mirror of
https://github.com/galaxyproject/galaxy.git
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pep8, cleanup in galaxy/buildapp
This commit is contained in:
Dannon Baker
@@ -6,8 +6,6 @@ import sys
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import os
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import os.path
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import atexit
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import warnings
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import glob
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from paste import httpexceptions
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import pkg_resources
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@@ -28,6 +26,7 @@ log = logging.getLogger( __name__ )
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class GalaxyWebApplication( galaxy.web.framework.webapp.WebApplication ):
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pass
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def app_factory( global_conf, **kwargs ):
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"""
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Return a wsgi application serving the root object
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@@ -41,7 +40,7 @@ def app_factory( global_conf, **kwargs ):
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else:
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try:
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from galaxy.app import UniverseApplication
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app = UniverseApplication( global_conf = global_conf, **kwargs )
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app = UniverseApplication( global_conf=global_conf, **kwargs )
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except:
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import traceback
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traceback.print_exc()
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@@ -65,8 +64,8 @@ def app_factory( global_conf, **kwargs ):
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webapp.add_route( '/datasets/:dataset_id/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None)
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webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None)
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webapp.add_route( '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param',
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controller='dataset', action='display_application', dataset_id=None, user_id=None,
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app_name = None, link_name = None, app_action = None, action_param = None )
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controller='dataset', action='display_application', dataset_id=None, user_id=None,
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app_name=None, link_name=None, app_action=None, action_param=None )
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webapp.add_route( '/u/:username/d/:slug/:filename', controller='dataset', action='display_by_username_and_slug', filename=None )
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webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' )
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webapp.add_route( '/u/:username/h/:slug', controller='history', action='display_by_username_and_slug' )
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@@ -103,7 +102,6 @@ def app_factory( global_conf, **kwargs ):
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log.error("Static middleware is enabled in your configuration but this is a uwsgi process. Refusing to wrap in static middleware.")
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else:
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webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=[ app.visualizations_registry ], **kwargs )
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#webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=None, **kwargs )
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if asbool(kwargs.get('pack_scripts', False)):
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log.warn( "The 'pack_scripts' option is deprecated" )
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pack_scripts()
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@@ -112,7 +110,6 @@ def app_factory( global_conf, **kwargs ):
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galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose()
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except:
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pass
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# Close any pooled database connections before forking
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try:
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galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose()
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except:
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@@ -137,32 +134,32 @@ def populate_api_routes( webapp, app ):
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controller='history_contents',
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path_prefix='/api/histories/:history_id/contents',
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parent_resources=dict( member_name='history', collection_name='histories' ),
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)
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)
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# Legacy access to HDA details via histories/:history_id/contents/:hda_id
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webapp.mapper.resource( 'content',
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'contents',
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controller='history_contents',
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name_prefix='history_',
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path_prefix='/api/histories/:history_id',
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parent_resources=dict( member_name='history', collection_name='histories' ) )
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webapp.mapper.connect("history_contents_display",
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"/api/histories/:history_id/contents/:history_content_id/display",
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controller="datasets",
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action="display",
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conditions=dict(method=["GET"]))
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'contents',
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controller='history_contents',
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name_prefix='history_',
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path_prefix='/api/histories/:history_id',
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parent_resources=dict( member_name='history', collection_name='histories' ) )
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webapp.mapper.connect( "history_contents_display",
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"/api/histories/:history_id/contents/:history_content_id/display",
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controller="datasets",
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action="display",
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conditions=dict(method=["GET"]))
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webapp.mapper.resource( 'user',
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'users',
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controller='group_users',
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name_prefix='group_',
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path_prefix='/api/groups/:group_id',
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parent_resources=dict( member_name='group', collection_name='groups' ) )
