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 populate_api_routes(webapp, app):
webapp.add_api_controllers('galaxy.webapps.galaxy.api', app)
valid_history_contents_types = [
'dataset',
'dataset_collection',
]
# Accesss HDA details via histories/{history_id}/contents/datasets/{hda_id}
webapp.mapper.resource(
"content_typed",
"{type:%s}s" % "|".join(valid_history_contents_types),
name_prefix="history_",
controller='history_contents',
path_prefix='/api/histories/{history_id}/contents',
parent_resources=dict(member_name='history',
collection_name='histories'),
)
# Legacy access to HDA details via histories/{history_id}/contents/{hda_id}
webapp.mapper.resource('content',
'contents',
controller='history_contents',
name_prefix='history_',
path_prefix='/api/histories/{history_id}',
parent_resources=dict(member_name='history',
collection_name='histories'))
webapp.mapper.connect(
"history_contents_display",
"/api/histories/{history_id}/contents/{history_content_id}/display",
controller="datasets",
action="display",
conditions=dict(method=["GET"]))
webapp.mapper.resource('user',
'users',
controller='group_users',
name_prefix='group_',
path_prefix='/api/groups/{group_id}',
parent_resources=dict(member_name='group',
collection_name='groups'))
webapp.mapper.resource('role',
'roles',
controller='group_roles',
name_prefix='group_',
path_prefix='/api/groups/{group_id}',
parent_resources=dict(member_name='group',
collection_name='groups'))
_add_item_tags_controller(
webapp,
name_prefix="history_content_",
path_prefix='/api/histories/{history_id}/contents/{history_content_id}'
)
webapp.mapper.connect('/api/histories/published',
action='published',
controller="histories",
conditions=dict(method=["GET"]))
webapp.mapper.connect('/api/histories/shared_with_me',
action='shared_with_me',
controller="histories")
_add_item_tags_controller(webapp,
name_prefix="history_",
path_prefix='/api/histories/{history_id}')
_add_item_tags_controller(webapp,
name_prefix="workflow_",
path_prefix='/api/workflows/{workflow_id}')
_add_item_annotation_controller(
webapp,
name_prefix="history_content_",
path_prefix='/api/histories/{history_id}/contents/{history_content_id}'
)
_add_item_annotation_controller(webapp,
name_prefix="history_",
path_prefix='/api/histories/{history_id}')
_add_item_annotation_controller(webapp,
name_prefix="workflow_",
path_prefix='/api/workflows/{workflow_id}')
_add_item_provenance_controller(
webapp,
name_prefix="history_content_",
path_prefix='/api/histories/{history_id}/contents/{history_content_id}'
)
webapp.mapper.resource('dataset', 'datasets', path_prefix='/api')
webapp.mapper.resource('tool_data', 'tool_data', path_prefix='/api')
webapp.mapper.connect(
'/api/tool_data/{id:.+?}/fields/{value:.+?}/files/{path:.+?}',
action='download_field_file',
controller="tool_data")
webapp.mapper.connect('/api/tool_data/{id:.+?}/fields/{value:.+?}',
action='show_field',
controller="tool_data")
webapp.mapper.connect('/api/tool_data/{id:.+?}/reload',
action='reload',
controller="tool_data")
webapp.mapper.resource('dataset_collection',
'dataset_collections',
path_prefix='/api/')
webapp.mapper.resource('sample', 'samples', path_prefix='/api')
webapp.mapper.resource('request', 'requests', path_prefix='/api')
webapp.mapper.resource('form', 'forms', path_prefix='/api')
webapp.mapper.resource('request_type', 'request_types', path_prefix='/api')
webapp.mapper.resource('role', 'roles', path_prefix='/api')
webapp.mapper.connect('/api/ftp_files', controller='remote_files')
webapp.mapper.resource('remote_file', 'remote_files', path_prefix='/api')
webapp.mapper.resource('group', 'groups', path_prefix='/api')
webapp.mapper.resource_with_deleted('quota', 'quotas', path_prefix='/api')
# =======================
# ====== TOOLS API ======
# =======================
webapp.mapper.connect('/api/tools/{id:.+?}/build',
action='build',
controller="tools")
webapp.mapper.connect('/api/tools/{id:.+?}/reload',
action='reload',
controller="tools")
webapp.mapper.connect('/api/tools/{id:.+?}/diagnostics',
action='diagnostics',
controller="tools")
webapp.mapper.connect('/api/tools/{id:.+?}/citations',
action='citations',
controller="tools")
webapp.mapper.connect('/api/tools/{id:.+?}/download',
action='download',
controller="tools")
webapp.mapper.connect('/api/tools/{id:.+?}',
action='show',
controller="tools")
webapp.mapper.resource('tool', 'tools', path_prefix='/api')
webapp.mapper.resource_with_deleted('user', 'users', path_prefix='/api')
webapp.mapper.resource('genome', 'genomes', path_prefix='/api')
webapp.mapper.resource('visualization',
'visualizations',
path_prefix='/api')
webapp.mapper.connect('/api/workflows/build_module',
action='build_module',
controller="workflows")
