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Source code for galaxy.model.tool_shed_install.mapping
from sqlalchemy import (
Boolean,
Column,
DateTime,
ForeignKey,
Integer,
MetaData,
String,
Table,
TEXT
)
from sqlalchemy.orm import (
mapper,
relation
)
from galaxy.model import tool_shed_install as install_model
from galaxy.model.base import ModelMapping
from galaxy.model.custom_types import (
MutableJSONType,
TrimmedString
)
from galaxy.model.orm.engine_factory import build_engine
from galaxy.model.orm.now import now
metadata = MetaData()
install_model.ToolShedRepository.table = Table("tool_shed_repository", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, default=now, onupdate=now),
Column("tool_shed", TrimmedString(255), index=True),
Column("name", TrimmedString(255), index=True),
Column("description", TEXT),
Column("owner", TrimmedString(255), index=True),
Column("installed_changeset_revision", TrimmedString(255)),
Column("changeset_revision", TrimmedString(255), index=True),
Column("ctx_rev", TrimmedString(10)),
Column("metadata", MutableJSONType, nullable=True),
Column("includes_datatypes", Boolean, index=True, default=False),
Column("tool_shed_status", MutableJSONType, nullable=True),
Column("deleted", Boolean, index=True, default=False),
Column("uninstalled", Boolean, default=False),
Column("dist_to_shed", Boolean, default=False),
Column("status", TrimmedString(255)),
Column("error_message", TEXT))
install_model.RepositoryRepositoryDependencyAssociation.table = Table('repository_repository_dependency_association', metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, default=now, onupdate=now),
Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True),
Column("repository_dependency_id", Integer, ForeignKey("repository_dependency.id"), index=True))
install_model.RepositoryDependency.table = Table("repository_dependency", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, default=now, onupdate=now),
Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True, nullable=False))
install_model.ToolDependency.table = Table("tool_dependency", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, default=now, onupdate=now),
Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True, nullable=False),
Column("name", TrimmedString(255)),
Column("version", TEXT),
Column("type", TrimmedString(40)),
Column("status", TrimmedString(255), nullable=False),
Column("error_message", TEXT))
install_model.ToolVersion.table = Table("tool_version", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, default=now, onupdate=now),
Column("tool_id", String(255)),
Column("tool_shed_repository_id", Integer, ForeignKey("tool_shed_repository.id"), index=True, nullable=True))
install_model.ToolVersionAssociation.table = Table("tool_version_association", metadata,
Column("id", Integer, primary_key=True),
Column("tool_id", Integer, ForeignKey("tool_version.id"), index=True, nullable=False),
Column("parent_id", Integer, ForeignKey("tool_version.id"), index=True, nullable=False))
install_model.MigrateTools.table = Table("migrate_tools", metadata,
Column("repository_id", TrimmedString(255)),
Column("repository_path", TEXT),
Column("version", Integer))
mapper(install_model.ToolShedRepository, install_model.ToolShedRepository.table,
properties=dict(tool_versions=relation(install_model.ToolVersion,
primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolVersion.table.c.tool_shed_repository_id),
backref='tool_shed_repository'),
tool_dependencies=relation(install_model.ToolDependency,
primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.ToolDependency.table.c.tool_shed_repository_id),
order_by=install_model.ToolDependency.table.c.name,
backref='tool_shed_repository'),
required_repositories=relation(install_model.RepositoryRepositoryDependencyAssociation,
primaryjoin=(install_model.ToolShedRepository.table.c.id == install_model.RepositoryRepositoryDependencyAssociation.table.c.tool_shed_repository_id))))
mapper(install_model.RepositoryRepositoryDependencyAssociation, install_model.RepositoryRepositoryDependencyAssociation.table,
properties=dict(repository=relation(install_model.ToolShedRepository,
primaryjoin=(install_model.RepositoryRepositoryDependencyAssociation.table.c.tool_shed_repository_id == install_model.ToolShedRepository.table.c.id)),
repository_dependency=relation(install_model.RepositoryDependency,
primaryjoin=(install_model.RepositoryRepositoryDependencyAssociation.table.c.repository_dependency_id == install_model.RepositoryDependency.table.c.id))))
mapper(install_model.RepositoryDependency, install_model.RepositoryDependency.table,
properties=dict(repository=relation(install_model.ToolShedRepository,
primaryjoin=(install_model.RepositoryDependency.table.c.tool_shed_repository_id == install_model.ToolShedRepository.table.c.id))))
mapper(install_model.ToolDependency, install_model.ToolDependency.table)
mapper(install_model.ToolVersion, install_model.ToolVersion.table,
properties=dict(
parent_tool_association=relation(install_model.ToolVersionAssociation,
primaryjoin=(install_model.ToolVersion.table.c.id == install_model.ToolVersionAssociation.table.c.tool_id)),
child_tool_association=relation(install_model.ToolVersionAssociation,
primaryjoin=(install_model.ToolVersion.table.c.id == install_model.ToolVersionAssociation.table.c.parent_id))))
mapper(install_model.ToolVersionAssociation, install_model.ToolVersionAssociation.table)
[docs]def init(url, engine_options=None, create_tables=False):
"""Connect mappings to the database"""
# Load the appropriate db module
engine_options = engine_options or {}
engine = build_engine(url, engine_options)
# Connect the metadata to the database.
metadata.bind = engine
result = ModelMapping([install_model], engine=engine)
# Create tables if needed
if create_tables:
metadata.create_all()
# metadata.engine.commit()
result.create_tables = create_tables
# load local galaxy security policy
return result