sdk/cwl/arvados_cwl/runner.py

   1 # Copyright (C) The Arvados Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: Apache-2.0
   4
   5 from future import standard_library
   6 standard_library.install_aliases()
   7 from future.utils import  viewvalues, viewitems
   8 from past.builtins import basestring
   9
  10 import os
  11 import sys
  12 import re
  13 import urllib.parse
  14 from functools import partial
  15 import logging
  16 import json
  17 import copy
  18 from collections import namedtuple
  19 from io import StringIO
  20 from typing import Mapping, Sequence
  21
  22 if os.name == "posix" and sys.version_info[0] < 3:
  23     import subprocess32 as subprocess
  24 else:
  25     import subprocess
  26
  27 from schema_salad.sourceline import SourceLine, cmap
  28
  29 from cwltool.command_line_tool import CommandLineTool
  30 import cwltool.workflow
  31 from cwltool.process import (scandeps, UnsupportedRequirement, normalizeFilesDirs,
  32                              shortname, Process, fill_in_defaults)
  33 from cwltool.load_tool import fetch_document
  34 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
  35 from cwltool.utils import aslist
  36 from cwltool.builder import substitute
  37 from cwltool.pack import pack
  38 from cwltool.update import INTERNAL_VERSION
  39 from cwltool.builder import Builder
  40 import schema_salad.validate as validate
  41
  42 import arvados.collection
  43 from .util import collectionUUID
  44 import ruamel.yaml as yaml
  45 from ruamel.yaml.comments import CommentedMap, CommentedSeq
  46
  47 import arvados_cwl.arvdocker
  48 from .pathmapper import ArvPathMapper, trim_listing, collection_pdh_pattern, collection_uuid_pattern
  49 from ._version import __version__
  50 from . import done
  51 from . context import ArvRuntimeContext
  52
  53 logger = logging.getLogger('arvados.cwl-runner')
  54
  55 def trim_anonymous_location(obj):
  56     """Remove 'location' field from File and Directory literals.
  57
  58     To make internal handling easier, literals are assigned a random id for
  59     'location'.  However, when writing the record back out, this can break
  60     reproducibility.  Since it is valid for literals not have a 'location'
  61     field, remove it.
  62
  63     """
  64
  65     if obj.get("location", "").startswith("_:"):
  66         del obj["location"]
  67
  68
  69 def remove_redundant_fields(obj):
  70     for field in ("path", "nameext", "nameroot", "dirname"):
  71         if field in obj:
  72             del obj[field]
  73
  74
  75 def find_defaults(d, op):
  76     if isinstance(d, list):
  77         for i in d:
  78             find_defaults(i, op)
  79     elif isinstance(d, dict):
  80         if "default" in d:
  81             op(d)
  82         else:
  83             for i in viewvalues(d):
  84                 find_defaults(i, op)
  85
  86 def make_builder(joborder, hints, requirements, runtimeContext):
  87     return Builder(
  88                  job=joborder,
  89                  files=[],               # type: List[Dict[Text, Text]]
  90                  bindings=[],            # type: List[Dict[Text, Any]]
  91                  schemaDefs={},          # type: Dict[Text, Dict[Text, Any]]
  92                  names=None,               # type: Names
  93                  requirements=requirements,        # type: List[Dict[Text, Any]]
  94                  hints=hints,               # type: List[Dict[Text, Any]]
  95                  resources={},           # type: Dict[str, int]
  96                  mutation_manager=None,    # type: Optional[MutationManager]
  97                  formatgraph=None,         # type: Optional[Graph]
  98                  make_fs_access=None,      # type: Type[StdFsAccess]
  99                  fs_access=None,           # type: StdFsAccess
 100                  job_script_provider=runtimeContext.job_script_provider, # type: Optional[Any]
 101                  timeout=runtimeContext.eval_timeout,             # type: float
 102                  debug=runtimeContext.debug,               # type: bool
 103                  js_console=runtimeContext.js_console,          # type: bool
 104                  force_docker_pull=runtimeContext.force_docker_pull,   # type: bool
 105                  loadListing="",         # type: Text
 106                  outdir="",              # type: Text
 107                  tmpdir="",              # type: Text
 108                  stagedir="",            # type: Text
 109                 )
 110
 111 def search_schemadef(name, reqs):
 112     for r in reqs:
 113         if r["class"] == "SchemaDefRequirement":
 114             for sd in r["types"]:
 115                 if sd["name"] == name:
 116                     return sd
 117     return None
 118
 119 primitive_types_set = frozenset(("null", "boolean", "int", "long",
 120                                  "float", "double", "string", "record",
 121                                  "array", "enum"))
 122
 123 def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discovered):
 124     if isinstance(inputschema, Sequence) and not isinstance(inputschema, basestring):
 125         # union type, collect all possible secondaryFiles
 126         for i in inputschema:
 127             set_secondary(fsaccess, builder, i, secondaryspec, primary, discovered)
 128         return
 129
 130     if isinstance(inputschema, basestring):
 131         sd = search_schemadef(inputschema, reversed(builder.hints+builder.requirements))
 132         if sd:
 133             inputschema = sd
 134         else:
 135             return
 136
 137     if "secondaryFiles" in inputschema:
 138         # set secondaryFiles, may be inherited by compound types.
