def upgrade():
if op.get_context().dialect.name == 'postgresql':
# INFO - G.M - 2018-11-27 - TO modify type in postgresq, we should
# create a new one set column type to this new one and remove old one
op.execute("ALTER TYPE authtype RENAME TO authtype_old;")
op.execute("ALTER TABLE users alter auth_type drop default;")
enum = sa.Enum(*new_auth_type_list, name='authtype')
enum.create(op.get_bind(), checkfirst=False)
with op.batch_alter_table('users') as batch_op:
batch_op.alter_column(
'auth_type',
type_=enum,
postgresql_using="auth_type::text::authtype",
server_default='INTERNAL'
)
op.execute("DROP TYPE authtype_old;")
else:
# INFO - G.M - 2018-11-27 - MYSQL case
enum = sa.Enum(*new_auth_type_list, name='authtype')
enum.create(op.get_bind(), checkfirst=False)
with op.batch_alter_table('users') as batch_op:
batch_op.alter_column(
'auth_type',
type_=enum,
)
def downgrade():
bind = op.get_bind()
insp = sa.engine.reflection.Inspector.from_engine(bind)
# Restore the size of the metric_name column.
with op.batch_alter_table('metrics', naming_convention=conv) as batch_op:
batch_op.alter_column(
'metric_name',
existing_type=sa.String(length=255),
type_=sa.String(length=512),
existing_nullable=True,
)
# Remove the previous missing uniqueness constraints.
for table, column in names.items():
with op.batch_alter_table(table, naming_convention=conv) as batch_op:
batch_op.drop_constraint(
generic_find_uq_constraint_name(
table,
{column, 'datasource_id'},
insp,
) or 'uq_{}_{}'.format(table, column),
type_='unique',
)
def downgrade():
with op.batch_alter_table('lti_user', naming_convention=convention) as batch_op:
batch_op.drop_column('lis_person_sourcedid')
with op.batch_alter_table('lti_context', naming_convention=convention) as batch_op:
batch_op.drop_column('lis_course_section_sourcedid')
batch_op.drop_column('lis_course_offering_sourcedid')
def downgrade():
### commands auto generated by Alembic - please adjust! ###
op.drop_table('ticket_transfer')
op.drop_table('ticket_checkin')
op.drop_table('ticket_attrib')
with op.batch_alter_table('ticket', schema=None) as batch_op:
batch_op.drop_index(batch_op.f('ix_ticket_type_id'))
batch_op.drop_index(batch_op.f('ix_ticket_paid'))
op.drop_table('ticket')
op.drop_table('payment_change')
op.drop_table('cfp_vote')
op.drop_table('cfp_message')
with op.batch_alter_table('bank_transaction', schema=None) as batch_op:
batch_op.drop_index('ix_bank_transaction_u1')
batch_op.drop_index(batch_op.f('ix_bank_transaction_fit_id'))
op.drop_table('bank_transaction')
with op.batch_alter_table('user_permission', schema=None) as batch_op:
batch_op.drop_index(batch_op.f('ix_user_permission_user_id'))
op.drop_table('user_permission')
with op.batch_alter_table('transaction', schema=None) as batch_op:
batch_op.drop_index(batch_op.f('ix_transaction_user_id'))
op.drop_table('transaction')
op.drop_table('ticket_price')
op.drop_table('proposal')
op.drop_table('payment')
op.drop_table('diversity')
with op.batch_alter_table('category_reviewers', schema=None) as batch_op:
batch_op.drop_index(batch_op.f('ix_category_reviewers_user_id'))
op.drop_table('category_reviewers')
with op.batch_alter_table('user', schema=None) as batch_op:
batch_op.drop_index(batch_op.f('ix_user_name'))
batch_op.drop_index(batch_op.f('ix_user_email'))
op.drop_table('user')
op.drop_table('ticket_type')
with op.batch_alter_table('proposal_version', schema=None) as batch_op:
batch_op.drop_index(batch_op.f('ix_proposal_version_transaction_id'))
batch_op.drop_index(batch_op.f('ix_proposal_version_operation_type'))
op.drop_table('proposal_version')
with op.batch_alter_table('permission', schema=None) as batch_op:
batch_op.drop_index(batch_op.f('ix_permission_name'))
op.drop_table('permission')
op.drop_table('feature_flag')
with op.batch_alter_table('cfp_vote_version', schema=None) as batch_op:
batch_op.drop_index(batch_op.f('ix_cfp_vote_version_transaction_id'))
batch_op.drop_index(batch_op.f('ix_cfp_vote_version_operation_type'))
op.drop_table('cfp_vote_version')
op.drop_table('category')
with op.batch_alter_table('bank_account', schema=None) as batch_op:
batch_op.drop_index('ix_bank_account_sort_code_acct_id')
op.drop_table('bank_account')
def downgrade():
### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('scenario', schema=None) as batch_op:
batch_op.drop_column('root_node')
op.create_table('ESP',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('score', sa.INTEGER(), nullable=True),
sa.Column('data', sa.VARCHAR(length=300), nullable=True),
sa.Column('xpath', sa.VARCHAR(length=500), nullable=True),
sa.PrimaryKeyConstraint('id')
)
op.create_table('contains',
sa.Column('esp_id', sa.INTEGER(), nullable=True),
sa.Column('scenario_id', sa.INTEGER(), nullable=True),
sa.ForeignKeyConstraint(['esp_id'], ['ESP.id'], ),
sa.ForeignKeyConstraint(['scenario_id'], ['scenario.id'], )
)
op.drop_table('scenario_groups')
op.drop_table('group_fields')
op.drop_table('group')
with op.batch_alter_table('field', schema=None) as batch_op:
batch_op.drop_index(batch_op.f('ix_field_name'))
op.drop_table('field')
def downgrade():
"""alexm: i believe this method is never called"""
with op.batch_alter_table(t2_name) as batch_op:
batch_op.drop_column("do_not_use")
with op.batch_alter_table(t1_name) as batch_op:
batch_op.drop_column("enabled")
def upgrade():
with op.batch_alter_table('lti_context', naming_convention=convention) as batch_op:
batch_op.add_column(sa.Column('lis_course_offering_sourcedid', sa.String(length=255), nullable=True))
batch_op.add_column(sa.Column('lis_course_section_sourcedid', sa.String(length=255), nullable=True))
with op.batch_alter_table('lti_user', naming_convention=convention) as batch_op:
batch_op.add_column(sa.Column('lis_person_sourcedid', sa.String(length=255), nullable=True))
def upgrade():
with op.batch_alter_table("deployments", schema=None) as batch_op:
batch_op.add_column(
sa.Column("credentials", sa.PickleType(), nullable=True))
connection = op.get_bind()
for deployment in connection.execute(deployments_helper.select()):
creds = [
["openstack",
{
"admin": deployment.admin,
"users": deployment.users
}]
]
connection.execute(
deployments_helper.update().where(
deployments_helper.c.id == deployment.id).values(
credentials=creds))
with op.batch_alter_table("deployments", schema=None) as batch_op:
batch_op.alter_column("credentials",
existing_type=sa.PickleType,
existing_nullable=True,
nullable=False)
batch_op.drop_column("admin")
batch_op.drop_column("users")
def downgrade():
with op.batch_alter_table("commits") as batch_op:
batch_op.alter_column('project_name', existing_type=sa.String(256),
type_=sa.String())
batch_op.alter_column('repo_dir', existing_type=sa.String(1024),
type_=sa.String())
batch_op.alter_column('distgit_dir', existing_type=sa.String(1024),
type_=sa.String())
batch_op.alter_column('commit_hash', existing_type=sa.String(64),
type_=sa.String())
batch_op.alter_column('distro_hash', existing_type=sa.String(64),
type_=sa.String())
batch_op.alter_column('distgit_dir', existing_type=sa.String(1024),
type_=sa.String())
batch_op.alter_column('commit_branch', existing_type=sa.String(256),
type_=sa.String())
batch_op.alter_column('status', existing_type=sa.String(64),
type_=sa.String())
batch_op.alter_column('rpms', existing_type=sa.Text(),
type_=sa.String())
batch_op.alter_column('notes', existing_type=sa.Text(),
type_=sa.String())
with op.batch_alter_table("projects") as batch_op:
batch_op.alter_column('project_name', existing_type=sa.String(256),
type_=sa.String())
def upgrade():
### commands auto generated by Alembic - please adjust! ###
op.create_table(
"favourite_calendar_events",
sa.Column("user_id", sa.Integer(), nullable=True),
sa.Column("event_id", sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(
["event_id"], ["calendar_event.id"], name=op.f("fk_favourite_calendar_events_event_id_calendar_event")
),
sa.ForeignKeyConstraint(["user_id"], ["user.id"], name=op.f("fk_favourite_calendar_events_user_id_user")),
)
with op.batch_alter_table(u"calendar_event", schema=None) as batch_op:
batch_op.add_column(sa.Column("end_dt", sa.DateTime(), nullable=False))
