2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b0ff7d6cfe40/
Changeset: b0ff7d6cfe40
User: jmchilton
Date: 2015-02-08 00:32:16+00:00
Summary: Rework control queue setup to work in non-web contexts.
Namely in the new lib/galaxy/main.py. I think this break down of the code makes more sense also since control queues aren't inheriently something web-y so lib/galaxy/app.py makes more sense for configuring them. Dannon feel free to reorganize if you dislike this particular organization - I just wanted to make sure lib/galaxy/main.py could share in the new stuff.
Affected #: 3 files
diff -r 5964dac35d2eb268097632ca65c3abbbdf624716 -r b0ff7d6cfe407ecae40dc761b0970ac2cfaa76e2 lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -144,6 +144,12 @@
self.model.engine.dispose()
+ def setup_control_queue(self):
+ self.control_worker = GalaxyQueueWorker(self, galaxy.queues.control_queue_from_config(self.config),
+ galaxy.queue_worker.control_message_to_task)
+ self.control_worker.daemon = True
+ self.control_worker.start()
+
def shutdown( self ):
self.workflow_scheduling_manager.shutdown()
self.job_manager.shutdown()
diff -r 5964dac35d2eb268097632ca65c3abbbdf624716 -r b0ff7d6cfe407ecae40dc761b0970ac2cfaa76e2 lib/galaxy/main.py
--- a/lib/galaxy/main.py
+++ b/lib/galaxy/main.py
@@ -101,6 +101,7 @@
global_conf={"__file__": config_builder.ini_path},
**kwds
)
+ app.setup_control_queue()
return app
diff -r 5964dac35d2eb268097632ca65c3abbbdf624716 -r b0ff7d6cfe407ecae40dc761b0970ac2cfaa76e2 lib/galaxy/webapps/galaxy/buildapp.py
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -123,14 +123,10 @@
@postfork
def postfork_setup():
from galaxy.app import app
- from galaxy.queue_worker import GalaxyQueueWorker
if app.config.is_uwsgi:
import uwsgi
app.config.server_name += ".%s" % uwsgi.worker_id()
- app.control_worker = GalaxyQueueWorker(app, galaxy.queues.control_queue_from_config(app.config),
- galaxy.queue_worker.control_message_to_task)
- app.control_worker.daemon = True
- app.control_worker.start()
+ app.setup_control_queue()
def populate_api_routes( webapp, app ):
https://bitbucket.org/galaxy/galaxy-central/commits/1b09e60f84db/
Changeset: 1b09e60f84db
User: jmchilton
Date: 2015-02-08 00:32:16+00:00
Summary: Fix running tool tests for recent control reworking.
Affected #: 1 file
diff -r b0ff7d6cfe407ecae40dc761b0970ac2cfaa76e2 -r 1b09e60f84db859ae49bed71c6f3fd838af612f5 lib/galaxy/webapps/galaxy/buildapp.py
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -47,6 +47,7 @@
# Create the Galaxy application unless passed in
if 'app' in kwargs:
app = kwargs.pop( 'app' )
+ galaxy.app.app = app
else:
try:
app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/527b11f07d81/
Changeset: 527b11f07d81
User: jmchilton
Date: 2015-02-07 02:33:49+00:00
Summary: Merged in JenCabral/galaxy-central/tool_shed_test_fix-DB_initialization (pull request #662)
Fix tool shed tests - create database directory
Affected #: 2 files
diff -r 3dd2ec31034db4febf1954c295b81604cca62169 -r 527b11f07d8107298c87293eb04469f2743e229e test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
--- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
+++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
@@ -407,6 +407,9 @@
else:
tempdir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir )
galaxy_db_path = os.path.join( tempdir, 'database' )
+ # Checks if galaxy_db_path exists, if not create it.
+ if not os.path.exists(galaxy_db_path):
+ os.makedirs(galaxy_db_path)
# Configure the paths Galaxy needs to install and test tools.
galaxy_file_path = os.path.join( galaxy_db_path, 'files' )
galaxy_tempfiles = tempfile.mkdtemp( dir=galaxy_test_tmp_dir )
diff -r 3dd2ec31034db4febf1954c295b81604cca62169 -r 527b11f07d8107298c87293eb04469f2743e229e test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py
--- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py
+++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py
@@ -255,6 +255,9 @@
else:
tempdir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir )
galaxy_db_path = os.path.join( tempdir, 'database' )
+ # Checks that galaxy_db_path exists and if not, create it.
+ if not os.path.exists(galaxy_db_path):
+ os.makedirs(galaxy_db_path)
# Configure the paths Galaxy needs to install and test tools.
galaxy_file_path = os.path.join( galaxy_db_path, 'files' )
galaxy_tempfiles = tempfile.mkdtemp( dir=galaxy_test_tmp_dir )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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