mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 23:49:37 +08:00
Remove reselect_tool_panel mako and controller endpoint.
This commit is contained in:
John Chilton
@@ -12,7 +12,6 @@ from galaxy.exceptions import ConfigDoesNotAllowException
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from galaxy.tool_shed.galaxy_install import install_manager
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from galaxy.tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
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from galaxy.tool_shed.galaxy_install.tools import tool_panel_manager
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from galaxy.tool_shed.util import tool_util
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from galaxy.tool_shed.util.repository_util import (
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create_or_update_tool_shed_repository,
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get_absolute_path_to_file_in_repository,
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@@ -368,172 +367,3 @@ class AdminToolshed(AdminGalaxy):
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except Exception:
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log.exception("Problem you know in here somewhere...")
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raise
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@web.expose
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@web.require_admin
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@legacy_tool_shed_endpoint
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def reselect_tool_panel_section(self, trans, **kwd):
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"""
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Select or change the tool panel section to contain the tools included in the tool shed repository
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being reinstalled. If there are updates available for the repository in the tool shed, the
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tool_dependencies and repository_dependencies associated with the updated changeset revision will
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have been retrieved from the tool shed and passed in the received kwd. In this case, the stored
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tool shed repository metadata from the Galaxy database will not be used since it is outdated.
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"""
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message = ""
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status = "done"
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repository_id = kwd.get("id", None)
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latest_changeset_revision = kwd.get("latest_changeset_revision", None)
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latest_ctx_rev = kwd.get("latest_ctx_rev", None)
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tool_shed_repository = get_installed_tool_shed_repository(trans.app, repository_id)
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repository_clone_url = common_util.generate_clone_url_for_installed_repository(trans.app, tool_shed_repository)
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metadata = tool_shed_repository.metadata_
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tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(
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trans.app, str(tool_shed_repository.tool_shed)
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)
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tool_path = tool_shed_repository.get_tool_relative_path(trans.app)[0]
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if latest_changeset_revision and latest_ctx_rev:
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# There are updates available in the tool shed for the repository, so use the received
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# dependency information which was retrieved from the tool shed.
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encoded_updated_repo_info_dict = kwd.get("updated_repo_info_dict", None)
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updated_repo_info_dict = encoding_util.tool_shed_decode(encoded_updated_repo_info_dict)
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readme_files_dict = updated_repo_info_dict.get("readme_files_dict", None)
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includes_data_managers = updated_repo_info_dict.get("includes_data_managers", False)
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includes_tool_dependencies = updated_repo_info_dict.get("includes_tool_dependencies", False)
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repo_info_dict = updated_repo_info_dict["repo_info_dict"]
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else:
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# There are no updates available from the tool shed for the repository, so use its locally stored metadata.
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includes_data_managers = False
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includes_tool_dependencies = False
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readme_files_dict = None
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tool_dependencies = None
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if metadata:
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if "data_manager" in metadata:
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includes_data_managers = True
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if "tool_dependencies" in metadata:
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includes_tool_dependencies = True
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# Since we're reinstalling, we need to send a request to the tool shed to get the README files.
