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Share tool_path resolution between the toolbox and tool discovery

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AbstractToolBox.__resolve_tool_path becomes the module-level
resolve_tool_path() in tool_util.toolbox.base and discover uses it,
dropping its own copy. This also fixes discover's fallback for confs
without a tool_path attribute: it guessed <root>/tools, while the
toolbox has always used config.tool_path; discover_tools_from_config
now takes that default (discover_tools passes config.tool_path).

Also hoists the MODEL_TOOLS_PATH import to module level - the parent
galaxy.tools package is imported with the subpackage anyway, so the
local import bought nothing.

Claude-Session: https://claude.ai/code/session_018L7ZmCv2ubKA3JNeSL8Pkr
This commit is contained in:
mvdbeek
2026-07-28 17:27:28 +02:00
parent 6585afa74c
commit 455d6e87e8
1 changed files with 18 additions and 12 deletions
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lib/galaxy/tool_util/toolbox/base.py
+18 -12
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@@ -171,6 +171,23 @@ class ToolLoadConfigurationConflict(Exception):
pass
def resolve_tool_path(tool_path: str | None, config_filename: str, default_tool_path: "StrPath | None" = None) -> str:
"""Resolve a tool conf's ``tool_path`` attribute to the directory its tool
files are relative to.
Expands the ``${tool_conf_dir}`` template; falls back to
``default_tool_path`` (the toolbox's ``tool_root_dir``, i.e.
``config.tool_path``) when the conf doesn't set one.
"""
if not tool_path:
# Default to backward compatible config setting.
return str(default_tool_path) if default_tool_path else ""
# Allow use of ${tool_conf_dir} in toolbox config files.
tool_conf_dir = os.path.dirname(config_filename)
tool_path_vars = {"tool_conf_dir": tool_conf_dir}
return string.Template(tool_path).safe_substitute(tool_path_vars)
class AbstractToolBox(ManagesIntegratedToolPanelMixin):
"""
Abstract container for managing a ToolPanel - containing tools and
@@ -389,7 +406,7 @@ class AbstractToolBox(ManagesIntegratedToolPanelMixin):
config_elems = []
tool_conf_type = "shed tool" if parsing_shed_tool_conf else "tool"
log.debug("Tool path for %s configuration %s is %s", tool_conf_type, config_filename, tool_path)
tool_path = self.__resolve_tool_path(tool_path, config_filename)
tool_path = resolve_tool_path(tool_path, config_filename, self._tool_root_dir)
# Only load the panel_dict under certain conditions.
load_panel_dict = not self._integrated_tool_panel_config_has_contents
for item in tool_conf_source.parse_items():
@@ -564,17 +581,6 @@ class AbstractToolBox(ManagesIntegratedToolPanelMixin):
tool_id = tool.id
return self._tool_panel.get_section_for_tool_id(tool_id)
def __resolve_tool_path(self, tool_path, config_filename):
if not tool_path:
# Default to backward compatible config setting.
tool_path = self._tool_root_dir
else:
# Allow use of __tool_conf_dir__ in toolbox config files.
tool_conf_dir = os.path.dirname(config_filename)
tool_path_vars = {"tool_conf_dir": tool_conf_dir}
tool_path = string.Template(tool_path).safe_substitute(tool_path_vars)
return tool_path
def add_tool_to_tool_panel_view(self, tool, view_panel_component):
self.__add_tool_to_tool_panel(tool, view_panel_component)