X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/d9eec0b9bf52b428b5506617590d87b2d92eb246..2e104941dbf1e4bf92e0632cadeb946be0595d67:/sdk/cwl/arvados_cwl/runner.py diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py index 72f347e439..2d13e6640b 100644 --- a/sdk/cwl/arvados_cwl/runner.py +++ b/sdk/cwl/arvados_cwl/runner.py @@ -4,31 +4,70 @@ 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, normalizeFilesDirs +from cwltool.process import get_feature, scandeps, UnsupportedRequirement, normalizeFilesDirs, shortname from cwltool.load_tool import fetch_document 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, $schemas, run, File and Directory + fields that represent external references. + + If workflowobj has an "id" field, this will reload the document to ensure + it is scanning the raw document prior to preprocessing. + """ + loaded = set() def loadref(b, u): joined = urlparse.urljoin(b, u) - if joined not in loaded: - loaded.add(joined) - return document_loader.fetch(urlparse.urljoin(b, u)) + defrg, _ = urlparse.urldefrag(joined) + if defrg not in loaded: + loaded.add(defrg) + # Use fetch_text to get raw file (before preprocessing). + text = document_loader.fetch_text(defrg) + if isinstance(text, bytes): + textIO = StringIO(text.decode('utf-8')) + else: + textIO = StringIO(text) + return yaml.safe_load(textIO) else: return {} @@ -37,30 +76,30 @@ def upload_dependencies(arvrunner, name, document_loader, else: loadref_fields = set(("$import",)) - sc = scandeps(uri, workflowobj, + 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", "$schemas", "path", "location")), + set(("$include", "$schemas", "location")), loadref) - files = [] - def visitFiles(path): - files.append(path) - - adjustFileObjs(sc, visitFiles) - adjustDirObjs(sc, visitFiles) - - normalizeFilesDirs(files) + normalizeFilesDirs(sc) if "id" in workflowobj: - files.append({"class": "File", "location": workflowobj["id"]}) + sc.append({"class": "File", "location": workflowobj["id"]}) - mapper = ArvPathMapper(arvrunner, files, "", + mapper = ArvPathMapper(arvrunner, sc, "", "keep:%s", "keep:%s/%s", name=name) def setloc(p): - p["location"] = mapper.mapper(p["location"]).target + 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) @@ -71,49 +110,89 @@ 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, submit_runner_ram=0, + name=None): 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 + self.name = name + + if submit_runner_ram: + self.submit_runner_ram = submit_runner_ram + else: + self.submit_runner_ram = 1024 + + if self.submit_runner_ram <= 0: + raise Exception("Value of --submit-runner-ram must be greater than zero") def update_pipeline_component(self, record): pass def arvados_job_spec(self, *args, **kwargs): - upload_docker(self.arvrunner, self.tool) - - self.name = os.path.basename(self.tool.tool["id"]) - - workflowmapper = upload_dependencies(self.arvrunner, - self.name, - self.tool.doc_loader, - self.tool.tool, - self.tool.tool["id"], - True) - - jobmapper = upload_dependencies(self.arvrunner, - os.path.basename(self.job_order.get("id", "#")), - self.tool.doc_loader, - self.job_order, - self.job_order.get("id", "#"), - False) - - if "id" in self.job_order: - del self.job_order["id"] - + if self.name is None: + self.name = os.path.basename(self.tool.tool["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: @@ -128,12 +207,18 @@ class Runner(object): else: processStatus = "permanentFail" - outputs = None + outputs = {} try: try: - outc = arvados.collection.Collection(record["output"]) - with outc.open("cwl.output.json") as f: - outputs = json.load(f) + 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) + if "cwl.output.json" in outc: + with outc.open("cwl.output.json") as f: + if f.size() > 0: + outputs = json.load(f) def keepify(fileobj): path = fileobj["location"] if not path.startswith("keep:"): @@ -141,7 +226,8 @@ class Runner(object): 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"]] + if record["uuid"] in self.arvrunner.processes: + del self.arvrunner.processes[record["uuid"]]