From 6196dcd3b321758ae8dfb84b22a59e1c77d8e933 Mon Sep 17 00:00:00 2001
From: Sebastiaan Huber <mail@sphuber.net>
Date: Fri, 5 Jul 2024 09:49:20 +0200
Subject: [PATCH] `SqliteDosStorage`: Make the migrator compatible with SQLite
(#6429)
The majority of the `SqliteDosStorage` piggy-backs off of the
`PsqlDosStorage` plugin. It also uses the `PsqlDosMigrator` as-is to
perform the database migrations. This is not safe however, as PostgreSQL
and SQLite do not have exactly the same syntax.
An example is the `main_0002` revision which was added to drop the
hashes of certain nodes. This uses the `#-` operator which is JSONB
specific syntax of PostgreSQL and is not supported by SQLite. Since this
migration was added before the `SqliteDosStorage` plugin was added, this
has never caused a problems as all profiles would be new, would not have
any nodes and therefore the SQL code of the migration would not actually
be executed.
In preparation for any future migrations that may need to be added, the
`SqliteDosStorage` now uses the `SqliteDosMigrator`. This subclasses the
`PsqlDosMigrator` as it can still use most of the functionality, but it
changes a few critical things. Most notably the location of the schema
versions which now are kept individually and are no longer lent from the
`core.psql_dos` plugin.
The initial version `main_0001_initial.py` is taken from the migration
`main_0000_initial.py` of the `core.sqlite_zip` storage plugin. The only
difference is that UUID fields are declared as `String(32)` instead of
`CHAR(32)`. The SQLAlchemy models that are automatically generated for
SQLite from the PostgreSQL-based models actually use the latter type.
See `aiida.storage.sqlite_zip.models:pg_to_sqlite`.
---
src/aiida/storage/migrations.py | 8 +
src/aiida/storage/psql_dos/migrator.py | 8 +-
src/aiida/storage/sqlite_dos/backend.py | 123 +++++++-
.../storage/sqlite_dos/migrations/env.py | 54 ++++
.../migrations/versions/main_0001_initial.py | 198 +++++++++++++
.../main_0002_recompute_hash_calc_job_node.py | 84 ++++++
.../storage/sqlite_zip/migrations/env.py | 2 +-
tests/cmdline/commands/test_status.py | 2 +
.../storage/sqlite_dos/migrations/conftest.py | 76 +++++
.../sqlite_dos/migrations/test_all_schema.py | 49 ++++
.../test_head_vs_orm_main_0002_.yml | 269 ++++++++++++++++++
.../test_all_schema/test_main_main_0001_.yml | 255 +++++++++++++++++
.../test_all_schema/test_main_main_0002_.yml | 255 +++++++++++++++++
13 files changed, 1360 insertions(+), 23 deletions(-)
create mode 100644 src/aiida/storage/migrations.py
create mode 100644 src/aiida/storage/sqlite_dos/migrations/env.py
create mode 100644 src/aiida/storage/sqlite_dos/migrations/versions/main_0001_initial.py
create mode 100644 src/aiida/storage/sqlite_dos/migrations/versions/main_0002_recompute_hash_calc_job_node.py
create mode 100644 tests/storage/sqlite_dos/migrations/conftest.py
create mode 100644 tests/storage/sqlite_dos/migrations/test_all_schema.py
create mode 100644 tests/storage/sqlite_dos/migrations/test_all_schema/test_head_vs_orm_main_0002_.yml
create mode 100644 tests/storage/sqlite_dos/migrations/test_all_schema/test_main_main_0001_.yml
create mode 100644 tests/storage/sqlite_dos/migrations/test_all_schema/test_main_main_0002_.yml
diff --git a/src/aiida/storage/migrations.py b/src/aiida/storage/migrations.py
new file mode 100644
index 0000000000..c37cbab641
--- /dev/null
+++ b/src/aiida/storage/migrations.py
@@ -0,0 +1,8 @@
+"""Module with common resources related to storage migrations."""
+
+TEMPLATE_INVALID_SCHEMA_VERSION = """
+Database schema version `{schema_version_database}` is incompatible with the required schema version `{schema_version_code}`.