batch_op.add_column(sa.Column("start_dt", sa.DateTime(), nullable=False))
batch_op.drop_column("end_tz")
batch_op.drop_column("start_tz")
batch_op.drop_column("start_utc")
batch_op.drop_column("end_local")
batch_op.drop_column("end_utc")
batch_op.drop_column("start_local")
with op.batch_alter_table(u"calendar_source", schema=None) as batch_op:
batch_op.add_column(sa.Column("priority", sa.Integer(), nullable=True))
batch_op.add_column(sa.Column("type", sa.String(), nullable=True))
with op.batch_alter_table(u"venue", schema=None) as batch_op:
batch_op.add_column(sa.Column("priority", sa.Integer(), nullable=True))
def downgrade():
with op.batch_alter_table("civotes") as batch_op:
batch_op.drop_constraint('civ_user_fk', type_='foreignkey')
with op.batch_alter_table("promotions") as batch_op:
batch_op.drop_constraint('prom_user_fk', type_='foreignkey')
with op.batch_alter_table("users") as batch_op:
batch_op.alter_column('username', existing_type=sa.String(255),
type_=sa.String(256))
with op.batch_alter_table("civotes") as batch_op:
batch_op.alter_column('user', existing_type=sa.String(255),
type_=sa.String(256))
batch_op.create_foreign_key(
constraint_name="civ_user_fk",
referent_table="users",
local_cols=["user"],
remote_cols=["username"])
with op.batch_alter_table("promotions") as batch_op:
batch_op.alter_column('user', existing_type=sa.String(255),
type_=sa.String(256))
batch_op.create_foreign_key(
constraint_name="prom_user_fk",
referent_table="users",
local_cols=["user"],
remote_cols=["username"])
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('user', schema=None) as batch_op:
batch_op.add_column(sa.Column('promo_opt_in', sa.Boolean(), nullable=False, server_default=expression.false()))
with op.batch_alter_table('user_version', schema=None) as batch_op:
batch_op.add_column(sa.Column('promo_opt_in', sa.Boolean(), autoincrement=False, nullable=True))
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('user_version', schema=None) as batch_op:
batch_op.drop_column('promo_opt_in')
with op.batch_alter_table('user', schema=None) as batch_op:
batch_op.drop_column('promo_opt_in')
def downgrade():
### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('task', schema=None) as batch_op:
batch_op.add_column(sa.Column('chunk_start', mysql.INTEGER(display_width=11), autoincrement=False, nullable=True))
batch_op.add_column(sa.Column('current_frame', mysql.INTEGER(display_width=11), autoincrement=False, nullable=True))
batch_op.add_column(sa.Column('chunk_end', mysql.INTEGER(display_width=11), autoincrement=False, nullable=True))
batch_op.drop_column('type')
batch_op.drop_column('settings')
batch_op.drop_column('name')
batch_op.drop_column('log')
batch_op.drop_column('activity')
with op.batch_alter_table('manager', schema=None) as batch_op:
batch_op.add_column(sa.Column('running_tasks', mysql.INTEGER(display_width=11), autoincrement=False, nullable=False))
batch_op.add_column(sa.Column('total_workers', mysql.INTEGER(display_width=11), autoincrement=False, nullable=True))
with op.batch_alter_table('job', schema=None) as batch_op:
batch_op.add_column(sa.Column('frame_start', mysql.INTEGER(display_width=11), autoincrement=False, nullable=True))
batch_op.add_column(sa.Column('current_frame', mysql.INTEGER(display_width=11), autoincrement=False, nullable=True))
batch_op.add_column(sa.Column('chunk_size', mysql.INTEGER(display_width=11), autoincrement=False, nullable=True))
batch_op.add_column(sa.Column('render_settings', mysql.VARCHAR(length=120), nullable=True))
batch_op.add_column(sa.Column('filepath', mysql.VARCHAR(length=256), nullable=True))
batch_op.add_column(sa.Column('frame_end', mysql.INTEGER(display_width=11), autoincrement=False, nullable=True))
batch_op.add_column(sa.Column('format', mysql.VARCHAR(length=10), nullable=True))
batch_op.drop_column('type')
batch_op.drop_column('settings')
def upgrade():
c = get_context()
# drop foreign keys for mysql
if isinstance(c.connection.engine.dialect, MySQLDialect):
insp = Inspector.from_engine(c.connection.engine)
for t in ['groups_resources_permissions', 'users_resources_permissions', 'resources']:
for constraint in insp.get_foreign_keys(t):
if constraint['referred_columns'] == ['resource_id']:
op.drop_constraint(constraint['name'], t, type='foreignkey')
with op.batch_alter_table('resources', schema=None) as batch_op:
batch_op.alter_column('resource_id',
type_=sa.Integer(), existing_type=sa.BigInteger(),
autoincrement=True)
with op.batch_alter_table('resources', schema=None) as batch_op:
batch_op.alter_column('parent_id',
type_=sa.Integer(), existing_type=sa.BigInteger())
with op.batch_alter_table('users_resources_permissions', schema=None) as batch_op:
batch_op.alter_column('resource_id',
type_=sa.Integer(), existing_type=sa.BigInteger())
batch_op.alter_column('resource_id',
type_=sa.Integer(), existing_type=sa.BigInteger())
# recreate foreign keys for mysql
if isinstance(c.connection.engine.dialect, MySQLDialect):
op.create_foreign_key("groups_resources_permissions_resource_fk",
'groups_resources_permissions',
"resources", ["resource_id"], ["resource_id"],
onupdate='CASCADE', ondelete='CASCADE')
op.create_foreign_key("users_resources_permissions_fk",
'users_resources_permissions',
"resources", ["resource_id"], ["resource_id"],
onupdate='CASCADE', ondelete='CASCADE')
def downgrade():
with op.batch_alter_table("deployments", schema=None) as batch_op:
batch_op.add_column(
sa.Column("users", sa.PickleType(),
nullable=True))
batch_op.add_column(
sa.Column("admin", sa.PickleType(), nullable=True))
connection = op.get_bind()
for deployment in connection.execute(deployments_helper.select()):
admin = None
users = []
for credentials in deployment.credentials:
if credentials[0] == "openstack":
admin = credentials[1].get("admin")
users = credentials[1].get("users", [])
connection.execute(
deployments_helper.update().where(
deployments_helper.c.id == deployment.id).values(
admin=admin, users=users))
with op.batch_alter_table("deployments", schema=None) as batch_op:
batch_op.alter_column("users",
existing_type=sa.PickleType,
existing_nullable=True,
nullable=False)
batch_op.drop_column("credentials")
def downgrade():
# insert selfevaltype_id column into Questions table
op.add_column(u'Questions', sa.Column('selfevaltype_id', sa.Integer(), nullable=True))
# populate the column - only populate the no comparison self evaluation type
type = text(
"SELECT id FROM SelfEvalTypes " +
"WHERE name='No Comparison with Another Answer'"
)
conn = op.get_bind()
res = conn.execute(type)
selfevaltype = res.fetchall()
populate = text(
"UPDATE Questions " +
"SET selfevaltype_id = "
"(SELECT qs.selfevaltypes_id " +
"FROM QuestionsAndSelfEvalTypes qs "
"WHERE Questions.id = qs.questions_id " +
"AND qs.selfevaltypes_id = " + str(selfevaltype[0][0]) + ')'
)
op.get_bind().execute(populate)
with op.batch_alter_table('Questions', naming_convention=convention) as batch_op:
batch_op.create_foreign_key('fk_Questions_selfevaltype_id_SelfEvalTypes', 'SelfEvalTypes',
['selfevaltype_id'], ['id'], ondelete="CASCADE")
with op.batch_alter_table('PostsForJudgements', naming_convention=convention) as batch_op:
batch_op.drop_column('selfeval')
op.drop_table('QuestionsAndSelfEvalTypes')
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table("message") as batch_op:
batch_op.alter_column("workflow_execution_uid", new_column_name="workflow_execution_id", type=UUIDType)
with op.batch_alter_table("scheduled_workflow") as batch_op:
batch_op.alter_column("uid", new_column_name="workflow_id", type=UUIDType, nullable=False)
def upgrade():
try:
with op.batch_alter_table(
"Criteria", naming_convention=convention, table_args=(UniqueConstraint("name"))
) as batch_op:
batch_op.drop_constraint("uq_Criteria_name", type_="unique")
except exc.InternalError:
with op.batch_alter_table(
"Criteria", naming_convention=convention, table_args=(UniqueConstraint("name"))
) as batch_op:
batch_op.drop_constraint("name", type_="unique")
except ValueError:
logging.warning("Drop unique constraint is not support for SQLite, dropping uq_Critiera_name ignored!")
