def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
"""Based on the configuration wrap `app` in a set of common and useful middleware."""
stack = application_stack
# Merge the global and local configurations
conf = global_conf.copy()
conf.update(local_conf)
debug = asbool(conf.get('debug', False))
# First put into place httpexceptions, which must be most closely
# wrapped around the application (it can interact poorly with
# other middleware):
app = wrap_if_allowed(app, stack, httpexceptions.make_middleware, name='paste.httpexceptions', args=(conf,))
# The recursive middleware allows for including requests in other
# requests or forwarding of requests, all on the server side.
if asbool(conf.get('use_recursive', True)):
from paste import recursive
app = wrap_if_allowed(app, stack, recursive.RecursiveMiddleware, args=(conf,))
# Various debug middleware that can only be turned on if the debug
# flag is set, either because they are insecure or greatly hurt
# performance
if debug:
# Middleware to check for WSGI compliance
if asbool(conf.get('use_lint', True)):
from paste import lint
app = wrap_if_allowed(app, stack, lint.make_middleware, name='paste.lint', args=(conf,))
# Middleware to run the python profiler on each request
if asbool(conf.get('use_profile', False)):
import profile
app = wrap_if_allowed(app, stack, profile.ProfileMiddleware, args=(conf,))
# Middleware that intercepts print statements and shows them on the
# returned page
if asbool(conf.get('use_printdebug', True)):
from paste.debug import prints
app = wrap_if_allowed(app, stack, prints.PrintDebugMiddleware, args=(conf,))
if debug and asbool(conf.get('use_interactive', False)):
# Interactive exception debugging, scary dangerous if publicly
# accessible, if not enabled we'll use the regular error printing
# middleware.
try:
from weberror import evalexception
app = wrap_if_allowed_or_fail(app, stack, evalexception.EvalException,
args=(conf,),
kwargs=dict(templating_formatters=build_template_error_formatters()))
except MiddlewareWrapUnsupported as exc:
log.warning(str(exc))
import galaxy.web.framework.middleware.error
app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
else:
# Not in interactive debug mode, just use the regular error middleware
import galaxy.web.framework.middleware.error
app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
# Transaction logging (apache access.log style)
if asbool(conf.get('use_translogger', True)):
from paste.translogger import TransLogger
app = wrap_if_allowed(app, stack, TransLogger)
# X-Forwarded-Host handling
from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware
app = wrap_if_allowed(app, stack, XForwardedHostMiddleware)
return app
def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
"""Based on the configuration wrap `app` in a set of common and useful middleware."""
stack = application_stack
# Merge the global and local configurations
conf = global_conf.copy()
conf.update(local_conf)
debug = asbool(conf.get('debug', False))
# First put into place httpexceptions, which must be most closely
# wrapped around the application (it can interact poorly with
# other middleware):
app = wrap_if_allowed(app, stack, httpexceptions.make_middleware, name='paste.httpexceptions', args=(conf,))
# The recursive middleware allows for including requests in other
# requests or forwarding of requests, all on the server side.
if asbool(conf.get('use_recursive', True)):
from paste import recursive
app = wrap_if_allowed(app, stack, recursive.RecursiveMiddleware, args=(conf,))
# Various debug middleware that can only be turned on if the debug
# flag is set, either because they are insecure or greatly hurt
# performance
if debug:
# Middleware to check for WSGI compliance
if asbool(conf.get('use_lint', True)):
from paste import lint
app = wrap_if_allowed(app, stack, lint.make_middleware, name='paste.lint', args=(conf,))
# Middleware to run the python profiler on each request
if asbool(conf.get('use_profile', False)):
import profile
app = wrap_if_allowed(app, stack, profile.ProfileMiddleware, args=(conf,))
# Middleware that intercepts print statements and shows them on the
# returned page
if asbool(conf.get('use_printdebug', True)):
from paste.debug import prints
app = wrap_if_allowed(app, stack, prints.PrintDebugMiddleware, args=(conf,))
if debug and asbool(conf.get('use_interactive', False)):
# Interactive exception debugging, scary dangerous if publicly
# accessible, if not enabled we'll use the regular error printing
# middleware.
try:
from weberror import evalexception
app = wrap_if_allowed_or_fail(app, stack, evalexception.EvalException,
args=(conf,),
kwargs=dict(templating_formatters=build_template_error_formatters()))
except MiddlewareWrapUnsupported as exc:
log.warning(str(exc))
import galaxy.web.framework.middleware.error
app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
else:
# Not in interactive debug mode, just use the regular error middleware
import galaxy.web.framework.middleware.error
app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
# Transaction logging (apache access.log style)
if asbool(conf.get('use_translogger', True)):
from paste.translogger import TransLogger
app = wrap_if_allowed(app, stack, TransLogger)
# X-Forwarded-Host handling
from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware
app = wrap_if_allowed(app, stack, XForwardedHostMiddleware)
return app
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:
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 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={}, **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_',
**load_app_kwds)
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 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('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.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',
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('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:
galaxy.webapps.tool_shed.model.mapping.metadata.bind.dispose()
except Exception:
log.exception(
"Unable to dispose of pooled tool_shed model database connections."
