X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/060d38d627bd1e51dd2b3c6e7de9af6aa7d7b6f3..418c57bce3aac1a22548e53e1018a1547d9efee4:/sdk/cwl/arvados_cwl/arvcontainer.py diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py index 4ab65d9d87..5c11babfc6 100644 --- a/sdk/cwl/arvados_cwl/arvcontainer.py +++ b/sdk/cwl/arvados_cwl/arvcontainer.py @@ -9,19 +9,20 @@ import urllib import time import datetime import ciso8601 +import uuid import ruamel.yaml as yaml from cwltool.errors import WorkflowException from cwltool.process import get_feature, UnsupportedRequirement, shortname -from cwltool.pathmapper import adjustFileObjs, adjustDirObjs +from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class from cwltool.utils import aslist import arvados.collection from .arvdocker import arv_docker_get_image from . import done -from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location +from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields from .fsaccess import CollectionFetcher from .pathmapper import NoFollowPathMapper, trim_listing from .perf import Perf @@ -41,18 +42,31 @@ class ArvadosContainer(object): pass def run(self, dry_run=False, pull_image=True, **kwargs): + # ArvadosCommandTool subclasses from cwltool.CommandLineTool, + # which calls makeJobRunner() to get a new ArvadosContainer + # object. The fields that define execution such as + # command_line, environment, etc are set on the + # ArvadosContainer object by CommandLineTool.job() before + # run() is called. + container_request = { "command": self.command_line, "owner_uuid": self.arvrunner.project_uuid, "name": self.name, "output_path": self.outdir, "cwd": self.outdir, - "priority": 1, + "priority": kwargs.get("priority"), "state": "Committed", "properties": {}, } runtime_constraints = {} + if self.arvrunner.secret_store.has_secret(self.command_line): + raise WorkflowException("Secret material leaked on command line, only file literals may contain secrets") + + if self.arvrunner.secret_store.has_secret(self.environment): + raise WorkflowException("Secret material leaked in environment, only file literals may contain secrets") + resources = self.builder.resources if resources is not None: runtime_constraints["vcpus"] = resources.get("cores", 1) @@ -68,6 +82,7 @@ class ArvadosContainer(object): "capacity": resources.get("tmpdirSize", 0) * 2**20 } } + secret_mounts = {} scheduling_parameters = {} rf = [self.pathmapper.mapper(f) for f in self.pathmapper.referenced_files] @@ -105,27 +120,55 @@ class ArvadosContainer(object): generatemapper = NoFollowPathMapper([self.generatefiles], "", "", separateDirs=False) + sorteditems = sorted(generatemapper.items(), None, key=lambda n: n[1].target) + + logger.debug("generatemapper is %s", sorteditems) + with Perf(metrics, "createfiles %s" % self.name): - for f, p in generatemapper.items(): + for f, p in sorteditems: if not p.target: pass - elif p.type in ("File", "Directory"): - source, path = self.arvrunner.fs_access.get_collection(p.resolved) - vwd.copy(path, p.target, source_collection=source) + elif p.type in ("File", "Directory", "WritableFile", "WritableDirectory"): + if p.resolved.startswith("_:"): + vwd.mkdirs(p.target) + else: + source, path = self.arvrunner.fs_access.get_collection(p.resolved) + vwd.copy(path, p.target, source_collection=source) elif p.type == "CreateFile": - with vwd.open(p.target, "w") as n: - n.write(p.resolved.encode("utf-8")) + if self.arvrunner.secret_store.has_secret(p.resolved): + secret_mounts["%s/%s" % (self.outdir, p.target)] = { + "kind": "text", + "content": self.arvrunner.secret_store.retrieve(p.resolved) + } + else: + with vwd.open(p.target, "w") as n: + n.write(p.resolved.encode("utf-8")) + + def keepemptydirs(p): + if isinstance(p, arvados.collection.RichCollectionBase): + if len(p) == 0: + p.open(".keep", "w").close() + else: + for c in p: + keepemptydirs(p[c]) + + keepemptydirs(vwd) with Perf(metrics, "generatefiles.save_new %s" % self.name): vwd.save_new() - for f, p in generatemapper.items(): - if not p.target: + prev = None + for f, p in sorteditems: + 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) mounts[mountpoint] = {"kind": "collection", "portable_data_hash": vwd.portable_data_hash(), "path": p.target} + if p.type.startswith("Writable"): + mounts[mountpoint]["writable"] = True + prev = p.target + "/" container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir} if self.environment: @@ -183,10 +226,11 @@ class ArvadosContainer(object): self.output_ttl = self.arvrunner.intermediate_output_ttl if self.output_ttl < 0: - raise WorkflowError("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"]) + raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"]) container_request["output_ttl"] = self.output_ttl container_request["mounts"] = mounts + container_request["secret_mounts"] = secret_mounts container_request["runtime_constraints"] = runtime_constraints container_request["scheduling_parameters"] = scheduling_parameters @@ -286,15 +330,25 @@ class RunnerContainer(Runner): """ adjustDirObjs(self.job_order, trim_listing) - adjustFileObjs(self.job_order, trim_anonymous_location) - adjustDirObjs(self.job_order, trim_anonymous_location) + visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location) + visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields) + + secret_mounts = {} + for param in sorted(self.job_order.keys()): + if self.secret_store.has_secret(self.job_order[param]): + mnt = "/secrets/s%d" % len(secret_mounts) + secret_mounts[mnt] = { + "kind": "text", + "content": self.secret_store.retrieve(self.job_order[param]) + } + self.job_order[param] = {"$include": mnt} container_req = { "owner_uuid": self.arvrunner.project_uuid, "name": self.name, "output_path": "/var/spool/cwl", "cwd": "/var/spool/cwl", - "priority": 1, + "priority": self.priority, "state": "Committed", "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image), "mounts": { @@ -311,11 +365,13 @@ class RunnerContainer(Runner): "writable": True } }, + "secret_mounts": secret_mounts, "runtime_constraints": { "vcpus": 1, "ram": 1024*1024 * self.submit_runner_ram, "API": True }, + "use_existing": self.enable_reuse, "properties": {} } @@ -329,7 +385,7 @@ class RunnerContainer(Runner): "portable_data_hash": "%s" % workflowcollection } else: - packed = packed_workflow(self.arvrunner, self.tool) + packed = packed_workflow(self.arvrunner, self.tool, self.merged_map) workflowpath = "/var/lib/cwl/workflow.json#main" container_req["mounts"]["/var/lib/cwl/workflow.json"] = { "kind": "json", @@ -338,7 +394,12 @@ class RunnerContainer(Runner): if self.tool.tool.get("id", "").startswith("arvwf:"): container_req["properties"]["template_uuid"] = self.tool.tool["id"][6:33] - command = ["arvados-cwl-runner", "--local", "--api=containers", "--no-log-timestamps"] + + # --local means execute the workflow instead of submitting a container request + # --api=containers means use the containers API + # --no-log-timestamps means don't add timestamps (the logging infrastructure does this) + # --disable-validate because we already validated so don't need to do it again + command = ["arvados-cwl-runner", "--local", "--api=containers", "--no-log-timestamps", "--disable-validate"] if self.output_name: command.append("--output-name=" + self.output_name) container_req["output_name"] = self.output_name @@ -363,6 +424,11 @@ class RunnerContainer(Runner): if self.arvrunner.trash_intermediate: command.append("--trash-intermediate") + if self.arvrunner.project_uuid: + command.append("--project-uuid="+self.arvrunner.project_uuid) + + command.append("--eval-timeout=%s" % self.arvrunner.eval_timeout) + command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"]) container_req["command"] = command