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'users',
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controller='group_users',
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name_prefix='group_',
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path_prefix='/api/groups/:group_id',
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parent_resources=dict( member_name='group', collection_name='groups' ) )
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webapp.mapper.resource( 'role',
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'roles',
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controller='group_roles',
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name_prefix='group_',
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path_prefix='/api/groups/:group_id',
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parent_resources=dict( member_name='group', collection_name='groups' ) )
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'roles',
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controller='group_roles',
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name_prefix='group_',
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path_prefix='/api/groups/:group_id',
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parent_resources=dict( member_name='group', collection_name='groups' ) )
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_add_item_tags_controller( webapp,
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name_prefix="history_content_",
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path_prefix='/api/histories/:history_id/contents/:history_content_id' )
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@@ -173,17 +170,17 @@ def populate_api_routes( webapp, app ):
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name_prefix="workflow_",
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path_prefix='/api/workflows/:workflow_id' )
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_add_item_annotation_controller( webapp,
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name_prefix="history_content_",
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path_prefix='/api/histories/:history_id/contents/:history_content_id' )
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name_prefix="history_content_",
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path_prefix='/api/histories/:history_id/contents/:history_content_id' )
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_add_item_annotation_controller( webapp,
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name_prefix="history_",
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path_prefix='/api/histories/:history_id' )
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name_prefix="history_",
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path_prefix='/api/histories/:history_id' )
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_add_item_annotation_controller( webapp,
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name_prefix="workflow_",
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path_prefix='/api/workflows/:workflow_id' )
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name_prefix="workflow_",
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path_prefix='/api/workflows/:workflow_id' )
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_add_item_provenance_controller( webapp,
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name_prefix="history_content_",
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path_prefix='/api/histories/:history_id/contents/:history_content_id' )
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name_prefix="history_content_",
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path_prefix='/api/histories/:history_id/contents/:history_content_id' )
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webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' )
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webapp.mapper.resource( 'tool_data', 'tool_data', path_prefix='/api' )
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@@ -216,27 +213,28 @@ def populate_api_routes( webapp, app ):
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webapp.mapper.resource( 'datatype',
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'datatypes',
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path_prefix='/api',
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collection={ 'sniffers': 'GET', 'mapping' : 'GET', 'converters': 'GET' },
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collection={ 'sniffers': 'GET', 'mapping': 'GET', 'converters': 'GET' },
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parent_resources=dict( member_name='datatype', collection_name='datatypes' ) )
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#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"]) )
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webapp.mapper.resource( 'search', 'search', path_prefix='/api' )
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webapp.mapper.resource( 'page', 'pages', path_prefix="/api")
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webapp.mapper.resource( 'revision', 'revisions',
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path_prefix='/api/pages/:page_id',
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controller='page_revisions',
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parent_resources=dict( member_name='page', collection_name='pages' ) )
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path_prefix='/api/pages/:page_id',
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controller='page_revisions',
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parent_resources=dict( member_name='page', collection_name='pages' ) )
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webapp.mapper.connect( "history_archive_export", "/api/histories/{id}/exports",
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controller="histories", action="archive_export", conditions=dict( method=[ "PUT" ] ) )
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webapp.mapper.connect( "history_archive_download", "/api/histories/{id}/exports/{jeha_id}",
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controller="histories", action="archive_download", conditions=dict( method=[ "GET" ] ) )
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webapp.mapper.connect( "history_archive_export",
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"/api/histories/{id}/exports", controller="histories",
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action="archive_export", conditions=dict( method=[ "PUT" ] ) )
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webapp.mapper.connect( "history_archive_download",
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"/api/histories/{id}/exports/{jeha_id}", controller="histories",
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action="archive_download", conditions=dict( method=[ "GET" ] ) )
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webapp.mapper.connect( "create_api_key", "/api/users/:user_id/api_key",
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controller="users", action="api_key", user_id=None, conditions=dict( method=["POST"] ) )
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controller="users", action="api_key", user_id=None,
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conditions=dict( method=["POST"] ) )
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# visualizations registry generic template renderer
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webapp.add_route( '/visualization/show/:visualization_name',
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controller='visualization', action='render', visualization_name=None )
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webapp.add_route( '/visualization/show/:visualization_name', controller='visualization', action='render', visualization_name=None )
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# Deprecated in favor of POST /api/workflows with 'workflow' in payload.
