Source code for galaxy.model.migrate.versions.0001_initial_tables

from __future__ import print_function

import datetime
import logging

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

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

log = logging.getLogger(__name__)
now = datetime.datetime.utcnow
metadata = MetaData()

# Tables as of changeset 1464:c7acaa1bb88f
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("password", TrimmedString(40), nullable=False),
    Column("external", Boolean, default=False))

History_table = Table("history", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, index=True, default=now, onupdate=now),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("name", TrimmedString(255)),
    Column("hid_counter", Integer, default=1),
    Column("deleted", Boolean, index=True, default=False),
    Column("purged", Boolean, index=True, default=False),
    Column("genome_build", TrimmedString(40)))

HistoryDatasetAssociation_table = Table("history_dataset_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("history_id", Integer, ForeignKey("history.id"), index=True),
    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("copied_from_history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), nullable=True),
    Column("hid", Integer),
    Column("name", TrimmedString(255)),
    Column("info", TrimmedString(255)),
    Column("blurb", TrimmedString(255)),
    Column("peek", TEXT),
    Column("extension", TrimmedString(64)),
    Column("metadata", MetadataType(), key="_metadata"),
    Column("parent_id", Integer, ForeignKey("history_dataset_association.id"), nullable=True),
    Column("designation", TrimmedString(255)),
    Column("deleted", Boolean, index=True, default=False),
    Column("visible", Boolean))

Dataset_table = Table("dataset", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, index=True, default=now, onupdate=now),
    Column("state", TrimmedString(64)),
    Column("deleted", Boolean, index=True, default=False),
    Column("purged", Boolean, index=True, default=False),
    Column("purgable", Boolean, default=True),
    Column("external_filename", TEXT),
    Column("_extra_files_path", TEXT),
    Column('file_size', Numeric(15, 0)))

ImplicitlyConvertedDatasetAssociation_table = Table("implicitly_converted_dataset_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("hda_id", Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True),
    Column("hda_parent_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
    Column("deleted", Boolean, index=True, default=False),
    Column("metadata_safe", Boolean, index=True, default=True),
    Column("type", TrimmedString(255)))

ValidationError_table = Table("validation_error", metadata,
    Column("id", Integer, primary_key=True),
    Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
    Column("message", TrimmedString(255)),
    Column("err_type", TrimmedString(64)),
    Column("attributes", TEXT))

Job_table = Table("job", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("history_id", Integer, ForeignKey("history.id"), index=True),
    Column("tool_id", String(255)),
    Column("tool_version", TEXT, default="1.0.0"),
    Column("state", String(64)),
    Column("info", TrimmedString(255)),
    Column("command_line", TEXT),
    Column("param_filename", String(1024)),
    Column("runner_name", String(255)),
    Column("stdout", TEXT),
    Column("stderr", TEXT),
    Column("traceback", TEXT),
    Column("session_id", Integer, ForeignKey("galaxy_session.id"), index=True, nullable=True),
    Column("job_runner_name", String(255)),
    Column("job_runner_external_id", String(255)))

JobParameter_table = Table("job_parameter", metadata,
    Column("id", Integer, primary_key=True),
    Column("job_id", Integer, ForeignKey("job.id"), index=True),
    Column("name", String(255)),
    Column("value", TEXT))

JobToInputDatasetAssociation_table = Table("job_to_input_dataset", metadata,
    Column("id", Integer, primary_key=True),
    Column("job_id", Integer, ForeignKey("job.id"), index=True),
    Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
    Column("name", String(255)))

JobToOutputDatasetAssociation_table = Table("job_to_output_dataset", metadata,
    Column("id", Integer, primary_key=True),
    Column("job_id", Integer, ForeignKey("job.id"), index=True),
    Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
    Column("name", String(255)))

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("history_id", Integer, ForeignKey("history.id"), index=True, nullable=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=True),
    Column("message", TrimmedString(1024)),
    Column("session_id", Integer, ForeignKey("galaxy_session.id"), index=True, nullable=True),
    Column("tool_id", String(255)))

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("current_history_id", Integer, ForeignKey("history.id"), nullable=True),
    Column("session_key", TrimmedString(255), index=True, unique=True),
    Column("is_valid", Boolean, default=False),
    Column("prev_session_id", Integer))

GalaxySessionToHistoryAssociation_table = Table("galaxy_session_to_history", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("session_id", Integer, ForeignKey("galaxy_session.id"), index=True),
    Column("history_id", Integer, ForeignKey("history.id"), index=True))

StoredWorkflow_table = Table("stored_workflow", 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=False),
    Column("latest_workflow_id", Integer,
           ForeignKey("workflow.id", use_alter=True, name='stored_workflow_latest_workflow_id_fk'), index=True),
    Column("name", TEXT),
    Column("deleted", Boolean, default=False))

Workflow_table = Table("workflow", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("stored_workflow_id", Integer, ForeignKey("stored_workflow.id"), index=True, nullable=False),
    Column("name", TEXT),
    Column("has_cycles", Boolean),
    Column("has_errors", Boolean))

WorkflowStep_table = Table("workflow_step", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("workflow_id", Integer, ForeignKey("workflow.id"), index=True, nullable=False),
    Column("type", String(64)),
    Column("tool_id", TEXT),
    Column("tool_version", TEXT),
    Column("tool_inputs", JSONType),
    Column("tool_errors", JSONType),
    Column("position", JSONType),
    Column("config", JSONType),
    Column("order_index", Integer))

WorkflowStepConnection_table = Table("workflow_step_connection", metadata,
    Column("id", Integer, primary_key=True),
    Column("output_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
    Column("input_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
    Column("output_name", TEXT),
    Column("input_name", TEXT))

StoredWorkflowUserShareAssociation_table = Table("stored_workflow_user_share_connection", metadata,
    Column("id", Integer, primary_key=True),
    Column("stored_workflow_id", Integer, ForeignKey("stored_workflow.id"), index=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True))

StoredWorkflowMenuEntry_table = Table("stored_workflow_menu_entry", metadata,
    Column("id", Integer, primary_key=True),
    Column("stored_workflow_id", Integer, ForeignKey("stored_workflow.id"), index=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("order_index", Integer))


[docs]def upgrade(migrate_engine):
    print(__doc__)
    metadata.bind = migrate_engine
    metadata.create_all()