)
# Return
return webapp
def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
"""Based on the configuration wrap `app` in a set of common and useful middleware."""
stack = application_stack
# Merge the global and local configurations
conf = global_conf.copy()
conf.update(local_conf)
debug = asbool(conf.get('debug', False))
interactive = asbool(conf.get('use_interactive', False))
# First put into place httpexceptions, which must be most closely
# wrapped around the application (it can interact poorly with
# other middleware):
app = wrap_if_allowed(app,
stack,
httpexceptions.make_middleware,
name='paste.httpexceptions',
args=(conf, ))
# Create a separate mapper for redirects to prevent conflicts.
redirect_mapper = routes.Mapper()
redirect_mapper = _map_redirects(redirect_mapper)
# Load the Routes middleware which we use for redirecting
app = wrap_if_allowed(app,
stack,
RoutesMiddleware,
args=(redirect_mapper, ))
# If we're using remote_user authentication, add middleware that
# protects Galaxy from improperly configured authentication in the
# upstream server
if asbool(conf.get('use_remote_user', False)):
from galaxy.webapps.tool_shed.framework.middleware.remoteuser import RemoteUser
app = wrap_if_allowed(
app,
stack,
RemoteUser,
kwargs=dict(
maildomain=conf.get('remote_user_maildomain', None),
display_servers=util.listify(conf.get('display_servers', '')),
admin_users=conf.get('admin_users', '').split(','),
remote_user_header=conf.get('remote_user_header',
'HTTP_REMOTE_USER'),
remote_user_secret_header=conf.get('remote_user_secret', None),
normalize_remote_user_email=conf.get(
'normalize_remote_user_email', False)))
# The recursive middleware allows for including requests in other
# requests or forwarding of requests, all on the server side.
if asbool(conf.get('use_recursive', True)):
from paste import recursive
app = wrap_if_allowed(app,
stack,
recursive.RecursiveMiddleware,
args=(conf, ))
# Transaction logging (apache access.log style)
if asbool(conf.get('use_translogger', True)):
from paste.translogger import TransLogger
app = wrap_if_allowed(app, stack, TransLogger)
# If sentry logging is enabled, log here before propogating up to
# the error middleware
# TODO sentry config is duplicated between tool_shed/galaxy, refactor this.
sentry_dsn = conf.get('sentry_dsn', None)
if sentry_dsn:
from galaxy.web.framework.middleware.sentry import Sentry
app = wrap_if_allowed(app, stack, Sentry, args=(sentry_dsn, ))
# X-Forwarded-Host handling
from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware
app = wrap_if_allowed(app, stack, XForwardedHostMiddleware)
# Various debug middleware that can only be turned on if the debug
# flag is set, either because they are insecure or greatly hurt
# performance.
if debug:
# Middleware to check for WSGI compliance
if asbool(conf.get('use_lint', True)):
from paste import lint
app = wrap_if_allowed(app,
stack,
lint.make_middleware,
name='paste.lint',
args=(conf, ))
# Middleware to run the python profiler on each request
if asbool(conf.get('use_profile', False)):
from paste.debug import profile
app = wrap_if_allowed(app,
stack,
profile.ProfileMiddleware,
args=(conf, ))
if interactive:
# Interactive exception debugging, scary dangerous if publicly
# accessible, if not enabled we'll use the regular error printing
# middleware.
try:
from weberror import evalexception
app = wrap_if_allowed_or_fail(
app,
stack,
evalexception.EvalException,
args=(conf, ),
kwargs=dict(
templating_formatters=build_template_error_formatters(
)))
except MiddlewareWrapUnsupported as exc:
log.warning(util.unicodify(exc))
import galaxy.web.framework.middleware.error
app = wrap_if_allowed(
app,
stack,
galaxy.web.framework.middleware.error.ErrorMiddleware,
args=(conf, ))
else:
# Not in interactive debug mode, just use the regular error middleware
import galaxy.web.framework.middleware.error
app = wrap_if_allowed(
app,
stack,
galaxy.web.framework.middleware.error.ErrorMiddleware,
args=(conf, ))
return app
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 wrap_in_middleware( app, global_conf, application_stack, **local_conf ):
"""
Based on the configuration wrap `app` in a set of common and useful
middleware.
