diff --git a/client/src/components/admin/Home.vue b/client/src/components/admin/Home.vue index 8f9f18e4384..fa16ffe346b 100644 --- a/client/src/components/admin/Home.vue +++ b/client/src/components/admin/Home.vue @@ -111,12 +111,6 @@ - A view of a version lineages for all installed tools. Useful for debugging. -
  • - - View Migration Stages - - - See the list of migration stages that moved sets of tools from the distribution to the Tool Shed. -
    • @@ -145,7 +139,6 @@ export default { }, }, computed: { - migrationStagesUrl: () => `${root}admin/review_tool_migration_stages`, // NOT ROUTER adminDataTypesUrl: () => `${root}admin/data_types`, adminDataTablesUrl: () => `${root}admin/data_tables`, adminDisplayApplicationsUrl: () => `${root}admin/display_applications`, diff --git a/client/src/entry/panels/admin-panel.js b/client/src/entry/panels/admin-panel.js index af5689f0888..3e78be30552 100644 --- a/client/src/entry/panels/admin-panel.js +++ b/client/src/entry/panels/admin-panel.js @@ -130,11 +130,6 @@ const AdminPanel = Backbone.View.extend({ target: "__use_router__", id: "admin-link-tool-versions", }, - { - title: _l("View Migration Stages"), - url: "admin/review_tool_migration_stages", - id: "admin-link-migrations", - }, { title: _l("View Error Logs"), url: "admin/error_stack", diff --git a/client/src/nls/es/locale.js b/client/src/nls/es/locale.js index 4d30b42441a..aa0897a1303 100644 --- a/client/src/nls/es/locale.js +++ b/client/src/nls/es/locale.js @@ -496,7 +496,6 @@ define({ "Download local tool": "Descargar herramienta local", "Tool lineage": "Linaje de herramientas", "Reload a tool's configuration": "Volver a cargar la configuración de una herramienta", - "Review tool migration stages": "Revisar las etapas de migración de la herramienta", "View Tool Error Logs": "Ver registros de error de la herramienta", "Manage Allowlist": "Administrar lista de permisos", "Manage Tool Dependencies": "Administrar dependencias de herramienta", @@ -730,7 +729,6 @@ define({ "Refresh history": "Actualizar historial", // ---------------------------------------------------------------------------- admin-panel "View error logs": "Ver registros de error", - "View migration stages": "Ver etapas de migración", "View lineage": "Ver linaje", "Manage dependencies": "Administrar dependencias", "Manage allowlist": "Administrar lista de permitidos", diff --git a/client/src/nls/fr/locale.js b/client/src/nls/fr/locale.js index 7c21a8c9f43..224dabd196e 100644 --- a/client/src/nls/fr/locale.js +++ b/client/src/nls/fr/locale.js @@ -218,7 +218,6 @@ define({ "Download local tool": "Télécharger un outil en local", "Tool lineage": "Affiliation des outils", "Reload a tool's configuration": "Recharger une configuration d'outils", - "Review tool migration stages": "Vérifier les étapes de migration d'outils", "View Tool Error Logs": "Voir les logs d'erreur d'outils", "Manage Allowlist": "Gérer la liste autorisée d'outils graphiques", "Manage Tool Dependencies": "Gérer les dépendances d'outils", @@ -370,7 +369,6 @@ define({ "Refresh history": false, // ---------------------------------------------------------------------------- admin-panel "View error logs": false, - "View migration stages": false, "View lineage": false, "Manage dependencies": false, "Manage allowlist": false, diff --git a/client/src/nls/ja/locale.js b/client/src/nls/ja/locale.js index 599cb6e288f..16a5aa8bf9c 100644 --- a/client/src/nls/ja/locale.js +++ b/client/src/nls/ja/locale.js @@ -251,7 +251,6 @@ define({ "Download local tool": "ローカルツールのダウンロード", "Tool lineage": "ツール系統", "Reload a tool's configuration": "ツールのコンフィグのリロード", - "Review tool migration stages": "ツール移行ステージのレビュー", "View Tool Error Logs": "ツールのエラーログ", "Manage Allowlist": "表示ホワイトリストの管理", "Manage Tool Dependencies": "ツール依存関係の管理", diff --git a/client/src/nls/locale.js b/client/src/nls/locale.js index 04b7d03aa1d..ee00ab2aaa3 100644 --- a/client/src/nls/locale.js +++ b/client/src/nls/locale.js @@ -218,7 +218,6 @@ define({ "Download local tool": false, "Tool lineage": false, "Reload a tool's configuration": false, - "Review tool migration stages": false, "View Tool Error Logs": false, "Manage Allowlist": false, "Manage Tool Dependencies": false, @@ -368,7 +367,6 @@ define({ "Refresh