[ARVADOS] updated: 1.1.4-27-g19da21a
Git user
git at public.curoverse.com
Thu Apr 12 20:58:51 EDT 2018
Summary of changes:
sdk/cwl/arvados_cwl/arvjob.py | 39 ++++++++++++++++++------------------
sdk/cwl/arvados_cwl/crunch_script.py | 3 ++-
sdk/cwl/arvados_cwl/runner.py | 3 +--
3 files changed, 23 insertions(+), 22 deletions(-)
via 19da21ab8e56154d7db15c2643524cb8348a7a8a (commit)
from e4c5f98f696c354638bbba22ee4a1db20a52837c (commit)
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commit 19da21ab8e56154d7db15c2643524cb8348a7a8a
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Thu Apr 12 20:54:57 2018 -0400
13108: crunch_script uses safeapi
Also take workflow lock on update_pipeline_component to prevent update races.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index e222152..decd692 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -184,27 +184,28 @@ class ArvadosJob(object):
self.output_callback({}, "permanentFail")
def update_pipeline_component(self, record):
- if self.arvrunner.pipeline:
- self.arvrunner.pipeline["components"][self.name] = {"job": record}
- with Perf(metrics, "update_pipeline_component %s" % self.name):
- self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(
- uuid=self.arvrunner.pipeline["uuid"],
- body={
- "components": self.arvrunner.pipeline["components"]
- }).execute(num_retries=self.arvrunner.num_retries)
- if self.arvrunner.uuid:
- try:
- job = self.arvrunner.api.jobs().get(uuid=self.arvrunner.uuid).execute()
- if job:
- components = job["components"]
- components[self.name] = record["uuid"]
- self.arvrunner.api.jobs().update(
- uuid=self.arvrunner.uuid,
+ with self.arvrunner.workflow_eval_lock:
+ if self.arvrunner.pipeline:
+ self.arvrunner.pipeline["components"][self.name] = {"job": record}
+ with Perf(metrics, "update_pipeline_component %s" % self.name):
+ self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(
+ uuid=self.arvrunner.pipeline["uuid"],
body={
- "components": components
+ "components": self.arvrunner.pipeline["components"]
}).execute(num_retries=self.arvrunner.num_retries)
- except Exception as e:
- logger.info("Error adding to components: %s", e)
+ if self.arvrunner.uuid:
+ try:
+ job = self.arvrunner.api.jobs().get(uuid=self.arvrunner.uuid).execute()
+ if job:
+ components = job["components"]
+ components[self.name] = record["uuid"]
+ self.arvrunner.api.jobs().update(
+ uuid=self.arvrunner.uuid,
+ body={
+ "components": components
+ }).execute(num_retries=self.arvrunner.num_retries)
+ except Exception as e:
+ logger.info("Error adding to components: %s", e)
def done(self, record):
try:
diff --git a/sdk/cwl/arvados_cwl/crunch_script.py b/sdk/cwl/arvados_cwl/crunch_script.py
index aaeffea..bf940ec 100644
--- a/sdk/cwl/arvados_cwl/crunch_script.py
+++ b/sdk/cwl/arvados_cwl/crunch_script.py
@@ -97,7 +97,8 @@ def run():
debug = job_order_object["arv:debug"]
del job_order_object["arv:debug"]
- runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
+ runner = arvados_cwl.ArvCwlRunner(api_client=arvados.safeapi.ThreadSafeApiCache(
+ api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4}),
output_name=output_name, output_tags=output_tags)
make_fs_access = functools.partial(CollectionFsAccess,
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 053c995..bf0eb08 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -400,5 +400,4 @@ class Runner(object):
else:
self.arvrunner.output_callback(outputs, processStatus)
finally:
- if record["uuid"] in self.arvrunner.processes:
- del self.arvrunner.processes[record["uuid"]]
+ self.arvrunner.process_done(record["uuid"])
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