X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/779c5400a4f376489f4abc8564f890f309ae3f20..f82ee19a440e31f05381511cf6c0d7932d804b9d:/sdk/cwl/arvados_cwl/__init__.py diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index 03f3132287..65a36f6877 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -8,6 +8,8 @@ import logging import os import sys import threading +import hashlib +from functools import partial import pkg_resources # part of setuptools from cwltool.errors import WorkflowException @@ -15,7 +17,6 @@ import cwltool.main import cwltool.workflow import arvados -import arvados.events import arvados.config from .arvcontainer import ArvadosContainer, RunnerContainer @@ -24,6 +25,8 @@ from .arvtool import ArvadosCommandTool from .fsaccess import CollectionFsAccess from cwltool.process import shortname, UnsupportedRequirement +from cwltool.pathmapper import adjustFileObjs +from cwltool.draft2tool import compute_checksums from arvados.api import OrderedJsonModel logger = logging.getLogger('arvados.cwl-runner') @@ -46,6 +49,8 @@ class ArvCwlRunner(object): self.num_retries = 4 self.uuid = None self.work_api = work_api + self.stop_polling = threading.Event() + self.poll_api = None if self.work_api is None: # todo: autodetect API to use. @@ -56,7 +61,8 @@ class ArvCwlRunner(object): def arvMakeTool(self, toolpath_object, **kwargs): if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool": - return ArvadosCommandTool(self, toolpath_object, work_api=self.work_api, **kwargs) + kwargs["work_api"] = self.work_api + return ArvadosCommandTool(self, toolpath_object, **kwargs) else: return cwltool.workflow.defaultMakeTool(toolpath_object, **kwargs) @@ -95,15 +101,62 @@ class ArvCwlRunner(object): finally: self.cond.release() + def poll_states(self): + """Poll status of jobs or containers listed in the processes dict. + + Runs in a separate thread. + """ + + while True: + self.stop_polling.wait(15) + if self.stop_polling.is_set(): + break + with self.lock: + keys = self.processes.keys() + if not keys: + continue + + if self.work_api == "containers": + table = self.poll_api.containers() + elif self.work_api == "jobs": + table = self.poll_api.jobs() + + try: + proc_states = table.list(filters=[["uuid", "in", keys]]).execute(num_retries=self.num_retries) + except Exception as e: + logger.warn("Error checking states on API server: %s", e) + continue + + for p in proc_states["items"]: + self.on_message({ + "object_uuid": p["uuid"], + "event_type": "update", + "properties": { + "new_attributes": p + } + }) + def get_uploaded(self): return self.uploaded.copy() def add_uploaded(self, src, pair): self.uploaded[src] = pair + def check_writable(self, obj): + if isinstance(obj, dict): + if obj.get("writable"): + raise UnsupportedRequirement("InitialWorkDir feature 'writable: true' not supported") + for v in obj.itervalues(): + self.check_writable(v) + if isinstance(obj, list): + for v in obj: + self.check_writable(v) + def arvExecutor(self, tool, job_order, **kwargs): self.debug = kwargs.get("debug") + tool.visit(self.check_writable) + if kwargs.get("quiet"): logger.setLevel(logging.WARN) logging.getLogger('arvados.arv-run').setLevel(logging.WARN) @@ -111,7 +164,8 @@ class ArvCwlRunner(object): useruuid = self.api.users().current().execute()["uuid"] self.project_uuid = kwargs.get("project_uuid") if kwargs.get("project_uuid") else useruuid self.pipeline = None - self.fs_access = CollectionFsAccess(kwargs["basedir"], api_client=self.api) + make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, api_client=self.api) + self.fs_access = make_fs_access(kwargs["basedir"]) if kwargs.get("create_template"): tmpl = RunnerTemplate(self, tool, job_order, kwargs.get("enable_reuse")) @@ -122,16 +176,18 @@ class ArvCwlRunner(object): self.debug = kwargs.get("debug") self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse") - kwargs["fs_access"] = self.fs_access + kwargs["make_fs_access"] = make_fs_access kwargs["enable_reuse"] = kwargs.get("enable_reuse") kwargs["use_container"] = True kwargs["tmpdir_prefix"] = "tmp" kwargs["on_error"] = "continue" + kwargs["compute_checksum"] = kwargs.get("compute_checksum") if self.work_api == "containers": kwargs["outdir"] = "/var/spool/cwl" kwargs["docker_outdir"] = "/var/spool/cwl" kwargs["tmpdir"] = "/tmp" + kwargs["docker_tmpdir"] = "/tmp" elif self.work_api == "jobs": kwargs["outdir"] = "$(task.outdir)" kwargs["docker_outdir"] = "$(task.outdir)" @@ -163,12 +219,9 @@ class ArvCwlRunner(object): runnerjob.run() return runnerjob.uuid - arvados.config.settings()["ARVADOS_DISABLE_WEBSOCKETS"] = "1" - - if self.work_api == "containers": - events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#container"]], self.on_message) - if self.work_api == "jobs": - events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message) + self.poll_api = arvados.api('v1') + self.polling_thread = threading.Thread(target=self.poll_states) + self.polling_thread.start() if runnerjob: jobiter = iter((runnerjob,)) @@ -198,7 +251,6 @@ class ArvCwlRunner(object): while self.processes: self.cond.wait(1) - events.close() except UnsupportedRequirement: raise except: @@ -214,6 +266,8 @@ class ArvCwlRunner(object): body={"priority": "0"}).execute(num_retries=self.num_retries) finally: self.cond.release() + self.stop_polling.set() + self.polling_thread.join() if self.final_status == "UnsupportedRequirement": raise UnsupportedRequirement("Check log for details.") @@ -224,6 +278,9 @@ class ArvCwlRunner(object): if self.final_output is None: raise WorkflowException("Workflow did not return a result.") + if kwargs.get("compute_checksum"): + adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access)) + return self.final_output @@ -290,6 +347,10 @@ def arg_parser(): # type: () -> argparse.ArgumentParser default=None, dest="work_api", help="Select work submission API, one of 'jobs' or 'containers'.") + parser.add_argument("--compute-checksum", action="store_true", default=False, + help="Compute checksum of contents while collecting outputs", + dest="compute_checksum") + parser.add_argument("workflow", type=str, nargs="?", default=None, help="The workflow to execute") parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.") @@ -321,4 +382,5 @@ def main(args, stdout, stderr, api_client=None): executor=runner.arvExecutor, makeTool=runner.arvMakeTool, versionfunc=versionstring, - job_order_object=job_order_object) + job_order_object=job_order_object, + make_fs_access=partial(CollectionFsAccess, api_client=api_client))