webapp.mapper.resource('workflow', 'workflows', path_prefix='/api')
webapp.mapper.resource_with_deleted('history',
'histories',
path_prefix='/api')
webapp.mapper.connect('/api/histories/{history_id}/citations',
action='citations',
controller="histories")
webapp.mapper.connect('dynamic_tool_confs',
'/api/configuration/dynamic_tool_confs',
controller="configuration",
action="dynamic_tool_confs")
webapp.mapper.connect('tool_lineages',
'/api/configuration/tool_lineages',
controller="configuration",
action="tool_lineages")
webapp.mapper.resource('configuration',
'configuration',
path_prefix='/api')
webapp.mapper.connect("configuration_version",
"/api/version",
controller="configuration",
action="version",
conditions=dict(method=["GET"]))
webapp.mapper.resource('datatype',
'datatypes',
path_prefix='/api',
collection={
'sniffers': 'GET',
'mapping': 'GET',
'converters': 'GET',
'edam_formats': 'GET'
},
parent_resources=dict(member_name='datatype',
collection_name='datatypes'))
webapp.mapper.resource('search', 'search', path_prefix='/api')
webapp.mapper.resource('page', 'pages', path_prefix="/api")
webapp.mapper.resource('revision',
'revisions',
path_prefix='/api/pages/{page_id}',
controller='page_revisions',
parent_resources=dict(member_name='page',
collection_name='pages'))
webapp.mapper.connect("history_archive_export",
"/api/histories/{id}/exports",
controller="histories",
action="archive_export",
conditions=dict(method=["PUT"]))
webapp.mapper.connect("history_archive_download",
"/api/histories/{id}/exports/{jeha_id}",
controller="histories",
action="archive_download",
conditions=dict(method=["GET"]))
webapp.mapper.connect("create_api_key",
"/api/users/{user_id}/api_key",
controller="users",
action="api_key",
user_id=None,
conditions=dict(method=["POST"]))
# visualizations registry generic template renderer
webapp.add_route('/visualization/show/{visualization_name}',
controller='visualization',
action='render',
visualization_name=None)
# Deprecated in favor of POST /api/workflows with 'workflow' in payload.
webapp.mapper.connect('import_workflow_deprecated',
'/api/workflows/upload',
controller='workflows',
action='import_new_workflow_deprecated',
conditions=dict(method=['POST']))
webapp.mapper.connect('workflow_dict',
'/api/workflows/{workflow_id}/download',
controller='workflows',
action='workflow_dict',
conditions=dict(method=['GET']))
# Preserve the following download route for now for dependent applications -- deprecate at some point
webapp.mapper.connect('workflow_dict',
'/api/workflows/download/{workflow_id}',
controller='workflows',
action='workflow_dict',
conditions=dict(method=['GET']))
# Deprecated in favor of POST /api/workflows with shared_workflow_id in payload.
webapp.mapper.connect('import_shared_workflow_deprecated',
'/api/workflows/import',
controller='workflows',
action='import_shared_workflow_deprecated',
conditions=dict(method=['POST']))
# route for creating/getting converted datasets
webapp.mapper.connect('/api/datasets/{dataset_id}/converted',
controller='datasets',
action='converted',
ext=None)
webapp.mapper.connect('/api/datasets/{dataset_id}/converted/{ext}',
controller='datasets',
action='converted')
# API refers to usages and invocations - these mean the same thing but the
# usage routes should be considered deprecated.
invoke_names = {
"invocations": "",
"usage": "_deprecated",
}
for noun, suffix in invoke_names.iteritems():
name = "%s%s" % (noun, suffix)
webapp.mapper.connect('list_workflow_%s' % name,
'/api/workflows/{workflow_id}/%s' % noun,
controller='workflows',
action='index_invocations',
conditions=dict(method=['GET']))
webapp.mapper.connect(
'workflow_%s_contents' % name,
'/api/workflows/{workflow_id}/%s/{invocation_id}' % noun,
controller='workflows',
action='show_invocation',
conditions=dict(method=['GET']))
webapp.mapper.connect(
'cancel_workflow_%s' % name,
'/api/workflows/{workflow_id}/%s/{invocation_id}' % noun,
controller='workflows',
action='cancel_invocation',
conditions=dict(method=['DELETE']))
webapp.mapper.connect(
'workflow_%s_step' % name,
'/api/workflows/{workflow_id}/%s/{invocation_id}/steps/{step_id}' %
noun,
controller='workflows',
action='invocation_step',
conditions=dict(method=['GET']))
webapp.mapper.connect(
'workflow_%s_step_update' % name,
'/api/workflows/{workflow_id}/%s/{invocation_id}/steps/{step_id}' %
noun,
controller='workflows',
action='update_invocation_step',
conditions=dict(method=['PUT']))
webapp.mapper.connect('workflow_%s' % name,
'/api/workflows/{workflow_id}/%s' % noun,
controller='workflows',
action='invoke',
conditions=dict(method=['POST']))
# ============================
# ===== AUTHENTICATE API =====
# ============================
webapp.mapper.connect('api_key_retrieval',
