Source code for galaxy.tools.toolbox.lineages.interface
import threading
import packaging.version
from galaxy.util.tool_version import remove_version_from_guid
[docs]class ToolLineageVersion(object):
""" 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). """
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]class ToolLineage(object):
""" Simple tool's loaded directly from file system with lineage
determined solely by PEP 440 versioning scheme.
"""
lineages_by_id = {}
lock = threading.Lock()
def __init__(self, tool_id, **kwds):
self.tool_id = tool_id
self._tool_versions = set()
@property
def tool_versions(self):
return sorted(self._tool_versions, key=packaging.version.parse)
@property
def tool_ids(self):
versionless_tool_id = remove_version_from_guid(self.tool_id)
tool_id = versionless_tool_id or self.tool_id
return ["%s/%s" % (tool_id, version) for version in self.tool_versions]
[docs] @staticmethod
def from_tool(tool):
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):
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):
if reverse:
return list(reversed(self.tool_ids))
return self.tool_ids
[docs] def to_dict(self):
return dict(
tool_id=self.tool_id,
tool_versions=list(self.tool_versions),
lineage_type='stock',
)