def paste_app_factory(global_conf, **kwargs):
"""
Return a wsgi application serving the root object
"""
kwargs = load_app_properties(kwds=kwargs)
# 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)
galaxy.app.app = app
except:
import traceback
traceback.print_exc()
sys.exit(1)
# Call app's shutdown method when the interpeter exits, this cleanly stops
# the various Galaxy application daemon threads
atexit.register(app.shutdown)
# Create the universe WSGI application
webapp = GalaxyWebApplication(app,
session_cookie='galaxysession',
name='galaxy')
webapp.add_ui_controllers('galaxy.webapps.galaxy.controllers', app)
# Force /history to go to view of current
webapp.add_route('/history', controller='history', action='view')
# Force /activate to go to the controller
webapp.add_route('/activate', controller='user', action='activate')
# These two routes handle our simple needs at the moment
webapp.add_route('/async/{tool_id}/{data_id}/{data_secret}',
controller='async',
action='index',
tool_id=None,
data_id=None,
data_secret=None)
webapp.add_route('/{controller}/{action}', action='index')
webapp.add_route('/{action}', controller='root', action='index')
# allow for subdirectories in extra_files_path
webapp.add_route('/datasets/{dataset_id}/display/{filename:.+?}',
controller='dataset',
action='display',
dataset_id=None,
filename=None)
webapp.add_route('/datasets/{dataset_id}/{action}/{filename}',
controller='dataset',
action='index',
dataset_id=None,
filename=None)
webapp.add_route(
'/display_application/{dataset_id}/{app_name}/{link_name}/{user_id}/{app_action}/{action_param}/{action_param_extra:.+?}',
controller='dataset',
action='display_application',
dataset_id=None,
user_id=None,
app_name=None,
link_name=None,
app_action=None,
action_param=None,
action_param_extra=None)
webapp.add_route('/u/{username}/d/{slug}/{filename}',
controller='dataset',
action='display_by_username_and_slug',
filename=None)
webapp.add_route('/u/{username}/p/{slug}',
controller='page',
action='display_by_username_and_slug')
webapp.add_route('/u/{username}/h/{slug}',
controller='history',
action='display_by_username_and_slug')
webapp.add_route('/u/{username}/w/{slug}',
controller='workflow',
action='display_by_username_and_slug')
webapp.add_route('/u/{username}/w/{slug}/{format}',
controller='workflow',
action='display_by_username_and_slug')
webapp.add_route('/u/{username}/v/{slug}',
controller='visualization',
action='display_by_username_and_slug')
webapp.add_route('/search', controller='search', action='index')
# TODO: Refactor above routes into external method to allow testing in
# isolation as well.
populate_api_routes(webapp, app)
# ==== Done
# Indicate that all configuration settings have been provided
webapp.finalize_config()
# Wrap the webapp in some useful middleware
if kwargs.get('middleware', True):
webapp = wrap_in_middleware(webapp, global_conf, **kwargs)
if asbool(kwargs.get('static_enabled', True)):
if process_is_uwsgi:
log.error(
"Static middleware is enabled in your configuration but this is a uwsgi process. Refusing to wrap in static middleware."
)
else:
webapp = wrap_in_static(
webapp,
global_conf,
plugin_frameworks=[app.visualizations_registry],
**kwargs)
# Close any pooled database connections before forking
try:
galaxy.model.mapping.metadata.bind.dispose()
except:
log.exception(
"Unable to dispose of pooled galaxy model database connections.")
try:
# This model may not actually be bound.
if galaxy.model.tool_shed_install.mapping.metadata.bind:
galaxy.model.tool_shed_install.mapping.metadata.bind.dispose()
except:
log.exception(
"Unable to dispose of pooled toolshed install model database connections."
)
if not process_is_uwsgi:
postfork_setup()
# Return
return webapp
def paste_app_factory( global_conf, **kwargs ):
"""
Return a wsgi application serving the root object
"""
kwargs = load_app_properties(
kwds=kwargs
)
# 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 )
galaxy.app.app = app
except:
import traceback
traceback.print_exc()
sys.exit( 1 )
# Call app's shutdown method when the interpeter exits, this cleanly stops
# the various Galaxy application daemon threads
atexit.register( app.shutdown )
# Create the universe WSGI application
webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' )
# STANDARD CONTROLLER ROUTES
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
# Force /history to go to view of current
webapp.add_route( '/history', controller='history', action='view' )
webapp.add_route( '/history/view/{id}', controller='history', action='view' )