# set existing criteria's active attribute to True using server_default
op.add_column(
"CriteriaAndCourses",
sa.Column("active", sa.Boolean(name="active"), default=True, server_default="1", nullable=False),
)
op.add_column(
"Criteria", sa.Column("public", sa.Boolean(name="public"), default=False, server_default="0", nullable=False)
)
# set the first criteria as public
t = {"name": "Which is better?", "public": True}
op.get_bind().execute(text("Update Criteria set public=:public where name=:name"), **t)
def downgrade():
op.drop_table('ensemble_data_file_variables')
op.drop_table('data_file_variables_qc_flags')
op.drop_table('data_file_variables')
with op.batch_alter_table('data_files', schema=None) as batch_op:
batch_op.drop_index('data_files_run_id_key')
op.drop_table('data_files')
with op.batch_alter_table('y_cell_bounds', schema=None) as batch_op:
batch_op.drop_index('y_c_b_grid_id_key')
op.drop_table('y_cell_bounds')
op.drop_table('variables')
with op.batch_alter_table('times', schema=None) as batch_op:
batch_op.drop_index('time_set_id_key')
op.drop_table('times')
with op.batch_alter_table('runs', schema=None) as batch_op:
batch_op.drop_index('runs_model_id_key')
batch_op.drop_index('runs_emission_id_key')
op.drop_table('runs')
op.drop_table('levels')
with op.batch_alter_table('climatological_times', schema=None) as batch_op:
batch_op.drop_index('climatological_times_time_set_id_key')
op.drop_table('climatological_times')
op.drop_table('variable_aliases')
op.drop_table('time_sets')
op.drop_table('qc_flags')
op.drop_table('models')
op.drop_table('level_sets')
op.drop_table('grids')
op.drop_table('ensembles')
op.drop_table('emissions')
def upgrade():
op.create_table(
'SelfEvalTypes',
sa.Column('id', sa.Integer(), nullable=True),
sa.Column('name', sa.String(length=255), nullable=False),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('name'),
mysql_charset='utf8',
mysql_collate='utf8_unicode_ci',
mysql_engine='InnoDB'
)
# populate table with a self evaluation type
insert = text(
"INSERT INTO SelfEvalTypes (name) " +
"VALUES ('No Comparison with Another Answer')"
)
op.get_bind().execute(insert)
with op.batch_alter_table('Questions', naming_convention=convention) as batch_op:
batch_op.add_column(sa.Column('selfevaltype_id', sa.Integer(), nullable=True))
with op.batch_alter_table('Questions', naming_convention=convention) as batch_op:
batch_op.create_foreign_key(
'fk_Questions_selfevaltype_id_SelfEvalTypes', 'SelfEvalTypes',
['selfevaltype_id'], ['id'], ondelete="CASCADE")
def upgrade():
### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('job', schema=None) as batch_op:
batch_op.add_column(sa.Column('settings', sa.Text(), nullable=True))
batch_op.add_column(sa.Column('type', sa.String(length=64), nullable=True))
batch_op.drop_column('format')
batch_op.drop_column('frame_end')
batch_op.drop_column('filepath')
batch_op.drop_column('render_settings')
batch_op.drop_column('chunk_size')
batch_op.drop_column('current_frame')
batch_op.drop_column('frame_start')
with op.batch_alter_table('manager', schema=None) as batch_op:
batch_op.drop_column('total_workers')
batch_op.drop_column('running_tasks')
with op.batch_alter_table('task', schema=None) as batch_op:
batch_op.add_column(sa.Column('activity', sa.String(length=128), nullable=True))
batch_op.add_column(sa.Column('log', sa.Text(), nullable=True))
batch_op.add_column(sa.Column('name', sa.String(length=64), nullable=True))
batch_op.add_column(sa.Column('settings', sa.Text(), nullable=True))
batch_op.add_column(sa.Column('type', sa.String(length=64), nullable=True))
batch_op.drop_column('chunk_end')
batch_op.drop_column('current_frame')
batch_op.drop_column('chunk_start')
def downgrade():
with op.batch_alter_table("register") as batch_op:
batch_op.create_unique_constraint(None, ['registration_no'])
with op.batch_alter_table("register_details") as batch_op:
batch_op.drop_column('amends')
batch_op.drop_column('cancelled_on')
def upgrade():
role_focus_user = op.create_table('role_focus_user',
sa.Column('role_focus_user_id', sa.Integer(), nullable=False),
sa.Column('role_focus_id', sa.Integer(), nullable=False),
sa.Column('user_id', sa.Integer(), nullable=True),
sa.Column('start_date', sa.DateTime(), nullable=True),
sa.Column('end_date', sa.DateTime(), nullable=True),
sa.ForeignKeyConstraint(['role_focus_id'], ['role_focus.role_focus_id'], name='fk_user_focus'),
sa.PrimaryKeyConstraint('role_focus_user_id')
)
with op.batch_alter_table('role', schema=None) as batch_op:
batch_op.add_column(sa.Column('duration', sa.Integer(), nullable=True))
batch_op.add_column(sa.Column('role_type', sa.Enum('leadlink', 'elected', 'assigned'), nullable=True))
for focus in connection.execute(focus_helper.select()):
op.bulk_insert(
role_focus_user,
[
{
'role_focus_user_id': focus.role_focus_id,
'role_focus_id': focus.role_focus_id,
'user_id' : focus.user_id,
},
]
)
with op.batch_alter_table('role_focus', schema=None) as batch_op:
batch_op.drop_column('user_id')
def downgrade():
### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('task', schema=None) as batch_op:
batch_op.alter_column('uuid',
existing_type=sa.String(length=256),
type_=sa.VARCHAR(),
existing_nullable=True)
batch_op.alter_column('user',
existing_type=sa.String(length=256),
type_=sa.VARCHAR(),
existing_nullable=True)
batch_op.alter_column('task',
existing_type=sa.String(length=256),
type_=sa.VARCHAR(),
existing_nullable=True)
with op.batch_alter_table('session', schema=None) as batch_op:
batch_op.alter_column('uuid',
existing_type=sa.String(length=256),
type_=sa.VARCHAR(),
existing_nullable=True)
batch_op.alter_column('user',
existing_type=sa.String(length=256),
type_=sa.VARCHAR(),
existing_nullable=True)
batch_op.alter_column('ua',
existing_type=sa.String(length=2048),
type_=sa.VARCHAR(),
existing_nullable=True)
batch_op.alter_column('ip',
existing_type=sa.String(length=256),
type_=sa.VARCHAR(),
existing_nullable=True)
def upgrade():
for table, _, col in TABLES_FKS:
inspector = reflection.Inspector.from_engine(op.get_bind())
fk_name = [fk['name'] for fk in
inspector.get_foreign_keys(table)
if col in fk['constrained_columns']]
try:
op.drop_constraint(fk_name[0], table, 'foreignkey')
except (NotImplementedError, IndexError):
pass
with op.batch_alter_table(table) as batch_op:
batch_op.alter_column(col, existing_type=sa.Integer,
type_=sa.String(255),
existing_nullable=False,
nullable=False)
for table in TABLES:
with op.batch_alter_table(table) as batch_op:
batch_op.alter_column("aim_id", existing_type=sa.Integer,
type_=sa.String(255),
existing_nullable=False,
nullable=False)
with op.batch_alter_table("aim_statuses") as batch_op:
batch_op.alter_column("resource_id", existing_type=sa.Integer,
type_=sa.String(255),
existing_nullable=False,
nullable=False)
for table, other, col in TABLES_FKS:
with op.batch_alter_table(table) as batch_op:
batch_op.create_foreign_key('fk_' + table + '_' + col,
other, [col], ['aim_id'])
def downgrade():
# revert table Judgements
op.add_column("Judgements", sa.Column('criteriaandcourses_id', sa.Integer(), nullable=True))
# populate column with the judgements' criteriaandcourses_id
update = text(
# rewrite into subquery to support SQLite. need more testing to verify
"UPDATE Judgements "
"SET criteriaandcourses_id = "
"(SELECT cc.id FROM CriteriaAndCourses cc "
"JOIN CriteriaAndQuestions cq ON cq.criteria_id = cc.criteria_id "
"JOIN Questions q ON cq.questions_id = q.id "
"JOIN Posts p ON q.posts_id = p.id "
"WHERE Judgements.criteriaandquestions_id = cq.id AND p.courses_id = cc.courses_id)"
# "UPDATE Judgements j " + \
# "JOIN CriteriaAndQuestions cq ON j.criteriaandquestions_id = cq.id " + \
# "JOIN Questions q ON cq.questions_id = q.id " + \
# "JOIN Posts p ON q.posts_id = p.id " + \
# "JOIN CriteriaAndCourses cc ON cq.criteria_id = cc.criteria_id AND p.courses_id = cc.courses_id " + \
# "SET j.criteriaandcourses_id = cc.id"
)
op.get_bind().execute(update)
with op.batch_alter_table('Judgements', naming_convention=convention) as batch_op:
