diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py index c1267c166db..f99abf7ce1a 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -890,33 +890,6 @@ class AdminGalaxy(controller.JSAppLauncher): repo_name_dependency_tups.append((repository_name, tool_dependencies)) return repo_name_dependency_tups - @web.expose - @web.require_admin - def review_tool_migration_stages(self, trans, **kwd): - message = escape(util.restore_text(kwd.get('message', ''))) - status = util.restore_text(kwd.get('status', 'done')) - migration_stages_dict = {} - # FIXME: this isn't valid in an installed context - migration_scripts_dir = os.path.abspath(os.path.join(trans.app.config.root, 'lib', 'galaxy', 'tool_shed', 'galaxy_install', 'migrate', 'versions')) - modules = os.listdir(migration_scripts_dir) - modules.sort() - modules.reverse() - for item in modules: - if not item.endswith('_tools.py') or item.startswith('0001_tools'): - continue - module = item.replace('.py', '') - migration_stage = int(module.replace('_tools', '')) - repo_name_dependency_tups = self.check_for_tool_dependencies(trans, migration_stage) - open_file_obj, file_name, description = imp.find_module(module, [migration_scripts_dir]) - imported_module = imp.load_module('upgrade', open_file_obj, file_name, description) - migration_info = imported_module.__doc__ - open_file_obj.close() - migration_stages_dict[migration_stage] = (migration_info, repo_name_dependency_tups) - return trans.fill_template('admin/review_tool_migration_stages.mako', - migration_stages_dict=migration_stages_dict, - message=message, - status=status) - @web.legacy_expose_api @web.require_admin def tool_versions_list(self, trans, **kwd): diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py index 1b093e2ee2f..e9c334ecb0c 100644 --- a/lib/tool_shed/test/base/twilltestcase.py +++ b/lib/tool_shed/test/base/twilltestcase.py @@ -1173,11 +1173,6 @@ class ShedTwillTestCase(DrivenFunctionalTestCase): self.visit_url('/repository/display_tool', params=params) self.check_for_strings(strings_displayed, strings_not_displayed) - def load_galaxy_tool_migrations_page(self, strings_displayed=None, strings_not_displayed=None): - url = '/admin/review_tool_migration_stages' - self.visit_galaxy_url(url) - self.check_for_strings(strings_displayed, strings_not_displayed) - def load_invalid_tool_page(self, repository, tool_xml, changeset_revision, strings_displayed=None, strings_not_displayed=None): params = { 'repository_id': self.security.encode_id(repository.id), diff --git a/templates/admin/review_tool_migration_stages.mako b/templates/admin/review_tool_migration_stages.mako deleted file mode 100644 index ebf96336a94..00000000000 --- a/templates/admin/review_tool_migration_stages.mako +++ /dev/null @@ -1,123 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif -<% -from markupsafe import escape -%> -
-
Tool migrations that can be performed on this Galaxy instance
-
-
-

- The list of tool migration stages below, displayed most recent to oldest, provides information about the repositories in the - main Galaxy tool shed that will be cloned at each stage if you run the shell command for that stage. This enables you to execute - the migration process for any stage at any time. -

-

- Keep in mind that tools included in a repository that you want to be displayed in the Galaxy tool panel when the repository is - installed must be defined in the tool_conf.xml (or equivalent) config file prior to execution of the migration process for a - stage. Executing a migration process multiple times will have no affect unless the repositories associated with that stage have been - uninstalled prior to the execution of the migration process. -

-

- When you initiate a migration process, the associated repositories will be cloned from the Galaxy tool shed at - http://toolshed.g2.bx.psu.edu. The location in which the tool repositories - will be installed is the value of the 'tool_path' attribute in the tag of the file named ./migrated_tool_conf.xml - (i.e., <toolbox tool_path="../shed_tools">). The default location setting is '../shed_tools', which may be problematic - for some cluster environments, so make sure to change it before you execute the installation process if appropriate. The configured location - must be outside of the Galaxy installation directory or it must be in a sub-directory protected by a properly configured .hgignore - file if the directory is within the Galaxy installation directory hierarchy. This is because tool shed repositories will be installed using - mercurial's clone feature, which creates .hg directories and associated mercurial repository files. Not having .hgignore properly - configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed repositories if they are - in directories that pose conflicts. See mercurial's .hgignore documentation at - http://mercurial.selenic.com/wiki/.hgignore for details. -

-
- - <% from tool_shed.util.basic_util import to_html_string %> - %for stage in migration_stages_dict.keys(): - <% - migration_command = 'sh ./scripts/migrate_tools/%04d_tools.sh' % stage - install_dependencies = '%s install_dependencies' % migration_command - migration_tup = migration_stages_dict[ stage ] - migration_info, repo_name_dependency_tups = migration_tup - repository_names = [] - for repo_name_dependency_tup in repo_name_dependency_tups: - repository_name, tool_dependencies = repo_name_dependency_tup - if repository_name not in repository_names: - repository_names.append( repository_name ) - if repository_names: - repository_names.sort() - repository_names = ', '.join( repository_names ) - %> - - - - - %for repo_name_dependency_tup in repo_name_dependency_tups: - <% repository_name, tool_dependencies = repo_name_dependency_tup %> - - - - %if tool_dependencies: - - - - %for tool_dependencies_tup in tool_dependencies: - <% - tool_dependency_name = escape( tool_dependencies_tup[0] ) - tool_dependency_version = escape( tool_dependencies_tup[1] ) - tool_dependency_type = escape( tool_dependencies_tup[2] ) - installation_requirements = escape( tool_dependencies_tup[3] ).replace( '\n', '
' ) - %> - - - - %endfor - %else: - - - - %endif - %endfor - %endfor -
Tool migration stage ${stage} - repositories: ${repository_names|h}
-
-

${to_html_string(migration_info)} Run commands from the Galaxy installation directory!

-

- %if tool_dependencies: - This migration stage includes tools that have tool dependencies that can be automatically installed. To install them, run:
- ${install_dependencies|h}

- To skip tool dependency installation run:
- ${migration_command|h} - %else: - ${migration_command|h} - %endif -

-
-
-
- Repository: ${repository_name|h} -
-
-
- Tool dependencies -
-
-
- Name: ${tool_dependency_name} Version: ${tool_dependency_version} Type: ${tool_dependency_type} -
-
- Requirements and installation information:
- ${installation_requirements} -
-
-
- No tool dependencies have been defined for this repository. -
-
-
-