April 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dannon: Fix more broken tooltips from the tipsy->bootstrap.tooltip() swap
by commits-noreply＠bitbucket.org 17 Apr '13

17 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/57b64ceac4b5/ Changeset: 57b64ceac4b5 User: dannon Date: 2013-04-17 14:40:24 Summary: Fix more broken tooltips from the tipsy->bootstrap.tooltip() swap Affected #: 1 file diff -r ec36ff4ec0f6baf7c6dc7af436b70a711cab94aa -r 57b64ceac4b5eaef10eb0f6c3cf94a87646901c2 templates/webapps/galaxy/workflow/editor.mako --- a/templates/webapps/galaxy/workflow/editor.mako +++ b/templates/webapps/galaxy/workflow/editor.mako @@ -1015,7 +1015,7 @@ ## Workflow name. <div id="workflow-name-area" class="form-row"><label>Name:</label> - <span id="workflow-name" class="tooltip editable-text" original-title="Click to rename workflow">${h.to_unicode( stored.name ) | h}</span> + <span id="workflow-name" class="tooltip editable-text" title="Click to rename workflow">${h.to_unicode( stored.name ) | h}</span></div> ## Workflow tags. <%namespace file="/tagging_common.mako" import="render_individual_tagging_element" /> @@ -1037,7 +1037,7 @@ ## Annotation elt. <div id="workflow-annotation-area" class="form-row"><label>Annotation / Notes:</label> - <div id="workflow-annotation" class="tooltip editable-text" original-title="Click to edit annotation"> + <div id="workflow-annotation" class="tooltip editable-text" title="Click to edit annotation"> %if annotation: ${h.to_unicode( annotation ) | h} %else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 7 new changesets
by commits-noreply＠bitbucket.org 17 Apr '13

17 Apr '13

7 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/83b09f742d31/ Changeset: 83b09f742d31 User: dannon Date: 2013-04-17 01:01:32 Summary: Refactor api auth logic, again. This should resolve remote_user API issues and correctly allow access by key or session. This also re-allows access to the API *without* a session in the case of key auth -- probably need to review and make sure we fail gracefully if we were counting on that anywhere Affected #: 2 files diff -r 46133ca43f322fe8b042ac0c0b393fe72579cecc -r 83b09f742d3134168ef3925c712e1c0e54f0aeb7 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -112,34 +112,25 @@ def expose_api_anonymous( func, to_json=True ): """ - Expose this function via the API but don't require an API key. + Expose this function via the API but don't require a set user. """ - return expose_api( func, to_json=to_json, key_required=False ) + return expose_api( func, to_json=to_json, user_required=False ) -def expose_api( func, to_json=True, key_required=True ): +def expose_api( func, to_json=True, user_required=True ): + """ + Expose this function via the API. + """ @wraps(func) def decorator( self, trans, *args, **kwargs ): def error( environ, start_response ): start_response( error_status, [('Content-type', 'text/plain')] ) return error_message error_status = '403 Forbidden' - #If no key supplied, we use the existing session which may be an anonymous user. - if key_required and not trans.user: - try: - if 'key' not in kwargs: - raise NoResultFound( 'No key provided' ) - provided_key = trans.sa_session.query( trans.app.model.APIKeys ).filter( trans.app.model.APIKeys.table.c.key == kwargs['key'] ).one() - except NoResultFound: - error_message = 'Provided API key is not valid.' - return error - if provided_key.user.deleted: - error_message = 'User account is deactivated, please contact an administrator.' - return error - newest_key = provided_key.user.api_keys[0] - if newest_key.key != provided_key.key: - error_message = 'Provided API key has expired.' - return error - trans.set_user( provided_key.user ) + if trans.error_message: + return trans.error_message + if user_required and trans.user is None: + error_message = "API Authentication Required for this request" + return error if trans.request.body: def extract_payload_from_request(trans, func, kwargs): content_type = trans.request.headers['content-type'] @@ -238,6 +229,7 @@ def form( *args, **kwargs ): return FormBuilder( *args, **kwargs ) + class WebApplication( base.WebApplication ): def __init__( self, galaxy_app, session_cookie='galaxysession', name=None ): @@ -326,6 +318,7 @@ controller_name = getattr( T, "controller_name", name ) self.add_api_controller( controller_name, T( app ) ) + class GalaxyWebTransaction( base.DefaultWebTransaction ): """ Encapsulates web transaction specific state for the Galaxy application @@ -346,13 +339,26 @@ # Flag indicating whether this is an API call and the API key user is an administrator self.api_inherit_admin = False self.__user = None - # Always have a valid galaxy session - self._ensure_valid_session( session_cookie ) - # Prevent deleted users from accessing Galaxy - if self.app.config.use_remote_user and self.galaxy_session.user.deleted: - self.response.send_redirect( url_for( '/static/user_disabled.html' ) ) - if self.app.config.require_login: - self._ensure_logged_in_user( environ, session_cookie ) + self.galaxy_session = None + self.error_message = None + if self.environ.get('is_api_request', False): + # With API requests, if there's a key, use it and associate the + # user with the transaction. + # If not, check for an active session but do not create one. + # If an error message is set here, it's sent back using + # trans.show_error in the response -- in expose_api. + self.error_message = self._authenticate_api( session_cookie ) + else: + #This is a web request, get or create session. + self._ensure_valid_session( session_cookie ) + if self.galaxy_session: + # When we've authenticated by session, we have to check the + # following. + # Prevent deleted users from accessing Galaxy + if self.app.config.use_remote_user and self.galaxy_session.user.deleted: + self.response.send_redirect( url_for( '/static/user_disabled.html' ) ) + if self.app.config.require_login: + self._ensure_logged_in_user( environ, session_cookie ) def setup_i18n( self ): locales = [] @@ -382,16 +388,17 @@ def get_user( self ): """Return the current user if logged in or None.""" - if self.__user: + if self.galaxy_session: + return self.galaxy_session.user + else: return self.__user - else: - return self.galaxy_session.user def set_user( self, user ): """Set the current user.""" - self.galaxy_session.user = user - self.sa_session.add( self.galaxy_session ) - self.sa_session.flush() + if self.galaxy_session: + self.galaxy_session.user = user + self.sa_session.add( self.galaxy_session ) + self.sa_session.flush() self.__user = user user = property( get_user, set_user ) @@ -473,6 +480,33 @@ except CookieError, e: log.warning( "Error setting httponly attribute in cookie '%s': %s" % ( name, e ) ) + def _authenticate_api( self, session_cookie ): + """ + Authenticate for the API via key or session (if available). + """ + api_key = self.request.params.get('key', None) + secure_id = self.get_cookie( name=session_cookie ) + if self.environ.get('is_api_request', False) and api_key: + # Sessionless API transaction, we just need to associate a user. + try: + provided_key = self.sa_session.query( self.app.model.APIKeys ).filter( self.app.model.APIKeys.table.c.key == api_key ).one() + except NoResultFound: + return 'Provided API key is not valid.' + if provided_key.user.deleted: + return 'User account is deactivated, please contact an administrator.' + newest_key = provided_key.user.api_keys[0] + if newest_key.key != provided_key.key: + return 'Provided API key has expired.' + self.set_user( provided_key.user ) + elif secure_id: + # API authentication via active session + # Associate user using existing session + self._ensure_valid_session( session_cookie ) + else: + # Anonymous API interaction -- anything but @expose_api_anonymous will fail past here. + self.user = None + self.galaxy_session = None + def _ensure_valid_session( self, session_cookie, create=True): """ Ensure that a valid Galaxy session exists and is available as @@ -505,26 +539,27 @@ .filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, self.app.model.GalaxySession.table.c.is_valid==True ) ) \ .first() - # If remote user is in use it can invalidate the session, so we need to to check some things now. - if self.app.config.use_remote_user: - assert "HTTP_REMOTE_USER" in self.environ, \ - "use_remote_user is set but no HTTP_REMOTE_USER variable" - remote_user_email = self.environ[ 'HTTP_REMOTE_USER' ] - if galaxy_session: - # An existing session, make sure correct association exists - if galaxy_session.user is None: - # No user, associate - galaxy_session.user = self.get_or_create_remote_user( remote_user_email ) - galaxy_session_requires_flush = True - elif galaxy_session.user.email != remote_user_email: - # Session exists but is not associated with the correct remote user - invalidate_existing_session = True + # If remote user is in use it can invalidate the session, so we need to to check some things now. + if self.app.config.use_remote_user: + #If this is an api request, and they've passed a key, we let this go. + assert "HTTP_REMOTE_USER" in self.environ, \ + "use_remote_user is set but no HTTP_REMOTE_USER variable" + remote_user_email = self.environ[ 'HTTP_REMOTE_USER' ] + if galaxy_session: + # An existing session, make sure correct association exists + if galaxy_session.user is None: + # No user, associate + galaxy_session.user = self.get_or_create_remote_user( remote_user_email ) + galaxy_session_requires_flush = True + elif galaxy_session.user.email != remote_user_email: + # Session exists but is not associated with the correct remote user + invalidate_existing_session = True + user_for_new_session = self.get_or_create_remote_user( remote_user_email ) + log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session", + remote_user_email, galaxy_session.user.email ) + else: + # No session exists, get/create user for new session user_for_new_session = self.get_or_create_remote_user( remote_user_email ) - log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session", - remote_user_email, galaxy_session.user.email ) - else: - # No session exists, get/create user for new session - user_for_new_session = self.get_or_create_remote_user( remote_user_email ) else: if galaxy_session is not None and galaxy_session.user and galaxy_session.user.external: # Remote user support is not enabled, but