From 533e3f9be0375dd1e3bde780553e1693f16a120d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 14:16:03 -0400
Subject: [PATCH 01/19] Remove reselect_tool_panel mako and controller
 endpoint.

---
 .../galaxy/controllers/admin_toolshed.py      | 170 ----------------
 .../reselect_tool_panel_section.mako          | 101 ----------
 .../select_tool_panel_section.mako            | 188 ------------------
 3 files changed, 459 deletions(-)
 delete mode 100644 templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
 delete mode 100644 templates/admin/tool_shed_repository/select_tool_panel_section.mako

diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index 4616f761d18..da081c95a64 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -12,7 +12,6 @@ from galaxy.exceptions import ConfigDoesNotAllowException
 from galaxy.tool_shed.galaxy_install import install_manager
 from galaxy.tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
 from galaxy.tool_shed.galaxy_install.tools import tool_panel_manager
-from galaxy.tool_shed.util import tool_util
 from galaxy.tool_shed.util.repository_util import (
     create_or_update_tool_shed_repository,
     get_absolute_path_to_file_in_repository,
@@ -368,172 +367,3 @@ class AdminToolshed(AdminGalaxy):
         except Exception:
             log.exception("Problem you know in here somewhere...")
             raise
-
-    @web.expose
-    @web.require_admin
-    @legacy_tool_shed_endpoint
-    def reselect_tool_panel_section(self, trans, **kwd):
-        """
-        Select or change the tool panel section to contain the tools included in the tool shed repository
-        being reinstalled.  If there are updates available for the repository in the tool shed, the
-        tool_dependencies and repository_dependencies associated with the updated changeset revision will
-        have been retrieved from the tool shed and passed in the received kwd.  In this case, the stored
-        tool shed repository metadata from the Galaxy database will not be used since it is outdated.
-        """
-        message = ""
-        status = "done"
-        repository_id = kwd.get("id", None)
-        latest_changeset_revision = kwd.get("latest_changeset_revision", None)
-        latest_ctx_rev = kwd.get("latest_ctx_rev", None)
-        tool_shed_repository = get_installed_tool_shed_repository(trans.app, repository_id)
-        repository_clone_url = common_util.generate_clone_url_for_installed_repository(trans.app, tool_shed_repository)
-        metadata = tool_shed_repository.metadata_
-        tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(
-            trans.app, str(tool_shed_repository.tool_shed)
-        )
-        tool_path = tool_shed_repository.get_tool_relative_path(trans.app)[0]
-        if latest_changeset_revision and latest_ctx_rev:
-            # There are updates available in the tool shed for the repository, so use the received
-            # dependency information which was retrieved from the tool shed.
-            encoded_updated_repo_info_dict = kwd.get("updated_repo_info_dict", None)
-            updated_repo_info_dict = encoding_util.tool_shed_decode(encoded_updated_repo_info_dict)
-            readme_files_dict = updated_repo_info_dict.get("readme_files_dict", None)
-            includes_data_managers = updated_repo_info_dict.get("includes_data_managers", False)
-            includes_tool_dependencies = updated_repo_info_dict.get("includes_tool_dependencies", False)
-            repo_info_dict = updated_repo_info_dict["repo_info_dict"]
-        else:
-            # There are no updates available from the tool shed for the repository, so use its locally stored metadata.
-            includes_data_managers = False
-            includes_tool_dependencies = False
-            readme_files_dict = None
-            tool_dependencies = None
-            if metadata:
-                if "data_manager" in metadata:
-                    includes_data_managers = True
-                if "tool_dependencies" in metadata:
-                    includes_tool_dependencies = True
-                # Since we're reinstalling, we need to send a request to the tool shed to get the README files.
-                params = dict(
-                    name=tool_shed_repository.name,
-                    owner=tool_shed_repository.owner,
-                    changeset_revision=tool_shed_repository.installed_changeset_revision,
-                )
-                pathspec = ["repository", "get_readme_files"]
-                raw_text = util.url_get(
-                    tool_shed_url,
-                    auth=self.app.tool_shed_registry.url_auth(tool_shed_url),
-                    pathspec=pathspec,
-                    params=params,
-                )
-                readme_files_dict = json.loads(raw_text)
-                tool_dependencies = metadata.get("tool_dependencies", None)
-            rdim = repository_dependency_manager.RepositoryDependencyInstallManager(trans.app)
-            repository_dependencies = rdim.get_repository_dependencies_for_installed_tool_shed_repository(
-                trans.app, tool_shed_repository
-            )
-            repo_info_dict = create_repo_info_dict(
-                trans.app,
-                repository_clone_url=repository_clone_url,
-                changeset_revision=tool_shed_repository.installed_changeset_revision,
-                ctx_rev=tool_shed_repository.ctx_rev,
-                repository_owner=tool_shed_repository.owner,
-                repository_name=tool_shed_repository.name,
-                tool_dependencies=tool_dependencies,
-                repository_dependencies=repository_dependencies,
-            )
-        irm = trans.app.installed_repository_manager
-        dependencies_for_repository_dict = irm.get_dependencies_for_repository(
-            tool_shed_url, repo_info_dict, includes_tool_dependencies, updating=True
-        )
-        includes_tool_dependencies = dependencies_for_repository_dict.get("includes_tool_dependencies", False)
-        includes_tools = dependencies_for_repository_dict.get("includes_tools", False)
-        includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get(
-            "includes_tools_for_display_in_tool_panel", False
-        )
-        installed_repository_dependencies = dependencies_for_repository_dict.get(
-            "installed_repository_dependencies", None
-        )
-        installed_tool_dependencies = dependencies_for_repository_dict.get("installed_tool_dependencies", None)
-        missing_repository_dependencies = dependencies_for_repository_dict.get("missing_repository_dependencies", None)
-        missing_tool_dependencies = dependencies_for_repository_dict.get("missing_tool_dependencies", None)
-        if installed_repository_dependencies or missing_repository_dependencies:
-            has_repository_dependencies = True
-        else:
-            has_repository_dependencies = False
-        if includes_tools_for_display_in_tool_panel:
-            # Get the location in the tool panel in which the tools were originally loaded.
-            if "tool_panel_section" in metadata:
-                tool_panel_dict = metadata["tool_panel_section"]
-                if tool_panel_dict:
-                    if tool_util.panel_entry_per_tool(tool_panel_dict):
-                        # The following forces everything to be loaded into 1 section (or no section) in the tool panel.
-                        tool_section_dicts = tool_panel_dict[next(iter(tool_panel_dict.keys()))]
-                        tool_section_dict = tool_section_dicts[0]
-                        original_section_name = tool_section_dict["name"]
-                    else:
-                        original_section_name = tool_panel_dict["name"]
-                else:
-                    original_section_name = ""
-            else:
-                original_section_name = ""
-            tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field(trans.app)
-            no_changes_check_box = CheckboxField("no_changes", value=True)
-            if original_section_name:
-                message += (
-                    "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>.  "
-                    % (escape(tool_shed_repository.name), original_section_name)
-                )
-                message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a "
-                message += "different section in the tool panel.  "
-                status = "warning"
-            else:
-                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.  "
-                message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section.  "
-                status = "warning"
-        else:
-            no_changes_check_box = None
-            original_section_name = ""
-            tool_panel_section_select_field = None
-        shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field(trans.app)
-        dd = dependency_display.DependencyDisplayer(trans.app)
-        containers_dict = dd.populate_containers_dict_for_new_install(
-            tool_shed_url=tool_shed_url,
-            tool_path=tool_path,
-            readme_files_dict=readme_files_dict,
-            installed_repository_dependencies=installed_repository_dependencies,
-            missing_repository_dependencies=missing_repository_dependencies,
-            installed_tool_dependencies=installed_tool_dependencies,
-            missing_tool_dependencies=missing_tool_dependencies,
-            updating=False,
-        )
-        # Since we're reinstalling we'll merge the list of missing repository dependencies into the list of
-        # installed repository dependencies since each displayed repository dependency will display a status,
-        # whether installed or missing.
-        containers_dict = dd.merge_missing_repository_dependencies_to_installed_container(containers_dict)
-        # Handle repository dependencies check box.
-        install_repository_dependencies_check_box = CheckboxField("install_repository_dependencies", value=True)
-        view = views.DependencyResolversView(self.app)
-        if view.installable_resolvers:
-            install_resolver_dependencies_check_box = CheckboxField("install_resolver_dependencies", value=True)
-        else:
-            install_resolver_dependencies_check_box = None
-        return trans.fill_template(
-            "/admin/tool_shed_repository/reselect_tool_panel_section.mako",
-            repository=tool_shed_repository,
-            no_changes_check_box=no_changes_check_box,
-            original_section_name=original_section_name,
-            includes_data_managers=includes_data_managers,
-            includes_tools=includes_tools,
-            includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
-            includes_tool_dependencies=includes_tool_dependencies,
-            has_repository_dependencies=has_repository_dependencies,
-            install_repository_dependencies_check_box=install_repository_dependencies_check_box,
-            install_resolver_dependencies_check_box=install_resolver_dependencies_check_box,
-            containers_dict=containers_dict,
-            tool_panel_section_select_field=tool_panel_section_select_field,
-            shed_tool_conf_select_field=shed_tool_conf_select_field,
-            encoded_repo_info_dict=encoding_util.tool_shed_encode(repo_info_dict),
-            repo_info_dict=repo_info_dict,
-            message=message,
-            status=status,
-        )
diff --git a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
deleted file mode 100644
index 447085d6a32..00000000000
--- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
+++ /dev/null
@@ -1,101 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" />
-<%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" />
-<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" />
-<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "library" )}
-</%def>
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-    ${container_javascripts()}
-</%def>
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="card">
-    <div class="card-body">
-        <form name="reselect_tool_panel_section" id="reselect_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='reinstall_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
-            <div class="form-row">
-                <input type="hidden" name="repo_info_dict" value="${encoded_repo_info_dict}" />
-            </div>
-            <div style="clear: both"></div>
-            <% readme_files_dict = containers_dict.get( 'readme_files', None ) %>
-            %if readme_files_dict:
-                <div class="form-row">
-                    <table class="colored" width="100%">
-                        <th bgcolor="#EBD9B2">Repository README files - may contain important installation or license information</th>
-                    </table>
-                </div>
-                ${render_readme_section( containers_dict )}
-                <div style="clear: both"></div>
-            %endif
-            %if has_repository_dependencies or includes_tool_dependencies:
-                <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 )}
-            %endif
-            %if shed_tool_conf_select_field:
-                <div class="form-row">
-                    <table class="colored" width="100%">
-                        <th bgcolor="#EBD9B2">Choose the configuration file whose tool_path setting will be used for installing repositories</th>
-                    </table>
-                </div>
-                <%
-                    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;">
-                        ${select_help|h}
-                    </div>
-                </div>
-                <div style="clear: both"></div>
-            %else:
-                <input type="hidden" name="shed_tool_conf" value="${shed_tool_conf|h}"/>
-            %endif
-            %if includes_tools_for_display_in_tool_panel:
-                <div style="clear: both"></div>
-                <div class="form-row">
-                    ${render_checkbox(no_changes_check_box)}
-                    <label style="display: inline;">No changes</label>
-                    <div class="toolParamHelp" style="clear: both;">
-                        Uncheck and select a different tool panel section to load the tools into a different section in the tool panel.
-                    </div>
-                </div>
-                <div class="form-row">
-                    <label>Add new tool panel section:</label>
-                    <input name="new_tool_panel_section_label" type="textfield" value="" 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>
-        </form>
-    </div>
-</div>
diff --git a/templates/admin/tool_shed_repository/select_tool_panel_section.mako b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
deleted file mode 100644
index 4c980982984..00000000000
--- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako
+++ /dev/null
@@ -1,188 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" />
-<%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" />
-<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" />
-<%namespace file="/webapps/tool_shed/common/common.mako" import="*" />
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "library" )}
-</%def>
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-    ${container_javascripts()}
-</%def>
-
-<%
-    # Handle the case where an uninstalled repository encountered errors during the process of being reinstalled.  In
-    # this case, the repository metadata is an empty dictionary, but one or both of has_repository_dependencies
-    # and includes_tool_dependencies may be True.  If either of these are True but we have no metadata, we cannot install
-    # repository dependencies on this pass.
-    if has_repository_dependencies:
-        repository_dependencies = containers_dict[ 'repository_dependencies' ]
-        missing_repository_dependencies = containers_dict[ 'missing_repository_dependencies' ]
-        if repository_dependencies or missing_repository_dependencies:
-            can_display_repository_dependencies = True
-        else:
-            can_display_repository_dependencies = False
-    else:
-        can_display_repository_dependencies = False
-    if includes_tool_dependencies:
-        tool_dependencies = containers_dict[ 'tool_dependencies' ]
-        missing_tool_dependencies = containers_dict[ 'missing_tool_dependencies' ]
-        if tool_dependencies or missing_tool_dependencies:
-            can_display_tool_dependencies = True
-        else:
-            can_display_tool_dependencies = False
-    else:
-        can_display_tool_dependencies = False
-    can_display_resolver_installation = install_resolver_dependencies_check_box is not None
-%>
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-<div class="warningmessage">
-    <p>
-        The Galaxy development team does not maintain the contents of many Galaxy Tool Shed repositories.  Some
-        repository tools may include code that produces malicious behavior, so be aware of what you are installing.
-    </p>
-    <p>
-        If you discover a repository that causes problems after installation, contact <a href="https://galaxyproject.org/support" target="_blank">Galaxy support</a>,
-        sending all necessary information, and appropriate action will be taken.
-    </p>
-    <p>
-        <a href="https://galaxyproject.org/toolshed/repository-features/#contact-repository-owner" target="_blank">Contact the repository owner</a> for
-        general questions or concerns.
-    </p>
-</div>
-<div class="card">
-    <div class="card-body">
-        <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install' )}" method="post" >
-            <div class="form-row">
-                <input type="hidden" name="includes_tools" value="${includes_tools}" />
-                <input type="hidden" name="includes_tool_dependencies" value="${includes_tool_dependencies}" />
-                <input type="hidden" name="requirements_status" value="${requirements_status}" />
-                <input type="hidden" name="includes_tools_for_display_in_tool_panel" value="${includes_tools_for_display_in_tool_panel}" />
-                <input type="hidden" name="tool_shed_url" value="${tool_shed_url}" />
-                <input type="hidden" name="encoded_repo_info_dicts" value="${encoded_repo_info_dicts}" />
-                <input type="hidden" name="updating" value="${updating}" />
-                <input type="hidden" name="updating_repository_id" value="${updating_repository_id}" />
-                <input type="hidden" name="updating_to_ctx_rev" value="${updating_to_ctx_rev}" />
-                <input type="hidden" name="updating_to_changeset_revision" value="${updating_to_changeset_revision}" />
-                <input type="hidden" name="encoded_updated_metadata" value="${encoded_updated_metadata}" />
-            </div>
-            <div style="clear: both"></div>
-            <% readme_files_dict = containers_dict.get( 'readme_files', None ) %>
-            %if readme_files_dict:
-                <div class="form-row">
-                    <table class="colored" width="100%">
-                        <th bgcolor="#EBD9B2">Repository README file - may contain important installation or license information</th>
-                    </table>
-                </div>
-                ${render_readme_section( containers_dict )}
-                <div style="clear: both"></div>
-            %endif
-            <%
-                if requirements_status and install_resolver_dependencies_check_box or includes_tool_dependencies:
-                    display_dependency_confirmation = True
-                else:
-                    display_dependency_confirmation = False
-            %>
-            %if requirements_status:
-                %if not install_resolver_dependencies_check_box and not includes_tool_dependencies:
-                <div class="form-row">
-                    <table class="colored" width="100%">
-                        <head>
-                            <th>
-                                <img src="${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>

