from future import standard_library
standard_library.install_aliases()
from future.utils import viewvalues, viewitems
+from past.builtins import basestring
import os
import sys
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
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
from .pathmapper import ArvPathMapper, trim_listing
from ._version import __version__
from . import done
+from . context import ArvRuntimeContext
logger = logging.getLogger('arvados.cwl-runner')
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)) and
+ not isinstance(inputschema["type"], basestring)):
+ # 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.get("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})(/.*)?$')
collection_pdh_pattern = re.compile(r'^keep:([0-9a-f]{32}\+\d+)(/.*)?')
loadref_fields = set(("$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"])
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)
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 throws an error if there are any
+ # missing required parameters, we don't want it to do that
+ # so make them all optional.
+ inputs_copy = copy.deepcopy(tool.tool["inputs"])
+ for i in inputs_copy:
+ if "null" not in i["type"]:
+ i["type"] = ["null"] + aslist(i["type"])
+
+ fill_in_defaults(inputs_copy,
+ 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,
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
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
projects / arvados.git / blobdiff