diff --git a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako deleted file mode 100644 index 366eeb3bd3c..00000000000 --- a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako +++ /dev/null @@ -1,94 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" /> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/tool_shed/common/common.mako" import="*" /> - -<% import os %> - -${render_galaxy_repository_actions( repository )} - -%if message: - ${render_msg( message, status )} -%endif - -
-

- The updates to the ${repository.name} repository require the following packages. Click the Install button to install them. - Installing some packages may take a while, but you can continue to use Galaxy during installation. -

-
- -
-
-
- - - - - - - %if tool_dependencies_dict: - %if install_tool_dependencies_check_box is not None: -
- - <% disabled = trans.app.tool_dependency_dir is None %> - ${render_checkbox(install_tool_dependencies_check_box, disabled=disabled)} -
- %if disabled: - Set the tool_dependency_dir configuration value in your Galaxy config to automatically handle tool dependencies. - %else: - Un-check to skip automatic handling of these tool dependencies. - %endif -
-
-
- %endif -
- - - - - - - - %for key, requirements_dict in tool_dependencies_dict.items(): - <% - readme_text = None - if key == 'set_environment': - key_name = ', '.join( [ environment_variable[ 'name' ] for environment_variable in requirements_dict ] ) - key_version = '' - install_dir = '' - else: - key_items = key.split( '/' ) - key_name = key_items[ 0 ] - key_version = key_items[ 1 ] - readme_text = requirements_dict.get( 'readme', None ) - install_dir = os.path.join( trans.app.tool_dependency_dir, - key_name, - key_version, - repository.owner, - repository.name, - repository.installed_changeset_revision ) - %> - %if not os.path.exists( install_dir ): - - - - - - %if readme_text: - - - %endif - %endif - %endfor -
New tool dependencies included in update
NameVersionInstall directory
${key_name|h}${key_version|h}${install_dir|h}
${key_name|h} ${key_version|h} requirements and installation information
${readme_text}
-
-
- %endif -
- -
-
-
-
diff --git a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/monitor_repository_installation.mako b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/monitor_repository_installation.mako deleted file mode 100644 index e42c3f034c7..00000000000 --- a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/monitor_repository_installation.mako +++ /dev/null @@ -1,70 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/admin/tool_shed_repository/common.mako" import="*" /> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${repository_installation_status_updater()} - ${repository_installation_updater()} - ${self.repository_installation_javascripts()} - - -<%def name="repository_installation_javascripts()"> - - - -%if context.get("message"): - ${render_msg( message, status )} -%endif - -%if tool_shed_repositories: -
-
Monitor installing tool shed repositories
-
- - - - - - - - - %for tool_shed_repository in tool_shed_repositories: - <% - encoded_repository_id = trans.security.encode_id( tool_shed_repository.id ) - ids_of_tool_dependencies_missing_or_being_installed = [ trans.security.encode_id( td.id ) for td in tool_shed_repository.tool_dependencies_missing_or_being_installed ] - link_to_manage_tool_dependencies = tool_shed_repository.status in [ trans.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ] - %> - - - - - - - - %endfor -
NameDescriptionOwnerRevisionStatus
${tool_shed_repository.name|h}${tool_shed_repository.description}${tool_shed_repository.owner}${tool_shed_repository.changeset_revision}
${tool_shed_repository.status|h}
-
-
-
-%else: - ${render_msg("There is no repository being installed.", "info")} -%endif diff --git a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/purge_repository_confirmation.mako b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/purge_repository_confirmation.mako deleted file mode 100644 index 36a7f562b66..00000000000 --- a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/purge_repository_confirmation.mako +++ /dev/null @@ -1,74 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" /> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "library" )} - - -<%def name="javascripts()"> - ${parent.javascripts()} - - -${render_galaxy_repository_actions( repository )} - -%if message: - ${render_msg( message, status )} -%endif - -
-

- Purging the repository named ${repository.name|h} will result in deletion of all records for the - following associated items from the database. Click the Purge button to purge this repository - and its associated items. -