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webapp.mapper.connect( 'import_workflow_deprecated', '/api/workflows/upload', controller='workflows', action='import_new_workflow_deprecated', conditions=dict( method=['POST'] ) )
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@@ -446,8 +444,8 @@ def populate_api_routes( webapp, app ):
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parent_resources=dict( member_name="job", collection_name="jobs" ) )
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_add_item_extended_metadata_controller( webapp,
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name_prefix="history_dataset_",
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path_prefix='/api/histories/:history_id/contents/:history_content_id' )
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name_prefix="history_dataset_",
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path_prefix='/api/histories/:history_id/contents/:history_content_id' )
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# ====================
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# ===== TOOLSHED =====
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@@ -463,46 +461,46 @@ def populate_api_routes( webapp, app ):
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# Galaxy API for tool shed features.
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webapp.mapper.resource( 'tool_shed_repository',
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'tool_shed_repositories',
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member={ 'repair_repository_revision' : 'POST',
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'exported_workflows' : 'GET',
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'import_workflow' : 'POST',
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'import_workflows' : 'POST' },
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collection={ 'get_latest_installable_revision' : 'POST',
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'reset_metadata_on_installed_repositories' : 'POST' },
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member={ 'repair_repository_revision': 'POST',
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'exported_workflows': 'GET',
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'import_workflow': 'POST',
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'import_workflows': 'POST' },
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collection={ 'get_latest_installable_revision': 'POST',
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'reset_metadata_on_installed_repositories': 'POST' },
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controller='tool_shed_repositories',
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name_prefix='tool_shed_repository_',
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path_prefix='/api',
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new={ 'install_repository_revision' : 'POST' },
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new={ 'install_repository_revision': 'POST' },
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parent_resources=dict( member_name='tool_shed_repository', collection_name='tool_shed_repositories' ) )
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# ==== Trace/Metrics Logger
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# Connect logger from app
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if app.trace_logger:
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webapp.trace_logger = app.trace_logger
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# metrics logging API
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#webapp.mapper.connect( "index", "/api/metrics",
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# webapp.mapper.connect( "index", "/api/metrics",
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# controller="metrics", action="index", conditions=dict( method=["GET"] ) )
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#webapp.mapper.connect( "show", "/api/metrics/{id}",
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# webapp.mapper.connect( "show", "/api/metrics/{id}",
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# controller="metrics", action="show", conditions=dict( method=["GET"] ) )
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webapp.mapper.connect( "create", "/api/metrics",
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controller="metrics", action="create", conditions=dict( method=["POST"] ) )
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webapp.mapper.connect( "create", "/api/metrics", controller="metrics",
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action="create", conditions=dict( method=["POST"] ) )
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def pack_scripts():
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from glob import glob
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from subprocess import call
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cmd = "java -jar scripts/yuicompressor.jar --type js static/scripts/%(fname)s -o static/scripts/packed/%(fname)s"
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raw_js= [os.path.basename(g) for g in glob( "static/scripts/*.js" )]
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raw_js = [os.path.basename(g) for g in glob( "static/scripts/*.js" )]
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for fname in raw_js:
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if os.path.exists('static/scripts/packed/%s' % fname):
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if os.path.getmtime('static/scripts/packed/%s' % fname) > os.path.getmtime('static/scripts/%s' % fname):
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continue # Skip, packed is newer than source.
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continue # Skip, packed is newer than source.
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d = dict( fname=fname )
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log.info("%(fname)s --> packed/%(fname)s" % d)
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call( cmd % d, shell=True )
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def _add_item_tags_controller( webapp, name_prefix, path_prefix, **kwd ):
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# Not just using map.resources because actions should be based on name not id
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controller = "%stags" % name_prefix
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@@ -511,24 +509,24 @@ def _add_item_tags_controller( webapp, name_prefix, path_prefix, **kwd ):
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map = webapp.mapper
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# Allow view items' tags.