 139         secondaryspec = inputschema["secondaryFiles"]
 140
 141     if (isinstance(inputschema["type"], (Mapping, Sequence)) and
 142         not isinstance(inputschema["type"], basestring)):
 143         # compound type (union, array, record)
 144         set_secondary(fsaccess, builder, inputschema["type"], secondaryspec, primary, discovered)
 145
 146     elif (inputschema["type"] == "record" and
 147           isinstance(primary, Mapping)):
 148         #
 149         # record type, find secondary files associated with fields.
 150         #
 151         for f in inputschema["fields"]:
 152             p = primary.get(shortname(f["name"]))
 153             if p:
 154                 set_secondary(fsaccess, builder, f, secondaryspec, p, discovered)
 155
 156     elif (inputschema["type"] == "array" and
 157           isinstance(primary, Sequence)):
 158         #
 159         # array type, find secondary files of elements
 160         #
 161         for p in primary:
 162             set_secondary(fsaccess, builder, {"type": inputschema["items"]}, secondaryspec, p, discovered)
 163
 164     elif (inputschema["type"] == "File" and
 165           secondaryspec and
 166           isinstance(primary, Mapping) and
 167           primary.get("class") == "File" and
 168           "secondaryFiles" not in primary):
 169         #
 170         # Found a file, check for secondaryFiles
 171         #
 172         primary["secondaryFiles"] = []
 173         for i, sf in enumerate(aslist(secondaryspec)):
 174             pattern = builder.do_eval(sf["pattern"], context=primary)
 175             if pattern is None:
 176                 continue
 177             sfpath = substitute(primary["location"], pattern)
 178             required = builder.do_eval(sf.get("required"), context=primary)
 179
 180             if fsaccess.exists(sfpath):
 181                 primary["secondaryFiles"].append({"location": sfpath, "class": "File"})
 182             elif required:
 183                 raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
 184                     "Required secondary file '%s' does not exist" % sfpath)
 185
 186         primary["secondaryFiles"] = cmap(primary["secondaryFiles"])
 187         if discovered is not None:
 188             discovered[primary["location"]] = primary["secondaryFiles"]
 189     elif inputschema["type"] not in primitive_types_set:
 190         set_secondary(fsaccess, builder, inputschema["type"], secondaryspec, primary, discovered)
 191
 192 def discover_secondary_files(fsaccess, builder, inputs, job_order, discovered=None):
 193     for inputschema in inputs:
 194         primary = job_order.get(shortname(inputschema["id"]))
 195         if isinstance(primary, (Mapping, Sequence)):
 196             set_secondary(fsaccess, builder, inputschema, None, primary, discovered)
 197
 198 def upload_dependencies(arvrunner, name, document_loader,
 199                         workflowobj, uri, loadref_run,
 200                         include_primary=True, discovered_secondaryfiles=None):
 201     """Upload the dependencies of the workflowobj document to Keep.
 202
 203     Returns a pathmapper object mapping local paths to keep references.  Also
 204     does an in-place update of references in "workflowobj".
 205
 206     Use scandeps to find $import, $include, $schemas, run, File and Directory
 207     fields that represent external references.
 208
 209     If workflowobj has an "id" field, this will reload the document to ensure
 210     it is scanning the raw document prior to preprocessing.
 211     """
 212
 213     loaded = set()
 214     def loadref(b, u):
 215         joined = document_loader.fetcher.urljoin(b, u)
 216         defrg, _ = urllib.parse.urldefrag(joined)
 217         if defrg not in loaded:
 218             loaded.add(defrg)
 219             # Use fetch_text to get raw file (before preprocessing).
 220             text = document_loader.fetch_text(defrg)
 221             if isinstance(text, bytes):
 222                 textIO = StringIO(text.decode('utf-8'))
 223             else:
 224                 textIO = StringIO(text)
 225             return yaml.safe_load(textIO)
 226         else:
 227             return {}
 228
 229     if loadref_run:
 230         loadref_fields = set(("$import", "run"))
 231     else:
 232         loadref_fields = set(("$import",))
 233
 234     scanobj = workflowobj
 235     if "id" in workflowobj and not workflowobj["id"].startswith("_:"):
 236         # Need raw file content (before preprocessing) to ensure
 237         # that external references in $include and $mixin are captured.
 238         scanobj = loadref("", workflowobj["id"])
 239
 240     sc_result = scandeps(uri, scanobj,
 241                   loadref_fields,
 242                   set(("$include", "$schemas", "location")),
 243                   loadref, urljoin=document_loader.fetcher.urljoin)
 244
 245     sc = []
 246     uuids = {}
 247
 248     def collect_uuids(obj):
 249         loc = obj.get("location", "")
 250         sp = loc.split(":")
 251         if sp[0] == "keep":
 252             # Collect collection uuids that need to be resolved to
 253             # portable data hashes
 254             gp = collection_uuid_pattern.match(loc)
 255             if gp:
 256                 uuids[gp.groups()[0]] = obj
 257             if collectionUUID in obj:
 258                 uuids[obj[collectionUUID]] = obj
 259
 260     def collect_uploads(obj):
 261         loc = obj.get("location", "")
 262         sp = loc.split(":")
 263         if len(sp) < 1:
 264             return
 265         if sp[0] in ("file", "http", "https"):
 266             # Record local files than need to be uploaded,
 267             # don't include file literals, keep references, etc.
 268             sc.append(obj)
 269         collect_uuids(obj)
 270
 271     visit_class(workflowobj, ("File", "Directory"), collect_uuids)
 272     visit_class(sc_result, ("File", "Directory"), collect_uploads)
 273
 274     # Resolve any collection uuids we found to portable data hashes
 275     # and assign them to uuid_map
 276     uuid_map = {}
 277     fetch_uuids = list(uuids.keys())
 278     while fetch_uuids:
 279         # For a large number of fetch_uuids, API server may limit
 280         # response size, so keep fetching from API server has nothing
 281         # more to give us.
 282         lookups = arvrunner.api.collections().list(
 283             filters=[["uuid", "in", fetch_uuids]],
 284             count="none",
 285             select=["uuid", "portable_data_hash"]).execute(
 286                 num_retries=arvrunner.num_retries)
 287
 288         if not lookups["items"]:
 289             break
 290
 291         for l in lookups["items"]:
 292             uuid_map[l["uuid"]] = l["portable_data_hash"]
 293
 294         fetch_uuids = [u for u in fetch_uuids if u not in uuid_map]
 295
 296     normalizeFilesDirs(sc)
 297
 298     if include_primary and "id" in workflowobj:
 299         sc.append({"class": "File", "location": workflowobj["id"]})
 300
 301     if "$schemas" in workflowobj:
 302         for s in workflowobj["$schemas"]:
 303             sc.append({"class": "File", "location": s})
 304
 305     def visit_default(obj):
 306         remove = [False]
 307         def ensure_default_location(f):
 308             if "location" not in f and "path" in f:
 309                 f["location"] = f["path"]
 310                 del f["path"]
 311             if "location" in f and not arvrunner.fs_access.exists(f["location"]):
 312                 # Doesn't exist, remove from list of dependencies to upload
 313                 sc[:] = [x for x in sc if x["location"] != f["location"]]
 314                 # Delete "default" from workflowobj
 315                 remove[0] = True
 316         visit_class(obj["default"], ("File", "Directory"), ensure_default_location)
 317         if remove[0]:
 318             del obj["default"]
 319
 320     find_defaults(workflowobj, visit_default)
 321
 322     discovered = {}
 323     def discover_default_secondary_files(obj):
 324         builder_job_order = {}
 325         for t in obj["inputs"]:
 326             builder_job_order[shortname(t["id"])] = t["default"] if "default" in t else None
 327         # Need to create a builder object to evaluate expressions.