'/api/authenticate/baseauth/',
controller='authenticate',
action='get_api_key',
conditions=dict(method=["GET"]))
# =======================
# ===== LIBRARY API =====
# =======================
webapp.mapper.connect('update_library',
'/api/libraries/{id}',
controller='libraries',
action='update',
conditions=dict(method=["PATCH", "PUT"]))
webapp.mapper.connect('show_library_permissions',
'/api/libraries/{encoded_library_id}/permissions',
controller='libraries',
action='get_permissions',
conditions=dict(method=["GET"]))
webapp.mapper.connect('set_library_permissions',
'/api/libraries/{encoded_library_id}/permissions',
controller='libraries',
action='set_permissions',
conditions=dict(method=["POST"]))
webapp.mapper.connect('show_ld_item',
'/api/libraries/datasets/{id}',
controller='lda_datasets',
action='show',
conditions=dict(method=["GET"]))
webapp.mapper.connect('load_ld',
'/api/libraries/datasets/',
controller='lda_datasets',
action='load',
conditions=dict(method=["POST"]))
webapp.mapper.connect(
'show_version_of_ld_item',
'/api/libraries/datasets/{encoded_dataset_id}/versions/{encoded_ldda_id}',
controller='lda_datasets',
action='show_version',
conditions=dict(method=["GET"]))
webapp.mapper.connect(
'show_legitimate_lda_roles',
'/api/libraries/datasets/{encoded_dataset_id}/permissions',
controller='lda_datasets',
action='show_roles',
conditions=dict(method=["GET"]))
webapp.mapper.connect(
'update_lda_permissions',
'/api/libraries/datasets/{encoded_dataset_id}/permissions',
controller='lda_datasets',
action='update_permissions',
conditions=dict(method=["POST"]))
webapp.mapper.connect('delete_lda_item',
'/api/libraries/datasets/{encoded_dataset_id}',
controller='lda_datasets',
action='delete',
conditions=dict(method=["DELETE"]))
webapp.mapper.connect('download_lda_items',
'/api/libraries/datasets/download/{format}',
controller='lda_datasets',
action='download',
conditions=dict(method=["POST", "GET"]))
webapp.mapper.resource_with_deleted('library',
'libraries',
path_prefix='/api')
webapp.mapper.resource('content',
'contents',
controller='library_contents',
name_prefix='library_',
path_prefix='/api/libraries/{library_id}',
parent_resources=dict(member_name='library',
collection_name='libraries'))
_add_item_extended_metadata_controller(
webapp,
name_prefix="library_dataset_",
path_prefix='/api/libraries/{library_id}/contents/{library_content_id}'
)
# =======================
# ===== FOLDERS API =====
# =======================
webapp.mapper.connect('add_history_datasets_to_library',
'/api/folders/{encoded_folder_id}/contents',
controller='folder_contents',
action='create',
conditions=dict(method=["POST"]))
webapp.mapper.connect('create_folder',
'/api/folders/{encoded_parent_folder_id}',
controller='folders',
action='create',
conditions=dict(method=["POST"]))
webapp.mapper.resource('folder', 'folders', path_prefix='/api')
webapp.mapper.connect('show_folder_permissions',
'/api/folders/{encoded_folder_id}/permissions',
controller='folders',
action='get_permissions',
conditions=dict(method=["GET"]))
webapp.mapper.connect('set_folder_permissions',
'/api/folders/{encoded_folder_id}/permissions',
controller='folders',
action='set_permissions',
conditions=dict(method=["POST"]))
webapp.mapper.resource('content',
'contents',
controller='folder_contents',
name_prefix='folder_',
path_prefix='/api/folders/{folder_id}',
parent_resources=dict(member_name='folder',
collection_name='folders'),
conditions=dict(method=["GET"]))
webapp.mapper.resource('job', 'jobs', path_prefix='/api')
webapp.mapper.connect('job_search',
'/api/jobs/search',
controller='jobs',
action='search',
conditions=dict(method=['POST']))
webapp.mapper.connect('job_inputs',
'/api/jobs/{id}/inputs',
controller='jobs',
action='inputs',
conditions=dict(method=['GET']))
webapp.mapper.connect('job_outputs',
'/api/jobs/{id}/outputs',
controller='jobs',
action='outputs',
conditions=dict(method=['GET']))
# Job files controllers. Only for consumption by remote job runners.
webapp.mapper.resource('file',
'files',
controller="job_files",
name_prefix="job_",
path_prefix='/api/jobs/{job_id}',
parent_resources=dict(member_name="job",
collection_name="jobs"))
_add_item_extended_metadata_controller(
webapp,
name_prefix="history_dataset_",
path_prefix='/api/histories/{history_id}/contents/{history_content_id}'
)
# ====================
# ===== TOOLSHED =====
# ====================
# Handle displaying tool help images and README file images contained in repositories installed from the tool shed.
webapp.add_route(
'/admin_toolshed/static/images/{repository_id}/{image_file:.+?}',
controller='admin_toolshed',
action='display_image_in_repository',
repository_id=None,
image_file=None)
