12278: Propagate --debug flag to jobs.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 794c99446c7bdf5ce442d714816d93f150a623ce..7fc62db9513e1793021b26b9d8d52ba405dada1f 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -297,6 +297,9 @@ class RunnerJob(Runner):
         if self.on_error:
             self.job_order["arv:on_error"] = self.on_error
 
+        if kwargs.get("debug"):
+            self.job_order["arv:debug"] = True
+
         return {
             "script": "cwl-runner",
             "script_version": "master",

diff --git a/sdk/cwl/arvados_cwl/crunch_script.py b/sdk/cwl/arvados_cwl/crunch_script.py
index 7fbbd29d50d72f385b5e1ea95f2b093405518baf..80235e426b7d8d2b47a26204980e3e70f56615f3 100644 (file)
--- a/sdk/cwl/arvados_cwl/crunch_script.py
+++ b/sdk/cwl/arvados_cwl/crunch_script.py
@@ -75,6 +75,8 @@ def run():
         output_tags = None
         enable_reuse = True
         on_error = "continue"
+        debug = False
+
         if "arv:output_name" in job_order_object:
             output_name = job_order_object["arv:output_name"]
             del job_order_object["arv:output_name"]
@@ -91,6 +93,10 @@ def run():
             on_error = job_order_object["arv:on_error"]
             del job_order_object["arv:on_error"]
 
+        if "arv:debug" in job_order_object:
+            debug = job_order_object["arv:debug"]
+            del job_order_object["arv:debug"]
+
         runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
                                           output_name=output_name, output_tags=output_tags)
 
@@ -108,7 +114,7 @@ def run():
         args.enable_reuse = enable_reuse
         args.on_error = on_error
         args.submit = False
-        args.debug = False
+        args.debug = debug
         args.quiet = False
         args.ignore_docker_for_reuse = False
         args.basedir = os.getcwd()