 328         builder = make_builder(builder_job_order,
 329                                obj.get("hints", []),
 330                                obj.get("requirements", []),
 331                                ArvRuntimeContext())
 332         discover_secondary_files(arvrunner.fs_access,
 333                                  builder,
 334                                  obj["inputs"],
 335                                  builder_job_order,
 336                                  discovered)
 337
 338     copied, _ = document_loader.resolve_all(copy.deepcopy(cmap(workflowobj)), base_url=uri, checklinks=False)
 339     visit_class(copied, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
 340
 341     for d in list(discovered):
 342         # Only interested in discovered secondaryFiles which are local
 343         # files that need to be uploaded.
 344         if d.startswith("file:"):
 345             sc.extend(discovered[d])
 346         else:
 347             del discovered[d]
 348
 349     mapper = ArvPathMapper(arvrunner, sc, "",
 350                            "keep:%s",
 351                            "keep:%s/%s",
 352                            name=name,
 353                            single_collection=True)
 354
 355     def setloc(p):
 356         loc = p.get("location")
 357         if loc and (not loc.startswith("_:")) and (not loc.startswith("keep:")):
 358             p["location"] = mapper.mapper(p["location"]).resolved
 359             return
 360
 361         if not loc:
 362             return
 363
 364         if collectionUUID in p:
 365             uuid = p[collectionUUID]
 366             if uuid not in uuid_map:
 367                 raise SourceLine(p, collectionUUID, validate.ValidationException).makeError(
 368                     "Collection uuid %s not found" % uuid)
 369             gp = collection_pdh_pattern.match(loc)
 370             if gp and uuid_map[uuid] != gp.groups()[0]:
 371                 # This file entry has both collectionUUID and a PDH
 372                 # location. If the PDH doesn't match the one returned
 373                 # the API server, raise an error.
 374                 raise SourceLine(p, "location", validate.ValidationException).makeError(
 375                     "Expected collection uuid %s to be %s but API server reported %s" % (
 376                         uuid, gp.groups()[0], uuid_map[p[collectionUUID]]))
 377
 378         gp = collection_uuid_pattern.match(loc)
 379         if not gp:
 380             return
 381         uuid = gp.groups()[0]
 382         if uuid not in uuid_map:
 383             raise SourceLine(p, "location", validate.ValidationException).makeError(
 384                 "Collection uuid %s not found" % uuid)
 385         p["location"] = "keep:%s%s" % (uuid_map[uuid], gp.groups()[1] if gp.groups()[1] else "")
 386         p[collectionUUID] = uuid
 387
 388     visit_class(workflowobj, ("File", "Directory"), setloc)
 389     visit_class(discovered, ("File", "Directory"), setloc)
 390
 391     if discovered_secondaryfiles is not None:
 392         for d in discovered:
 393             discovered_secondaryfiles[mapper.mapper(d).resolved] = discovered[d]
 394
 395     if "$schemas" in workflowobj:
 396         sch = CommentedSeq()
 397         for s in workflowobj["$schemas"]:
 398             sch.append(mapper.mapper(s).resolved)
 399         workflowobj["$schemas"] = sch
 400
 401     return mapper
 402
 403
 404 def upload_docker(arvrunner, tool):
 405     """Uploads Docker images used in CommandLineTool objects."""
 406
 407     if isinstance(tool, CommandLineTool):
 408         (docker_req, docker_is_req) = tool.get_requirement("DockerRequirement")
 409         if docker_req:
 410             if docker_req.get("dockerOutputDirectory") and arvrunner.work_api != "containers":
 411                 # TODO: can be supported by containers API, but not jobs API.