there is an existing @@ -605,6 +640,7 @@ pass if self.request.path not in allowed_paths: self.response.send_redirect( url_for( controller='root', action='index' ) ) + def __create_new_session( self, prev_galaxy_session=None, user_for_new_session=None ): """ Create a new GalaxySession for this request, possibly with a connection @@ -627,6 +663,7 @@ # The new session should be associated with the user galaxy_session.user = user_for_new_session return galaxy_session + def get_or_create_remote_user( self, remote_user_email ): """ Create a remote user with the email remote_user_email and return it @@ -671,11 +708,13 @@ self.app.security_agent.user_set_default_permissions( user ) #self.log_event( "Automatically created account '%s'", user.email ) return user + def __update_session_cookie( self, name='galaxysession' ): """ Update the session cookie to match the current session. """ self.set_cookie( self.security.encode_guid( self.galaxy_session.session_key ), name=name, path=self.app.config.cookie_path ) + def handle_user_login( self, user ): """ Login a new user (possibly newly created) @@ -701,9 +740,9 @@ except: users_last_session = None last_accessed = False - if prev_galaxy_session.current_history and \ - not prev_galaxy_session.current_history.deleted and \ - prev_galaxy_session.current_history.datasets: + if (prev_galaxy_session.current_history and not + prev_galaxy_session.current_history.deleted and + prev_galaxy_session.current_history.datasets): if prev_galaxy_session.current_history.user is None or prev_galaxy_session.current_history.user == user: # If the previous galaxy session had a history, associate it with the new # session, but only if it didn't belong to a different user. @@ -714,10 +753,9 @@ user.total_disk_usage += hda.quota_amount( user ) elif self.galaxy_session.current_history: history = self.galaxy_session.current_history - if not history and \ - users_last_session and \ - users_last_session.current_history and \ - not users_last_session.current_history.deleted: + if (not history and users_last_session and + users_last_session.current_history and not + users_last_session.current_history.deleted): history = users_last_session.current_history elif not history: history = self.get_history( create=True ) @@ -736,6 +774,8 @@ self.sa_session.flush() # This method is not called from the Galaxy reports, so the cookie will always be galaxysession self.__update_session_cookie( name=cookie_name ) + + def handle_user_logout( self, logout_all=False ): """ Logout the current user: @@ -988,6 +1028,7 @@ return True return False + class FormBuilder( object ): """ Simple class describing an HTML form @@ -999,17 +1040,22 @@ self.submit_text = submit_text self.inputs = [] self.use_panels = use_panels + def add_input( self, type, name, label, value=None, error=None, help=None, use_label=True ): self.inputs.append( FormInput( type, label, name, value, error, help, use_label ) ) return self + def add_text( self, name, label, value=None, error=None, help=None ): return self.add_input( 'text', label, name, value, error, help ) + def add_password( self, name, label, value=None, error=None, help=None ): return self.add_input( 'password', label, name, value, error, help ) + def add_select( self, name, label, value=None, options=[], error=None, help=None, use_label=True ): self.inputs.append( SelectInput( name, label, value=value, options=options, error=error, help=help, use_label=use_label ) ) return self + class FormInput( object ): """ Simple class describing a form input element @@ -1023,12 +1069,14 @@ self.help = help self.use_label = use_label + class SelectInput( FormInput ): """ A select form input. """ def __init__( self, name, label, value=None, options=[], error=None, help=None, use_label=True ): FormInput.__init__( self, "select", name, label, value=value, error=error, help=help, use_label=use_label ) self.options = options + class FormData( object ): """ Class for passing data about a form to a template, very rudimentary, could @@ -1038,6 +1086,7 @@ self.values = Bunch() self.errors = Bunch() + class Bunch( dict ): """ Bunch based on a dict @@ -1047,3 +1096,4 @@ return self[key] def __setattr__( self, key, value ): self[key] = value + diff -r 46133ca43f322fe8b042ac0c0b393fe72579cecc -r 83b09f742d3134168ef3925c712e1c0e54f0aeb7 lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py +++ b/lib/galaxy/web/framework/base.py @@ -138,6 +138,7 @@ environ[ 'is_api_request' ] = True controllers = self.api_controllers else: + environ[ 'is_api_request' ] = False controllers = self.controllers if map == None: raise httpexceptions.HTTPNotFound( "No route for " + path_info ) https://bitbucket.org/galaxy/galaxy-central/commits/bf323c3cf3c2/ Changeset: bf323c3cf3c2 User: dannon Date: 2013-04-17 01:03:39 Summary: Cleanup spacing in framework/base.py Affected #: 1 file diff -r 83b09f742d3134168ef3925c712e1c0e54f0aeb7 -r bf323c3cf3c28ebbecb7491abb87e58bf7f7a028 lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py +++ b/lib/galaxy/web/framework/base.py @@ -44,20 +44,21 @@ self.resource( member_name, collection_name, **kwargs ) routes.Mapper.resource_with_deleted = __resource_with_deleted + class WebApplication( object ): """ A simple web application which maps requests to objects using routes, - and to methods on those objects in the CherryPy style. Thus simple + and to methods on those objects in the CherryPy style. Thus simple argument mapping in the CherryPy style occurs automatically, but more complicated encoding of arguments in the PATH_INFO can be performed with routes. """ def __init__( self ): """ - Create a new web application object. To actually connect some - controllers use `add_controller` and `add_route`. Call + Create a new web application object. To actually connect some + controllers use `add_controller` and `add_route`. Call `finalize_config` when all controllers and routes have been added - and `__call__` to handle a request (WSGI style). + and `__call__` to handle a request (WSGI style). """ self.controllers = dict() self.api_controllers = dict() @@ -69,36 +70,41 @@ self.transaction_factory = DefaultWebTransaction # Set if trace logging is enabled self.trace_logger = None + def add_ui_controller( self, controller_name, controller ): """ Add a controller class to this application. A controller class has methods which handle web requests. To connect a URL to a controller's method use `add_route`. """ - log.debug( "Enabling '%s' controller, class: %s", + log.debug( "Enabling '%s' controller, class: %s", controller_name, controller.__class__.__name__ ) self.controllers[ controller_name ] = controller + def add_api_controller( self, controller_name, controller ): log.debug( "Enabling '%s' API controller, class: %s", controller_name, controller.__class__.__name__ ) self.api_controllers[ controller_name ] = controller + def add_route( self, route, **kwargs ): """ Add a route to match a URL with a method. Accepts all keyword arguments of `routes.Mapper.connect`. Every route should result in - at least a controller value which corresponds to one of the - objects added with `add_controller`. It optionally may yield an + at least a controller value which corresponds to one of the + objects added with `add_controller`. It optionally may yield an `action` argument which will be used to locate the method to call on the controller. Additional arguments will be passed to the - method as keyword args. + method as keyword args. """ self.mapper.connect( route, **kwargs ) + def set_transaction_factory( self, transaction_factory ): """ Use the callable `transaction_factory` to create the transaction which will be passed to requests. """ self.transaction_factory = transaction_factory + def finalize_config( self ): """ Call when application is completely configured and ready to serve @@ -106,6 +112,7 @@ """ # Create/compile the regular expressions for route mapping self.mapper.create_regs( self.controllers.keys() ) + def trace( self, **fields ): if self.trace_logger: self.trace_logger.log( "WebApplication", **fields ) @@ -173,7 +180,7 @@ raise httpexceptions.HTTPNotFound( "Action not exposed for " + path_info ) # Is the method callable if not callable( method ): - raise httpexceptions.HTTPNotFound( "Action not callable for " + path_info ) + raise httpexceptions.HTTPNotFound( "Action not callable for " + path_info ) # Combine mapper args and query string / form args and call kwargs = trans.request.params.mixed() kwargs.update( map ) @@ -196,14 +203,14 @@ elif isinstance( body, tarfile.ExFileObject ): # Stream the tarfile member back to the browser body = iterate_file( body ) - start_response( trans.response.wsgi_status(), + start_response( trans.response.wsgi_status(), trans.response.wsgi_headeritems() ) return body else: - start_response( trans.response.wsgi_status(), + start_response( trans.response.wsgi_status(), trans.response.wsgi_headeritems() ) return self.make_body_iterable( trans, body ) - + def make_body_iterable( self, trans, body ): if isinstance( body, ( types.GeneratorType, list, tuple ) ): # Recursively stream the iterable @@ -223,7 +230,8 @@ Allow handling of exceptions raised in controller methods. """ return False - + + class WSGIEnvironmentProperty( object ): """ Descriptor that delegates a property to a key in the environ member of the @@ -237,6 +245,7 @@ if obj is None: return self return obj.environ.get( self.key, self.default ) + class LazyProperty( object ): """ Property that replaces itself with a calculated value the first time @@ -250,12 +259,13 @@ setattr( obj, self.func.func_name, value ) return value lazy_property = LazyProperty - + + class DefaultWebTransaction( object ): """ - Wraps the state of a single web transaction (request/response cycle). + Wraps the state of a single web transaction (request/response cycle). - TODO: Provide hooks to allow application specific state to be included + TODO: Provide hooks to allow application specific state to be included in here. """ def __init__( self, environ ): @@ -274,7 +284,7 @@ return self.environ['beaker.session'] else: return None - + # For request.params, override cgi.FieldStorage.make_file to create persistent # tempfiles. Necessary for externalizing the upload tool. It's a little hacky # but for performance reasons it's way better to use Paste's tempfile than to @@ -290,12 +300,13 @@ if