#
# 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 .runner import make_builder
+from ._version import __version__
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()))))
+ 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"):
+ 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."""
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:
+ self.hints.append({"class": "DockerRequirement",
+ "dockerPull": "arvados/jobs:"+__version__})
+
self.arvrunner = arvrunner
def make_job_runner(self, runtimeContext):
if runtimeContext.work_api == "containers":
- return partial(ArvadosContainer, self.arvrunner)
- 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)
- def make_path_mapper(self, reffiles, stagedir, runtimeContext):
+ def make_path_mapper(self, reffiles, stagedir, runtimeContext, separateDirs):
if runtimeContext.work_api == "containers":
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()
+ 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":
dockerReq, is_req = self.get_requirement("DockerRequirement")
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)
projects / arvados.git / blobdiff