def app_factory(global_conf, load_app_kwds=None, **kwargs):
"""Return a wsgi application serving the root object"""
# Create the Galaxy application unless passed in
load_app_kwds = load_app_kwds or {}
kwargs = load_app_properties(kwds=kwargs, **load_app_kwds)
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, app.application_stack,
**kwargs)
if asbool(kwargs.get('static_enabled', True)):
webapp = wrap_if_allowed(webapp,
app.application_stack,
build_url_map,
args=(global_conf, ),
kwargs=kwargs)
return webapp
def app_factory(global_conf, load_app_kwds={}, **kwargs):
"""Return a wsgi application serving the root object"""
# Create the Galaxy application unless passed in
kwargs = load_app_properties(kwds=kwargs, **load_app_kwds)
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, 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=kwargs)
# Close any pooled database connections before forking
try:
galaxy.model.mapping.metadata.bind.dispose()
except Exception:
log.exception(
"Unable to dispose of pooled galaxy model database connections.")
# Return
return webapp
def app_factory(global_conf, load_app_kwds=None, **kwargs):
"""Return a wsgi application serving the root object"""
# Create the Galaxy tool shed application unless passed in
load_app_kwds = load_app_kwds or {}
kwargs = load_app_properties(kwds=kwargs,
config_prefix='TOOL_SHED_CONFIG_',
**load_app_kwds)
if 'app' in kwargs:
app = kwargs.pop('app')
else:
try:
from tool_shed.webapp.app import UniverseApplication
app = UniverseApplication(global_conf=global_conf, **kwargs)
except Exception:
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')
# Enable 'hg clone' functionality on repos by letting hgwebapp handle the request
webapp.add_route('/repos/*path_info',
controller='hg',
action='handle_request',
path_info='/')
# Add the web API. # A good resource for RESTful services - https://routes.readthedocs.io/en/latest/restful.html
webapp.add_api_controllers('tool_shed.webapp.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.connect('repositories_in_category',
'/api/categories/{category_id}/repositories',
controller='categories',
action='get_repositories',
conditions=dict(method=["GET"]))
webapp.mapper.connect('show_updates_for_repository',
'/api/repositories/updates',
controller='repositories',
action='updates',
conditions=dict(method=["GET"]))
webapp.mapper.resource('repository',
'repositories',
controller='repositories',
collection={
'add_repository_registry_entry': 'POST',
'get_repository_revision_install_info': 'GET',
'get_ordered_installable_revisions': 'GET',
'get_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',
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('repository_get_metadata',
'/api/repositories/{id}/metadata',
controller='repositories',
action='metadata',
conditions=dict(method=["GET"]))
webapp.mapper.connect('repository_show_tools',
'/api/repositories/{id}/{changeset}/show_tools',
controller='repositories',
action='show_tools',
conditions=dict(method=["GET"]))
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('json',
'/api/tools/json',
controller='tools',
action='json',
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, 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=kwargs)
# Close any pooled database connections before forking
try:
tool_shed.webapp.model.mapping.metadata.bind.dispose()
except Exception:
log.exception(
"Unable to dispose of pooled tool_shed model database connections."
)
# Return
return webapp