From 0d61a37a71e693adbcc9dfbb6aab622a8b2e0ea9 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 14:23:50 -0400
Subject: [PATCH 02/19] Remove now unused function from dependency_display.

---
 .../galaxy_install/dependency_display.py      | 95 -------------------
 1 file changed, 95 deletions(-)

diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py
index 5c4c8cf0e56..cc3c06672f5 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -7,12 +7,10 @@ from galaxy import util
 from tool_shed.galaxy_install.utility_containers import GalaxyUtilityContainerManager
 from tool_shed.util import (
     common_util,
-    container_util,
     readme_util,
     repository_util,
     tool_dependency_util,
 )
-from tool_shed.utility_containers import utility_container_manager
 
 log = logging.getLogger(__name__)
 
@@ -259,99 +257,6 @@ class DependencyDisplayer:
             missing_tool_dependencies = None
         return tool_dependencies, missing_tool_dependencies
 
-    def merge_containers_dicts_for_new_install(self, containers_dicts):
-        """
-        When installing one or more tool shed repositories for the first time, the received list of
-        containers_dicts contains a containers_dict for each repository being installed.  Since the
-        repositories are being installed for the first time, all entries are None except the repository
-        dependencies and tool dependencies.  The entries for missing dependencies are all None since
-        they have previously been merged into the installed dependencies.  This method will merge the
-        dependencies entries into a single container and return it for display.
-        """
-        new_containers_dict = dict(
-            readme_files=None,
-            datatypes=None,
-            missing_repository_dependencies=None,
-            repository_dependencies=None,
-            missing_tool_dependencies=None,
-            tool_dependencies=None,
-            invalid_tools=None,
-            valid_tools=None,
-            workflows=None,
-        )
-        if containers_dicts:
-            lock = threading.Lock()
-            lock.acquire(True)
-            try:
-                repository_dependencies_root_folder = None
-                tool_dependencies_root_folder = None
-                # Use a unique folder id (hopefully the following is).
-                folder_id = 867
-                for old_container_dict in containers_dicts:
-                    # Merge repository_dependencies.
-                    old_container_repository_dependencies_root = old_container_dict["repository_dependencies"]
-                    if old_container_repository_dependencies_root:
-                        if repository_dependencies_root_folder is None:
-                            repository_dependencies_root_folder = utility_container_manager.Folder(
-                                id=folder_id, key="root", label="root", parent=None
-                            )
-                            folder_id += 1
-                            repository_dependencies_folder = utility_container_manager.Folder(
-                                id=folder_id,
-                                key="merged",
-                                label="Repository dependencies",
-                                parent=repository_dependencies_root_folder,
-                            )
-                            folder_id += 1
-                        # The old_container_repository_dependencies_root will be a root folder containing a single sub_folder.
-                        old_container_repository_dependencies_folder = (
-                            old_container_repository_dependencies_root.folders[0]
-                        )
-                        # Change the folder id so it won't confict with others being merged.
-                        old_container_repository_dependencies_folder.id = folder_id
-                        folder_id += 1
-                        repository_components_tuple = container_util.get_components_from_key(
-                            old_container_repository_dependencies_folder.key
-                        )
-                        components_list = repository_util.extract_components_from_tuple(repository_components_tuple)
-                        name = components_list[1]
-                        # Generate the label by retrieving the repository name.
-                        old_container_repository_dependencies_folder.label = str(name)
-                        repository_dependencies_folder.folders.append(old_container_repository_dependencies_folder)
-                    # Merge tool_dependencies.
-                    old_container_tool_dependencies_root = old_container_dict["tool_dependencies"]
-                    if old_container_tool_dependencies_root:
-                        if tool_dependencies_root_folder is None:
-                            tool_dependencies_root_folder = utility_container_manager.Folder(
-                                id=folder_id, key="root", label="root", parent=None
-                            )
-                            folder_id += 1
-                            tool_dependencies_folder = utility_container_manager.Folder(
-                                id=folder_id,
-                                key="merged",
-                                label="Tool dependencies",
-                                parent=tool_dependencies_root_folder,
-                            )
-                            folder_id += 1
-                        else:
-                            td_list = [td.listify for td in tool_dependencies_folder.tool_dependencies]
-                            # The old_container_tool_dependencies_root will be a root folder containing a single sub_folder.
-                            old_container_tool_dependencies_folder = old_container_tool_dependencies_root.folders[0]
-                            for td in old_container_tool_dependencies_folder.tool_dependencies:
-                                if td.listify not in td_list:
-                                    tool_dependencies_folder.tool_dependencies.append(td)
-                if repository_dependencies_root_folder:
-                    repository_dependencies_root_folder.folders.append(repository_dependencies_folder)
-                    new_containers_dict["repository_dependencies"] = repository_dependencies_root_folder
-                if tool_dependencies_root_folder:
-                    tool_dependencies_root_folder.folders.append(tool_dependencies_folder)
-                    new_containers_dict["tool_dependencies"] = tool_dependencies_root_folder
-            except Exception as e:
-                log.debug(f"Exception in merge_containers_dicts_for_new_install: {e}")
-            finally:
-                lock.release()
-        return new_containers_dict
-
     def merge_missing_repository_dependencies_to_installed_container(self, containers_dict):
         """
         Merge the list of missing repository dependencies into the list of installed

From 03f3f0ee0a85fc3019e4b6d53b2ac6f7152549f9 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 14:37:41 -0400
Subject: [PATCH 03/19] Improved dependency imports in readme_util.

---
 lib/tool_shed/util/readme_util.py | 31 +++++++++++++++----------------
 1 file changed, 15 insertions(+), 16 deletions(-)

diff --git a/lib/tool_shed/util/readme_util.py b/lib/tool_shed/util/readme_util.py
index e573f4bd6cd..3e5cabaf900 100644
--- a/lib/tool_shed/util/readme_util.py
+++ b/lib/tool_shed/util/readme_util.py
@@ -4,20 +4,21 @@ import os
 
 from mako.template import Template
 
-import tool_shed.util.shed_util_common as suc
 from galaxy import web
+from galaxy.tool_shed.util import basic_util
+from galaxy.tool_shed.util.hg_util import (
+    get_changectx_for_changeset,
+    get_file_context_from_ctx,
+)
+from galaxy.tool_shed.util.repository_util import get_repo_info_tuple_contents
+from galaxy.tool_shed.util.shed_util_common import set_image_paths
 from galaxy.util import (
     rst_to_html,
     unicodify,
     url_get,
 )
-from tool_shed.util import (
-    basic_util,
-    common_util,
-    hg_util,
-    metadata_util,
-    repository_util,
-)
+from galaxy.util.tool_shed.common_util import get_tool_shed_url_from_tool_shed_registry
+from tool_shed.util.metadata_util import get_latest_downloadable_changeset_revision
 
 log = logging.getLogger(__name__)
 
