from cwltool.draft2tool import revmap_file, CommandLineTool
from cwltool.load_tool import fetch_document
from cwltool.builder import Builder
-from cwltool.pathmapper import PathMapper
import arvados.collection
from .arvdocker import arv_docker_get_image
from .runner import Runner
+from .pathmapper import InitialWorkDirPathMapper
from . import done
logger = logging.getLogger('arvados.cwl-runner')
if self.generatefiles["listing"]:
vwd = arvados.collection.Collection()
script_parameters["task.vwd"] = {}
- generatemapper = PathMapper([self.generatefiles], self.outdir,
- ".", separateDirs=False)
+ generatemapper = InitialWorkDirPathMapper([self.generatefiles], "", "",
+ separateDirs=False)
for f, p in generatemapper.items():
if p.type == "CreateFile":
with vwd.open(p.target, "w") as n:
vwd.save_new()
for f, p in generatemapper.items():
if p.type == "File":
- script_parameters["task.vwd"][p.target] = self.pathmapper.mapper(f).target
+ script_parameters["task.vwd"][p.target] = p.resolved
if p.type == "CreateFile":
script_parameters["task.vwd"][p.target] = "$(task.keep)/%s/%s" % (vwd.portable_data_hash(), p.target)