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Source code for tool_shed.tools.tool_version_manager

import logging

from sqlalchemy import and_

from tool_shed.util import hg_util
from tool_shed.util import metadata_util
from tool_shed.util import repository_util

log = logging.getLogger(__name__)

[docs]class ToolVersionManager(object):
[docs] def __init__(self, app): self.app = app
[docs] def get_tool_version(self, tool_id): context = self.app.install_model.context return context.query(self.app.install_model.ToolVersion) \ .filter(self.app.install_model.ToolVersion.table.c.tool_id == tool_id) \ .first()
[docs] def get_tool_version_association(self, parent_tool_version, tool_version): """ Return a ToolVersionAssociation if one exists that associates the two received tool_versions. This function is called only from Galaxy. """ context = self.app.install_model.context return context.query(self.app.install_model.ToolVersionAssociation) \ .filter(and_(self.app.install_model.ToolVersionAssociation.table.c.parent_id == parent_tool_version.id, self.app.install_model.ToolVersionAssociation.table.c.tool_id == tool_version.id)) \ .first()
[docs] def get_version_lineage_for_tool(self, repository_id, repository_metadata, guid): """ Return the tool version lineage chain in descendant order for the received guid contained in the received repsitory_metadata.tool_versions. This function is called only from the Tool Shed. """ repository = repository_util.get_repository_by_id(self.app, repository_id) repo = hg_util.get_repo_for_repository(self.app, repository=repository) # Initialize the tool lineage version_lineage = [guid] # Get all ancestor guids of the received guid. current_child_guid = guid for changeset in hg_util.reversed_upper_bounded_changelog(repo, repository_metadata.changeset_revision): ctx = repo[changeset] rm = metadata_util.get_repository_metadata_by_changeset_revision(self.app, repository_id, str(ctx)) if rm: parent_guid = rm.tool_versions.get(current_child_guid, None) if parent_guid: version_lineage.append(parent_guid) current_child_guid = parent_guid # Get all descendant guids of the received guid. current_parent_guid = guid for changeset in hg_util.reversed_lower_upper_bounded_changelog(repo, repository_metadata.changeset_revision, repository.tip(self.app)): ctx = repo[changeset] rm = metadata_util.get_repository_metadata_by_changeset_revision(self.app, repository_id, str(ctx)) if rm: tool_versions = rm.tool_versions for child_guid, parent_guid in tool_versions.items(): if parent_guid == current_parent_guid: version_lineage.insert(0, child_guid) current_parent_guid = child_guid break return version_lineage