self.outerboundary: self.read_lines_to_outerboundary() else: - self.read_lines_to_eof() + self.read_lines_to_eof() cgi.FieldStorage = FieldStorage + class Request( webob.Request ): """ - Encapsulates an HTTP request. + Encapsulates an HTTP request. """ def __init__( self, environ ): """ @@ -330,7 +341,7 @@ return self.environ['SCRIPT_NAME'] + self.environ['PATH_INFO'] @lazy_property def browser_url( self ): - return self.base + self.path + return self.base + self.path # Descriptors that map properties to the associated environment ## scheme = WSGIEnvironmentProperty( 'wsgi.url_scheme' ) ## remote_addr = WSGIEnvironmentProperty( 'REMOTE_ADDR' ) @@ -341,6 +352,7 @@ ## query_string = WSGIEnvironmentProperty( 'QUERY_STRING' ) ## path_info = WSGIEnvironmentProperty( 'PATH_INFO' ) + class Response( object ): """ Describes an HTTP response. Currently very simple since the actual body @@ -353,18 +365,22 @@ self.status = "200 OK" self.headers = HeaderDict( { "content-type": "text/html" } ) self.cookies = SimpleCookie() + def set_content_type( self, type ): """ Sets the Content-Type header """ self.headers[ "content-type" ] = type + def get_content_type( self ): return self.headers[ "content-type" ] + def send_redirect( self, url ): """ Send an HTTP redirect response to (target `url`) """ raise httpexceptions.HTTPFound( url, headers=self.wsgi_headeritems() ) + def wsgi_headeritems( self ): """ Return headers in format appropriate for WSGI `start_response` @@ -376,10 +392,11 @@ header, value = str( crumb ).split( ': ', 1 ) result.append( ( header, value ) ) return result + def wsgi_status( self ): """ Return status line in format appropriate for WSGI `start_response` - """ + """ if isinstance( self.status, int ): exception = httpexceptions.get_exception( self.status ) return "%d %s" % ( exception.code, exception.title ) @@ -404,7 +421,7 @@ # Fall back on sending the file in chunks else: body = iterate_file( body ) - start_response( trans.response.wsgi_status(), + start_response( trans.response.wsgi_status(), trans.response.wsgi_headeritems() ) return body https://bitbucket.org/galaxy/galaxy-central/commits/356965791008/ Changeset: 356965791008 User: dannon Date: 2013-04-17 01:06:42 Summary: Cleanup in framework/__init__.py Affected #: 1 file diff -r bf323c3cf3c28ebbecb7491abb87e58bf7f7a028 -r 356965791008f24aa26dc8043259765dcc0e7f7e lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -713,7 +713,8 @@ """ Update the session cookie to match the current session. """ - self.set_cookie( self.security.encode_guid( self.galaxy_session.session_key ), name=name, path=self.app.config.cookie_path ) + self.set_cookie( self.security.encode_guid(self.galaxy_session.session_key ), + name=name, path=self.app.config.cookie_path ) def handle_user_login( self, user ): """ @@ -800,11 +801,13 @@ self.__update_session_cookie( name='galaxysession' ) elif self.webapp.name == 'tool_shed': self.__update_session_cookie( name='galaxycommunitysession' ) + def get_galaxy_session( self ): """ Return the current galaxy session """ return self.galaxy_session + def get_history( self, create=False ): """ Load the current history, creating a new one only if there is not @@ -819,12 +822,15 @@ log.debug( "This request returned None from get_history(): %s" % self.request.browser_url ) return None return history + def set_history( self, history ): if history and not history.deleted: self.galaxy_session.current_history = history self.sa_session.add( self.galaxy_session ) self.sa_session.flush() + history = property( get_history, set_history ) + def new_history( self, name=None ): """ Create a new history and associate it with the current session and @@ -849,6 +855,7 @@ self.sa_session.add_all( ( self.galaxy_session, history ) ) self.sa_session.flush() return history + def get_current_user_roles( self ): user = self.get_user() if user: @@ -856,27 +863,34 @@ else: roles = [] return roles + def user_is_admin( self ): if self.api_inherit_admin: return True admin_users = [ x.strip() for x in self.app.config.get( "admin_users", "" ).split( "," ) ] return self.user and admin_users and self.user.email in admin_users + def user_can_do_run_as( self ): run_as_users = self.app.config.get( "api_allow_run_as", "" ).split( "," ) return self.user and run_as_users and self.user.email in run_as_users + def get_toolbox(self): """Returns the application toolbox""" return self.app.toolbox + @base.lazy_property def template_context( self ): return dict() + @property def model( self ): return self.app.model + def make_form_data( self, name, **kwargs ): rval = self.template_context[name] = FormData() rval.values.update( kwargs ) return rval + def set_message( self, message, type=None ): """ Convenience method for setting the 'message' and 'message_type' @@ -885,12 +899,14 @@ self.template_context['message'] = message if type: self.template_context['status'] = type + def get_message( self ): """ Convenience method for getting the 'message' element of the template context. """ return self.template_context['message'] + def show_message( self, message, type='info', refresh_frames=[], cont=None, use_panels=False, active_view="" ): """ Convenience method for displaying a simple page with a single message. @@ -902,21 +918,25 @@ refreshed when the message is displayed """ return self.fill_template( "message.mako", status=type, message=message, refresh_frames=refresh_frames, cont=cont, use_panels=use_panels, active_view=active_view ) + def show_error_message( self, message, refresh_frames=[], use_panels=False, active_view="" ): """ Convenience method for displaying an error message. See `show_message`. """ return self.show_message( message, 'error', refresh_frames, use_panels=use_panels, active_view=active_view ) + def show_ok_message( self, message, refresh_frames=[], use_panels=False, active_view="" ): """ Convenience method for displaying an ok message. See `show_message`. """ return self.show_message( message, 'done', refresh_frames, use_panels=use_panels, active_view=active_view ) + def show_warn_message( self, message, refresh_frames=[], use_panels=False, active_view="" ): """ Convenience method for displaying an warn message. See `show_message`. """ return self.show_message( message, 'warning', refresh_frames, use_panels=use_panels, active_view=active_view ) + def show_form( self, form, header=None, template="form.mako", use_panels=False, active_view="" ): """ Convenience method for displaying a simple page with a single HTML @@ -924,6 +944,7 @@ """ return self.fill_template( template, form=form, header=header, use_panels=( form.use_panels or use_panels ), active_view=active_view ) + def fill_template(self, filename, **kwargs): """ Fill in a template, putting any keyword arguments on the context. @@ -937,6 +958,7 @@ template = Template( file=os.path.join(self.app.config.template_path, filename), searchList=[kwargs, self.template_context, dict(caller=self, t=self, h=helpers, util=util, request=self.request, response=self.response, app=self.app)] ) return str( template ) + def fill_template_mako( self, filename, **kwargs ): template = self.webapp.mako_template_lookup.get_template( filename ) template.output_encoding = 'utf-8' @@ -944,6 +966,7 @@ data.update( self.template_context ) data.update( kwargs ) return template.render( **data ) + def stream_template_mako( self, filename, **kwargs ): template = self.webapp.mako_template_lookup.get_template( filename ) template.output_encoding = 'utf-8' @@ -961,6 +984,7 @@ template.render_context( context ) return [] return render + def fill_template_string(self, template_string, context=None, **kwargs): """ Fill in a template, putting any keyword arguments on the context. https://bitbucket.org/galaxy/galaxy-central/commits/18c73eeb77fe/ Changeset: 18c73eeb77fe User: dannon Date: 2013-04-17 01:07:02 Summary: Merge with galaxy-central Affected #: 1 file diff -r 356965791008f24aa26dc8043259765dcc0e7f7e -r 18c73eeb77feba055b2240412006dc3ce2e49fb0 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -770,6 +770,10 @@ else: pos = source.tell() + # If last line is a comment, there are no data lines. + if line.startswith( "#" ): + return [] + # Match chrom naming format. if line: dataset_chrom = line.split()[0] @@ -1272,7 +1276,7 @@ class IntervalIndexDataProvider( FilterableMixin, GenomeDataProvider ): """ - Interval index files used only for GFF files. + Interval index files used for GFF, Pileup files. """ col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } @@ -1282,20 +1286,26 @@ source = open( self.original_dataset.file_name ) index = Indexes( self.converted_dataset.file_name ) out = open( filename, 'w' ) - + for region in regions: # Write data from region. chrom = region.chrom start = region.start end = region.end - for start, end, offset in index.find(chrom, start, end): + for start, end, offset in index.find( chrom, start, end ): source.seek( offset ) - - reader = GFFReaderWrapper( source, fix_strand=True ) - feature = reader.next() - for interval in feature.intervals: - out.write( '\t'.join( interval.fields ) + '\n' ) - + + # HACK: write differently depending on original dataset format. + if self.original_dataset.ext not in [ 'gff', 'gff3', 'gtf' ]: + line = source.readline() + out.write( line ) + else: + reader = GFFReaderWrapper( source, fix_strand=True ) + feature = reader.next() + for interval in feature.intervals: + out.write( '\t'.join( interval.fields ) + '\n' ) + + source.close() out.close() def get_iterator( self, chrom, start, end, **kwargs ): https://bitbucket.org/galaxy/galaxy-central/commits/94caae7433a7/ Changeset: 94caae7433a7 User: dannon Date: 2013-04-17 03:38:38 Summary: Disable select2 for Input Dataset steps on the run workflow page. Affected #: 1 file Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/60d7b1a9ebec/ Changeset: 60d7b1a9ebec User: dannon Date: 2013-04-17 03:47:17 Summary: Update multiselect tooltip, now functional. Was still using tipsy's 'original-title' attribute. Affected #: 1 file Diff not available. https://bitbucket.org/galaxy/galaxy-central/commits/ec36ff4ec0f6/ Changeset: ec36ff4ec0f6 User: dannon Date: 2013-04-17 04:27:07 Summary: Add tooltips for (un)linking icon on run workflow page. Affected #: 1 file Diff not available. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Enable IntervalIndex data provider to work with pileup datasets.
