From a3d9ad884385fdeea5302169fd5df8344aed7e87 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 7 Jun 2019 11:44:48 -0400
Subject: [PATCH] Handle extended remote metadata.
---
docker/coexecutor/Dockerfile | 2 +-
pulsar/client/staging/__init__.py | 2 +-
setup.py | 1 +
3 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/docker/coexecutor/Dockerfile b/docker/coexecutor/Dockerfile
index 7d55e69a..a97ce20e 100644
--- a/docker/coexecutor/Dockerfile
+++ b/docker/coexecutor/Dockerfile
@@ -19,4 +19,4 @@ RUN pip install -U pip && pip install wheel kombu pykube poster
ADD pulsar_app-*.dev0-py2.py3-none-any.whl /pulsar_app-*.dev0-py2.py3-none-any.whl
-RUN pip install /pulsar_app-*.dev0-py2.py3-none-any.whl
+RUN pip install /pulsar_app-*.dev0-py2.py3-none-any.whl[galaxy_extended_metadata]
diff --git a/pulsar/client/staging/__init__.py b/pulsar/client/staging/__init__.py
index 86cb2158..00e16c5d 100644
--- a/pulsar/client/staging/__init__.py
+++ b/pulsar/client/staging/__init__.py
@@ -14,7 +14,7 @@ from galaxy.util.bunch import Bunch
from ..util import PathHelper
COMMAND_VERSION_FILENAME = "COMMAND_VERSION"
-DEFAULT_DYNAMIC_COLLECTION_PATTERN = [r"primary_.*|galaxy.json|metadata_.*|dataset_\d+\.dat|__instrument_.*|dataset_\d+_files.+"]
+DEFAULT_DYNAMIC_COLLECTION_PATTERN = [r"primary_.*|galaxy.json|metadata_.*|dataset_\d+\.dat|__instrument_.*|dataset_\d+_files.+|outputs_populated/.*"]
class ClientJobDescription(object):
diff --git a/setup.py b/setup.py
index d9cd7db6..8e9c406e 100644
--- a/setup.py
+++ b/setup.py
@@ -111,6 +111,7 @@ setup(
install_requires=requirements,
extras_require={
':python_version=="2.7"': py27_requirements,
+ 'galaxy_extended_metadata': ['galaxy-job-execution>=19.9.0.dev0'],
},
license="Apache License 2.0",
zip_safe=False,
--
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