batch_op.create_foreign_key('fk_Judgements_criteriaandcourses_id_CriteriaAndCourses', 'CriteriaAndCourses',
['criteriaandcourses_id'], ['id'], ondelete="CASCADE")
batch_op.alter_column('criteriaandcourses_id', nullable=False, existing_type=sa.Integer())
batch_op.drop_constraint('fk_Judgements_criteriaandquestions_id_CriteriaAndQuestions',
'foreignkey')
# batch_op.drop_index("criteriaandquestions_id")
batch_op.drop_column("criteriaandquestions_id")
# revert table Scores
op.add_column('Scores', sa.Column('criteriaandcourses_id', sa.Integer(), nullable=True))
# populate column with the scores' criteriaandcourses_id
update = text(
# rewrite into subquery to support SQLite. need more testing to verify
"UPDATE Scores "
"SET criteriaandcourses_id = "
"(SELECT cc.id FROM CriteriaAndCourses cc "
"JOIN CriteriaAndQuestions cq ON cq.criteria_id = cc.criteria_id "
"JOIN Questions q ON cq.questions_id = q.id "
"JOIN Posts p ON q.posts_id = p.id "
"WHERE Scores.criteriaandquestions_id = cq.id AND p.courses_id = cc.courses_id)"
# "UPDATE Scores s " + \
# "JOIN CriteriaAndQuestions cq ON s.criteriaandquestions_id = cq.id " + \
# "JOIN Questions q ON cq.questions_id = q.id " + \
# "JOIN Posts p ON q.posts_id = p.id " + \
# "JOIN CriteriaAndCourses cc ON cq.criteria_id = cc.criteria_id AND p.courses_id = cc.courses_id " + \
# "SET s.criteriaandcourses_id = cc.id"
)
op.get_bind().execute(update)
with op.batch_alter_table('Scores', naming_convention=convention) as batch_op:
batch_op.create_foreign_key('fk_Scores_criteriaandcourses_id_CriteriaAndCourses', 'CriteriaAndCourses',
['criteriaandcourses_id'], ['id'], ondelete="CASCADE")
batch_op.alter_column('criteriaandcourses_id', nullable=False, existing_type=sa.Integer())
batch_op.drop_constraint('fk_Scores_criteriaandquestions_id_CriteriaAndQuestions', 'foreignkey')
# batch_op.drop_index('criteriaandquestions_id')
batch_op.drop_column('criteriaandquestions_id')
# drop table CriteriaAndQuestions
op.drop_table('CriteriaAndQuestions')
def downgrade():
with op.batch_alter_table('Criteria', naming_convention=convention,
table_args=(UniqueConstraint('name'))) as batch_op:
batch_op.create_unique_constraint('uq_Criteria_name', ['name'])
batch_op.drop_column('public')
with op.batch_alter_table('CriteriaAndCourses', naming_convention=convention) as batch_op:
batch_op.drop_column('active')
def downgrade():
with op.batch_alter_table('submissions', schema=None) as batch_op:
batch_op.drop_column('archived')
with op.batch_alter_table('comments', schema=None) as batch_op:
batch_op.alter_column(
'author', existing_type=sa.VARCHAR(), nullable=False)
def upgrade():
table_prefix = context.config.get_main_option('table_prefix')
op.drop_table(table_prefix + 'template')
table_name = table_prefix + 'environment_schema_values'
with op.batch_alter_table(table_name) as batch:
batch.drop_constraint(table_name + '_schema_id_fkey', 'foreignkey')
batch.alter_column(
'schema_id',
new_column_name='resource_definition_id',
existing_type=sa.Integer(),
)
op.rename_table(table_name, table_prefix + 'resource_values')
op.rename_table(table_prefix + 'schema',
table_prefix + 'resource_definition')
with op.batch_alter_table(table_prefix + 'resource_definition') as batch:
batch.drop_column('namespace_id')
op.drop_table(table_prefix + 'namespace')
table_name = table_prefix + 'resource_values'
with op.batch_alter_table(table_name) as batch:
batch.create_foreign_key(
table_name + '_resource_definition_id_fkey',
table_prefix + 'resource_definition',
['resource_definition_id'],
['id'],
)
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.create_table(
'user', sa.Column('id', sa.Integer(), nullable=False),
sa.Column('username', sa.String(length=200), nullable=True),
sa.Column('email', sa.String(length=200), nullable=True),
sa.Column('password_hash', sa.String(length=150), nullable=True),
sa.Column('about_me', sa.String(length=300), nullable=True),
sa.Column('nickname', sa.String(length=150), nullable=True),
sa.Column('last_seen', sa.DateTime(), nullable=True),
sa.PrimaryKeyConstraint('id', name=op.f('pk_user')))
with op.batch_alter_table('user', schema=None) as batch_op:
batch_op.create_index(batch_op.f('ix_user_email'), ['email'],
unique=True)
batch_op.create_index(batch_op.f('ix_user_username'), ['username'],
unique=True)
op.create_table(
'followers', sa.Column('follower_id', sa.Integer(), nullable=True),
sa.Column('followed_id', sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(['followed_id'], ['user.id'],
name=op.f('fk_followers_followed_id_user')),
sa.ForeignKeyConstraint(['follower_id'], ['user.id'],
name=op.f('fk_followers_follower_id_user')))
op.create_table(
'post', sa.Column('id', sa.Integer(), nullable=False),
sa.Column('title', sa.String(length=200), nullable=True),
sa.Column('sphere', sa.String(length=200), nullable=True),
sa.Column('description', sa.String(length=800), nullable=True),
sa.Column('officialLink', sa.String(length=300), nullable=True),
sa.Column('timestamp', sa.DateTime(), nullable=True),
sa.Column('user_id', sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(['user_id'], ['user.id'],
name=op.f('fk_post_user_id_user')),
sa.PrimaryKeyConstraint('id', name=op.f('pk_post')))
with op.batch_alter_table('post', schema=None) as batch_op:
batch_op.create_index(batch_op.f('ix_post_description'),
['description'],
unique=False)
batch_op.create_index(batch_op.f('ix_post_officialLink'),
['officialLink'],
unique=False)
batch_op.create_index(batch_op.f('ix_post_sphere'), ['sphere'],
unique=False)
batch_op.create_index(batch_op.f('ix_post_timestamp'), ['timestamp'],
unique=False)
batch_op.create_index(batch_op.f('ix_post_title'), ['title'],
unique=True)
op.create_table(
'software', sa.Column('id', sa.Integer(), nullable=False),
sa.Column('title', sa.String(length=200), nullable=True),
sa.Column('description', sa.String(length=800), nullable=True),
sa.Column('downloadLink', sa.String(length=300), nullable=True),
sa.Column('activeDevelopment', sa.String(length=200), nullable=True),
sa.Column('license', sa.String(length=200), nullable=True),
sa.Column('owner', sa.String(length=200), nullable=True),
sa.Column('dateCreation', sa.String(length=300), nullable=True),
sa.Column('dateRelease', sa.String(length=300), nullable=True),
sa.Column('timestamp', sa.DateTime(), nullable=True),
sa.Column('user_id', sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(['user_id'], ['user.id'],
name=op.f('fk_software_user_id_user')),
sa.PrimaryKeyConstraint('id', name=op.f('pk_software')))
with op.batch_alter_table('software', schema=None) as batch_op:
batch_op.create_index(batch_op.f('ix_software_activeDevelopment'),
['activeDevelopment'],
unique=False)
batch_op.create_index(batch_op.f('ix_software_dateCreation'),
['dateCreation'],
unique=False)
batch_op.create_index(batch_op.f('ix_software_dateRelease'),
['dateRelease'],
unique=False)
batch_op.create_index(batch_op.f('ix_software_description'),
['description'],
unique=False)
batch_op.create_index(batch_op.f('ix_software_downloadLink'),
['downloadLink'],
unique=False)
batch_op.create_index(batch_op.f('ix_software_license'), ['license'],
unique=False)
batch_op.create_index(batch_op.f('ix_software_owner'), ['owner'],
unique=False)
batch_op.create_index(batch_op.f('ix_software_timestamp'),
['timestamp'],
unique=False)
batch_op.create_index(batch_op.f('ix_software_title'), ['title'],
unique=True)
op.create_table(
'category', sa.Column('id', sa.Integer(), nullable=False),
sa.Column('category', sa.String(length=200), nullable=True),
sa.Column('timestamp', sa.DateTime(), nullable=True),
sa.Column('postCategory_id', sa.Integer(), nullable=True),
sa.Column('softwareCategory_id', sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(['postCategory_id'], ['post.id'],
name=op.f('fk_category_postCategory_id_post')),
sa.ForeignKeyConstraint(
['softwareCategory_id'], ['software.id'],
name=op.f('fk_category_softwareCategory_id_software')),
sa.PrimaryKeyConstraint('id', name=op.f('pk_category')))
with op.batch_alter_table('category', schema=None) as batch_op:
batch_op.create_index(batch_op.f('ix_category_category'), ['category'],
