From f2be4ce3cd677f12269e0f9a73ba2428c30f662e Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 3 May 2019 14:02:43 -0400
Subject: [PATCH] Revisions to Kubernetes coexecution pods.
- Don't hardcode the job ID - it makes Galaxy mapping tricky, seems to be not reason to anyway.
- Don't assume tool execution container has bash.
- Rev to this version of Pulsar.
---
docker/coexecutor/Dockerfile | 4 ++--
pulsar/client/client.py | 4 ++--
pulsar/managers/unqueued.py | 3 +--
test/integration_test.py | 1 -
test/manager_coexecution_test.py | 4 +---
5 files changed, 6 insertions(+), 10 deletions(-)
diff --git a/docker/coexecutor/Dockerfile b/docker/coexecutor/Dockerfile
index b81016bf..de491753 100644
--- a/docker/coexecutor/Dockerfile
+++ b/docker/coexecutor/Dockerfile
@@ -17,8 +17,8 @@ RUN apt-get update \
RUN pip install -U pip && pip install wheel
-ADD pulsar_app-0.9.0-py2.py3-none-any.whl /pulsar_app-0.9.0-py2.py3-none-any.whl
+ADD pulsar_app-0.10.0.dev0-py2.py3-none-any.whl /pulsar_app-0.10.0.dev0-py2.py3-none-any.whl
-RUN pip install /pulsar_app-0.9.0-py2.py3-none-any.whl
+RUN pip install /pulsar_app-0.10.0.dev0-py2.py3-none-any.whl
RUN pip install kombu pykube poster
diff --git a/pulsar/client/client.py b/pulsar/client/client.py
index 06603a4a..cfe7ccf2 100644
--- a/pulsar/client/client.py
+++ b/pulsar/client/client.py
@@ -31,7 +31,7 @@ CACHE_WAIT_SECONDS = 3
TOOL_EXECUTION_CONTAINER_COMMAND_TEMPLATE = """
path='%s/command_line';
while [ ! -e $path ];
- do sleep 1; echo 'waiting for job script...';
+ do sleep 1; echo "waiting for job script $path";
done;
echo 'running script';
sh $path;
@@ -410,7 +410,7 @@ class MessageCoexecutionPodJobClient(BaseMessageJobClient):
tool_container_spec = {
"name": "tool-container",
"image": tool_container_image,
- "command": ["bash"],
+ "command": ["sh"],
"args": ["-c", command],
"workingDir": "/",
"volumeMounts": volume_mounts,
diff --git a/pulsar/managers/unqueued.py b/pulsar/managers/unqueued.py
index 8ebeaced..79bdb06e 100644
--- a/pulsar/managers/unqueued.py
+++ b/pulsar/managers/unqueued.py
@@ -188,10 +188,9 @@ class CoexecutionManager(BaseUnqueuedManager):
def __init__(self, name, app, **kwds):
super(CoexecutionManager, self).__init__(name, app, **kwds)
- self.singleton_job_id = "0"
def setup_job(self, input_job_id, tool_id, tool_version):
- return self._setup_job_for_job_id(self.singleton_job_id, tool_id, tool_version)
+ return self._setup_job_for_job_id(input_job_id, tool_id, tool_version)
def get_status(self, job_id):
return self._get_status(job_id)
diff --git a/test/integration_test.py b/test/integration_test.py
index 9f1bf855..ebbcb509 100644
--- a/test/integration_test.py
+++ b/test/integration_test.py
@@ -257,7 +257,6 @@ class ExternalQueueIntegrationTests(IntegrationTests):
k8s_enabled=True,
container="conda/miniconda2",
remote_pulsar_app_config=remote_pulsar_app_config,
- job_id="0",
**self.default_kwargs
)
diff --git a/test/manager_coexecution_test.py b/test/manager_coexecution_test.py
index 4e48d02d..0bcbfbfb 100644
--- a/test/manager_coexecution_test.py
+++ b/test/manager_coexecution_test.py
@@ -17,11 +17,9 @@ class Coexecutor(object):
self.command_line = None
def monitor(self):
- singleton_job_id = "0"
-
while not self.has_command_line:
try:
- command_line = self.manager.read_command_line(singleton_job_id)
+ command_line = self.manager.read_command_line("123")
except (IOError, ValueError):
continue
if not command_line:
--
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