1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/31564ea924e7/ changeset: 31564ea924e7 user: greg date: 2012-07-03 19:53:09 summary: Clarify up status column display in the tool shed repository grids, and fix a method signature bug. affected #: 4 files diff -r f6b32f963f6114e8ee86853a6311836b8dd5cdd3 -r 31564ea924e7911a04eecc9157d1817d68febd97 lib/galaxy/tool_shed/__init__.py --- a/lib/galaxy/tool_shed/__init__.py +++ b/lib/galaxy/tool_shed/__init__.py @@ -52,5 +52,5 @@ if installed_repository_dict[ 'converter_path' ]: galaxy.util.shed_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) if installed_repository_dict[ 'display_path' ]: - galaxy.util.shed_util.load_installed_display_applications( installed_repository_dict, deactivate=deactivate ) + galaxy.util.shed_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) \ No newline at end of file diff -r f6b32f963f6114e8ee86853a6311836b8dd5cdd3 -r 31564ea924e7911a04eecc9157d1817d68febd97 lib/galaxy/tool_shed/migrate/check.py --- a/lib/galaxy/tool_shed/migrate/check.py +++ b/lib/galaxy/tool_shed/migrate/check.py @@ -127,7 +127,7 @@ msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n" msg += "sh ./scripts/migrate_tools/%04d_tools.sh install_dependencies\n" % latest_tool_migration_script_number msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n" - msg += "Tool dependencies can be installed after the repositories have been installed, but installing them now is better.\n\n" + msg += "Tool dependencies can be installed after the repositories have been installed as well.\n\n" msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n" msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n" msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these files should be\n" diff -r f6b32f963f6114e8ee86853a6311836b8dd5cdd3 -r 31564ea924e7911a04eecc9157d1817d68febd97 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1279,7 +1279,7 @@ except: pass return repository_dict -def load_installed_display_applications( installed_repository_dict, deactivate=False ): +def load_installed_display_applications( app, installed_repository_dict, deactivate=False ): # Load or deactivate proprietary datatype display applications app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict, deactivate=deactivate ) def make_tmp_directory(): diff -r f6b32f963f6114e8ee86853a6311836b8dd5cdd3 -r 31564ea924e7911a04eecc9157d1817d68febd97 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -30,6 +30,7 @@ return tool_shed_repository.changeset_revision class StatusColumn( grids.TextColumn ): def get_value( self, trans, grid, tool_shed_repository ): + status_label = tool_shed_repository.status if tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING, trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS, trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES, @@ -45,12 +46,12 @@ elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.INSTALLED ]: if tool_shed_repository.missing_tool_dependencies: bgcolor = trans.model.ToolShedRepository.states.WARNING + status_label = '%s, missing dependencies' % status_label else: bgcolor = trans.model.ToolShedRepository.states.OK else: bgcolor = trans.model.ToolShedRepository.states.ERROR - rval = '<div class="count-box state-color-%s">' % bgcolor - rval += '%s</div>' % tool_shed_repository.status + rval = '<div class="count-box state-color-%s">%s</div>' % ( bgcolor, status_label ) return rval class ToolShedColumn( grids.TextColumn ): def get_value( self, trans, grid, tool_shed_repository ): @@ -121,6 +122,7 @@ return tool_shed_repository.changeset_revision class StatusColumn( grids.TextColumn ): def get_value( self, trans, grid, tool_shed_repository ): + status_label = tool_shed_repository.status if tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING, trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS, trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES, @@ -136,12 +138,13 @@ elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.INSTALLED ]: if tool_shed_repository.missing_tool_dependencies: bgcolor = trans.model.ToolShedRepository.states.WARNING + status_label = '%s, missing dependencies' % status_label else: bgcolor = trans.model.ToolShedRepository.states.OK else: bgcolor = trans.model.ToolShedRepository.states.ERROR rval = '<div class="count-box state-color-%s" id="RepositoryStatus-%s">%s</div>' % \ - ( bgcolor, trans.security.encode_id( tool_shed_repository.id ), tool_shed_repository.status ) + ( bgcolor, trans.security.encode_id( tool_shed_repository.id ), status_label ) return rval webapp = "galaxy" @@ -223,8 +226,8 @@ bgcolor = trans.model.ToolDependency.states.ERROR elif tool_dependency.status in [ trans.model.ToolDependency.installation_status.INSTALLED ]: bgcolor = trans.model.ToolDependency.states.OK - rval = '<div class="count-box state-color-%s" id="ToolDependencyStatus-%s">' % ( bgcolor, trans.security.encode_id( tool_dependency.id ) ) - rval += '%s</div>' % tool_dependency.status + rval = '<div class="count-box state-color-%s" id="ToolDependencyStatus-%s">%s</div>' % \ + ( bgcolor, trans.security.encode_id( tool_dependency.id ), tool_dependency.status ) return rval webapp = "galaxy" @@ -408,7 +411,7 @@ if installed_repository_dict[ 'converter_path' ]: load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=True ) if installed_repository_dict[ 'display_path' ]: - load_installed_display_applications( installed_repository_dict, deactivate=True ) + load_installed_display_applications( trans.app, installed_repository_dict, deactivate=True ) if remove_from_disk_checked: try: # Remove the repository from disk. 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