-from __future__ import division
-from builtins import next
-from builtins import object
-from builtins import str
-from future.utils import viewvalues, viewitems
-
-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
# Don't send validation warnings to runtime status,
# they're noisy and unhelpful.
return
# Don't send validation warnings to runtime status,
# they're noisy and unhelpful.
return
page = keys[:pageSize]
try:
proc_states = table.list(filters=[["uuid", "in", page]], select=["uuid", "container_uuid", "state", "log_uuid",
page = keys[:pageSize]
try:
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)
+ "output_uuid", "modified_at", "properties",
+ "runtime_constraints"]).execute(num_retries=self.num_retries)
except Exception as e:
logger.warning("Temporary error checking states on API server: %s", e)
remain_wait = self.poll_interval
except Exception as e:
logger.warning("Temporary error checking states on API server: %s", e)
remain_wait = self.poll_interval
if obj.get("class") == "InplaceUpdateRequirement":
if obj["inplaceUpdate"] and parentfield == "requirements":
raise SourceLine(obj, "class", UnsupportedRequirement).makeError("InplaceUpdateRequirement not supported for keep collections.")
if obj.get("class") == "InplaceUpdateRequirement":
if obj["inplaceUpdate"] and parentfield == "requirements":
raise SourceLine(obj, "class", UnsupportedRequirement).makeError("InplaceUpdateRequirement not supported for keep collections.")
self.check_features(v, parentfield=k)
elif isinstance(obj, list):
for i,v in enumerate(obj):
self.check_features(v, parentfield=k)
elif isinstance(obj, list):
for i,v in enumerate(obj):
if git_info[g]:
logger.info(" %s: %s", g.split("#", 1)[1], git_info[g])
if git_info[g]:
logger.info(" %s: %s", g.split("#", 1)[1], git_info[g])
workbench1 = self.api.config()["Services"]["Workbench1"]["ExternalURL"]
workbench2 = self.api.config()["Services"]["Workbench2"]["ExternalURL"]
controller = self.api.config()["Services"]["Controller"]["ExternalURL"]
workbench1 = self.api.config()["Services"]["Workbench1"]["ExternalURL"]
workbench2 = self.api.config()["Services"]["Workbench2"]["ExternalURL"]
controller = self.api.config()["Services"]["Controller"]["ExternalURL"]
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
# 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,
+ if runtimeContext.print_keep_deps:
+ # Just find and print out all the collection dependencies and exit
+ print_keep_deps(self, runtimeContext, merged_map, tool)
+ return (None, "success")
+
# 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()
- logger.error("Workflow is deadlocked, no runnable processes and not waiting on any pending processes.")
+ if self.final_status is None:
+ logger.error("Workflow is deadlocked, no runnable processes and not waiting on any pending processes.")
if runtimeContext.submit and isinstance(tool, Runner):
logger.info("Final output collection %s", tool.final_output)
if workbench2 or workbench1:
if runtimeContext.submit and isinstance(tool, Runner):
logger.info("Final output collection %s", tool.final_output)
if workbench2 or workbench1: