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15954: Merge branch 'master'
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
arvtool.py
diff --git
a/sdk/cwl/arvados_cwl/arvtool.py
b/sdk/cwl/arvados_cwl/arvtool.py
index 4fc02a0166455c13f6853cbce714fd6d7f2d90f4..704edaccb903eb83f1e66c983eb007fe1c4f8711 100644
(file)
--- a/
sdk/cwl/arvados_cwl/arvtool.py
+++ b/
sdk/cwl/arvados_cwl/arvtool.py
@@
-3,7
+3,6
@@
# SPDX-License-Identifier: Apache-2.0
from cwltool.command_line_tool import CommandLineTool, ExpressionTool
# SPDX-License-Identifier: Apache-2.0
from cwltool.command_line_tool import CommandLineTool, ExpressionTool
-from .arvjob import ArvadosJob
from .arvcontainer import ArvadosContainer
from .pathmapper import ArvPathMapper
from .runner import make_builder
from .arvcontainer import ArvadosContainer
from .pathmapper import ArvPathMapper
from .runner import make_builder
@@
-48,8
+47,6
@@
class ArvadosCommandTool(CommandLineTool):
def make_job_runner(self, runtimeContext):
if runtimeContext.work_api == "containers":
return partial(ArvadosContainer, self.arvrunner, runtimeContext)
def make_job_runner(self, runtimeContext):
if runtimeContext.work_api == "containers":
return partial(ArvadosContainer, self.arvrunner, runtimeContext)
- elif runtimeContext.work_api == "jobs":
- return partial(ArvadosJob, self.arvrunner)
else:
raise Exception("Unsupported work_api %s", runtimeContext.work_api)
else:
raise Exception("Unsupported work_api %s", runtimeContext.work_api)
@@
-58,10
+55,6
@@
class ArvadosCommandTool(CommandLineTool):
return ArvPathMapper(self.arvrunner, reffiles+runtimeContext.extra_reffiles, runtimeContext.basedir,
"/keep/%s",
"/keep/%s/%s")
return ArvPathMapper(self.arvrunner, reffiles+runtimeContext.extra_reffiles, runtimeContext.basedir,
"/keep/%s",
"/keep/%s/%s")
- elif runtimeContext.work_api == "jobs":
- return ArvPathMapper(self.arvrunner, reffiles, runtimeContext.basedir,
- "$(task.keep)/%s",
- "$(task.keep)/%s/%s")
def job(self, joborder, output_callback, runtimeContext):
builder = make_builder(joborder, self.hints, self.requirements, runtimeContext)
def job(self, joborder, output_callback, runtimeContext):
builder = make_builder(joborder, self.hints, self.requirements, runtimeContext)
@@
-75,11
+68,6
@@
class ArvadosCommandTool(CommandLineTool):
else:
runtimeContext.outdir = "/var/spool/cwl"
runtimeContext.docker_outdir = "/var/spool/cwl"
else:
runtimeContext.outdir = "/var/spool/cwl"
runtimeContext.docker_outdir = "/var/spool/cwl"
- elif runtimeContext.work_api == "jobs":
- runtimeContext.outdir = "$(task.outdir)"
- runtimeContext.docker_outdir = "$(task.outdir)"
- runtimeContext.tmpdir = "$(task.tmpdir)"
- runtimeContext.docker_tmpdir = "$(task.tmpdir)"
return super(ArvadosCommandTool, self).job(joborder, output_callback, runtimeContext)
class ArvadosExpressionTool(ExpressionTool):
return super(ArvadosCommandTool, self).job(joborder, output_callback, runtimeContext)
class ArvadosExpressionTool(ExpressionTool):