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This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.webapps.galaxy.buildapp

"""
Provides factory methods to assemble the Galaxy web application
"""
import atexit
import logging
import sys
import threading
import traceback

from paste import httpexceptions

import galaxy.app
import galaxy.datatypes.registry
import galaxy.model
import galaxy.model.mapping
import galaxy.web.framework
import galaxy.web.framework.webapp
from galaxy import util
from galaxy.util import asbool
from galaxy.util.properties import load_app_properties
from galaxy.webapps.util import (
    build_template_error_formatters,
    MiddlewareWrapUnsupported,
    wrap_if_allowed,
    wrap_if_allowed_or_fail
)

log = logging.getLogger(__name__)


[docs]class GalaxyWebApplication(galaxy.web.framework.webapp.WebApplication): pass
[docs]def app_factory(global_conf, load_app_kwds={}, **kwargs): """ Return a wsgi application serving the root object """ kwargs = load_app_properties( kwds=kwargs, **load_app_kwds ) # 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 Exception: traceback.print_exc() sys.exit(1) # Call app's shutdown method when the interpeter exits, this cleanly stops # the various Galaxy application daemon threads app.application_stack.register_postfork_function(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') # Authentication endpoints. webapp.add_route('/authnz/', controller='authnz', action='index', provider=None) webapp.add_route('/authnz/{provider}/login', controller='authnz', action='login', provider=None) webapp.add_route('/authnz/{provider}/callback', controller='authnz', action='callback', provider=None) webapp.add_route('/authnz/{provider}/disconnect', controller='authnz', action='disconnect', provider=None) # 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('/admin/data_tables', 'admin') webapp.add_client_route('/admin/data_types', 'admin') webapp.add_client_route('/admin/data_manager{path_info:.*}', 'admin') webapp.add_client_route('/admin/error_stack', 'admin') webapp.add_client_route('/admin/users', 'admin') webapp.add_client_route('/admin/display_applications', 'admin') webapp.add_client_route('/admin/roles', 'admin') webapp.add_client_route('/admin/forms', 'admin') webapp.add_client_route('/admin/groups', 'admin') webapp.add_client_route('/admin/repositories', 'admin') webapp.add_client_route('/admin/tool_versions', 'admin') webapp.add_client_route('/admin/quotas', 'admin') webapp.add_client_route('/admin/form/{form_id}', 'admin') webapp.add_client_route('/admin/api_keys', 'admin') 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('/openids/list') webapp.add_client_route('/visualizations') webapp.add_client_route('/visualizations/edit') webapp.add_client_route('/visualizations/sharing') webapp.add_client_route('/visualizations/list_published') webapp.add_client_route('/visualizations/list') webapp.add_client_route('/pages/list') webapp.add_client_route('/pages/list_published') webapp.add_client_route('/pages/create') webapp.add_client_route('/pages/edit') webapp.add_client_route('/pages/sharing') webapp.add_client_route('/histories/citations') webapp.add_client_route('/histories/list') webapp.add_client_route('/histories/import') webapp.add_client_route('/histories/list_published') webapp.add_client_route('/histories/list_shared') webapp.add_client_route('/histories/rename') webapp.add_client_route('/histories/sharing') webapp.add_client_route('/histories/permissions') webapp.add_client_route('/histories/view') webapp.add_client_route('/histories/show_structure') webapp.add_client_route('/datasets/list') webapp.add_client_route('/datasets/edit') webapp.add_client_route('/datasets/error') webapp.add_client_route('/workflows/list') webapp.add_client_route('/workflows/list_published') webapp.add_client_route('/workflows/create') webapp.add_client_route('/workflows/run') webapp.add_client_route('/workflows/import') 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 Exception: 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 Exception: 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
[docs]def uwsgi_app(): return galaxy.web.framework.webapp.build_native_uwsgi_app(app_factory, "galaxy")
# For backwards compatibility uwsgi_app_factory = uwsgi_app
[docs]def postfork_setup(): from galaxy.app import app app.control_worker.bind_and_start() app.application_stack.log_startup()
