from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size
from .perf import Perf
from .pathmapper import NoFollowPathMapper
-from .task_queue import TaskQueue
+from cwltool.task_queue import TaskQueue
from .context import ArvLoadingContext, ArvRuntimeContext
from ._version import __version__
from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing, visit_class
+from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing, visit_class
from cwltool.command_line_tool import compute_checksums
from cwltool.load_tool import load_tool
}).execute(num_retries=self.num_retries)
except Exception:
logger.exception("Setting container output")
- return
+ raise
def apply_reqs(self, job_order_object, tool):
if "https://w3id.org/cwl/cwl#requirements" in job_order_object:
def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
self.debug = runtimeContext.debug
+ workbench1 = self.api.config()["Services"]["Workbench1"]["ExternalURL"]
+ workbench2 = self.api.config()["Services"]["Workbench2"]["ExternalURL"]
+ controller = self.api.config()["Services"]["Controller"]["ExternalURL"]
+ logger.info("Using cluster %s (%s)", self.api.config()["ClusterID"], workbench2 or workbench1 or controller)
+
updated_tool.visit(self.check_features)
self.project_uuid = runtimeContext.project_uuid
uuid=existing_uuid,
submit_runner_ram=runtimeContext.submit_runner_ram,
name=runtimeContext.name,
- merged_map=merged_map),
+ merged_map=merged_map,
+ submit_runner_image=runtimeContext.submit_runner_image),
"success")
self.apply_reqs(job_order, tool)
if runtimeContext.submit and isinstance(tool, Runner):
logger.info("Final output collection %s", tool.final_output)
+ if workbench2 or workbench1:
+ logger.info("Output at %scollections/%s", workbench2 or workbench1, tool.final_output)
else:
if self.output_name is None:
self.output_name = "Output of %s" % (shortname(tool.tool["id"]))