mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge pull request #13163 from ic4f/dev_migrate_tools_cleanup
Remove migrate tools-related code
This commit is contained in:
Marius van den Beek
@@ -111,12 +111,6 @@
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</strong>
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- A view of a version lineages for all installed tools. Useful for debugging.
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</li>
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<li>
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<strong>
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<a :href="migrationStagesUrl">View Migration Stages</a>
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</strong>
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- See the list of migration stages that moved sets of tools from the distribution to the Tool Shed.
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</li>
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</ul>
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</div>
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</template>
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@@ -145,7 +139,6 @@ export default {
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},
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},
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computed: {
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migrationStagesUrl: () => `${root}admin/review_tool_migration_stages`, // NOT ROUTER
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adminDataTypesUrl: () => `${root}admin/data_types`,
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adminDataTablesUrl: () => `${root}admin/data_tables`,
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adminDisplayApplicationsUrl: () => `${root}admin/display_applications`,
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@@ -130,11 +130,6 @@ const AdminPanel = Backbone.View.extend({
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target: "__use_router__",
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id: "admin-link-tool-versions",
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},
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{
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title: _l("View Migration Stages"),
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url: "admin/review_tool_migration_stages",
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id: "admin-link-migrations",
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},
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{
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title: _l("View Error Logs"),
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url: "admin/error_stack",
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@@ -496,7 +496,6 @@ define({
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"Download local tool": "Descargar herramienta local",
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"Tool lineage": "Linaje de herramientas",
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"Reload a tool's configuration": "Volver a cargar la configuración de una herramienta",
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"Review tool migration stages": "Revisar las etapas de migración de la herramienta",
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"View Tool Error Logs": "Ver registros de error de la herramienta",
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"Manage Allowlist": "Administrar lista de permisos",
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"Manage Tool Dependencies": "Administrar dependencias de herramienta",
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@@ -730,7 +729,6 @@ define({
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"Refresh history": "Actualizar historial",
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// ---------------------------------------------------------------------------- admin-panel
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"View error logs": "Ver registros de error",
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"View migration stages": "Ver etapas de migración",
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"View lineage": "Ver linaje",
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"Manage dependencies": "Administrar dependencias",
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"Manage allowlist": "Administrar lista de permitidos",
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@@ -218,7 +218,6 @@ define({
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"Download local tool": "Télécharger un outil en local",
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"Tool lineage": "Affiliation des outils",
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"Reload a tool's configuration": "Recharger une configuration d'outils",
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"Review tool migration stages": "Vérifier les étapes de migration d'outils",
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"View Tool Error Logs": "Voir les logs d'erreur d'outils",
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"Manage Allowlist": "Gérer la liste autorisée d'outils graphiques",
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"Manage Tool Dependencies": "Gérer les dépendances d'outils",
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@@ -370,7 +369,6 @@ define({
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"Refresh history": false,
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// ---------------------------------------------------------------------------- admin-panel
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"View error logs": false,
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"View migration stages": false,
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"View lineage": false,
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"Manage dependencies": false,
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"Manage allowlist": false,
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@@ -251,7 +251,6 @@ define({
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"Download local tool": "ローカルツールのダウンロード",
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"Tool lineage": "ツール系統",
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"Reload a tool's configuration": "ツールのコンフィグのリロード",
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"Review tool migration stages": "ツール移行ステージのレビュー",
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"View Tool Error Logs": "ツールのエラーログ",
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"Manage Allowlist": "表示ホワイトリストの管理",
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"Manage Tool Dependencies": "ツール依存関係の管理",
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@@ -218,7 +218,6 @@ define({
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"Download local tool": false,
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"Tool lineage": false,
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"Reload a tool's configuration": false,
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"Review tool migration stages": false,
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"View Tool Error Logs": false,
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"Manage Allowlist": false,
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"Manage Tool Dependencies": false,
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@@ -368,7 +367,6 @@ define({
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"Refresh history": false,
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// ---------------------------------------------------------------------------- admin-panel
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"View error logs": false,
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"View migration stages": false,
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"View lineage": false,
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"Manage dependencies": false,
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"Manage allowlist": false,
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@@ -227,7 +227,6 @@ define({
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"Download local tool": false,
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"Tool lineage": false,
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"Reload a tool's configuration": false,
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"Review tool migration stages": false,
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"View Tool Error Logs": false,
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"Manage Display Whitelist": false,
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"Manage Tool Dependencies": false,
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@@ -384,7 +383,6 @@ define({
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"Refresh history": "刷新历史记录",
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// ---------------------------------------------------------------------------- admin-panel
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"View error logs": false,
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"View migration stages": false,
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"View lineage": false,
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"Manage dependencies": false,
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"Manage whitelist": false,
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@@ -692,7 +692,6 @@ admin:
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jobs: '#admin-link-jobs'
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local_data: '#admin-link-local-data'
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metadata: '#admin-link-metadata'
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migrations: '#admin-link-migrations'
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tool_versions: '#admin-link-tool-versions'
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toolshed: '#admin-link-toolshed'
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users: '#admin-link-users'
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@@ -12,11 +12,6 @@ from galaxy.util.tool_shed import encoding_util, xml_util
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log = logging.getLogger(__name__)
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REPOSITORY_OWNER = 'devteam'
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# not valid for installed Galaxy, fix
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MIGRATE_DIR = os.path.abspath(os.path.join(
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os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'galaxy', 'tool_shed', 'galaxy_install', 'migrate'))
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TOOL_MIGRATION_SCRIPTS_DIR = os.path.join(MIGRATE_DIR, 'scripts')
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TOOL_MIGRATION_VERSIONS_DIR = os.path.join(MIGRATE_DIR, 'versions')
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def accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies):
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@@ -1,6 +1,4 @@
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import imp
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import logging
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import os
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from sqlalchemy import false, func
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@@ -18,9 +16,7 @@ from galaxy.util import (
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nice_size,
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pretty_print_time_interval,
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sanitize_text,
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url_get
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)
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from galaxy.util.tool_shed import common_util, encoding_util
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from galaxy.web import url_for
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from galaxy.web.framework.helpers import grids, time_ago
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from galaxy.webapps.base import controller
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@@ -861,62 +857,6 @@ class AdminGalaxy(controller.JSAppLauncher):
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action='users',
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message="Invalid user selected", status="error"))
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def check_for_tool_dependencies(self, trans, migration_stage):
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# Get the 000x_tools.xml file associated with migration_stage.