[docs]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.connect("history_contents_update_permissions", "/api/histories/{history_id}/contents/{history_content_id}/permissions", controller="history_contents", action="update_permissions", conditions=dict(method=["PUT"])) webapp.mapper.connect("history_contents_extra_files", "/api/histories/{history_id}/contents/{history_content_id}/extra_files", controller="datasets", action="extra_files", conditions=dict(method=["GET"])) webapp.mapper.connect("history_contents_metadata_file", "/api/histories/{history_id}/contents/{history_content_id}/metadata_file", controller="datasets", action="get_metadata_file", 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") webapp.mapper.connect('cloud_storage', '/api/cloud/storage/', controller='cloud', action='index', conditions=dict(method=["GET"])) webapp.mapper.connect('cloud_storage_get', '/api/cloud/storage/get', controller='cloud', action='get', conditions=dict(method=["POST"])) webapp.mapper.connect('cloud_storage_send', '/api/cloud/storage/send', controller='cloud', action='send', conditions=dict(method=["POST"])) _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('form', 'forms', path_prefix='/api') webapp.mapper.resource('role', 'roles', path_prefix='/api') webapp.mapper.resource('upload', 'uploads', 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') webapp.mapper.connect('/api/cloud/authz/', action='index', controller='cloudauthz', conditions=dict(method=["GET"])) webapp.mapper.connect('/api/cloud/authz/', action='create', controller='cloudauthz', conditions=dict(method=["POST"])) webapp.mapper.connect('get_custom_builds_metadata', '/api/histories/{id}/custom_builds_metadata', controller='histories', action='get_custom_builds_metadata', conditions=dict(method=["GET"])) # ======================= # ====== TOOLS API ====== # ======================= webapp.mapper.connect('/api/tools/fetch', action='fetch', controller='tools', conditions=dict(method=["POST"])) webapp.mapper.connect('/api/tools/all_requirements', action='all_requirements', controller="tools") webapp.mapper.connect('/api/tools/error_stack', action='error_stack', controller="tools") 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/tests_summary', action='tests_summary', controller="tools") webapp.mapper.connect('/api/tools/{id:.+?}/test_data_path', action='test_data_path', controller="tools") webapp.mapper.connect('/api/tools/{id:.+?}/test_data_download', action='test_data_download', controller="tools") webapp.mapper.connect('/api/tools/{id:.+?}/test_data', action='test_data', 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:.+?}/requirements', action='requirements', controller="tools") webapp.mapper.connect('/api/tools/{id:.+?}/install_dependencies', action='install_dependencies', controller="tools", conditions=dict(method=["POST"])) webapp.mapper.connect('/api/tools/{id:.+?}/dependencies', action='install_dependencies', controller="tools", conditions=dict(method=["POST"])) webapp.mapper.connect('/api/tools/{id:.+?}/dependencies', action='uninstall_dependencies', controller="tools", conditions=dict(method=["DELETE"])) webapp.mapper.connect('/api/tools/{id:.+?}/build_dependency_cache', action='build_dependency_cache', controller="tools", conditions=dict(method=["POST"])) webapp.mapper.connect('/api/tools/{id:.+?}', action='show', controller="tools") webapp.mapper.resource('tool', 'tools', path_prefix='/api') webapp.mapper.connect('/api/dependency_resolvers/clean', action="clean", controller="tool_dependencies", conditions=dict(method=["POST"])) webapp.mapper.connect('/api/dependency_resolvers/dependency', action="manager_dependency", controller="tool_dependencies", conditions=dict(method=["GET"])) webapp.mapper.connect('/api/dependency_resolvers/dependency', action="install_dependency", controller="tool_dependencies", conditions=dict(method=["POST"])) webapp.mapper.connect('/api/dependency_resolvers/requirements', action="manager_requirements", controller="tool_dependencies") webapp.mapper.connect('/api/dependency_resolvers/{id}/clean', action="clean", controller="tool_dependencies", conditions=dict(method=["POST"])) webapp.mapper.connect('/api/dependency_resolvers/{id}/dependency', action="resolver_dependency", controller="tool_dependencies", conditions=dict(method=["GET"])) webapp.mapper.connect('/api/dependency_resolvers/{id}/dependency', action="install_dependency", controller="tool_dependencies", conditions=dict(method=["POST"])) webapp.mapper.connect('/api/dependency_resolvers/{id}/requirements', action="resolver_requirements", controller="tool_dependencies") webapp.mapper.resource('dependency_resolver', 'dependency_resolvers', controller="tool_dependencies", path_prefix='api') webapp.mapper.resource_with_deleted('user', 'users', path_prefix='/api') webapp.mapper.resource('genome', 'genomes', path_prefix='/api') webapp.mapper.connect('/api/genomes/{id}/indexes', controller='genomes', action='indexes') webapp.mapper.connect('/api/genomes/{id}/sequences', controller='genomes', action='sequences') webapp.mapper.resource('visualization', 