# THIS IS A TEMPORARY ROUTE FOR THE 17.01 RELEASE
# This route supports the previous hide/delete-all-hidden functionality in a history.
# It will be removed after 17.01.
webapp.add_route( '/history/adjust_hidden', controller='history', action='adjust_hidden')
# Force /activate to go to the controller
webapp.add_route( '/activate', controller='user', action='activate' )
webapp.add_route( '/login', controller='root', action='login' )
# These two routes handle our simple needs at the moment
webapp.add_route( '/async/{tool_id}/{data_id}/{data_secret}', controller='async', action='index', tool_id=None, data_id=None, data_secret=None )
webapp.add_route( '/{controller}/{action}', action='index' )
webapp.add_route( '/{action}', controller='root', action='index' )
# allow for subdirectories in extra_files_path
webapp.add_route( '/datasets/{dataset_id}/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None)
webapp.add_route( '/datasets/{dataset_id}/{action}/{filename}', controller='dataset', action='index', dataset_id=None, filename=None)
webapp.add_route( '/display_application/{dataset_id}/{app_name}/{link_name}/{user_id}/{app_action}/{action_param}/{action_param_extra:.+?}',
controller='dataset', action='display_application', dataset_id=None, user_id=None,
app_name=None, link_name=None, app_action=None, action_param=None, action_param_extra=None )
webapp.add_route( '/u/{username}/d/{slug}/{filename}', controller='dataset', action='display_by_username_and_slug', filename=None )
webapp.add_route( '/u/{username}/p/{slug}', controller='page', action='display_by_username_and_slug' )
webapp.add_route( '/u/{username}/h/{slug}', controller='history', action='display_by_username_and_slug' )
webapp.add_route( '/u/{username}/w/{slug}', controller='workflow', action='display_by_username_and_slug' )
webapp.add_route( '/u/{username}/w/{slug}/{format}', controller='workflow', action='display_by_username_and_slug' )
webapp.add_route( '/u/{username}/v/{slug}', controller='visualization', action='display_by_username_and_slug' )
webapp.add_route( '/search', controller='search', action='index' )
# TODO: Refactor above routes into external method to allow testing in
# isolation as well.
populate_api_routes( webapp, app )
# CLIENTSIDE ROUTES
# The following are routes that are handled completely on the clientside.
# The following routes don't bootstrap any information, simply provide the
# base analysis interface at which point the application takes over.
webapp.add_client_route( '/tours' )
webapp.add_client_route( '/tours/{tour_id}' )
webapp.add_client_route( '/user' )
webapp.add_client_route( '/user/{form_id}' )
# ==== Done
# Indicate that all configuration settings have been provided
webapp.finalize_config()
# Wrap the webapp in some useful middleware
if kwargs.get( 'middleware', True ):
webapp = wrap_in_middleware(webapp, global_conf, app.application_stack, **kwargs)
if asbool( kwargs.get( 'static_enabled', True) ):
webapp = wrap_if_allowed(webapp, app.application_stack, wrap_in_static,
args=(global_conf,),
kwargs=dict(plugin_frameworks=[app.visualizations_registry], **kwargs))
# Close any pooled database connections before forking
try:
galaxy.model.mapping.metadata.bind.dispose()
except:
log.exception("Unable to dispose of pooled galaxy model database connections.")
try:
# This model may not actually be bound.
if galaxy.model.tool_shed_install.mapping.metadata.bind:
galaxy.model.tool_shed_install.mapping.metadata.bind.dispose()
except:
log.exception("Unable to dispose of pooled toolshed install model database connections.")