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params = dict(
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name=tool_shed_repository.name,
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owner=tool_shed_repository.owner,
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changeset_revision=tool_shed_repository.installed_changeset_revision,
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)
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pathspec = ["repository", "get_readme_files"]
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raw_text = util.url_get(
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tool_shed_url,
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auth=self.app.tool_shed_registry.url_auth(tool_shed_url),
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pathspec=pathspec,
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params=params,
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)
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readme_files_dict = json.loads(raw_text)
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tool_dependencies = metadata.get("tool_dependencies", None)
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rdim = repository_dependency_manager.RepositoryDependencyInstallManager(trans.app)
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repository_dependencies = rdim.get_repository_dependencies_for_installed_tool_shed_repository(
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trans.app, tool_shed_repository
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)
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repo_info_dict = create_repo_info_dict(
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trans.app,
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repository_clone_url=repository_clone_url,
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changeset_revision=tool_shed_repository.installed_changeset_revision,
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ctx_rev=tool_shed_repository.ctx_rev,
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repository_owner=tool_shed_repository.owner,
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repository_name=tool_shed_repository.name,
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tool_dependencies=tool_dependencies,
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repository_dependencies=repository_dependencies,
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)
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irm = trans.app.installed_repository_manager
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dependencies_for_repository_dict = irm.get_dependencies_for_repository(
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tool_shed_url, repo_info_dict, includes_tool_dependencies, updating=True
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)
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includes_tool_dependencies = dependencies_for_repository_dict.get("includes_tool_dependencies", False)
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includes_tools = dependencies_for_repository_dict.get("includes_tools", False)
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includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get(
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"includes_tools_for_display_in_tool_panel", False
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)
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installed_repository_dependencies = dependencies_for_repository_dict.get(
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"installed_repository_dependencies", None
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)
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installed_tool_dependencies = dependencies_for_repository_dict.get("installed_tool_dependencies", None)
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missing_repository_dependencies = dependencies_for_repository_dict.get("missing_repository_dependencies", None)
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missing_tool_dependencies = dependencies_for_repository_dict.get("missing_tool_dependencies", None)
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if installed_repository_dependencies or missing_repository_dependencies:
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has_repository_dependencies = True
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else:
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has_repository_dependencies = False
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if includes_tools_for_display_in_tool_panel:
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# Get the location in the tool panel in which the tools were originally loaded.
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if "tool_panel_section" in metadata:
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tool_panel_dict = metadata["tool_panel_section"]
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if tool_panel_dict:
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if tool_util.panel_entry_per_tool(tool_panel_dict):
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# The following forces everything to be loaded into 1 section (or no section) in the tool panel.
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tool_section_dicts = tool_panel_dict[next(iter(tool_panel_dict.keys()))]
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tool_section_dict = tool_section_dicts[0]
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original_section_name = tool_section_dict["name"]
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else:
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original_section_name = tool_panel_dict["name"]
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else:
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original_section_name = ""
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else:
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original_section_name = ""
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tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field(trans.app)
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no_changes_check_box = CheckboxField("no_changes", value=True)
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if original_section_name:
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message += (
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"The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. "
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% (escape(tool_shed_repository.name), original_section_name)
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)
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message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a "
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message += "different section in the tool panel. "
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status = "warning"
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else:
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message += f"The tools contained in your <b>{escape(tool_shed_repository.name)}</b> repository were last loaded into the tool panel outside of any sections. "
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message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section. "
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status = "warning"
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else:
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no_changes_check_box = None
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original_section_name = ""
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tool_panel_section_select_field = None
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shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field(trans.app)
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dd = dependency_display.DependencyDisplayer(trans.app)
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containers_dict = dd.populate_containers_dict_for_new_install(
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tool_shed_url=tool_shed_url,
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tool_path=tool_path,
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readme_files_dict=readme_files_dict,
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installed_repository_dependencies=installed_repository_dependencies,
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missing_repository_dependencies=missing_repository_dependencies,
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installed_tool_dependencies=installed_tool_dependencies,
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missing_tool_dependencies=missing_tool_dependencies,
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updating=False,
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)
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# Since we're reinstalling we'll merge the list of missing repository dependencies into the list of
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# installed repository dependencies since each displayed repository dependency will display a status,
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# whether installed or missing.
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containers_dict = dd.merge_missing_repository_dependencies_to_installed_container(containers_dict)
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# Handle repository dependencies check box.