'visualizations', path_prefix='/api') webapp.mapper.connect('/api/visualizations/{id}/sharing', action='sharing', controller="visualizations", conditions=dict(method=["GET", "POST"])) webapp.mapper.resource('plugins', 'plugins', path_prefix='/api') webapp.mapper.connect('/api/workflows/build_module', action='build_module', controller="workflows") webapp.mapper.connect('/api/workflows/menu', action='get_workflow_menu', controller="workflows", conditions=dict(method=["GET"])) webapp.mapper.connect('/api/workflows/menu', action='set_workflow_menu', controller="workflows", conditions=dict(method=["PUT"])) 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('/api/histories/{id}/sharing', action='sharing', controller="histories", conditions=dict(method=["GET", "POST"])) 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.connect( '/api/configuration/toolbox', controller="configuration", action="reload_toolbox", conditions=dict(method=["PUT"]) ) 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.connect("api_whoami", "/api/whoami", controller='configuration', action='whoami', conditions=dict(method=["GET"])) webapp.mapper.connect("api_decode", "/api/configuration/decode/{encoded_id}", controller='configuration', action='decode_id', conditions=dict(method=["GET"])) webapp.mapper.resource('datatype', 'datatypes', path_prefix='/api', collection={'sniffers': 'GET', 'mapping': 'GET', 'converters': 'GET', 'edam_data': '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.connect('/api/pages/{id}/sharing', action='sharing', controller="pages", conditions=dict(method=["GET", "POST"])) 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('/api/histories/{history_id}/contents/archive', controller='history_contents', action='archive') webapp.mapper.connect('/api/histories/{history_id}/contents/archive/{filename}{.format}', controller='history_contents', action='archive') webapp.mapper.connect("/api/histories/{history_id}/contents/dataset_collections/{id}/download", controller='history_contents', action='download_dataset_collection', conditions=dict(method=["GET"])) webapp.mapper.connect("/api/dataset_collections/{id}/download", controller='history_contents', action='download_dataset_collection', conditions=dict(method=["GET"])) webapp.mapper.connect("/api/histories/{history_id}/jobs_summary", action="index_jobs_summary", controller='history_contents', conditions=dict(method=["GET"])) webapp.mapper.connect("/api/histories/{history_id}/contents/{type:%s}s/{id}/jobs_summary" % "|".join(valid_history_contents_types), action="show_jobs_summary", controller='history_contents', conditions=dict(method=["GET"])) # ---- visualizations registry ---- generic template renderer # @deprecated: this route should be considered deprecated webapp.add_route('/visualization/show/{visualization_name}', controller='visualization', action='render', visualization_name=None) # provide an alternate route to visualization plugins that's closer to their static assets # (/plugins/visualizations/{visualization_name}/static) and allow them to use relative urls to those webapp.mapper.connect('visualization_plugin', '/plugins/visualizations/{visualization_name}/show', controller='visualization', action='render') webapp.mapper.connect('saved_visualization', '/plugins/visualizations/{visualization_name}/saved', controller='visualization', action='saved') # same with IE's webapp.mapper.connect('interactive_environment_plugin', '/plugins/interactive_environments/{visualization_name}/show', controller='visualization', action='render') webapp.mapper.connect('saved_interactive_environment', '/plugins/interactive_environments/{visualization_name}/saved', controller='visualization', action='saved') # 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'])) webapp.mapper.connect('show_versions', '/api/workflows/{workflow_id}/versions', controller='workflows', action='show_versions', 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') webapp.mapper.connect('/api/datasets/{dataset_id}/permissions', controller='datasets', action='update_permissions', conditions=dict(method=["PUT"])) # 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.items(): 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( 'list_invocations', '/api/invocations', 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"])) # ====================================== # ====== DISPLAY APPLICATIONS API ====== # ====================================== webapp.mapper.connect('index', '/api/display_applications', controller='display_applications', action='index', conditions=dict(method=["GET"])) webapp.mapper.connect('reload', '/api/display_applications/reload', controller='display_applications', action='reload', conditions=dict(method=["POST"])) # ===================== # ===== TOURS