from cwltool.errors import WorkflowException
import cwltool.workflow
-from schema_salad.sourceline import SourceLine
+from schema_salad.sourceline import SourceLine, cmap
import schema_salad.validate as validate
from schema_salad.ref_resolver import file_uri, uri_file_path
import arvados_cwl.util
from .arvcontainer import RunnerContainer, cleanup_name_for_collection
-from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder
+from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder, update_from_merged_map
from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool
-from .arvworkflow import ArvadosWorkflow, upload_workflow
+from .arvworkflow import ArvadosWorkflow, upload_workflow, make_workflow_record
from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size
from .perf import Perf
from .pathmapper import NoFollowPathMapper
kind = 'error'
elif record.levelno >= logging.WARNING:
kind = 'warning'
+ if kind == 'warning' and record.name == "salad":
+ # Don't send validation warnings to runtime status,
+ # they're noisy and unhelpful.
+ return
if kind is not None and self.updatingRuntimeStatus is not True:
self.updatingRuntimeStatus = True
try:
arvargs.thread_count = 1
arvargs.collection_cache_size = None
arvargs.git_info = True
+ arvargs.submit = False
+ arvargs.defer_downloads = False
self.api = api_client
self.processes = {}
self.toplevel_runtimeContext.make_fs_access = partial(CollectionFsAccess,
collection_cache=self.collection_cache)
+ self.defer_downloads = arvargs.submit and arvargs.defer_downloads
+
validate_cluster_target(self, self.toplevel_runtimeContext)
activity statuses, for example in the RuntimeStatusLoggingHandler.
"""
- if kind not in ('error', 'warning'):
+ if kind not in ('error', 'warning', 'activity'):
# Ignore any other status kind
return
runtime_status = current.get('runtime_status', {})
original_updatemessage = updatemessage = runtime_status.get(kind, "")
- if not updatemessage:
+ if kind == "activity" or not updatemessage:
updatemessage = message
# Subsequent messages tacked on in detail
while keys:
page = keys[:pageSize]
try:
- proc_states = table.list(filters=[["uuid", "in", page]]).execute(num_retries=self.num_retries)
- except Exception:
- logger.exception("Error checking states on API server: %s")
+ 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)
+ except Exception as e:
+ logger.warning("Temporary error checking states on API server: %s", e)
remain_wait = self.poll_interval
continue
def arv_executor(self, updated_tool, job_order, runtimeContext, logger=None):
self.debug = runtimeContext.debug
+ self.runtime_status_update("activity", "initialization")
+
git_info = self.get_git_info(updated_tool) if self.git_info else {}
if git_info:
logger.info("Git provenance")
self.project_uuid = runtimeContext.project_uuid
+ self.runtime_status_update("activity", "data transfer")
+
# Upload local file references in the job order.
with Perf(metrics, "upload_job_order"):
- job_order = upload_job_order(self, "%s input" % runtimeContext.name,
+ job_order, jobmapper = upload_job_order(self, "%s input" % runtimeContext.name,
updated_tool, job_order, runtimeContext)
+ # determine if we are submitting or directly executing the workflow.
+ #
# the last clause means: if it is a command line tool, and we
# are going to wait for the result, and always_submit_runner
# is false, then we don't submit a runner process.
loadingContext = self.loadingContext.copy()
loadingContext.do_validate = False
loadingContext.disable_js_validation = True
- if submitting and not self.fast_submit:
- loadingContext.do_update = False
- # Document may have been auto-updated. Reload the original
- # document with updating disabled because we want to
- # submit the document with its original CWL version, not
- # the auto-updated one.
