import logging import re import copy import json import time from cwltool.process import get_feature, shortname, UnsupportedRequirement from cwltool.errors import WorkflowException from cwltool.draft2tool import revmap_file, CommandLineTool from cwltool.load_tool import fetch_document from cwltool.builder import Builder from cwltool.pathmapper import adjustFileObjs, adjustDirObjs from schema_salad.sourceline import SourceLine import ruamel.yaml as yaml import arvados.collection from arvados.errors import ApiError from .arvdocker import arv_docker_get_image from .runner import Runner, arvados_jobs_image, packed_workflow, upload_workflow_collection, trim_anonymous_location from .pathmapper import VwdPathMapper, trim_listing from .perf import Perf from . import done from ._version import __version__ logger = logging.getLogger('arvados.cwl-runner') metrics = logging.getLogger('arvados.cwl-runner.metrics') crunchrunner_re = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.(tmpdir|outdir|keep)\)=(.*)") crunchrunner_git_commit = 'a3f2cb186e437bfce0031b024b2157b73ed2717d' class ArvadosJob(object): """Submit and manage a Crunch job for executing a CWL CommandLineTool.""" def __init__(self, runner): self.arvrunner = runner self.running = False self.uuid = None def run(self, dry_run=False, pull_image=True, **kwargs): script_parameters = { "command": self.command_line } runtime_constraints = {} with Perf(metrics, "generatefiles %s" % self.name): if self.generatefiles["listing"]: vwd = arvados.collection.Collection(api_client=self.arvrunner.api, keep_client=self.arvrunner.keep_client, num_retries=self.arvrunner.num_retries) script_parameters["task.vwd"] = {} generatemapper = VwdPathMapper([self.generatefiles], "", "", separateDirs=False) with Perf(metrics, "createfiles %s" % self.name): for f, p in generatemapper.items(): if p.type == "CreateFile": with vwd.open(p.target, "w") as n: n.write(p.resolved.encode("utf-8")) if vwd: with Perf(metrics, "generatefiles.save_new %s" % self.name): vwd.save_new() for f, p in generatemapper.items(): if p.type == "File": script_parameters["task.vwd"][p.target] = p.resolved if p.type == "CreateFile": script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target) script_parameters["task.env"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir} if self.environment: script_parameters["task.env"].update(self.environment) if self.stdin: script_parameters["task.stdin"] = self.stdin if self.stdout: script_parameters["task.stdout"] = self.stdout if self.stderr: script_parameters["task.stderr"] = self.stderr if self.successCodes: script_parameters["task.successCodes"] = self.successCodes if self.temporaryFailCodes: script_parameters["task.temporaryFailCodes"] = self.temporaryFailCodes if self.permanentFailCodes: script_parameters["task.permanentFailCodes"] = self.permanentFailCodes with Perf(metrics, "arv_docker_get_image %s" % self.name): (docker_req, docker_is_req) = get_feature(self, "DockerRequirement") if docker_req and kwargs.get("use_container") is not False: if docker_req.get("dockerOutputDirectory"): raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError( "Option 'dockerOutputDirectory' of DockerRequirement not supported.") runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvrunner.project_uuid) else: runtime_constraints["docker_image"] = "arvados/jobs" resources = self.builder.resources if resources is not None: runtime_constraints["min_cores_per_node"] = resources.get("cores", 1) runtime_constraints["min_ram_mb_per_node"] = resources.get("ram") runtime_constraints["min_scratch_mb_per_node"] = resources.get("tmpdirSize", 0) + resources.get("outdirSize", 0) runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints") if runtime_req: if "keep_cache" in runtime_req: runtime_constraints["keep_cache_mb_per_task"] = runtime_req["keep_cache"] runtime_constraints["min_ram_mb_per_node"] += runtime_req["keep_cache"] if "outputDirType" in runtime_req: if runtime_req["outputDirType"] == "local_output_dir": script_parameters["task.keepTmpOutput"] = False elif runtime_req["outputDirType"] == "keep_output_dir": script_parameters["task.keepTmpOutput"] = True filters = [["repository", "=", "arvados"], ["script", "=", "crunchrunner"], ["script_version", "in git", crunchrunner_git_commit]] if not self.arvrunner.ignore_docker_for_reuse: filters.append(["docker_image_locator", "in docker", runtime_constraints["docker_image"]]) enable_reuse = kwargs.get("enable_reuse", True) if enable_reuse: reuse_req, _ = get_feature(self, "http://arvados.org/cwl#ReuseRequirement") if reuse_req: enable_reuse = reuse_req["enableReuse"] try: with Perf(metrics, "create %s" % self.name): response = self.arvrunner.api.jobs().create( body={ "owner_uuid": self.arvrunner.project_uuid, "script": "crunchrunner", "repository": "arvados", "script_version": "master", "minimum_script_version": crunchrunner_git_commit, "script_parameters": {"tasks": [script_parameters]}, "runtime_constraints": runtime_constraints }, filters=filters, find_or_create=enable_reuse ).execute(num_retries=self.arvrunner.num_retries) self.arvrunner.processes[response["uuid"]] = self self.update_pipeline_component(response) if response["state"] == "Complete": logger.info("%s reused job %s", self.arvrunner.label(self), response["uuid"]) # Give read permission to the desired project on reused jobs if response["owner_uuid"] != self.arvrunner.project_uuid: try: self.arvrunner.api.links().create(body={ 'link_class': 'permission', 'name': 'can_read', 'tail_uuid': self.arvrunner.project_uuid, 'head_uuid': response["uuid"], }).execute(num_retries=self.arvrunner.num_retries) except ApiError as e: # The user might not have "manage" access on the job: log # a message and continue. logger.info("Creating read permission on job %s: %s", response["uuid"], e) with Perf(metrics, "done %s" % self.name): self.done(response) else: logger.info("%s %s is %s", self.arvrunner.label(self), response["uuid"], response["state"]) except Exception as e: logger.exception("%s error" % (self.arvrunner.label(self))) self.output_callback({}, "permanentFail") def update_pipeline_component(self, record): if self.arvrunner.pipeline: self.arvrunner.pipeline["components"][self.name] = {"job": record} with Perf(metrics, "update_pipeline_component %s" % self.name): self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(uuid=self.arvrunner.pipeline["uuid"], body={ "components": self.arvrunner.pipeline["components"] }).execute(num_retries=self.arvrunner.num_retries) if self.arvrunner.uuid: try: job = self.arvrunner.api.jobs().get(uuid=self.arvrunner.uuid).execute() if job: components = job["components"] components[self.name] = record["uuid"] self.arvrunner.api.jobs().update(uuid=self.arvrunner.uuid, body={ "components": components }).execute(num_retries=self.arvrunner.num_retries) except Exception as e: logger.info("Error adding to components: %s", e) def done(self, record): try: self.update_pipeline_component(record) except: pass try: if record["state"] == "Complete": processStatus = "success" else: processStatus = "permanentFail" outputs = {} try: if record["output"]: with Perf(metrics, "inspect log %s" % self.name): logc = arvados.collection.CollectionReader(record["log"], api_client=self.arvrunner.api, keep_client=self.arvrunner.keep_client, num_retries=self.arvrunner.num_retries) log = logc.open(logc.keys()[0]) dirs = {} tmpdir = None outdir = None keepdir = None for l in log: # Determine the tmpdir, outdir and keepdir paths from # the job run. Unfortunately, we can't take the first # values we find (which are expected to be near the # top) and stop scanning because if the node fails and # the job restarts on a different node these values # will different runs, and we need to know about the # final run that actually produced output. g = crunchrunner_re.match(l) if g: dirs[g.group(1)] = g.group(2) if processStatus == "permanentFail": done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self)) with Perf(metrics, "output collection %s" % self.name): outputs = done.done(self, record, dirs["tmpdir"], dirs["outdir"], dirs["keep"]) except WorkflowException as e: logger.error("%s unable to collect output from %s:\n%s", self.arvrunner.label(self), record["output"], e, exc_info=(e if self.arvrunner.debug else False)) processStatus = "permanentFail" except Exception as e: logger.exception("Got unknown exception while collecting output for job %s:", self.name) processStatus = "permanentFail" # Note: Currently, on error output_callback is expecting an empty dict, # anything else will fail. if not isinstance(outputs, dict): logger.error("Unexpected output type %s '%s'", type(outputs), outputs) outputs = {} processStatus = "permanentFail" finally: self.output_callback(outputs, processStatus) if record["uuid"] in self.arvrunner.processes: del self.arvrunner.processes[record["uuid"]] class RunnerJob(Runner): """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner.""" def arvados_job_spec(self, dry_run=False, pull_image=True, **kwargs): """Create an Arvados job specification for this workflow. The returned dict can be used to create a job (i.e., passed as the +body+ argument to jobs().create()), or as a component in a pipeline template or pipeline instance. """ if self.tool.tool["id"].startswith("keep:"): self.job_order["cwl:tool"] = self.tool.tool["id"][5:] else: packed = packed_workflow(self.arvrunner, self.tool) wf_pdh = upload_workflow_collection(self.arvrunner, self.name, packed) self.job_order["cwl:tool"] = "%s/workflow.cwl#main" % wf_pdh adjustDirObjs(self.job_order, trim_listing) adjustFileObjs(self.job_order, trim_anonymous_location) adjustDirObjs(self.job_order, trim_anonymous_location) if