by commits-noreply＠bitbucket.org 16 Apr '13

16 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/98b6216e42f5/ Changeset: 98b6216e42f5 User: jgoecks Date: 2013-04-17 01:01:50 Summary: Enable IntervalIndex data provider to work with pileup datasets. Affected #: 1 file diff -r 46133ca43f322fe8b042ac0c0b393fe72579cecc -r 98b6216e42f5beec89052cccf7c98820b978bf92 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -770,6 +770,10 @@ else: pos = source.tell() + # If last line is a comment, there are no data lines. + if line.startswith( "#" ): + return [] + # Match chrom naming format. if line: dataset_chrom = line.split()[0] @@ -1272,7 +1276,7 @@ class IntervalIndexDataProvider( FilterableMixin, GenomeDataProvider ): """ - Interval index files used only for GFF files. + Interval index files used for GFF, Pileup files. """ col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } @@ -1282,20 +1286,26 @@ source = open( self.original_dataset.file_name ) index = Indexes( self.converted_dataset.file_name ) out = open( filename, 'w' ) - + for region in regions: # Write data from region. chrom = region.chrom start = region.start end = region.end - for start, end, offset in index.find(chrom, start, end): + for start, end, offset in index.find( chrom, start, end ): source.seek( offset ) - - reader = GFFReaderWrapper( source, fix_strand=True ) - feature = reader.next() - for interval in feature.intervals: - out.write( '\t'.join( interval.fields ) + '\n' ) - + + # HACK: write differently depending on original dataset format. + if self.original_dataset.ext not in [ 'gff', 'gff3', 'gtf' ]: + line = source.readline() + out.write( line ) + else: + reader = GFFReaderWrapper( source, fix_strand=True ) + feature = reader.next() + for interval in feature.intervals: + out.write( '\t'.join( interval.fields ) + '\n' ) + + source.close() out.close() def get_iterator( self, chrom, start, end, **kwargs ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Make a data_sources attribute for data types and remove get_track_type because it is no longer needed.
by commits-noreply＠bitbucket.org 16 Apr '13

16 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/46133ca43f32/ Changeset: 46133ca43f32 User: jgoecks Date: 2013-04-17 00:11:09 Summary: Make a data_sources attribute for data types and remove get_track_type because it is no longer needed. Affected #: 8 files diff -r da3b931de04c93ddae85e4999b6911948fdf0b34 -r 46133ca43f322fe8b042ac0c0b393fe72579cecc lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -95,6 +95,7 @@ """Class describing a BAM binary file""" file_ext = "bam" track_type = "ReadTrack" + data_sources = { "data": "bai", "index": [ "bigwig", "summary_tree" ] } MetadataElement( name="bam_index", desc="BAM Index File", param=metadata.FileParameter, file_ext="bai", readonly=True, no_value=None, visible=False, optional=True ) @@ -246,9 +247,7 @@ return dataset.peek except: return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) ) - def get_track_type( self ): - return self.track_type, { "data": "bai", "index": [ "bigwig", "summary_tree" ] } - + Binary.register_sniffable_binary_format("bam", "bam", Bam) class H5( Binary ): @@ -327,6 +326,7 @@ http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq351v1 """ track_type = "LineTrack" + data_sources = { "data_standalone": "bigwig" } def __init__( self, **kwd ): Binary.__init__( self, **kwd ) @@ -352,20 +352,18 @@ return dataset.peek except: return "Binary UCSC %s file (%s)" % ( self._name, data.nice_size( dataset.get_size() ) ) - def get_track_type( self ): - return self.track_type, {"data_standalone": "bigwig"} - + Binary.register_sniffable_binary_format("bigwig", "bigwig", BigWig) class BigBed(BigWig): """BigBed support from UCSC.""" + data_sources = { "data_standalone": "bigbed" } + def __init__( self, **kwd ): Binary.__init__( self, **kwd ) self._magic = 0x8789F2EB self._name = "BigBed" - def get_track_type( self ): - return self.track_type, {"data_standalone": "bigbed"} Binary.register_sniffable_binary_format("bigbed", "bigbed", BigBed) diff -r da3b931de04c93ddae85e4999b6911948fdf0b34 -r 46133ca43f322fe8b042ac0c0b393fe72579cecc lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -100,6 +100,9 @@ # Trackster track type. track_type = None + # Data sources. + data_sources = {} + def __init__(self, **kwd): """Initialize the datatype""" object.__init__(self, **kwd) diff -r da3b931de04c93ddae85e4999b6911948fdf0b34 -r 46133ca43f322fe8b042ac0c0b393fe72579cecc lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -47,6 +47,7 @@ file_ext = "interval" line_class = "region" track_type = "FeatureTrack" + data_sources = { "data": "tabix", "index": "summary_tree" } """Add metadata elements""" MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) @@ -329,18 +330,13 @@ def get_track_resolution( self, dataset, start, end): return None - - def get_track_type( self ): - return self.track_type, {"data": "tabix", "index": "summary_tree"} class BedGraph( Interval ): """Tab delimited chrom/start/end/datavalue dataset""" file_ext = "bedgraph" track_type = "LineTrack" - - def get_track_type( self ): - return self.track_type, { "data": "bigwig", "index": "bigwig" } + data_sources = { "data": "bigwig", "index": "bigwig" } def as_ucsc_display_file( self, dataset, **kwd ): """ @@ -358,6 +354,7 @@ class Bed( Interval ): """Tab delimited data in BED format""" file_ext = "bed" + data_sources = {"data": "tabix", "index": "summary_tree", "feature_search": "fli"} """Add metadata elements""" MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) @@ -512,9 +509,6 @@ else: return False return True except: return False - - def get_track_type( self ): - return self.track_type, {"data": "tabix", "index": "summary_tree", "feature_search": "fli"} class BedStrict( Bed ): """Tab delimited data in strict BED format - no non-standard columns allowed""" @@ -574,6 +568,7 @@ """Tab delimited data in Gff format""" file_ext = "gff" column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ] + data_sources = { "data": "interval_index", "index": "summary_tree", "feature_search": "fli" } """Add metadata elements""" MetadataElement( name="columns", default=9, desc="Number of columns", readonly=True, visible=False ) @@ -785,10 +780,6 @@ return True except: return False - - def get_track_type( self ): - return self.track_type, {"data": "interval_index", "index": "summary_tree", "feature_search": "fli"} - class Gff3( Gff ): """Tab delimited data in Gff3 format""" @@ -969,6 +960,7 @@ """Tab delimited data in wiggle format""" file_ext = "wig" track_type = "LineTrack" + data_sources = { "data": "bigwig", "index": "bigwig" } MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False ) @@ -1149,9 +1141,6 @@ resolution = min( resolution, 100000 ) resolution = max( resolution, 1 ) return resolution - - def get_track_type( self ): - return self.track_type, { "data": "bigwig", "index": "bigwig" } class CustomTrack ( Tabular ): """UCSC CustomTrack""" @@ -1295,6 +1284,7 @@ file_ext = "encodepeak" column_names = [ 'Chrom', 'Start', 'End', 'Name', 'Score', 'Strand', 'SignalValue', 'pValue', 'qValue', 'Peak' ] + data_sources = { "data": "tabix", "index": "summary_tree" } """Add metadata elements""" MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) @@ -1306,9 +1296,6 @@ def sniff( self, filename ): return False - def get_track_type( self ): - return self.track_type, {"data": "tabix", "index": "summary_tree"} - class ChromatinInteractions( Interval ): ''' Chromatin interactions obtained from 3C/5C/Hi-C experiments. @@ -1316,6 +1303,7 @@ file_ext = "chrint" track_type = "DiagonalHeatmapTrack" + data_sources = { "data": "tabix", "index": "summary_tree" } column_names = [ 'Chrom1', 'Start1', 'End1', 'Chrom2', 'Start2', 'End2', 'Value' ] @@ -1332,11 +1320,6 @@ def sniff( self, filename ): return False - - def get_track_type( self ): - return self.track_type, {"data": "tabix", "index": "summary_tree"} - - if __name__ == '__main__': import doctest, sys diff -r da3b931de04c93ddae85e4999b6911948fdf0b34 -r 46133ca43f322fe8b042ac0c0b393fe72579cecc lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -359,6 +359,7 @@ class Sam( Tabular ): file_ext = 'sam' track_type = "ReadTrack" + data_sources = { "data": "bam", "index": "summary_tree" } def __init__(self, **kwd): """Initialize taxonomy datatype""" @@ -469,13 +470,11 @@ raise Exception('Result %s from %s' % (result, cmd)) merge = staticmethod(merge) - def get_track_type( self ): - return