1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6133a80c7a08/ Changeset: 6133a80c7a08 User: dannon Date: 2015-02-05 14:45:15+00:00 Summary: pep8, cleanup in galaxy/buildapp Affected #: 1 file
diff -r cca00d61df85a6ecd1be49265f0c92e7482b91f9 -r 6133a80c7a08b88f1e7d2e83456acdc329b88b47 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -6,8 +6,6 @@ import os import os.path import atexit -import warnings -import glob
from paste import httpexceptions import pkg_resources @@ -28,6 +26,7 @@ class GalaxyWebApplication( galaxy.web.framework.webapp.WebApplication ): pass
+ def app_factory( global_conf, **kwargs ): """ Return a wsgi application serving the root object @@ -41,7 +40,7 @@ else: try: from galaxy.app import UniverseApplication - app = UniverseApplication( global_conf = global_conf, **kwargs ) + app = UniverseApplication( global_conf=global_conf, **kwargs ) except: import traceback traceback.print_exc() @@ -65,8 +64,8 @@ webapp.add_route( '/datasets/:dataset_id/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None) webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None) webapp.add_route( '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param', - controller='dataset', action='display_application', dataset_id=None, user_id=None, - app_name = None, link_name = None, app_action = None, action_param = None ) + controller='dataset', action='display_application', dataset_id=None, user_id=None, + app_name=None, link_name=None, app_action=None, action_param=None ) webapp.add_route( '/u/:username/d/:slug/:filename', controller='dataset', action='display_by_username_and_slug', filename=None ) webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' ) webapp.add_route( '/u/:username/h/:slug', controller='history', action='display_by_username_and_slug' ) @@ -103,7 +102,6 @@ log.error("Static middleware is enabled in your configuration but this is a uwsgi process. Refusing to wrap in static middleware.") else: webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=[ app.visualizations_registry ], **kwargs ) - #webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=None, **kwargs ) if asbool(kwargs.get('pack_scripts', False)): log.warn( "The 'pack_scripts' option is deprecated" ) pack_scripts() @@ -112,7 +110,6 @@ galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose() except: pass - # Close any pooled database connections before forking try: galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose() except: @@ -137,32 +134,32 @@ 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"])) + 'contents', + controller='history_contents', + name_prefix='history_', + path_prefix='/api/histories/:history_id', + parent_resources=dict( member_name='history', collection_name='histories' ) ) + webapp.mapper.connect( "history_contents_display", + "/api/histories/:history_id/contents/:history_content_id/display", + controller="datasets", + action="display", + conditions=dict(method=["GET"])) webapp.mapper.resource( 'user', - 'users', - controller='group_users', - name_prefix='group_', - path_prefix='/api/groups/:group_id', - parent_resources=dict( member_name='group', collection_name='groups' ) ) + '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' ) ) + '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' ) @@ -173,17 +170,17 @@ 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' ) + 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' ) + name_prefix="history_", + path_prefix='/api/histories/:history_id' ) _add_item_annotation_controller( webapp, - name_prefix="workflow_", - path_prefix='/api/workflows/:workflow_id' ) + 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' ) + 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' ) @@ -216,27 +213,28 @@ webapp.mapper.resource( 'datatype', 'datatypes', path_prefix='/api', - collection={ 'sniffers': 'GET', 'mapping' : 'GET', 'converters': 'GET' }, + collection={ 'sniffers': 'GET', 'mapping': 'GET', 'converters': 'GET' }, parent_resources=dict( member_name='datatype', collection_name='datatypes' ) ) - #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) webapp.mapper.resource( 'page', 'pages', path_prefix="/api") webapp.mapper.resource( 'revision', 'revisions', - path_prefix='/api/pages/:page_id', - controller='page_revisions', - parent_resources=dict( member_name='page', collection_name='pages' ) ) + 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( "history_archive_export", + "/api/histories/{id}/exports", controller="histories", + action="archive_export", conditions=dict( method=[ "PUT" ] ) ) + webapp.mapper.connect( "history_archive_download", + "/api/histories/{id}/exports/{jeha_id}", controller="histories", + action="archive_download", conditions=dict( method=[ "GET" ] ) )
