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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]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