self.track_type, {"data": "bam", "index": "summary_tree"} - class Pileup( Tabular ): """Tab delimited data in pileup (6- or 10-column) format""" file_ext = "pileup" line_class = "genomic coordinate" + data_sources = { "data": "interval_index" } """Add metadata elements""" MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) @@ -527,10 +526,6 @@ return True except: return False - - def get_track_type( self ): - return self.track_type, { "data": "interval_index" } - class ElandMulti( Tabular ): file_ext = 'elandmulti' @@ -541,6 +536,7 @@ class Vcf( Tabular ): """ Variant Call Format for describing SNPs and other simple genome variations. """ track_type = "VariantTrack" + data_sources = { "data": "tabix", "index": "summary_tree" } file_ext = 'vcf' column_names = [ 'Chrom', 'Pos', 'ID', 'Ref', 'Alt', 'Qual', 'Filter', 'Info', 'Format', 'data' ] @@ -557,9 +553,6 @@ """Returns formated html of peek""" return Tabular.make_html_table( self, dataset, column_names=self.column_names ) - def get_track_type( self ): - return self.track_type, { "data": "tabix", "index": "summary_tree" } - class Eland( Tabular ): """Support for the export.txt.gz file used by Illumina's ELANDv2e aligner""" file_ext = '_export.txt.gz' diff -r da3b931de04c93ddae85e4999b6911948fdf0b34 -r 46133ca43f322fe8b042ac0c0b393fe72579cecc lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1333,10 +1333,9 @@ with entries of type (<datasource_type> : {<datasource_name>, <indexing_message>}). """ - track_type, data_sources = self.datatype.get_track_type() data_sources_dict = {} msg = None - for source_type, source_list in data_sources.iteritems(): + for source_type, source_list in self.datatype.data_sources.iteritems(): data_source = None if source_type == "data_standalone": # Nothing to do. diff -r da3b931de04c93ddae85e4999b6911948fdf0b34 -r 46133ca43f322fe8b042ac0c0b393fe72579cecc lib/galaxy/visualization/data_providers/registry.py --- a/lib/galaxy/visualization/data_providers/registry.py +++ b/lib/galaxy/visualization/data_providers/registry.py @@ -83,12 +83,12 @@ elif original_dataset: # No name, so look up a provider name from datatype's information. - # Dataset must have get_track_type function to get data. - if not hasattr( original_dataset.datatype, 'get_track_type'): + # Dataset must have data sources to get data. + if not original_dataset.datatype.data_sources: return None # Get data provider mapping and data provider. - _ , data_provider_mapping = original_dataset.datatype.get_track_type() + data_provider_mapping = original_dataset.datatype.data_sources if 'data_standalone' in data_provider_mapping: data_provider = self.get_data_provider( trans, name=data_provider_mapping[ 'data_standalone' ], diff -r da3b931de04c93ddae85e4999b6911948fdf0b34 -r 46133ca43f322fe8b042ac0c0b393fe72579cecc lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -590,12 +590,11 @@ except KeyError: prefs = {} - track_type, _ = dataset.datatype.get_track_type() track_data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='data' ) return { - "track_type": track_type, + "track_type": dataset.datatype.track_type, "name": track_dict['name'], "hda_ldda": track_dict.get("hda_ldda", "hda"), "dataset_id": trans.security.encode_id( dataset.id ), @@ -666,10 +665,8 @@ Returns track configuration dict for a dataset. """ # Get data provider. - track_type, _ = dataset.datatype.get_track_type() track_data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset ) - if isinstance( dataset, trans.app.model.HistoryDatasetAssociation ): hda_ldda = "hda" elif isinstance( dataset, trans.app.model.LibraryDatasetDatasetAssociation ): @@ -677,7 +674,7 @@ # Get track definition. return { - "track_type": track_type, + "track_type": dataset.datatype.track_type, "name": dataset.name, "hda_ldda": hda_ldda, "dataset_id": trans.security.encode_id( dataset.id ), diff -r da3b931de04c93ddae85e4999b6911948fdf0b34 -r 46133ca43f322fe8b042ac0c0b393fe72579cecc lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -225,7 +225,7 @@ data_provider = data_provider_registry.get_data_provider( trans, original_dataset=input_dataset, source='data' ) if data_provider and not data_provider.converted_dataset: # Can convert but no converted dataset yet, so return message about why. - _, data_sources = input_dataset.datatype.get_track_type() + data_sources = input_dataset.datatype.data_sources msg = input_dataset.convert_dataset( trans, data_sources[ 'data' ] ) if msg is not None: messages_list.append( msg ) @@ -311,7 +311,7 @@ input_dataset = jida.dataset if input_dataset is None: #optional dataset and dataset wasn't selected tool_params[ jida.name ] = None - elif run_on_regions and hasattr( input_dataset.datatype, 'get_track_type' ): + elif run_on_regions and 'data' in input_dataset.datatype.data_sources: # Dataset is indexed and hence a subset can be extracted and used # as input. @@ -324,8 +324,7 @@ subset_dataset = subset_dataset_association.subset else: # Need to create subset. - track_type, data_sources = input_dataset.datatype.get_track_type() - data_source = data_sources[ 'data' ] + data_source = input_dataset.datatype.data_sources[ 'data' ] converted_dataset = input_dataset.get_converted_dataset( trans, data_source ) deps = input_dataset.get_converted_dataset_deps( trans, data_source ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Add pileup to interval_index converter.
by commits-noreply＠bitbucket.org 16 Apr '13

16 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/da3b931de04c/ Changeset: da3b931de04c User: jgoecks Date: 2013-04-16 23:45:52 Summary: Add pileup to interval_index converter. Affected #: 4 files diff -r e0354c9d5497fa9d169df6a7aa44c8132718f92c -r da3b931de04c93ddae85e4999b6911948fdf0b34 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -159,7 +159,9 @@ <converter file="encodepeak_to_summary_tree_converter.xml" target_datatype="summary_tree"/></datatype><datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/> - <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" /> + <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true"> + <converter file="pileup_to_interval_index_converter.xml" target_datatype="interval_index"/> + </datatype><datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/><datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /><datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> diff -r e0354c9d5497fa9d169df6a7aa44c8132718f92c -r da3b931de04c93ddae85e4999b6911948fdf0b34 lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py --- /dev/null +++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py @@ -0,0 +1,39 @@ +#!/usr/bin/env python + +""" +Convert from pileup file to interval index file. + +usage: %prog <options> in_file out_file +""" + +from __future__ import division + +import sys, fileinput, optparse +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from galaxy.visualization.tracks.summary import * +from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed +from bx.interval_index_file import Indexes + +def main(): + + # Read options, args. + parser = optparse.OptionParser() + (options, args) = parser.parse_args() + input_fname, output_fname = args + + # Do conversion. + index = Indexes() + offset = 0 + for line in open( input_fname, "r" ): + chrom, start = line.split()[ 0:2 ] + # Pileup format is 1-based. + start = int( start ) - 1 + index.add( chrom, start, start + 1, offset ) + offset += len( line ) + + index.write( open(output_fname, "w") ) + +if __name__ == "__main__": + main() + \ No newline at end of file diff -r e0354c9d5497fa9d169df6a7aa44c8132718f92c -r da3b931de04c93ddae85e4999b6911948fdf0b34 lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml @@ -0,0 +1,15 @@ +<tool id="CONVERTER_pileup_to_interval_index_0" name="Convert Pileup to Interval Index" version="1.0.0" hidden="true"> + + <command interpreter="python">pileup_to_interval_index_converter.py $input $output + </command> + <inputs> + <page> + <param format="pileup" name="input" type="data" label="Choose Pileup file"/> + </page> + </inputs> + <outputs> + <data format="interval_index" name="output"/> + </outputs> + <help> + </help> +</tool> diff -r e0354c9d5497fa9d169df6a7aa44c8132718f92c -r da3b931de04c93ddae85e4999b6911948fdf0b34 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -527,6 +527,10 @@ return True except: return False + + def get_track_type( self ): + return self.track_type, { "data": "interval_index" } + class ElandMulti( Tabular ): file_ext = 'elandmulti' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 16 Apr '13