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install_repository_dependencies_check_box = CheckboxField("install_repository_dependencies", value=True)
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view = views.DependencyResolversView(self.app)
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if view.installable_resolvers:
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install_resolver_dependencies_check_box = CheckboxField("install_resolver_dependencies", value=True)
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else:
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install_resolver_dependencies_check_box = None
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return trans.fill_template(
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"/admin/tool_shed_repository/reselect_tool_panel_section.mako",
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repository=tool_shed_repository,
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no_changes_check_box=no_changes_check_box,
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original_section_name=original_section_name,
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includes_data_managers=includes_data_managers,
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includes_tools=includes_tools,
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includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
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includes_tool_dependencies=includes_tool_dependencies,
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has_repository_dependencies=has_repository_dependencies,
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install_repository_dependencies_check_box=install_repository_dependencies_check_box,
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install_resolver_dependencies_check_box=install_resolver_dependencies_check_box,
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containers_dict=containers_dict,
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tool_panel_section_select_field=tool_panel_section_select_field,
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shed_tool_conf_select_field=shed_tool_conf_select_field,
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encoded_repo_info_dict=encoding_util.tool_shed_encode(repo_info_dict),
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repo_info_dict=repo_info_dict,
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message=message,
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status=status,
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)
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@@ -1,101 +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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<%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" />
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<%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" />
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<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" />
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<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
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<%def name="stylesheets()">
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${parent.stylesheets()}
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${h.css( "library" )}
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</%def>
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<%def name="javascripts()">
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${parent.javascripts()}
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${container_javascripts()}
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</%def>
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%if message:
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${render_msg( message, status )}
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%endif
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<div class="card">
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<div class="card-body">
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<form name="reselect_tool_panel_section" id="reselect_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='reinstall_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
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<div class="form-row">
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<input type="hidden" name="repo_info_dict" value="${encoded_repo_info_dict}" />
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</div>
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<div style="clear: both"></div>
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<% readme_files_dict = containers_dict.get( 'readme_files', None ) %>
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%if readme_files_dict:
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<div class="form-row">
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<table class="colored" width="100%">
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<th bgcolor="#EBD9B2">Repository README files - may contain important installation or license information</th>
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</table>
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</div>
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${render_readme_section( containers_dict )}
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<div style="clear: both"></div>
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%endif
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%if has_repository_dependencies or includes_tool_dependencies:
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<div class="form-row">
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<table class="colored" width="100%">
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<th bgcolor="#EBD9B2">Confirm dependency installation</th>
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</table>
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</div>
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${render_dependencies_section( install_resolver_dependencies_check_box, install_repository_dependencies_check_box, containers_dict, revision_label=None, export=False )}
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%endif
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%if shed_tool_conf_select_field:
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<div class="form-row">
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<table class="colored" width="100%">
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<th bgcolor="#EBD9B2">Choose the configuration file whose tool_path setting will be used for installing repositories</th>
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</table>
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</div>
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<%
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if len( shed_tool_conf_select_field.options ) == 1:
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select_help = "Your Galaxy instance is configured with 1 shed-related tool configuration file, so repositories will be "
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select_help += "installed using its <b>tool_path</b> setting."
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else:
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select_help = "Your Galaxy instance is configured with %d shed-related tool configuration files, " % len( shed_tool_conf_select_field.options )
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select_help += "so select the file whose <b>tool_path</b> setting you want used for installing repositories."
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%>
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<div class="form-row">
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<label>Shed tool configuration file:</label>
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${render_select(shed_tool_conf_select_field)}
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<div class="toolParamHelp" style="clear: both;">
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${select_help|h}
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</div>
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</div>
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<div style="clear: both"></div>
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%else:
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<input type="hidden" name="shed_tool_conf" value="${shed_tool_conf|h}"/>
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%endif
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%if includes_tools_for_display_in_tool_panel:
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<div style="clear: both"></div>
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<div class="form-row">
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${render_checkbox(no_changes_check_box)}
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<label style="display: inline;">No changes</label>
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<div class="toolParamHelp" style="clear: both;">
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Uncheck and select a different tool panel section to load the tools into a different section in the tool panel.
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</div>
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</div>
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<div class="form-row">
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<label>Add new tool panel section:</label>
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<input name="new_tool_panel_section_label" type="textfield" value="" size="40"/>
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<div class="toolParamHelp" style="clear: both;">
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Add a new tool panel section to contain the installed tools (optional).
