def app_factory( global_conf, **kwargs ):
"""Return a wsgi application serving the root object"""
# Create the Galaxy application unless passed in
kwargs = load_app_properties(
kwds=kwargs
)
if 'app' in kwargs:
app = kwargs.pop( 'app' )
else:
from galaxy.webapps.reports.app import UniverseApplication
app = UniverseApplication( global_conf=global_conf, **kwargs )
atexit.register( app.shutdown )
# Create the universe WSGI application
webapp = ReportsWebApplication( app, session_cookie='galaxyreportssession', name="reports" )
add_ui_controllers( webapp, app )
# These two routes handle our simple needs at the moment
webapp.add_route( '/{controller}/{action}', controller="root", action='index' )
webapp.add_route( '/{action}', controller='root', action='index' )
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, **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.")
# Return
return webapp
def app_factory( global_conf, **kwargs ):
"""Return a wsgi application serving the root object"""
# Create the Galaxy application unless passed in
kwargs = load_app_properties(
kwds=kwargs
)
if 'app' in kwargs:
app = kwargs.pop( 'app' )
else:
from galaxy.webapps.reports.app import UniverseApplication
app = UniverseApplication( global_conf=global_conf, **kwargs )
atexit.register( app.shutdown )
# Create the universe WSGI application
webapp = ReportsWebApplication( app, session_cookie='galaxyreportssession', name="reports" )
add_ui_controllers( webapp, app )
# These two routes handle our simple needs at the moment
webapp.add_route( '/{controller}/{action}', controller="root", action='index' )
webapp.add_route( '/{action}', controller='root', action='index' )
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, **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.")
# Return
return webapp
def app_factory( global_conf, **kwargs ):
"""Return a wsgi application serving the root object"""
# Create the Galaxy tool shed application unless passed in
kwargs = load_app_properties(
kwds=kwargs,
config_prefix='TOOL_SHED_CONFIG_'
)
if 'app' in kwargs:
app = kwargs.pop( 'app' )
else:
try:
from galaxy.webapps.tool_shed.app import UniverseApplication
app = UniverseApplication( global_conf=global_conf, **kwargs )
except:
import traceback
import sys
traceback.print_exc()
sys.exit( 1 )
atexit.register( app.shutdown )
# Create the universe WSGI application
webapp = CommunityWebApplication( app, session_cookie='galaxycommunitysession', name="tool_shed" )
add_ui_controllers( webapp, app )
webapp.add_route( '/view/{owner}', controller='repository', action='sharable_owner' )
webapp.add_route( '/view/{owner}/{name}', controller='repository', action='sharable_repository' )
webapp.add_route( '/view/{owner}/{name}/{changeset_revision}', controller='repository', action='sharable_repository_revision' )
# Handle displaying tool help images and README file images for tools contained in repositories.
webapp.add_route( '/repository/static/images/{repository_id}/{image_file:.+?}',
controller='repository',
action='display_image_in_repository',
repository_id=None,
image_file=None )
webapp.add_route( '/{controller}/{action}', action='index' )
webapp.add_route( '/{action}', controller='repository', action='index' )
webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' )
# Add the web API. # A good resource for RESTful services - http://routes.readthedocs.org/en/latest/restful.html
webapp.add_api_controllers( 'galaxy.webapps.tool_shed.api', app )
webapp.mapper.connect( 'api_key_retrieval',
'/api/authenticate/baseauth/',
controller='authenticate',
action='get_tool_shed_api_key',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'group',
'/api/groups/',
controller='groups',
action='index',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'group',
'/api/groups/',
controller='groups',
action='create',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'group',
'/api/groups/{encoded_id}',
controller='groups',
action='show',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.resource( 'category',
'categories',
controller='categories',
name_prefix='category_',
path_prefix='/api',
parent_resources=dict( member_name='category', collection_name='categories' ) )
webapp.mapper.resource( 'repository',
'repositories',
controller='repositories',
collection={ 'add_repository_registry_entry' : 'POST',
'get_repository_revision_install_info' : 'GET',
'get_ordered_installable_revisions' : 'GET',
'remove_repository_registry_entry' : 'POST',
'repository_ids_for_setting_metadata' : 'GET',
'reset_metadata_on_repositories' : 'POST',
'reset_metadata_on_repository' : 'POST' },
name_prefix='repository_',
path_prefix='/api',
new={ 'import_capsule' : 'POST' },
parent_resources=dict( member_name='repository', collection_name='repositories' ) )
webapp.mapper.resource( 'repository_revision',
'repository_revisions',
member={ 'repository_dependencies' : 'GET',
'export' : 'POST' },