webapp.mapper.connect( "create_api_key", "/api/users/:user_id/api_key", - controller="users", action="api_key", user_id=None, conditions=dict( method=["POST"] ) ) + controller="users", action="api_key", user_id=None, + conditions=dict( method=["POST"] ) )
# visualizations registry generic template renderer - webapp.add_route( '/visualization/show/:visualization_name', - controller='visualization', action='render', visualization_name=None ) + webapp.add_route( '/visualization/show/:visualization_name', controller='visualization', action='render', visualization_name=None )
# Deprecated in favor of POST /api/workflows with 'workflow' in payload. webapp.mapper.connect( 'import_workflow_deprecated', '/api/workflows/upload', controller='workflows', action='import_new_workflow_deprecated', conditions=dict( method=['POST'] ) ) @@ -446,8 +444,8 @@ 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' ) + name_prefix="history_dataset_", + path_prefix='/api/histories/:history_id/contents/:history_content_id' )
# ==================== # ===== TOOLSHED ===== @@ -463,46 +461,46 @@ # 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' }, + 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' }, + 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", + # webapp.mapper.connect( "index", "/api/metrics", # controller="metrics", action="index", conditions=dict( method=["GET"] ) ) - #webapp.mapper.connect( "show", "/api/metrics/{id}", + # 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"] ) ) + webapp.mapper.connect( "create", "/api/metrics", controller="metrics", + action="create", conditions=dict( method=["POST"] ) )
def pack_scripts(): from glob import glob from subprocess import call cmd = "java -jar scripts/yuicompressor.jar --type js static/scripts/%(fname)s -o static/scripts/packed/%(fname)s" - raw_js= [os.path.basename(g) for g in glob( "static/scripts/*.js" )] + raw_js = [os.path.basename(g) for g in glob( "static/scripts/*.js" )] for fname in raw_js: if os.path.exists('static/scripts/packed/%s' % fname): if os.path.getmtime('static/scripts/packed/%s' % fname) > os.path.getmtime('static/scripts/%s' % fname): - continue # Skip, packed is newer than source. + continue # Skip, packed is newer than source. d = dict( fname=fname ) log.info("%(fname)s --> packed/%(fname)s" % d) call( cmd % d, shell=True )
+ 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 @@ -511,24 +509,24 @@ map = webapp.mapper # Allow view items' tags. map.connect(name, path, - controller=controller, action="index", - conditions=dict(method=["GET"])) + 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"])) + 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"])) + 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"])) + 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"])) + controller=controller, action="show", + conditions=dict(method=["GET"]))
def _add_item_extended_metadata_controller( webapp, name_prefix, path_prefix, **kwd ): @@ -536,11 +534,13 @@ 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 @@ -566,11 +566,11 @@ # upstream server if asbool(conf.get( 'use_remote_user', False )): from galaxy.web.framework.middleware.remoteuser import RemoteUser - app = RemoteUser( app, maildomain = conf.get( 'remote_user_maildomain', None ), - display_servers = util.listify( conf.get( 'display_servers', '' ) ), - admin_users = conf.get( 'admin_users', '' ).split( ',' ), - remote_user_header = conf.get( 'remote_user_header', 'HTTP_REMOTE_USER' ), - remote_user_secret_header = conf.get('remote_user_secret', None) ) + app = RemoteUser( app, maildomain=conf.get( 'remote_user_maildomain', None ), + display_servers=util.listify( conf.get( 'display_servers', '' ) ), + admin_users=conf.get( 'admin_users', '' ).split( ',' ), + remote_user_header=conf.get( 'remote_user_header', 'HTTP_REMOTE_USER' ), + remote_user_secret_header=conf.get('remote_user_secret', None) ) # 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)): @@ -626,6 +626,7 @@ log.debug( "Enabling 'Request ID' middleware" ) return app
+ def wrap_in_static( app, global_conf, plugin_frameworks=None, **local_conf ): from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static urlmap, cache_time = galaxy.web.framework.webapp.build_url_map( app, global_conf, local_conf ) @@ -642,6 +643,7 @@ # URL mapper becomes the root webapp return urlmap
+ def build_template_error_formatters(): """ Build a list of template error formatters for WebError. When an error @@ -651,6 +653,7 @@ formatters = [] # Formatter for mako import mako.exceptions + def mako_html_data( exc_value ): if isinstance( exc_value, ( mako.exceptions.CompileException, mako.exceptions.SyntaxException ) ): return mako.exceptions.html_error_template().render( full=False, css=False )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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