history": false, // ---------------------------------------------------------------------------- admin-panel "View error logs": false, - "View migration stages": false, "View lineage": false, "Manage dependencies": false, "Manage allowlist": false, diff --git a/client/src/nls/zh/locale.js b/client/src/nls/zh/locale.js index f250ad35ecc..a5578adb383 100644 --- a/client/src/nls/zh/locale.js +++ b/client/src/nls/zh/locale.js @@ -227,7 +227,6 @@ define({ "Download local tool": false, "Tool lineage": false, "Reload a tool's configuration": false, - "Review tool migration stages": false, "View Tool Error Logs": false, "Manage Display Whitelist": false, "Manage Tool Dependencies": false, @@ -384,7 +383,6 @@ define({ "Refresh history": "刷新历史记录", // ---------------------------------------------------------------------------- admin-panel "View error logs": false, - "View migration stages": false, "View lineage": false, "Manage dependencies": false, "Manage whitelist": false, diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml index 1c042093f85..df325801d68 100644 --- a/lib/galaxy/selenium/navigation.yml +++ b/lib/galaxy/selenium/navigation.yml @@ -692,7 +692,6 @@ admin: jobs: '#admin-link-jobs' local_data: '#admin-link-local-data' metadata: '#admin-link-metadata' - migrations: '#admin-link-migrations' tool_versions: '#admin-link-tool-versions' toolshed: '#admin-link-toolshed' users: '#admin-link-users' diff --git a/lib/galaxy/util/tool_shed/common_util.py b/lib/galaxy/util/tool_shed/common_util.py index 2188ae76302..23d593c0062 100644 --- a/lib/galaxy/util/tool_shed/common_util.py +++ b/lib/galaxy/util/tool_shed/common_util.py @@ -12,11 +12,6 @@ from galaxy.util.tool_shed import encoding_util, xml_util log = logging.getLogger(__name__) REPOSITORY_OWNER = 'devteam' -# not valid for installed Galaxy, fix -MIGRATE_DIR = os.path.abspath(os.path.join( - os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'galaxy', 'tool_shed', 'galaxy_install', 'migrate')) -TOOL_MIGRATION_SCRIPTS_DIR = os.path.join(MIGRATE_DIR, 'scripts') -TOOL_MIGRATION_VERSIONS_DIR = os.path.join(MIGRATE_DIR, 'versions') def accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies): diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py index c1267c166db..82633bda08e 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -1,6 +1,4 @@ -import imp import logging -import os from sqlalchemy import false, func @@ -18,9 +16,7 @@ from galaxy.util import ( nice_size, pretty_print_time_interval, sanitize_text, - url_get ) -from galaxy.util.tool_shed import common_util, encoding_util from galaxy.web import url_for from galaxy.web.framework.helpers import grids, time_ago from galaxy.webapps.base import controller @@ -861,62 +857,6 @@ class AdminGalaxy(controller.JSAppLauncher): action='users', message="Invalid user selected", status="error")) - def check_for_tool_dependencies(self, trans, migration_stage): - # Get the 000x_tools.xml file associated with migration_stage. - tools_xml_file_path = os.path.abspath(os.path.join(common_util.TOOL_MIGRATION_SCRIPTS_DIR, '%04d_tools.xml' % migration_stage)) - tree = util.parse_xml(tools_xml_file_path) - root = tree.getroot() - tool_shed = root.get('name') - shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, tool_shed) - repo_name_dependency_tups = [] - if shed_url: - for elem in root: - if elem.tag == 'repository': - tool_dependencies = [] - tool_dependencies_dict = {} - repository_name = elem.get('name') - changeset_revision = elem.get('changeset_revision') - params = dict(name=repository_name, owner='devteam', changeset_revision=changeset_revision) - pathspec = ['repository', 'get_tool_dependencies'] - text = url_get(shed_url, auth=self.app.tool_shed_registry.url_auth(shed_url), pathspec=pathspec, params=params) - if text: - tool_dependencies_dict = encoding_util.tool_shed_decode(text) - for requirements_dict in tool_dependencies_dict.values(): - tool_dependency_name = requirements_dict['name'] - tool_dependency_version = requirements_dict['version'] - tool_dependency_type = requirements_dict['type'] - tool_dependency_readme = requirements_dict.get('readme', '') - tool_dependencies.append((tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme)) - 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. -
    -
    -
    -