- with Perf(metrics, "load_tool original"):
- tool = load_tool(updated_tool.tool["id"], loadingContext)
- else:
- tool = updated_tool
+ tool = updated_tool
# Upload direct dependencies of workflow steps, get back mapping of files to keep references.
# Also uploads docker images.
with Perf(metrics, "upload_workflow_deps"):
merged_map = upload_workflow_deps(self, tool, runtimeContext)
else:
+ # in the fast submit case, we are running a workflow that
+ # has already been uploaded to Arvados, so we assume all
+ # the dependencies have been pinned to keep references and
+ # there is nothing to do.
merged_map = {}
- # Recreate process object (ArvadosWorkflow or
- # ArvadosCommandTool) because tool document may have been
- # updated by upload_workflow_deps in ways that modify
- # inheritance of hints or requirements.
loadingContext.loader = tool.doc_loader
loadingContext.avsc_names = tool.doc_schema
loadingContext.metadata = tool.metadata
- with Perf(metrics, "load_tool"):
- tool = load_tool(tool.tool, loadingContext)
+ loadingContext.skip_resolve_all = True
- if runtimeContext.update_workflow or runtimeContext.create_workflow:
- # Create a pipeline template or workflow record and exit.
- if self.work_api == "containers":
- uuid = upload_workflow(self, tool, job_order,
- runtimeContext.project_uuid,
- runtimeContext,
- uuid=runtimeContext.update_workflow,
- submit_runner_ram=runtimeContext.submit_runner_ram,
- name=runtimeContext.name,
- merged_map=merged_map,
- submit_runner_image=runtimeContext.submit_runner_image,
- git_info=git_info)
+ workflow_wrapper = None
+ if submitting and not self.fast_submit:
+ # upload workflow and get back the workflow wrapper
+
+ workflow_wrapper = upload_workflow(self, tool, job_order,
+ runtimeContext.project_uuid,
+ runtimeContext,
+ uuid=runtimeContext.update_workflow,
+ submit_runner_ram=runtimeContext.submit_runner_ram,
+ name=runtimeContext.name,
+ merged_map=merged_map,
+ submit_runner_image=runtimeContext.submit_runner_image,
+ git_info=git_info,
+ set_defaults=(runtimeContext.update_workflow or runtimeContext.create_workflow),
+ jobmapper=jobmapper)
+
+ if runtimeContext.update_workflow or runtimeContext.create_workflow:
+ # We're registering the workflow, so create or update
+ # the workflow record and then exit.
+ uuid = make_workflow_record(self, workflow_wrapper, runtimeContext.name, tool,
+ runtimeContext.project_uuid, runtimeContext.update_workflow)
self.stdout.write(uuid + "\n")
return (None, "success")
+ # Did not register a workflow, we're going to submit
+ # it instead.
+ loadingContext.loader.idx.clear()
+ loadingContext.loader.idx["_:main"] = workflow_wrapper
+ workflow_wrapper["id"] = "_:main"
+
+ # Reload the minimal wrapper workflow.
+ self.fast_submit = True
+ tool = load_tool(workflow_wrapper, loadingContext)
+ loadingContext.loader.idx["_:main"] = workflow_wrapper
+
+ if not submitting:
+ # If we are going to run the workflow now (rather than
+ # submit it), we need to update the workflow document
+ # replacing file references with keep references. If we
+ # are just going to construct a run submission, we don't
+ # need to do this.
+ update_from_merged_map(tool, merged_map)
+
self.apply_reqs(job_order, tool)
self.ignore_docker_for_reuse = runtimeContext.ignore_docker_for_reuse
runnerjob = None
if runtimeContext.submit:
- # Submit a runner job to run the workflow for us.
+ # We are submitting instead of running immediately.
+ #
+ # Create a "Runner job" that when run() is invoked,
+ # creates the container request to run the workflow.
if self.work_api == "containers":
if submitting:
- tool = RunnerContainer(self, updated_tool,
- tool, loadingContext, runtimeContext.enable_reuse,
+ loadingContext.metadata = updated_tool.metadata.copy()
+ tool = RunnerContainer(self, tool, loadingContext, runtimeContext.enable_reuse,
self.output_name,
self.output_tags,
submit_runner_ram=runtimeContext.submit_runner_ram,
runtimeContext)
if runtimeContext.submit and not runtimeContext.wait:
+ # User provided --no-wait so submit the container request,
+ # get the container request uuid, print it out, and exit.
runnerjob = next(jobiter)
runnerjob.run(runtimeContext)
self.stdout.write(runnerjob.uuid+"\n")
return (None, "success")
+ # We either running the workflow directly, or submitting it
+ # and will wait for a final result.
+
+ self.runtime_status_update("activity", "workflow execution")
+
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"))