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</div>
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</div>
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<div class="form-row">
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<label>Select existing tool panel section:</label>
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${render_select(tool_panel_section_select_field)}
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<div class="toolParamHelp" style="clear: both;">
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Choose an existing section in your tool panel to contain the installed tools (optional).
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</div>
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</div>
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%endif
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<div class="form-row">
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<input type="submit" name="select_tool_panel_section_button" value="Install"/>
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</div>
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</form>
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</div>
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</div>
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@@ -1,188 +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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<%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" />
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<%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" />
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<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" />
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<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
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<%def name="stylesheets()">
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${parent.stylesheets()}
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${h.css( "library" )}
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</%def>
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<%def name="javascripts()">
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${parent.javascripts()}
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${container_javascripts()}
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</%def>
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<%
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# Handle the case where an uninstalled repository encountered errors during the process of being reinstalled. In
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# this case, the repository metadata is an empty dictionary, but one or both of has_repository_dependencies
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# and includes_tool_dependencies may be True. If either of these are True but we have no metadata, we cannot install
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# repository dependencies on this pass.
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if has_repository_dependencies:
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repository_dependencies = containers_dict[ 'repository_dependencies' ]
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missing_repository_dependencies = containers_dict[ 'missing_repository_dependencies' ]
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if repository_dependencies or missing_repository_dependencies:
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can_display_repository_dependencies = True
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else:
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can_display_repository_dependencies = False
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else:
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can_display_repository_dependencies = False
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if includes_tool_dependencies:
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tool_dependencies = containers_dict[ 'tool_dependencies' ]
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missing_tool_dependencies = containers_dict[ 'missing_tool_dependencies' ]
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if tool_dependencies or missing_tool_dependencies:
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can_display_tool_dependencies = True
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else:
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can_display_tool_dependencies = False
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else:
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can_display_tool_dependencies = False
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can_display_resolver_installation = install_resolver_dependencies_check_box is not None
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%>
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%if message:
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${render_msg( message, status )}
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%endif
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<div class="warningmessage">
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<p>
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The Galaxy development team does not maintain the contents of many Galaxy Tool Shed repositories. Some
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repository tools may include code that produces malicious behavior, so be aware of what you are installing.
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</p>
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<p>
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If you discover a repository that causes problems after installation, contact <a href="https://galaxyproject.org/support" target="_blank">Galaxy support</a>,
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sending all necessary information, and appropriate action will be taken.
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</p>
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<p>
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<a href="https://galaxyproject.org/toolshed/repository-features/#contact-repository-owner" target="_blank">Contact the repository owner</a> for
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general questions or concerns.
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</p>
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</div>
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<div class="card">
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<div class="card-body">
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<form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install' )}" method="post" >
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<div class="form-row">
