X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/757ee383a605de73773544001a4e61717e19ece8..94dcdefbf8fe264daa28c5b15f68b304c683e390:/sdk/cwl/arvados_cwl/arvcontainer.py diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py index 0b8f2ca707..742906c616 100644 --- a/sdk/cwl/arvados_cwl/arvcontainer.py +++ b/sdk/cwl/arvados_cwl/arvcontainer.py @@ -17,7 +17,7 @@ import uuid import math import arvados_cwl.util -import ruamel.yaml as yaml +import ruamel.yaml from cwltool.errors import WorkflowException from cwltool.process import UnsupportedRequirement, shortname @@ -37,6 +37,9 @@ from ._version import __version__ logger = logging.getLogger('arvados.cwl-runner') metrics = logging.getLogger('arvados.cwl-runner.metrics') +def cleanup_name_for_collection(name): + return name.replace("/", " ") + class ArvadosContainer(JobBase): """Submit and manage a Crunch container request for executing a CWL CommandLineTool.""" @@ -88,6 +91,8 @@ class ArvadosContainer(JobBase): container_request["state"] = "Committed" container_request.setdefault("properties", {}) + container_request["properties"]["cwl_input"] = self.joborder + runtime_constraints = {} if runtimeContext.project_uuid: @@ -199,7 +204,7 @@ class ArvadosContainer(JobBase): if not runtimeContext.current_container: runtimeContext.current_container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger) - vwd.save_new(name=info["name"], + vwd.save_new(name=intermediate_collection_info["name"], owner_uuid=runtimeContext.project_uuid, ensure_unique_name=True, trash_at=intermediate_collection_info["trash_at"], @@ -245,11 +250,7 @@ class ArvadosContainer(JobBase): container_request["container_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, runtimeContext.pull_image, - runtimeContext.project_uuid, - runtimeContext.force_docker_pull, - runtimeContext.tmp_outdir_prefix, - runtimeContext.match_local_docker, - runtimeContext.copy_deps) + runtimeContext) network_req, _ = self.get_requirement("NetworkAccess") if network_req: @@ -259,10 +260,22 @@ class ArvadosContainer(JobBase): if api_req: runtime_constraints["API"] = True + use_disk_cache = (self.arvrunner.api.config()["Containers"].get("DefaultKeepCacheRAM", 0) == 0) + + keep_cache_type_req, _ = self.get_requirement("http://arvados.org/cwl#KeepCacheTypeRequirement") + if keep_cache_type_req: + if "keepCacheType" in keep_cache_type_req: + if keep_cache_type_req["keepCacheType"] == "ram_cache": + use_disk_cache = False + runtime_req, _ = self.get_requirement("http://arvados.org/cwl#RuntimeConstraints") if runtime_req: if "keep_cache" in runtime_req: - runtime_constraints["keep_cache_ram"] = math.ceil(runtime_req["keep_cache"] * 2**20) + if use_disk_cache: + # If DefaultKeepCacheRAM is zero it means we should use disk cache. + runtime_constraints["keep_cache_disk"] = math.ceil(runtime_req["keep_cache"] * 2**20) + else: + runtime_constraints["keep_cache_ram"] = math.ceil(runtime_req["keep_cache"] * 2**20) if "outputDirType" in runtime_req: if runtime_req["outputDirType"] == "local_output_dir": # Currently the default behavior. @@ -320,7 +333,7 @@ class ArvadosContainer(JobBase): if runtimeContext.submit_runner_cluster: extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster - container_request["output_name"] = "Output for step %s" % (self.name) + container_request["output_name"] = cleanup_name_for_collection("Output from step %s" % (self.name)) container_request["output_ttl"] = self.output_ttl container_request["mounts"] = mounts container_request["secret_mounts"] = secret_mounts @@ -344,10 +357,13 @@ class ArvadosContainer(JobBase): output_properties_req, _ = self.get_requirement("http://arvados.org/cwl#OutputCollectionProperties") if output_properties_req: - for pr in output_properties_req["processProperties"]: - container_request["output_properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"]) - - output_properties.update(intermediate_collection_info["properties"]) + if self.arvrunner.api._rootDesc["revision"] >= "20220510": + container_request["output_properties"] = {} + for pr in output_properties_req["outputProperties"]: + container_request["output_properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"]) + else: + logger.warning("%s API revision is %s, revision %s is required to support setting properties on output collections.", + self.arvrunner.label(self), self.arvrunner.api._rootDesc["revision"], "20220510") if runtimeContext.runnerjob.startswith("arvwf:"): wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")] @@ -431,6 +447,13 @@ class ArvadosContainer(JobBase): if container["output"]: outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep") + + properties = record["properties"].copy() + properties["cwl_output"] = outputs + self.arvrunner.api.container_requests().update( + uuid=self.uuid, + body={"container_request": {"properties": properties}} + ).execute(num_retries=self.arvrunner.num_retries) except WorkflowException as e: # Only include a stack trace if in debug mode. # A stack trace may obfuscate more useful output about the workflow. @@ -447,7 +470,7 @@ class ArvadosContainer(JobBase): class RunnerContainer(Runner): """Submit and manage a container that runs arvados-cwl-runner.""" - def arvados_job_spec(self, runtimeContext): + def arvados_job_spec(self, runtimeContext, git_info): """Create an Arvados container request for this workflow. The returned dict can be used to create a container passed as @@ -508,15 +531,28 @@ class RunnerContainer(Runner): "kind": "collection", "portable_data_hash": "%s" % workflowcollection } + elif self.embedded_tool.tool.get("id", "").startswith("arvwf:"): + uuid, frg = urllib.parse.urldefrag(self.embedded_tool.tool["id"]) + workflowpath = "/var/lib/cwl/workflow.json#" + frg + packedtxt = self.loadingContext.loader.fetch_text(uuid) + yaml = ruamel.yaml.YAML(typ='safe', pure=True) + packed = yaml.load(packedtxt) + container_req["mounts"]["/var/lib/cwl/workflow.json"] = { + "kind": "json", + "content": packed + } + container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33] else: - packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext) + main = self.loadingContext.loader.idx["_:main"] + if main.get("id") == "_:main": + del main["id"] workflowpath = "/var/lib/cwl/workflow.json#main" container_req["mounts"]["/var/lib/cwl/workflow.json"] = { "kind": "json", - "content": packed + "content": main } - if self.embedded_tool.tool.get("id", "").startswith("arvwf:"): - container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33] + + container_req["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in git_info.items()}) properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties") if properties_req: @@ -580,6 +616,15 @@ class RunnerContainer(Runner): if runtimeContext.enable_preemptible is False: command.append("--disable-preemptible") + if runtimeContext.varying_url_params: + command.append("--varying-url-params="+runtimeContext.varying_url_params) + + if runtimeContext.prefer_cached_downloads: + command.append("--prefer-cached-downloads") + + if self.fast_parser: + command.append("--fast-parser") + command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"]) container_req["command"] = command @@ -589,7 +634,7 @@ class RunnerContainer(Runner): def run(self, runtimeContext): runtimeContext.keepprefix = "keep:" - job_spec = self.arvados_job_spec(runtimeContext) + job_spec = self.arvados_job_spec(runtimeContext, self.git_info) if runtimeContext.project_uuid: job_spec["owner_uuid"] = runtimeContext.project_uuid