Merge branch '19744-acr-crunchstat' refs #19744

[arvados.git] / sdk / cwl / arvados_cwl / executor.py

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 330dba3dbe9f9ee5401f476b096753f39bd9ccb8..432b380aabcd90c4c91ff3d7d72a9af29ab52823 100644 (file)
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -70,7 +70,7 @@ class RuntimeStatusLoggingHandler(logging.Handler):
             kind = 'error'
         elif record.levelno >= logging.WARNING:
             kind = 'warning'
-        if kind == 'warning' and record.name == "salad":
+        if kind == 'warning' and record.name in ("salad", "crunchstat_summary"):
             # Don't send validation warnings to runtime status,
             # they're noisy and unhelpful.
             return
@@ -146,6 +146,7 @@ class ArvCwlExecutor(object):
         self.stdout = stdout
         self.fast_submit = False
         self.git_info = arvargs.git_info
+        self.debug = False
 
         if keep_client is not None:
             self.keep_client = keep_client
@@ -369,7 +370,8 @@ The 'jobs' API is no longer supported.
                     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
@@ -603,6 +605,8 @@ The 'jobs' API is no longer supported.
                 if git_info[g]:
                     logger.info("  %s: %s", g.split("#", 1)[1], git_info[g])
 
+        runtimeContext.git_info = git_info
+
         workbench1 = self.api.config()["Services"]["Workbench1"]["ExternalURL"]
         workbench2 = self.api.config()["Services"]["Workbench2"]["ExternalURL"]
         controller = self.api.config()["Services"]["Controller"]["ExternalURL"]
@@ -729,7 +733,7 @@ The 'jobs' API is no longer supported.
 
             if runtimeContext.print_keep_deps:
                 # Just find and print out all the collection dependencies and exit
-                print_keep_deps(tool)
+                print_keep_deps(self, runtimeContext, merged_map, tool)
                 return (None, "success")
 
             # Did not register a workflow, we're going to submit
@@ -874,7 +878,8 @@ The 'jobs' API is no longer supported.
                     if (self.task_queue.in_flight + len(self.processes)) > 0:
                         self.workflow_eval_lock.wait(3)
                     else:
-                        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.")
                         break
 
                 if self.stop_polling.is_set():
@@ -924,6 +929,11 @@ The 'jobs' API is no longer supported.
         if self.final_output is None:
             raise WorkflowException("Workflow did not return a result.")
 
+        if runtimeContext.usage_report_notes:
+            logger.info("Steps with low resource utilization (possible optimization opportunities):")
+            for x in runtimeContext.usage_report_notes:
+                logger.info("  %s", x)
+
         if runtimeContext.submit and isinstance(tool, Runner):
             logger.info("Final output collection %s", tool.final_output)
             if workbench2 or workbench1: