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Source code for galaxy.tool_util.toolbox.lineages.factory

from typing import (

from galaxy.util.tool_version import remove_version_from_guid
from .interface import ToolLineage

[docs]class LineageMap: """Map each unique tool id to a lineage object."""
[docs] def __init__(self, app): self.lineage_map: Dict[str, ToolLineage] = {} self.app = app
[docs] def register(self, tool) -> ToolLineage: tool_id = tool.id versionless_tool_id = remove_version_from_guid(tool_id) lineage: ToolLineage if versionless_tool_id not in self.lineage_map: lineage = ToolLineage.from_tool(tool) else: lineage = self.lineage_map[versionless_tool_id] # A lineage for a tool with the same versionless_tool_id exists, # but this lineage may not have the current tools' version, # so we add tool.version to the lineage lineage.register_version(tool.version) if versionless_tool_id and versionless_tool_id not in self.lineage_map: self.lineage_map[versionless_tool_id] = lineage if tool_id not in self.lineage_map: self.lineage_map[tool_id] = lineage return self.lineage_map[tool_id]
[docs] def get(self, tool_id) -> Optional[ToolLineage]: """ Get lineage for `tool_id`. By preference the lineage for a version-agnostic tool_id is returned. Falls back to fetching the lineage only when this fails. This happens when the tool_id does not contain a version. """ lineage = self._get_versionless(tool_id) if lineage: return lineage if tool_id not in self.lineage_map: toolbox = None try: toolbox = self.app.toolbox except AttributeError: # We're building the lineage map while building the toolbox, # so app.toolbox may not be available. # TODO: is the fallback really needed / can it be fixed by improving _get_versionless ? pass tool = toolbox and toolbox._tools_by_id.get(tool_id) if tool: lineage = ToolLineage.from_tool(tool) if lineage: self.lineage_map[tool_id] = lineage return self.lineage_map.get(tool_id)
def _get_versionless(self, tool_id) -> Optional[ToolLineage]: versionless_tool_id = remove_version_from_guid(tool_id) return self.lineage_map.get(versionless_tool_id, None)
__all__ = ("LineageMap",)