X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/ad4344e21db3c894869d09fdcb09e3202bf9cf78..a605fc29fd7f79b2882625c99a72e998157fa5bc:/sdk/cwl/arvados_cwl/__init__.py diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index 0452486b2a..c90f890268 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -24,14 +24,15 @@ import arvados.config from .arvcontainer import ArvadosContainer, RunnerContainer from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate +from. runner import Runner from .arvtool import ArvadosCommandTool from .arvworkflow import ArvadosWorkflow, upload_workflow from .fsaccess import CollectionFsAccess from .perf import Perf -from .pathmapper import InitialWorkDirPathMapper +from .pathmapper import FinalOutputPathMapper from cwltool.pack import pack -from cwltool.process import shortname, UnsupportedRequirement +from cwltool.process import shortname, UnsupportedRequirement, getListing from cwltool.pathmapper import adjustFileObjs, adjustDirObjs from cwltool.draft2tool import compute_checksums from arvados.api import OrderedJsonModel @@ -47,7 +48,7 @@ class ArvCwlRunner(object): """ - def __init__(self, api_client, work_api=None): + def __init__(self, api_client, work_api=None, keep_client=None, output_name=None): self.api = api_client self.processes = {} self.lock = threading.Lock() @@ -62,6 +63,11 @@ class ArvCwlRunner(object): self.poll_api = None self.pipeline = None self.final_output_collection = None + self.output_name = output_name + if keep_client is not None: + self.keep_client = keep_client + else: + self.keep_client = arvados.keep.KeepClient(api_client=self.api, num_retries=self.num_retries) if self.work_api is None: # todo: autodetect API to use. @@ -176,35 +182,46 @@ class ArvCwlRunner(object): adjustDirObjs(outputObj, capture) adjustFileObjs(outputObj, capture) - generatemapper = InitialWorkDirPathMapper(files, "", "", - separateDirs=False) + generatemapper = FinalOutputPathMapper(files, "", "", separateDirs=False) - final = arvados.collection.Collection() + final = arvados.collection.Collection(api_client=self.api, + keep_client=self.keep_client, + num_retries=self.num_retries) srccollections = {} for k,v in generatemapper.items(): sp = k.split("/") srccollection = sp[0][5:] if srccollection not in srccollections: - srccollections[srccollection] = arvados.collection.CollectionReader(srccollection) + srccollections[srccollection] = arvados.collection.CollectionReader( + srccollection, + api_client=self.api, + keep_client=self.keep_client, + num_retries=self.num_retries) reader = srccollections[srccollection] try: - final.copy("/".join(sp[1:]), v.target, source_collection=reader, overwrite=False) + srcpath = "/".join(sp[1:]) if len(sp) > 1 else "." + final.copy(srcpath, v.target, source_collection=reader, overwrite=False) except IOError as e: logger.warn("While preparing output collection: %s", e) def rewrite(fileobj): - fileobj["location"] = generatemapper.mapper(fileobj["location"]) + fileobj["location"] = generatemapper.mapper(fileobj["location"]).target + for k in ("basename", "size", "listing"): + if k in fileobj: + del fileobj[k] - adjustDirObjs(outputObj, capture) - adjustFileObjs(outputObj, capture) + adjustDirObjs(outputObj, rewrite) + adjustFileObjs(outputObj, rewrite) with final.open("cwl.output.json", "w") as f: - json.dump(outputObj, f, indent=4) + json.dump(outputObj, f, sort_keys=True, indent=4, separators=(',',': ')) final.save_new(name=name, owner_uuid=self.project_uuid, ensure_unique_name=True) - logger.info("Final output collection %s (%s)", final.portable_data_hash(), final.manifest_locator()) + logger.info("Final output collection %s \"%s\" (%s)", final.portable_data_hash(), + final.api_response()["name"], + final.manifest_locator()) self.final_output_collection = final @@ -216,7 +233,9 @@ class ArvCwlRunner(object): useruuid = self.api.users().current().execute()["uuid"] self.project_uuid = kwargs.get("project_uuid") if kwargs.get("project_uuid") else useruuid self.pipeline = None - make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, api_client=self.api) + make_fs_access = kwargs.get("make_fs_access") or partial(CollectionFsAccess, + api_client=self.api, + keep_client=self.keep_client) self.fs_access = make_fs_access(kwargs["basedir"]) if kwargs.get("create_template"): @@ -255,9 +274,9 @@ class ArvCwlRunner(object): self.output_callback, **kwargs).next() else: - runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse")) + runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name) else: - runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse")) + runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name) if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and not self.work_api == "containers": # Create pipeline for local run @@ -338,14 +357,16 @@ class ArvCwlRunner(object): if self.final_output is None: raise WorkflowException("Workflow did not return a result.") - if kwargs.get("compute_checksum"): - adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access)) - - if kwargs.get("submit"): + if kwargs.get("submit") and isinstance(runnerjob, Runner): logger.info("Final output collection %s", runnerjob.final_output) else: - self.make_output_collection("Output of %s" % (shortname(tool.tool["id"])), - self.final_output) + if self.output_name is None: + self.output_name = "Output of %s" % (shortname(tool.tool["id"])) + self.make_output_collection(self.output_name, self.final_output) + + if kwargs.get("compute_checksum"): + adjustDirObjs(self.final_output, partial(getListing, self.fs_access)) + adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access)) return self.final_output @@ -394,6 +415,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser help="") 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) parser.add_argument("--ignore-docker-for-reuse", action="store_true", help="Ignore Docker image version when deciding whether to reuse past jobs.", default=False) @@ -431,13 +453,14 @@ def add_arv_hints(): res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml') cache["http://arvados.org/cwl"] = res.read() res.close() - _, cwlnames, _, _ = cwltool.process.get_schema("v1.0") + document_loader, cwlnames, _, _ = cwltool.process.get_schema("v1.0") _, extnames, _, _ = schema_salad.schema.load_schema("http://arvados.org/cwl", cache=cache) for n in extnames.names: if not cwlnames.has_name("http://arvados.org/cwl#"+n, ""): cwlnames.add_name("http://arvados.org/cwl#"+n, "", extnames.get_name(n, "")) + document_loader.idx["http://arvados.org/cwl#"+n] = {} -def main(args, stdout, stderr, api_client=None): +def main(args, stdout, stderr, api_client=None, keep_client=None): parser = arg_parser() job_order_object = None @@ -450,7 +473,7 @@ def main(args, stdout, stderr, api_client=None): try: if api_client is None: api_client=arvados.api('v1', model=OrderedJsonModel()) - runner = ArvCwlRunner(api_client, work_api=arvargs.work_api) + runner = ArvCwlRunner(api_client, work_api=arvargs.work_api, keep_client=keep_client, output_name=arvargs.output_name) except Exception as e: logger.error(e) return 1