-
- -
-
Purge tool shed repository ${repository.name|h}
-
- <% - tool_versions = 0 - tool_dependencies = 0 - required_repositories = 0 - orphan_repository_repository_dependency_association_records = 0 - orphan_repository_dependency_records = 0 - # Count this repository's tool version lineage chain links that will be purged. - for tool_version in repository.tool_versions: - for tool_version_association in tool_version.parent_tool_association: - tool_versions += 1 - for tool_version_association in tool_version.child_tool_association: - tool_versions += 1 - tool_versions += 1 - # Count this repository's associated tool dependencies that will be purged. - for tool_dependency in repository.tool_dependencies: - tool_dependencies += 1 - # Count this repository's associated required repositories that will be purged. - for rrda in repository.required_repositories: - required_repositories += 1 - # Count any "orphan" repository_dependency records associated with the repository but not with any - # repository_repository_dependency_association records that will be purged. - for orphan_repository_dependency in \ - trans.sa_session.query( trans.app.install_model.RepositoryDependency ) \ - .filter( trans.app.install_model.RepositoryDependency.table.c.tool_shed_repository_id == repository.id ): - for orphan_rrda in \ - trans.sa_session.query( trans.app.install_model.RepositoryRepositoryDependencyAssociation ) \ - .filter( trans.app.install_model.RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id == orphan_repository_dependency.id ): - orphan_repository_repository_dependency_association_records += 1 - orphan_repository_dependency_records += 1 - %> - - - - - - -
Tool version records${tool_versions|h}
Tool dependency records${tool_dependencies|h}
Repository dependency records${required_repositories|h}
Orphan repository_repository_dependency_association records${orphan_repository_repository_dependency_association_records|h}
Orphan repository_dependency records${orphan_repository_dependency_records|h}
-
-
- -
-
-
- diff --git a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako b/lib/tool_shed/webapp/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako deleted file mode 100644 index d901b6d08e8..00000000000 --- a/lib/tool_shed/webapp/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako +++ /dev/null @@ -1,101 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" /> -<%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" /> -<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /> -<%namespace file="/webapps/tool_shed/common/common.mako" import="*" /> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "library" )} - - -<%def name="javascripts()"> - ${parent.javascripts()} - ${container_javascripts()} - - -%if message: - ${render_msg( message, status )} -%endif - -
-
-
-
- -
-
- <% readme_files_dict = containers_dict.get( 'readme_files', None ) %> - %if readme_files_dict: -
- - -
Repository README files - may contain important installation or license information
-
- ${render_readme_section( containers_dict )} -
- %endif - %if has_repository_dependencies or includes_tool_dependencies: -
- - -
Confirm dependency installation
-
- ${render_dependencies_section( install_resolver_dependencies_check_box, install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict, revision_label=None, export=False )} - %endif - %if shed_tool_conf_select_field: -
- - -
Choose the configuration file whose tool_path setting will be used for installing repositories
-
- <% - if len( shed_tool_conf_select_field.options ) == 1: - select_help = "Your Galaxy instance is configured with 1 shed-related tool configuration file, so repositories will be " - select_help += "installed using its tool_path setting." - else: - select_help = "Your Galaxy instance is configured with %d shed-related tool configuration files, " % len( shed_tool_conf_select_field.options ) - select_help += "so select the file whose tool_path setting you want used for installing repositories." - %> -
- - ${render_select(shed_tool_conf_select_field)} -
- ${select_help|h} -
-
-
- %else: - - %endif - %if includes_tools_for_display_in_tool_panel: -
-
- ${render_checkbox(no_changes_check_box)} - -
- Uncheck and select a different tool panel section to load the tools into a different section in the tool panel. -
-
-
- - -
- Add a new tool panel section to contain the installed tools (optional). -
-
-
- - ${render_select(tool_panel_section_select_field)} -
- Choose an existing section in your tool panel to contain the installed tools (optional). -
-
- %endif -
- -
-
-
-