"""
webapp = app
stack = application_stack
# Merge the global and local configurations
conf = global_conf.copy()
conf.update(local_conf)
debug = asbool( conf.get( 'debug', False ) )
# First put into place httpexceptions, which must be most closely
# wrapped around the application (it can interact poorly with
# other middleware):
app = wrap_if_allowed( app, stack, httpexceptions.make_middleware, name='paste.httpexceptions', args=(conf,) )
# Statsd request timing and profiling
statsd_host = conf.get('statsd_host', None)
if statsd_host:
from galaxy.web.framework.middleware.statsd import StatsdMiddleware
app = wrap_if_allowed( app, stack, StatsdMiddleware,
args=( statsd_host,
conf.get('statsd_port', 8125),
conf.get('statsd_prefix', 'galaxy') ) )
log.debug( "Enabling 'statsd' middleware" )
# graphite request timing and profiling
graphite_host = conf.get('graphite_host', None)
if graphite_host:
from galaxy.web.framework.middleware.graphite import GraphiteMiddleware
app = wrap_if_allowed( app, stack, GraphiteMiddleware,
args=( graphite_host,
conf.get('graphite_port', 2003),
conf.get('graphite_prefix', 'galaxy') ) )
log.debug( "Enabling 'graphite' middleware" )
# If we're using remote_user authentication, add middleware that
# protects Galaxy from improperly configured authentication in the
# upstream server
single_user = conf.get( 'single_user', None )
use_remote_user = asbool(conf.get( 'use_remote_user', False )) or single_user
if use_remote_user:
from galaxy.web.framework.middleware.remoteuser import RemoteUser
app = wrap_if_allowed( app, stack, RemoteUser,
kwargs=dict(
maildomain=conf.get('remote_user_maildomain', None),
display_servers=util.listify( conf.get('display_servers', '')),
single_user=single_user,
admin_users=conf.get('admin_users', '').split(','),
remote_user_header=conf.get('remote_user_header', 'HTTP_REMOTE_USER'),
remote_user_secret_header=conf.get('remote_user_secret', None),
normalize_remote_user_email=conf.get('normalize_remote_user_email', False)) )
# The recursive middleware allows for including requests in other
# requests or forwarding of requests, all on the server side.
if asbool(conf.get('use_recursive', True)):
from paste import recursive
app = wrap_if_allowed( app, stack, recursive.RecursiveMiddleware, args=(conf,) )
# If sentry logging is enabled, log here before propogating up to
# the error middleware
sentry_dsn = conf.get( 'sentry_dsn', None )
if sentry_dsn:
from galaxy.web.framework.middleware.sentry import Sentry
app = wrap_if_allowed( app, stack, Sentry, args=(sentry_dsn,) )
# Various debug middleware that can only be turned on if the debug
# flag is set, either because they are insecure or greatly hurt
# performance
if debug:
# Middleware to check for WSGI compliance
if asbool( conf.get( 'use_lint', False ) ):
from paste import lint
app = wrap_if_allowed( app, stack, lint.make_middleware, name='paste.lint', args=(conf,) )
# Middleware to run the python profiler on each request
if asbool( conf.get( 'use_profile', False ) ):
from paste.debug import profile
app = wrap_if_allowed( app, stack, profile.ProfileMiddleware, args=(conf,) )
if debug and asbool( conf.get( 'use_interactive', False ) ):
