X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/1275b20bc802424a69abd8a76b1c9e3de9657419..704dd826a498db11a052fe77a4953b0caa245c10:/sdk/cwl/arvados_cwl/__init__.py diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index 044b490843..4701b4d8f1 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -22,7 +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 @@ -111,8 +110,7 @@ class ArvCwlRunner(object): kwargs["fetcher_constructor"] = partial(CollectionFetcher, api_client=self.api, fs_access=CollectionFsAccess("", collection_cache=self.collection_cache), - num_retries=self.num_retries, - overrides=kwargs.get("override_tools")) + 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) @@ -226,13 +224,16 @@ class ArvCwlRunner(object): 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): @@ -281,7 +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] @@ -367,8 +368,7 @@ class ArvCwlRunner(object): # Upload direct dependencies of workflow steps, get back mapping of files to keep references. # Also uploads docker images. - override_tools = {} - upload_workflow_deps(self, tool, override_tools) + merged_map = upload_workflow_deps(self, tool) # Reload tool object which may have been updated by # upload_workflow_deps @@ -376,8 +376,7 @@ class ArvCwlRunner(object): makeTool=self.arv_make_tool, loader=tool.doc_loader, avsc_names=tool.doc_schema, - metadata=tool.metadata, - override_tools=override_tools) + metadata=tool.metadata) # Upload local file references in the job order. job_order = upload_job_order(self, "%s input" % kwargs["name"], @@ -391,7 +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") @@ -400,10 +400,12 @@ 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") + self.eval_timeout = kwargs.get("eval_timeout") kwargs["make_fs_access"] = make_fs_access kwargs["enable_reuse"] = kwargs.get("enable_reuse") @@ -412,6 +414,8 @@ class ArvCwlRunner(object): kwargs["compute_checksum"] = kwargs.get("compute_checksum") if self.work_api == "containers": + if self.ignore_docker_for_reuse: + raise validate.ValidationException("--ignore-docker-for-reuse not supported with containers API.") kwargs["outdir"] = "/var/spool/cwl" kwargs["docker_outdir"] = "/var/spool/cwl" kwargs["tmpdir"] = "/tmp" @@ -438,7 +442,8 @@ class ArvCwlRunner(object): name=kwargs.get("name"), on_error=kwargs.get("on_error"), submit_runner_image=kwargs.get("submit_runner_image"), - intermediate_output_ttl=kwargs.get("intermediate_output_ttl")) + 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, @@ -446,7 +451,8 @@ 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"), + 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( @@ -554,7 +560,7 @@ 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) @@ -750,7 +756,6 @@ 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,