X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/72c6ba534706ddd929d11bf7800c7a483c9656af..e8d1a643cdbc3a5f4c0e5c745da58d9f7e1248d8:/sdk/cwl/arvados_cwl/arvcontainer.py diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py index 03b4e07c76..fb23c2ccf7 100644 --- a/sdk/cwl/arvados_cwl/arvcontainer.py +++ b/sdk/cwl/arvados_cwl/arvcontainer.py @@ -33,6 +33,7 @@ from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_ from .fsaccess import CollectionFetcher from .pathmapper import NoFollowPathMapper, trim_listing from .perf import Perf +from ._version import __version__ logger = logging.getLogger('arvados.cwl-runner') metrics = logging.getLogger('arvados.cwl-runner.metrics') @@ -123,6 +124,8 @@ class ArvadosContainer(JobBase): "kind": "collection", "portable_data_hash": pdh } + if pdh in self.pathmapper.pdh_to_uuid: + mounts[targetdir]["uuid"] = self.pathmapper.pdh_to_uuid[pdh] if len(sp) == 2: if tp == "Directory": path = sp[1] @@ -147,21 +150,28 @@ class ArvadosContainer(JobBase): with Perf(metrics, "createfiles %s" % self.name): for f, p in sorteditems: if not p.target: - pass - elif p.type in ("File", "Directory", "WritableFile", "WritableDirectory"): + continue + + if p.target.startswith("/"): + dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:] + else: + dst = p.target + + if p.type in ("File", "Directory", "WritableFile", "WritableDirectory"): if p.resolved.startswith("_:"): - vwd.mkdirs(p.target) + vwd.mkdirs(dst) else: source, path = self.arvrunner.fs_access.get_collection(p.resolved) - vwd.copy(path, p.target, source_collection=source) + vwd.copy(path or ".", dst, source_collection=source) elif p.type == "CreateFile": if self.arvrunner.secret_store.has_secret(p.resolved): - secret_mounts["%s/%s" % (self.outdir, p.target)] = { + mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target) + secret_mounts[mountpoint] = { "kind": "text", "content": self.arvrunner.secret_store.retrieve(p.resolved) } else: - with vwd.open(p.target, "w") as n: + with vwd.open(dst, "w") as n: n.write(p.resolved) def keepemptydirs(p): @@ -188,10 +198,14 @@ class ArvadosContainer(JobBase): if (not p.target or self.arvrunner.secret_store.has_secret(p.resolved) or (prev is not None and p.target.startswith(prev))): continue - mountpoint = "%s/%s" % (self.outdir, p.target) + if p.target.startswith("/"): + dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:] + else: + dst = p.target + mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target) mounts[mountpoint] = {"kind": "collection", "portable_data_hash": vwd.portable_data_hash(), - "path": p.target} + "path": dst} if p.type.startswith("Writable"): mounts[mountpoint]["writable"] = True prev = p.target + "/" @@ -216,13 +230,17 @@ class ArvadosContainer(JobBase): (docker_req, docker_is_req) = self.get_requirement("DockerRequirement") if not docker_req: - docker_req = {"dockerImageId": "arvados/jobs"} + docker_req = {"dockerImageId": "arvados/jobs:"+__version__} container_request["container_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, runtimeContext.pull_image, runtimeContext.project_uuid) + network_req, _ = self.get_requirement("NetworkAccess") + if network_req: + runtime_constraints["API"] = network_req["networkAccess"] + api_req, _ = self.get_requirement("http://arvados.org/cwl#APIRequirement") if api_req: runtime_constraints["API"] = True @@ -254,7 +272,7 @@ class ArvadosContainer(JobBase): if self.output_ttl < 0: raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"]) - if self.timelimit is not None: + if self.timelimit is not None and self.timelimit > 0: scheduling_parameters["max_run_time"] = self.timelimit extra_submit_params = {} @@ -270,6 +288,9 @@ class ArvadosContainer(JobBase): enable_reuse = runtimeContext.enable_reuse if enable_reuse: + reuse_req, _ = self.get_requirement("WorkReuse") + if reuse_req: + enable_reuse = reuse_req["enableReuse"] reuse_req, _ = self.get_requirement("http://arvados.org/cwl#ReuseRequirement") if reuse_req: enable_reuse = reuse_req["enableReuse"] @@ -306,6 +327,7 @@ class ArvadosContainer(JobBase): logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"]) except Exception: logger.exception("%s got an error", self.arvrunner.label(self)) + logger.debug("Container request was %s", container_request) self.output_callback({}, "permanentFail") def done(self, record): @@ -329,8 +351,8 @@ class ArvadosContainer(JobBase): else: processStatus = "permanentFail" - if processStatus == "permanentFail": - logc = arvados.collection.CollectionReader(container["log"], + if processStatus == "permanentFail" and record["log_uuid"]: + logc = arvados.collection.CollectionReader(record["log_uuid"], api_client=self.arvrunner.api, keep_client=self.arvrunner.keep_client, num_retries=self.arvrunner.num_retries) @@ -353,8 +375,8 @@ class ArvadosContainer(JobBase): if container["output"]: outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep") except WorkflowException as e: - # Only include a stack trace if in debug mode. - # A stack trace may obfuscate more useful output about the workflow. + # Only include a stack trace if in debug mode. + # A stack trace may obfuscate more useful output about the workflow. logger.error("%s unable to collect output from %s:\n%s", self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False)) processStatus = "permanentFail" @@ -416,7 +438,7 @@ class RunnerContainer(Runner): "ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)), "API": True }, - "use_existing": self.enable_reuse, + "use_existing": False, # Never reuse the runner container - see #15497. "properties": {} } @@ -483,6 +505,9 @@ class RunnerContainer(Runner): if self.arvrunner.project_uuid: command.append("--project-uuid="+self.arvrunner.project_uuid) + if self.enable_dev: + command.append("--enable-dev") + command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"]) container_req["command"] = command @@ -525,6 +550,7 @@ class RunnerContainer(Runner): container = self.arvrunner.api.containers().get( uuid=record["container_uuid"] ).execute(num_retries=self.arvrunner.num_retries) + container["log"] = record["log_uuid"] except Exception: logger.exception("%s while getting runner container", self.arvrunner.label(self)) self.arvrunner.output_callback({}, "permanentFail")