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tools_xml_file_path = os.path.abspath(os.path.join(common_util.TOOL_MIGRATION_SCRIPTS_DIR, '%04d_tools.xml' % migration_stage))
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tree = util.parse_xml(tools_xml_file_path)
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root = tree.getroot()
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tool_shed = root.get('name')
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shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, tool_shed)
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repo_name_dependency_tups = []
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if shed_url:
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for elem in root:
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if elem.tag == 'repository':
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tool_dependencies = []
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tool_dependencies_dict = {}
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repository_name = elem.get('name')
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changeset_revision = elem.get('changeset_revision')
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params = dict(name=repository_name, owner='devteam', changeset_revision=changeset_revision)
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pathspec = ['repository', 'get_tool_dependencies']
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text = url_get(shed_url, auth=self.app.tool_shed_registry.url_auth(shed_url), pathspec=pathspec, params=params)
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if text:
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tool_dependencies_dict = encoding_util.tool_shed_decode(text)
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for requirements_dict in tool_dependencies_dict.values():
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tool_dependency_name = requirements_dict['name']
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tool_dependency_version = requirements_dict['version']
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tool_dependency_type = requirements_dict['type']
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tool_dependency_readme = requirements_dict.get('readme', '')
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tool_dependencies.append((tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme))
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repo_name_dependency_tups.append((repository_name, tool_dependencies))
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return repo_name_dependency_tups
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@web.expose
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@web.require_admin
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def review_tool_migration_stages(self, trans, **kwd):
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message = escape(util.restore_text(kwd.get('message', '')))
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status = util.restore_text(kwd.get('status', 'done'))
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migration_stages_dict = {}
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# FIXME: this isn't valid in an installed context
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migration_scripts_dir = os.path.abspath(os.path.join(trans.app.config.root, 'lib', 'galaxy', 'tool_shed', 'galaxy_install', 'migrate', 'versions'))
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modules = os.listdir(migration_scripts_dir)
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modules.sort()
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modules.reverse()
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for item in modules:
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if not item.endswith('_tools.py') or item.startswith('0001_tools'):
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continue
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module = item.replace('.py', '')
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migration_stage = int(module.replace('_tools', ''))
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repo_name_dependency_tups = self.check_for_tool_dependencies(trans, migration_stage)
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open_file_obj, file_name, description = imp.find_module(module, [migration_scripts_dir])
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imported_module = imp.load_module('upgrade', open_file_obj, file_name, description)
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migration_info = imported_module.__doc__
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open_file_obj.close()
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migration_stages_dict[migration_stage] = (migration_info, repo_name_dependency_tups)
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return trans.fill_template('admin/review_tool_migration_stages.mako',
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migration_stages_dict=migration_stages_dict,
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message=message,
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status=status)
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@web.legacy_expose_api
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@web.require_admin
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def tool_versions_list(self, trans, **kwd):
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@@ -1173,11 +1173,6 @@ class ShedTwillTestCase(DrivenFunctionalTestCase):
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self.visit_url('/repository/display_tool', params=params)
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self.check_for_strings(strings_displayed, strings_not_displayed)
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def load_galaxy_tool_migrations_page(self, strings_displayed=None, strings_not_displayed=None):
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url = '/admin/review_tool_migration_stages'
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self.visit_galaxy_url(url)
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self.check_for_strings(strings_displayed, strings_not_displayed)
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def load_invalid_tool_page(self, repository, tool_xml, changeset_revision, strings_displayed=None, strings_not_displayed=None):
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params = {
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'repository_id': self.security.encode_id(repository.id),
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@@ -1,123 +0,0 @@
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<%inherit file="/base.mako"/>
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<%namespace file="/message.mako" import="render_msg" />
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%if message:
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${render_msg( message, status )}
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%endif
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<%
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from markupsafe import escape
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%>
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<div class="card">
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<div class="card-header">Tool migrations that can be performed on this Galaxy instance</div>
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<div class="card-body">
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<div class="form-row">
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<p>
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The list of tool migration stages below, displayed most recent to oldest, provides information about the repositories in the
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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
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the migration process for any stage at any time.