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<input type="hidden" name="includes_tools" value="${includes_tools}" />
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<input type="hidden" name="includes_tool_dependencies" value="${includes_tool_dependencies}" />
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<input type="hidden" name="requirements_status" value="${requirements_status}" />
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<input type="hidden" name="includes_tools_for_display_in_tool_panel" value="${includes_tools_for_display_in_tool_panel}" />
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<input type="hidden" name="tool_shed_url" value="${tool_shed_url}" />
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<input type="hidden" name="encoded_repo_info_dicts" value="${encoded_repo_info_dicts}" />
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<input type="hidden" name="updating" value="${updating}" />
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<input type="hidden" name="updating_repository_id" value="${updating_repository_id}" />
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<input type="hidden" name="updating_to_ctx_rev" value="${updating_to_ctx_rev}" />
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<input type="hidden" name="updating_to_changeset_revision" value="${updating_to_changeset_revision}" />
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<input type="hidden" name="encoded_updated_metadata" value="${encoded_updated_metadata}" />
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</div>
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<div style="clear: both"></div>
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<% readme_files_dict = containers_dict.get( 'readme_files', None ) %>
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%if readme_files_dict:
|
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<div class="form-row">
|
||||
<table class="colored" width="100%">
|
||||
<th bgcolor="#EBD9B2">Repository README file - may contain important installation or license information</th>
|
||||
</table>
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||||
</div>
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${render_readme_section( containers_dict )}
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<div style="clear: both"></div>
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%endif
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<%
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||||
if requirements_status and install_resolver_dependencies_check_box or includes_tool_dependencies:
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display_dependency_confirmation = True
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else:
|
||||
display_dependency_confirmation = False
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%>
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||||
%if requirements_status:
|
||||
%if not install_resolver_dependencies_check_box and not includes_tool_dependencies:
|
||||
<div class="form-row">
|
||||
<table class="colored" width="100%">
|
||||
<head>
|
||||
<th>
|
||||
<img src="${h.url_for('/static')}/images/icon_error_sml.gif" title='Cannot install dependencies'/>
|
||||
This repository requires dependencies that cannot be installed through the Tool Shed
|
||||
</th>
|
||||
</head>
|
||||
</table>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<p>This repository defines tool requirements that cannot be installed through the Tool Shed.</p>
|
||||
<p>Please activate Conda dependency resolution, activate Docker dependency resolution, setup Environment Modules
|
||||
or manually satisfy the dependencies listed below.</p>
|
||||
<p>For details see <a target="_blank" href="https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html">the dependency resolver documentation.</a></p>
|
||||
</div>
|
||||
%endif
|
||||
<div class="form-row">
|
||||
<table class="colored" width="100%">
|
||||
<th bgcolor="#EBD9B2">The following tool dependencies are required by the current repository</th>
|
||||
</table>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
${render_tool_dependency_resolver( requirements_status, prepare_for_install=True )}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
%endif
|
||||
%if can_display_repository_dependencies or display_dependency_confirmation:
|
||||
<div class="form-row">
|
||||
<table class="colored" width="100%">
|
||||
<th bgcolor="#EBD9B2">Confirm dependency installation</th>
|
||||
</table>
|
||||
</div>
|
||||
${render_dependencies_section( install_resolver_dependencies_check_box, install_repository_dependencies_check_box, containers_dict, revision_label=None, export=False, requirements_status=requirements_status )}
|
||||
<div style="clear: both"></div>
|
||||
%endif
|
||||
%if shed_tool_conf_select_field:
|
||||
%if includes_tools_for_display_in_tool_panel:
|
||||
<div class="form-row">
|
||||
<table class="colored" width="100%">
|
||||
<th bgcolor="#EBD9B2">Choose the tool panel section to contain the installed tools (optional)</th>
|
||||
</table>
|
||||
</div>
|
||||
<div class="detail-section">
|
||||
%endif
|
||||
<%
|
||||
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 <b>tool_path</b> 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 <b>tool_path</b> setting you want used for installing repositories."
|
||||
%>
|
||||
<div class="form-row">
|
||||
<label>Shed tool configuration file:</label>
|
||||
${render_select(shed_tool_conf_select_field)}
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
${select_help|h}
|
||||
</div>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%else:
|
||||
<input type="hidden" name="shed_tool_conf" value="${shed_tool_conf|h}"/>
|
||||
%endif
|
||||
%if includes_tools_for_display_in_tool_panel:
|
||||
<div class="form-row">
|
||||
<label>Add new tool panel section:</label>
|
||||
<input name="new_tool_panel_section_label" type="textfield" value="${new_tool_panel_section_label|h}" size="40"/>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Add a new tool panel section to contain the installed tools (optional).
|
||||
</div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Select existing tool panel section:</label>
|
||||
${render_select(tool_panel_section_select_field)}
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Choose an existing section in your tool panel to contain the installed tools (optional).
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
<div class="form-row">
|
||||
<input type="submit" name="select_tool_panel_section_button" value="Install"/>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
%if includes_tools_for_display_in_tool_panel:
|
||||
Clicking <b>Install</b> without selecting a tool panel section will load the installed tools into the tool panel outside of any sections.
|
||||
%endif
|
||||
</div>
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
Reference in New Issue
Block a user