reuse", True)
+ ).execute(num_retries=self.arvrunner.num_retries)
self.arvrunner.jobs[response["uuid"]] = self
tmpdir = None
outdir = None
keepdir = None
- for l in log.readlines():
+ for l in log:
+ # Determine the tmpdir, outdir and keepdir 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
+ # the job restarts on a different node these values
+ # will different runs, and we need to know about the
+ # final run that actually produced output.
+
g = tmpdirre.match(l)
if g:
tmpdir = g.group(1)
g = keepre.match(l)
if g:
keepdir = g.group(1)
- if tmpdir and outdir and keepdir:
- break
+
+ colname = "Output %s of %s" % (record["output"][0:7], self.name)
+
+ # check if collection already exists with same owner, name and content
+ collection_exists = self.arvrunner.api.collections().list(
+ filters=[["owner_uuid", "=", self.arvrunner.project_uuid],
+ ['portable_data_hash', '=', record["output"]],
+ ["name", "=", colname]]
+ ).execute(num_retries=self.arvrunner.num_retries)
+
+ if not collection_exists["items"]:
+ # Create a collection located in the same project as the
+ # pipeline with the contents of the output.
+ # First, get output record.
+ collections = self.arvrunner.api.collections().list(
+ limit=1,
+ filters=[['portable_data_hash', '=', record["output"]]],
+ select=["manifest_text"]
+ ).execute(num_retries=self.arvrunner.num_retries)
+
+ if not collections["items"]:
+ raise WorkflowException(
+ "Job output '%s' cannot be found on API server" % (
+ record["output"]))
+
+ # Create new collection in the parent project
+ # with the output contents.
+ self.arvrunner.api.collections().create(body={
+ "owner_uuid": self.arvrunner.project_uuid,
+ "name": colname,
+ "portable_data_hash": record["output"],
+ "manifest_text": collections["items"][0]["manifest_text"]
+ }, ensure_unique_name=True).execute(
+ num_retries=self.arvrunner.num_retries)
self.builder.outdir = outdir
self.builder.pathmapper.keepdir = keepdir
outputs = self.collect_outputs("keep:" + record["output"])
+ except WorkflowException as e:
+ logger.error("Error while collecting job outputs:\n%s", e, exc_info=(e if self.arvrunner.debug else False))
+ processStatus = "permanentFail"
except Exception as e:
- logger.exception("Got exception while collecting job outputs:")
+ logger.exception("Got unknown exception while collecting job outputs:")
processStatus = "permanentFail"
self.output_callback(outputs, processStatus)
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={
+ "owner_uuid": self.arvrunner.project_uuid,
+ "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):
+ """Convert container-local paths to and from Keep collection ids."""
+
def __init__(self, arvrunner, referenced_files, basedir,
- collection_pattern, file_pattern, **kwargs):
+ 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, 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=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:
dry_run=kwargs.get("dry_run"),
num_retries=3,
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
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
def add_uploaded(self, src, pair):
self.uploaded[src] = pair
- def upload_docker(self, tool):
- pass
-
- def submit(self, tool, job_order, input_basedir, args, **kwargs):
- files = set()
- def visitFiles(self, path):
- files.add(path)
-
- adjustFiles(process.scandeps("", tool.tool,
- set(("run")),
- set(("$schemas", "path"))),
- visitFiles)
- adjustFiles(job_order, visitFiles)
-
- mapper = ArvPathMapper(self, files, "",
- "$(task.keep)/%s",
- "$(task.keep)/%s/%s",
- **kwargs)
-
- job_order = adjustFiles(job_order, lambda p: mapper.mapper(p))
+ def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
+ self.debug = args.debug
- response = self.api.jobs().create(body={
- "script": "cwl-runner",
- "script_version": "8654-arv-jobs-cwl-runner",
- "repository": "arvados",
- "script_parameters": job_order,
- "runtime_constraints": {
- "docker_image": "arvados/jobs"
- }
- }, find_or_create=args.enable_reuse).execute(num_retries=self.num_retries)
- print response["uuid"]
- return None
+ 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
- def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
if args.submit:
- self.submit(tool, job_order, input_basedir, args, **kwargs)
- return
+ 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)
- try:
- self.api.collections().get(uuid=crunchrunner_pdh).execute()
- except arvados.errors.ApiError as e:
- import httplib2
- h = httplib2.Http(ca_certs=arvados.util.ca_certs_path())
- resp, content = h.request(crunchrunner_download, "GET")
- resp2, content2 = h.request(certs_download, "GET")
- with arvados.collection.Collection() as col:
- with col.open("crunchrunner", "w") as f:
- f.write(content)
- with col.open("ca-certificates.crt", "w") as f:
- f.write(content2)
-
- col.save_new("crunchrunner binary", ensure_unique_name=True)
-
+ self.debug = args.debug
+ self.ignore_docker_for_reuse = args.ignore_docker_for_reuse
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"]}
- logger.info("Pipeline instance %s", self.pipeline["uuid"])
+ 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)
- jobiter = tool.job(job_order,
- input_basedir,
- self.output_callback,
- docker_outdir="$(task.outdir)",
- **kwargs)
+ logger.info("Pipeline instance %s", self.pipeline["uuid"])
+
+ jobiter = tool.job(job_order,
+ input_basedir,
+ self.output_callback,
+ docker_outdir="$(task.outdir)",
+ **kwargs)
try:
self.cond.acquire()
if sys.exc_info()[0] is KeyboardInterrupt:
logger.error("Interrupted, marking pipeline as failed")
else:
- logger.exception("Caught unhandled exception, marking pipeline as failed")
- self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
- body={"state": "Failed"}).execute(num_retries=self.num_retries)
+ 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))
+ 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."""
+
+ arvcwlpkg = pkg_resources.require("arvados-cwl-runner")
+ arvpkg = pkg_resources.require("arvados-python-client")
+ cwlpkg = pkg_resources.require("cwltool")
+
+ return "%s %s, %s %s, %s %s" % (sys.argv[0], arvcwlpkg[0].version,
+ "arvados-python-client", arvpkg[0].version,
+ "cwltool", cwlpkg[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")
- parser.add_argument("--submit", type=str, help="Submit job and print job uuid.")
+ parser.add_argument("--ignore-docker-for-reuse", action="store_true",
+ help="Ignore Docker image version when deciding whether to reuse past jobs.",
+ default=False)
+
+ exgroup = parser.add_mutually_exclusive_group()
+ exgroup.add_argument("--submit", action="store_true", help="Submit workflow to run on Arvados.",
+ 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 = 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="Submit workflow runner job and exit.",
+ 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 / blobdiff