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</p>
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<p>
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Keep in mind that tools included in a repository that you want to be displayed in the Galaxy tool panel when the repository is
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installed must be defined in the <b>tool_conf.xml</b> (or equivalent) config file prior to execution of the migration process for a
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stage. Executing a migration process multiple times will have no affect unless the repositories associated with that stage have been
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uninstalled prior to the execution of the migration process.
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</p>
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<p>
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When you initiate a migration process, the associated repositories will be cloned from the Galaxy tool shed at
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<a href="http://toolshed.g2.bx.psu.edu" target="_blank">http://toolshed.g2.bx.psu.edu</a>. The location in which the tool repositories
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will be installed is the value of the 'tool_path' attribute in the <tool> tag of the file named ./migrated_tool_conf.xml
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(i.e., <b><toolbox tool_path="../shed_tools"></b>). The default location setting is <b>'../shed_tools'</b>, which may be problematic
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for some cluster environments, so make sure to change it before you execute the installation process if appropriate. The configured location
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must be outside of the Galaxy installation directory or it must be in a sub-directory protected by a properly configured <b>.hgignore</b>
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file if the directory is within the Galaxy installation directory hierarchy. This is because tool shed repositories will be installed using
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mercurial's clone feature, which creates .hg directories and associated mercurial repository files. Not having <b>.hgignore</b> properly
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configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed repositories if they are
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in directories that pose conflicts. See mercurial's .hgignore documentation at
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<a href="http://mercurial.selenic.com/wiki/.hgignore" target="_blank">http://mercurial.selenic.com/wiki/.hgignore</a> for details.
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</p>
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</div>
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<table class="grid">
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<% from tool_shed.util.basic_util import to_html_string %>
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%for stage in migration_stages_dict.keys():
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<%
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migration_command = 'sh ./scripts/migrate_tools/%04d_tools.sh' % stage
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install_dependencies = '%s install_dependencies' % migration_command
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migration_tup = migration_stages_dict[ stage ]
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migration_info, repo_name_dependency_tups = migration_tup
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repository_names = []
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for repo_name_dependency_tup in repo_name_dependency_tups:
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repository_name, tool_dependencies = repo_name_dependency_tup
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if repository_name not in repository_names:
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repository_names.append( repository_name )
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if repository_names:
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repository_names.sort()
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repository_names = ', '.join( repository_names )
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%>
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<tr><td bgcolor="#D8D8D8"><b>Tool migration stage ${stage} - repositories: ${repository_names|h}</b></td></tr>
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<tr>
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<td bgcolor="#FFFFCC">
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<div class="form-row">
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<p>${to_html_string(migration_info)} <b>Run commands from the Galaxy installation directory!</b></p>
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<p>
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%if tool_dependencies:
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This migration stage includes tools that have tool dependencies that can be automatically installed. To install them, run:<br/>
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<b>${install_dependencies|h}</b><br/><br/>
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To skip tool dependency installation run:<br/>
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<b>${migration_command|h}</b>
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%else:
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<b>${migration_command|h}</b>
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%endif
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</p>
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</div>
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</td>
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</tr>
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%for repo_name_dependency_tup in repo_name_dependency_tups:
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<% repository_name, tool_dependencies = repo_name_dependency_tup %>
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<tr>
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<td bgcolor="#DADFEF">
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<div class="form-row">
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<b>Repository:</b> ${repository_name|h}
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</div>
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</td>
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</tr>
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%if tool_dependencies:
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<tr>
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<td>
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<div class="form-row">
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<b>Tool dependencies</b>
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</div>
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</td>
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</tr>
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%for tool_dependencies_tup in tool_dependencies:
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<%
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tool_dependency_name = escape( tool_dependencies_tup[0] )
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tool_dependency_version = escape( tool_dependencies_tup[1] )
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tool_dependency_type = escape( tool_dependencies_tup[2] )
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installation_requirements = escape( tool_dependencies_tup[3] ).replace( '\n', '<br/>' )
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%>
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<tr>
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<td>
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<div class="form-row">
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<b>Name:</b> ${tool_dependency_name} <b>Version:</b> ${tool_dependency_version} <b>Type:</b> ${tool_dependency_type}
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</div>
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<div class="form-row">
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<b>Requirements and installation information:</b><br/>
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${installation_requirements}
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</div>
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</td>
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</tr>
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%endfor
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%else:
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<tr>
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<td>
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<div class="form-row">
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No tool dependencies have been defined for this repository.
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</div>
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</td>
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</tr>
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%endif
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%endfor
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%endfor
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</table>
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</div>
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</div>
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Reference in New Issue
Block a user