Source code for tool_shed.webapp.model.migrate.versions.0001_initial_tables

"""
Migration script to create initial tables.
"""

import datetime
import logging
import sys

from sqlalchemy import (
    Boolean,
    Column,
    DateTime,
    ForeignKey,
    Index,
    Integer,
    MetaData,
    String,
    Table,
    TEXT,
    UniqueConstraint,
)

# Need our custom types, but don't import anything else from model
from galaxy.model.custom_types import TrimmedString

now = datetime.datetime.utcnow
log = logging.getLogger(__name__)
log.setLevel(logging.DEBUG)
handler = logging.StreamHandler(sys.stdout)
format = "%(name)s %(levelname)s %(asctime)s %(message)s"
formatter = logging.Formatter(format)
handler.setFormatter(formatter)
log.addHandler(handler)

metadata = MetaData()

User_table = Table(
    "galaxy_user",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("email", TrimmedString(255), nullable=False),
    Column("username", String(255), index=True),
    Column("password", TrimmedString(40), nullable=False),
    Column("external", Boolean, default=False),
    Column("deleted", Boolean, index=True, default=False),
    Column("purged", Boolean, index=True, default=False),
)

Group_table = Table(
    "galaxy_group",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("name", String(255), index=True, unique=True),
    Column("deleted", Boolean, index=True, default=False),
)

Role_table = Table(
    "role",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("name", String(255), index=True, unique=True),
    Column("description", TEXT),
    Column("type", String(40), index=True),
    Column("deleted", Boolean, index=True, default=False),
)

UserGroupAssociation_table = Table(
    "user_group_association",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
)

UserRoleAssociation_table = Table(
    "user_role_association",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
)

GroupRoleAssociation_table = Table(
    "group_role_association",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
)

GalaxySession_table = Table(
    "galaxy_session",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True),
    Column("remote_host", String(255)),
    Column("remote_addr", String(255)),
    Column("referer", TEXT),
    Column(
        "session_key", TrimmedString(255), index=True, unique=True
    ),  # unique 128 bit random number coerced to a string
    Column("is_valid", Boolean, default=False),
    Column("prev_session_id", Integer),
)  # saves a reference to the previous session so we have a way to chain them together

Tool_table = Table(
    "tool",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("guid", TrimmedString(255), index=True, unique=True),
    Column("tool_id", TrimmedString(255), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("newer_version_id", Integer, ForeignKey("tool.id"), nullable=True),
    Column("name", TrimmedString(255), index=True),
    Column("description", TEXT),
    Column("user_description", TEXT),
    Column("version", TrimmedString(255)),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("external_filename", TEXT),
    Column("deleted", Boolean, index=True, default=False),
)

Event_table = Table(
    "event",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("state", TrimmedString(255), index=True),
    Column("comment", TEXT),
)

ToolEventAssociation_table = Table(
    "tool_event_association",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
    Column("event_id", Integer, ForeignKey("event.id"), index=True),
)

Category_table = Table(
    "category",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("name", TrimmedString(255), index=True, unique=True),
    Column("description", TEXT),
    Column("deleted", Boolean, index=True, default=False),
)

ToolCategoryAssociation_table = Table(
    "tool_category_association",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
    Column("category_id", Integer, ForeignKey("category.id"), index=True),
)

Tag_table = Table(
    "tag",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("type", Integer),
    Column("parent_id", Integer, ForeignKey("tag.id")),
    Column("name", TrimmedString(255)),
    UniqueConstraint("name"),
)

ToolTagAssociation_table = Table(
    "tool_tag_association",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("user_tname", TrimmedString(255), index=True),
    Column("value", TrimmedString(255), index=True),
    Column("user_value", TrimmedString(255), index=True),
)

ToolAnnotationAssociation_table = Table(
    "tool_annotation_association",
    metadata,
    Column("id", Integer, primary_key=True),
    Column("tool_id", Integer, ForeignKey("tool.id"), index=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("annotation", TEXT),
)


[docs]def upgrade(migrate_engine):
    print(__doc__)
    metadata.bind = migrate_engine
    metadata.create_all()
    Index(
        "ix_tool_annotation_association_annotation", ToolAnnotationAssociation_table.c.annotation, mysql_length=767
    ).create()


[docs]def downgrade(migrate_engine):
    # Operations to reverse the above upgrade go here.
    pass