# Galaxy API for tool shed features.
webapp.mapper.resource(
'tool_shed_repository',
'tool_shed_repositories',
member={
'repair_repository_revision': 'POST',
'exported_workflows': 'GET',
'import_workflow': 'POST',
'import_workflows': 'POST'
},
collection={
'get_latest_installable_revision': 'POST',
'reset_metadata_on_installed_repositories': 'POST'
},
controller='tool_shed_repositories',
name_prefix='tool_shed_repository_',
path_prefix='/api',
new={'install_repository_revision': 'POST'},
parent_resources=dict(member_name='tool_shed_repository',
collection_name='tool_shed_repositories'))
# ==== Trace/Metrics Logger
# Connect logger from app
if app.trace_logger:
webapp.trace_logger = app.trace_logger
# metrics logging API
# webapp.mapper.connect( "index", "/api/metrics",
# controller="metrics", action="index", conditions=dict( method=["GET"] ) )
# webapp.mapper.connect( "show", "/api/metrics/{id}",
# controller="metrics", action="show", conditions=dict( method=["GET"] ) )
webapp.mapper.connect("create",
"/api/metrics",
controller="metrics",
action="create",
conditions=dict(method=["POST"]))
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 populate_api_routes( webapp, app ):
webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app )
valid_history_contents_types = [
'dataset',
'dataset_collection',
]
# Accesss HDA details via histories/{history_id}/contents/datasets/{hda_id}
webapp.mapper.resource( "content_typed",
"{type:%s}s" % "|".join( valid_history_contents_types ),
name_prefix="history_",
controller='history_contents',
path_prefix='/api/histories/{history_id}/contents',
parent_resources=dict( member_name='history', collection_name='histories' ),
)
# Legacy access to HDA details via histories/{history_id}/contents/{hda_id}
webapp.mapper.resource( 'content',
'contents',
controller='history_contents',
name_prefix='history_',
path_prefix='/api/histories/{history_id}',
parent_resources=dict( member_name='history', collection_name='histories' ) )
webapp.mapper.connect( "history_contents_display",
"/api/histories/{history_id}/contents/{history_content_id}/display",
controller="datasets",
action="display",
conditions=dict(method=["GET"]))
webapp.mapper.resource( 'user',
'users',
controller='group_users',
name_prefix='group_',
path_prefix='/api/groups/{group_id}',
parent_resources=dict( member_name='group', collection_name='groups' ) )
webapp.mapper.resource( 'role',
'roles',
controller='group_roles',
name_prefix='group_',
path_prefix='/api/groups/{group_id}',
parent_resources=dict( member_name='group', collection_name='groups' ) )
_add_item_tags_controller( webapp,
name_prefix="history_content_",
path_prefix='/api/histories/{history_id}/contents/{history_content_id}' )
webapp.mapper.connect( '/api/histories/published', action='published', controller="histories", conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( '/api/histories/shared_with_me', action='shared_with_me', controller="histories" )
_add_item_tags_controller( webapp,
name_prefix="history_",
path_prefix='/api/histories/{history_id}' )
_add_item_tags_controller( webapp,
name_prefix="workflow_",
path_prefix='/api/workflows/{workflow_id}' )
_add_item_annotation_controller( webapp,
name_prefix="history_content_",
path_prefix='/api/histories/{history_id}/contents/{history_content_id}' )
_add_item_annotation_controller( webapp,
name_prefix="history_",
path_prefix='/api/histories/{history_id}' )
_add_item_annotation_controller( webapp,
name_prefix="workflow_",
path_prefix='/api/workflows/{workflow_id}' )
_add_item_provenance_controller( webapp,
name_prefix="history_content_",
path_prefix='/api/histories/{history_id}/contents/{history_content_id}' )
webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' )
webapp.mapper.resource( 'tool_data', 'tool_data', path_prefix='/api' )
webapp.mapper.connect( '/api/tool_data/{id:.+?}/fields/{value:.+?}/files/{path:.+?}', action='download_field_file', controller="tool_data" )
webapp.mapper.connect( '/api/tool_data/{id:.+?}/fields/{value:.+?}', action='show_field', controller="tool_data" )
webapp.mapper.connect( '/api/tool_data/{id:.+?}/reload', action='reload', controller="tool_data" )
webapp.mapper.resource( 'dataset_collection', 'dataset_collections', path_prefix='/api/')
webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' )
webapp.mapper.resource( 'request', 'requests', path_prefix='/api' )
webapp.mapper.resource( 'form', 'forms', path_prefix='/api' )
webapp.mapper.resource( 'request_type', 'request_types', path_prefix='/api' )
webapp.mapper.resource( 'role', 'roles', path_prefix='/api' )
webapp.mapper.connect( '/api/ftp_files', controller='remote_files' )
webapp.mapper.resource( 'remote_file', 'remote_files', path_prefix='/api' )
webapp.mapper.resource( 'group', 'groups', path_prefix='/api' )
webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' )
# =======================
# ====== TOOLS API ======
# =======================
webapp.mapper.connect( '/api/tools/{id:.+?}/build', action='build', controller="tools" )
webapp.mapper.connect( '/api/tools/{id:.+?}/reload', action='reload', controller="tools" )
webapp.mapper.connect( '/api/tools/{id:.+?}/diagnostics', action='diagnostics', controller="tools" )
webapp.mapper.connect( '/api/tools/{id:.+?}/citations', action='citations', controller="tools" )
webapp.mapper.connect( '/api/tools/{id:.+?}/download', action='download', controller="tools" )
webapp.mapper.connect( '/api/tools/{id:.+?}', action='show', controller="tools" )
webapp.mapper.resource( 'tool', 'tools', path_prefix='/api' )
webapp.mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' )
webapp.mapper.resource( 'genome', 'genomes', path_prefix='/api' )
webapp.mapper.resource( 'visualization', 'visualizations', path_prefix='/api' )
webapp.mapper.connect( '/api/workflows/build_module', action='build_module', controller="workflows" )
webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' )
webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' )
webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" )
webapp.mapper.connect(
'dynamic_tool_confs',
'/api/configuration/dynamic_tool_confs',
controller="configuration",
action="dynamic_tool_confs"
)
webapp.mapper.connect(
'tool_lineages',
'/api/configuration/tool_lineages',
controller="configuration",
action="tool_lineages"
)
webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' )
webapp.mapper.connect( "configuration_version",
"/api/version", controller="configuration",
action="version", conditions=dict( method=[ "GET" ] ) )
webapp.mapper.resource( 'datatype',
'datatypes',
path_prefix='/api',
collection={ 'sniffers': 'GET', 'mapping': 'GET', 'converters': 'GET', 'edam_formats': 'GET' },
parent_resources=dict( member_name='datatype', collection_name='datatypes' ) )
webapp.mapper.resource( 'search', 'search', path_prefix='/api' )
webapp.mapper.resource( 'page', 'pages', path_prefix="/api")
webapp.mapper.resource( 'revision', 'revisions',
path_prefix='/api/pages/{page_id}',
controller='page_revisions',
parent_resources=dict( member_name='page', collection_name='pages' ) )
webapp.mapper.connect( "history_archive_export",
"/api/histories/{id}/exports", controller="histories",
action="archive_export", conditions=dict( method=[ "PUT" ] ) )
webapp.mapper.connect( "history_archive_download",
"/api/histories/{id}/exports/{jeha_id}", controller="histories",
action="archive_download", conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( "create_api_key", "/api/users/{user_id}/api_key",
controller="users", action="api_key", user_id=None,
conditions=dict( method=["POST"] ) )
# visualizations registry generic template renderer
webapp.add_route( '/visualization/show/{visualization_name}', controller='visualization', action='render', visualization_name=None )