self.output_name: self.job_order["arv:output_name"] = self.output_name if self.output_tags: self.job_order["arv:output_tags"] = self.output_tags self.job_order["arv:enable_reuse"] = self.enable_reuse if self.on_error: self.job_order["arv:on_error"] = self.on_error return { "script": "cwl-runner", "script_version": "master", "minimum_script_version": "570509ab4d2ef93d870fd2b1f2eab178afb1bad9", "repository": "arvados", "script_parameters": self.job_order, "runtime_constraints": { "docker_image": arvados_jobs_image(self.arvrunner, self.jobs_image), "min_ram_mb_per_node": self.submit_runner_ram } } def run(self, *args, **kwargs): job_spec = self.arvados_job_spec(*args, **kwargs) job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid) job = self.arvrunner.api.jobs().create( body=job_spec, find_or_create=self.enable_reuse ).execute(num_retries=self.arvrunner.num_retries) for k,v in job_spec["script_parameters"].items(): if v is False or v is None or isinstance(v, dict): job_spec["script_parameters"][k] = {"value": v} del job_spec["owner_uuid"] job_spec["job"] = job self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().create( body={ "owner_uuid": self.arvrunner.project_uuid, "name": self.name, "components": {"cwl-runner": job_spec }, "state": "RunningOnServer"}).execute(num_retries=self.arvrunner.num_retries) logger.info("Created pipeline %s", self.arvrunner.pipeline["uuid"]) if kwargs.get("wait") is False: self.uuid = self.arvrunner.pipeline["uuid"] return self.uuid = job["uuid"] self.arvrunner.processes[self.uuid] = self if job["state"] in ("Complete", "Failed", "Cancelled"): self.done(job) class RunnerTemplate(object): """An Arvados pipeline template that invokes a CWL workflow.""" type_to_dataclass = { 'boolean': 'boolean', 'File': 'File', 'Directory': 'Collection', 'float': 'number', 'int': 'number', 'string': 'text', } def __init__(self, runner, tool, job_order, enable_reuse, uuid, submit_runner_ram=0, name=None): self.runner = runner self.tool = tool self.job = RunnerJob( runner=runner, tool=tool, job_order=job_order, enable_reuse=enable_reuse, output_name=None, output_tags=None, submit_runner_ram=submit_runner_ram, name=name) self.uuid = uuid def pipeline_component_spec(self): """Return a component that Workbench and a-r-p-i will understand. Specifically, translate CWL input specs to Arvados pipeline format, like {"dataclass":"File","value":"xyz"}. """ spec = self.job.arvados_job_spec() # Most of the component spec is exactly the same as the job # spec (script, script_version, etc.). # spec['script_parameters'] isn't right, though. A component # spec's script_parameters hash is a translation of # self.tool.tool['inputs'] with defaults/overrides taken from # the job order. So we move the job parameters out of the way # and build a new spec['script_parameters']. job_params = spec['script_parameters'] spec['script_parameters'] = {} for param in self.tool.tool['inputs']: param = copy.deepcopy(param) # Data type and "required" flag... types = param['type'] if not isinstance(types, list): types = [types] param['required'] = 'null' not in types non_null_types = [t for t in types if t != "null"] if len(non_null_types) == 1: the_type = [c for c in non_null_types][0] dataclass = None if isinstance(the_type, basestring): dataclass = self.type_to_dataclass.get(the_type) if dataclass: param['dataclass'] = dataclass # Note: If we didn't figure out a single appropriate # dataclass, we just left that attribute out. We leave # the "type" attribute there in any case, which might help # downstream. # Title and description... title = param.pop('label', '') descr = param.pop('doc', '').rstrip('\n') if title: param['title'] = title if descr: param['description'] = descr # Fill in the value from the current job order, if any. param_id = shortname(param.pop('id')) value = job_params.get(param_id) if value is None: pass elif not isinstance(value, dict): param['value'] = value elif param.get('dataclass') in ('File', 'Collection') and value.get('location'): param['value'] = value['location'][5:] spec['script_parameters'][param_id] = param spec['script_parameters']['cwl:tool'] = job_params['cwl:tool'] return spec def save(self): body = { "components": { self.job.name: self.pipeline_component_spec(), }, "name": self.job.name, } if self.runner.project_uuid: body["owner_uuid"] = self.runner.project_uuid if self.uuid: self.runner.api.pipeline_templates().update( uuid=self.uuid, body=body).execute( num_retries=self.runner.num_retries) logger.info("Updated template %s", self.uuid) else: self.uuid = self.runner.api.pipeline_templates().create( body=body, ensure_unique_name=True).execute( num_retries=self.runner.num_retries)['uuid'] logger.info("Created template %s", self.uuid)