mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-13 00:44:55 +08:00
Nicola Soranzo
a353b2e88f
using: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 . ```
114 lines
6.3 KiB
Python
114 lines
6.3 KiB
Python
import logging
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from sqlalchemy import and_, or_
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from tool_shed.util import hg_util
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from tool_shed.util import metadata_util
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from tool_shed.util import repository_util
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log = logging.getLogger(__name__)
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class ToolVersionManager(object):
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def __init__(self, app):
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self.app = app
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def get_tool_version(self, tool_id):
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context = self.app.install_model.context
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return context.query(self.app.install_model.ToolVersion) \
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.filter(self.app.install_model.ToolVersion.table.c.tool_id == tool_id) \
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.first()
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def get_tool_version_association(self, parent_tool_version, tool_version):
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"""
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Return a ToolVersionAssociation if one exists that associates the two
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received tool_versions. This function is called only from Galaxy.
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"""
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context = self.app.install_model.context
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return context.query(self.app.install_model.ToolVersionAssociation) \
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.filter(and_(self.app.install_model.ToolVersionAssociation.table.c.parent_id == parent_tool_version.id,
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self.app.install_model.ToolVersionAssociation.table.c.tool_id == tool_version.id)) \
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.first()
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def get_version_lineage_for_tool(self, repository_id, repository_metadata, guid):
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"""
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Return the tool version lineage chain in descendant order for the received
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guid contained in the received repsitory_metadata.tool_versions. This function
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is called only from the Tool Shed.
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"""
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repository = repository_util.get_repository_by_id(self.app, repository_id)
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repo = hg_util.get_repo_for_repository(self.app, repository=repository, repo_path=None, create=False)
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# Initialize the tool lineage
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version_lineage = [guid]
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# Get all ancestor guids of the received guid.
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current_child_guid = guid
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for changeset in hg_util.reversed_upper_bounded_changelog(repo, repository_metadata.changeset_revision):
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ctx = repo.changectx(changeset)
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rm = metadata_util.get_repository_metadata_by_changeset_revision(self.app, repository_id, str(ctx))
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if rm:
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parent_guid = rm.tool_versions.get(current_child_guid, None)
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if parent_guid:
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version_lineage.append(parent_guid)
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current_child_guid = parent_guid
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# Get all descendant guids of the received guid.
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current_parent_guid = guid
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for changeset in hg_util.reversed_lower_upper_bounded_changelog(repo,
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repository_metadata.changeset_revision,
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repository.tip(self.app)):
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ctx = repo.changectx(changeset)
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rm = metadata_util.get_repository_metadata_by_changeset_revision(self.app, repository_id, str(ctx))
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if rm:
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tool_versions = rm.tool_versions
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for child_guid, parent_guid in tool_versions.items():
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if parent_guid == current_parent_guid:
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version_lineage.insert(0, child_guid)
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current_parent_guid = child_guid
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break
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return version_lineage
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def handle_tool_versions(self, tool_version_dicts, tool_shed_repository):
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"""
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Using the list of tool_version_dicts retrieved from the Tool Shed (one per changeset
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revision up to the currently installed changeset revision), create the parent / child
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pairs of tool versions. Each dictionary contains { tool id : parent tool id } pairs.
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This function is called only from Galaxy.
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"""
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context = self.app.install_model.context
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for tool_version_dict in tool_version_dicts:
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for tool_guid, parent_id in tool_version_dict.items():
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tool_version_using_tool_guid = self.get_tool_version(tool_guid)
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tool_version_using_parent_id = self.get_tool_version(parent_id)
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if not tool_version_using_tool_guid:
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tool_version_using_tool_guid = \
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self.app.install_model.ToolVersion(tool_id=tool_guid,
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tool_shed_repository=tool_shed_repository)
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context.add(tool_version_using_tool_guid)
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context.flush()
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if not tool_version_using_parent_id:
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tool_version_using_parent_id = \
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self.app.install_model.ToolVersion(tool_id=parent_id,
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tool_shed_repository=tool_shed_repository)
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context.add(tool_version_using_parent_id)
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context.flush()
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# Remove existing wrong tool version associations having
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# tool_version_using_parent_id as parent or
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# tool_version_using_tool_guid as child.
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context.query(self.app.install_model.ToolVersionAssociation) \
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.filter(or_(and_(self.app.install_model.ToolVersionAssociation.table.c.parent_id == tool_version_using_parent_id.id,
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self.app.install_model.ToolVersionAssociation.table.c.tool_id != tool_version_using_tool_guid.id),
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and_(self.app.install_model.ToolVersionAssociation.table.c.parent_id != tool_version_using_parent_id.id,
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self.app.install_model.ToolVersionAssociation.table.c.tool_id == tool_version_using_tool_guid.id))) \
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.delete()
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context.flush()
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tool_version_association = \
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self.get_tool_version_association(tool_version_using_parent_id,
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tool_version_using_tool_guid)
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if not tool_version_association:
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# Associate the two versions as parent / child.
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tool_version_association = \
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self.app.install_model.ToolVersionAssociation(tool_id=tool_version_using_tool_guid.id,
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parent_id=tool_version_using_parent_id.id)
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context.add(tool_version_association)
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context.flush()
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