app.application_stack.register_postfork_function(postfork_setup)
for th in threading.enumerate():
if th.is_alive():
log.debug("Prior to webapp return, Galaxy thread %s is alive.", th)
# Return
return webapp
def app_factory(global_conf, **kwargs):
"""
Return a wsgi application serving the root object
"""
kwargs = load_app_properties(kwds=kwargs)
# Create the Galaxy application unless passed in
if 'app' in kwargs:
app = kwargs.pop('app')
else:
try:
from galaxy.app import UniverseApplication
app = UniverseApplication(global_conf=global_conf, **kwargs)
except:
import traceback
traceback.print_exc()
sys.exit(1)
# Call app's shutdown method when the interpeter exits, this cleanly stops
# the various Galaxy application daemon threads
atexit.register(app.shutdown)
# Create the universe WSGI application
webapp = GalaxyWebApplication(app,
session_cookie='galaxysession',
name='galaxy')
webapp.add_ui_controllers('galaxy.webapps.galaxy.controllers', app)
# Force /history to go to /root/history -- needed since the tests assume this
webapp.add_route('/history', controller='root', action='history')
# Force /activate to go to the controller
webapp.add_route('/activate', controller='user', action='activate')
# These two routes handle our simple needs at the moment
webapp.add_route('/async/:tool_id/:data_id/:data_secret',
controller='async',
action='index',
tool_id=None,
data_id=None,
data_secret=None)
webapp.add_route('/:controller/:action', action='index')
webapp.add_route('/:action', controller='root', action='index')
# allow for subdirectories in extra_files_path
webapp.add_route('/datasets/:dataset_id/display/{filename:.+?}',
controller='dataset',
action='display',
dataset_id=None,
filename=None)
webapp.add_route('/datasets/:dataset_id/:action/:filename',
controller='dataset',
action='index',
dataset_id=None,
filename=None)
webapp.add_route(
'/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param',
controller='dataset',
action='display_application',
dataset_id=None,
user_id=None,
app_name=None,
link_name=None,
app_action=None,
action_param=None)
webapp.add_route('/u/:username/d/:slug/:filename',
controller='dataset',
action='display_by_username_and_slug',
filename=None)
webapp.add_route('/u/:username/p/:slug',
controller='page',
action='display_by_username_and_slug')
webapp.add_route('/u/:username/h/:slug',
controller='history',
action='display_by_username_and_slug')
webapp.add_route('/u/:username/w/:slug',
controller='workflow',
action='display_by_username_and_slug')
webapp.add_route('/u/:username/w/:slug/:format',
controller='workflow',
action='display_by_username_and_slug')
webapp.add_route('/u/:username/v/:slug',
controller='visualization',
action='display_by_username_and_slug')
webapp.add_route('/search', controller='search', action='index')
# TODO: Refactor above routes into external method to allow testing in
# isolation as well.
populate_api_routes(webapp, app)
# ==== Done
# Indicate that all configuration settings have been provided
webapp.finalize_config()
# Wrap the webapp in some useful middleware
if kwargs.get('middleware', True):
webapp = wrap_in_middleware(webapp, global_conf, **kwargs)
if asbool(kwargs.get('static_enabled', True)):
webapp = wrap_in_static(
webapp,
global_conf,
plugin_frameworks=[app.visualizations_registry],
**kwargs)
#webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=None, **kwargs )
if asbool(kwargs.get('pack_scripts', False)):
pack_scripts()
# Close any pooled database connections before forking
try:
galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose(
)
except:
pass
# Close any pooled database connections before forking
try:
galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose(
)
except:
pass
# Return
return webapp
def paste_app_factory( global_conf, **kwargs ):
"""
Return a wsgi application serving the root object
"""
kwargs = load_app_properties(
kwds=kwargs
)
# 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 )
galaxy.app.app = app
except:
import traceback
traceback.print_exc()
sys.exit( 1 )
# Call app's shutdown method when the interpeter exits, this cleanly stops
# the various Galaxy application daemon threads
atexit.register( app.shutdown )
# Create the universe WSGI application
webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' )
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
# Force /history to go to view of current
webapp.add_route( '/history', controller='history', action='view' )
# Force /activate to go to the controller
webapp.add_route( '/activate', controller='user', action='activate' )
webapp.add_route( '/login', controller='root', action='login' )
# These two routes handle our simple needs at the moment
webapp.add_route( '/async/{tool_id}/{data_id}/{data_secret}', controller='async', action='index', tool_id=None, data_id=None, data_secret=None )
webapp.add_route( '/{controller}/{action}', action='index' )
webapp.add_route( '/{action}', controller='root', action='index' )
# allow for subdirectories in extra_files_path
webapp.add_route( '/datasets/{dataset_id}/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None)
webapp.add_route( '/datasets/{dataset_id}/{action}/{filename}', controller='dataset', action='index', dataset_id=None, filename=None)
webapp.add_route( '/display_application/{dataset_id}/{app_name}/{link_name}/{user_id}/{app_action}/{action_param}/{action_param_extra:.+?}',
controller='dataset', action='display_application', dataset_id=None, user_id=None,
app_name=None, link_name=None, app_action=None, action_param=None, action_param_extra=None )
webapp.add_route( '/u/{username}/d/{slug}/{filename}', controller='dataset', action='display_by_username_and_slug', filename=None )
webapp.add_route( '/u/{username}/p/{slug}', controller='page', action='display_by_username_and_slug' )
webapp.add_route( '/u/{username}/h/{slug}', controller='history', action='display_by_username_and_slug' )
webapp.add_route( '/u/{username}/w/{slug}', controller='workflow', action='display_by_username_and_slug' )
webapp.add_route( '/u/{username}/w/{slug}/{format}', controller='workflow', action='display_by_username_and_slug' )
webapp.add_route( '/u/{username}/v/{slug}', controller='visualization', action='display_by_username_and_slug' )
webapp.add_route( '/search', controller='search', action='index' )