# Deprecated in favor of POST /api/workflows with 'workflow' in payload.
webapp.mapper.connect( 'import_workflow_deprecated',
'/api/workflows/upload',
controller='workflows',
action='import_new_workflow_deprecated',
conditions=dict( method=['POST'] ) )
webapp.mapper.connect( 'workflow_dict',
'/api/workflows/{workflow_id}/download',
controller='workflows',
action='workflow_dict',
conditions=dict( method=['GET'] ) )
# Preserve the following download route for now for dependent applications -- deprecate at some point
webapp.mapper.connect( 'workflow_dict',
'/api/workflows/download/{workflow_id}',
controller='workflows',
action='workflow_dict',
conditions=dict( method=['GET'] ) )
# Deprecated in favor of POST /api/workflows with shared_workflow_id in payload.
webapp.mapper.connect( 'import_shared_workflow_deprecated',
'/api/workflows/import',
controller='workflows',
action='import_shared_workflow_deprecated',
conditions=dict( method=['POST'] ) )
# route for creating/getting converted datasets
webapp.mapper.connect( '/api/datasets/{dataset_id}/converted', controller='datasets', action='converted', ext=None )
webapp.mapper.connect( '/api/datasets/{dataset_id}/converted/{ext}', controller='datasets', action='converted' )
# API refers to usages and invocations - these mean the same thing but the
# usage routes should be considered deprecated.
invoke_names = {
"invocations": "",
"usage": "_deprecated",
}
for noun, suffix in invoke_names.iteritems():
name = "%s%s" % (noun, suffix)
webapp.mapper.connect(
'list_workflow_%s' % name,
'/api/workflows/{workflow_id}/%s' % noun,
controller='workflows',
action='index_invocations',
conditions=dict(method=['GET'])
)
webapp.mapper.connect(
'workflow_%s_contents' % name,
'/api/workflows/{workflow_id}/%s/{invocation_id}' % noun,
controller='workflows',
action='show_invocation',
conditions=dict(method=['GET'])
)
webapp.mapper.connect(
'cancel_workflow_%s' % name,
'/api/workflows/{workflow_id}/%s/{invocation_id}' % noun,
controller='workflows',
action='cancel_invocation',
conditions=dict(method=['DELETE'])
)
webapp.mapper.connect(
'workflow_%s_step' % name,
'/api/workflows/{workflow_id}/%s/{invocation_id}/steps/{step_id}' % noun,
controller='workflows',
action='invocation_step',
conditions=dict(method=['GET'])
)
webapp.mapper.connect(
'workflow_%s_step_update' % name,
'/api/workflows/{workflow_id}/%s/{invocation_id}/steps/{step_id}' % noun,
controller='workflows',
action='update_invocation_step',
conditions=dict(method=['PUT'])
)
webapp.mapper.connect(
'workflow_%s' % name,
'/api/workflows/{workflow_id}/%s' % noun,
controller='workflows',
action='invoke',
conditions=dict( method=['POST'] )
)
# ============================
# ===== AUTHENTICATE API =====
# ============================
webapp.mapper.connect( 'api_key_retrieval',
'/api/authenticate/baseauth/',
controller='authenticate',
action='get_api_key',
conditions=dict( method=[ "GET" ] ) )
# =======================
# ===== LIBRARY API =====
# =======================
webapp.mapper.connect( 'update_library',
'/api/libraries/{id}',
controller='libraries',
action='update',
conditions=dict( method=[ "PATCH", "PUT" ] ) )
webapp.mapper.connect( 'show_library_permissions',
'/api/libraries/{encoded_library_id}/permissions',
controller='libraries',
action='get_permissions',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'set_library_permissions',
'/api/libraries/{encoded_library_id}/permissions',
controller='libraries',
action='set_permissions',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'show_ld_item',
'/api/libraries/datasets/{id}',
controller='lda_datasets',
action='show',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'load_ld',
'/api/libraries/datasets/',
controller='lda_datasets',
action='load',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'show_version_of_ld_item',
'/api/libraries/datasets/{encoded_dataset_id}/versions/{encoded_ldda_id}',
controller='lda_datasets',
action='show_version',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'show_legitimate_lda_roles',
'/api/libraries/datasets/{encoded_dataset_id}/permissions',
controller='lda_datasets',
action='show_roles',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'update_lda_permissions',
'/api/libraries/datasets/{encoded_dataset_id}/permissions',
controller='lda_datasets',
action='update_permissions',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'delete_lda_item',
'/api/libraries/datasets/{encoded_dataset_id}',
controller='lda_datasets',
action='delete',
conditions=dict( method=[ "DELETE" ] ) )
webapp.mapper.connect( 'download_lda_items',
'/api/libraries/datasets/download/{format}',
controller='lda_datasets',
action='download',
conditions=dict( method=[ "POST", "GET" ] ) )
webapp.mapper.resource_with_deleted( 'library',
'libraries',
path_prefix='/api' )
webapp.mapper.resource( 'content',
