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

import threading
from typing import (

import packaging.version
from sortedcontainers import SortedSet

from galaxy.util.tool_version import remove_version_from_guid

[docs]class ToolLineageVersion: """Represents a single tool in a lineage. If lineage is based around GUIDs that somehow encode the version (either using GUID or a simple tool id and a version)."""
[docs] def __init__(self, id, version): self.id = id self.version = version
@property def id_based(self): """Return True if the lineage is defined by GUIDs (in this case the indexer of the tools (i.e. the ToolBox) should ignore the tool_version (because it is encoded in the GUID and managed externally). """ return self.version is None
[docs] def to_dict(self): return dict( id=self.id, version=self.version, )
[docs]class ToolLineage: """Simple tool's loaded directly from file system with lineage determined solely by PEP 440 versioning scheme. """ lineages_by_id: Dict[str, "ToolLineage"] = {} lock = threading.Lock()
[docs] def __init__(self, tool_id, **kwds): self.tool_id = tool_id self.tool_versions = SortedSet(key=packaging.version.parse)
@property def tool_ids(self) -> List[str]: versionless_tool_id = remove_version_from_guid(self.tool_id) tool_id = versionless_tool_id or self.tool_id return [f"{tool_id}/{version}" for version in self.tool_versions]
[docs] @staticmethod def from_tool(tool) -> "ToolLineage": tool_id = tool.id lineages_by_id = ToolLineage.lineages_by_id with ToolLineage.lock: if tool_id not in lineages_by_id: lineages_by_id[tool_id] = ToolLineage(tool_id) lineage = lineages_by_id[tool_id] lineage.register_version(tool.version) return lineage
[docs] def register_version(self, tool_version) -> None: assert tool_version is not None self.tool_versions.add(str(tool_version))
[docs] def get_versions(self): """ Return an ordered list of lineages (ToolLineageVersion) in this chain, from oldest to newest. """ return [ ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions) ]
[docs] def get_version_ids(self, reverse=False) -> List[str]: if reverse: return list(reversed(self.tool_ids)) return self.tool_ids
[docs] def to_dict(self) -> Dict[str, Any]: return dict( tool_id=self.tool_id, tool_versions=list(self.tool_versions), lineage_type="stock", )