16 Apr '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0a3c911778ae/ Changeset: 0a3c911778ae User: jmchilton Date: 2013-04-16 04:48:52 Summary: Consolidate logic for determining user's FTP directory. Affected #: 3 files diff -r 788cd3d065413b2611d82375a5d0d562775ea529 -r 0a3c911778aebded1d40c5e12b05959a761a0276 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -475,7 +475,7 @@ if trans is None or trans.user is None: user_ftp_dir = None else: - user_ftp_dir = os.path.join( trans.app.config.ftp_upload_dir, trans.user.email ) + user_ftp_dir = trans.user_ftp_dir return form_builder.FTPFileField( self.name, user_ftp_dir, trans.app.config.ftp_upload_site, value = value ) def from_html( self, value, trans=None, other_values={} ): try: diff -r 788cd3d065413b2611d82375a5d0d562775ea529 -r 0a3c911778aebded1d40c5e12b05959a761a0276 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -270,7 +270,7 @@ if file_bunch.path and ftp_files is not None: warnings.append( "All FTP uploaded file selections were ignored." ) elif ftp_files is not None and trans.user is not None: # look for files uploaded via FTP - user_ftp_dir = os.path.join( trans.app.config.ftp_upload_dir, trans.user.email ) + user_ftp_dir = trans.user_ftp_dir for ( dirpath, dirnames, filenames ) in os.walk( user_ftp_dir ): for filename in filenames: for ftp_filename in ftp_files: @@ -318,7 +318,7 @@ ftp_files = [] # TODO: warning to the user (could happen if session has become invalid) else: - user_ftp_dir = os.path.join( trans.app.config.ftp_upload_dir, trans.user.email ) + user_ftp_dir = trans.user_ftp_dir for ( dirpath, dirnames, filenames ) in os.walk( user_ftp_dir ): for filename in filenames: path = relpath( os.path.join( dirpath, filename ), user_ftp_dir ) diff -r 788cd3d065413b2611d82375a5d0d562775ea529 -r 0a3c911778aebded1d40c5e12b05959a761a0276 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -958,6 +958,10 @@ def ncbi_builds( self ): return util.dlnames['ncbi'] + @property + def user_ftp_dir( self ): + return os.path.join( self.app.config.ftp_upload_dir, self.user.email ) + def db_dataset_for( self, dbkey ): """ Returns the db_file dataset associated/needed by `dataset`, or `None`. https://bitbucket.org/galaxy/galaxy-central/commits/0d2a9d0dbd2d/ Changeset: 0d2a9d0dbd2d User: jmchilton Date: 2013-04-16 05:00:14 Summary: Implement new property ftp_uplod_dir_identifier which defaults to 'email' but can be changed to 'username' to allow FTP directories based on usernames instead of e-mail addresses. I setup ProFTP + mod_ldap and it does not have the same flexibility the SQL driver has so this change is required at the Galaxy level. Affected #: 2 files diff -r 0a3c911778aebded1d40c5e12b05959a761a0276 -r 0d2a9d0dbd2db8a31f570b13acaf0caa9b245b09 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -166,6 +166,7 @@ self.enable_whoosh_library_search = string_as_bool( kwargs.get( 'enable_whoosh_library_search', False ) ) self.whoosh_index_dir = resolve_path( kwargs.get( "whoosh_index_dir", "database/whoosh_indexes" ), self.root ) self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None ) + self.ftp_upload_dir_identifier = kwargs.get( 'ftp_uplod_dir_identifier', 'email' ) # attribute on user - email, username, id, etc... self.ftp_upload_site = kwargs.get( 'ftp_upload_site', None ) self.allow_library_path_paste = kwargs.get( 'allow_library_path_paste', False ) self.disable_library_comptypes = kwargs.get( 'disable_library_comptypes', '' ).lower().split( ',' ) diff -r 0a3c911778aebded1d40c5e12b05959a761a0276 -r 0d2a9d0dbd2db8a31f570b13acaf0caa9b245b09 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -960,7 +960,8 @@ @property def user_ftp_dir( self ): - return os.path.join( self.app.config.ftp_upload_dir, self.user.email ) + identifier = self.app.config.ftp_upload_dir_identifier + return os.path.join( self.app.config.ftp_upload_dir, getattr(self.user, identifier) ) def db_dataset_for( self, dbkey ): """ https://bitbucket.org/galaxy/galaxy-central/commits/8b74c635ca3b/ Changeset: 8b74c635ca3b User: jmchilton Date: 2013-04-16 14:44:54 Summary: Fix typo in previous FTP upload commit. Affected #: 1 file diff -r 0d2a9d0dbd2db8a31f570b13acaf0caa9b245b09 -r 8b74c635ca3bb266eb0ad2b08aa17836e500add2 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -166,7 +166,7 @@ self.enable_whoosh_library_search = string_as_bool( kwargs.get( 'enable_whoosh_library_search', False ) ) self.whoosh_index_dir = resolve_path( kwargs.get( "whoosh_index_dir", "database/whoosh_indexes" ), self.root ) self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None ) - self.ftp_upload_dir_identifier = kwargs.get( 'ftp_uplod_dir_identifier', 'email' ) # attribute on user - email, username, id, etc... + self.ftp_upload_dir_identifier = kwargs.get( 'ftp_upload_dir_identifier', 'email' ) # attribute on user - email, username, id, etc... self.ftp_upload_site = kwargs.get( 'ftp_upload_site', None ) self.allow_library_path_paste = kwargs.get( 'allow_library_path_paste', False ) self.disable_library_comptypes = kwargs.get( 'disable_library_comptypes', '' ).lower().split( ',' ) https://bitbucket.org/galaxy/galaxy-central/commits/e0354c9d5497/ Changeset: e0354c9d5497 User: natefoo Date: 2013-04-16 22:17:33 Summary: Merged in jmchilton/galaxy-central-multi-input-tool-fixes-2 (pull request #157) Increased flexibility for FTP directory configuration. Affected #: 4 files diff -r bbb229927c688213e67ba62998a64526ca948a19 -r e0354c9d5497fa9d169df6a7aa44c8132718f92c lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -166,6 +166,7 @@ self.enable_whoosh_library_search = string_as_bool( kwargs.get( 'enable_whoosh_library_search', False ) ) self.whoosh_index_dir = resolve_path( kwargs.get( "whoosh_index_dir", "database/whoosh_indexes" ), self.root ) self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None ) + self.ftp_upload_dir_identifier = kwargs.get( 'ftp_upload_dir_identifier', 'email' ) # attribute on user - email, username, id, etc... self.ftp_upload_site = kwargs.get( 'ftp_upload_site', None ) self.allow_library_path_paste = kwargs.get( 'allow_library_path_paste', False ) self.disable_library_comptypes = kwargs.get( 'disable_library_comptypes', '' ).lower().split( ',' ) diff -r bbb229927c688213e67ba62998a64526ca948a19 -r e0354c9d5497fa9d169df6a7aa44c8132718f92c lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -475,7 +475,7 @@ if trans is None or trans.user is None: user_ftp_dir = None else: - user_ftp_dir = os.path.join( trans.app.config.ftp_upload_dir, trans.user.email ) + user_ftp_dir = trans.user_ftp_dir return form_builder.FTPFileField( self.name, user_ftp_dir, trans.app.config.ftp_upload_site, value = value ) def from_html( self, value, trans=None, other_values={} ): try: diff -r bbb229927c688213e67ba62998a64526ca948a19 -r e0354c9d5497fa9d169df6a7aa44c8132718f92c lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -270,7 +270,7 @@ if file_bunch.path and ftp_files is not None: warnings.append( "All FTP uploaded file selections were ignored." ) elif ftp_files is not None and trans.user is not None: # look for files uploaded via FTP - user_ftp_dir = os.path.join( trans.app.config.ftp_upload_dir, trans.user.email ) + user_ftp_dir = trans.user_ftp_dir for ( dirpath, dirnames, filenames ) in os.walk( user_ftp_dir ): for filename in filenames: for ftp_filename in ftp_files: @@ -318,7 +318,7 @@ ftp_files = [] # TODO: warning to the user (could happen if session has become invalid) else: - user_ftp_dir = os.path.join( trans.app.config.ftp_upload_dir, trans.user.email ) + user_ftp_dir = trans.user_ftp_dir for ( dirpath, dirnames, filenames ) in os.walk( user_ftp_dir ): for filename in filenames: path = relpath( os.path.join( dirpath, filename ), user_ftp_dir ) diff -r bbb229927c688213e67ba62998a64526ca948a19 -r e0354c9d5497fa9d169df6a7aa44c8132718f92c lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -960,6 +960,11 @@ def ncbi_builds( self ): return util.dlnames['ncbi'] + @property + def user_ftp_dir( self ): + identifier = self.app.config.ftp_upload_dir_identifier + return os.path.join( self.app.config.ftp_upload_dir, getattr(self.user, identifier) ) + def db_dataset_for( self, dbkey ): """ Returns the db_file dataset associated/needed by `dataset`, or `None`. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes to make support for recently introduced prior_installation_required atribute for ordering installation of tool shed repositories backward compatible to the 12/20/12 Galaxy release.
