Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Create and use a temporary shed_data_manager_conf.xml #662

Merged
merged 1 commit into from
Apr 13, 2017
Merged

Create and use a temporary shed_data_manager_conf.xml #662

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
21 changes: 15 additions & 6 deletions planemo/galaxy/config.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,10 @@
from galaxy.tools.deps import docker_util
from galaxy.tools.deps.commands import argv_to_str

from six import iteritems
from six import (
add_metaclass,
iteritems
)
from six.moves.urllib.request import urlopen
from six.moves.urllib.request import urlretrieve

Expand Down Expand Up @@ -79,6 +82,10 @@
</toolbox>
"""

SHED_DATA_MANAGER_CONF_TEMPLATE = """<?xml version="1.0"?>
<data_managers>
</data_managers>
"""

EMPTY_JOB_METRICS_TEMPLATE = """<?xml version="1.0"?>
<job_metrics>
Expand Down Expand Up @@ -281,7 +288,6 @@ def config_join(*args):

tool_conf = config_join("tool_conf.xml")

tool_conf = config_join("tool_conf.xml")
shed_tool_path = kwds.get("shed_tool_path") or config_join("shed_tools")
_ensure_directory(shed_tool_path)

Expand Down Expand Up @@ -393,7 +399,8 @@ def config_join(*args):

tool_conf = config_join("tool_conf.xml")

tool_conf = config_join("tool_conf.xml")
shed_data_manager_config_file = config_join("shed_data_manager_conf.xml")

shed_tool_path = kwds.get("shed_tool_path") or config_join("shed_tools")
_ensure_directory(shed_tool_path)

Expand Down Expand Up @@ -461,6 +468,7 @@ def config_join(*args):
amqp_internal_connection="sqlalchemy+sqlite://",
migrated_tools_config=empty_tool_conf,
test_data_dir=test_data_dir, # TODO: make gx respect this
shed_data_manager_config_file=shed_data_manager_config_file,
))
_handle_container_resolution(ctx, kwds, properties)
write_file(config_join("logging.ini"), _sub(LOGGING_TEMPLATE, template_args))
Expand Down Expand Up @@ -502,6 +510,8 @@ def config_join(*args):
# Write a new shed_tool_conf.xml if needed.
write_file(shed_tool_conf, shed_tool_conf_contents, force=False)

write_file(shed_data_manager_config_file, SHED_DATA_MANAGER_CONF_TEMPLATE)

pid_file = kwds.get("pid_file") or config_join("galaxy.pid")

yield LocalGalaxyConfig(
Expand Down Expand Up @@ -578,15 +588,14 @@ def _config_directory(ctx, **kwds):
shutil.rmtree(config_directory)


@add_metaclass(abc.ABCMeta)
class GalaxyConfig(object):
"""Abstraction around a Galaxy instance.

This requires more than just an API connection and assumes access to files
etc....
"""

__metaclass__ = abc.ABCMeta

@abc.abstractproperty
def kill(self):
"""Stop the running instance."""
Expand Down Expand Up @@ -1167,7 +1176,7 @@ def _build_env_for_galaxy(properties, template_args):


def _build_test_env(properties, env):
# Keeping these environment variables around for a little while but they
# Keeping these environment variables around for a little while but
# many are probably not needed as of the following commit.
# https://bitbucket.org/galaxy/galaxy-central/commits/d7dd1f9
test_property_variants = {
Expand Down