API ===== # ===================== webapp.mapper.connect('index', '/api/tours', controller='tours', action='index', conditions=dict(method=["GET"])) webapp.mapper.connect('show', '/api/tours/{tour_id}', controller='tours', action='show', conditions=dict(method=["GET"])) webapp.mapper.connect('update_tour', '/api/tours/{tour_id}', controller='tours', action='update_tour', conditions=dict(method=["POST"])) # ================================ # ===== USERS API ===== # ================================ webapp.mapper.connect('api_key', '/api/users/{id}/api_key', controller='users', action='api_key', conditions=dict(method=["POST"])) webapp.mapper.connect('get_api_key', '/api/users/{id}/api_key/inputs', controller='users', action='get_api_key', conditions=dict(method=["GET"])) webapp.mapper.connect('set_api_key', '/api/users/{id}/api_key/inputs', controller='users', action='set_api_key', conditions=dict(method=["PUT"])) webapp.mapper.connect('get_information', '/api/users/{id}/information/inputs', controller='users', action='get_information', conditions=dict(method=["GET"])) webapp.mapper.connect('set_information', '/api/users/{id}/information/inputs', controller='users', action='set_information', conditions=dict(method=["PUT"])) webapp.mapper.connect('get_password', '/api/users/{id}/password/inputs', controller='users', action='get_password', conditions=dict(method=["GET"])) webapp.mapper.connect('set_password', '/api/users/{id}/password/inputs', controller='users', action='set_password', conditions=dict(method=["PUT"])) webapp.mapper.connect('get_permissions', '/api/users/{id}/permissions/inputs', controller='users', action='get_permissions', conditions=dict(method=["GET"])) webapp.mapper.connect('set_permissions', '/api/users/{id}/permissions/inputs', controller='users', action='set_permissions', conditions=dict(method=["PUT"])) webapp.mapper.connect('get_toolbox_filters', '/api/users/{id}/toolbox_filters/inputs', controller='users', action='get_toolbox_filters', conditions=dict(method=["GET"])) webapp.mapper.connect('set_toolbox_filters', '/api/users/{id}/toolbox_filters/inputs', controller='users', action='set_toolbox_filters', conditions=dict(method=["PUT"])) webapp.mapper.connect('get_communication', '/api/users/{id}/communication/inputs', controller='users', action='get_communication', conditions=dict(method=["GET"])) webapp.mapper.connect('set_communication', '/api/users/{id}/communication/inputs', controller='users', action='set_communication', conditions=dict(method=["PUT"])) webapp.mapper.connect('get_custom_builds', '/api/users/{id}/custom_builds', controller='users', action='get_custom_builds', conditions=dict(method=["GET"])) webapp.mapper.connect('add_custom_builds', '/api/users/{id}/custom_builds/{key}', controller='users', action='add_custom_builds', conditions=dict(method=["PUT"])) webapp.mapper.connect('delete_custom_builds', '/api/users/{id}/custom_builds/{key}', controller='users', action='delete_custom_builds', conditions=dict(method=["DELETE"])) # ======================== # ===== WEBHOOKS API ===== # ======================== webapp.mapper.connect('get_all_webhooks', '/api/webhooks', controller='webhooks', action='all_webhooks', conditions=dict(method=['GET'])) webapp.mapper.connect('get_webhook_data', '/api/webhooks/{webhook_id}/data', controller='webhooks', action='webhook_data', 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"])) # POST for legacy reasons, but this should be a PUT. webapp.mapper.connect('set_library_permissions', '/api/libraries/{encoded_library_id}/permissions', controller='libraries', action='set_permissions', conditions=dict(method=["POST", "PUT"])) webapp.mapper.connect('show_ld_item', '/api/libraries/datasets/{id}', controller='library_datasets', action='show', conditions=dict(method=["GET"])) webapp.mapper.connect('load_ld', '/api/libraries/datasets/', controller='library_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='library_datasets', action='show_version', conditions=dict(method=["GET"])) webapp.mapper.connect('update_ld', '/api/libraries/datasets/{encoded_dataset_id}', controller='library_datasets', action='update', conditions=dict(method=["PATCH"])) webapp.mapper.connect('show_legitimate_ld_roles', '/api/libraries/datasets/{encoded_dataset_id}/permissions', controller='library_datasets', action='show_roles', conditions=dict(method=["GET"])) webapp.mapper.connect('update_ld_permissions', '/api/libraries/datasets/{encoded_dataset_id}/permissions', controller='library_datasets', action='update_permissions', conditions=dict(method=["POST"])) webapp.mapper.connect('delete_ld_item', '/api/libraries/datasets/{encoded_dataset_id}', controller='library_datasets', action='delete', conditions=dict(method=["DELETE"])) webapp.mapper.connect('download_ld_items', '/api/libraries/datasets/download/{format}', controller='library_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'])) webapp.mapper.connect('resume', '/api/jobs/{id}/resume', controller='jobs', action='resume', conditions=dict(method=['PUT'])) webapp.mapper.connect('job_error', '/api/jobs/{id}/error', controller='jobs', action='error', conditions=dict(method=['POST'])) # 