@@ -31,9 +32,7 @@ def build_readme_files_dict(app, repository, changeset_revision, metadata, tool_
     if app.name == "galaxy":
         can_use_disk_files = True
     else:
-        latest_downloadable_changeset_revision = metadata_util.get_latest_downloadable_changeset_revision(
-            app, repository
-        )
+        latest_downloadable_changeset_revision = get_latest_downloadable_changeset_revision(app, repository)
         can_use_disk_files = changeset_revision == latest_downloadable_changeset_revision
     readme_files_dict = {}
     if metadata:
@@ -59,7 +58,7 @@ def build_readme_files_dict(app, repository, changeset_revision, metadata, tool_
                         if text_of_reasonable_length.find(".. image:: ") >= 0:
                             # Handle image display for README files that are contained in repositories in the tool shed or installed into Galaxy.
                             try:
-                                text_of_reasonable_length = suc.set_image_paths(
+                                text_of_reasonable_length = set_image_paths(
                                     app,
                                     text_of_reasonable_length,
                                     encoded_repository_id=app.security.encode_id(repository.id),
@@ -85,9 +84,9 @@ def build_readme_files_dict(app, repository, changeset_revision, metadata, tool_
                 else:
                     # We must be in the tool shed and have an old changeset_revision, so we need to retrieve the file contents from the repository manifest.
                     repo = repository.hg_repo
-                    ctx = hg_util.get_changectx_for_changeset(repo, changeset_revision)
+                    ctx = get_changectx_for_changeset(repo, changeset_revision)
                     if ctx:
-                        fctx = hg_util.get_file_context_from_ctx(ctx, readme_file_name)
+                        fctx = get_file_context_from_ctx(ctx, readme_file_name)
                         if fctx and fctx not in ["DELETED"]:
                             try:
                                 text = unicodify(fctx.data())
@@ -115,9 +114,9 @@ def get_readme_files_dict_for_display(app, tool_shed_url, repo_info_dict):
         repository_owner,
         repository_dependencies,
         installed_td,
-    ) = repository_util.get_repo_info_tuple_contents(repo_info_tuple)
+    ) = get_repo_info_tuple_contents(repo_info_tuple)
     # Handle changing HTTP protocols over time.
-    tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed_url)
+    tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, tool_shed_url)
     params = dict(name=name, owner=repository_owner, changeset_revision=changeset_revision)
     pathspec = ["repository", "get_readme_files"]
     raw_text = url_get(

From 6915c5c5561dfbe169b7b1dc074ea4269e1cab25 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 14:43:49 -0400
Subject: [PATCH 04/19] Cleanup up imports in dependency_display.py.

---
 .../galaxy_install/dependency_display.py      | 36 +++++++++++--------
 1 file changed, 21 insertions(+), 15 deletions(-)

diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py
index cc3c06672f5..bde25e80488 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -1,16 +1,22 @@
 import json
 import logging
 import os
-import threading
 
 from galaxy import util
-from tool_shed.galaxy_install.utility_containers import GalaxyUtilityContainerManager
-from tool_shed.util import (
-    common_util,
-    readme_util,
-    repository_util,
-    tool_dependency_util,
+from galaxy.tool_shed.util.common_util import (
+    get_tool_shed_url_from_tool_shed_registry,
+    parse_repository_dependency_tuple,
 )
+from galaxy.tool_shed.util.repository_util import (
+    get_repo_info_tuple_contents,
+    repository_was_previously_installed,
+)
+from galaxy.tool_shed.util.tool_dependency_util import (
+    get_tool_dependency_by_name_type_repository,
+    get_tool_dependency_by_name_version_type_repository,
+)
+from tool_shed.galaxy_install.utility_containers import GalaxyUtilityContainerManager
+from tool_shed.util.readme_util import build_readme_files_dict
 
 log = logging.getLogger(__name__)
 
@@ -70,7 +76,7 @@ class DependencyDisplayer:
                             prior_installation_required,
                             only_if_compiling_contained_td,
                             error,
-                        ) = common_util.parse_repository_dependency_tuple(
+                        ) = parse_repository_dependency_tuple(
                             repository_dependency_tup, contains_error=True
                         )
                         if error:
@@ -103,7 +109,7 @@ class DependencyDisplayer:
                                 changeset_revision,
                                 pir,
                                 oicct,
-                            ) = common_util.parse_repository_dependency_tuple(rd_tup)
+                            ) = parse_repository_dependency_tuple(rd_tup)
                             if util.asbool(pir):
                                 pir_str = "True"
                             else:
@@ -211,7 +217,7 @@ class DependencyDisplayer:
                         name = td_info_dict["name"]
                         version = None
                         type = td_info_dict["type"]
-                        tool_dependency = tool_dependency_util.get_tool_dependency_by_name_type_repository(
+                        tool_dependency = get_tool_dependency_by_name_type_repository(
                             self.app, repository, name, type
                         )
                         if tool_dependency:
@@ -234,7 +240,7 @@ class DependencyDisplayer:
                     name = val["name"]
                     version = val["version"]
                     type = val["type"]
-                    tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type_repository(
+                    tool_dependency = get_tool_dependency_by_name_version_type_repository(
                         self.app, repository, name, version, type
                     )
                     if tool_dependency:
@@ -391,7 +397,7 @@ class DependencyDisplayer:
                     self.app.install_model.ToolShedRepository.installation_status.INSTALLED,
                 ]:
                     # Since we're reinstalling, we need to send a request to the tool shed to get the README files.
-                    tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(self.app, tool_shed_url)
+                    tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, tool_shed_url)
                     params = dict(
                         name=str(repository.name),
                         owner=str(repository.owner),
@@ -406,7 +412,7 @@ class DependencyDisplayer:
                     )
                     readme_files_dict = json.loads(raw_text)
                 else:
-                    readme_files_dict = readme_util.build_readme_files_dict(
+                    readme_files_dict = build_readme_files_dict(
                         self.app, repository, repository.changeset_revision, repository.metadata_, tool_path
                     )
             else:
@@ -519,7 +525,7 @@ class DependencyDisplayer:
                         repository_owner,
                         repository_dependencies,
                         tool_dependencies,
-                    ) = repository_util.get_repo_info_tuple_contents(repo_info_tuple)
+                    ) = get_repo_info_tuple_contents(repo_info_tuple)
                     if tool_dependencies:
                         # Add the install_dir attribute to the tool_dependencies.
                         tool_dependencies = self.add_installation_directories_to_tool_dependencies(tool_dependencies)
@@ -527,7 +533,7 @@ class DependencyDisplayer:
                         (
                             required_repository,
                             installed_changeset_revision,
-                        ) = repository_util.repository_was_previously_installed(
+                        ) = repository_was_previously_installed(
                             self.app, tool_shed_url, name, repo_info_tuple, from_tip=False
                         )
                         if required_repository:

From 2dd9065926ab4e01ed7e165bf51d1bcd4a49a2ee Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 14:56:34 -0400
Subject: [PATCH 05/19] Mark dependency_display internal-only methods as such.

---
 .../galaxy_install/dependency_display.py      | 38 +++++++++----------
 1 file changed, 19 insertions(+), 19 deletions(-)

diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py
index bde25e80488..15a77f33880 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -25,7 +25,7 @@ class DependencyDisplayer:
     def __init__(self, app):
         self.app = app
 
-    def add_installation_directories_to_tool_dependencies(self, tool_dependencies):
+    def _add_installation_directories_to_tool_dependencies(self, tool_dependencies):
         """
         Determine the path to the installation directory for each of the received
         tool dependencies.  This path will be displayed within the tool dependencies
@@ -172,7 +172,7 @@ class DependencyDisplayer:
                         for env_requirements_dict in requirements_dict:
                             name = env_requirements_dict["name"]
                             type = env_requirements_dict["type"]
-                            if self.tool_dependency_is_orphan(type, name, None, tools):
+                            if self._tool_dependency_is_orphan(type, name, None, tools):
                                 if not has_orphan_set_environment_dependencies:
                                     has_orphan_set_environment_dependencies = True
                                 set_environment_orphans_str += f"<b>* name:</b> {name}, <b>type:</b> {type}<br/>"
@@ -181,7 +181,7 @@ class DependencyDisplayer:
                         name = requirements_dict["name"]
                         type = requirements_dict["type"]
                         version = requirements_dict["version"]
-                        if self.tool_dependency_is_orphan(type, name, version, tools):
+                        if self._tool_dependency_is_orphan(type, name, version, tools):
                             if not has_orphan_package_dependencies:
                                 has_orphan_package_dependencies = True
                             package_orphans_str += (
@@ -203,7 +203,7 @@ class DependencyDisplayer:
             message += set_environment_orphans_str
         return message
 
-    def get_installed_and_missing_tool_dependencies_for_installed_repository(self, repository, all_tool_dependencies):
+    def _get_installed_and_missing_tool_dependencies_for_installed_repository(self, repository, all_tool_dependencies):
         """
         Return the lists of installed tool dependencies and missing tool dependencies for a Tool Shed
         repository that has been installed into Galaxy.
@@ -263,7 +263,7 @@ class DependencyDisplayer:
             missing_tool_dependencies = None
         return tool_dependencies, missing_tool_dependencies
 
-    def merge_missing_repository_dependencies_to_installed_container(self, containers_dict):
+    def _merge_missing_repository_dependencies_to_installed_container(self, containers_dict):
         """
         Merge the list of missing repository dependencies into the list of installed
         repository dependencies.
@@ -295,7 +295,7 @@ class DependencyDisplayer:
         containers_dict["missing_repository_dependencies"] = None
         return containers_dict
 
-    def merge_missing_tool_dependencies_to_installed_container(self, containers_dict):
+    def _merge_missing_tool_dependencies_to_installed_container(self, containers_dict):
         """
         Merge the list of missing tool dependencies into the list of installed tool
         dependencies.
@@ -343,7 +343,7 @@ class DependencyDisplayer:
         or for an installed repository that is being updated and the updates include newly
         defined repository (and possibly tool) dependencies.
         """
-        installed_tool_dependencies, missing_tool_dependencies = self.populate_tool_dependencies_dicts(
+        installed_tool_dependencies, missing_tool_dependencies = self._populate_tool_dependencies_dicts(
             tool_shed_url=tool_shed_url,
             tool_path=tool_path,
             repository_installed_tool_dependencies=installed_tool_dependencies,
@@ -372,9 +372,9 @@ class DependencyDisplayer:
             # the missing_repository_dependencies container contents to the installed_repository_dependencies
             # container.  When updating an installed repository, merging will result in losing newly defined
             # dependencies included in the updates.
-            containers_dict = self.merge_missing_repository_dependencies_to_installed_container(containers_dict)
+            containers_dict = self._merge_missing_repository_dependencies_to_installed_container(containers_dict)
             # Merge the missing_tool_dependencies container contents to the installed_tool_dependencies container.
-            containers_dict = self.merge_missing_tool_dependencies_to_installed_container(containers_dict)
+            containers_dict = self._merge_missing_tool_dependencies_to_installed_container(containers_dict)
         return containers_dict
 
     def populate_containers_dict_from_repository_metadata(
@@ -433,11 +433,11 @@ class DependencyDisplayer:
             (
                 repository_installed_tool_dependencies,
                 repository_missing_tool_dependencies,
-            ) = self.get_installed_and_missing_tool_dependencies_for_installed_repository(
+            ) = self._get_installed_and_missing_tool_dependencies_for_installed_repository(
                 repository, repository_tool_dependencies
             )
             if reinstalling:
-                installed_tool_dependencies, missing_tool_dependencies = self.populate_tool_dependencies_dicts(
+                installed_tool_dependencies, missing_tool_dependencies = self._populate_tool_dependencies_dicts(
                     tool_shed_url,
                     tool_path,
                     repository_installed_tool_dependencies,
@@ -485,7 +485,7 @@ class DependencyDisplayer:
             )
         return containers_dict
 
