X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f40364c4d42e111b9da3873afcfaed2b49e7f182..8de691c25eac0454f8f30cfa35eccff15642e330:/sdk/cwl/arvados_cwl/runner.py diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py index 6978b5469a..c55e976924 100644 --- a/sdk/cwl/arvados_cwl/runner.py +++ b/sdk/cwl/arvados_cwl/runner.py @@ -1,12 +1,15 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + import os import urlparse from functools import partial import logging import json -import re import subprocess -from cStringIO import StringIO +from StringIO import StringIO from schema_salad.sourceline import SourceLine @@ -15,7 +18,7 @@ from cwltool.draft2tool import CommandLineTool import cwltool.workflow from cwltool.process import get_feature, scandeps, UnsupportedRequirement, normalizeFilesDirs, shortname from cwltool.load_tool import fetch_document -from cwltool.pathmapper import adjustFileObjs, adjustDirObjs +from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class from cwltool.utils import aslist from cwltool.builder import substitute from cwltool.pack import pack @@ -24,29 +27,41 @@ import arvados.collection import ruamel.yaml as yaml from .arvdocker import arv_docker_get_image -from .pathmapper import ArvPathMapper +from .pathmapper import ArvPathMapper, trim_listing from ._version import __version__ from . import done logger = logging.getLogger('arvados.cwl-runner') -cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r".*") +def trim_anonymous_location(obj): + """Remove 'location' field from File and Directory literals. -def trim_listing(obj): - """Remove 'listing' field from Directory objects that are keep references. + To make internal handling easier, literals are assigned a random id for + 'location'. However, when writing the record back out, this can break + reproducibility. Since it is valid for literals not have a 'location' + field, remove it. - When Directory objects represent Keep references, it redundant and - potentially very expensive to pass fully enumerated Directory objects - between instances of cwl-runner (e.g. a submitting a job, or using the - RunInSingleContainer feature), so delete the 'listing' field when it is - safe to do so. """ - if obj.get("location", "").startswith("keep:") and "listing" in obj: - del obj["listing"] if obj.get("location", "").startswith("_:"): del obj["location"] +def remove_redundant_fields(obj): + for field in ("path", "nameext", "nameroot", "dirname"): + if field in obj: + del obj[field] + +def find_defaults(d, op): + if isinstance(d, list): + for i in d: + find_defaults(i, op) + elif isinstance(d, dict): + if "default" in d: + op(d) + else: + for i in d.itervalues(): + find_defaults(i, op) + def upload_dependencies(arvrunner, name, document_loader, workflowobj, uri, loadref_run, include_primary=True): """Upload the dependencies of the workflowobj document to Keep. @@ -98,10 +113,32 @@ def upload_dependencies(arvrunner, name, document_loader, if include_primary and "id" in workflowobj: sc.append({"class": "File", "location": workflowobj["id"]}) + if "$schemas" in workflowobj: + for s in workflowobj["$schemas"]: + sc.append({"class": "File", "location": s}) + + def capture_default(obj): + remove = [False] + def add_default(f): + if "location" not in f and "path" in f: + f["location"] = f["path"] + del f["path"] + if "location" in f and not arvrunner.fs_access.exists(f["location"]): + # Remove from sc + sc[:] = [x for x in sc if x["location"] != f["location"]] + # Delete "default" from workflowobj + remove[0] = True + visit_class(obj["default"], ("File", "Directory"), add_default) + if remove[0]: + del obj["default"] + + find_defaults(workflowobj, capture_default) + mapper = ArvPathMapper(arvrunner, sc, "", "keep:%s", "keep:%s/%s", - name=name) + name=name, + single_collection=True) def setloc(p): if "location" in p and (not p["location"].startswith("_:")) and (not p["location"].startswith("keep:")): @@ -109,11 +146,18 @@ def upload_dependencies(arvrunner, name, document_loader, adjustFileObjs(workflowobj, setloc) adjustDirObjs(workflowobj, setloc) + if "$schemas" in workflowobj: + sch = [] + for s in workflowobj["$schemas"]: + sch.append(mapper.mapper(s).resolved) + workflowobj["$schemas"] = sch + return mapper def upload_docker(arvrunner, tool): - """Visitor which uploads Docker images referenced in CommandLineTool objects.""" + """Uploads Docker images used in CommandLineTool objects.""" + if isinstance(tool, CommandLineTool): (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement") if docker_req: @@ -122,6 +166,11 @@ def upload_docker(arvrunner, tool): raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError( "Option 'dockerOutputDirectory' of DockerRequirement not supported.") arv_docker_get_image(arvrunner.api, docker_req, True, arvrunner.project_uuid) + else: + arv_docker_get_image(arvrunner.api, {"dockerPull": "arvados/jobs"}, True, arvrunner.project_uuid) + elif isinstance(tool, cwltool.workflow.Workflow): + for s in tool.steps: + upload_docker(arvrunner, s.embedded_tool) def packed_workflow(arvrunner, tool): """Create a packed workflow. @@ -177,9 +226,10 @@ def upload_job_order(arvrunner, name, tool, job_order): return job_order -def upload_workflow_deps(arvrunner, tool): +def upload_workflow_deps(arvrunner, tool, override_tools): # Ensure that Docker images needed by this workflow are available - tool.visit(partial(upload_docker, arvrunner)) + + upload_docker(arvrunner, tool) document_loader = tool.doc_loader @@ -193,6 +243,7 @@ def upload_workflow_deps(arvrunner, tool): False, include_primary=False) document_loader.idx[deptool["id"]] = deptool + override_tools[deptool["id"]] = json.dumps(deptool) tool.visit(upload_tool_deps) @@ -205,17 +256,49 @@ def arvados_jobs_image(arvrunner, img): raise Exception("Docker image %s is not available\n%s" % (img, e) ) return img +def upload_workflow_collection(arvrunner, name, packed): + collection = arvados.collection.Collection(api_client=arvrunner.api, + keep_client=arvrunner.keep_client, + num_retries=arvrunner.num_retries) + with collection.open("workflow.cwl", "w") as f: + f.write(json.dumps(packed, indent=2, sort_keys=True, separators=(',',': '))) + + filters = [["portable_data_hash", "=", collection.portable_data_hash()], + ["name", "like", name+"%"]] + if arvrunner.project_uuid: + filters.append(["owner_uuid", "=", arvrunner.project_uuid]) + exists = arvrunner.api.collections().list(filters=filters).execute(num_retries=arvrunner.num_retries) + + if exists["items"]: + logger.info("Using collection %s", exists["items"][0]["uuid"]) + else: + collection.save_new(name=name, + owner_uuid=arvrunner.project_uuid, + ensure_unique_name=True, + num_retries=arvrunner.num_retries) + logger.info("Uploaded to %s", collection.manifest_locator()) + + return collection.portable_data_hash() + + class Runner(object): """Base class for runner processes, which submit an instance of arvados-cwl-runner and wait for the final result.""" def __init__(self, runner, tool, job_order, enable_reuse, output_name, output_tags, submit_runner_ram=0, - name=None, on_error=None, submit_runner_image=None): + name=None, on_error=None, submit_runner_image=None, + intermediate_output_ttl=0): self.arvrunner = runner self.tool = tool self.job_order = job_order self.running = False + if enable_reuse: + # If reuse is permitted by command line arguments but + # disabled by the workflow itself, disable it. + reuse_req, _ = get_feature(self.tool, "http://arvados.org/cwl#ReuseRequirement") + if reuse_req: + enable_reuse = reuse_req["enableReuse"] self.enable_reuse = enable_reuse self.uuid = None self.final_output = None @@ -224,11 +307,12 @@ class Runner(object): self.name = name self.on_error = on_error self.jobs_image = submit_runner_image or "arvados/jobs:"+__version__ + self.intermediate_output_ttl = intermediate_output_ttl if submit_runner_ram: self.submit_runner_ram = submit_runner_ram else: - self.submit_runner_ram = 1024 + self.submit_runner_ram = 3000 if self.submit_runner_ram <= 0: raise Exception("Value of --submit-runner-ram must be greater than zero")