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map.connect(name, path,
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controller=controller, action="index",
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conditions=dict(method=["GET"]))
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controller=controller, action="index",
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conditions=dict(method=["GET"]))
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# Allow remove tag from item
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map.connect("%s_delete" % name, "%s/tags/:tag_name" % path_prefix,
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controller=controller, action="delete",
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conditions=dict(method=["DELETE"]))
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controller=controller, action="delete",
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conditions=dict(method=["DELETE"]))
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# Allow create a new tag with from name
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map.connect("%s_create" % name, "%s/tags/:tag_name" % path_prefix,
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controller=controller, action="create",
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conditions=dict(method=["POST"]))
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controller=controller, action="create",
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conditions=dict(method=["POST"]))
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# Allow update tag value
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map.connect("%s_update" % name, "%s/tags/:tag_name" % path_prefix,
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controller=controller, action="update",
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conditions=dict(method=["PUT"]))
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controller=controller, action="update",
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conditions=dict(method=["PUT"]))
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# Allow show tag by name
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map.connect("%s_show" % name, "%s/tags/:tag_name" % path_prefix,
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controller=controller, action="show",
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conditions=dict(method=["GET"]))
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controller=controller, action="show",
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conditions=dict(method=["GET"]))
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def _add_item_extended_metadata_controller( webapp, name_prefix, path_prefix, **kwd ):
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@@ -536,11 +534,13 @@ def _add_item_extended_metadata_controller( webapp, name_prefix, path_prefix, **
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name = "%sextended_metadata" % name_prefix
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webapp.mapper.resource(name, "extended_metadata", path_prefix=path_prefix, controller=controller)
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def _add_item_annotation_controller( webapp, name_prefix, path_prefix, **kwd ):
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controller = "%sannotations" % name_prefix
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name = "%sannotation" % name_prefix
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webapp.mapper.resource(name, "annotation", path_prefix=path_prefix, controller=controller)
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def _add_item_provenance_controller( webapp, name_prefix, path_prefix, **kwd ):
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controller = "%sprovenance" % name_prefix
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name = "%sprovenance" % name_prefix
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@@ -566,11 +566,11 @@ def wrap_in_middleware( app, global_conf, **local_conf ):
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# upstream server
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if asbool(conf.get( 'use_remote_user', False )):
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from galaxy.web.framework.middleware.remoteuser import RemoteUser
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app = RemoteUser( app, maildomain = conf.get( 'remote_user_maildomain', None ),
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display_servers = util.listify( conf.get( 'display_servers', '' ) ),
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admin_users = conf.get( 'admin_users', '' ).split( ',' ),
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remote_user_header = conf.get( 'remote_user_header', 'HTTP_REMOTE_USER' ),
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remote_user_secret_header = conf.get('remote_user_secret', None) )
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app = RemoteUser( app, maildomain=conf.get( 'remote_user_maildomain', None ),
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display_servers=util.listify( conf.get( 'display_servers', '' ) ),
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admin_users=conf.get( 'admin_users', '' ).split( ',' ),
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remote_user_header=conf.get( 'remote_user_header', 'HTTP_REMOTE_USER' ),
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remote_user_secret_header=conf.get('remote_user_secret', None) )
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# The recursive middleware allows for including requests in other
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# requests or forwarding of requests, all on the server side.
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if asbool(conf.get('use_recursive', True)):
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@@ -626,6 +626,7 @@ def wrap_in_middleware( app, global_conf, **local_conf ):
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log.debug( "Enabling 'Request ID' middleware" )
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return app
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def wrap_in_static( app, global_conf, plugin_frameworks=None, **local_conf ):
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from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static
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urlmap, cache_time = galaxy.web.framework.webapp.build_url_map( app, global_conf, local_conf )
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@@ -642,6 +643,7 @@ def wrap_in_static( app, global_conf, plugin_frameworks=None, **local_conf ):
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# URL mapper becomes the root webapp
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return urlmap
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def build_template_error_formatters():
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"""
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Build a list of template error formatters for WebError. When an error
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@@ -651,6 +653,7 @@ def build_template_error_formatters():
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formatters = []
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# Formatter for mako
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import mako.exceptions
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def mako_html_data( exc_value ):
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if isinstance( exc_value, ( mako.exceptions.CompileException, mako.exceptions.SyntaxException ) ):
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return mako.exceptions.html_error_template().render( full=False, css=False )
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