-    def populate_tool_dependencies_dicts(
+    def _populate_tool_dependencies_dicts(
         self,
         tool_shed_url,
         tool_path,
@@ -503,14 +503,14 @@ class DependencyDisplayer:
             repository_installed_tool_dependencies = {}
         else:
             # Add the install_dir attribute to the tool_dependencies.
-            repository_installed_tool_dependencies = self.add_installation_directories_to_tool_dependencies(
+            repository_installed_tool_dependencies = self._add_installation_directories_to_tool_dependencies(
                 repository_installed_tool_dependencies
             )
         if repository_missing_tool_dependencies is None:
             repository_missing_tool_dependencies = {}
         else:
             # Add the install_dir attribute to the tool_dependencies.
-            repository_missing_tool_dependencies = self.add_installation_directories_to_tool_dependencies(
+            repository_missing_tool_dependencies = self._add_installation_directories_to_tool_dependencies(
                 repository_missing_tool_dependencies
             )
         if required_repo_info_dicts:
@@ -528,7 +528,7 @@ class DependencyDisplayer:
                     ) = get_repo_info_tuple_contents(repo_info_tuple)
                     if tool_dependencies:
                         # Add the install_dir attribute to the tool_dependencies.
-                        tool_dependencies = self.add_installation_directories_to_tool_dependencies(tool_dependencies)
+                        tool_dependencies = self._add_installation_directories_to_tool_dependencies(tool_dependencies)
                         # The required_repository may have been installed with a different changeset revision.
                         (
                             required_repository,
@@ -540,13 +540,13 @@ class DependencyDisplayer:
                             (
                                 required_repository_installed_tool_dependencies,
                                 required_repository_missing_tool_dependencies,
-                            ) = self.get_installed_and_missing_tool_dependencies_for_installed_repository(
+                            ) = self._get_installed_and_missing_tool_dependencies_for_installed_repository(
                                 required_repository, tool_dependencies
                             )
                             if required_repository_installed_tool_dependencies:
                                 # Add the install_dir attribute to the tool_dependencies.
                                 required_repository_installed_tool_dependencies = (
-                                    self.add_installation_directories_to_tool_dependencies(
+                                    self._add_installation_directories_to_tool_dependencies(
                                         required_repository_installed_tool_dependencies
                                     )
                                 )
@@ -556,7 +556,7 @@ class DependencyDisplayer:
                             if required_repository_missing_tool_dependencies:
                                 # Add the install_dir attribute to the tool_dependencies.
                                 required_repository_missing_tool_dependencies = (
-                                    self.add_installation_directories_to_tool_dependencies(
+                                    self._add_installation_directories_to_tool_dependencies(
                                         required_repository_missing_tool_dependencies
                                     )
                                 )
@@ -569,7 +569,7 @@ class DependencyDisplayer:
             missing_tool_dependencies = repository_missing_tool_dependencies
         return installed_tool_dependencies, missing_tool_dependencies
 
-    def tool_dependency_is_orphan(self, type, name, version, tools):
+    def _tool_dependency_is_orphan(self, type, name, version, tools):
         """
         Determine if the combination of the received type, name and version is defined in the <requirement>
         tag for at least one tool in the received list of tools.  If not, the tool dependency defined by the

From fcc58d54111fa178247a4c540ae55f1bf7f400ac Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 15:10:17 -0400
Subject: [PATCH 06/19] Improved dependency imports for toolshed.

---
 lib/tool_shed/utility_containers/__init__.py | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/lib/tool_shed/utility_containers/__init__.py b/lib/tool_shed/utility_containers/__init__.py
index 1058b3169a8..a4e244ead7a 100644
--- a/lib/tool_shed/utility_containers/__init__.py
+++ b/lib/tool_shed/utility_containers/__init__.py
@@ -2,11 +2,12 @@ import logging
 import threading
 
 from galaxy import util
-from tool_shed.util import (
-    common_util,
-    container_util,
-    readme_util,
+from galaxy.tool_shed.util.common_util import parse_repository_dependency_tuple
+from galaxy.tool_shed.util.container_util import (
+    generate_repository_dependencies_key_for_repository,
+    STRSEP,
 )
+from tool_shed.util.readme_util import build_readme_files_dict
 from . import utility_container_manager
 
 log = logging.getLogger(__name__)
@@ -166,8 +167,8 @@ class ToolShedUtilityContainerManager(utility_container_manager.UtilityContainer
                     prior_installation_required,
                     only_if_compiling_contained_td,
                     error,
-                ) = common_util.parse_repository_dependency_tuple(invalid_repository_dependency, contains_error=True)
-                key = container_util.generate_repository_dependencies_key_for_repository(
+                ) = parse_repository_dependency_tuple(invalid_repository_dependency, contains_error=True)
+                key = generate_repository_dependencies_key_for_repository(
                     toolshed,
                     name,
                     owner,
@@ -300,7 +301,7 @@ class ToolShedUtilityContainerManager(utility_container_manager.UtilityContainer
                 # Readme files container.
                 if metadata:
                     if "readme_files" not in exclude and "readme_files" in metadata:
-                        readme_files_dict = readme_util.build_readme_files_dict(
+                        readme_files_dict = build_readme_files_dict(
                             self.app, repository, changeset_revision, metadata
                         )
                         folder_id, readme_files_root_folder = self.build_readme_files_folder(
@@ -363,4 +364,4 @@ class ToolShedUtilityContainerManager(utility_container_manager.UtilityContainer
         return containers_dict
 
     def generate_tool_dependencies_key(self, name, version, type):
-        return f"{str(name)}{container_util.STRSEP}{str(version)}{container_util.STRSEP}{str(type)}"
+        return f"{str(name)}{STRSEP}{str(version)}{STRSEP}{str(type)}"

From 1326745b65a255a2f5b62b4ccd2b648c58346a59 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 15:11:42 -0400
Subject: [PATCH 07/19] Remove unused methods in dependency_display.py.

---
 .../galaxy_install/dependency_display.py      | 198 ------------------
 1 file changed, 198 deletions(-)

diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py
index 15a77f33880..15100bafe73 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -263,120 +263,6 @@ class DependencyDisplayer:
             missing_tool_dependencies = None
         return tool_dependencies, missing_tool_dependencies
 
-    def _merge_missing_repository_dependencies_to_installed_container(self, containers_dict):
-        """
-        Merge the list of missing repository dependencies into the list of installed
-        repository dependencies.
-        """
-        missing_rd_container_root = containers_dict.get("missing_repository_dependencies", None)
-        if missing_rd_container_root:
-            # The missing_rd_container_root will be a root folder containing a single sub_folder.
-            missing_rd_container = missing_rd_container_root.folders[0]
-            installed_rd_container_root = containers_dict.get("repository_dependencies", None)
-            # The installed_rd_container_root will be a root folder containing a single sub_folder.
-            if installed_rd_container_root:
-                installed_rd_container = installed_rd_container_root.folders[0]
-                installed_rd_container.label = "Repository dependencies"
-                for index, rd in enumerate(missing_rd_container.repository_dependencies):
-                    # Skip the header row.
-                    if index == 0:
-                        continue
-                    installed_rd_container.repository_dependencies.append(rd)
-                installed_rd_container_root.folders = [installed_rd_container]
-                containers_dict["repository_dependencies"] = installed_rd_container_root
-            else:
-                # Change the folder label from 'Missing repository dependencies' to be
-                # 'Repository dependencies' for display.
-                root_container = containers_dict["missing_repository_dependencies"]
-                for sub_container in root_container.folders:
-                    # There should only be 1 sub-folder.
-                    sub_container.label = "Repository dependencies"
-                containers_dict["repository_dependencies"] = root_container
-        containers_dict["missing_repository_dependencies"] = None
-        return containers_dict
-
-    def _merge_missing_tool_dependencies_to_installed_container(self, containers_dict):
-        """
-        Merge the list of missing tool dependencies into the list of installed tool
-        dependencies.
-        """
-        missing_td_container_root = containers_dict.get("missing_tool_dependencies", None)
-        if missing_td_container_root:
-            # The missing_td_container_root will be a root folder containing a single sub_folder.
-            missing_td_container = missing_td_container_root.folders[0]
-            installed_td_container_root = containers_dict.get("tool_dependencies", None)
-            # The installed_td_container_root will be a root folder containing a single sub_folder.
-            if installed_td_container_root:
-                installed_td_container = installed_td_container_root.folders[0]
-                installed_td_container.label = "Tool dependencies"
-                for index, td in enumerate(missing_td_container.tool_dependencies):
-                    # Skip the header row.
-                    if index == 0:
-                        continue
-                    installed_td_container.tool_dependencies.append(td)
-                installed_td_container_root.folders = [installed_td_container]
-                containers_dict["tool_dependencies"] = installed_td_container_root
-            else:
-                # Change the folder label from 'Missing tool dependencies' to be
-                # 'Tool dependencies' for display.
-                root_container = containers_dict["missing_tool_dependencies"]
-                for sub_container in root_container.folders:
-                    # There should only be 1 subfolder.
-                    sub_container.label = "Tool dependencies"
-                containers_dict["tool_dependencies"] = root_container
-        containers_dict["missing_tool_dependencies"] = None
-        return containers_dict
-
-    def populate_containers_dict_for_new_install(
-        self,
-        tool_shed_url,
-        tool_path,
-        readme_files_dict,
-        installed_repository_dependencies,
-        missing_repository_dependencies,
-        installed_tool_dependencies,
-        missing_tool_dependencies,
-        updating=False,
-    ):
-        """
-        Return the populated containers for a repository being installed for the first time
-        or for an installed repository that is being updated and the updates include newly
-        defined repository (and possibly tool) dependencies.
-        """
-        installed_tool_dependencies, missing_tool_dependencies = self._populate_tool_dependencies_dicts(
-            tool_shed_url=tool_shed_url,
-            tool_path=tool_path,
-            repository_installed_tool_dependencies=installed_tool_dependencies,
-            repository_missing_tool_dependencies=missing_tool_dependencies,
-            required_repo_info_dicts=None,
-        )
-        # Most of the repository contents are set to None since we don't yet know what they are.
-        gucm = GalaxyUtilityContainerManager(self.app)
-        containers_dict = gucm.build_repository_containers(
-            repository=None,
-            invalid_tools=None,
-            missing_repository_dependencies=missing_repository_dependencies,
-            missing_tool_dependencies=missing_tool_dependencies,
-            readme_files_dict=readme_files_dict,
-            repository_dependencies=installed_repository_dependencies,
-            tool_dependencies=installed_tool_dependencies,
-            valid_tools=None,
-            valid_data_managers=None,
-            invalid_data_managers=None,
-            data_managers_errors=None,
-            new_install=True,
-            reinstalling=False,
-        )
-        if not updating:
-            # If we installing a new repository and not updaing an installed repository, we can merge
-            # the missing_repository_dependencies container contents to the installed_repository_dependencies
-            # container.  When updating an installed repository, merging will result in losing newly defined
-            # dependencies included in the updates.
-            containers_dict = self._merge_missing_repository_dependencies_to_installed_container(containers_dict)
-            # Merge the missing_tool_dependencies container contents to the installed_tool_dependencies container.
-            containers_dict = self._merge_missing_tool_dependencies_to_installed_container(containers_dict)
-        return containers_dict
-
     def populate_containers_dict_from_repository_metadata(
         self, tool_shed_url, tool_path, repository, reinstalling=False, required_repo_info_dicts=None
     ):
@@ -485,90 +371,6 @@ class DependencyDisplayer:
             )
         return containers_dict
 
