X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/92ce0b4ffb51c957ddc0a6e36f7dfba2c819b38f..6c43be47cb3756a0e6ffc924572259d1a1c8f2c3:/sdk/cwl/arvados_cwl/__init__.py diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index af74808e1d..136d5aec15 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -3,397 +3,28 @@ # Implement cwl-runner interface for submitting and running jobs on Arvados. import argparse -import arvados -import arvados.collection -import arvados.commands.keepdocker -import arvados.commands.run -import arvados.events -import arvados.util -import copy -import cwltool.docker -from cwltool.draft2tool import revmap_file, remove_hostfs, CommandLineTool -from cwltool.errors import WorkflowException -import cwltool.main -import cwltool.workflow -import fnmatch -from functools import partial -import json import logging import os -import pkg_resources # part of setuptools -import re import sys import threading -from cwltool.load_tool import fetch_document -from cwltool.builder import Builder -import urlparse -from .arvcontainer import ArvadosContainer -from .arvjob import ArvadosJob -from .arvdocker import arv_docker_get_image - -from cwltool.process import shortname, get_feature, adjustFiles, adjustFileObjs, scandeps, UnsupportedRequirement -from arvados.api import OrderedJsonModel - -logger = logging.getLogger('arvados.cwl-runner') -logger.setLevel(logging.INFO) - -class CollectionFsAccess(cwltool.process.StdFsAccess): - """Implement the cwltool FsAccess interface for Arvados Collections.""" - - def __init__(self, basedir): - super(CollectionFsAccess, self).__init__(basedir) - self.collections = {} - - def get_collection(self, path): - p = path.split("/") - if p[0].startswith("keep:") and arvados.util.keep_locator_pattern.match(p[0][5:]): - pdh = p[0][5:] - if pdh not in self.collections: - self.collections[pdh] = arvados.collection.CollectionReader(pdh) - return (self.collections[pdh], "/".join(p[1:])) - else: - return (None, path) - - def _match(self, collection, patternsegments, parent): - if not patternsegments: - return [] - - if not isinstance(collection, arvados.collection.RichCollectionBase): - return [] - - ret = [] - # iterate over the files and subcollections in 'collection' - for filename in collection: - if patternsegments[0] == '.': - # Pattern contains something like "./foo" so just shift - # past the "./" - ret.extend(self._match(collection, patternsegments[1:], parent)) - elif fnmatch.fnmatch(filename, patternsegments[0]): - cur = os.path.join(parent, filename) - if len(patternsegments) == 1: - ret.append(cur) - else: - ret.extend(self._match(collection[filename], patternsegments[1:], cur)) - return ret - - def glob(self, pattern): - collection, rest = self.get_collection(pattern) - patternsegments = rest.split("/") - return self._match(collection, patternsegments, "keep:" + collection.manifest_locator()) - - def open(self, fn, mode): - collection, rest = self.get_collection(fn) - if collection: - return collection.open(rest, mode) - else: - return open(self._abs(fn), mode) - - def exists(self, fn): - collection, rest = self.get_collection(fn) - if collection: - return collection.exists(rest) - else: - return os.path.exists(self._abs(fn)) - - - -class RunnerJob(object): - """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner.""" - - def __init__(self, runner, tool, job_order, enable_reuse): - self.arvrunner = runner - self.tool = tool - self.job_order = job_order - self.running = False - self.enable_reuse = enable_reuse - - def update_pipeline_component(self, record): - pass - - def upload_docker(self, tool): - if isinstance(tool, CommandLineTool): - (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement") - if docker_req: - arv_docker_get_image(self.arvrunner.api, docker_req, True, self.arvrunner.project_uuid) - elif isinstance(tool, cwltool.workflow.Workflow): - for s in tool.steps: - self.upload_docker(s.embedded_tool) - - 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. - """ - self.upload_docker(self.tool) - - workflowfiles = set() - jobfiles = set() - workflowfiles.add(self.tool.tool["id"]) - - self.name = os.path.basename(self.tool.tool["id"]) - - def visitFiles(files, path): - files.add(path) - return path - - document_loader, workflowobj, uri = fetch_document(self.tool.tool["id"]) - def loadref(b, u): - return document_loader.fetch(urlparse.urljoin(b, u)) - - sc = scandeps(uri, workflowobj, - set(("$import", "run")), - set(("$include", "$schemas", "path")), - loadref) - adjustFiles(sc, partial(visitFiles, workflowfiles)) - adjustFiles(self.job_order, partial(visitFiles, jobfiles)) - - workflowmapper = ArvPathMapper(self.arvrunner, workflowfiles, "", - "%s", - "%s/%s", - name=self.name, - **kwargs) - - jobmapper = ArvPathMapper(self.arvrunner, jobfiles, "", - "%s", - "%s/%s", - name=os.path.basename(self.job_order.get("id", "#")), - **kwargs) - - adjustFiles(self.job_order, lambda p: jobmapper.mapper(p)[1]) - - if "id" in self.job_order: - del