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Source code for galaxy.webapps.tool_shed.model.mapping
"""
Details of how the data model objects are mapped onto the relational database
are encapsulated here.
"""
import logging
from sqlalchemy import Boolean, Column, DateTime, desc, false, ForeignKey, Integer, MetaData, not_, String, Table, TEXT, true, UniqueConstraint
from sqlalchemy.orm import backref, mapper, relation
import galaxy.webapps.tool_shed.model
import galaxy.webapps.tool_shed.util.hgweb_config
import galaxy.webapps.tool_shed.util.shed_statistics as shed_statistics
from galaxy.model.base import ModelMapping
from galaxy.model.custom_types import JSONType, TrimmedString
from galaxy.model.orm.engine_factory import build_engine
from galaxy.model.orm.now import now
from galaxy.webapps.tool_shed.model import APIKeys, Category, Component, ComponentReview
from galaxy.webapps.tool_shed.model import GalaxySession, Group, GroupRoleAssociation
from galaxy.webapps.tool_shed.model import PasswordResetToken, Repository, RepositoryCategoryAssociation
from galaxy.webapps.tool_shed.model import RepositoryMetadata, RepositoryRatingAssociation
from galaxy.webapps.tool_shed.model import RepositoryReview, RepositoryRoleAssociation, Role
from galaxy.webapps.tool_shed.model import Tag, User, UserGroupAssociation, UserRoleAssociation
from galaxy.webapps.tool_shed.security import CommunityRBACAgent
log = logging.getLogger(__name__)
metadata = MetaData()
APIKeys.table = Table("api_keys", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("key", TrimmedString(32), index=True, unique=True))
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("new_repo_alert", Boolean, default=False),
Column("deleted", Boolean, index=True, default=False),
Column("purged", Boolean, index=True, default=False))
PasswordResetToken.table = Table("password_reset_token", metadata,
Column("token", String(32), primary_key=True, unique=True, index=True),
Column("expiration_time", DateTime),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True))
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))
RepositoryRoleAssociation.table = Table("repository_role_association", metadata,
Column("id", Integer, primary_key=True),
Column("repository_id", Integer, ForeignKey("repository.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
Column("last_action", DateTime))
Repository.table = Table("repository", 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),
Column("type", TrimmedString(255), index=True),
Column("remote_repository_url", TrimmedString(255)),
Column("homepage_url", TrimmedString(255)),
Column("description", TEXT),
Column("long_description", TEXT),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("private", Boolean, default=False),
Column("deleted", Boolean, index=True, default=False),
Column("email_alerts", JSONType, nullable=True),
Column("times_downloaded", Integer),
Column("deprecated", Boolean, default=False))
RepositoryMetadata.table = Table("repository_metadata", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, default=now, onupdate=now),
Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
Column("changeset_revision", TrimmedString(255), index=True),
Column("numeric_revision", Integer, index=True),
Column("metadata", JSONType, nullable=True),
Column("tool_versions", JSONType, nullable=True),
Column("malicious", Boolean, default=False),
Column("downloadable", Boolean, default=True),
Column("missing_test_components", Boolean, default=False, index=True),
Column("has_repository_dependencies", Boolean, default=False, index=True),
Column("includes_datatypes", Boolean, default=False, index=True),
Column("includes_tools", Boolean, default=False, index=True),
Column("includes_tool_dependencies", Boolean, default=False, index=True),
Column("includes_workflows", Boolean, default=False, index=True))
RepositoryReview.table = Table("repository_review", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, default=now, onupdate=now),
Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
Column("changeset_revision", TrimmedString(255), index=True),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
Column("approved", TrimmedString(255)),
Column("rating", Integer, index=True),
Column("deleted", Boolean, index=True, default=False))
ComponentReview.table = Table("component_review", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, default=now, onupdate=now),
Column("repository_review_id", Integer, ForeignKey("repository_review.id"), index=True),
Column("component_id", Integer, ForeignKey("component.id"), index=True),
Column("comment", TEXT),
Column("private", Boolean, default=False),
Column("approved", TrimmedString(255)),
Column("rating", Integer),
Column("deleted", Boolean, index=True, default=False))
Component.table = Table("component", metadata,
Column("id", Integer, primary_key=True),
Column("name", TrimmedString(255)),
Column("description", TEXT))
RepositoryRatingAssociation.table = Table("repository_rating_association", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, default=now, onupdate=now),
Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("rating", Integer, index=True),
Column("comment", TEXT))
RepositoryCategoryAssociation.table = Table("repository_category_association", metadata,
Column("id", Integer, primary_key=True),
Column("repository_id", Integer, ForeignKey("repository.id"), index=True),
Column("category_id", Integer, ForeignKey("category.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))
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"))