# Interactive exception debugging, scary dangerous if publicly
# accessible, if not enabled we'll use the regular error printing
# middleware.
try:
from weberror import evalexception
app = wrap_if_allowed_or_fail( app, stack, evalexception.EvalException,
args=(conf,),
kwargs=dict(templating_formatters=build_template_error_formatters()) )
except MiddlewareWrapUnsupported as exc:
log.warning(str(exc))
import galaxy.web.framework.middleware.error
app = wrap_if_allowed( app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,) )
else:
# Not in interactive debug mode, just use the regular error middleware
import galaxy.web.framework.middleware.error
app = wrap_if_allowed( app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,) )
# Transaction logging (apache access.log style)
if asbool( conf.get( 'use_translogger', True ) ):
from galaxy.web.framework.middleware.translogger import TransLogger
app = wrap_if_allowed( app, stack, TransLogger )
# X-Forwarded-Host handling
from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware
app = wrap_if_allowed( app, stack, XForwardedHostMiddleware )
# Request ID middleware
from galaxy.web.framework.middleware.request_id import RequestIDMiddleware
app = wrap_if_allowed( app, stack, RequestIDMiddleware )
# api batch call processing middleware
from galaxy.web.framework.middleware.batch import BatchMiddleware
app = wrap_if_allowed( app, stack, BatchMiddleware, args=(webapp, {}) )
return app
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, load_app_kwds={}, **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_',
**load_app_kwds
)
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 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 - 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.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',
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('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:
galaxy.webapps.tool_shed.model.mapping.metadata.bind.dispose()
except Exception:
log.exception("Unable to dispose of pooled tool_shed model database connections.")
# Return
return webapp
def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
"""Based on the configuration wrap `app` in a set of common and useful middleware."""
stack = application_stack
# Merge the global and local configurations
conf = global_conf.copy()
conf.update(local_conf)
debug = asbool(conf.get('debug', False))
interactive = asbool(conf.get('use_interactive', False))
# First put into place httpexceptions, which must be most closely
# wrapped around the application (it can interact poorly with
# other middleware):
app = wrap_if_allowed(app, stack, httpexceptions.make_middleware, name='paste.httpexceptions', args=(conf,))
# Create a separate mapper for redirects to prevent conflicts.
redirect_mapper = routes.Mapper()
redirect_mapper = _map_redirects(redirect_mapper)
# Load the Routes middleware which we use for redirecting
app = wrap_if_allowed(app, stack, RoutesMiddleware, args=(redirect_mapper,))
# If we're using remote_user authentication, add middleware that
# protects Galaxy from improperly configured authentication in the
# upstream server
if asbool(conf.get('use_remote_user', False)):
from galaxy.webapps.tool_shed.framework.middleware.remoteuser import RemoteUser
app = wrap_if_allowed(app, stack, RemoteUser,
kwargs=dict(
maildomain=conf.get('remote_user_maildomain', None),
display_servers=util.listify(conf.get('display_servers', '')),
admin_users=conf.get('admin_users', '').split(','),
remote_user_header=conf.get('remote_user_header', 'HTTP_REMOTE_USER'),
remote_user_secret_header=conf.get('remote_user_secret', None),
normalize_remote_user_email=conf.get('normalize_remote_user_email', False)))
# The recursive middleware allows for including requests in other
# requests or forwarding of requests, all on the server side.
if asbool(conf.get('use_recursive', True)):
from paste import recursive
app = wrap_if_allowed(app, stack, recursive.RecursiveMiddleware, args=(conf,))
# Transaction logging (apache access.log style)
if asbool(conf.get('use_translogger', True)):
from paste.translogger import TransLogger
app = wrap_if_allowed(app, stack, TransLogger)
# If sentry logging is enabled, log here before propogating up to
# the error middleware
# TODO sentry config is duplicated between tool_shed/galaxy, refactor this.
sentry_dsn = conf.get('sentry_dsn', None)
if sentry_dsn:
from galaxy.web.framework.middleware.sentry import Sentry
app = wrap_if_allowed(app, stack, Sentry, args=(sentry_dsn,))
# X-Forwarded-Host handling
from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware
app = wrap_if_allowed(app, stack, XForwardedHostMiddleware)
# Various debug middleware that can only be turned on if the debug
# flag is set, either because they are insecure or greatly hurt
# performance.
if debug:
# Middleware to check for WSGI compliance
if asbool(conf.get('use_lint', True)):
from paste import lint
app = wrap_if_allowed(app, stack, lint.make_middleware, name='paste.lint', args=(conf,))
# Middleware to run the python profiler on each request
if asbool(conf.get('use_profile', False)):
from paste.debug import profile
app = wrap_if_allowed(app, stack, profile.ProfileMiddleware, args=(conf,))
if interactive:
# Interactive exception debugging, scary dangerous if publicly
# accessible, if not enabled we'll use the regular error printing
# middleware.
try:
from weberror import evalexception
app = wrap_if_allowed_or_fail(app, stack, evalexception.EvalException,
args=(conf,),
kwargs=dict(templating_formatters=build_template_error_formatters()))
except MiddlewareWrapUnsupported as exc:
log.warning(str(exc))
import galaxy.web.framework.middleware.error
app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
else:
# Not in interactive debug mode, just use the regular error middleware
import galaxy.web.framework.middleware.error
app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
return app