unique=False)
batch_op.create_index(batch_op.f('ix_category_timestamp'),
['timestamp'],
unique=False)
op.create_table(
'comment', sa.Column('id', sa.Integer(), nullable=False),
sa.Column('name', sa.String(length=200), nullable=True),
sa.Column('email', sa.String(length=200), nullable=True),
sa.Column('text', sa.String(length=600), nullable=True),
sa.Column('timestamp', sa.DateTime(), nullable=True),
sa.Column('postComment_id', sa.Integer(), nullable=True),
sa.Column('softwareComment_id', sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(['postComment_id'], ['post.id'],
name=op.f('fk_comment_postComment_id_post')),
sa.ForeignKeyConstraint(
['softwareComment_id'], ['software.id'],
name=op.f('fk_comment_softwareComment_id_software')),
sa.PrimaryKeyConstraint('id', name=op.f('pk_comment')))
with op.batch_alter_table('comment', schema=None) as batch_op:
batch_op.create_index(batch_op.f('ix_comment_email'), ['email'],
unique=False)
batch_op.create_index(batch_op.f('ix_comment_name'), ['name'],
unique=False)
batch_op.create_index(batch_op.f('ix_comment_text'), ['text'],
unique=False)
batch_op.create_index(batch_op.f('ix_comment_timestamp'),
['timestamp'],
unique=False)
op.create_table(
'favorites_post', sa.Column('favorite_id', sa.Integer(),
nullable=True),
sa.ForeignKeyConstraint(
['favorite_id'], ['post.id'],
name=op.f('fk_favorites_post_favorite_id_post')))
op.create_table(
'favorites_software',
sa.Column('favorite_id', sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(
['favorite_id'], ['software.id'],
name=op.f('fk_favorites_software_favorite_id_software')))
op.create_table(
'report', sa.Column('id', sa.Integer(), nullable=False),
sa.Column('name', sa.String(length=200), nullable=True),
sa.Column('description', sa.String(length=500), nullable=True),
sa.Column('type', sa.String(length=200), nullable=True),
sa.Column('timestamp', sa.DateTime(), nullable=True),
sa.Column('postReport_id', sa.Integer(), nullable=True),
sa.Column('softwareReport_id', sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(['postReport_id'], ['post.id'],
name=op.f('fk_report_postReport_id_post')),
sa.ForeignKeyConstraint(
['softwareReport_id'], ['software.id'],
name=op.f('fk_report_softwareReport_id_software')),
sa.PrimaryKeyConstraint('id', name=op.f('pk_report')))
with op.batch_alter_table('report', schema=None) as batch_op:
batch_op.create_index(batch_op.f('ix_report_description'),
['description'],
unique=False)
batch_op.create_index(batch_op.f('ix_report_name'), ['name'],
unique=False)
batch_op.create_index(batch_op.f('ix_report_timestamp'), ['timestamp'],
unique=False)
batch_op.create_index(batch_op.f('ix_report_type'), ['type'],
unique=False)
op.create_table(
'similar', sa.Column('id', sa.Integer(), nullable=False),
sa.Column('name', sa.String(length=200), nullable=True),
sa.Column('timestamp', sa.DateTime(), nullable=True),
sa.Column('postSimilar_id', sa.Integer(), nullable=True),
sa.Column('softwareSimilare_id', sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(['postSimilar_id'], ['post.id'],
name=op.f('fk_similar_postSimilar_id_post')),
sa.ForeignKeyConstraint(
['softwareSimilare_id'], ['software.id'],
name=op.f('fk_similar_softwareSimilare_id_software')),
sa.PrimaryKeyConstraint('id', name=op.f('pk_similar')))
with op.batch_alter_table('similar', schema=None) as batch_op:
batch_op.create_index(batch_op.f('ix_similar_name'), ['name'],
unique=False)
batch_op.create_index(batch_op.f('ix_similar_timestamp'),
['timestamp'],
unique=False)
op.create_table(
'tag', sa.Column('id', sa.Integer(), nullable=False),
sa.Column('tag', sa.String(length=200), nullable=True),
sa.Column('timestamp', sa.DateTime(), nullable=True),
sa.Column('postTag_id', sa.Integer(), nullable=True),
sa.Column('softwareTag_id', sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(['postTag_id'], ['post.id'],
name=op.f('fk_tag_postTag_id_post')),
sa.ForeignKeyConstraint(['softwareTag_id'], ['software.id'],
name=op.f('fk_tag_softwareTag_id_software')),
sa.PrimaryKeyConstraint('id', name=op.f('pk_tag')))
with op.batch_alter_table('tag', schema=None) as batch_op:
batch_op.create_index(batch_op.f('ix_tag_tag'), ['tag'], unique=False)
batch_op.create_index(batch_op.f('ix_tag_timestamp'), ['timestamp'],
unique=False)
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('tags', schema=None) as batch_op:
batch_op.drop_constraint(batch_op.f('fk_tags_software_id_software'),
type_='foreignkey')
batch_op.drop_column('software_id')
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('match', schema=None) as batch_op:
batch_op.add_column(sa.Column('scoresheet', sa.String(),
nullable=True))
def downgrade():
with op.batch_alter_table("misc") as batch_op:
batch_op.drop_column('daemon_debug_mode')
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('user', schema=None) as batch_op:
batch_op.drop_index('ix_user_token')
batch_op.drop_column('token_expiration')
batch_op.drop_column('token')
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('match', schema=None) as batch_op:
batch_op.drop_column('scoresheet')
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('question', schema=None) as batch_op:
batch_op.drop_constraint(batch_op.f('fk_question_user_id_user'), type_='foreignkey')
batch_op.drop_column('user_id')
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('users', schema=None) as batch_op:
batch_op.drop_column('last_recived_comments_read_time')
def upgrade():
# so Sqlite DOES NOT support ALTER operations so to update columns you gotta do batch updates
with op.batch_alter_table('blacklist') as batch_op:
batch_op.alter_column('added_at',
nullable=False,
server_default=sa.func.current_timestamp())
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.create_table(
'patients', sa.Column('id', sa.Integer(), nullable=False),
sa.Column('name', sa.String(length=255), nullable=True),
sa.Column('case_number', sa.String(length=255), nullable=True),
sa.Column('sex', sa.String(length=255), nullable=False),
sa.Column('date', sa.Date(), nullable=False),
sa.Column('address', sa.String(length=255), nullable=True),
sa.Column('timestamp', sa.DateTime(), nullable=True),
sa.Column('deleted', sa.Boolean(), nullable=True),
sa.PrimaryKeyConstraint('id', name=op.f('pk_patients')))
with op.batch_alter_table('patients', schema=None) as batch_op:
batch_op.create_index(batch_op.f('ix_patients_timestamp'),
['timestamp'],
unique=False)
op.create_table('roles', sa.Column('id', sa.Integer(), nullable=False),
sa.Column('slug', sa.String(length=255), nullable=True),
sa.Column('name', sa.String(length=255), nullable=True),
sa.Column('default', sa.Boolean(), nullable=True),
sa.Column('deleted', sa.Boolean(), nullable=True),
sa.PrimaryKeyConstraint('id', name=op.f('pk_roles')),
sa.UniqueConstraint('slug', name=op.f('uq_roles_slug')))
with op.batch_alter_table('roles', schema=None) as batch_op:
batch_op.create_index(batch_op.f('ix_roles_default'), ['default'],
unique=False)
op.create_table(
'diseases', sa.Column('id', sa.Integer(), nullable=False),
sa.Column('collected_date', sa.DateTime(), nullable=True),
sa.Column('age', sa.Integer(), nullable=True),
sa.Column('disease_type', sa.String(length=255), nullable=True),
sa.Column('type', sa.String(length=255), nullable=True),
sa.Column('tnm', sa.String(length=255), nullable=True),
sa.Column('period', sa.String(length=255), nullable=True),
sa.Column('pathological_immunohistochemistry',
sa.String(length=255),
nullable=True),
sa.Column('operation_date', sa.DateTime(), nullable=True),
sa.Column('pathological_information',
sa.String(length=255),
nullable=True),
sa.Column('Typing', sa.String(length=255), nullable=True),
sa.Column('hypertension', sa.String(length=255), nullable=True),
sa.Column('diabetes', sa.String(length=255), nullable=True),
sa.Column('history_of_cancer', sa.String(length=255), nullable=True),
sa.Column('systemic_diseases', sa.String(length=255), nullable=True),
sa.Column('family_history', sa.String(length=255), nullable=True),
sa.Column('antiviral_therapy', sa.String(length=255), nullable=True),