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) webapp.mapper.connect('tool_shed_contents', '/api/tool_shed/contents', controller='toolshed', action='show', conditions=dict(method=["GET"])) webapp.mapper.connect('tool_shed_category_contents', '/api/tool_shed/category', controller='toolshed', action='category', conditions=dict(method=["GET"])) webapp.mapper.connect('tool_shed_repository_details', '/api/tool_shed/repository', controller='toolshed', action='repository', conditions=dict(method=["GET"])) webapp.mapper.connect('tool_sheds', '/api/tool_shed', controller='toolshed', action='index', conditions=dict(method=["GET"])) webapp.mapper.connect('tool_shed_search', '/api/tool_shed/search', controller='toolshed', action='search', conditions=dict(method=["GET", "POST"])) webapp.mapper.connect('tool_shed_status', '/api/tool_shed/status', controller='toolshed', action='status', conditions=dict(method=["GET", "POST"])) webapp.mapper.connect('shed_tool_json', '/api/tool_shed/tool_json', controller='toolshed', action='tool_json', conditions=dict(method=["GET"])) webapp.mapper.connect('tool_shed_repository', '/api/tool_shed_repositories/:id/status', controller='tool_shed_repositories', action='status', conditions=dict(method=["GET"])) webapp.mapper.connect('install_repository', '/api/tool_shed_repositories', controller='tool_shed_repositories', action='install_repository_revision', conditions=dict(method=['POST'])) webapp.mapper.connect('install_repository', '/api/tool_shed_repositories/install', controller='tool_shed_repositories', action='install', conditions=dict(method=['POST'])) webapp.mapper.connect('check_for_updates', '/api/tool_shed_repositories/check_for_updates', controller='tool_shed_repositories', action='check_for_updates', conditions=dict(method=['GET'])) webapp.mapper.connect('tool_shed_repository', '/api/tool_shed_repositories', controller='tool_shed_repositories', action='uninstall_repository', conditions=dict(method=["DELETE"])) webapp.mapper.connect('tool_shed_repository', '/api/tool_shed_repositories/{id}', controller='tool_shed_repositories', action='uninstall_repository', conditions=dict(method=["DELETE"])) # 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 _add_item_tags_controller(webapp, name_prefix, path_prefix, **kwd): # Not just using map.resources because actions should be based on name not id controller = "%stags" % name_prefix name = "%stag" % name_prefix path = "%s/tags" % path_prefix map = webapp.mapper # Allow view items' tags. map.connect(name, path, controller=controller, action="index", conditions=dict(method=["GET"])) # Allow remove tag from item map.connect("%s_delete" % name, "%s/tags/{tag_name}" % path_prefix, controller=controller, action="delete", conditions=dict(method=["DELETE"])) # Allow create a new tag with from name map.connect("%s_create" % name, "%s/tags/{tag_name}" % path_prefix, controller=controller, action="create", conditions=dict(method=["POST"])) # Allow update tag value map.connect("%s_update" % name, "%s/tags/{tag_name}" % path_prefix, controller=controller, action="update", conditions=dict(method=["PUT"])) # Allow show tag by name map.connect("%s_show" % name, "%s/tags/{tag_name}" % path_prefix, controller=controller, action="show", conditions=dict(method=["GET"])) def _add_item_extended_metadata_controller(webapp, name_prefix, path_prefix, **kwd): controller = "%sextended_metadata" % name_prefix name = "%sextended_metadata" % name_prefix webapp.mapper.resource(name, "extended_metadata", path_prefix=path_prefix, controller=controller) def _add_item_annotation_controller(webapp, name_prefix, path_prefix, **kwd): controller = "%sannotations" % name_prefix name = "%sannotation" % name_prefix webapp.mapper.resource(name, "annotation", path_prefix=path_prefix, controller=controller) def _add_item_provenance_controller(webapp, name_prefix, path_prefix, **kwd): controller = "%sprovenance" % name_prefix name = "%sprovenance" % name_prefix webapp.mapper.resource(name, "provenance", path_prefix=path_prefix, controller=controller)