-    def _populate_tool_dependencies_dicts(
-        self,
-        tool_shed_url,
-        tool_path,
-        repository_installed_tool_dependencies,
-        repository_missing_tool_dependencies,
-        required_repo_info_dicts,
-    ):
-        """
-        Return the populated installed_tool_dependencies and missing_tool_dependencies dictionaries
-        for all repositories defined by entries in the received required_repo_info_dicts.
-        """
-        installed_tool_dependencies = None
-        missing_tool_dependencies = None
-        if repository_installed_tool_dependencies is None:
-            repository_installed_tool_dependencies = {}
-        else:
-            # Add the install_dir attribute to the tool_dependencies.
-            repository_installed_tool_dependencies = self._add_installation_directories_to_tool_dependencies(
-                repository_installed_tool_dependencies
-            )
-        if repository_missing_tool_dependencies is None:
-            repository_missing_tool_dependencies = {}
-        else:
-            # Add the install_dir attribute to the tool_dependencies.
-            repository_missing_tool_dependencies = self._add_installation_directories_to_tool_dependencies(
-                repository_missing_tool_dependencies
-            )
-        if required_repo_info_dicts:
-            # Handle the tool dependencies defined for each of the repository's repository dependencies.
-            for rid in required_repo_info_dicts:
-                for name, repo_info_tuple in rid.items():
-                    (
-                        description,
-                        repository_clone_url,
-                        changeset_revision,
-                        ctx_rev,
-                        repository_owner,
-                        repository_dependencies,
-                        tool_dependencies,
-                    ) = get_repo_info_tuple_contents(repo_info_tuple)
-                    if tool_dependencies:
-                        # Add the install_dir attribute to the tool_dependencies.
-                        tool_dependencies = self._add_installation_directories_to_tool_dependencies(tool_dependencies)
-                        # The required_repository may have been installed with a different changeset revision.
-                        (
-                            required_repository,
-                            installed_changeset_revision,
-                        ) = repository_was_previously_installed(
-                            self.app, tool_shed_url, name, repo_info_tuple, from_tip=False
-                        )
-                        if required_repository:
-                            (
-                                required_repository_installed_tool_dependencies,
-                                required_repository_missing_tool_dependencies,
-                            ) = self._get_installed_and_missing_tool_dependencies_for_installed_repository(
-                                required_repository, tool_dependencies
-                            )
-                            if required_repository_installed_tool_dependencies:
-                                # Add the install_dir attribute to the tool_dependencies.
-                                required_repository_installed_tool_dependencies = (
-                                    self._add_installation_directories_to_tool_dependencies(
-                                        required_repository_installed_tool_dependencies
-                                    )
-                                )
-                                for td_key, td_dict in required_repository_installed_tool_dependencies.items():
-                                    if td_key not in repository_installed_tool_dependencies:
-                                        repository_installed_tool_dependencies[td_key] = td_dict
-                            if required_repository_missing_tool_dependencies:
-                                # Add the install_dir attribute to the tool_dependencies.
-                                required_repository_missing_tool_dependencies = (
-                                    self._add_installation_directories_to_tool_dependencies(
-                                        required_repository_missing_tool_dependencies
-                                    )
-                                )
-                                for td_key, td_dict in required_repository_missing_tool_dependencies.items():
-                                    if td_key not in repository_missing_tool_dependencies:
-                                        repository_missing_tool_dependencies[td_key] = td_dict
-        if repository_installed_tool_dependencies:
-            installed_tool_dependencies = repository_installed_tool_dependencies
-        if repository_missing_tool_dependencies:
-            missing_tool_dependencies = repository_missing_tool_dependencies
-        return installed_tool_dependencies, missing_tool_dependencies
-
     def _tool_dependency_is_orphan(self, type, name, version, tools):
         """
         Determine if the combination of the received type, name and version is defined in the <requirement>

From 401328a6dd7e5f80b89d3ea19b354fee696ee874 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 15:24:47 -0400
Subject: [PATCH 08/19] Remove no-op Lock in utility containers.

---
 lib/tool_shed/galaxy_install/utility_containers/__init__.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/lib/tool_shed/galaxy_install/utility_containers/__init__.py b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
index 223d2bf1bde..14f2d5c46c6 100644
--- a/lib/tool_shed/galaxy_install/utility_containers/__init__.py
+++ b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
@@ -1,5 +1,4 @@
 import logging
-import threading
 
 from tool_shed.utility_containers import utility_container_manager
 
@@ -50,8 +49,6 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
             changeset_revision = repository.changeset_revision
         else:
             changeset_revision = None
-        lock = threading.Lock()
-        lock.acquire(True)
         try:
             folder_id = 0
             # Invalid tools container.
@@ -133,6 +130,4 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
                 containers_dict["invalid_data_managers"] = invalid_data_managers_root_folder
         except Exception as e:
             log.debug(f"Exception in build_repository_containers: {str(e)}")
-        finally:
-            lock.release()
         return containers_dict

From 6dfb59f9ce4cf4849906c1d4e04a25626ac9e98d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 15:25:46 -0400
Subject: [PATCH 09/19] Simplify dependency_display now that it is used for a
 lot less.

---
 .../galaxy/controllers/admin_toolshed.py      |  4 --
 .../galaxy_install/dependency_display.py      | 62 ++-----------------
 .../utility_containers/__init__.py            |  9 ---
 3 files changed, 6 insertions(+), 69 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index da081c95a64..b96866a37f2 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -170,11 +170,7 @@ class AdminToolshed(AdminGalaxy):
             message = "The repository information has been updated."
         dd = dependency_display.DependencyDisplayer(trans.app)
         containers_dict = dd.populate_containers_dict_from_repository_metadata(
-            tool_shed_url=tool_shed_url,
-            tool_path=tool_path,
             repository=repository,
-            reinstalling=False,
-            required_repo_info_dicts=None,
         )
         view = views.DependencyResolversView(self.app)
         tool_requirements_d = suc.get_requirements_from_repository(repository)
diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py
index 15100bafe73..2cb03b3c82d 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -3,20 +3,12 @@ import logging
 import os
 
 from galaxy import util
-from galaxy.tool_shed.util.common_util import (
-    get_tool_shed_url_from_tool_shed_registry,
-    parse_repository_dependency_tuple,
-)
-from galaxy.tool_shed.util.repository_util import (
-    get_repo_info_tuple_contents,
-    repository_was_previously_installed,
-)
+from galaxy.tool_shed.util.common_util import parse_repository_dependency_tuple
 from galaxy.tool_shed.util.tool_dependency_util import (
     get_tool_dependency_by_name_type_repository,
     get_tool_dependency_by_name_version_type_repository,
 )
 from tool_shed.galaxy_install.utility_containers import GalaxyUtilityContainerManager
-from tool_shed.util.readme_util import build_readme_files_dict
 
 log = logging.getLogger(__name__)
 
@@ -264,7 +256,7 @@ class DependencyDisplayer:
         return tool_dependencies, missing_tool_dependencies
 
     def populate_containers_dict_from_repository_metadata(
-        self, tool_shed_url, tool_path, repository, reinstalling=False, required_repo_info_dicts=None
+        self, repository
     ):
         """
         Retrieve necessary information from the received repository's metadata to populate the
@@ -276,33 +268,6 @@ class DependencyDisplayer:
         if metadata:
             # Handle invalid tools.
             invalid_tools = metadata.get("invalid_tools", None)
-            # Handle README files.
-            if repository.has_readme_files:
-                if reinstalling or repository.status not in [
-                    self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED,
-                    self.app.install_model.ToolShedRepository.installation_status.INSTALLED,
-                ]:
-                    # Since we're reinstalling, we need to send a request to the tool shed to get the README files.
-                    tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, tool_shed_url)
-                    params = dict(
-                        name=str(repository.name),
-                        owner=str(repository.owner),
-                        changeset_revision=str(repository.installed_changeset_revision),
-                    )
-                    pathspec = ["repository", "get_readme_files"]
-                    raw_text = util.url_get(
-                        tool_shed_url,
-                        auth=self.app.tool_shed_registry.url_auth(tool_shed_url),
-                        pathspec=pathspec,
-                        params=params,
-                    )
-                    readme_files_dict = json.loads(raw_text)
-                else:
-                    readme_files_dict = build_readme_files_dict(
-                        self.app, repository, repository.changeset_revision, repository.metadata_, tool_path
-                    )
-            else:
-                readme_files_dict = None
             # Handle repository dependencies.
             (
                 installed_repository_dependencies,
@@ -322,17 +287,8 @@ class DependencyDisplayer:
             ) = self._get_installed_and_missing_tool_dependencies_for_installed_repository(
                 repository, repository_tool_dependencies
             )
-            if reinstalling:
-                installed_tool_dependencies, missing_tool_dependencies = self._populate_tool_dependencies_dicts(
-                    tool_shed_url,
-                    tool_path,
-                    repository_installed_tool_dependencies,
-                    repository_missing_tool_dependencies,
-                    required_repo_info_dicts,
-                )
-            else:
-                installed_tool_dependencies = repository_installed_tool_dependencies
-                missing_tool_dependencies = repository_missing_tool_dependencies
+            installed_tool_dependencies = repository_installed_tool_dependencies
+            missing_tool_dependencies = repository_missing_tool_dependencies
             # Handle valid tools.
             valid_tools = metadata.get("tools", None)
             # Handle Data Managers
@@ -349,7 +305,7 @@ class DependencyDisplayer:
                 invalid_tools=invalid_tools,
                 missing_repository_dependencies=missing_repository_dependencies,
                 missing_tool_dependencies=missing_tool_dependencies,
-                readme_files_dict=readme_files_dict,
+                readme_files_dict=None,
                 repository_dependencies=installed_repository_dependencies,
                 tool_dependencies=installed_tool_dependencies,
                 valid_tools=valid_tools,
@@ -357,17 +313,11 @@ class DependencyDisplayer:
                 invalid_data_managers=invalid_data_managers,
                 data_managers_errors=data_managers_errors,
                 new_install=False,
-                reinstalling=reinstalling,
+                reinstalling=False,
             )
         else:
             containers_dict = dict(
-                datatypes=None,
-                invalid_tools=None,
-                readme_files_dict=None,
                 repository_dependencies=None,
-                tool_dependencies=None,
-                valid_tools=None,
-                workflows=None,
             )
         return containers_dict
 
diff --git a/lib/tool_shed/galaxy_install/utility_containers/__init__.py b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
index 14f2d5c46c6..d9ad93bd7e1 100644
--- a/lib/tool_shed/galaxy_install/utility_containers/__init__.py
+++ b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
@@ -30,17 +30,8 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
         display during installation to Galaxy.
         """
         containers_dict = dict(
-            datatypes=None,
-            invalid_tools=None,
-            missing_tool_dependencies=None,
-            readme_files=None,
             repository_dependencies=None,
             missing_repository_dependencies=None,
-            tool_dependencies=None,
-            valid_tools=None,
-            workflows=None,
-            valid_data_managers=None,
-            invalid_data_managers=None,
         )
         # Some of the tool dependency folders will include links to display tool dependency information, and
         # some of these links require the repository id.  However we need to be careful because sometimes the

From e6519265ad234276de81523564e4e54c403866d3 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 15:27:03 -0400
Subject: [PATCH 10/19] Remove unused container invalid_tools.

