X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/ec2af1a4d13bbbdeedb83295d6177f7317cd8302..2eaa77dc327c024f2faa3fbd322e7054454b6442:/sdk/cwl/arvados_cwl/runner.py diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py index 1b5d8a4ea9..3bbcb8b091 100644 --- a/sdk/cwl/arvados_cwl/runner.py +++ b/sdk/cwl/arvados_cwl/runner.py @@ -4,97 +4,183 @@ from functools import partial import logging import json import re +from cStringIO import StringIO import cwltool.draft2tool from cwltool.draft2tool import CommandLineTool import cwltool.workflow -from cwltool.process import get_feature, scandeps, UnsupportedRequirement +from cwltool.process import get_feature, scandeps, UnsupportedRequirement, normalizeFilesDirs, shortname from cwltool.load_tool import fetch_document -from cwltool.pathmapper import adjustFileObjs +from cwltool.pathmapper import adjustFileObjs, adjustDirObjs +from cwltool.utils import aslist +from cwltool.builder import substitute import arvados.collection +import ruamel.yaml as yaml from .arvdocker import arv_docker_get_image from .pathmapper import ArvPathMapper +from ._version import __version__ logger = logging.getLogger('arvados.cwl-runner') -cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$") +cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r".*") + +def trim_listing(obj): + """Remove 'listing' field from Directory objects that are keep references. + + When Directory objects represent Keep references, it redundant and + potentially very expensive to pass fully enumerated Directory objects + between instances of cwl-runner (e.g. a submitting a job, or using the + RunInSingleContainer feature), so delete the 'listing' field when it is + safe to do so. + """ + + if obj.get("location", "").startswith("keep:") and "listing" in obj: + del obj["listing"] + if obj.get("location", "").startswith("_:"): + del obj["location"] + +def upload_dependencies(arvrunner, name, document_loader, + workflowobj, uri, loadref_run): + """Upload the dependencies of the workflowobj document to Keep. + + Returns a pathmapper object mapping local paths to keep references. Also + does an in-place update of references in "workflowobj". + + Use scandeps to find $import, $include, $schemas, run, File and Directory + fields that represent external references. + + If workflowobj has an "id" field, this will reload the document to ensure + it is scanning the raw document prior to preprocessing. + """ + + loaded = set() + def loadref(b, u): + joined = urlparse.urljoin(b, u) + defrg, _ = urlparse.urldefrag(joined) + if defrg not in loaded: + loaded.add(defrg) + # Use fetch_text to get raw file (before preprocessing). + text = document_loader.fetch_text(defrg) + if isinstance(text, bytes): + textIO = StringIO(text.decode('utf-8')) + else: + textIO = StringIO(text) + return yaml.safe_load(textIO) + else: + return {} + + if loadref_run: + loadref_fields = set(("$import", "run")) + else: + loadref_fields = set(("$import",)) + + scanobj = workflowobj + if "id" in workflowobj: + # Need raw file content (before preprocessing) to ensure + # that external references in $include and $mixin are captured. + scanobj = loadref("", workflowobj["id"]) + + sc = scandeps(uri, scanobj, + loadref_fields, + set(("$include", "$schemas", "location")), + loadref) + + normalizeFilesDirs(sc) + + if "id" in workflowobj: + sc.append({"class": "File", "location": workflowobj["id"]}) + + mapper = ArvPathMapper(arvrunner, sc, "", + "keep:%s", + "keep:%s/%s", + name=name) + + def setloc(p): + if "location" in p and (not p["location"].startswith("_:")) and (not p["location"].startswith("keep:")): + p["location"] = mapper.mapper(p["location"]).resolved + adjustFileObjs(workflowobj, setloc) + adjustDirObjs(workflowobj, setloc) + + return mapper + + +def upload_docker(arvrunner, tool): + if isinstance(tool, CommandLineTool): + (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement") + if docker_req: + if docker_req.get("dockerOutputDirectory"): + # TODO: can be supported by containers API, but not jobs API. + raise UnsupportedRequirement("Option 'dockerOutputDirectory' of DockerRequirement not supported.") + arv_docker_get_image(arvrunner.api, docker_req, True, arvrunner.project_uuid) + elif isinstance(tool, cwltool.workflow.Workflow): + for