1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/81d637b6fdad/ changeset: 81d637b6fdad user: greg date: 2012-06-30 23:49:07 summary: Miscellaneous fixes for installing tool shed repositories. affected #: 2 files diff -r f3c8c73009c90025a068fc7eaf1641ebd1f3cc47 -r 81d637b6fdad65d74fdccd02c7d71e0e6eaf37dd lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -86,15 +86,18 @@ operations = [ grids.GridOperation( "Get updates", allow_multiple=False, condition=( lambda item: not item.deleted ), - async_compatible=False ), + async_compatible=False, + url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='get updates' ) ), grids.GridOperation( "Deactivate or uninstall", allow_multiple=False, condition=( lambda item: not item.deleted ), - async_compatible=False ), + async_compatible=False, + url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='deactivate or uninstall' ) ), grids.GridOperation( "Activate or reinstall", allow_multiple=False, condition=( lambda item: item.deleted ), - async_compatible=False ) ] + async_compatible=False, + url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='activate or reinstall' ) ) ] standard_filters = [] default_filter = dict( deleted="False" ) num_rows_per_page = 50 @@ -589,43 +592,38 @@ if file_name == shed_tool_conf: tool_path = shed_tool_conf_dict[ 'tool_path' ] break - if includes_tools and ( new_tool_panel_section or tool_panel_section ): - if new_tool_panel_section: - section_id = new_tool_panel_section.lower().replace( ' ', '_' ) - new_section_key = 'section_%s' % str( section_id ) - if new_section_key in trans.app.toolbox.tool_panel: - # Appending a tool to an existing section in trans.app.toolbox.tool_panel - log.debug( "Appending to tool panel section: %s" % new_tool_panel_section ) - tool_section = trans.app.toolbox.tool_panel[ new_section_key ] - else: - # Appending a new section to trans.app.toolbox.tool_panel - log.debug( "Loading new tool panel section: %s" % new_tool_panel_section ) - elem = Element( 'section' ) - elem.attrib[ 'name' ] = new_tool_panel_section - elem.attrib[ 'id' ] = section_id - elem.attrib[ 'version' ] = '' - tool_section = tools.ToolSection( elem ) - trans.app.toolbox.tool_panel[ new_section_key ] = tool_section - else: - section_key = 'section_%s' % tool_panel_section - tool_section = trans.app.toolbox.tool_panel[ section_key ] - else: - tool_section = None # Make sure all tool_shed_repository records exist. - new_tool_shed_repositories = [] + created_or_updated_tool_shed_repositories = [] for name, repo_info_tuple in repo_info_dict.items(): description, repository_clone_url, changeset_revision, ctx_rev = repo_info_tuple clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, name ) owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) ) # Make sure the repository was not already installed. - installed_changeset_revision = self.repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple, clone_dir ) - if installed_changeset_revision: - message = "Tool shed repository <b>%s</b> with owner <b>%s</b> and changeset revision <b>%s</b> " % ( name, owner, changeset_revision ) - message += "was previously installed using changeset revision <b>%s</b>. You can get " % installed_changeset_revision - message += "the latest updates for the installed repository using the <b>Get updates</b> option from the repository's " - message += "<b>Repository Actions</b> pop-up menu." + installed_tool_shed_repository, installed_changeset_revision = self.repository_was_previously_installed( trans, + tool_shed_url, + name, + repo_info_tuple, + clone_dir ) + if installed_tool_shed_repository: + message = "The tool shed repository <b>%s</b> with owner <b>%s</b> and changeset revision <b>%s</b> " % ( name, owner, changeset_revision ) + if installed_changeset_revision != changeset_revision: + message += "was previously installed using changeset revision <b>%s</b>. " % installed_changeset_revision + else: + message += "was previously installed. " + if installed_tool_shed_repository.uninstalled: + message += "The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. " + elif installed_tool_shed_repository.deleted: + message += "The repository has been deactivated, however, so activate the original repository instead of installing it again. " + if installed_changeset_revision != changeset_revision: + message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's " + message += "<b>Repository Actions</b> pop-up menu. " status = 'error' + if len( repo_info_dict ) == 1: + new_kwd = dict( message=message, status=status ) + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='browse_repositories', + **new_kwd ) ) else: print "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name tool_shed_repository = create_or_update_tool_shed_repository( app=trans.app, @@ -639,9 +637,31 @@ current_changeset_revision=changeset_revision, owner=owner, dist_to_shed=False ) - new_tool_shed_repositories.append( tool_shed_repository ) - if new_tool_shed_repositories: - tsrids_list = [ trans.security.encode_id( tsr.id ) for tsr in new_tool_shed_repositories ] + created_or_updated_tool_shed_repositories.append( tool_shed_repository ) + if created_or_updated_tool_shed_repositories: + if includes_tools and ( new_tool_panel_section or tool_panel_section ): + if new_tool_panel_section: + section_id = new_tool_panel_section.lower().replace( ' ', '_' ) + tool_panel_section_key = 'section_%s' % str( section_id ) + if tool_panel_section_key in trans.app.toolbox.tool_panel: + # Appending a tool to an existing section in trans.app.toolbox.tool_panel + log.debug( "Appending to tool panel section: %s" % new_tool_panel_section ) + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + # Appending a new section to trans.app.toolbox.tool_panel + log.debug( "Loading new tool panel section: %s" % new_tool_panel_section ) + elem = Element( 'section' ) + elem.attrib[ 'name' ] = new_tool_panel_section + elem.attrib[ 'id' ] = section_id + elem.attrib[ 'version' ] = '' + tool_section = tools.ToolSection( elem ) + trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section + else: + tool_panel_section_key = 'section_%s' % tool_panel_section + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + tool_section = None + tsrids_list = [ trans.security.encode_id( tsr.id ) for tsr in created_or_updated_tool_shed_repositories ] new_kwd = dict( includes_tool_dependencies=kwd.get( 'includes_tool_dependencies', False ), includes_tools=kwd.get( 'includes_tools', False ), install_tool_dependencies=install_tool_dependencies, @@ -652,7 +672,7 @@ status=status, tool_panel_section=kwd.get( 'tool_panel_section', '' ), tool_path=tool_path, - tool_section=tool_section, + tool_panel_section_key=tool_panel_section_key, tool_shed_repository_ids=tsrids_list, tool_shed_url=kwd[ 'tool_shed_url' ] ) encoded_kwd = tool_shed_encode( new_kwd ) @@ -760,6 +780,11 @@ tool_path = kwd[ 'tool_path' ] includes_tool_dependencies = util.string_as_bool( kwd[ 'includes_tool_dependencies' ] ) install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) + tool_panel_section_key = kwd.get( 'tool_panel_section_key', None ) + if tool_panel_section_key: + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + tool_section = None for tool_shed_repository in tool_shed_repositories: # Clone each repository to the configured location. update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.CLONING ) @@ -777,7 +802,7 @@ repository_clone_url=repository_clone_url, relative_install_dir=relative_install_dir, tool_shed=tool_shed_repository.tool_shed, - tool_section=kwd.get( 'tool_section', '' ), + tool_section=tool_section, shed_tool_conf=kwd.get( 'shed_tool_conf', '' ) ) trans.sa_session.refresh( tool_shed_repository ) metadata = tool_shed_repository.metadata @@ -1262,25 +1287,29 @@ def repository_was_previously_installed( self, trans, tool_shed_url, repository_name, repo_info_tuple, clone_dir ): # Handle case where the repository was previously installed using an older changeset_revsion, but later the repository was updated # in the tool shed and now we're trying to install the latest changeset revision of the same repository instead of updating the one - # that was previously installed. + # that was previously installed. We'll look in the database instead of on disk since the repository may be uninstalled. description, repository_clone_url, changeset_revision, ctx_rev = repo_info_tuple - if os.path.exists( clone_dir ): - # The installed changeset revision already exists on disk. - return changeset_revision repository_owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) ) + tool_shed = get_tool_shed_from_clone_url( repository_clone_url ) + # Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset + # revision to see if it was previously installed using one of them. url = '%s/repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy&no_reset=true' % \ ( tool_shed_url, url_for( '/', qualified=True ), repository_name, repository_owner, changeset_revision ) response = urllib2.urlopen( url ) text = response.read() response.close() if text: - clone_path, clone_directory = os.path.split( clone_dir ) + #clone_path, clone_directory = os.path.split( clone_dir ) changeset_revisions = util.listify( text ) for previous_changeset_revision in changeset_revisions: - new_clone_dir = os.path.join( clone_path, previous_changeset_revision ) - if os.path.exists( new_clone_dir ): - return previous_changeset_revision - return None + tool_shed_repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( trans.app, + tool_shed, + repository_name, + repository_owner, + previous_changeset_revision ) + if tool_shed_repository and tool_shed_repository.status not in [ trans.model.ToolShedRepository.installation_status.NEW ]: + return tool_shed_repository, previous_changeset_revision + return None, None @web.expose @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): diff -r f3c8c73009c90025a068fc7eaf1641ebd1f3cc47 -r 81d637b6fdad65d74fdccd02c7d71e0e6eaf37dd templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako --- a/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako +++ b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako @@ -23,7 +23,7 @@ <div class="toolForm"><div class="toolFormTitle">${repository.name}</div><div class="toolFormBody"> - <form name="uninstall_repository" id="uninstall_repository" action="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <form name="deactivate_or_uninstall_repository" id="deactivate_or_uninstall_repository" action="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"><label>Description:</label> ${repository.description} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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