X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/e030e175bf4093eb7cdecd9c534548ad2b9a2b05..35852356dd9bb2e29e8aebb208e063d9fe924316:/sdk/cwl/arvados_cwl/runner.py diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py index 9385bde63c..68b2fd827a 100644 --- a/sdk/cwl/arvados_cwl/runner.py +++ b/sdk/cwl/arvados_cwl/runner.py @@ -5,6 +5,7 @@ from future import standard_library standard_library.install_aliases() from future.utils import viewvalues, viewitems +from past.builtins import basestring import os import sys @@ -13,8 +14,10 @@ import urllib.parse from functools import partial import logging import json +import copy from collections import namedtuple from io import StringIO +from typing import Mapping, Sequence if os.name == "posix" and sys.version_info[0] < 3: import subprocess32 as subprocess @@ -25,12 +28,15 @@ from schema_salad.sourceline import SourceLine, cmap from cwltool.command_line_tool import CommandLineTool import cwltool.workflow -from cwltool.process import scandeps, UnsupportedRequirement, normalizeFilesDirs, shortname, Process +from cwltool.process import (scandeps, UnsupportedRequirement, normalizeFilesDirs, + shortname, Process, fill_in_defaults) from cwltool.load_tool import fetch_document from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class from cwltool.utils import aslist from cwltool.builder import substitute from cwltool.pack import pack +from cwltool.update import INTERNAL_VERSION +from cwltool.builder import Builder import schema_salad.validate as validate import arvados.collection @@ -41,6 +47,7 @@ import arvados_cwl.arvdocker from .pathmapper import ArvPathMapper, trim_listing from ._version import __version__ from . import done +from . context import ArvRuntimeContext logger = logging.getLogger('arvados.cwl-runner') @@ -75,20 +82,116 @@ def find_defaults(d, op): for i in viewvalues(d): find_defaults(i, op) -def setSecondary(t, fileobj, discovered): - if isinstance(fileobj, dict) and fileobj.get("class") == "File": - if "secondaryFiles" not in fileobj: - fileobj["secondaryFiles"] = cmap([{"location": substitute(fileobj["location"], sf), "class": "File"} for sf in t["secondaryFiles"]]) - if discovered is not None: - discovered[fileobj["location"]] = fileobj["secondaryFiles"] - elif isinstance(fileobj, list): - for e in fileobj: - setSecondary(t, e, discovered) - -def discover_secondary_files(inputs, job_order, discovered=None): - for t in inputs: - if shortname(t["id"]) in job_order and t.get("secondaryFiles"): - setSecondary(t, job_order[shortname(t["id"])], discovered) +def make_builder(joborder, hints, requirements, runtimeContext): + return Builder( + job=joborder, + files=[], # type: List[Dict[Text, Text]] + bindings=[], # type: List[Dict[Text, Any]] + schemaDefs={}, # type: Dict[Text, Dict[Text, Any]] + names=None, # type: Names + requirements=requirements, # type: List[Dict[Text, Any]] + hints=hints, # type: List[Dict[Text, Any]] + resources={}, # type: Dict[str, int] + mutation_manager=None, # type: Optional[MutationManager] + formatgraph=None, # type: Optional[Graph] + make_fs_access=None, # type: Type[StdFsAccess] + fs_access=None, # type: StdFsAccess + job_script_provider=runtimeContext.job_script_provider, # type: Optional[Any] + timeout=runtimeContext.eval_timeout, # type: float + debug=runtimeContext.debug, # type: bool + js_console=runtimeContext.js_console, # type: bool + force_docker_pull=runtimeContext.force_docker_pull, # type: bool + loadListing="", # type: Text + outdir="", # type: Text + tmpdir="", # type: Text + stagedir="", # type: Text + ) + +def search_schemadef(name, reqs): + for r in reqs: + if r["class"] == "SchemaDefRequirement": + for sd in r["types"]: + if sd["name"] == name: + return sd + return None + +primitive_types_set = frozenset(("null", "boolean", "int", "long", + "float", "double", "string", "record", + "array", "enum")) + +def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discovered): + if isinstance(inputschema, Sequence) and not isinstance(inputschema, basestring): + # union type, collect all possible secondaryFiles + for i in inputschema: + set_secondary(fsaccess, builder, i, secondaryspec, primary, discovered) + return + + if isinstance(inputschema, basestring): + sd = search_schemadef(inputschema, reversed(builder.hints+builder.requirements)) + if sd: + inputschema = sd + else: + return + + if "secondaryFiles" in inputschema: + # set secondaryFiles, may be inherited by compound types. + secondaryspec = inputschema["secondaryFiles"] + + if isinstance(inputschema["type"], (Mapping, Sequence)): + # compound type (union, array, record) + set_secondary(fsaccess, builder, inputschema["type"], secondaryspec, primary, discovered) + + elif (inputschema["type"] == "record" and + isinstance(primary, Mapping)): + # + # record type, find secondary files associated with fields. + # + for f in inputschema["fields"]: + p = primary.get(shortname(f["name"])) + if p: + set_secondary(fsaccess, builder, f, secondaryspec, p, discovered) + + elif (inputschema["type"] == "array" and + isinstance(primary, Sequence)): + # + # array type, find secondary files of elements + # + for p in primary: + set_secondary(fsaccess, builder, {"type": inputschema["items"]}, secondaryspec, p, discovered) + + elif (inputschema["type"] == "File" and + secondaryspec and + isinstance(primary, Mapping) and + primary.get("class") == "File" and + "secondaryFiles" not in primary): + # + # Found a file, check for secondaryFiles + # + primary["secondaryFiles"] = [] + for i, sf in enumerate(aslist(secondaryspec)): + pattern = builder.do_eval(sf["pattern"], context=primary) + if pattern is None: + continue + sfpath = substitute(primary["location"], pattern) + required = builder.do_eval(sf["required"], context=primary) + + if fsaccess.exists(sfpath): + primary["secondaryFiles"].append({"location": sfpath, "class": "File"}) + elif required: + raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError( + "Required secondary file '%s' does not exist" % sfpath) + + primary["secondaryFiles"] = cmap(primary["secondaryFiles"]) + if discovered is not None: + discovered[primary["location"]] = primary["secondaryFiles"] + elif inputschema["type"] not in primitive_types_set: + set_secondary(fsaccess, builder, inputschema["type"], secondaryspec, primary, discovered) + +def discover_secondary_files(fsaccess, builder, inputs, job_order, discovered=None): + for inputschema in inputs: + primary = job_order.get(shortname(inputschema["id"])) + if isinstance(primary, (Mapping, Sequence)): + set_secondary(fsaccess, builder, inputschema, None, primary, discovered) collection_uuid_pattern = re.compile(r'^keep:([a-z0-9]{5}-4zz18-[a-z0-9]{15})(/.*)?$') collection_pdh_pattern = re.compile(r'^keep:([0-9a-f]{32}\+\d+)(/.*)?') @@ -130,7 +233,7 @@ def upload_dependencies(arvrunner, name, document_loader, loadref_fields = set(("$import",)) scanobj = workflowobj - if "id" in workflowobj: + if "id" in workflowobj and not workflowobj["id"].startswith("_:"): # Need raw file content (before preprocessing) to ensure # that external references in $include and $mixin are captured. scanobj = loadref("", workflowobj["id"]) @@ -219,8 +322,18 @@ def upload_dependencies(arvrunner, name, document_loader, discovered = {} def discover_default_secondary_files(obj): - discover_secondary_files(obj["inputs"], - {shortname(t["id"]): t["default"] for t in obj["inputs"] if "default" in t}, + builder_job_order = {} + for t in obj["inputs"]: + builder_job_order[shortname(t["id"])] = t["default"] if "default" in t else None + # Need to create a builder object to evaluate expressions. + builder = make_builder(builder_job_order, + obj.get("hints", []), + obj.get("requirements", []), + ArvRuntimeContext()) + discover_secondary_files(arvrunner.fs_access, + builder, + obj["inputs"], + builder_job_order, discovered) visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files) @@ -354,7 +467,21 @@ def upload_job_order(arvrunner, name, tool, job_order): object with 'location' updated to the proper keep references. """ - discover_secondary_files(tool.tool["inputs"], job_order) + # Make a copy of the job order and set defaults. + builder_job_order = copy.copy(job_order) + fill_in_defaults(tool.tool["inputs"], + builder_job_order, + arvrunner.fs_access) + # Need to create a builder object to evaluate expressions. + builder = make_builder(builder_job_order, + tool.hints, + tool.requirements, + ArvRuntimeContext()) + # Now update job_order with secondaryFiles + discover_secondary_files(arvrunner.fs_access, + builder, + tool.tool["inputs"], + job_order) jobmapper = upload_dependencies(arvrunner, name, @@ -451,6 +578,10 @@ class Runner(Process): collection_cache_size=256, collection_cache_is_default=True): + loadingContext = loadingContext.copy() + loadingContext.metadata = loadingContext.metadata.copy() + loadingContext.metadata["cwlVersion"] = INTERNAL_VERSION + super(Runner, self).__init__(tool.tool, loadingContext) self.arvrunner = runner @@ -474,6 +605,7 @@ class Runner(Process): self.intermediate_output_ttl = intermediate_output_ttl self.priority = priority self.secret_store = secret_store + self.enable_dev = loadingContext.enable_dev self.submit_runner_cores = 1 self.submit_runner_ram = 1024 # defaut 1 GiB