controller='repository_revisions',
name_prefix='repository_revision_',
path_prefix='/api',
parent_resources=dict( member_name='repository_revision', collection_name='repository_revisions' ) )
webapp.mapper.resource( 'user',
'users',
controller='users',
name_prefix='user_',
path_prefix='/api',
parent_resources=dict( member_name='user', collection_name='users' ) )
webapp.mapper.connect( 'update_repository',
'/api/repositories/{id}',
controller='repositories',
action='update',
conditions=dict( method=[ "PATCH", "PUT" ] ) )
webapp.mapper.connect( 'repository_create_changeset_revision',
'/api/repositories/{id}/changeset_revision',
controller='repositories',
action='create_changeset_revision',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'create_repository',
'/api/repositories',
controller='repositories',
action='create',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'tools',
'/api/tools',
controller='tools',
action='index',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( "version", "/api/version", controller="configuration", action="version", conditions=dict( method=[ "GET" ] ) )
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, **kwargs )
# Close any pooled database connections before forking
try:
galaxy.webapps.tool_shed.model.mapping.metadata.bind.dispose()
except:
log.exception("Unable to dispose of pooled tool_shed model database connections.")
# 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')
# 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"""
# Create the Galaxy tool shed application unless passed in
if 'app' in kwargs:
app = kwargs.pop( 'app' )
else:
try:
from galaxy.webapps.tool_shed.app import UniverseApplication
app = UniverseApplication( global_conf=global_conf, **kwargs )
except:
import traceback, sys
traceback.print_exc()
sys.exit( 1 )
atexit.register( app.shutdown )
# Create the universe WSGI application
webapp = CommunityWebApplication( app, session_cookie='galaxycommunitysession', name="tool_shed" )
add_ui_controllers( webapp, app )
webapp.add_route( '/view/{owner}', controller='repository', action='sharable_owner' )
webapp.add_route( '/view/{owner}/{name}', controller='repository', action='sharable_repository' )
webapp.add_route( '/view/{owner}/{name}/{changeset_revision}', controller='repository', action='sharable_repository_revision' )
# Handle displaying tool help images and README file images for tools contained in repositories.
webapp.add_route( '/repository/static/images/:repository_id/:image_file',
controller='repository',
action='display_image_in_repository',
repository_id=None,
image_file=None )
webapp.add_route( '/:controller/:action', action='index' )
webapp.add_route( '/:action', controller='repository', action='index' )
webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' )
# Add the web API. # A good resource for RESTful services - http://routes.readthedocs.org/en/latest/restful.html
webapp.add_api_controllers( 'galaxy.webapps.tool_shed.api', app )
webapp.mapper.connect( 'api_key_retrieval',
'/api/authenticate/baseauth/',
controller='authenticate',
action='get_tool_shed_api_key',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'repo_search',
'/api/search/',
controller='search',
action='search',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.resource( 'category',
'categories',
controller='categories',
name_prefix='category_',
path_prefix='/api',
parent_resources=dict( member_name='category', collection_name='categories' ) )
webapp.mapper.resource( 'repository',
'repositories',
controller='repositories',
collection={ 'add_repository_registry_entry' : 'POST',
'get_repository_revision_install_info' : 'GET',
'get_ordered_installable_revisions' : 'GET',
'remove_repository_registry_entry' : 'POST',
'repository_ids_for_setting_metadata' : 'GET',
'reset_metadata_on_repositories' : 'POST',
'reset_metadata_on_repository' : 'POST' },
name_prefix='repository_',
path_prefix='/api',
new={ 'import_capsule' : 'POST' },
parent_resources=dict( member_name='repository', collection_name='repositories' ) )
webapp.mapper.resource( 'repository_revision',
'repository_revisions',
member={ 'repository_dependencies' : 'GET',
'export' : 'POST' },
controller='repository_revisions',
name_prefix='repository_revision_',
path_prefix='/api',
parent_resources=dict( member_name='repository_revision', collection_name='repository_revisions' ) )
webapp.mapper.resource( 'user',
'users',
controller='users',
name_prefix='user_',
path_prefix='/api',
parent_resources=dict( member_name='user', collection_name='users' ) )
webapp.mapper.connect( 'repository_create_changeset_revision',
'/api/repositories/:id/changeset_revision',
controller='repositories',
action='create_changeset_revision',
conditions=dict( method=[ "POST" ] ) )
webapp.finalize_config()
# Wrap the webapp in some useful middleware
if kwargs.get( 'middleware', True ):
webapp = wrap_in_middleware( webapp, global_conf, **kwargs )