# TODO: Refactor above routes into external method to allow testing in
# isolation as well.
populate_api_routes( webapp, app )
# ==== Done
# Indicate that all configuration settings have been provided
webapp.finalize_config()
# Wrap the webapp in some useful middleware
if kwargs.get( 'middleware', True ):
webapp = wrap_in_middleware( webapp, global_conf, **kwargs )
if asbool( kwargs.get( 'static_enabled', True) ):
if process_is_uwsgi:
log.error("Static middleware is enabled in your configuration but this is a uwsgi process. Refusing to wrap in static middleware.")
else:
webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=[ app.visualizations_registry ], **kwargs )
# Close any pooled database connections before forking
try:
galaxy.model.mapping.metadata.bind.dispose()
except:
log.exception("Unable to dispose of pooled galaxy model database connections.")
try:
# This model may not actually be bound.
if galaxy.model.tool_shed_install.mapping.metadata.bind:
galaxy.model.tool_shed_install.mapping.metadata.bind.dispose()
except:
log.exception("Unable to dispose of pooled toolshed install model database connections.")
if not process_is_uwsgi:
postfork_setup()
# Return
return webapp
def app_factory( global_conf, **kwargs ):
"""
Return a wsgi application serving the root object
"""
# Create the Galaxy application unless passed in
if 'app' in kwargs:
app = kwargs.pop( 'app' )
else:
try:
from galaxy.app import UniverseApplication
app = UniverseApplication( global_conf = global_conf, **kwargs )
except:
import traceback
traceback.print_exc()
sys.exit( 1 )
# Call app's shutdown method when the interpeter exits, this cleanly stops
# the various Galaxy application daemon threads
atexit.register( app.shutdown )
# Create the universe WSGI application
webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' )
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
# Force /history to go to /root/history -- needed since the tests assume this
webapp.add_route( '/history', controller='root', action='history' )
# Force /activate to go to the controller
webapp.add_route( '/activate', controller='user', action='activate' )
# These two routes handle our simple needs at the moment
webapp.add_route( '/async/:tool_id/:data_id/:data_secret', controller='async', action='index', tool_id=None, data_id=None, data_secret=None )
webapp.add_route( '/:controller/:action', action='index' )
webapp.add_route( '/:action', controller='root', action='index' )
# allow for subdirectories in extra_files_path
webapp.add_route( '/datasets/:dataset_id/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None)
webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None)
webapp.add_route( '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param',
controller='dataset', action='display_application', dataset_id=None, user_id=None,
app_name = None, link_name = None, app_action = None, action_param = None )
webapp.add_route( '/u/:username/d/:slug/:filename', controller='dataset', action='display_by_username_and_slug', filename=None )
webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' )
webapp.add_route( '/u/:username/h/:slug', controller='history', action='display_by_username_and_slug' )
webapp.add_route( '/u/:username/w/:slug', controller='workflow', action='display_by_username_and_slug' )
webapp.add_route( '/u/:username/w/:slug/:format', controller='workflow', action='display_by_username_and_slug' )
webapp.add_route( '/u/:username/v/:slug', controller='visualization', action='display_by_username_and_slug' )
webapp.add_route( '/search', controller='search', action='index' )
