X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/c043e133b2646037ed630d571e91dbf77344f855..8a2035547ad8bf6abad6a4a03bb0b59211a00932:/sdk/cwl/arvados_cwl/__init__.py diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index 3c7de77ebf..71ddd17221 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -1,4 +1,7 @@ #!/usr/bin/env python +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 # Implement cwl-runner interface for submitting and running work on Arvados, using # either the Crunch jobs API or Crunch containers API. @@ -19,7 +22,6 @@ from cwltool.errors import WorkflowException import cwltool.main import cwltool.workflow import cwltool.process -import schema_salad from schema_salad.sourceline import SourceLine import arvados @@ -74,6 +76,9 @@ class ArvCwlRunner(object): self.output_name = output_name self.output_tags = output_tags self.project_uuid = None + self.intermediate_output_ttl = 0 + self.intermediate_output_collections = [] + self.trash_intermediate = False if keep_client is not None: self.keep_client = keep_client @@ -106,6 +111,7 @@ class ArvCwlRunner(object): api_client=self.api, fs_access=CollectionFsAccess("", collection_cache=self.collection_cache), num_retries=self.num_retries) + kwargs["resolver"] = partial(collectionResolver, self.api, num_retries=self.num_retries) if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool": return ArvadosCommandTool(self, toolpath_object, **kwargs) elif "class" in toolpath_object and toolpath_object["class"] == "Workflow": @@ -202,20 +208,37 @@ class ArvCwlRunner(object): def add_uploaded(self, src, pair): self.uploaded[src] = pair + def add_intermediate_output(self, uuid): + if uuid: + self.intermediate_output_collections.append(uuid) + + def trash_intermediate_output(self): + logger.info("Cleaning up intermediate output collections") + for i in self.intermediate_output_collections: + try: + self.api.collections().delete(uuid=i).execute(num_retries=self.num_retries) + except: + logger.warn("Failed to delete intermediate output: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False)) + if sys.exc_info()[0] is KeyboardInterrupt: + break + def check_features(self, obj): if isinstance(obj, dict): - if obj.get("writable"): - raise SourceLine(obj, "writable", UnsupportedRequirement).makeError("InitialWorkDir feature 'writable: true' not supported") + if obj.get("writable") and self.work_api != "containers": + raise SourceLine(obj, "writable", UnsupportedRequirement).makeError("InitialWorkDir feature 'writable: true' not supported with --api=jobs") if obj.get("class") == "DockerRequirement": if obj.get("dockerOutputDirectory"): - # TODO: can be supported by containers API, but not jobs API. - raise SourceLine(obj, "dockerOutputDirectory", UnsupportedRequirement).makeError( - "Option 'dockerOutputDirectory' of DockerRequirement not supported.") + if self.work_api != "containers": + raise SourceLine(obj, "dockerOutputDirectory", UnsupportedRequirement).makeError( + "Option 'dockerOutputDirectory' of DockerRequirement not supported with --api=jobs.") + if not obj.get("dockerOutputDirectory").startswith('/'): + raise SourceLine(obj, "dockerOutputDirectory", validate.ValidationException).makeError( + "Option 'dockerOutputDirectory' must be an absolute path.") for v in obj.itervalues(): self.check_features(v) elif isinstance(obj, list): for i,v in enumerate(obj): - with SourceLine(obj, i, UnsupportedRequirement): + with SourceLine(obj, i, UnsupportedRequirement, logger.isEnabledFor(logging.DEBUG)): self.check_features(v) def make_output_collection(self, name, tagsString, outputObj): @@ -259,7 +282,7 @@ class ArvCwlRunner(object): def rewrite(fileobj): fileobj["location"] = generatemapper.mapper(fileobj["location"]).target - for k in ("basename", "listing", "contents"): + for k in ("listing", "contents", "nameext", "nameroot", "dirname"): if k in fileobj: del fileobj[k] @@ -329,12 +352,23 @@ class ArvCwlRunner(object): collection_cache=self.collection_cache) self.fs_access = make_fs_access(kwargs["basedir"]) + + self.trash_intermediate = kwargs["trash_intermediate"] + if self.trash_intermediate and self.work_api != "containers": + raise Exception("--trash-intermediate is only supported with --api=containers.") + + self.intermediate_output_ttl = kwargs["intermediate_output_ttl"] + if self.intermediate_output_ttl and self.work_api != "containers": + raise Exception("--intermediate-output-ttl is only supported with --api=containers.") + if self.intermediate_output_ttl < 0: + raise Exception("Invalid value %d for --intermediate-output-ttl, cannot be less than zero" % self.intermediate_output_ttl) + if not kwargs.get("name"): kwargs["name"] = self.name = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"]) # Upload direct dependencies of workflow steps, get back mapping of files to keep references. # Also uploads docker images. - upload_workflow_deps(self, tool) + merged_map = upload_workflow_deps(self, tool) # Reload tool object which may have been updated by # upload_workflow_deps @@ -356,7 +390,8 @@ class ArvCwlRunner(object): kwargs.get("enable_reuse"), uuid=existing_uuid, submit_runner_ram=kwargs.get("submit_runner_ram"), - name=kwargs["name"]) + name=kwargs["name"], + merged_map=merged_map) tmpl.save() # cwltool.main will write our return value to stdout. return (tmpl.uuid, "success") @@ -365,7 +400,8 @@ class ArvCwlRunner(object): self.project_uuid, uuid=existing_uuid, submit_runner_ram=kwargs.get("submit_runner_ram"), - name=kwargs["name"]), + name=kwargs["name"], + merged_map=merged_map), "success") self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse") @@ -390,14 +426,8 @@ class ArvCwlRunner(object): if kwargs.get("submit"): # Submit a runner job to run the