# With the tables defined we can define the mappers and setup the relationships between the model objects.
mapper(User, User.table,
properties=dict(active_repositories=relation(Repository, primaryjoin=((Repository.table.c.user_id == User.table.c.id) & (not_(Repository.table.c.deleted))), order_by=(Repository.table.c.name)),
galaxy_sessions=relation(GalaxySession, order_by=desc(GalaxySession.table.c.update_time)),
api_keys=relation(APIKeys, backref="user", order_by=desc(APIKeys.table.c.create_time))))
mapper(PasswordResetToken, PasswordResetToken.table,
properties=dict(user=relation(User, backref="reset_tokens")))
mapper(APIKeys, APIKeys.table, properties={})
mapper(Group, Group.table,
properties=dict(users=relation(UserGroupAssociation)))
mapper(Role, Role.table,
properties=dict(
repositories=relation(RepositoryRoleAssociation,
primaryjoin=((Role.table.c.id == RepositoryRoleAssociation.table.c.role_id) & (RepositoryRoleAssociation.table.c.repository_id == Repository.table.c.id))),
users=relation(UserRoleAssociation,
primaryjoin=((Role.table.c.id == UserRoleAssociation.table.c.role_id) & (UserRoleAssociation.table.c.user_id == User.table.c.id))),
groups=relation(GroupRoleAssociation,
primaryjoin=((Role.table.c.id == GroupRoleAssociation.table.c.role_id) & (GroupRoleAssociation.table.c.group_id == Group.table.c.id)))))
mapper(RepositoryRoleAssociation, RepositoryRoleAssociation.table,
properties=dict(
repository=relation(Repository),
role=relation(Role)))
mapper(UserGroupAssociation, UserGroupAssociation.table,
properties=dict(user=relation(User, backref="groups"),
group=relation(Group, backref="members")))
mapper(UserRoleAssociation, UserRoleAssociation.table,
properties=dict(
user=relation(User, backref="roles"),
non_private_roles=relation(User,
backref="non_private_roles",
primaryjoin=((User.table.c.id == UserRoleAssociation.table.c.user_id) & (UserRoleAssociation.table.c.role_id == Role.table.c.id) & not_(Role.table.c.name == User.table.c.email))),
role=relation(Role)))
mapper(GroupRoleAssociation, GroupRoleAssociation.table,
properties=dict(
group=relation(Group, backref="roles"),
role=relation(Role)))
mapper(GalaxySession, GalaxySession.table,
properties=dict(user=relation(User)))
mapper(Tag, Tag.table,
properties=dict(children=relation(Tag, backref=backref('parent', remote_side=[Tag.table.c.id]))))
mapper(Category, Category.table,
properties=dict(repositories=relation(RepositoryCategoryAssociation,
secondary=Repository.table,
primaryjoin=(Category.table.c.id == RepositoryCategoryAssociation.table.c.category_id),
secondaryjoin=(RepositoryCategoryAssociation.table.c.repository_id == Repository.table.c.id))))
mapper(Repository, Repository.table,
properties=dict(
categories=relation(RepositoryCategoryAssociation),
ratings=relation(RepositoryRatingAssociation, order_by=desc(RepositoryRatingAssociation.table.c.update_time), backref="repositories"),
user=relation(User),
downloadable_revisions=relation(RepositoryMetadata,
primaryjoin=((Repository.table.c.id == RepositoryMetadata.table.c.repository_id) & (RepositoryMetadata.table.c.downloadable == true())),
order_by=desc(RepositoryMetadata.table.c.update_time)),
metadata_revisions=relation(RepositoryMetadata,
order_by=desc(RepositoryMetadata.table.c.update_time)),
roles=relation(RepositoryRoleAssociation),