# TEST FOR UWSGI -- TODO save this somewhere so we only have to do it once.
is_uwsgi = False
try:
# The uwsgi module is automatically injected by the parent uwsgi
# process and only exists that way. If anything works, this is a
# uwsgi-managed process.
import uwsgi
is_uwsgi = uwsgi.numproc
is_uwsgi = True
except ImportError:
# This is not a uwsgi process, or something went horribly wrong.
pass
if asbool( kwargs.get( 'static_enabled', True) ):
if 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, **kwargs )
# Close any pooled database connections before forking
try:
galaxy.webapps.tool_shed.model.mapping.metadata.bind.dispose()
except:
log.exception("Unable to dispose of pooled tool_shed model database connections.")
# Return
return webapp
def app_factory( global_conf, **kwargs ):
"""Return a wsgi application serving the root object"""
# Create the Galaxy tool shed application unless passed in
if 'app' in kwargs:
app = kwargs.pop( 'app' )
else:
try:
from galaxy.webapps.tool_shed.app import UniverseApplication
app = UniverseApplication( global_conf=global_conf, **kwargs )
except:
import traceback
import sys
traceback.print_exc()
sys.exit( 1 )
atexit.register( app.shutdown )
# Create the universe WSGI application
webapp = CommunityWebApplication( app, session_cookie='galaxycommunitysession', name="tool_shed" )
add_ui_controllers( webapp, app )
webapp.add_route( '/view/{owner}', controller='repository', action='sharable_owner' )
webapp.add_route( '/view/{owner}/{name}', controller='repository', action='sharable_repository' )
webapp.add_route( '/view/{owner}/{name}/{changeset_revision}', controller='repository', action='sharable_repository_revision' )
# Handle displaying tool help images and README file images for tools contained in repositories.
webapp.add_route( '/repository/static/images/{repository_id}/{image_file:.+?}',
controller='repository',
action='display_image_in_repository',
repository_id=None,
image_file=None )
webapp.add_route( '/{controller}/{action}', action='index' )
webapp.add_route( '/{action}', controller='repository', action='index' )
webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' )
# Add the web API. # A good resource for RESTful services - http://routes.readthedocs.org/en/latest/restful.html
webapp.add_api_controllers( 'galaxy.webapps.tool_shed.api', app )
webapp.mapper.connect( 'api_key_retrieval',
'/api/authenticate/baseauth/',
controller='authenticate',
action='get_tool_shed_api_key',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'group',
'/api/groups/',
controller='groups',
action='index',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'group',
'/api/groups/',
controller='groups',
action='create',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'group',
'/api/groups/{encoded_id}',
controller='groups',
action='show',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.resource( 'category',
'categories',
controller='categories',
name_prefix='category_',
path_prefix='/api',
parent_resources=dict( member_name='category', collection_name='categories' ) )
webapp.mapper.resource( 'repository',
'repositories',
controller='repositories',
collection={ 'add_repository_registry_entry' : 'POST',
'get_repository_revision_install_info' : 'GET',
'get_ordered_installable_revisions' : 'GET',
'remove_repository_registry_entry' : 'POST',
'repository_ids_for_setting_metadata' : 'GET',
'reset_metadata_on_repositories' : 'POST',
'reset_metadata_on_repository' : 'POST' },
name_prefix='repository_',
path_prefix='/api',
new={ 'import_capsule' : 'POST' },
parent_resources=dict( member_name='repository', collection_name='repositories' ) )
webapp.mapper.resource( 'repository_revision',
'repository_revisions',
member={ 'repository_dependencies' : 'GET',
'export' : 'POST' },
controller='repository_revisions',
name_prefix='repository_revision_',
path_prefix='/api',
parent_resources=dict( member_name='repository_revision', collection_name='repository_revisions' ) )
webapp.mapper.resource( 'user',
'users',
controller='users',
name_prefix='user_',
path_prefix='/api',
parent_resources=dict( member_name='user', collection_name='users' ) )
webapp.mapper.connect( 'update_repository',
'/api/repositories/{id}',
controller='repositories',
action='update',
conditions=dict( method=[ "PATCH", "PUT" ] ) )
webapp.mapper.connect( 'repository_create_changeset_revision',
'/api/repositories/{id}/changeset_revision',
controller='repositories',
action='create_changeset_revision',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'create_repository',
'/api/repositories',
controller='repositories',
action='create',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'tools',
'/api/tools',
controller='tools',
action='index',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( "version", "/api/version", controller="configuration", action="version", conditions=dict( method=[ "GET" ] ) )
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, **kwargs )
# Close any pooled database connections before forking
try:
galaxy.webapps.tool_shed.model.mapping.metadata.bind.dispose()
except:
log.exception("Unable to dispose of pooled tool_shed model database connections.")