workflow for us. if self.work_api == "containers": - if tool.tool["class"] == "CommandLineTool": + if tool.tool["class"] == "CommandLineTool" and kwargs.get("wait"): kwargs["runnerjob"] = tool.tool["id"] - upload_dependencies(self, - kwargs["name"], - tool.doc_loader, - tool.tool, - tool.tool["id"], - False) runnerjob = tool.job(job_order, self.output_callback, **kwargs).next() @@ -408,7 +438,9 @@ class ArvCwlRunner(object): submit_runner_ram=kwargs.get("submit_runner_ram"), name=kwargs.get("name"), on_error=kwargs.get("on_error"), - submit_runner_image=kwargs.get("submit_runner_image")) + submit_runner_image=kwargs.get("submit_runner_image"), + intermediate_output_ttl=kwargs.get("intermediate_output_ttl"), + merged_map=merged_map) elif self.work_api == "jobs": runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name, @@ -416,9 +448,9 @@ class ArvCwlRunner(object): submit_runner_ram=kwargs.get("submit_runner_ram"), name=kwargs.get("name"), on_error=kwargs.get("on_error"), - submit_runner_image=kwargs.get("submit_runner_image")) - - if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and self.work_api == "jobs": + submit_runner_image=kwargs.get("submit_runner_image"), + merged_map=merged_map) + elif "cwl_runner_job" not in kwargs and self.work_api == "jobs": # Create pipeline for local run self.pipeline = self.api.pipeline_instances().create( body={ @@ -512,6 +544,9 @@ class ArvCwlRunner(object): adjustDirObjs(self.final_output, partial(get_listing, self.fs_access)) adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access)) + if self.trash_intermediate and self.final_status == "success": + self.trash_intermediate_output() + return (self.final_output, self.final_status) @@ -522,7 +557,7 @@ def versionstring(): arvpkg = pkg_resources.require("arvados-python-client") cwlpkg = pkg_resources.require("cwltool") - return "%s %s %s, %s %s, %s %s" % (sys.argv[0], __version__, arvcwlpkg[0].version, + return "%s %s, %s %s, %s %s" % (sys.argv[0], arvcwlpkg[0].version, "arvados-python-client", arvpkg[0].version, "cwltool", cwlpkg[0].version) @@ -539,7 +574,12 @@ def arg_parser(): # type: () -> argparse.ArgumentParser help="Time to wait for a Javascript expression to evaluate before giving an error, default 20s.", type=float, default=20) - parser.add_argument("--version", action="store_true", help="Print version and exit") + + exgroup = parser.add_mutually_exclusive_group() + exgroup.add_argument("--print-dot", action="store_true", + help="Print workflow visualization in graphviz format and exit") + exgroup.add_argument("--version", action="store_true", help="Print version and exit") + exgroup.add_argument("--validate", action="store_true", help="Validate CWL document only.") exgroup = parser.add_mutually_exclusive_group() exgroup.add_argument("--verbose", action="store_true", help="Default logging") @@ -553,10 +593,10 @@ def arg_parser(): # type: () -> argparse.ArgumentParser exgroup = parser.add_mutually_exclusive_group() exgroup.add_argument("--enable-reuse", action="store_true", default=True, dest="enable_reuse", - help="") + help="Enable job or container reuse (default)") exgroup.add_argument("--disable-reuse", action="store_false", default=True, dest="enable_reuse", - help="") + help="Disable job or container reuse") 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) @@ -589,7 +629,8 @@ def arg_parser(): # type: () -> argparse.ArgumentParser parser.add_argument("--api", type=str, default=None, dest="work_api", - help="Select work submission API, one of 'jobs' or 'containers'. Default is 'jobs' if that API is available, otherwise 'containers'.") + choices=("jobs", "containers"), + help="Select work submission API. Default is 'jobs' if that API is available, otherwise 'containers'.") parser.add_argument("--compute-checksum", action="store_true", default=False, help="Compute checksum of contents while collecting outputs", @@ -611,6 +652,22 @@ def arg_parser(): # type: () -> argparse.ArgumentParser help="Desired workflow behavior when a step fails. One of 'stop' or 'continue'. " "Default is 'continue'.", default="continue", choices=("stop", "continue")) + parser.add_argument("--enable-dev", action="store_true", + help="Enable loading and running development versions " + "of CWL spec.", default=False) + + parser.add_argument("--intermediate-output-ttl", type=int, metavar="N", + help="If N > 0, intermediate output collections will be trashed N seconds after creation. Default is 0 (don't trash).", + default=0) + + exgroup = parser.add_mutually_exclusive_group() + exgroup.add_argument("--trash-intermediate", action="store_true", + default=False, dest="trash_intermediate", + help="Immediately trash intermediate outputs on workflow success.") + exgroup.add_argument("--no-trash-intermediate", action="store_false", + default=False, dest="trash_intermediate", + help="Do not trash intermediate outputs (default).") + 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.") @@ -628,7 +685,9 @@ def add_arv_hints(): "http://arvados.org/cwl#RuntimeConstraints", "http://arvados.org/cwl#PartitionRequirement", "http://arvados.org/cwl#APIRequirement", - "http://commonwl.org/cwltool#LoadListingRequirement" + "http://commonwl.org/cwltool#LoadListingRequirement", + "http://arvados.org/cwl#IntermediateOutput", + "http://arvados.org/cwl#ReuseRequirement" ]) def main(args, stdout, stderr, api_client=None, keep_client=None): @@ -694,7 +753,7 @@ def main(args, stdout, stderr, api_client=None, keep_client=None): arvargs.conformance_test = None arvargs.use_container = True arvargs.relax_path_checks = True - arvargs.validate = None + arvargs.print_supported_versions = False make_fs_access = partial(CollectionFsAccess, collection_cache=runner.collection_cache)