sa.Column('preoperative_tumor_treatment',
sa.String(length=255),
nullable=True),
sa.Column('blood_lipids', sa.String(length=255), nullable=True),
sa.Column('biochemical_indicators',
sa.String(length=255),
nullable=True),
sa.Column('lymphocyte', sa.String(length=255), nullable=True),
sa.Column('Neutrophils', sa.String(length=255), nullable=True),
sa.Column('after_AEP', sa.String(length=255), nullable=True),
sa.Column('after_CEA', sa.String(length=255), nullable=True),
sa.Column('after_CA19_9', sa.String(length=255), nullable=True),
sa.Column('HBV_DNA', sa.String(length=255), nullable=True),
sa.Column('hepatitis_B_surface_antigen',
sa.String(length=255),
nullable=True),
sa.Column('surface_antibody', sa.String(length=255), nullable=True),
sa.Column('E_antigen', sa.String(length=255), nullable=True),
sa.Column('E_antibody', sa.String(length=255), nullable=True),
sa.Column('core_antibody', sa.String(length=255), nullable=True),
sa.Column('smoking', sa.String(length=255), nullable=True),
sa.Column('treatment', sa.Text(), nullable=True),
sa.Column('timestamp', sa.DateTime(), nullable=True),
sa.Column('deleted', sa.Boolean(), nullable=True),
sa.Column('patient_id', sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(['patient_id'], ['patients.id'],
name=op.f('fk_diseases_patient_id_patients')),
sa.PrimaryKeyConstraint('id', name=op.f('pk_diseases')))
with op.batch_alter_table('diseases', schema=None) as batch_op:
batch_op.create_index(batch_op.f('ix_diseases_timestamp'),
['timestamp'],
unique=False)
op.create_table(
'users', sa.Column('id', sa.Integer(), nullable=False),
sa.Column('username', sa.String(length=64), nullable=True),
sa.Column('email', sa.String(length=120), nullable=True),
sa.Column('password_hash', sa.String(length=128), nullable=True),
sa.Column('name', sa.String(length=64), nullable=True),
sa.Column('location', sa.String(length=64), nullable=True),
sa.Column('about_me', sa.Text(), nullable=True),
sa.Column('member_since', sa.DateTime(), nullable=True),
sa.Column('last_seen', sa.DateTime(), nullable=True),
sa.Column('deleted', sa.Boolean(), nullable=True),
sa.Column('confirmed', sa.Boolean(), nullable=True),
sa.Column('role_id', sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(['role_id'], ['roles.id'],
name=op.f('fk_users_role_id_roles')),
sa.PrimaryKeyConstraint('id', name=op.f('pk_users')))
with op.batch_alter_table('users', schema=None) as batch_op:
batch_op.create_index(batch_op.f('ix_users_email'), ['email'],
unique=True)
batch_op.create_index(batch_op.f('ix_users_username'), ['username'],
unique=True)
op.create_table(
'sequence', sa.Column('sequence_id', sa.Integer(), nullable=False),
sa.Column('batch', sa.String(length=255), nullable=True),
sa.Column('id', sa.String(length=255), nullable=True),
sa.Column('gao_lab_id', sa.String(length=255), nullable=True),
sa.Column('introduction', sa.Text(), nullable=True),
sa.Column('sample_origin', sa.String(length=255), nullable=True),
sa.Column('collected_date', sa.DATE(), nullable=True),
sa.Column('timestamp', sa.DateTime(), nullable=True),
sa.Column('deleted', sa.Boolean(), nullable=True),
sa.Column('author_id', sa.Integer(), nullable=True),
sa.Column('disease_id', sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(['author_id'], ['users.id'],
name=op.f('fk_sequence_author_id_users')),
sa.ForeignKeyConstraint(['disease_id'], ['diseases.id'],
name=op.f('fk_sequence_disease_id_diseases')),
sa.PrimaryKeyConstraint('sequence_id', name=op.f('pk_sequence')))
with op.batch_alter_table('sequence', schema=None) as batch_op:
batch_op.create_index(batch_op.f('ix_sequence_timestamp'),
['timestamp'],
unique=False)
op.create_table(
'results', sa.Column('id', sa.Integer(), nullable=False),
sa.Column('name_1', sa.String(length=255), nullable=True),
sa.Column('data_quality_input', sa.Float(), nullable=True),
sa.Column('data_quality_bam', sa.Float(), nullable=True),
sa.Column('data_quality_bam_input', sa.Float(), nullable=True),
sa.Column('data_Quality_uniq_bam', sa.Float(), nullable=True),
sa.Column('data_Quality_uniq_nodup_bam', sa.Float(), nullable=True),
sa.Column('data_Quality_uniq_nodup_bam_input',
sa.Float(),
nullable=True),
sa.Column('coverage', sa.Float(), nullable=True),
sa.Column('timestamp', sa.DateTime(), nullable=True),
sa.Column('deleted', sa.Boolean(), nullable=True),
sa.Column('sequence_id', sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(['sequence_id'], ['sequence.id'],
name=op.f('fk_results_sequence_id_sequence')),
sa.PrimaryKeyConstraint('id', name=op.f('pk_results')))
with op.batch_alter_table('results', schema=None) as batch_op:
batch_op.create_index(batch_op.f('ix_results_timestamp'),
['timestamp'],
unique=False)
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('person_has_role', schema=None) as batch_op:
batch_op.drop_constraint('_person_has_role_function_uc',
type_='unique')
batch_op.drop_column('function')
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('question', schema=None) as batch_op:
batch_op.add_column(sa.Column('user_id', sa.Integer(), nullable=False))
batch_op.create_foreign_key(batch_op.f('fk_question_user_id_user'), 'user', ['user_id'], ['id'], ondelete='CASCADE')
def downgrade():
with op.batch_alter_table("puppet") as batch_op:
batch_op.drop_column('is_bot')
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.create_table(
"khandaker_mojo_medication_item",
sa.Column(
"medicationtable_id",
sa.Integer(),
nullable=False,
comment="FK to medicationtable",
),
sa.Column(
"seqnum",
sa.Integer(),
nullable=False,
comment="Sequence number of this medication",
),
sa.Column(
"medication_name",
sa.UnicodeText(),
nullable=True,
comment="Medication name",
),
sa.Column(
"chemical_name",
sa.UnicodeText(),
nullable=True,
comment="Chemical name for study team",
),
sa.Column("dose", sa.UnicodeText(), nullable=True, comment="Dose"),
sa.Column("frequency",
sa.UnicodeText(),
nullable=True,
comment="Frequency"),
sa.Column(
"duration_months",
sa.Float(),
nullable=True,
comment="Duration (months)",
),
sa.Column(
"indication",
sa.UnicodeText(),
nullable=True,
comment="Indication (what is the medication used for?)",
),
sa.Column(
"response",
sa.Integer(),
nullable=True,
comment=("1 = treats all symptoms, 2 = most symptoms, 3 = some"
" symptoms, 4 = no symptoms)"),
),
sa.Column(
"_pk",
sa.Integer(),
autoincrement=True,
nullable=False,
comment="(SERVER) Primary key (on the server)",
),
sa.Column(
"_device_id",
sa.Integer(),
nullable=False,
comment="(SERVER) ID of the source tablet device",
),
sa.Column(
"_era",
sa.String(length=32),
nullable=False,
comment=(
"(SERVER) 'NOW', or when this row was preserved and removed"
" from the source device (UTC ISO 8601)"),
),
sa.Column(
"_current",
sa.Boolean(),
nullable=False,
comment="(SERVER) Is the row current (1) or not (0)?",
),
sa.Column(
"_when_added_exact",
PendulumDateTimeAsIsoTextColType(length=32),
nullable=True,
comment="(SERVER) Date/time this row was added (ISO 8601)",
),
sa.Column(
"_when_added_batch_utc",
sa.DateTime(),
nullable=True,
comment=(
"(SERVER) Date/time of the upload batch that added this row"
" (DATETIME in UTC)"),
),
sa.Column(
"_adding_user_id",
sa.Integer(),
nullable=True,
comment="(SERVER) ID of user that added this row",
),
sa.Column(
"_when_removed_exact",
PendulumDateTimeAsIsoTextColType(length=32),
nullable=True,
comment=("(SERVER) Date/time this row was removed, i.e. made not"
" current (ISO 8601)"),
),
sa.Column(
"_when_removed_batch_utc",
sa.DateTime(),
nullable=True,
comment=(
"(SERVER) Date/time of the upload batch that removed this row"
" (DATETIME in UTC)"),
),
sa.Column(
"_removing_user_id",
sa.Integer(),
nullable=True,
comment="(SERVER) ID of user that removed this row",
),
sa.Column(
"_preserving_user_id",
sa.Integer(),
nullable=True,
comment="(SERVER) ID of user that preserved this row",
),
sa.Column(
"_forcibly_preserved",
sa.Boolean(),
nullable=True,
comment=("(SERVER) Forcibly preserved by superuser (rather than"
" normally preserved by tablet)?"),
),
sa.Column(
"_predecessor_pk",
sa.Integer(),
nullable=True,
