X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/e838828374ceed5ef6da260939251e86f72b6f27..7bdffdeb9ccec113d1d9b848423be60d85a501ed:/sdk/cwl/arvados_cwl/arvtool.py

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index 4fc02a0166..86fecc0a1d 100644
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -3,20 +3,36 @@
 # 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 ._version import __version__
 from functools import partial
 from schema_salad.sourceline import SourceLine
 from cwltool.errors import WorkflowException
+from arvados.util import portable_data_hash_pattern
 
 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()))))
+                                                                                                     ", ".join(list(arvrunner.api._rootDesc["remoteHosts"].keys()))))
+    if runtimeContext.project_uuid:
+        cluster_target = runtimeContext.submit_runner_cluster or arvrunner.api._rootDesc["uuidPrefix"]
+        if not runtimeContext.project_uuid.startswith(cluster_target):
+            raise WorkflowException("Project uuid '%s' should start with id of target cluster '%s'" % (runtimeContext.project_uuid, cluster_target))
+
+        try:
+            if runtimeContext.project_uuid[5:12] == '-tpzed-':
+                arvrunner.api.users().get(uuid=runtimeContext.project_uuid).execute()
+            else:
+                proj = arvrunner.api.groups().get(uuid=runtimeContext.project_uuid).execute()
+                if proj["group_class"] != "project":
+                    raise Exception("not a project, group_class is '%s'" % (proj["group_class"]))
+        except Exception as e:
+            raise WorkflowException("Invalid project uuid '%s': %s" % (runtimeContext.project_uuid, e))
+
 def set_cluster_target(tool, arvrunner, builder, runtimeContext):
     cluster_target_req = None
     for field in ("hints", "requirements"):
@@ -43,13 +59,21 @@ class ArvadosCommandTool(CommandLineTool):
 
     def __init__(self, arvrunner, toolpath_object, loadingContext):
         super(ArvadosCommandTool, self).__init__(toolpath_object, loadingContext)
+
+        (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
+        if not docker_req:
+            if portable_data_hash_pattern.match(loadingContext.default_docker_image):
+                self.hints.append({"class": "DockerRequirement",
+                                   "http://arvados.org/cwl#dockerCollectionPDH": loadingContext.default_docker_image})
+            else:
+                self.hints.append({"class": "DockerRequirement",
+                                   "dockerPull": loadingContext.default_docker_image})
+
         self.arvrunner = arvrunner
 
     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)
 
@@ -58,13 +82,9 @@ 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)
+        builder = make_builder(joborder, self.hints, self.requirements, runtimeContext, self.metadata)
         runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
 
         if runtimeContext.work_api == "containers":
@@ -75,11 +95,6 @@ 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):