1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/3bdb4291e5e6/ changeset: 3bdb4291e5e6 user: carlfeberhard date: 2013-02-22 20:58:50 summary: Fix to new-style display_application url mapping/formation; display_applications/link_generator: clean up affected #: 2 files

diff -r 5f10f61335fbcfb7982a879edc80325f5a73402f -r 3bdb4291e5e666c4d4b86e184b4599e61b847864 lib/galaxy/datatypes/display_applications/link_generator.py --- a/lib/galaxy/datatypes/display_applications/link_generator.py +++ b/lib/galaxy/datatypes/display_applications/link_generator.py @@ -1,4 +1,6 @@ -"""Separating Transaction based elements of display applications from datatypes. +"""Classes to generate links for display applications. + +Separating Transaction based elements of display applications from datatypes. """

import urllib @@ -10,19 +12,22 @@

from galaxy import util from galaxy.web import url_for - from galaxy.datatypes.interval import Interval, Gff, Wiggle, CustomTrack

+#TODO: Ideally, these classes would be instantiated in the trans (or some other semi-persistant fixture) +# Currently, these are instantiated per HDA which is not the best solution + +#TODO: these could be extended to handle file_function and parse/contain the builds.txt files

def get_display_app_link_generator( display_app_name ): """Returns an instance of the proper link generator class based on the display_app_name or DisplayAppLinkGenerator - if the name is unrecognized. + if the display_app_name is unrecognized. """ if display_app_name == 'ucsc': return UCSCDisplayAppLinkGenerator()

- if display_app_name == 'gbrowse': + elif display_app_name == 'gbrowse': return GBrowseDisplayAppLinkGenerator()

return DisplayAppLinkGenerator() @@ -58,9 +63,10 @@

class UCSCDisplayAppLinkGenerator( DisplayAppLinkGenerator ): - """Class for UCSC display application link generators. + """Class for generating links to display data in the + UCSC genome browser.

- This class returns UCSC main and test links for the following datatypes: + This class returns links for the following datatypes and their subclasses: Interval, Wiggle, Gff, CustomTrack """ def __init__( self ): @@ -69,7 +75,6 @@ def _link_function_from_datatype( self, datatype ): """Dispatch to proper link generating function based on datatype. """ - # they're all the same if( ( isinstance( datatype, Interval ) ) or ( isinstance( datatype, Wiggle ) ) or ( isinstance( datatype, Gff ) ) @@ -83,8 +88,6 @@ and content of dataset. """ # this is a refactor of Interval.ucsc_links, GFF.ucsc_links, Wiggle.ucsc_links, and CustomTrack.ucsc_links - # ...which are all the same function - #TODO: app vars can be moved into init (and base_url as well) chrom, start, stop = dataset.datatype.get_estimated_display_viewport( dataset ) if chrom is None: @@ -107,10 +110,11 @@

class GBrowseDisplayAppLinkGenerator( DisplayAppLinkGenerator ): - """Class for UCSC display application link generators. + """Class for generating links to display data in the + GBrowse genome browser.

- This class returns UCSC main and test links for the following datatypes: - Interval, Wiggle, Gff, CustomTrack + This class returns links for the following datatypes and their subclasses: + Gff, Wiggle """ def __init__( self ): self.display_app_name = 'gbrowse' @@ -118,7 +122,6 @@ def _link_function_from_datatype( self, datatype ): """Dispatch to proper link generating function based on datatype. """ - # they're all the same if( ( isinstance( datatype, Gff ) ) or ( isinstance( datatype, Wiggle ) ) ): return self.gbrowse_links

diff -r 5f10f61335fbcfb7982a879edc80325f5a73402f -r 3bdb4291e5e666c4d4b86e184b4599e61b847864 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -244,7 +244,7 @@ def get_display_app_url( display_app_link, hda, trans ): web_url_for = routes.URLGenerator( trans.webapp.mapper, trans.environ ) dataset_hash, user_hash = util.encode_dataset_user( trans, hda, None ) - return web_url_for( controller='/dataset', + return web_url_for( controller='dataset', action="display_application", dataset_id=dataset_hash, user_id=user_hash, @@ -280,4 +280,3 @@ display_apps.append( dict( label=hda.datatype.get_display_label( display_app_name ), links=app_links ) )

return display_apps -

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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