comment="(SERVER) PK of predecessor record, prior to modification",
),
sa.Column(
"_successor_pk",
sa.Integer(),
nullable=True,
comment=(
"(SERVER) PK of successor record (after modification) or NULL"
" (whilst live, or after deletion)"),
),
sa.Column(
"_manually_erased",
sa.Boolean(),
nullable=True,
comment="(SERVER) Record manually erased (content destroyed)?",
),
sa.Column(
"_manually_erased_at",
PendulumDateTimeAsIsoTextColType(length=32),
nullable=True,
comment="(SERVER) Date/time of manual erasure (ISO 8601)",
),
sa.Column(
"_manually_erasing_user_id",
sa.Integer(),
nullable=True,
comment="(SERVER) ID of user that erased this row manually",
),
sa.Column(
"_camcops_version",
SemanticVersionColType(length=147),
nullable=True,
comment="(SERVER) CamCOPS version number of the uploading device",
),
sa.Column(
"_addition_pending",
sa.Boolean(),
nullable=False,
comment="(SERVER) Addition pending?",
),
sa.Column(
"_removal_pending",
sa.Boolean(),
nullable=True,
comment="(SERVER) Removal pending?",
),
sa.Column(
"_group_id",
sa.Integer(),
nullable=False,
comment="(SERVER) ID of group to which this record belongs",
),
sa.Column(
"id",
sa.Integer(),
nullable=False,
comment="(TASK) Primary key (task ID) on the tablet device",
),
sa.Column(
"when_last_modified",
PendulumDateTimeAsIsoTextColType(length=32),
nullable=True,
comment=(
"(STANDARD) Date/time this row was last modified on the source"
" tablet device (ISO 8601)"),
),
sa.Column(
"_move_off_tablet",
sa.Boolean(),
nullable=True,
comment="(SERVER/TABLET) Record-specific preservation pending?",
),
sa.ForeignKeyConstraint(
["_adding_user_id"],
["_security_users.id"],
name=op.f("fk_khandaker_mojo_medication_item__adding_user_id"),
),
sa.ForeignKeyConstraint(
["_device_id"],
["_security_devices.id"],
name=op.f("fk_khandaker_mojo_medication_item__device_id"),
),
sa.ForeignKeyConstraint(
["_group_id"],
["_security_groups.id"],
name=op.f("fk_khandaker_mojo_medication_item__group_id"),
),
sa.ForeignKeyConstraint(
["_manually_erasing_user_id"],
["_security_users.id"],
name=op.f(
"fk_khandaker_mojo_medication_item__manually_erasing_user_id"),
),
sa.ForeignKeyConstraint(
["_preserving_user_id"],
["_security_users.id"],
name=op.f("fk_khandaker_mojo_medication_item__preserving_user_id"),
),
sa.ForeignKeyConstraint(
["_removing_user_id"],
["_security_users.id"],
name=op.f("fk_khandaker_mojo_medication_item__removing_user_id"),
),
sa.PrimaryKeyConstraint(
"_pk", name=op.f("pk_khandaker_mojo_medication_item")),
mysql_charset="utf8mb4 COLLATE utf8mb4_unicode_ci",
mysql_engine="InnoDB",
mysql_row_format="DYNAMIC",
)
with op.batch_alter_table("khandaker_mojo_medication_item",
schema=None) as batch_op:
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_medication_item__current"),
["_current"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_medication_item__device_id"),
["_device_id"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_medication_item__era"),
["_era"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_medication_item__group_id"),
["_group_id"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_medication_item__pk"),
["_pk"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_medication_item_id"),
["id"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_medication_item_when_last_modified"),
["when_last_modified"],
unique=False,
)
op.create_table(
"khandaker_mojo_medicationtherapy",
sa.Column(
"patient_id",
sa.Integer(),
nullable=False,
comment="(TASK) Foreign key to patient.id (for this device/era)",
),
sa.Column(
"when_created",
PendulumDateTimeAsIsoTextColType(length=32),
nullable=False,
comment=(
"(TASK) Date/time this task instance was created (ISO 8601)"),
),
sa.Column(
"when_firstexit",
PendulumDateTimeAsIsoTextColType(length=32),
nullable=True,
comment=(
"(TASK) Date/time of the first exit from this task (ISO 8601)"
),
),
sa.Column(
"firstexit_is_finish",
sa.Boolean(),
nullable=True,
comment=("(TASK) Was the first exit from the task because it was"
" finished (1)?"),
),
sa.Column(
"firstexit_is_abort",
sa.Boolean(),
nullable=True,
comment=("(TASK) Was the first exit from this task because it was"
" aborted (1)?"),
),
sa.Column(
"editing_time_s",
sa.Float(),
nullable=True,
comment="(TASK) Time spent editing (s)",
),
sa.Column(
"_pk",
sa.Integer(),
autoincrement=True,
nullable=False,
comment="(SERVER) Primary key (on the server)",
),
sa.Column(
"_device_id",
sa.Integer(),
nullable=False,
comment="(SERVER) ID of the source tablet device",
),
sa.Column(
"_era",
sa.String(length=32),
nullable=False,
comment=(
"(SERVER) 'NOW', or when this row was preserved and removed"
" from the source device (UTC ISO 8601)"),
),
sa.Column(
"_current",
sa.Boolean(),
nullable=False,
comment="(SERVER) Is the row current (1) or not (0)?",
),
sa.Column(
"_when_added_exact",
PendulumDateTimeAsIsoTextColType(length=32),
nullable=True,
comment="(SERVER) Date/time this row was added (ISO 8601)",
),
sa.Column(
"_when_added_batch_utc",
sa.DateTime(),
nullable=True,
comment=(
"(SERVER) Date/time of the upload batch that added this row"
" (DATETIME in UTC)"),
),
sa.Column(
"_adding_user_id",
sa.Integer(),
nullable=True,
comment="(SERVER) ID of user that added this row",
),
sa.Column(
"_when_removed_exact",
PendulumDateTimeAsIsoTextColType(length=32),
nullable=True,
comment=("(SERVER) Date/time this row was removed, i.e. made not"
" current (ISO 8601)"),
),
sa.Column(
"_when_removed_batch_utc",
sa.DateTime(),
nullable=True,
comment=(
"(SERVER) Date/time of the upload batch that removed this row"
" (DATETIME in UTC)"),
),
sa.Column(
"_removing_user_id",
sa.Integer(),
nullable=True,
comment="(SERVER) ID of user that removed this row",
),
sa.Column(
"_preserving_user_id",
sa.Integer(),
nullable=True,
comment="(SERVER) ID of user that preserved this row",
),
sa.Column(
"_forcibly_preserved",
sa.Boolean(),
nullable=True,
comment=("(SERVER) Forcibly preserved by superuser (rather than"
" normally preserved by tablet)?"),
),
sa.Column(
"_predecessor_pk",
sa.Integer(),
nullable=True,
comment="(SERVER) PK of predecessor record, prior to modification",
),
sa.Column(
"_successor_pk",
sa.Integer(),
nullable=True,
comment=(
"(SERVER) PK of successor record (after modification) or NULL"
" (whilst live, or after deletion)"),
),
sa.Column(
"_manually_erased",
sa.Boolean(),
nullable=True,
comment="(SERVER) Record manually erased (content destroyed)?",
),
sa.Column(
"_manually_erased_at",
PendulumDateTimeAsIsoTextColType(length=32),
nullable=True,
comment="(SERVER) Date/time of manual erasure (ISO 8601)",
),
sa.Column(
"_manually_erasing_user_id",
sa.Integer(),
nullable=True,
comment="(SERVER) ID of user that erased this row manually",
),
sa.Column(
"_camcops_version",
SemanticVersionColType(length=147),
nullable=True,
comment="(SERVER) CamCOPS version number of the uploading device",
),
sa.Column(
"_addition_pending",
sa.Boolean(),
nullable=False,
comment="(SERVER) Addition pending?",
),
sa.Column(
"_removal_pending",
sa.Boolean(),
nullable=True,
comment="(SERVER) Removal pending?",
),
sa.Column(
"_group_id",
sa.Integer(),
nullable=False,
comment="(SERVER) ID of group to which this record belongs",
),
sa.Column(
"id",
sa.Integer(),
nullable=False,
comment="(TASK) Primary key (task ID) on the tablet device",
),
sa.Column(
"when_last_modified",
PendulumDateTimeAsIsoTextColType(length=32),
nullable=True,
comment=(
"(STANDARD) Date/time this row was last modified on the source"
" tablet device (ISO 8601)"),
),
sa.Column(
"_move_off_tablet",
sa.Boolean(),
nullable=True,
comment="(SERVER/TABLET) Record-specific preservation pending?",
),
sa.ForeignKeyConstraint(
["_adding_user_id"],
["_security_users.id"],
name=op.f("fk_khandaker_mojo_medicationtherapy__adding_user_id"),
),
sa.ForeignKeyConstraint(
["_device_id"],
["_security_devices.id"],
name=op.f("fk_khandaker_mojo_medicationtherapy__device_id"),
),
sa.ForeignKeyConstraint(
["_group_id"],
["_security_groups.id"],
name=op.f("fk_khandaker_mojo_medicationtherapy__group_id"),
),
sa.ForeignKeyConstraint(
["_manually_erasing_user_id"],
["_security_users.id"],
name=op.
