#!/usr/bin/env python
+# Implement cwl-runner interface for submitting and running jobs on Arvados.
+
import argparse
import arvados
import arvados.events
logger = logging.getLogger('arvados.cwl-runner')
logger.setLevel(logging.INFO)
-crunchrunner_pdh = "ff6fc71e593081ef9733afacaeee15ea+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_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
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["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": "8654-arv-jobs-cwl-runner",
+ "script_version": "master",
"repository": "arvados",
"script_parameters": self.job_order,
"runtime_constraints": {
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, name=None, **kwargs):
self._pathmap = arvrunner.get_uploaded()
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 = {}
logger.setLevel(logging.WARN)
logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
- 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)
-
useruuid = self.api.users().current().execute()["uuid"]
self.project_uuid = args.project_uuid if args.project_uuid else useruuid
self.pipeline = None
events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
+ 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
return self.final_output
def versionstring():
- cwlpkg = pkg_resources.require("cwltool")
- arvpkg = pkg_resources.require("arvados-python-client")
+ """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],
- "arvados-cwl-runner", arvcwlpkg[0].version,
- "arvados-python-client", cwlpkg[0].version,
- "cwltool", arvpkg[0].version)
+ 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", action="store_true", help="Submit job and print job uuid.",
- default=False)
- parser.add_argument("--wait", action="store_true", help="Wait for completion after submitting cwl-runner job.",
+ 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:
if api_client is None:
api_client=arvados.api('v1', model=OrderedJsonModel())
projects / arvados.git / blobdiff