'contents',
controller='library_contents',
name_prefix='library_',
path_prefix='/api/libraries/{library_id}',
parent_resources=dict( member_name='library', collection_name='libraries' ) )
_add_item_extended_metadata_controller( webapp,
name_prefix="library_dataset_",
path_prefix='/api/libraries/{library_id}/contents/{library_content_id}' )
# =======================
# ===== FOLDERS API =====
# =======================
webapp.mapper.connect( 'add_history_datasets_to_library',
'/api/folders/{encoded_folder_id}/contents',
controller='folder_contents',
action='create',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'create_folder',
'/api/folders/{encoded_parent_folder_id}',
controller='folders',
action='create',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'delete_folder',
'/api/folders/{encoded_folder_id}',
controller='folders',
action='delete',
conditions=dict( method=[ "DELETE" ] ) )
webapp.mapper.connect( 'update_folder',
'/api/folders/{encoded_folder_id}',
controller='folders',
action='update',
conditions=dict( method=[ "PATCH", "PUT" ] ) )
webapp.mapper.resource( 'folder',
'folders',
path_prefix='/api' )
webapp.mapper.connect( 'show_folder_permissions',
'/api/folders/{encoded_folder_id}/permissions',
controller='folders',
action='get_permissions',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'set_folder_permissions',
'/api/folders/{encoded_folder_id}/permissions',
controller='folders',
action='set_permissions',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.resource( 'content',
'contents',
controller='folder_contents',
name_prefix='folder_',
path_prefix='/api/folders/{folder_id}',
parent_resources=dict( member_name='folder', collection_name='folders' ),
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.resource( 'job',
'jobs',
path_prefix='/api' )
webapp.mapper.connect( 'job_search', '/api/jobs/search', controller='jobs', action='search', conditions=dict( method=['POST'] ) )
webapp.mapper.connect( 'job_inputs', '/api/jobs/{id}/inputs', controller='jobs', action='inputs', conditions=dict( method=['GET'] ) )
webapp.mapper.connect( 'job_outputs', '/api/jobs/{id}/outputs', controller='jobs', action='outputs', conditions=dict( method=['GET'] ) )
webapp.mapper.connect( 'build_for_rerun', '/api/jobs/{id}/build_for_rerun', controller='jobs', action='build_for_rerun', conditions=dict( method=['GET'] ) )
# Job files controllers. Only for consumption by remote job runners.
webapp.mapper.resource( 'file',
'files',
controller="job_files",
name_prefix="job_",
path_prefix='/api/jobs/{job_id}',
parent_resources=dict( member_name="job", collection_name="jobs" ) )
_add_item_extended_metadata_controller( webapp,
name_prefix="history_dataset_",
path_prefix='/api/histories/{history_id}/contents/{history_content_id}' )
# ====================
# ===== TOOLSHED =====
# ====================
# Handle displaying tool help images and README file images contained in repositories installed from the tool shed.
webapp.add_route( '/admin_toolshed/static/images/{repository_id}/{image_file:.+?}',
controller='admin_toolshed',
action='display_image_in_repository',
repository_id=None,
image_file=None )
# Galaxy API for tool shed features.
webapp.mapper.resource( 'tool_shed_repository',
'tool_shed_repositories',
member={ 'repair_repository_revision': 'POST',
'exported_workflows': 'GET',
'import_workflow': 'POST',
'import_workflows': 'POST' },
collection={ 'get_latest_installable_revision': 'POST',
'reset_metadata_on_installed_repositories': 'POST' },
controller='tool_shed_repositories',
name_prefix='tool_shed_repository_',
path_prefix='/api',
new={ 'install_repository_revision': 'POST' },
parent_resources=dict( member_name='tool_shed_repository', collection_name='tool_shed_repositories' ) )
# ==== Trace/Metrics Logger
# Connect logger from app
if app.trace_logger:
webapp.trace_logger = app.trace_logger
# metrics logging API
# webapp.mapper.connect( "index", "/api/metrics",
# controller="metrics", action="index", conditions=dict( method=["GET"] ) )
# webapp.mapper.connect( "show", "/api/metrics/{id}",
# controller="metrics", action="show", conditions=dict( method=["GET"] ) )
webapp.mapper.connect( "create", "/api/metrics", controller="metrics",
action="create", conditions=dict( method=["POST"] ) )
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 populate_api_routes( webapp, app ):
webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app )
valid_history_contents_types = [
'dataset',
'dataset_collection',
]
# Accesss HDA details via histories/:history_id/contents/datasets/:hda_id
webapp.mapper.resource( "content_typed",
"{type:%s}s" % "|".join( valid_history_contents_types ),
name_prefix="history_",
controller='history_contents',
path_prefix='/api/histories/:history_id/contents',
parent_resources=dict( member_name='history', collection_name='histories' ),
)