[docs]def wrap_in_middleware(app, global_conf, application_stack, **local_conf): """ Based on the configuration wrap `app` in a set of common and useful middleware. """ webapp = app stack = application_stack # Merge the global and local configurations conf = global_conf.copy() conf.update(local_conf) debug = asbool(conf.get('debug', False)) # First put into place httpexceptions, which must be most closely # wrapped around the application (it can interact poorly with # other middleware): app = wrap_if_allowed(app, stack, httpexceptions.make_middleware, name='paste.httpexceptions', args=(conf,)) # Statsd request timing and profiling statsd_host = conf.get('statsd_host', None) if statsd_host: from galaxy.web.framework.middleware.statsd import StatsdMiddleware app = wrap_if_allowed(app, stack, StatsdMiddleware, args=(statsd_host, conf.get('statsd_port', 8125), conf.get('statsd_prefix', 'galaxy'), conf.get('statsd_influxdb', False))) log.debug("Enabling 'statsd' middleware") # If we're using remote_user authentication, add middleware that # protects Galaxy from improperly configured authentication in the # upstream server single_user = conf.get('single_user', None) use_remote_user = asbool(conf.get('use_remote_user', False)) or single_user if use_remote_user: from galaxy.web.framework.middleware.remoteuser import RemoteUser app = wrap_if_allowed(app, stack, RemoteUser, kwargs=dict( maildomain=conf.get('remote_user_maildomain', None), display_servers=util.listify(conf.get('display_servers', '')), single_user=single_user, admin_users=conf.get('admin_users', '').split(','), remote_user_header=conf.get('remote_user_header', 'HTTP_REMOTE_USER'), remote_user_secret_header=conf.get('remote_user_secret', None), normalize_remote_user_email=conf.get('normalize_remote_user_email', False))) # The recursive middleware allows for including requests in other # requests or forwarding of requests, all on the server side. if asbool(conf.get('use_recursive', True)): from paste import recursive app = wrap_if_allowed(app, stack, recursive.RecursiveMiddleware, args=(conf,)) # If sentry logging is enabled, log here before propogating up to # the error middleware sentry_dsn = conf.get('sentry_dsn', None) sentry_sloreq = float(conf.get('sentry_sloreq_threshold', 0)) if sentry_dsn: from galaxy.web.framework.middleware.sentry import Sentry app = wrap_if_allowed(app, stack, Sentry, args=(sentry_dsn, sentry_sloreq)) # Various debug middleware that can only be turned on if the debug # flag is set, either because they are insecure or greatly hurt # performance if debug: # Middleware to check for WSGI compliance if asbool(conf.get('use_lint', False)): from paste import lint app = wrap_if_allowed(app, stack, lint.make_middleware, name='paste.lint', args=(conf,)) # Middleware to run the python profiler on each request if asbool(conf.get('use_profile', False)): from paste.debug import profile app = wrap_if_allowed(app, stack, profile.ProfileMiddleware, args=(conf,)) if debug and asbool(conf.get('use_interactive', False)): # Interactive exception debugging, scary dangerous if publicly # accessible, if not enabled we'll use the regular error printing # middleware. try: from weberror import evalexception app = wrap_if_allowed_or_fail(app, stack, evalexception.EvalException, args=(conf,), kwargs=dict(templating_formatters=build_template_error_formatters())) except MiddlewareWrapUnsupported as exc: log.warning(str(exc)) import galaxy.web.framework.middleware.error app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,)) else: # Not in interactive debug mode, just use the regular error middleware import galaxy.web.framework.middleware.error app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,)) # Transaction logging (apache access.log style) if asbool(conf.get('use_translogger', True)): from galaxy.web.framework.middleware.translogger import TransLogger app = wrap_if_allowed(app, stack, TransLogger) # X-Forwarded-Host handling from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware app = wrap_if_allowed(app, stack, XForwardedHostMiddleware) # Request ID middleware from galaxy.web.framework.middleware.request_id import RequestIDMiddleware app = wrap_if_allowed(app, stack, RequestIDMiddleware) # api batch call processing middleware from galaxy.web.framework.middleware.batch import BatchMiddleware app = wrap_if_allowed(app, stack, BatchMiddleware, args=(webapp, {})) if asbool(conf.get('enable_per_request_sql_debugging', False)): from galaxy.web.framework.middleware.sqldebug import SQLDebugMiddleware app = wrap_if_allowed(app, stack, SQLDebugMiddleware, args=(webapp, {})) return app
[docs]def wrap_in_static(app, global_conf, plugin_frameworks=None, **local_conf): urlmap, cache_time = galaxy.web.framework.webapp.build_url_map(app, global_conf, local_conf) return urlmap