---
 lib/tool_shed/galaxy_install/dependency_display.py         | 3 ---
 .../galaxy_install/utility_containers/__init__.py          | 7 -------
 2 files changed, 10 deletions(-)

diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py
index 2cb03b3c82d..0dee318c917 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -266,8 +266,6 @@ class DependencyDisplayer:
         """
         metadata = repository.metadata_
         if metadata:
-            # Handle invalid tools.
-            invalid_tools = metadata.get("invalid_tools", None)
             # Handle repository dependencies.
             (
                 installed_repository_dependencies,
@@ -302,7 +300,6 @@ class DependencyDisplayer:
             gucm = GalaxyUtilityContainerManager(self.app)
             containers_dict = gucm.build_repository_containers(
                 repository=repository,
-                invalid_tools=invalid_tools,
                 missing_repository_dependencies=missing_repository_dependencies,
                 missing_tool_dependencies=missing_tool_dependencies,
                 readme_files_dict=None,
diff --git a/lib/tool_shed/galaxy_install/utility_containers/__init__.py b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
index d9ad93bd7e1..56c23303345 100644
--- a/lib/tool_shed/galaxy_install/utility_containers/__init__.py
+++ b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
@@ -12,7 +12,6 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
     def build_repository_containers(
         self,
         repository,
-        invalid_tools,
         missing_repository_dependencies,
         missing_tool_dependencies,
         readme_files_dict,
@@ -42,12 +41,6 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
             changeset_revision = None
         try:
             folder_id = 0
-            # Invalid tools container.
-            if invalid_tools:
-                folder_id, invalid_tools_root_folder = self.build_invalid_tools_folder(
-                    folder_id, invalid_tools, changeset_revision, repository=repository, label="Invalid tools"
-                )
-                containers_dict["invalid_tools"] = invalid_tools_root_folder
             # Readme files container.
             if readme_files_dict:
                 folder_id, readme_files_root_folder = self.build_readme_files_folder(folder_id, readme_files_dict)

From 8e6fc9dcc78a76e0dca49f51e08b047be1e36bbc Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 15:27:55 -0400
Subject: [PATCH 11/19] Remove unused container readme files.

---
 lib/tool_shed/galaxy_install/dependency_display.py          | 1 -
 lib/tool_shed/galaxy_install/utility_containers/__init__.py | 5 -----
 2 files changed, 6 deletions(-)

diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py
index 0dee318c917..0fe28bb3006 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -302,7 +302,6 @@ class DependencyDisplayer:
                 repository=repository,
                 missing_repository_dependencies=missing_repository_dependencies,
                 missing_tool_dependencies=missing_tool_dependencies,
-                readme_files_dict=None,
                 repository_dependencies=installed_repository_dependencies,
                 tool_dependencies=installed_tool_dependencies,
                 valid_tools=valid_tools,
diff --git a/lib/tool_shed/galaxy_install/utility_containers/__init__.py b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
index 56c23303345..0e9dab9bc8b 100644
--- a/lib/tool_shed/galaxy_install/utility_containers/__init__.py
+++ b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
@@ -14,7 +14,6 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
         repository,
         missing_repository_dependencies,
         missing_tool_dependencies,
-        readme_files_dict,
         repository_dependencies,
         tool_dependencies,
         valid_tools,
@@ -41,10 +40,6 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
             changeset_revision = None
         try:
             folder_id = 0
-            # Readme files container.
-            if readme_files_dict:
-                folder_id, readme_files_root_folder = self.build_readme_files_folder(folder_id, readme_files_dict)
-                containers_dict["readme_files"] = readme_files_root_folder
             # Installed repository dependencies container.
             if repository_dependencies:
                 if new_install:

From 25e830fa8128ff1ec08961f2bed0cf36dcb97b69 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 15:29:47 -0400
Subject: [PATCH 12/19] Remove more unused containers.

---
 .../galaxy_install/dependency_display.py      | 14 ----------
 .../utility_containers/__init__.py            | 28 -------------------
 2 files changed, 42 deletions(-)

diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py
index 0fe28bb3006..949b3fc168b 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -287,16 +287,6 @@ class DependencyDisplayer:
             )
             installed_tool_dependencies = repository_installed_tool_dependencies
             missing_tool_dependencies = repository_missing_tool_dependencies
-            # Handle valid tools.
-            valid_tools = metadata.get("tools", None)
-            # Handle Data Managers
-            valid_data_managers = None
-            invalid_data_managers = None
-            data_managers_errors = None
-            if "data_manager" in metadata:
-                valid_data_managers = metadata["data_manager"].get("data_managers", None)
-                invalid_data_managers = metadata["data_manager"].get("invalid_data_managers", None)
-                data_managers_errors = metadata["data_manager"].get("messages", None)
             gucm = GalaxyUtilityContainerManager(self.app)
             containers_dict = gucm.build_repository_containers(
                 repository=repository,
@@ -304,10 +294,6 @@ class DependencyDisplayer:
                 missing_tool_dependencies=missing_tool_dependencies,
                 repository_dependencies=installed_repository_dependencies,
                 tool_dependencies=installed_tool_dependencies,
-                valid_tools=valid_tools,
-                valid_data_managers=valid_data_managers,
-                invalid_data_managers=invalid_data_managers,
-                data_managers_errors=data_managers_errors,
                 new_install=False,
                 reinstalling=False,
             )
diff --git a/lib/tool_shed/galaxy_install/utility_containers/__init__.py b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
index 0e9dab9bc8b..670fec127a5 100644
--- a/lib/tool_shed/galaxy_install/utility_containers/__init__.py
+++ b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
@@ -16,10 +16,6 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
         missing_tool_dependencies,
         repository_dependencies,
         tool_dependencies,
-        valid_tools,
-        valid_data_managers,
-        invalid_data_managers,
-        data_managers_errors,
         new_install=False,
         reinstalling=False,
     ):
@@ -34,10 +30,6 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
         # Some of the tool dependency folders will include links to display tool dependency information, and
         # some of these links require the repository id.  However we need to be careful because sometimes the
         # repository object is None.
-        if repository:
-            changeset_revision = repository.changeset_revision
-        else:
-            changeset_revision = None
         try:
             folder_id = 0
             # Installed repository dependencies container.
@@ -87,26 +79,6 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
                     reinstalling=reinstalling,
                 )
                 containers_dict["missing_tool_dependencies"] = missing_tool_dependencies_root_folder
-            # Valid tools container.
-            if valid_tools:
-                folder_id, valid_tools_root_folder = self.build_tools_folder(
-                    folder_id, valid_tools, repository, changeset_revision, label="Valid tools"
-                )
-                containers_dict["valid_tools"] = valid_tools_root_folder
-            # Workflows container.
-            if valid_data_managers:
-                folder_id, valid_data_managers_root_folder = self.build_data_managers_folder(
-                    folder_id=folder_id, data_managers=valid_data_managers, label="Valid Data Managers"
-                )
-                containers_dict["valid_data_managers"] = valid_data_managers_root_folder
-            if invalid_data_managers or data_managers_errors:
-                folder_id, invalid_data_managers_root_folder = self.build_invalid_data_managers_folder(
-                    folder_id=folder_id,
-                    data_managers=invalid_data_managers,
-                    error_messages=data_managers_errors,
-                    label="Invalid Data Managers",
-                )
-                containers_dict["invalid_data_managers"] = invalid_data_managers_root_folder
         except Exception as e:
             log.debug(f"Exception in build_repository_containers: {str(e)}")
         return containers_dict

From dea1d0e12f40c3f12f7be2ff1c36593d9131c1dd Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 15:31:05 -0400
Subject: [PATCH 13/19] Remove more unused parameters to
 GalaxyUtilityContainerManager

---
 .../galaxy_install/dependency_display.py      |  3 ---
 .../utility_containers/__init__.py            | 21 ++++++-------------
 2 files changed, 6 insertions(+), 18 deletions(-)

diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py
index 949b3fc168b..5a05818da74 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -289,13 +289,10 @@ class DependencyDisplayer:
             missing_tool_dependencies = repository_missing_tool_dependencies
             gucm = GalaxyUtilityContainerManager(self.app)
             containers_dict = gucm.build_repository_containers(
-                repository=repository,
                 missing_repository_dependencies=missing_repository_dependencies,
                 missing_tool_dependencies=missing_tool_dependencies,
                 repository_dependencies=installed_repository_dependencies,
                 tool_dependencies=installed_tool_dependencies,
-                new_install=False,
-                reinstalling=False,
             )
         else:
             containers_dict = dict(
diff --git a/lib/tool_shed/galaxy_install/utility_containers/__init__.py b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
index 670fec127a5..02b92be217a 100644
--- a/lib/tool_shed/galaxy_install/utility_containers/__init__.py
+++ b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
@@ -11,13 +11,10 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
 
     def build_repository_containers(
         self,
-        repository,
         missing_repository_dependencies,
         missing_tool_dependencies,
         repository_dependencies,
         tool_dependencies,
-        new_install=False,
-        reinstalling=False,
     ):
         """
         Return a dictionary of containers for the received repository's dependencies and readme files for
@@ -34,10 +31,7 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
             folder_id = 0
             # Installed repository dependencies container.
             if repository_dependencies:
-                if new_install:
-                    label = "Repository dependencies"
-                else:
-                    label = "Installed repository dependencies"
+                label = "Installed repository dependencies"
                 folder_id, repository_dependencies_root_folder = self.build_repository_dependencies_folder(
                     folder_id=folder_id, repository_dependencies=repository_dependencies, label=label, installed=True
                 )
@@ -53,18 +47,15 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
                 containers_dict["missing_repository_dependencies"] = missing_repository_dependencies_root_folder
             # Installed tool dependencies container.
             if tool_dependencies:
-                if new_install:
-                    label = "Tool dependencies"
-                else:
-                    label = "Installed tool dependencies"
+                label = "Installed tool dependencies"
                 # We only want to display the Status column if the tool_dependency is missing.
                 folder_id, tool_dependencies_root_folder = self.build_tool_dependencies_folder(
                     folder_id,
                     tool_dependencies,
                     label=label,
                     missing=False,
-                    new_install=new_install,
-                    reinstalling=reinstalling,
+                    new_install=False,
+                    reinstalling=False,
                 )
                 containers_dict["tool_dependencies"] = tool_dependencies_root_folder
             # Missing tool dependencies container.
@@ -75,8 +66,8 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
                     missing_tool_dependencies,
                     label="Missing tool dependencies",
                     missing=True,
-                    new_install=new_install,
-                    reinstalling=reinstalling,
+                    new_install=False,
+                    reinstalling=False,
                 )
                 containers_dict["missing_tool_dependencies"] = missing_tool_dependencies_root_folder
         except Exception as e:

From f734fb81595fab4eb757d4c1aa92b70ef09e37f0 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 15:33:57 -0400
Subject: [PATCH 14/19] Remove tool dependency related folders in container
 dict.