# Legacy access to HDA details via histories/:history_id/contents/:hda_id
webapp.mapper.resource( 'content',
'contents',
controller='history_contents',
name_prefix='history_',
path_prefix='/api/histories/:history_id',
parent_resources=dict( member_name='history', collection_name='histories' ) )
webapp.mapper.connect("history_contents_display",
"/api/histories/:history_id/contents/:history_content_id/display",
controller="datasets",
action="display",
conditions=dict(method=["GET"]))
webapp.mapper.resource( 'user',
'users',
controller='group_users',
name_prefix='group_',
path_prefix='/api/groups/:group_id',
parent_resources=dict( member_name='group', collection_name='groups' ) )
webapp.mapper.resource( 'role',
'roles',
controller='group_roles',
name_prefix='group_',
path_prefix='/api/groups/:group_id',
parent_resources=dict( member_name='group', collection_name='groups' ) )
_add_item_tags_controller( webapp,
name_prefix="history_content_",
path_prefix='/api/histories/:history_id/contents/:history_content_id' )
_add_item_tags_controller( webapp,
name_prefix="history_",
path_prefix='/api/histories/:history_id' )
_add_item_tags_controller( webapp,
name_prefix="workflow_",
path_prefix='/api/workflows/:workflow_id' )
_add_item_annotation_controller( webapp,
name_prefix="history_content_",
path_prefix='/api/histories/:history_id/contents/:history_content_id' )
_add_item_annotation_controller( webapp,
name_prefix="history_",
path_prefix='/api/histories/:history_id' )
_add_item_annotation_controller( webapp,
name_prefix="workflow_",
path_prefix='/api/workflows/:workflow_id' )
_add_item_provenance_controller( webapp,
name_prefix="history_content_",
path_prefix='/api/histories/:history_id/contents/:history_content_id' )
webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' )
webapp.mapper.resource( 'dataset_collection', 'dataset_collections', path_prefix='/api/')
webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' )
webapp.mapper.resource( 'request', 'requests', path_prefix='/api' )
webapp.mapper.resource( 'form', 'forms', path_prefix='/api' )
webapp.mapper.resource( 'request_type', 'request_types', path_prefix='/api' )
webapp.mapper.resource( 'role', 'roles', path_prefix='/api' )
webapp.mapper.resource( 'ftp_file', 'ftp_files', path_prefix='/api' )
webapp.mapper.resource( 'group', 'groups', path_prefix='/api' )
webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' )
webapp.mapper.connect( '/api/tools/{id:.+?}/citations', action='citations', controller="tools" )
webapp.mapper.connect( '/api/tools/{id:.+?}', action='show', controller="tools" )
webapp.mapper.resource( 'tool', 'tools', path_prefix='/api' )
webapp.mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' )
webapp.mapper.resource( 'genome', 'genomes', path_prefix='/api' )
webapp.mapper.resource( 'visualization', 'visualizations', path_prefix='/api' )
webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' )
webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' )
webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" )
webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' )
webapp.mapper.resource( 'datatype',
'datatypes',
path_prefix='/api',
collection={ 'sniffers': 'GET' },
parent_resources=dict( member_name='datatype', collection_name='datatypes' ) )
#webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) )
webapp.mapper.resource( 'search', 'search', path_prefix='/api' )
webapp.mapper.resource( 'page', 'pages', path_prefix="/api")
webapp.mapper.resource( 'revision', 'revisions',
path_prefix='/api/pages/:page_id',
controller='page_revisions',
parent_resources=dict( member_name='page', collection_name='pages' ) )
webapp.mapper.connect( "history_archive_export", "/api/histories/{id}/exports",
controller="histories", action="archive_export", conditions=dict( method=[ "PUT" ] ) )
webapp.mapper.connect( "history_archive_download", "/api/histories/{id}/exports/{jeha_id}",
controller="histories", action="archive_download", conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( "create_api_key", "/api/users/:user_id/api_key",
controller="users", action="api_key", user_id=None, conditions=dict( method=["POST"] ) )
# visualizations registry generic template renderer
webapp.add_route( '/visualization/show/:visualization_name',
controller='visualization', action='render', visualization_name=None )
# Deprecated in favor of POST /api/workflows with 'workflow' in payload.
webapp.mapper.connect( 'import_workflow_deprecated', '/api/workflows/upload', controller='workflows', action='import_new_workflow_deprecated', conditions=dict( method=['POST'] ) )
webapp.mapper.connect( 'workflow_dict', '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) )
# Preserve the following download route for now for dependent applications -- deprecate at some point
webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) )