f("fk_khandaker_mojo_medicationtherapy__manually_erasing_user_id"),
),
sa.ForeignKeyConstraint(
["_preserving_user_id"],
["_security_users.id"],
name=op.f(
"fk_khandaker_mojo_medicationtherapy__preserving_user_id"),
),
sa.ForeignKeyConstraint(
["_removing_user_id"],
["_security_users.id"],
name=op.f("fk_khandaker_mojo_medicationtherapy__removing_user_id"),
),
sa.PrimaryKeyConstraint(
"_pk", name=op.f("pk_khandaker_mojo_medicationtherapy")),
mysql_charset="utf8mb4 COLLATE utf8mb4_unicode_ci",
mysql_engine="InnoDB",
mysql_row_format="DYNAMIC",
)
with op.batch_alter_table("khandaker_mojo_medicationtherapy",
schema=None) as batch_op:
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_medicationtherapy__current"),
["_current"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_medicationtherapy__device_id"),
["_device_id"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_medicationtherapy__era"),
["_era"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_medicationtherapy__group_id"),
["_group_id"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_medicationtherapy__pk"),
["_pk"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_medicationtherapy_id"),
["id"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_medicationtherapy_patient_id"),
["patient_id"],
unique=False,
)
batch_op.create_index(
batch_op.f(
"ix_khandaker_mojo_medicationtherapy_when_last_modified"),
["when_last_modified"],
unique=False,
)
op.create_table(
"khandaker_mojo_therapy_item",
sa.Column(
"medicationtable_id",
sa.Integer(),
nullable=False,
comment="FK to medicationtable",
),
sa.Column(
"seqnum",
sa.Integer(),
nullable=False,
comment="Sequence number of this therapy",
),
sa.Column("therapy",
sa.UnicodeText(),
nullable=True,
comment="Therapy"),
sa.Column("frequency",
sa.UnicodeText(),
nullable=True,
comment="Frequency"),
sa.Column(
"sessions_completed",
sa.Integer(),
nullable=True,
comment="Sessions completed",
),
sa.Column(
"sessions_planned",
sa.Integer(),
nullable=True,
comment="Total number of sessions planned",
),
sa.Column(
"indication",
sa.UnicodeText(),
nullable=True,
comment="Indication (what is the medication used for?)",
),
sa.Column(
"response",
sa.Integer(),
nullable=True,
comment=("1 = treats all symptoms, 2 = most symptoms, 3 = some"
" symptoms, 4 = no symptoms)"),
),
sa.Column(
"_pk",
sa.Integer(),
autoincrement=True,
nullable=False,
comment="(SERVER) Primary key (on the server)",
),
sa.Column(
"_device_id",
sa.Integer(),
nullable=False,
comment="(SERVER) ID of the source tablet device",
),
sa.Column(
"_era",
sa.String(length=32),
nullable=False,
comment=(
"(SERVER) 'NOW', or when this row was preserved and removed"
" from the source device (UTC ISO 8601)"),
),
sa.Column(
"_current",
sa.Boolean(),
nullable=False,
comment="(SERVER) Is the row current (1) or not (0)?",
),
sa.Column(
"_when_added_exact",
PendulumDateTimeAsIsoTextColType(length=32),
nullable=True,
comment="(SERVER) Date/time this row was added (ISO 8601)",
),
sa.Column(
"_when_added_batch_utc",
sa.DateTime(),
nullable=True,
comment=(
"(SERVER) Date/time of the upload batch that added this row"
" (DATETIME in UTC)"),
),
sa.Column(
"_adding_user_id",
sa.Integer(),
nullable=True,
comment="(SERVER) ID of user that added this row",
),
sa.Column(
"_when_removed_exact",
PendulumDateTimeAsIsoTextColType(length=32),
nullable=True,
comment=("(SERVER) Date/time this row was removed, i.e. made not"
" current (ISO 8601)"),
),
sa.Column(
"_when_removed_batch_utc",
sa.DateTime(),
nullable=True,
comment=(
"(SERVER) Date/time of the upload batch that removed this row"
" (DATETIME in UTC)"),
),
sa.Column(
"_removing_user_id",
sa.Integer(),
nullable=True,
comment="(SERVER) ID of user that removed this row",
),
sa.Column(
"_preserving_user_id",
sa.Integer(),
nullable=True,
comment="(SERVER) ID of user that preserved this row",
),
sa.Column(
"_forcibly_preserved",
sa.Boolean(),
nullable=True,
comment=("(SERVER) Forcibly preserved by superuser (rather than"
" normally preserved by tablet)?"),
),
sa.Column(
"_predecessor_pk",
sa.Integer(),
nullable=True,
comment="(SERVER) PK of predecessor record, prior to modification",
),
sa.Column(
"_successor_pk",
sa.Integer(),
nullable=True,
comment=(
"(SERVER) PK of successor record (after modification) or NULL"
" (whilst live, or after deletion)"),
),
sa.Column(
"_manually_erased",
sa.Boolean(),
nullable=True,
comment="(SERVER) Record manually erased (content destroyed)?",
),
sa.Column(
"_manually_erased_at",
PendulumDateTimeAsIsoTextColType(length=32),
nullable=True,
comment="(SERVER) Date/time of manual erasure (ISO 8601)",
),
sa.Column(
"_manually_erasing_user_id",
sa.Integer(),
nullable=True,
comment="(SERVER) ID of user that erased this row manually",
),
sa.Column(
"_camcops_version",
SemanticVersionColType(length=147),
nullable=True,
comment="(SERVER) CamCOPS version number of the uploading device",
),
sa.Column(
"_addition_pending",
sa.Boolean(),
nullable=False,
comment="(SERVER) Addition pending?",
),
sa.Column(
"_removal_pending",
sa.Boolean(),
nullable=True,
comment="(SERVER) Removal pending?",
),
sa.Column(
"_group_id",
sa.Integer(),
nullable=False,
comment="(SERVER) ID of group to which this record belongs",
),
sa.Column(
"id",
sa.Integer(),
nullable=False,
comment="(TASK) Primary key (task ID) on the tablet device",
),
sa.Column(
"when_last_modified",
PendulumDateTimeAsIsoTextColType(length=32),
nullable=True,
comment=(
"(STANDARD) Date/time this row was last modified on the source"
" tablet device (ISO 8601)"),
),
sa.Column(
"_move_off_tablet",
sa.Boolean(),
nullable=True,
comment="(SERVER/TABLET) Record-specific preservation pending?",
),
sa.ForeignKeyConstraint(
["_adding_user_id"],
["_security_users.id"],
name=op.f("fk_khandaker_mojo_therapy_item__adding_user_id"),
),
sa.ForeignKeyConstraint(
["_device_id"],
["_security_devices.id"],
name=op.f("fk_khandaker_mojo_therapy_item__device_id"),
),
sa.ForeignKeyConstraint(
["_group_id"],
["_security_groups.id"],
name=op.f("fk_khandaker_mojo_therapy_item__group_id"),
),
sa.ForeignKeyConstraint(
["_manually_erasing_user_id"],
["_security_users.id"],
name=op.f(
"fk_khandaker_mojo_therapy_item__manually_erasing_user_id"),
),
sa.ForeignKeyConstraint(
["_preserving_user_id"],
["_security_users.id"],
name=op.f("fk_khandaker_mojo_therapy_item__preserving_user_id"),
),
sa.ForeignKeyConstraint(
["_removing_user_id"],
["_security_users.id"],
name=op.f("fk_khandaker_mojo_therapy_item__removing_user_id"),
),
sa.PrimaryKeyConstraint("_pk",
name=op.f("pk_khandaker_mojo_therapy_item")),
mysql_charset="utf8mb4 COLLATE utf8mb4_unicode_ci",
mysql_engine="InnoDB",
mysql_row_format="DYNAMIC",
)
with op.batch_alter_table("khandaker_mojo_therapy_item",
schema=None) as batch_op:
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_therapy_item__current"),
["_current"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_therapy_item__device_id"),
["_device_id"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_therapy_item__era"),
["_era"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_therapy_item__group_id"),
["_group_id"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_therapy_item__pk"),
["_pk"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_therapy_item_id"),
["id"],
unique=False,
)
batch_op.create_index(
batch_op.f("ix_khandaker_mojo_therapy_item_when_last_modified"),
["when_last_modified"],
unique=False,
)
def upgrade():
with op.batch_alter_table("puppet") as batch_op:
batch_op.add_column(sa.Column('is_bot', sa.Boolean(), nullable=True))
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('releases', schema=None) as batch_op:
batch_op.drop_index(batch_op.f('ix_releases_timestamp'))
op.drop_table('releases')