 412                 raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
 413                     "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
 414             arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, docker_req, True, arvrunner.project_uuid)
 415         else:
 416             arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, {"dockerPull": "arvados/jobs"}, True, arvrunner.project_uuid)
 417     elif isinstance(tool, cwltool.workflow.Workflow):
 418         for s in tool.steps:
 419             upload_docker(arvrunner, s.embedded_tool)
 420
 421
 422 def packed_workflow(arvrunner, tool, merged_map):
 423     """Create a packed workflow.
 424
 425     A "packed" workflow is one where all the components have been combined into a single document."""
 426
 427     rewrites = {}
 428     packed = pack(arvrunner.loadingContext, tool.tool["id"],
 429                   rewrite_out=rewrites,
 430                   loader=tool.doc_loader)
 431
 432     rewrite_to_orig = {v: k for k,v in viewitems(rewrites)}
 433
 434     def visit(v, cur_id):
 435         if isinstance(v, dict):
 436             if v.get("class") in ("CommandLineTool", "Workflow"):
 437                 if "id" not in v:
 438                     raise SourceLine(v, None, Exception).makeError("Embedded process object is missing required 'id' field")
 439                 cur_id = rewrite_to_orig.get(v["id"], v["id"])
 440             if "location" in v and not v["location"].startswith("keep:"):
 441                 v["location"] = merged_map[cur_id].resolved[v["location"]]
 442             if "location" in v and v["location"] in merged_map[cur_id].secondaryFiles:
 443                 v["secondaryFiles"] = merged_map[cur_id].secondaryFiles[v["location"]]
 444             if v.get("class") == "DockerRequirement":
 445                 v["http://arvados.org/cwl#dockerCollectionPDH"] = arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, v, True, arvrunner.project_uuid)
 446             for l in v:
 447                 visit(v[l], cur_id)
 448         if isinstance(v, list):
 449             for l in v:
 450                 visit(l, cur_id)
 451     visit(packed, None)
 452     return packed
 453
 454
 455 def tag_git_version(packed):
 456     if tool.tool["id"].startswith("file://"):
 457         path = os.path.dirname(tool.tool["id"][7:])
 458         try:
 459             githash = subprocess.check_output(['git', 'log', '--first-parent', '--max-count=1', '--format=%H'], stderr=subprocess.STDOUT, cwd=path).strip()
 460         except (OSError, subprocess.CalledProcessError):
 461             pass
 462         else:
 463             packed["http://schema.org/version"] = githash
 464
 465
 466 def upload_job_order(arvrunner, name, tool, job_order):
 467     """Upload local files referenced in the input object and return updated input
 468     object with 'location' updated to the proper keep references.
 469     """
 470
 471     # Make a copy of the job order and set defaults.
 472     builder_job_order = copy.copy(job_order)
 473
 474     # fill_in_defaults throws an error if there are any
 475     # missing required parameters, we don't want it to do that
 476     # so make them all optional.
 477     inputs_copy = copy.deepcopy(tool.tool["inputs"])
 478     for i in inputs_copy:
 479         if "null" not in i["type"]:
 480             i["type"] = ["null"] + aslist(i["type"])
 481
 482     fill_in_defaults(inputs_copy,
 483                      builder_job_order,
 484                      arvrunner.fs_access)
 485     # Need to create a builder object to evaluate expressions.
 486     builder = make_builder(builder_job_order,
 487                            tool.hints,
 488                            tool.requirements,
 489                            ArvRuntimeContext())
 490     # Now update job_order with secondaryFiles
 491     discover_secondary_files(arvrunner.fs_access,
 492                              builder,
 493                              tool.tool["inputs"],
 494                              job_order)
 495
 496     jobmapper = upload_dependencies(arvrunner,
 497                                     name,
 498                                     tool.doc_loader,
 499                                     job_order,
 500                                     job_order.get("id", "#"),
 501                                     False)
 502
 503     if "id" in job_order:
 504         del job_order["id"]
 505
 506     # Need to filter this out, gets added by cwltool when providing
 507     # parameters on the command line.
