import sys
import threading
import hashlib
+import copy
+import json
from functools import partial
import pkg_resources # part of setuptools
from .arvcontainer import ArvadosContainer, RunnerContainer
from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
+from. runner import Runner
from .arvtool import ArvadosCommandTool
-from .arvworkflow import ArvadosWorkflow
+from .arvworkflow import ArvadosWorkflow, upload_workflow
from .fsaccess import CollectionFsAccess
-from .arvworkflow import upload_workflow
from .perf import Perf
-from cwltool.pack import pack
+from .pathmapper import FinalOutputPathMapper
-from cwltool.process import shortname, UnsupportedRequirement
-from cwltool.pathmapper import adjustFileObjs
+from cwltool.pack import pack
+from cwltool.process import shortname, UnsupportedRequirement, getListing
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
from cwltool.draft2tool import compute_checksums
from arvados.api import OrderedJsonModel
logger = logging.getLogger('arvados.cwl-runner')
+metrics = logging.getLogger('arvados.cwl-runner.metrics')
logger.setLevel(logging.INFO)
+
class ArvCwlRunner(object):
"""Execute a CWL tool or workflow, submit work (using either jobs or
containers API), wait for them to complete, and report output.
"""
- def __init__(self, api_client, work_api=None):
+ def __init__(self, api_client, work_api=None, keep_client=None, output_name=None):
self.api = api_client
self.processes = {}
self.lock = threading.Lock()
self.work_api = work_api
self.stop_polling = threading.Event()
self.poll_api = None
+ self.pipeline = None
+ self.final_output_collection = None
+ self.output_name = output_name
+ if keep_client is not None:
+ self.keep_client = keep_client
+ else:
+ self.keep_client = arvados.keep.KeepClient(api_client=self.api, num_retries=self.num_retries)
if self.work_api is None:
# todo: autodetect API to use.
self.cond.acquire()
j = self.processes[uuid]
logger.info("Job %s (%s) is %s", j.name, uuid, event["properties"]["new_attributes"]["state"])
- with Perf(logger, "done %s" % j.name):
+ with Perf(metrics, "done %s" % j.name):
j.done(event["properties"]["new_attributes"])
self.cond.notify()
finally:
for v in obj:
self.check_writable(v)
+ def make_output_collection(self, name, outputObj):
+ outputObj = copy.deepcopy(outputObj)
+
+ files = []
+ def capture(fileobj):
+ files.append(fileobj)
+
+ adjustDirObjs(outputObj, capture)
+ adjustFileObjs(outputObj, capture)
+
+ generatemapper = FinalOutputPathMapper(files, "", "", separateDirs=False)
+
+ final = arvados.collection.Collection(api_client=self.api,
+ keep_client=self.keep_client,
+ num_retries=self.num_retries)
+
+ srccollections = {}
+ for k,v in generatemapper.items():
+ sp = k.split("/")
+ srccollection = sp[0][5:]
+ if srccollection not in srccollections:
+ srccollections[srccollection] = arvados.collection.CollectionReader(
+ srccollection,
+ api_client=self.api,
+ keep_client=self.keep_client,
+ num_retries=self.num_retries)
+ reader = srccollections[srccollection]
+ try:
+ srcpath = "/".join(sp[1:]) if len(sp) > 1 else "."
+ final.copy(srcpath, v.target, source_collection=reader, overwrite=False)
+ except IOError as e:
+ logger.warn("While preparing output collection: %s", e)
+
+ def rewrite(fileobj):
+ fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
+ for k in ("basename", "size", "listing"):
+ if k in fileobj:
+ del fileobj[k]
+
+ adjustDirObjs(outputObj, rewrite)
+ adjustFileObjs(outputObj, rewrite)
+
+ with final.open("cwl.output.json", "w") as f:
+ json.dump(outputObj, f, sort_keys=True, indent=4, separators=(',',': '))
+
+ final.save_new(name=name, owner_uuid=self.project_uuid, ensure_unique_name=True)
+
+ logger.info("Final output collection %s \"%s\" (%s)", final.portable_data_hash(),
+ final.api_response()["name"],
+ final.manifest_locator())
+
+ self.final_output_collection = final
+
def arv_executor(self, tool, job_order, **kwargs):
self.debug = kwargs.get("debug")
useruuid = self.api.users().current().execute()["uuid"]
self.project_uuid = kwargs.get("project_uuid") if kwargs.get("project_uuid") else useruuid
self.pipeline = None
- make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, api_client=self.api)
+ make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess,
+ api_client=self.api,
+ keep_client=self.keep_client)
self.fs_access = make_fs_access(kwargs["basedir"])
if kwargs.get("create_template"):
self.output_callback,
**kwargs).next()
else:
- runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"))
+ runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name)
else:
- runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"))
+ runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name)
if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and not self.work_api == "containers":