# 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 app_factory(global_conf, **kwargs):
"""Return a wsgi application serving the root object"""
# Create the Galaxy tool shed application unless passed in
if 'app' in kwargs:
app = kwargs.pop('app')
else:
try:
from galaxy.webapps.tool_shed.app import UniverseApplication
app = UniverseApplication(global_conf=global_conf, **kwargs)
except:
import traceback, sys
traceback.print_exc()
sys.exit(1)
atexit.register(app.shutdown)
# Create the universe WSGI application
webapp = CommunityWebApplication(app,
session_cookie='galaxycommunitysession',
name="tool_shed")
add_ui_controllers(webapp, app)
webapp.add_route('/view/{owner}',
controller='repository',
action='sharable_owner')
webapp.add_route('/view/{owner}/{name}',
controller='repository',
action='sharable_repository')
webapp.add_route('/view/{owner}/{name}/{changeset_revision}',
controller='repository',
action='sharable_repository_revision')
# Handle displaying tool help images and README file images for tools contained in repositories.
webapp.add_route('/repository/static/images/:repository_id/:image_file',
controller='repository',
action='display_image_in_repository',
repository_id=None,
image_file=None)
webapp.add_route('/:controller/:action', action='index')
webapp.add_route('/:action', controller='repository', action='index')
webapp.add_route('/repos/*path_info',
controller='hg',
action='handle_request',
path_info='/')
# Add the web API. # A good resource for RESTful services - http://routes.readthedocs.org/en/latest/restful.html
webapp.add_api_controllers('galaxy.webapps.tool_shed.api', app)
webapp.mapper.connect('api_key_retrieval',
'/api/authenticate/baseauth/',
controller='authenticate',
action='get_tool_shed_api_key',
conditions=dict(method=["GET"]))
webapp.mapper.connect('repo_search',
'/api/search/',
controller='search',
action='search',
conditions=dict(method=["GET"]))
webapp.mapper.resource('category',
'categories',
controller='categories',
name_prefix='category_',
path_prefix='/api',
parent_resources=dict(member_name='category',
collection_name='categories'))
webapp.mapper.resource('repository',
'repositories',
controller='repositories',
collection={
'add_repository_registry_entry': 'POST',
'get_repository_revision_install_info': 'GET',
'get_ordered_installable_revisions': 'GET',
'remove_repository_registry_entry': 'POST',
'repository_ids_for_setting_metadata': 'GET',
'reset_metadata_on_repositories': 'POST',
'reset_metadata_on_repository': 'POST'
},
name_prefix='repository_',
path_prefix='/api',
new={'import_capsule': 'POST'},
parent_resources=dict(
member_name='repository',
collection_name='repositories'))
webapp.mapper.resource('repository_revision',
'repository_revisions',
member={
'repository_dependencies': 'GET',
'export': 'POST'
},
controller='repository_revisions',
name_prefix='repository_revision_',
path_prefix='/api',
parent_resources=dict(
member_name='repository_revision',
collection_name='repository_revisions'))
webapp.mapper.resource('user',
'users',
controller='users',
name_prefix='user_',
path_prefix='/api',
parent_resources=dict(member_name='user',
collection_name='users'))
webapp.mapper.connect('repository_create_changeset_revision',
'/api/repositories/:id/changeset_revision',
controller='repositories',
action='create_changeset_revision',
conditions=dict(method=["POST"]))
webapp.mapper.connect('create_repository',
'/api/repositories',
controller='repositories',
action='create',
conditions=dict(method=["POST"]))
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, **kwargs)
# Close any pooled database connections before forking
try:
galaxy.webapps.tool_shed.model.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
def app_factory(global_conf, **kwargs):
"""Return a wsgi application serving the root object"""
# Create the Galaxy tool shed application unless passed in
if 'app' in kwargs:
app = kwargs.pop('app')
else:
try:
from galaxy.webapps.tool_shed.app import UniverseApplication
app = UniverseApplication(global_conf=global_conf, **kwargs)
except:
import traceback, sys
traceback.print_exc()
sys.exit(1)
atexit.register(app.shutdown)
# Create the universe WSGI application
webapp = CommunityWebApplication(app,
session_cookie='galaxycommunitysession',
name="tool_shed")
add_ui_controllers(webapp, app)
webapp.add_route('/view/{owner}',
controller='repository',
action='sharable_owner')
webapp.add_route('/view/{owner}/{name}',
controller='repository',
action='sharable_repository')
webapp.add_route('/view/{owner}/{name}/{changeset_revision}',
controller='repository',
action='sharable_repository_revision')