---
 .../galaxy_install/dependency_display.py      | 75 -------------------
 .../utility_containers/__init__.py            | 27 -------
 2 files changed, 102 deletions(-)

diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py
index 5a05818da74..46b0b34be61 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -1,13 +1,8 @@
-import json
 import logging
 import os
 
 from galaxy import util
 from galaxy.tool_shed.util.common_util import parse_repository_dependency_tuple
-from galaxy.tool_shed.util.tool_dependency_util import (
-    get_tool_dependency_by_name_type_repository,
-    get_tool_dependency_by_name_version_type_repository,
-)
 from tool_shed.galaxy_install.utility_containers import GalaxyUtilityContainerManager
 
 log = logging.getLogger(__name__)
@@ -195,66 +190,6 @@ class DependencyDisplayer:
             message += set_environment_orphans_str
         return message
 
-    def _get_installed_and_missing_tool_dependencies_for_installed_repository(self, repository, all_tool_dependencies):
-        """
-        Return the lists of installed tool dependencies and missing tool dependencies for a Tool Shed
-        repository that has been installed into Galaxy.
-        """
-        if all_tool_dependencies:
-            tool_dependencies = {}
-            missing_tool_dependencies = {}
-            for td_key, val in all_tool_dependencies.items():
-                if td_key in ["set_environment"]:
-                    for index, td_info_dict in enumerate(val):
-                        name = td_info_dict["name"]
-                        version = None
-                        type = td_info_dict["type"]
-                        tool_dependency = get_tool_dependency_by_name_type_repository(
-                            self.app, repository, name, type
-                        )
-                        if tool_dependency:
-                            td_info_dict["repository_id"] = repository.id
-                            td_info_dict["tool_dependency_id"] = tool_dependency.id
-                            if tool_dependency.status:
-                                tool_dependency_status = str(tool_dependency.status)
-                            else:
-                                tool_dependency_status = "Never installed"
-                            td_info_dict["status"] = tool_dependency_status
-                            val[index] = td_info_dict
-                            if (
-                                tool_dependency.status
-                                == self.app.install_model.ToolDependency.installation_status.INSTALLED
-                            ):
-                                tool_dependencies[td_key] = val
-                            else:
-                                missing_tool_dependencies[td_key] = val
-                else:
-                    name = val["name"]
-                    version = val["version"]
-                    type = val["type"]
-                    tool_dependency = get_tool_dependency_by_name_version_type_repository(
-                        self.app, repository, name, version, type
-                    )
-                    if tool_dependency:
-                        val["repository_id"] = repository.id
-                        val["tool_dependency_id"] = tool_dependency.id
-                        if tool_dependency.status:
-                            tool_dependency_status = str(tool_dependency.status)
-                        else:
-                            tool_dependency_status = "Never installed"
-                        val["status"] = tool_dependency_status
-                        if (
-                            tool_dependency.status
-                            == self.app.install_model.ToolDependency.installation_status.INSTALLED
-                        ):
-                            tool_dependencies[td_key] = val
-                        else:
-                            missing_tool_dependencies[td_key] = val
-        else:
-            tool_dependencies = None
-            missing_tool_dependencies = None
-        return tool_dependencies, missing_tool_dependencies
-
     def populate_containers_dict_from_repository_metadata(
         self, repository
     ):
@@ -279,20 +214,10 @@ class DependencyDisplayer:
                 if repository_tool_dependencies is None:
                     repository_tool_dependencies = {}
                 repository_tool_dependencies.update(repository_invalid_tool_dependencies)
-            (
-                repository_installed_tool_dependencies,
-                repository_missing_tool_dependencies,
-            ) = self._get_installed_and_missing_tool_dependencies_for_installed_repository(
-                repository, repository_tool_dependencies
-            )
-            installed_tool_dependencies = repository_installed_tool_dependencies
-            missing_tool_dependencies = repository_missing_tool_dependencies
             gucm = GalaxyUtilityContainerManager(self.app)
             containers_dict = gucm.build_repository_containers(
                 missing_repository_dependencies=missing_repository_dependencies,
-                missing_tool_dependencies=missing_tool_dependencies,
                 repository_dependencies=installed_repository_dependencies,
-                tool_dependencies=installed_tool_dependencies,
             )
         else:
             containers_dict = dict(
diff --git a/lib/tool_shed/galaxy_install/utility_containers/__init__.py b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
index 02b92be217a..260c7a7bbc5 100644
--- a/lib/tool_shed/galaxy_install/utility_containers/__init__.py
+++ b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
@@ -12,9 +12,7 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
     def build_repository_containers(
         self,
         missing_repository_dependencies,
-        missing_tool_dependencies,
         repository_dependencies,
-        tool_dependencies,
     ):
         """
         Return a dictionary of containers for the received repository's dependencies and readme files for
@@ -45,31 +43,6 @@ class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerMa
                     installed=False,
                 )
                 containers_dict["missing_repository_dependencies"] = missing_repository_dependencies_root_folder
-            # Installed tool dependencies container.
-            if tool_dependencies:
-                label = "Installed tool dependencies"
-                # We only want to display the Status column if the tool_dependency is missing.
-                folder_id, tool_dependencies_root_folder = self.build_tool_dependencies_folder(
-                    folder_id,
-                    tool_dependencies,
-                    label=label,
-                    missing=False,
-                    new_install=False,
-                    reinstalling=False,
-                )
-                containers_dict["tool_dependencies"] = tool_dependencies_root_folder
-            # Missing tool dependencies container.
-            if missing_tool_dependencies:
-                # We only want to display the Status column if the tool_dependency is missing.
-                folder_id, missing_tool_dependencies_root_folder = self.build_tool_dependencies_folder(
-                    folder_id,
-                    missing_tool_dependencies,
-                    label="Missing tool dependencies",
-                    missing=True,
-                    new_install=False,
-                    reinstalling=False,
-                )
-                containers_dict["missing_tool_dependencies"] = missing_tool_dependencies_root_folder
         except Exception as e:
             log.debug(f"Exception in build_repository_containers: {str(e)}")
         return containers_dict

From 4f603d68f7a9057539d8da833953143da3855b0c Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 15:41:45 -0400
Subject: [PATCH 15/19] Refactor utility container stuff to avoid galaxy ->
 tool shed imports.

---
 .../tool_shed/util}/utility_container_manager.py                | 0
 lib/tool_shed/galaxy_install/utility_containers/__init__.py     | 2 +-
 lib/tool_shed/utility_containers/__init__.py                    | 2 +-
 3 files changed, 2 insertions(+), 2 deletions(-)
 rename lib/{tool_shed/utility_containers => galaxy/tool_shed/util}/utility_container_manager.py (100%)

diff --git a/lib/tool_shed/utility_containers/utility_container_manager.py b/lib/galaxy/tool_shed/util/utility_container_manager.py
similarity index 100%
rename from lib/tool_shed/utility_containers/utility_container_manager.py
rename to lib/galaxy/tool_shed/util/utility_container_manager.py
diff --git a/lib/tool_shed/galaxy_install/utility_containers/__init__.py b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
index 260c7a7bbc5..7561ab21820 100644
--- a/lib/tool_shed/galaxy_install/utility_containers/__init__.py
+++ b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.utility_containers import utility_container_manager
+from galaxy.tool_shed.util import utility_container_manager
 
 log = logging.getLogger(__name__)
 
diff --git a/lib/tool_shed/utility_containers/__init__.py b/lib/tool_shed/utility_containers/__init__.py
index a4e244ead7a..37d99394e3b 100644
--- a/lib/tool_shed/utility_containers/__init__.py
+++ b/lib/tool_shed/utility_containers/__init__.py
@@ -2,13 +2,13 @@ import logging
 import threading
 
 from galaxy import util
+from galaxy.tool_shed.util import utility_container_manager
 from galaxy.tool_shed.util.common_util import parse_repository_dependency_tuple
 from galaxy.tool_shed.util.container_util import (
     generate_repository_dependencies_key_for_repository,
     STRSEP,
 )
 from tool_shed.util.readme_util import build_readme_files_dict
-from . import utility_container_manager
 
 log = logging.getLogger(__name__)
 

From be49c8edd1c6fd2098571bef4d4bf07b4d741442 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 15:44:22 -0400
Subject: [PATCH 16/19] Rework GalaxyUtilityContainerManager to avoid a
 Galaxy-> Tool Shed import.

---
 .../galaxy_install/dependency_display.py      | 45 ++++++++++++++++-
 .../utility_containers/__init__.py            | 48 -------------------
 lib/tool_shed/utility_containers/__init__.py  |  6 +--
 3 files changed, 46 insertions(+), 53 deletions(-)
 delete mode 100644 lib/tool_shed/galaxy_install/utility_containers/__init__.py

diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py
index 46b0b34be61..f51824037f6 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -3,7 +3,7 @@ import os
 
 from galaxy import util
 from galaxy.tool_shed.util.common_util import parse_repository_dependency_tuple
-from tool_shed.galaxy_install.utility_containers import GalaxyUtilityContainerManager
+from galaxy.tool_shed.util import utility_container_manager
 
 log = logging.getLogger(__name__)
 
@@ -251,3 +251,46 @@ class DependencyDisplayer:
                         if req_name == name and req_type == type:
                             return False
         return True
+
+
+class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerManager):
+    def __init__(self, app):
+        self.app = app
+
+    def build_repository_containers(
+        self,
+        missing_repository_dependencies,
+        repository_dependencies,
+    ):
+        """
+        Return a dictionary of containers for the received repository's dependencies and readme files for
+        display during installation to Galaxy.
+        """
+        containers_dict = dict(
+            repository_dependencies=None,
+            missing_repository_dependencies=None,
+        )
+        # Some of the tool dependency folders will include links to display tool dependency information, and
+        # some of these links require the repository id.  However we need to be careful because sometimes the
+        # repository object is None.
+        try:
+            folder_id = 0
+            # Installed repository dependencies container.
+            if repository_dependencies:
+                label = "Installed repository dependencies"
+                folder_id, repository_dependencies_root_folder = self.build_repository_dependencies_folder(
+                    folder_id=folder_id, repository_dependencies=repository_dependencies, label=label, installed=True
+                )
+                containers_dict["repository_dependencies"] = repository_dependencies_root_folder
+            # Missing repository dependencies container.
+            if missing_repository_dependencies:
+                folder_id, missing_repository_dependencies_root_folder = self.build_repository_dependencies_folder(
+                    folder_id=folder_id,
+                    repository_dependencies=missing_repository_dependencies,
+                    label="Missing repository dependencies",
+                    installed=False,
+                )
+                containers_dict["missing_repository_dependencies"] = missing_repository_dependencies_root_folder
+        except Exception as e:
+            log.debug(f"Exception in build_repository_containers: {str(e)}")
+        return containers_dict
diff --git a/lib/tool_shed/galaxy_install/utility_containers/__init__.py b/lib/tool_shed/galaxy_install/utility_containers/__init__.py
deleted file mode 100644
index 7561ab21820..00000000000
--- a/lib/tool_shed/galaxy_install/utility_containers/__init__.py
+++ /dev/null
@@ -1,48 +0,0 @@
-import logging
-
-from galaxy.tool_shed.util import utility_container_manager
-
-log = logging.getLogger(__name__)
-
-
-class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerManager):
-    def __init__(self, app):
-        self.app = app
-
-    def build_repository_containers(
-        self,
-        missing_repository_dependencies,
-        repository_dependencies,
-    ):
-        """
-        Return a dictionary of containers for the received repository's dependencies and readme files for
-        display during installation to Galaxy.
-        """
-        containers_dict = dict(
-            repository_dependencies=None,
-            missing_repository_dependencies=None,
-        )
-        # Some of the tool dependency folders will include links to display tool dependency information, and
-        # some of these links require the repository id.  However we need to be careful because sometimes the
-        # repository object is None.
-        try:
-            folder_id = 0
-            # Installed repository dependencies container.
-            if repository_dependencies:
-                label = "Installed repository dependencies"
-                folder_id, repository_dependencies_root_folder = self.build_repository_dependencies_folder(
-                    folder_id=folder_id, repository_dependencies=repository_dependencies, label=label, installed=True
-                )
-                containers_dict["repository_dependencies"] = repository_dependencies_root_folder
-            # Missing repository dependencies container.
-            if missing_repository_dependencies:
-                folder_id, missing_repository_dependencies_root_folder = self.build_repository_dependencies_folder(
-                    folder_id=folder_id,
-                    repository_dependencies=missing_repository_dependencies,
-                    label="Missing repository dependencies",
-                    installed=False,
-                )
-                containers_dict["missing_repository_dependencies"] = missing_repository_dependencies_root_folder
-        except Exception as e:
-            log.debug(f"Exception in build_repository_containers: {str(e)}")
-        return containers_dict
diff --git a/lib/tool_shed/utility_containers/__init__.py b/lib/tool_shed/utility_containers/__init__.py
index 37d99394e3b..5d0c5b7700c 100644
--- a/lib/tool_shed/utility_containers/__init__.py
+++ b/lib/tool_shed/utility_containers/__init__.py
@@ -3,11 +3,11 @@ import threading
 
 from galaxy import util
 from galaxy.tool_shed.util import utility_container_manager
-from galaxy.tool_shed.util.common_util import parse_repository_dependency_tuple
 from galaxy.tool_shed.util.container_util import (
     generate_repository_dependencies_key_for_repository,
     STRSEP,
 )
+from galaxy.util.tool_shed.common_util import parse_repository_dependency_tuple
 from tool_shed.util.readme_util import build_readme_files_dict
 
 log = logging.getLogger(__name__)
@@ -301,9 +301,7 @@ class ToolShedUtilityContainerManager(utility_container_manager.UtilityContainer
                 # Readme files container.
                 if metadata:
                     if "readme_files" not in exclude and "readme_files" in metadata:
-                        readme_files_dict = build_readme_files_dict(
-                            self.app, repository, changeset_revision, metadata
-                        )
+                        readme_files_dict = build_readme_files_dict(self.app, repository, changeset_revision, metadata)
                         folder_id, readme_files_root_folder = self.build_readme_files_folder(
                             folder_id, readme_files_dict
                         )

From ead32bcfc5e6f6fe5feaaaa6c416b55ff7e2be75 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 15:46:19 -0400
Subject: [PATCH 17/19] Move dependency_display to avoid Galaxy -> Tool Shed
 import.