# TODO: Refactor above routes into external method to allow testing in
# isolation as well.
populate_api_routes( webapp, app )
# ==== Done
# Indicate that all configuration settings have been provided
webapp.finalize_config()
# Wrap the webapp in some useful middleware
if kwargs.get( 'middleware', True ):
webapp = wrap_in_middleware( webapp, global_conf, **kwargs )
if asbool( kwargs.get( 'static_enabled', True ) ):
webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=[ app.visualizations_registry ], **kwargs )
#webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=None, **kwargs )
if asbool(kwargs.get('pack_scripts', False)):
pack_scripts()
# Close any pooled database connections before forking
try:
galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose()
except:
pass
# Close any pooled database connections before forking
try:
galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose()
except:
pass
# Return
return webapp
def paste_app_factory( global_conf, **kwargs ):
"""
Return a wsgi application serving the root object
"""
kwargs = load_app_properties(
kwds=kwargs
)
# 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 )
galaxy.app.app = app
except:
import traceback
traceback.print_exc()
sys.exit( 1 )
# Call app's shutdown method when the interpeter exits, this cleanly stops
# the various Galaxy application daemon threads
atexit.register( app.shutdown )
# Create the universe WSGI application
webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' )
# STANDARD CONTROLLER ROUTES
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
# Force /history to go to view of current
webapp.add_route( '/history', controller='history', action='view' )
webapp.add_route( '/history/view/{id}', controller='history', action='view' )
# Force /activate to go to the controller
webapp.add_route( '/activate', controller='user', action='activate' )
# These two routes handle our simple needs at the moment
webapp.add_route( '/async/{tool_id}/{data_id}/{data_secret}', controller='async', action='index', tool_id=None, data_id=None, data_secret=None )
webapp.add_route( '/{controller}/{action}', action='index' )
webapp.add_route( '/{action}', controller='root', action='index' )
# allow for subdirectories in extra_files_path
webapp.add_route( '/datasets/{dataset_id}/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None)
webapp.add_route( '/datasets/{dataset_id}/{action}/{filename}', controller='dataset', action='index', dataset_id=None, filename=None)
webapp.add_route( '/display_application/{dataset_id}/{app_name}/{link_name}/{user_id}/{app_action}/{action_param}/{action_param_extra:.+?}',
controller='dataset', action='display_application', dataset_id=None, user_id=None,
app_name=None, link_name=None, app_action=None, action_param=None, action_param_extra=None )
webapp.add_route( '/u/{username}/d/{slug}/{filename}', controller='dataset', action='display_by_username_and_slug', filename=None )
webapp.add_route( '/u/{username}/p/{slug}', controller='page', action='display_by_username_and_slug' )
webapp.add_route( '/u/{username}/h/{slug}', controller='history', action='display_by_username_and_slug' )
webapp.add_route( '/u/{username}/w/{slug}', controller='workflow', action='display_by_username_and_slug' )
webapp.add_route( '/u/{username}/w/{slug}/{format}', controller='workflow', action='display_by_username_and_slug' )
webapp.add_route( '/u/{username}/v/{slug}', controller='visualization', action='display_by_username_and_slug' )
# TODO: Refactor above routes into external method to allow testing in
# isolation as well.
populate_api_routes( webapp, app )
# CLIENTSIDE ROUTES
# The following are routes that are handled completely on the clientside.
# The following routes don't bootstrap any information, simply provide the
# base analysis interface at which point the application takes over.
webapp.add_client_route( '/tours' )
webapp.add_client_route( '/tours/{tour_id}' )
webapp.add_client_route( '/user' )
webapp.add_client_route( '/user/{form_id}' )
webapp.add_client_route( '/custom_builds' )
# ==== Done
# Indicate that all configuration settings have been provided
webapp.finalize_config()
# Wrap the webapp in some useful middleware
if kwargs.get( 'middleware', True ):
webapp = wrap_in_middleware(webapp, global_conf, app.application_stack, **kwargs)
if asbool( kwargs.get( 'static_enabled', True) ):
webapp = wrap_if_allowed(webapp, app.application_stack, wrap_in_static,
args=(global_conf,),
kwargs=dict(plugin_frameworks=[app.visualizations_registry], **kwargs))
# Close any pooled database connections before forking
try:
galaxy.model.mapping.metadata.bind.dispose()
except:
log.exception("Unable to dispose of pooled galaxy model database connections.")
try:
# This model may not actually be bound.
if galaxy.model.tool_shed_install.mapping.metadata.bind:
galaxy.model.tool_shed_install.mapping.metadata.bind.dispose()
except:
log.exception("Unable to dispose of pooled toolshed install model database connections.")
app.application_stack.register_postfork_function(postfork_setup)
for th in threading.enumerate():
if th.is_alive():
log.debug("Prior to webapp return, Galaxy thread %s is alive.", th)
# Return
return webapp