s in tool.steps: + upload_docker(arvrunner, s.embedded_tool) + +def upload_instance(arvrunner, name, tool, job_order): + upload_docker(arvrunner, tool) + + for t in tool.tool["inputs"]: + def setSecondary(fileobj): + if isinstance(fileobj, dict) and fileobj.get("class") == "File": + if "secondaryFiles" not in fileobj: + fileobj["secondaryFiles"] = [{"location": substitute(fileobj["location"], sf), "class": "File"} for sf in t["secondaryFiles"]] + + if isinstance(fileobj, list): + for e in fileobj: + setSecondary(e) + + if shortname(t["id"]) in job_order and t.get("secondaryFiles"): + setSecondary(job_order[shortname(t["id"])]) + + workflowmapper = upload_dependencies(arvrunner, + name, + tool.doc_loader, + tool.tool, + tool.tool["id"], + True) + jobmapper = upload_dependencies(arvrunner, + os.path.basename(job_order.get("id", "#")), + tool.doc_loader, + job_order, + job_order.get("id", "#"), + False) + + if "id" in job_order: + del job_order["id"] + + return workflowmapper + +def arvados_jobs_image(arvrunner): + img = "arvados/jobs:"+__version__ + try: + arv_docker_get_image(arvrunner.api, {"dockerPull": img}, True, arvrunner.project_uuid) + except Exception as e: + raise Exception("Docker image %s is not available\n%s" % (img, e) ) + return img class Runner(object): - def __init__(self, runner, tool, job_order, enable_reuse): + def __init__(self, runner, tool, job_order, enable_reuse, output_name, output_tags): self.arvrunner = runner self.tool = tool self.job_order = job_order self.running = False self.enable_reuse = enable_reuse self.uuid = None + self.final_output = None + self.output_name = output_name + self.output_tags = output_tags 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, *args, **kwargs): - self.upload_docker(self.tool) - - workflowfiles = [] - jobfiles = [] - workflowfiles.append({"class":"File", "location": self.tool.tool["id"]}) - self.name = os.path.basename(self.tool.tool["id"]) - - def visitFiles(files, path): - files.append(path) - - document_loader, workflowobj, uri = fetch_document(self.tool.tool["id"]) - loaded = set() - def loadref(b, u): - joined = urlparse.urljoin(b, u) - if joined not in loaded: - loaded.add(joined) - return document_loader.fetch(urlparse.urljoin(b, u)) - else: - return {} - - sc = scandeps(uri, workflowobj, - set(("$import", "run")), - set(("$include", "$schemas", "path", "location")), - loadref) - adjustFileObjs(sc, partial(visitFiles, workflowfiles)) - adjustFileObjs(self.job_order, partial(visitFiles, jobfiles)) - - keepprefix = kwargs.get("keepprefix", "") - workflowmapper = ArvPathMapper(self.arvrunner, workflowfiles, "", - keepprefix+"%s", - keepprefix+"%s/%s", - name=self.name, - **kwargs) - - jobmapper = ArvPathMapper(self.arvrunner, jobfiles, "", - keepprefix+"%s", - keepprefix+"%s/%s", - name=os.path.basename(self.job_order.get("id", "#")), - **kwargs) - - def setloc(p): - p["location"] = jobmapper.mapper(p["location"])[1] - adjustFileObjs(self.job_order, setloc) - - if "id" in self.job_order: - del self.job_order["id"] - + workflowmapper = upload_instance(self.arvrunner, self.name, self.tool, self.job_order) + adjustDirObjs(self.job_order, trim_listing) return workflowmapper - def done(self, record): if record["state"] == "Complete": if record.get("exit_code") is not None: @@ -109,10 +195,14 @@ class Runner(object): else: processStatus = "permanentFail" - outputs = None + outputs = {} try: try: - outc = arvados.collection.Collection(record["output"]) + self.final_output = record["output"] + outc = arvados.collection.CollectionReader(self.final_output, + api_client=self.arvrunner.api, + keep_client=self.arvrunner.keep_client, + num_retries=self.arvrunner.num_retries) with outc.open("cwl.output.json") as f: outputs = json.load(f) def keepify(fileobj): @@ -120,8 +210,9 @@ class Runner(object): if not path.startswith("keep:"): fileobj["location"] = "keep:%s/%s" % (record["output"], path) adjustFileObjs(outputs, keepify) + adjustDirObjs(outputs, keepify) except Exception as e: - logger.error("While getting final output object: %s", e) + logger.exception("While getting final output object: %s", e) self.arvrunner.output_callback(outputs, processStatus) finally: del self.arvrunner.processes[record["uuid"]]