---
 .../tool_shed/util}/dependency_display.py              | 10 +++-------
 .../webapps/galaxy/controllers/admin_toolshed.py       |  2 +-
 lib/tool_shed/webapp/controllers/repository.py         |  2 +-
 lib/tool_shed/webapp/controllers/upload.py             |  2 +-
 4 files changed, 6 insertions(+), 10 deletions(-)
 rename lib/{tool_shed/galaxy_install => galaxy/tool_shed/util}/dependency_display.py (98%)

diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/galaxy/tool_shed/util/dependency_display.py
similarity index 98%
rename from lib/tool_shed/galaxy_install/dependency_display.py
rename to lib/galaxy/tool_shed/util/dependency_display.py
index f51824037f6..1d27431e495 100644
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/galaxy/tool_shed/util/dependency_display.py
@@ -2,8 +2,8 @@ import logging
 import os
 
 from galaxy import util
-from galaxy.tool_shed.util.common_util import parse_repository_dependency_tuple
 from galaxy.tool_shed.util import utility_container_manager
+from galaxy.util.tool_shed.common_util import parse_repository_dependency_tuple
 
 log = logging.getLogger(__name__)
 
@@ -63,9 +63,7 @@ class DependencyDisplayer:
                             prior_installation_required,
                             only_if_compiling_contained_td,
                             error,
-                        ) = parse_repository_dependency_tuple(
-                            repository_dependency_tup, contains_error=True
-                        )
+                        ) = parse_repository_dependency_tuple(repository_dependency_tup, contains_error=True)
                         if error:
                             message += f"{error}  "
             else:
@@ -190,9 +188,7 @@ class DependencyDisplayer:
             message += set_environment_orphans_str
         return message
 
-    def populate_containers_dict_from_repository_metadata(
-        self, repository
-    ):
+    def populate_containers_dict_from_repository_metadata(self, repository):
         """
         Retrieve necessary information from the received repository's metadata to populate the
         containers_dict for display.  This method is called only from Galaxy (not the tool shed)
diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index b96866a37f2..a5e2d32550a 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -25,7 +25,7 @@ from galaxy.util.tool_shed import (
     encoding_util,
 )
 from galaxy.web.form_builder import CheckboxField
-from tool_shed.galaxy_install import dependency_display
+from galaxy.tool_shed.util import dependency_display
 from tool_shed.util import shed_util_common as suc
 from tool_shed.util.repository_util import create_repo_info_dict
 from tool_shed.util.web_util import escape
diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py
index bb694d404bf..bcbb6873d1d 100644
--- a/lib/tool_shed/webapp/controllers/repository.py
+++ b/lib/tool_shed/webapp/controllers/repository.py
@@ -24,6 +24,7 @@ from galaxy import (
     util,
     web,
 )
+from galaxy.tool_shed.util import dependency_display
 from galaxy.tools.repositories import ValidationContext
 from galaxy.web.form_builder import (
     CheckboxField,
@@ -32,7 +33,6 @@ from galaxy.web.form_builder import (
 from galaxy.web.legacy_framework import grids
 from galaxy.webapps.base.controller import BaseUIController
 from tool_shed.dependencies.repository import relation_builder
-from tool_shed.galaxy_install import dependency_display
 from tool_shed.metadata import repository_metadata_manager
 from tool_shed.tools import (
     tool_validator,
diff --git a/lib/tool_shed/webapp/controllers/upload.py b/lib/tool_shed/webapp/controllers/upload.py
index b4ea9b5631d..ef3ef730dd7 100644
--- a/lib/tool_shed/webapp/controllers/upload.py
+++ b/lib/tool_shed/webapp/controllers/upload.py
@@ -10,10 +10,10 @@ from galaxy import (
     util,
     web,
 )
+from galaxy.tool_shed.util import dependency_display
 from galaxy.util import checkers
 from galaxy.webapps.base.controller import BaseUIController
 from tool_shed.dependencies import attribute_handlers
-from tool_shed.galaxy_install import dependency_display
 from tool_shed.metadata import repository_metadata_manager
 from tool_shed.repository_types import util as rt_util
 from tool_shed.tools.data_table_manager import ShedToolDataTableManager

From 217a21b4f6a028439140f6069d849319de65b0f4 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 15:52:09 -0400
Subject: [PATCH 18/19] Another attempt to cleanup imports of admin_toolshed.

---
 .../galaxy/controllers/admin_toolshed.py      | 30 ++++++++++++-------
 1 file changed, 20 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index a5e2d32550a..a8d1c5e4b3f 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -12,12 +12,19 @@ from galaxy.exceptions import ConfigDoesNotAllowException
 from galaxy.tool_shed.galaxy_install import install_manager
 from galaxy.tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
 from galaxy.tool_shed.galaxy_install.tools import tool_panel_manager
+from galaxy.tool_shed.util import dependency_display
 from galaxy.tool_shed.util.repository_util import (
     create_or_update_tool_shed_repository,
     get_absolute_path_to_file_in_repository,
     get_installed_tool_shed_repository,
     get_tool_shed_repository_by_id,
 )
+from galaxy.tool_shed.util.shed_util_common import (
+    clean_dependency_relationships,
+    get_ctx_rev,
+    get_tool_panel_config_tool_path_install_dir,
+    have_shed_tool_conf_for_install,
+)
 from galaxy.tool_util.deps import views
 from galaxy.util import unicodify
 from galaxy.util.tool_shed import (
@@ -25,9 +32,12 @@ from galaxy.util.tool_shed import (
     encoding_util,
 )
 from galaxy.web.form_builder import CheckboxField
-from galaxy.tool_shed.util import dependency_display
-from tool_shed.util import shed_util_common as suc
 from tool_shed.util.repository_util import create_repo_info_dict
+from tool_shed.util.shed_util_common import (
+    get_repository_type_from_tool_shed,
+    get_requirements_from_repository,
+    get_tool_dependency_definition_metadata_from_tool_shed,
+)
 from tool_shed.util.web_util import escape
 from .admin import AdminGalaxy
 
@@ -153,7 +163,7 @@ class AdminToolshed(AdminGalaxy):
         tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(repository.tool_shed))
         description = kwd.get("description", repository.description)
         status = "ok"
-        _, tool_path, _ = suc.get_tool_panel_config_tool_path_install_dir(trans.app, repository)
+        _, tool_path, _ = get_tool_panel_config_tool_path_install_dir(trans.app, repository)
         if repository.in_error_state:
             message = "This repository is not installed correctly (see the <b>Repository installation error</b> below).  Choose "
             message += "<b>Reset to install</b> from the <b>Repository Actions</b> menu, correct problems if necessary and try "
@@ -173,7 +183,7 @@ class AdminToolshed(AdminGalaxy):
             repository=repository,
         )
         view = views.DependencyResolversView(self.app)
-        tool_requirements_d = suc.get_requirements_from_repository(repository)
+        tool_requirements_d = get_requirements_from_repository(repository)
         requirements_status = view.get_requirements_status(tool_requirements_d, repository.installed_tool_dependencies)
         management_dict = {
             "status": status,
@@ -206,9 +216,9 @@ class AdminToolshed(AdminGalaxy):
             install_repository_dependencies = CheckboxField.is_checked(kwd.get("install_repository_dependencies", ""))
             install_tool_dependencies = CheckboxField.is_checked(kwd.get("install_tool_dependencies", ""))
             install_resolver_dependencies = CheckboxField.is_checked(kwd.get("install_resolver_dependencies", ""))
-            if not suc.have_shed_tool_conf_for_install(trans.app):
+            if not have_shed_tool_conf_for_install(trans.app):
                 raise Exception("No valid shed tool configuration file available, please configure one")
-            shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir(
+            shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir(
                 trans.app, tool_shed_repository
             )
             repository_clone_url = common_util.generate_clone_url_for_installed_repository(
@@ -240,19 +250,19 @@ class AdminToolshed(AdminGalaxy):
                     # Just in case the tool_section.id differs from tool_panel_section_id, which it shouldn't...
                     tool_panel_section_id = str(tool_section.id)
             if tool_shed_repository.status == trans.install_model.ToolShedRepository.installation_status.UNINSTALLED:
-                repository_type = suc.get_repository_type_from_tool_shed(
+                repository_type = get_repository_type_from_tool_shed(
                     trans.app, tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner
                 )
                 if repository_type == rt_util.TOOL_DEPENDENCY_DEFINITION:
                     # Repositories of type tool_dependency_definition must get the latest
                     # metadata from the Tool Shed since they have only a single installable
                     # revision.
-                    raw_text = suc.get_tool_dependency_definition_metadata_from_tool_shed(
+                    raw_text = get_tool_dependency_definition_metadata_from_tool_shed(
                         trans.app, tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner
                     )
                     new_meta = json.loads(raw_text)
                     # Clean up old repository dependency and tool dependency relationships.
-                    suc.clean_dependency_relationships(trans, new_meta, tool_shed_repository, tool_shed_url)
+                    clean_dependency_relationships(trans, new_meta, tool_shed_repository, tool_shed_url)
                 # The repository's status must be updated from 'Uninstalled' to 'New' when initiating reinstall
                 # so the repository_installation_updater will function.
                 tool_shed_repository = create_or_update_tool_shed_repository(
@@ -268,7 +278,7 @@ class AdminToolshed(AdminGalaxy):
                     owner=tool_shed_repository.owner,
                     dist_to_shed=tool_shed_repository.dist_to_shed,
                 )
-            ctx_rev = suc.get_ctx_rev(
+            ctx_rev = get_ctx_rev(
                 trans.app,
                 tool_shed_url,
                 tool_shed_repository.name,

From 6547e421f8d3796ef8d7657ea35bfa194ac5c6e2 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 17 Oct 2022 17:01:28 -0400
Subject: [PATCH 19/19] linting fixes for admin_toolshed.py.

---
 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
index a8d1c5e4b3f..ea077071571 100644
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -160,10 +160,8 @@ class AdminToolshed(AdminGalaxy):
         repository = get_installed_tool_shed_repository(trans.app, repository_id)
         if repository is None:
             return trans.show_error_message("Invalid repository specified.")
-        tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, str(repository.tool_shed))
         description = kwd.get("description", repository.description)
         status = "ok"
-        _, tool_path, _ = get_tool_panel_config_tool_path_install_dir(trans.app, repository)
         if repository.in_error_state:
             message = "This repository is not installed correctly (see the <b>Repository installation error</b> below).  Choose "
             message += "<b>Reset to install</b> from the <b>Repository Actions</b> menu, correct problems if necessary and try "