reviews=relation(RepositoryReview,
primaryjoin=((Repository.table.c.id == RepositoryReview.table.c.repository_id))),
reviewers=relation(User,
secondary=RepositoryReview.table,
primaryjoin=(Repository.table.c.id == RepositoryReview.table.c.repository_id),
secondaryjoin=(RepositoryReview.table.c.user_id == User.table.c.id))))
mapper(RepositoryMetadata, RepositoryMetadata.table,
properties=dict(repository=relation(Repository),
reviews=relation(RepositoryReview,
foreign_keys=[RepositoryMetadata.table.c.repository_id, RepositoryMetadata.table.c.changeset_revision],
primaryjoin=((RepositoryMetadata.table.c.repository_id == RepositoryReview.table.c.repository_id) & (RepositoryMetadata.table.c.changeset_revision == RepositoryReview.table.c.changeset_revision)))))
mapper(RepositoryReview, RepositoryReview.table,
properties=dict(repository=relation(Repository,
primaryjoin=(RepositoryReview.table.c.repository_id == Repository.table.c.id)),
# Take care when using the mapper below! It should be used only when a new review is being created for a repository change set revision.
# Keep in mind that repository_metadata records can be removed from the database for certain change set revisions when metadata is being
# reset on a repository!
repository_metadata=relation(RepositoryMetadata,
foreign_keys=[RepositoryReview.table.c.repository_id, RepositoryReview.table.c.changeset_revision],
primaryjoin=((RepositoryReview.table.c.repository_id == RepositoryMetadata.table.c.repository_id) & (RepositoryReview.table.c.changeset_revision == RepositoryMetadata.table.c.changeset_revision)),
backref='review'),
user=relation(User, backref="repository_reviews"),
component_reviews=relation(ComponentReview,
primaryjoin=((RepositoryReview.table.c.id == ComponentReview.table.c.repository_review_id) & (ComponentReview.table.c.deleted == false()))),
private_component_reviews=relation(ComponentReview,
primaryjoin=((RepositoryReview.table.c.id == ComponentReview.table.c.repository_review_id) & (ComponentReview.table.c.deleted == false()) & (ComponentReview.table.c.private == true())))))
mapper(ComponentReview, ComponentReview.table,
properties=dict(repository_review=relation(RepositoryReview),
component=relation(Component,
primaryjoin=(ComponentReview.table.c.component_id == Component.table.c.id))))
mapper(Component, Component.table)
mapper(RepositoryRatingAssociation, RepositoryRatingAssociation.table,
properties=dict(repository=relation(Repository), user=relation(User)))
mapper(RepositoryCategoryAssociation, RepositoryCategoryAssociation.table,
properties=dict(
category=relation(Category),
repository=relation(Repository)))
[docs]def init(file_path, url, engine_options={}, create_tables=False):
"""Connect mappings to the database"""
# Create the database engine
engine = build_engine(url, engine_options)
# Connect the metadata to the database.
metadata.bind = engine
result = ModelMapping([galaxy.webapps.tool_shed.model], engine=engine)
if create_tables:
metadata.create_all()
result.create_tables = create_tables
# Load local tool shed security policy
result.security_agent = CommunityRBACAgent(result)
result.shed_counter = shed_statistics.ShedCounter(result)
result.hgweb_config_manager = galaxy.webapps.tool_shed.util.hgweb_config.HgWebConfigManager()
return result