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 e0997db5bbb4fbeade9c1d324dbd30c9462db911..704edaccb903eb83f1e66c983eb007fe1c4f8711 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -2,12 +2,40 @@
 #
 # SPDX-License-Identifier: Apache-2.0
 
-from cwltool.command_line_tool import CommandLineTool
-from .arvjob import ArvadosJob
+from cwltool.command_line_tool import CommandLineTool, ExpressionTool
 from .arvcontainer import ArvadosContainer
 from .pathmapper import ArvPathMapper
-from .context import ClusterTarget
+from .runner import make_builder
 from functools import partial
+from schema_salad.sourceline import SourceLine
+from cwltool.errors import WorkflowException
+
+def validate_cluster_target(arvrunner, runtimeContext):
+    if (runtimeContext.submit_runner_cluster and
+        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(list(arvrunner.api._rootDesc["remoteHosts"].keys()))))
+def set_cluster_target(tool, arvrunner, builder, runtimeContext):
+    cluster_target_req = None
+    for field in ("hints", "requirements"):
+        if field not in tool:
+            continue
+        for item in tool[field]:
+            if item["class"] == "http://arvados.org/cwl#ClusterTarget":
+                cluster_target_req = item
+
+    if cluster_target_req is None:
+        return runtimeContext
+
+    with SourceLine(cluster_target_req, None, WorkflowException, runtimeContext.debug):
+        runtimeContext = runtimeContext.copy()
+        runtimeContext.submit_runner_cluster = builder.do_eval(cluster_target_req.get("cluster_id")) or runtimeContext.submit_runner_cluster
+        runtimeContext.project_uuid = builder.do_eval(cluster_target_req.get("project_uuid")) or runtimeContext.project_uuid
+        validate_cluster_target(arvrunner, runtimeContext)
+
+    return runtimeContext
+
 
 class ArvadosCommandTool(CommandLineTool):
     """Wrap cwltool CommandLineTool to override selected methods."""
@@ -18,9 +46,7 @@ class ArvadosCommandTool(CommandLineTool):
 
     def make_job_runner(self, runtimeContext):
         if runtimeContext.work_api == "containers":
-            return partial(ArvadosContainer, self.arvrunner, runtimeContext.cluster_target)
-        elif runtimeContext.work_api == "jobs":
-            return partial(ArvadosJob, self.arvrunner)
+            return partial(ArvadosContainer, self.arvrunner, runtimeContext)
         else:
             raise Exception("Unsupported work_api %s", runtimeContext.work_api)
 
@@ -29,27 +55,10 @@ 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):
-
-        # Workaround for #13365
-        builderargs = runtimeContext.copy()
-        builderargs.toplevel = True
-        builderargs.tmp_outdir_prefix = ""
-        builder = self._init_job(joborder, builderargs)
-        joborder = builder.job
-
-        runtimeContext = runtimeContext.copy()
-
-        cluster_target_req, _ = self.get_requirement("http://arvados.org/cwl#ClusterTarget")
-        if runtimeContext.cluster_target is None or runtimeContext.cluster_target.instance != id(cluster_target_req):
-            runtimeContext.cluster_target = ClusterTarget(id(cluster_target_req),
-                                                          builder.do_eval(cluster_target_req.get("clusterID")),
-                                                          builder.do_eval(cluster_target_req.get("ownerUUID")))
+        builder = make_builder(joborder, self.hints, self.requirements, runtimeContext)
+        runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
 
         if runtimeContext.work_api == "containers":
             dockerReq, is_req = self.get_requirement("DockerRequirement")
@@ -59,9 +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)