# Handle displaying tool help images and README file images for tools contained in repositories.
webapp.add_route('/repository/static/images/:repository_id/:image_file',
controller='repository',
action='display_image_in_repository',
repository_id=None,
image_file=None)
webapp.add_route('/:controller/:action', action='index')
webapp.add_route('/:action', controller='repository', action='index')
webapp.add_route('/repos/*path_info',
controller='hg',
action='handle_request',
path_info='/')
# Add the web API. # A good resource for RESTful services - http://routes.readthedocs.org/en/latest/restful.html
webapp.add_api_controllers('galaxy.webapps.tool_shed.api', app)
webapp.mapper.connect('api_key_retrieval',
'/api/authenticate/baseauth/',
controller='authenticate',
action='get_tool_shed_api_key',
conditions=dict(method=["GET"]))
webapp.mapper.connect('repo_search',
'/api/search/',
controller='search',
action='search',
conditions=dict(method=["GET"]))
webapp.mapper.resource('category',
'categories',
controller='categories',
name_prefix='category_',
path_prefix='/api',
parent_resources=dict(member_name='category',
collection_name='categories'))
webapp.mapper.resource('repository',
'repositories',
controller='repositories',
collection={
'add_repository_registry_entry': 'POST',
'get_repository_revision_install_info': 'GET',
'get_ordered_installable_revisions': 'GET',
'remove_repository_registry_entry': 'POST',
'repository_ids_for_setting_metadata': 'GET',
'reset_metadata_on_repositories': 'POST',
'reset_metadata_on_repository': 'POST'
},
name_prefix='repository_',
path_prefix='/api',
new={'import_capsule': 'POST'},
parent_resources=dict(
member_name='repository',
collection_name='repositories'))
webapp.mapper.resource('repository_revision',
'repository_revisions',
member={
'repository_dependencies': 'GET',
'export': 'POST'
},
controller='repository_revisions',
name_prefix='repository_revision_',
path_prefix='/api',
parent_resources=dict(
member_name='repository_revision',
collection_name='repository_revisions'))
webapp.mapper.resource('user',
'users',
controller='users',
name_prefix='user_',
path_prefix='/api',
parent_resources=dict(member_name='user',
collection_name='users'))
webapp.mapper.connect('repository_create_changeset_revision',
'/api/repositories/:id/changeset_revision',
controller='repositories',
action='create_changeset_revision',
conditions=dict(method=["POST"]))
webapp.finalize_config()
# Wrap the webapp in some useful middleware
if kwargs.get('middleware', True):
webapp = wrap_in_middleware(webapp, global_conf, **kwargs)
# TEST FOR UWSGI -- TODO save this somewhere so we only have to do it once.
is_uwsgi = False
try:
# The uwsgi module is automatically injected by the parent uwsgi
# process and only exists that way. If anything works, this is a
# uwsgi-managed process.
import uwsgi
is_uwsgi = uwsgi.numproc
is_uwsgi = True
except ImportError:
# This is not a uwsgi process, or something went horribly wrong.
pass
if asbool(kwargs.get('static_enabled', True)):
if 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, **kwargs)
# Close any pooled database connections before forking
try:
galaxy.webapps.tool_shed.model.mapping.metadata.bind.dispose()
except:
log.exception(
"Unable to dispose of pooled tool_shed model database connections."
)
# Return
return webapp
