# SPDX-License-Identifier: Apache-2.0
from cwltool.command_line_tool import CommandLineTool
+from cwltool.builder import Builder
from .arvjob import ArvadosJob
from .arvcontainer import ArvadosContainer
from .pathmapper import ArvPathMapper
return runtimeContext
+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
+ )
+
class ArvadosCommandTool(CommandLineTool):
"""Wrap cwltool CommandLineTool to override selected methods."""
"$(task.keep)/%s/%s")
def job(self, joborder, output_callback, runtimeContext):
- builder = self._init_job(joborder, runtimeContext)
+ builder = make_builder(joborder, self.hints, self.requirements, runtimeContext)
runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
if runtimeContext.work_api == "containers":
from cwltool.process import shortname
from cwltool.workflow import Workflow, WorkflowException, WorkflowStep
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
-from cwltool.builder import Builder
from cwltool.context import LoadingContext
import ruamel.yaml as yaml
from .runner import (upload_dependencies, packed_workflow, upload_workflow_collection,
trim_anonymous_location, remove_redundant_fields, discover_secondary_files)
from .pathmapper import ArvPathMapper, trim_listing
-from .arvtool import ArvadosCommandTool, set_cluster_target
+from .arvtool import ArvadosCommandTool, set_cluster_target, make_builder
from .perf import Perf
logger = logging.getLogger('arvados.cwl-runner')
runtimeContext = runtimeContext.copy()
runtimeContext.toplevel = True # Preserve behavior for #13365
- builder = self._init_job({shortname(k): v for k,v in joborder.items()}, runtimeContext)
+ builder = make_builder({shortname(k): v for k,v in joborder.items()}, self.hints, self.requirements, runtimeContext)
runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
return super(ArvadosWorkflowStep, self).job(joborder, output_callback, runtimeContext)