 508     if "job_order" in job_order:
 509         del job_order["job_order"]
 510
 511     return job_order
 512
 513 FileUpdates = namedtuple("FileUpdates", ["resolved", "secondaryFiles"])
 514
 515 def upload_workflow_deps(arvrunner, tool):
 516     # Ensure that Docker images needed by this workflow are available
 517
 518     upload_docker(arvrunner, tool)
 519
 520     document_loader = tool.doc_loader
 521
 522     merged_map = {}
 523
 524     def upload_tool_deps(deptool):
 525         if "id" in deptool:
 526             discovered_secondaryfiles = {}
 527             pm = upload_dependencies(arvrunner,
 528                                      "%s dependencies" % (shortname(deptool["id"])),
 529                                      document_loader,
 530                                      deptool,
 531                                      deptool["id"],
 532                                      False,
 533                                      include_primary=False,
 534                                      discovered_secondaryfiles=discovered_secondaryfiles)
 535             document_loader.idx[deptool["id"]] = deptool
 536             toolmap = {}
 537             for k,v in pm.items():
 538                 toolmap[k] = v.resolved
 539             merged_map[deptool["id"]] = FileUpdates(toolmap, discovered_secondaryfiles)
 540
 541     tool.visit(upload_tool_deps)
 542
 543     return merged_map
 544
 545 def arvados_jobs_image(arvrunner, img):
 546     """Determine if the right arvados/jobs image version is available.  If not, try to pull and upload it."""
 547
 548     try:
 549         return arvados_cwl.arvdocker.arv_docker_get_image(arvrunner.api, {"dockerPull": img}, True, arvrunner.project_uuid)
 550     except Exception as e:
 551         raise Exception("Docker image %s is not available\n%s" % (img, e) )
 552
 553
 554 def upload_workflow_collection(arvrunner, name, packed):
 555     collection = arvados.collection.Collection(api_client=arvrunner.api,
 556                                                keep_client=arvrunner.keep_client,
 557                                                num_retries=arvrunner.num_retries)
 558     with collection.open("workflow.cwl", "w") as f:
 559         f.write(json.dumps(packed, indent=2, sort_keys=True, separators=(',',': ')))
 560
 561     filters = [["portable_data_hash", "=", collection.portable_data_hash()],
 562                ["name", "like", name+"%"]]
 563     if arvrunner.project_uuid:
 564         filters.append(["owner_uuid", "=", arvrunner.project_uuid])
 565     exists = arvrunner.api.collections().list(filters=filters).execute(num_retries=arvrunner.num_retries)
 566
 567     if exists["items"]:
 568         logger.info("Using collection %s", exists["items"][0]["uuid"])
 569     else:
 570         collection.save_new(name=name,
 571                             owner_uuid=arvrunner.project_uuid,
 572                             ensure_unique_name=True,
 573                             num_retries=arvrunner.num_retries)
 574         logger.info("Uploaded to %s", collection.manifest_locator())
 575
 576     return collection.portable_data_hash()
 577
 578
 579 class Runner(Process):
 580     """Base class for runner processes, which submit an instance of
 581     arvados-cwl-runner and wait for the final result."""
 582
 583     def __init__(self, runner, updated_tool,
 584                  tool, loadingContext, enable_reuse,
 585                  output_name, output_tags, submit_runner_ram=0,
 586                  name=None, on_error=None, submit_runner_image=None,
 587                  intermediate_output_ttl=0, merged_map=None,
 588                  priority=None, secret_store=None,
 589                  collection_cache_size=256,
 590                  collection_cache_is_default=True):
 591
 592         loadingContext = loadingContext.copy()
 593         loadingContext.metadata = updated_tool.metadata.copy()
 594
 595         super(Runner, self).__init__(updated_tool.tool, loadingContext)
 596
 597         self.arvrunner = runner
 598         self.embedded_tool = tool
 599         self.job_order = None
 600         self.running = False
 601         if enable_reuse:
 602             # If reuse is permitted by command line arguments but
 603             # disabled by the workflow itself, disable it.