self.job_order["id"] - - self.job_order["cwl:tool"] = workflowmapper.mapper(self.tool.tool["id"])[1] - return { - "script": "cwl-runner", - "script_version": "master", - "repository": "arvados", - "script_parameters": self.job_order, - "runtime_constraints": { - "docker_image": "arvados/jobs" - } - } - - def run(self, *args, **kwargs): - job_spec = self.arvados_job_spec(*args, **kwargs) - job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid) - - response = self.arvrunner.api.jobs().create( - body=job_spec, - find_or_create=self.enable_reuse - ).execute(num_retries=self.arvrunner.num_retries) - - self.uuid = response["uuid"] - self.arvrunner.jobs[self.uuid] = self - - logger.info("Submitted job %s", response["uuid"]) - - if kwargs.get("submit"): - self.pipeline = self.arvrunner.api.pipeline_instances().create( - body={ - "owner_uuid": self.arvrunner.project_uuid, - "name": shortname(self.tool.tool["id"]), - "components": {"cwl-runner": {"job": {"uuid": self.uuid, "state": response["state"]} } }, - "state": "RunningOnClient"}).execute(num_retries=self.arvrunner.num_retries) - - if response["state"] in ("Complete", "Failed", "Cancelled"): - self.done(response) - - def done(self, record): - if record["state"] == "Complete": - processStatus = "success" - else: - processStatus = "permanentFail" - - outputs = None - try: - try: - outc = arvados.collection.Collection(record["output"]) - with outc.open("cwl.output.json") as f: - outputs = json.load(f) - def keepify(path): - if not path.startswith("keep:"): - return "keep:%s/%s" % (record["output"], path) - adjustFiles(outputs, keepify) - except Exception as e: - logger.error("While getting final output object: %s", e) - self.arvrunner.output_callback(outputs, processStatus) - finally: - del self.arvrunner.jobs[record["uuid"]] - - -class RunnerTemplate(object): - """An Arvados pipeline template that invokes a CWL workflow.""" - - type_to_dataclass = { - 'boolean': 'boolean', - 'File': 'File', - 'float': 'number', - 'int': 'number', - 'string': 'text', - } - - def __init__(self, runner, tool, job_order, enable_reuse): - self.runner = runner - self.tool = tool - self.job = RunnerJob( - runner=runner, - tool=tool, - job_order=job_order, - enable_reuse=enable_reuse) - - 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 = set(types) - set(['null']) - if len(non_null_types) == 1: - the_type = [c for c in non_null_types][0] - 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('description', '').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') == 'File' and value.get('path'): - param['value'] = value['path'] - - spec['script_parameters'][param_id] = param - spec['script_parameters']['cwl:tool'] = job_params['cwl:tool'] - return spec - - def save(self): - job_spec = self.pipeline_component_spec() - response = self.runner.api.pipeline_templates().create(body={ - "components": { - self.job.name: job_spec, - }, - "name": self.job.name, - "owner_uuid": self.runner.project_uuid, - }, ensure_unique_name=True).execute(num_retries=self.runner.num_retries) - self.uuid = response["uuid"] - logger.info("Created template %s", self.uuid) - - -class ArvPathMapper(cwltool.pathmapper.PathMapper): - """Convert container-local paths to and from Keep collection ids.""" - - def __init__(self, arvrunner, referenced_files, input_basedir, - collection_pattern, file_pattern, name=None, **kwargs): - self._pathmap = arvrunner.get_uploaded() - uploadfiles = set() - - pdh_path = re.compile(r'^keep:[0-9a-f]{32}\+\d+/.+') - - for src in referenced_files: - if isinstance(src, basestring) and pdh_path.match(src): - self._pathmap[src] = (src, collection_pattern % src[5:]) - if "#" in src: - src = src[:src.index("#")] - if src not in self._pathmap: - ab = cwltool.pathmapper.abspath(src, input_basedir) - st = arvados.commands.run.statfile("", ab, fnPattern=file_pattern) - if kwargs.get("conformance_test"): - self._pathmap[src] = (src, ab) - elif isinstance(st, arvados.commands.run.UploadFile): - uploadfiles.add((src, ab, st)) - elif isinstance(st, arvados.commands.run.ArvFile): - self._pathmap[src] = (ab, st.fn) - else: - raise cwltool.workflow.WorkflowException("Input file path '%s' is invalid" % st) - - if uploadfiles: - arvados.commands.run.uploadfiles([u[2] for u in uploadfiles], - arvrunner.api, - dry_run=kwargs.get("dry_run"), - num_retries=3, - fnPattern=file_pattern, - name=name, - project=arvrunner.project_uuid) - - for src, ab, st in uploadfiles: - arvrunner.add_uploaded(src, (ab, st.fn)) - self._pathmap[src] = (ab, st.fn) - - self.keepdir = None - - def reversemap(self, target): - if target.startswith("keep:"): - return (target, target) - elif self.keepdir and target.startswith(self.keepdir): - return (target, "keep:" + target[len(self.keepdir)+1:]) - else: - return super(ArvPathMapper, self).reversemap(target) - +import pkg_resources # part of setuptools -class ArvadosCommandTool(CommandLineTool): - """Wrap cwltool CommandLineTool to override selected methods.""" +from cwltool.errors import WorkflowException +import cwltool.main +import cwltool.workflow - def __init__(self, arvrunner, toolpath_object, crunch2, **kwargs): - super(ArvadosCommandTool, self).