by commits-noreply＠bitbucket.org 16 Apr '13

16 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bbb229927c68/ Changeset: bbb229927c68 User: greg Date: 2013-04-16 21:55:07 Summary: Fixes to make support for recently introduced prior_installation_required atribute for ordering installation of tool shed repositories backward compatible to the 12/20/12 Galaxy release. Affected #: 5 files diff -r cf7a0098c612499d03aafb2f62084ebbcf99e55f -r bbb229927c688213e67ba62998a64526ca948a19 lib/galaxy/webapps/tool_shed/util/container_util.py --- a/lib/galaxy/webapps/tool_shed/util/container_util.py +++ b/lib/galaxy/webapps/tool_shed/util/container_util.py @@ -1031,14 +1031,18 @@ changeset_revision = items[ 3 ] if len( items ) == 5: prior_installation_required = asbool( str( items[ 4 ] ) ) + return toolshed_base_url, repository_name, repository_owner, changeset_revision, prior_installation_required else: - # Metadata should have been reset on the repository that contains the definition for this repository_dependency. In the meantime we'll - # default the prior_installation_required to False. - prior_installation_required = False - return toolshed_base_url, repository_name, repository_owner, changeset_revision, prior_installation_required + # For backward compatibility to the 12/20/12 Galaxy release we have to return the following, and callers must handle exceptions. + return toolshed_base_url, repository_name, repository_owner, changeset_revision def handle_repository_dependencies_container_entry( trans, repository_dependencies_folder, rd_key, rd_value, folder_id, repository_dependency_id, folder_keys ): - toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required = get_components_from_key( rd_key ) + try: + toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required = get_components_from_key( rd_key ) + except ValueError: + # For backward compatibility to the 12/20/12 Galaxy release, default prior_installation_required to False. + toolshed, repository_name, repository_owner, changeset_revision = get_components_from_key( rd_key ) + prior_installation_required = False folder = get_folder( repository_dependencies_folder, rd_key ) label = generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, @@ -1114,7 +1118,12 @@ return False def key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, prior_installation_required, key ): - toolshed_base_url, key_name, key_owner, key_changeset_revision, key_prior_installation_required = get_components_from_key( key ) + try: + toolshed_base_url, key_name, key_owner, key_changeset_revision, key_prior_installation_required = get_components_from_key( key ) + except ValueError: + # For backward compatibility to the 12/20/12 Galaxy release, default key_prior_installation_required to False. + toolshed_base_url, key_name, key_owner, key_changeset_revision = get_components_from_key( key ) + key_prior_installation_required = False return repository_name == key_name and \ repository_owner == key_owner and \ changeset_revision == key_changeset_revision and \ diff -r cf7a0098c612499d03aafb2f62084ebbcf99e55f -r bbb229927c688213e67ba62998a64526ca948a19 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -478,8 +478,12 @@ old_container_repository_dependencies_folder.id = folder_id folder_id += 1 # Generate the label by retrieving the repository name. - toolshed, name, owner, changeset_revision, prior_installation_required = \ - container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) + try: + toolshed, name, owner, changeset_revision, prior_installation_required = \ + container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) + except ValueError: + # For backward compatibility to the 12/20/12 Galaxy release. + toolshed, name, owner, changeset_revision = container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) old_container_repository_dependencies_folder.label = str( name ) repository_dependencies_folder.folders.append( old_container_repository_dependencies_folder ) # Merge tool_dependencies. diff -r cf7a0098c612499d03aafb2f62084ebbcf99e55f -r bbb229927c688213e67ba62998a64526ca948a19 lib/tool_shed/tool_shed_registry.py --- a/lib/tool_shed/tool_shed_registry.py +++ b/lib/tool_shed/tool_shed_registry.py @@ -42,9 +42,8 @@ Following more what galaxy.demo_sequencer.controllers.common does might be more appropriate at some stage... """ - log.debug( 'Looking for url %s' % url ) for shed_name, shed_url in self.tool_sheds.items(): if shed_url.find( url ) >= 0: - log.debug( 'Found %s -> %s' % ( shed_name, shed_url ) ) return self.tool_sheds_auth[ shed_name ] + log.debug( "Invalid url '%s' received by tool shed registry's password_manager_for_url method." % str( url ) ) return None diff -r cf7a0098c612499d03aafb2f62084ebbcf99e55f -r bbb229927c688213e67ba62998a64526ca948a19 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -263,8 +263,13 @@ for key, val in repository_dependencies.items(): if key in [ 'root_key', 'description' ]: continue - toolshed, name, owner, changeset_revision, prior_installation_required = container_util.get_components_from_key( key ) - components_list = [ toolshed, name, owner, changeset_revision, prior_installation_required ] + try: + toolshed, name, owner, changeset_revision, prior_installation_required = container_util.get_components_from_key( key ) + components_list = [ toolshed, name, owner, changeset_revision, prior_installation_required ] + except ValueError: + # For backward compatibility to the 12/20/12 Galaxy release, default prior_installation_required to False in the caller. + toolshed, name, owner, changeset_revision = container_util.get_components_from_key( key ) + components_list = [ toolshed, name, owner, changeset_revision ] if components_list not in required_repository_tups: required_repository_tups.append( components_list ) for components_list in val: @@ -279,7 +284,7 @@ encoded_required_repository_tups.append( encoding_util.encoding_sep.join( required_repository_tup ) ) encoded_required_repository_str = encoding_util.encoding_sep2.join( encoded_required_repository_tups ) encoded_required_repository_str = encoding_util.tool_shed_encode( encoded_required_repository_str ) - url = suc.url_join( tool_shed_url, '/repository/get_required_repo_info_dict?encoded_str=%s' % encoded_required_repository_str ) + url = suc.url_join( tool_shed_url, '/repository/get_required_repo_info_dict?encoded_str=%s' % encoded_required_repository_str ) text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) if text: required_repo_info_dict = json.from_json_string( text ) diff -r cf7a0098c612499d03aafb2f62084ebbcf99e55f -r bbb229927c688213e67ba62998a64526ca948a19 lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -33,8 +33,12 @@ if key in [ 'root_key', 'description' ]: continue dependent_repository = None - dependent_toolshed, dependent_name, dependent_owner, dependent_changeset_revision, dependent_prior_installation_required = \ - container_util.get_components_from_key( key ) + try: + dependent_toolshed, dependent_name, dependent_owner, dependent_changeset_revision, dependent_prior_installation_required = \ + container_util.get_components_from_key( key ) + except ValueError: + # For backward compatibility to the 12/20/12 Galaxy release. + dependent_toolshed, dependent_name, dependent_owner, dependent_changeset_revision = container_util.get_components_from_key( key ) for tsr in tool_shed_repositories: # Get the the tool_shed_repository defined by name, owner and changeset_revision. This is the repository that will be # dependent upon each of the tool shed repositories contained in val. @@ -350,13 +354,22 @@ # We have the updated changset revision. updated_key_rd_dicts.append( new_key_rd_dict ) else: - toolshed, repository_name, repository_owner, repository_changeset_revision, prior_installation_required = \ - container_util.get_components_from_key( key ) + try: + toolshed, repository_name, repository_owner, repository_changeset_revision, prior_installation_required = \ + container_util.get_components_from_key( key ) + except ValueError: + # For backward compatibility to the 12/20/12 Galaxy release. + toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key ) message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \ ( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) ) log.debug( message ) else: - toolshed, repository_name, repository_owner, repository_changeset_revision, prior_installation_required = container_util.get_components_from_key( key ) + try: + toolshed, repository_name, repository_owner, repository_changeset_revision, prior_installation_required = \ + container_util.get_components_from_key( key ) + except ValueError: + # For backward compatibility to the 12/20/12 Galaxy release. + toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key ) message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \ ( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) ) log.debug( message ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Add a track_type attribute to data types and use instead of burying track type in get_track_type function.
by commits-noreply＠bitbucket.org 16 Apr '13

16 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cf7a0098c612/ Changeset: cf7a0098c612 User: jgoecks Date: 2013-04-16 21:32:46 Summary: Add a track_type attribute to data types and use instead of burying track type in get_track_type function. Affected #: 5 files diff -r 270ef5007ae876bfbaa3110d6666432751152323 -r cf7a0098c612499d03aafb2f62084ebbcf99e55f lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -94,6 +94,8 @@ class Bam( Binary ): """Class describing a BAM binary file""" file_ext = "bam" + track_type = "ReadTrack" + MetadataElement( name="bam_index", desc="BAM Index File", param=metadata.FileParameter, file_ext="bai", readonly=True, no_value=None, visible=False, optional=True ) def _get_samtools_version( self ): @@ -245,7 +247,7 @@ except: return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) ) def get_track_type( self ): - return "ReadTrack", { "data": "bai", "index": [ "bigwig", "summary_tree" ] } + return self.track_type, { "data": "bai", "index": [ "bigwig", "summary_tree" ] } Binary.register_sniffable_binary_format("bam", "bam", Bam) @@ -324,6 +326,8 @@ The supplemental info in the paper has the binary details: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq351v1 """ + track_type = "LineTrack" + def __init__( self, **kwd ): Binary.__init__( self, **kwd ) self._magic = 0x888FFC26 @@ -349,18 +353,19 @@ except: return "Binary UCSC %s file (%s)" % ( self._name, data.nice_size( dataset.get_size() ) ) def get_track_type( self ): - return "LineTrack", {"data_standalone": "bigwig"} + return self.track_type, {"data_standalone": "bigwig"} Binary.register_sniffable_binary_format("bigwig", "bigwig", BigWig) class BigBed(BigWig): """BigBed support from UCSC.""" + def __init__( self, **kwd ): Binary.__init__( self, **kwd ) self._magic = 0x8789F2EB self._name = "BigBed" def get_track_type( self ): - return "LineTrack", {"data_standalone": "bigbed"} + return self.track_type, {"data_standalone": "bigbed"} Binary.register_sniffable_binary_format("bigbed", "bigbed", BigBed) diff -r 270ef5007ae876bfbaa3110d6666432751152323 -r cf7a0098c612499d03aafb2f62084ebbcf99e55f lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -97,6 +97,9 @@ #A per datatype setting (inherited): max file size (in bytes) for setting optional metadata _max_optional_metadata_filesize = None + # Trackster track type. + track_type = None + def __init__(self, **kwd): """Initialize the datatype""" object.