-from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder, update_from_merged_map
+from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder, update_from_merged_map, print_keep_deps
from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool
from .arvworkflow import ArvadosWorkflow, upload_workflow, make_workflow_record
from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size
from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool
from .arvworkflow import ArvadosWorkflow, upload_workflow, make_workflow_record
from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size
runtime_status = current.get('runtime_status', {})
original_updatemessage = updatemessage = runtime_status.get(kind, "")
runtime_status = current.get('runtime_status', {})
original_updatemessage = updatemessage = runtime_status.get(kind, "")
- proc_states = table.list(filters=[["uuid", "in", page]]).execute(num_retries=self.num_retries)
+ proc_states = table.list(filters=[["uuid", "in", page]], select=["uuid", "container_uuid", "state", "log_uuid",
+ "output_uuid", "modified_at", "properties"]).execute(num_retries=self.num_retries)
def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
self.debug = runtimeContext.debug
def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
self.debug = runtimeContext.debug
if runtimeContext.update_workflow and self.project_uuid is None:
# If we are updating a workflow, make sure anything that
# gets uploaded goes into the same parent project, unless
if runtimeContext.update_workflow and self.project_uuid is None:
# If we are updating a workflow, make sure anything that
# gets uploaded goes into the same parent project, unless
# Upload local file references in the job order.
with Perf(metrics, "upload_job_order"):
job_order, jobmapper = upload_job_order(self, "%s input" % runtimeContext.name,
# Upload local file references in the job order.
with Perf(metrics, "upload_job_order"):
job_order, jobmapper = upload_job_order(self, "%s input" % runtimeContext.name,
# are going to wait for the result, and always_submit_runner
# is false, then we don't submit a runner process.
# are going to wait for the result, and always_submit_runner
# is false, then we don't submit a runner process.
# upload workflow and get back the workflow wrapper
workflow_wrapper = upload_workflow(self, tool, job_order,
# upload workflow and get back the workflow wrapper
workflow_wrapper = upload_workflow(self, tool, job_order,
# Did not register a workflow, we're going to submit
# it instead.
loadingContext.loader.idx.clear()
# Did not register a workflow, we're going to submit
# it instead.
loadingContext.loader.idx.clear()
# We either running the workflow directly, or submitting it
# and will wait for a final result.
# We either running the workflow directly, or submitting it
# and will wait for a final result.
current_container = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
if current_container:
logger.info("Running inside container %s", current_container.get("uuid"))
current_container = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger)
if current_container:
logger.info("Running inside container %s", current_container.get("uuid"))