# Deprecated in favor of POST /api/workflows with shared_workflow_id in payload.
webapp.mapper.connect( 'import_shared_workflow_deprecated', '/api/workflows/import', controller='workflows', action='import_shared_workflow_deprecated', conditions=dict( method=['POST'] ) )
webapp.mapper.connect( 'workflow_usage', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_usage', conditions=dict(method=['GET']))
webapp.mapper.connect( 'workflow_usage_contents', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='workflow_usage_contents', conditions=dict(method=['GET']))
# ============================
# ===== AUTHENTICATE API =====
# ============================
webapp.mapper.connect( 'api_key_retrieval',
'/api/authenticate/baseauth/',
controller='authenticate',
action='get_api_key',
conditions=dict( method=[ "GET" ] ) )
# =======================
# ===== LIBRARY API =====
# =======================
webapp.mapper.connect( 'update_library',
'/api/libraries/:id',
controller='libraries',
action='update',
conditions=dict( method=[ "PATCH", "PUT" ] ) )
webapp.mapper.connect( 'show_library_permissions',
'/api/libraries/:encoded_library_id/permissions',
controller='libraries',
action='get_permissions',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'set_library_permissions',
'/api/libraries/:encoded_library_id/permissions',
controller='libraries',
action='set_permissions',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'show_ld_item',
'/api/libraries/datasets/:id',
controller='lda_datasets',
action='show',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'load_ld',
'/api/libraries/datasets/',
controller='lda_datasets',
action='load',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'show_version_of_ld_item',
'/api/libraries/datasets/:encoded_dataset_id/versions/:encoded_ldda_id',
controller='lda_datasets',
action='show_version',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'show_legitimate_lda_roles',
'/api/libraries/datasets/:encoded_dataset_id/permissions',
controller='lda_datasets',
action='show_roles',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'update_lda_permissions',
'/api/libraries/datasets/:encoded_dataset_id/permissions',
controller='lda_datasets',
action='update_permissions',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'delete_lda_item',
'/api/libraries/datasets/:encoded_dataset_id',
controller='lda_datasets',
action='delete',
conditions=dict( method=[ "DELETE" ] ) )
webapp.mapper.connect( 'download_lda_items',
'/api/libraries/datasets/download/:format',
controller='lda_datasets',
action='download',
conditions=dict( method=[ "POST", "GET" ] ) )
webapp.mapper.resource_with_deleted( 'library',
'libraries',
path_prefix='/api' )
webapp.mapper.resource( 'content',
'contents',
controller='library_contents',
name_prefix='library_',
path_prefix='/api/libraries/:library_id',
parent_resources=dict( member_name='library', collection_name='libraries' ) )
_add_item_extended_metadata_controller( webapp,
name_prefix="library_dataset_",
path_prefix='/api/libraries/:library_id/contents/:library_content_id' )
# =======================
# ===== FOLDERS API =====
# =======================
webapp.mapper.connect( 'add_history_datasets_to_library',
'/api/folders/:encoded_folder_id/contents',
controller='folder_contents',
action='create',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.connect( 'create_folder',
'/api/folders/:encoded_parent_folder_id',
controller='folders',
action='create',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.resource( 'folder',
'folders',
path_prefix='/api' )
webapp.mapper.connect( 'show_folder_permissions',
'/api/folders/:encoded_folder_id/permissions',
controller='folders',
action='get_permissions',
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( 'set_folder_permissions',
'/api/folders/:encoded_folder_id/permissions',
controller='folders',
action='set_permissions',
conditions=dict( method=[ "POST" ] ) )
webapp.mapper.resource( 'content',
'contents',
controller='folder_contents',
name_prefix='folder_',
path_prefix='/api/folders/:folder_id',
parent_resources=dict( member_name='folder', collection_name='folders' ),
conditions=dict( method=[ "GET" ] ) )
webapp.mapper.resource( 'job',
'jobs',
path_prefix='/api' )
webapp.mapper.connect( 'job_search', '/api/jobs/search', controller='jobs', action='search', conditions=dict( method=['POST'] ) )
webapp.mapper.connect( 'job_inputs', '/api/jobs/{id}/inputs', controller='jobs', action='inputs', conditions=dict( method=['GET'] ) )
webapp.mapper.connect( 'job_outputs', '/api/jobs/{id}/outputs', controller='jobs', action='outputs', conditions=dict( method=['GET'] ) )
# Job files controllers. Only for consumption by remote job runners.
webapp.mapper.resource( 'file',
'files',
controller="job_files",
name_prefix="job_",
path_prefix='/api/jobs/:job_id',
parent_resources=dict( member_name="job", collection_name="jobs" ) )
_add_item_extended_metadata_controller( webapp,
name_prefix="history_dataset_",
path_prefix='/api/histories/:history_id/contents/:history_content_id' )
# ====================
# ===== TOOLSHED =====
# ====================
# Handle displaying tool help images and README file images contained in repositories installed from the tool shed.
webapp.add_route( '/admin_toolshed/static/images/:repository_id/{image_file:.+?}',
controller='admin_toolshed',
action='display_image_in_repository',
repository_id=None,
image_file=None )
# Galaxy API for tool shed features.
webapp.mapper.resource( 'tool_shed_repository',
'tool_shed_repositories',
member={ 'repair_repository_revision' : 'POST',
'exported_workflows' : 'GET',
'import_workflow' : 'POST',
'import_workflows' : 'POST' },
collection={ 'get_latest_installable_revision' : 'POST',
'reset_metadata_on_installed_repositories' : 'POST' },
controller='tool_shed_repositories',
name_prefix='tool_shed_repository_',
path_prefix='/api',
new={ 'install_repository_revision' : 'POST' },
parent_resources=dict( member_name='tool_shed_repository', collection_name='tool_shed_repositories' ) )
# ==== Trace/Metrics Logger
# Connect logger from app
if app.trace_logger:
webapp.trace_logger = app.trace_logger
# metrics logging API
#webapp.mapper.connect( "index", "/api/metrics",
# controller="metrics", action="index", conditions=dict( method=["GET"] ) )
#webapp.mapper.connect( "show", "/api/metrics/{id}",
# controller="metrics", action="show", conditions=dict( method=["GET"] ) )
webapp.mapper.connect( "create", "/api/metrics",
controller="metrics", action="create", conditions=dict( method=["POST"] ) )
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