__init__(toolpath_object, **kwargs) - self.arvrunner = arvrunner - self.crunch2 = crunch2 +import arvados +import arvados.events - def makeJobRunner(self): - if self.crunch2: - return ArvadosContainer(self.arvrunner) - else: - return ArvadosJob(self.arvrunner) +from .arvcontainer import ArvadosContainer, RunnerContainer +from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate +from .arvtool import ArvadosCommandTool - def makePathMapper(self, reffiles, **kwargs): - if self.crunch2: - return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"], - "/keep/%s", - "/keep/%s/%s", - **kwargs) - else: - return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"], - "$(task.keep)/%s", - "$(task.keep)/%s/%s", - **kwargs) +from cwltool.process import shortname, UnsupportedRequirement +from arvados.api import OrderedJsonModel +logger = logging.getLogger('arvados.cwl-runner') +logger.setLevel(logging.INFO) class ArvCwlRunner(object): """Execute a CWL tool or workflow, submit crunch jobs, wait for them to @@ -475,7 +106,10 @@ class ArvCwlRunner(object): return tmpl.uuid if kwargs.get("submit"): - runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse")) + if self.crunch2: + runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse")) + else: + runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse")) if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and not self.crunch2: # Create pipeline for local run @@ -510,56 +144,54 @@ class ArvCwlRunner(object): kwargs["outdir"] = "$(task.outdir)" kwargs["tmpdir"] = "$(task.tmpdir)" - if kwargs.get("conformance_test"): - return cwltool.main.single_job_executor(tool, job_order, **kwargs) + if kwargs.get("submit"): + jobiter = iter((runnerjob,)) else: - if kwargs.get("submit"): - jobiter = iter((runnerjob,)) - else: - if "cwl_runner_job" in kwargs: - self.uuid = kwargs.get("cwl_runner_job").get('uuid') - jobiter = tool.job(job_order, - self.output_callback, - docker_outdir="$(task.outdir)", - **kwargs) - - try: - self.cond.acquire() - # Will continue to hold the lock for the duration of this code - # except when in cond.wait(), at which point on_message can update - # job state and process output callbacks. - - for runnable in jobiter: - if runnable: - runnable.run(**kwargs) - else: - if self.jobs: - self.cond.wait(1) - else: - logger.error("Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs.") - break - - while self.jobs: - self.cond.wait(1) - - events.close() - except UnsupportedRequirement: - raise - except: - if sys.exc_info()[0] is KeyboardInterrupt: - logger.error("Interrupted, marking pipeline as failed") + if "cwl_runner_job" in kwargs: + self.uuid = kwargs.get("cwl_runner_job").get('uuid') + jobiter = tool.job(job_order, + self.output_callback, + docker_outdir="$(task.outdir)", + **kwargs) + + try: + self.cond.acquire() + # Will continue to hold the lock for the duration of this code + # except when in cond.wait(), at which point on_message can update + # job state and process output callbacks. + + for runnable in jobiter: + if runnable: + runnable.run(**kwargs) else: - logger.error("Caught unhandled exception, marking pipeline as failed. Error was: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False)) - if self.pipeline: - self.api.pipeline_instances().update(uuid=self.pipeline["uuid"], - body={"state": "Failed"}).execute(num_retries=self.num_retries) - finally: - self.cond.release() + if self.jobs: + self.cond.wait(1) + else: + logger.error("Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs.") + break + + while self.jobs: + self.cond.wait(1) + + events.close() + except UnsupportedRequirement: + raise + except: + if sys.exc_info()[0] is KeyboardInterrupt: + logger.error("Interrupted, marking pipeline as failed") + else: + logger.error("Caught unhandled exception, marking pipeline as failed. Error was: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False)) + if self.pipeline: + self.api.pipeline_instances().update(uuid=self.pipeline["uuid"], + body={"state": "Failed"}).execute(num_retries=self.num_retries) + finally: + self.cond.release() - if self.final_output is None: - raise cwltool.workflow.WorkflowException("Workflow did not return a result.") + if self.final_output is None: + raise cwltool.workflow.WorkflowException("Workflow did not return a result.") + + return self.final_output - return self.final_output def versionstring(): """Print version string of key packages for provenance and debugging.""" @@ -572,6 +204,7 @@ def versionstring(): "arvados-python-client", arvpkg[0].version, "cwltool", cwlpkg[0].version) + def arg_parser(): # type: () -> argparse.ArgumentParser parser = argparse.ArgumentParser(description='Arvados executor for Common Workflow Language') @@ -634,6 +267,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser return parser + def main(args, stdout, stderr, api_client=None): parser = arg_parser()