# Create pipeline for local run
# except when in cond.wait(), at which point on_message can update
# job state and process output callbacks.
+ loopperf = Perf(metrics, "jobiter")
+ loopperf.__enter__()
for runnable in jobiter:
+ loopperf.__exit__()
if runnable:
- with Perf(logger, "run"):
+ with Perf(metrics, "run"):
runnable.run(**kwargs)
else:
if self.processes:
else:
logger.error("Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs.")
break
+ loopperf.__enter__()
+ loopperf.__exit__()
while self.processes:
self.cond.wait(1)
if self.final_output is None:
raise WorkflowException("Workflow did not return a result.")
+ if kwargs.get("submit") and isinstance(runnerjob, Runner):
+ logger.info("Final output collection %s", runnerjob.final_output)
+ else:
+ if self.output_name is None:
+ self.output_name = "Output of %s" % (shortname(tool.tool["id"]))
+ self.make_output_collection(self.output_name, self.final_output)
+
if kwargs.get("compute_checksum"):
+ adjustDirObjs(self.final_output, partial(getListing, self.fs_access))
adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
return self.final_output
exgroup.add_argument("--quiet", action="store_true", help="Only print warnings and errors.")
exgroup.add_argument("--debug", action="store_true", help="Print even more logging")
+ parser.add_argument("--metrics", action="store_true", help="Print timing metrics")
+
parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool")
exgroup = parser.add_mutually_exclusive_group()
help="")
parser.add_argument("--project-uuid", type=str, metavar="UUID", help="Project that will own the workflow jobs, if not provided, will go to home project.")
+ parser.add_argument("--output-name", type=str, help="Name to use for collection that stores the final output.", default=None)
parser.add_argument("--ignore-docker-for-reuse", action="store_true",
help="Ignore Docker image version when deciding whether to reuse past jobs.",
default=False)
def add_arv_hints():
cache = {}
res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
- cache["https://w3id.org/cwl/arv-cwl-schema.yml"] = res.read()
+ cache["http://arvados.org/cwl"] = res.read()
res.close()
- _, cwlnames, _, _ = cwltool.process.get_schema("v1.0")
- _, extnames, _, _ = schema_salad.schema.load_schema("https://w3id.org/cwl/arv-cwl-schema.yml", cache=cache)
+ document_loader, cwlnames, _, _ = cwltool.process.get_schema("v1.0")
+ _, extnames, _, _ = schema_salad.schema.load_schema("http://arvados.org/cwl", cache=cache)
for n in extnames.names:
- cwlnames.add_name("http://arvados.org/cwl#"+n, "", extnames.get_name(n, ""))
+ if not cwlnames.has_name("http://arvados.org/cwl#"+n, ""):
+ cwlnames.add_name("http://arvados.org/cwl#"+n, "", extnames.get_name(n, ""))
+ document_loader.idx["http://arvados.org/cwl#"+n] = {}
-def main(args, stdout, stderr, api_client=None):
+def main(args, stdout, stderr, api_client=None, keep_client=None):
parser = arg_parser()
job_order_object = None
try:
if api_client is None:
api_client=arvados.api('v1', model=OrderedJsonModel())
- runner = ArvCwlRunner(api_client, work_api=arvargs.work_api)
+ runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, keep_client=keep_client, output_name=arvargs.output_name)
except Exception as e:
logger.error(e)
return 1
logger.setLevel(logging.WARN)
logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
+ if arvargs.metrics:
+ metrics.setLevel(logging.DEBUG)
+ logging.getLogger("cwltool.metrics").setLevel(logging.DEBUG)
+
arvargs.conformance_test = None
arvargs.use_container = True
projects / arvados.git / blobdiff