__init__(self, **kwd) @@ -561,7 +564,7 @@ Returns a list of visualizations for datatype. """ - if hasattr( self, 'get_track_type' ): + if self.track_type: return [ 'trackster', 'circster' ] return [] diff -r 270ef5007ae876bfbaa3110d6666432751152323 -r cf7a0098c612499d03aafb2f62084ebbcf99e55f lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -46,6 +46,7 @@ """Tab delimited data containing interval information""" file_ext = "interval" line_class = "region" + track_type = "FeatureTrack" """Add metadata elements""" MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) @@ -330,15 +331,16 @@ return None def get_track_type( self ): - return "FeatureTrack", {"data": "tabix", "index": "summary_tree"} + return self.track_type, {"data": "tabix", "index": "summary_tree"} class BedGraph( Interval ): """Tab delimited chrom/start/end/datavalue dataset""" file_ext = "bedgraph" + track_type = "LineTrack" def get_track_type( self ): - return "LineTrack", { "data": "bigwig", "index": "bigwig" } + return self.track_type, { "data": "bigwig", "index": "bigwig" } def as_ucsc_display_file( self, dataset, **kwd ): """ @@ -512,7 +514,7 @@ except: return False def get_track_type( self ): - return "FeatureTrack", {"data": "tabix", "index": "summary_tree", "feature_search": "fli"} + return self.track_type, {"data": "tabix", "index": "summary_tree", "feature_search": "fli"} class BedStrict( Bed ): """Tab delimited data in strict BED format - no non-standard columns allowed""" @@ -785,7 +787,7 @@ return False def get_track_type( self ): - return "FeatureTrack", {"data": "interval_index", "index": "summary_tree", "feature_search": "fli"} + return self.track_type, {"data": "interval_index", "index": "summary_tree", "feature_search": "fli"} class Gff3( Gff ): @@ -966,6 +968,7 @@ class Wiggle( Tabular, _RemoteCallMixin ): """Tab delimited data in wiggle format""" file_ext = "wig" + track_type = "LineTrack" MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False ) @@ -1148,7 +1151,7 @@ return resolution def get_track_type( self ): - return "LineTrack", { "data": "bigwig", "index": "bigwig" } + return self.track_type, { "data": "bigwig", "index": "bigwig" } class CustomTrack ( Tabular ): """UCSC CustomTrack""" @@ -1304,7 +1307,7 @@ return False def get_track_type( self ): - return "FeatureTrack", {"data": "tabix", "index": "summary_tree"} + return self.track_type, {"data": "tabix", "index": "summary_tree"} class ChromatinInteractions( Interval ): ''' @@ -1312,6 +1315,7 @@ ''' file_ext = "chrint" + track_type = "DiagonalHeatmapTrack" column_names = [ 'Chrom1', 'Start1', 'End1', 'Chrom2', 'Start2', 'End2', 'Value' ] @@ -1330,7 +1334,7 @@ return False def get_track_type( self ): - return "DiagonalHeatmapTrack", {"data": "tabix", "index": "summary_tree"} + return self.track_type, {"data": "tabix", "index": "summary_tree"} diff -r 270ef5007ae876bfbaa3110d6666432751152323 -r cf7a0098c612499d03aafb2f62084ebbcf99e55f lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -163,7 +163,7 @@ # Use default mime type as per datatype spec mimetype = self.datatypes_by_extension[ extension ].get_mime() self.mimetypes_by_extension[ extension ] = mimetype - if hasattr( datatype_class, "get_track_type" ): + if datatype_class.track_type: self.available_tracks.append( extension ) if display_in_upload: self.upload_file_formats.append( extension ) diff -r 270ef5007ae876bfbaa3110d6666432751152323 -r cf7a0098c612499d03aafb2f62084ebbcf99e55f lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -358,6 +358,8 @@ class Sam( Tabular ): file_ext = 'sam' + track_type = "ReadTrack" + def __init__(self, **kwd): """Initialize taxonomy datatype""" Tabular.__init__( self, **kwd ) @@ -468,7 +470,7 @@ merge = staticmethod(merge) def get_track_type( self ): - return "ReadTrack", {"data": "bam", "index": "summary_tree"} + return self.track_type, {"data": "bam", "index": "summary_tree"} class Pileup( Tabular ): """Tab delimited data in pileup (6- or 10-column) format""" @@ -525,8 +527,7 @@ return True except: return False - - + class ElandMulti( Tabular ): file_ext = 'elandmulti' @@ -535,6 +536,7 @@ class Vcf( Tabular ): """ Variant Call Format for describing SNPs and other simple genome variations. """ + track_type = "VariantTrack" file_ext = 'vcf' column_names = [ 'Chrom', 'Pos', 'ID', 'Ref', 'Alt', 'Qual', 'Filter', 'Info', 'Format', 'data' ] @@ -552,7 +554,7 @@ return Tabular.make_html_table( self, dataset, column_names=self.column_names ) def get_track_type( self ): - return "VariantTrack", { "data": "tabix", "index": "summary_tree" } + return self.track_type, { "data": "tabix", "index": "summary_tree" } class Eland( Tabular ): """Support for the export.txt.gz file used by Illumina's ELANDv2e aligner""" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Added info_only option to install and test script.
by commits-noreply＠bitbucket.org 16 Apr '13

16 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/270ef5007ae8/ Changeset: 270ef5007ae8 User: inithello Date: 2013-04-16 21:28:23 Summary: Added info_only option to install and test script. Affected #: 1 file diff -r 95c90c1d90294032a0db5f3cb9312a967ac00e49 -r 270ef5007ae876bfbaa3110d6666432751152323 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -265,9 +265,8 @@ tool_id = parts[ -2 ] return tool_id, tool_version -def get_tool_test_errors_from_api( tool_shed_url, metadata_dict ): - params = dict() - api_path = metadata_dict[ 'url' ].split( '/' ) +def get_tool_test_errors_from_api( tool_shed_url, metadata_revision_id ): + api_path = [ 'api', 'repository_revisions', metadata_revision_id ] api_url = get_api_url( base=tool_shed_url, parts=api_path ) repository_metadata = json_from_url( api_url ) if repository_metadata[ 'tool_test_errors' ] is None: @@ -292,7 +291,10 @@ params[ 'tools_functionally_correct' ] = 'false' params[ 'do_not_test' ] = 'false' params[ 'tool_test_errors' ] = test_results_dict - return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params, return_formatted=False ) + if '-info_only' in sys.argv: + return {} + else: + return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params, return_formatted=False ) def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config ) @@ -332,8 +334,6 @@ galaxy_test_file_dir = os.environ.get( 'GALAXY_INSTALL_TEST_FILE_DIR', default_galaxy_test_file_dir ) if not os.path.isabs( galaxy_test_file_dir ): galaxy_test_file_dir = os.path.abspath( galaxy_test_file_dir ) - # Set up the tool dependency path for the Galaxy instance. - tool_dependency_dir = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR', None ) use_distributed_object_store = os.environ.get( 'GALAXY_INSTALL_TEST_USE_DISTRIBUTED_OBJECT_STORE', False ) if not os.path.isdir( galaxy_test_tmp_dir ): os.mkdir( galaxy_test_tmp_dir ) @@ -363,9 +363,12 @@ new_repos_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) galaxy_tempfiles = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) galaxy_shed_tool_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir, prefix='shed_tools' ) - galaxy_migrated_tool_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) - galaxy_tool_dependency_dir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) - os.environ[ 'GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR' ] = galaxy_tool_dependency_dir + galaxy_migrated_tool_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + # Set up the tool dependency path for the Galaxy instance. + tool_dependency_dir = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR', None ) + if tool_dependency_dir is None: + tool_dependency_dir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + os.environ[ 'GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR' ] = tool_dependency_dir if 'GALAXY_INSTALL_TEST_DBURI' in os.environ: database_connection = os.environ[ 'GALAXY_INSTALL_TEST_DBURI' ] else: @@ -422,7 +425,7 @@ tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ], tool_data_path = tool_data_path, tool_data_table_config_path = galaxy_tool_data_table_conf_file, - tool_dependency_dir = galaxy_tool_dependency_dir, + tool_dependency_dir = tool_dependency_dir, tool_path = tool_path, tool_parse_help = False, tool_sheds_config_file = galaxy_tool_sheds_conf_file, @@ -625,7 +628,7 @@ # }, # ] # } - repository_status = get_tool_test_errors_from_api( galaxy_tool_shed_url, repository_info_dict ) + repository_status = get_tool_test_errors_from_api( galaxy_tool_shed_url, metadata_revision_id ) if 'test_environment' not in repository_status: repository_status[ 'test_environment' ] = {} test_environment = get_test_environment( repository_status[ 'test_environment' ] ) @@ -775,6 +778,8 @@ print "####################################################################################" print "# %s - repository installation and testing script completed." % now print "# Repository revisions tested: %d" % repositories_tested + if '-info_only' in sys.argv: + print "# -info_only set, not updating the tool shed." if repositories_tested > 0: if repositories_passed: print '# ----------------------------------------------------------------------------------' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Rewrite RawVcfDataProvider for completeness and efficiency.
by commits-noreply＠bitbucket.org 16 Apr '13

16 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/95c90c1d9029/ Changeset: 95c90c1d9029 User: jgoecks Date: 2013-04-16 20:36:27 Summary: Rewrite RawVcfDataProvider for completeness and efficiency. Affected #: 1 file diff -r 6e91867769eab9e97353cd0e6363393c8077aadc -r 95c90c1d90294032a0db5f3cb9312a967ac00e49 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -759,29 +759,41 @@ """ def get_iterator( self, chrom, start, end, **kwargs ): - # Read first line in order to match chrom naming format. - line = source.readline() - dataset_chrom = line.split()[0] - if not _chrom_naming_matches( chrom, dataset_chrom ): - chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) - # Undo read. - source.seek( 0 ) + source = open( self.original_dataset.file_name ) + + # Skip comments. + pos = 0 + line = None + for line in source: + if not line.startswith("#"): + break + else: + pos = source.tell() + + # Match chrom naming format. + if line: + dataset_chrom = line.split()[0] + if not _chrom_naming_matches( chrom, dataset_chrom ): + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + + def line_in_region( vcf_line, chrom, start, end ): + """ Returns true if line is in region. """ + variant_chrom, variant_start = vcf_line.split()[ 0:2 ] + # VCF format is 1-based. + variant_start = int( variant_start ) - 1 + return variant_chrom == chrom and variant_start >= start and variant_start <= end def line_filter_iter(): - for line in open( self.original_dataset.file_name ): - if line.startswith("#"): - continue - variant = line.split() - variant_chrom, variant_start, id, ref, alts = variant[ 0:5 ] - variant_start = int( variant_start ) - longest_alt = -1 - for alt in alts: - if len( alt ) > longest_alt: - longest_alt = len( alt ) - variant_end = variant_start + abs( len( ref ) - longest_alt ) - if variant_chrom != chrom or variant_start > end or variant_end < start: - continue + """ Yields lines in source that are in region chrom:start-end """ + # Yield data line read above. + if line_in_region( line, chrom, start, end ): yield line + + # Search for and yield other data lines. + for data_line in source: + if line_in_region( data_line, chrom, start, end ): + print chrom, start, end, ">>>", data_line, + yield data_line return line_filter_iter() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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