X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/9c0ea426167e01ea69ff022a811803aa95a302d4..c5f67bbc40e8f6a98854b1bf67fc6a98cff80790:/sdk/cwl/arvados_cwl/arvtool.py

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index cd319e55b1..704edaccb9 100644
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -2,11 +2,10 @@
 #
 # SPDX-License-Identifier: Apache-2.0
 
-from cwltool.command_line_tool import CommandLineTool
-from cwltool.builder import Builder
-from .arvjob import ArvadosJob
+from cwltool.command_line_tool import CommandLineTool, ExpressionTool
 from .arvcontainer import ArvadosContainer
 from .pathmapper import ArvPathMapper
+from .runner import make_builder
 from functools import partial
 from schema_salad.sourceline import SourceLine
 from cwltool.errors import WorkflowException
@@ -16,7 +15,7 @@ def validate_cluster_target(arvrunner, runtimeContext):
         runtimeContext.submit_runner_cluster not in arvrunner.api._rootDesc["remoteHosts"] and
         runtimeContext.submit_runner_cluster != arvrunner.api._rootDesc["uuidPrefix"]):
         raise WorkflowException("Unknown or invalid cluster id '%s' known remote clusters are %s" % (runtimeContext.submit_runner_cluster,
-                                                                                                  ", ".join(arvrunner.api._rootDesc["remoteHosts"].keys())))
+                                                                                                  ", ".join(list(arvrunner.api._rootDesc["remoteHosts"].keys()))))
 def set_cluster_target(tool, arvrunner, builder, runtimeContext):
     cluster_target_req = None
     for field in ("hints", "requirements"):
@@ -37,30 +36,6 @@ def set_cluster_target(tool, arvrunner, builder, runtimeContext):
 
     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."""
@@ -72,8 +47,6 @@ class ArvadosCommandTool(CommandLineTool):
     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)
 
@@ -82,10 +55,6 @@ class ArvadosCommandTool(CommandLineTool):
             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)
@@ -99,9 +68,16 @@ class ArvadosCommandTool(CommandLineTool):
             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):
+    def __init__(self, arvrunner, toolpath_object, loadingContext):
+        super(ArvadosExpressionTool, self).__init__(toolpath_object, loadingContext)
+        self.arvrunner = arvrunner
+
+    def job(self,
+            job_order,         # type: Mapping[Text, Text]
+            output_callback,  # type: Callable[[Any, Any], Any]
+            runtimeContext     # type: RuntimeContext
+           ):
+        return super(ArvadosExpressionTool, self).job(job_order, self.arvrunner.get_wrapped_callback(output_callback), runtimeContext)