 604             reuse_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ReuseRequirement")
 605             if reuse_req:
 606                 enable_reuse = reuse_req["enableReuse"]
 607         self.enable_reuse = enable_reuse
 608         self.uuid = None
 609         self.final_output = None
 610         self.output_name = output_name
 611         self.output_tags = output_tags
 612         self.name = name
 613         self.on_error = on_error
 614         self.jobs_image = submit_runner_image or "arvados/jobs:"+__version__
 615         self.intermediate_output_ttl = intermediate_output_ttl
 616         self.priority = priority
 617         self.secret_store = secret_store
 618         self.enable_dev = loadingContext.enable_dev
 619
 620         self.submit_runner_cores = 1
 621         self.submit_runner_ram = 1024  # defaut 1 GiB
 622         self.collection_cache_size = collection_cache_size
 623
 624         runner_resource_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#WorkflowRunnerResources")
 625         if runner_resource_req:
 626             if runner_resource_req.get("coresMin"):
 627                 self.submit_runner_cores = runner_resource_req["coresMin"]
 628             if runner_resource_req.get("ramMin"):
 629                 self.submit_runner_ram = runner_resource_req["ramMin"]
 630             if runner_resource_req.get("keep_cache") and collection_cache_is_default:
 631                 self.collection_cache_size = runner_resource_req["keep_cache"]
 632
 633         if submit_runner_ram:
 634             # Command line / initializer overrides default and/or spec from workflow
 635             self.submit_runner_ram = submit_runner_ram
 636
 637         if self.submit_runner_ram <= 0:
 638             raise Exception("Value of submit-runner-ram must be greater than zero")
 639
 640         if self.submit_runner_cores <= 0:
 641             raise Exception("Value of submit-runner-cores must be greater than zero")
 642
 643         self.merged_map = merged_map or {}
 644
 645     def job(self,
 646             job_order,         # type: Mapping[Text, Text]
 647             output_callbacks,  # type: Callable[[Any, Any], Any]
 648             runtimeContext     # type: RuntimeContext
 649            ):  # type: (...) -> Generator[Any, None, None]
 650         self.job_order = job_order
 651         self._init_job(job_order, runtimeContext)
 652         yield self
 653
 654     def update_pipeline_component(self, record):
 655         pass
 656
 657     def done(self, record):
 658         """Base method for handling a completed runner."""
 659
 660         try:
 661             if record["state"] == "Complete":
 662                 if record.get("exit_code") is not None:
 663                     if record["exit_code"] == 33:
 664                         processStatus = "UnsupportedRequirement"
 665                     elif record["exit_code"] == 0:
 666                         processStatus = "success"
 667                     else:
 668                         processStatus = "permanentFail"
 669                 else:
 670                     processStatus = "success"
 671             else:
 672                 processStatus = "permanentFail"
 673
 674             outputs = {}
 675
 676             if processStatus == "permanentFail":
 677                 logc = arvados.collection.CollectionReader(record["log"],
 678                                                            api_client=self.arvrunner.api,
 679                                                            keep_client=self.arvrunner.keep_client,
 680                                                            num_retries=self.arvrunner.num_retries)
 681                 done.logtail(logc, logger.error, "%s (%s) error log:" % (self.arvrunner.label(self), record["uuid"]), maxlen=40)
 682
 683             self.final_output = record["output"]
 684             outc = arvados.collection.CollectionReader(self.final_output,
 685                                                        api_client=self.arvrunner.api,
 686                                                        keep_client=self.arvrunner.keep_client,
 687                                                        num_retries=self.arvrunner.num_retries)
 688             if "cwl.output.json" in outc:
 689                 with outc.open("cwl.output.json", "rb") as f:
 690                     if f.size() > 0:
 691                         outputs = json.loads(f.read().decode())
 692             def keepify(fileobj):
 693                 path = fileobj["location"]
 694                 if not path.startswith("keep:"):
 695                     fileobj["location"] = "keep:%s/%s" % (record["output"], path)
 696             adjustFileObjs(outputs, keepify)
 697             adjustDirObjs(outputs, keepify)
 698         except Exception:
 699             logger.exception("[%s] While getting final output object", self.name)
 700             self.arvrunner.output_callback({}, "permanentFail")
 701         else:
 702             self.arvrunner.output_callback(outputs, processStatus)