+To migrate the database schema version to the current one, run the following command:
+
+ verdi -p {profile_name} storage migrate
+""" # noqa: E501
diff --git a/src/aiida/storage/psql_dos/migrator.py b/src/aiida/storage/psql_dos/migrator.py
index 3ea36b9307..5251fd49de 100644
--- a/src/aiida/storage/psql_dos/migrator.py
+++ b/src/aiida/storage/psql_dos/migrator.py
@@ -33,6 +33,7 @@
from aiida.common import exceptions
from aiida.manage.configuration.profile import Profile
from aiida.storage.log import MIGRATE_LOGGER
+from aiida.storage.migrations import TEMPLATE_INVALID_SCHEMA_VERSION
from aiida.storage.psql_dos.models.settings import DbSetting
from aiida.storage.psql_dos.utils import create_sqlalchemy_engine
@@ -46,13 +47,6 @@
verdi -p {profile_name} storage migrate
"""
-TEMPLATE_INVALID_SCHEMA_VERSION = """
-Database schema version `{schema_version_database}` is incompatible with the required schema version `{schema_version_code}`.
-To migrate the database schema version to the current one, run the following command:
-
- verdi -p {profile_name} storage migrate
-""" # noqa: E501
-
ALEMBIC_REL_PATH = 'migrations'
REPOSITORY_UUID_KEY = 'repository|uuid'
diff --git a/src/aiida/storage/sqlite_dos/backend.py b/src/aiida/storage/sqlite_dos/backend.py
index 3b13764b3d..7be70f4a1c 100644
--- a/src/aiida/storage/sqlite_dos/backend.py
+++ b/src/aiida/storage/sqlite_dos/backend.py
@@ -10,31 +10,36 @@
from __future__ import annotations
+import pathlib
from functools import cached_property, lru_cache
from pathlib import Path
from shutil import rmtree
from typing import TYPE_CHECKING, Optional
from uuid import uuid4
+from alembic.config import Config
from disk_objectstore import Container, backup_utils
from pydantic import BaseModel, Field, field_validator
-from sqlalchemy import insert
+from sqlalchemy import insert, inspect, select
from sqlalchemy.orm import scoped_session, sessionmaker
from aiida.common import exceptions
from aiida.common.log import AIIDA_LOGGER
-from aiida.manage import Profile
+from aiida.manage.configuration.profile import Profile
from aiida.manage.configuration.settings import AIIDA_CONFIG_FOLDER
from aiida.orm.implementation import BackendEntity
+from aiida.storage.log import MIGRATE_LOGGER
from aiida.storage.psql_dos.models.settings import DbSetting
from aiida.storage.sqlite_zip import models, orm
-from aiida.storage.sqlite_zip.migrator import get_schema_version_head
from aiida.storage.sqlite_zip.utils import create_sqla_engine
+from ..migrations import TEMPLATE_INVALID_SCHEMA_VERSION
from ..psql_dos import PsqlDosBackend
-from ..psql_dos.migrator import REPOSITORY_UUID_KEY, PsqlDosMigrator
+from ..psql_dos.migrator import PsqlDosMigrator
if TYPE_CHECKING:
+ from disk_objectstore import Container
+
from aiida.orm.entities import EntityTypes
from aiida.repository.backend import DiskObjectStoreRepositoryBackend
@@ -45,15 +50,26 @@
FILENAME_CONTAINER = 'container'
+ALEMBIC_REL_PATH = 'migrations'
+
+REPOSITORY_UUID_KEY = 'repository|uuid'
+
+
class SqliteDosMigrator(PsqlDosMigrator):
- """Storage implementation using Sqlite database and disk-objectstore container.
+ """Class for validating and migrating `sqlite_dos` storage instances.
- This storage backend is not recommended for use in production. The sqlite database is not the most performant and it
- does not support all the ``QueryBuilder`` functionality that is supported by the ``core.psql_dos`` storage backend.
- This storage is ideally suited for use cases that want to test or demo AiiDA as it requires no server but just a
- folder on the local filesystem.
+ .. important:: This class should only be accessed via the storage backend class (apart from for test purposes)
+
+ The class subclasses the ``PsqlDosMigrator``. It essentially changes two things in the implementation:
+
+ * Changes the path to the migration version files. This allows custom migrations to be written for SQLite-based
+ storage plugins, which is necessary since the PSQL-based migrations may use syntax that is not compatible.
+ * The logic for validating the storage is significantly simplified since the SQLite-based storage plugins do not
+ have to take legacy Django-based implementations into account.
"""
+ alembic_version_tbl_name = 'alembic_version'
+
def __init__(self, profile: Profile) -> None:
filepath_database = Path(profile.storage_config['filepath']) / FILENAME_DATABASE
filepath_database.touch()
@@ -91,6 +107,86 @@ def initialise_database(self) -> None:
context.stamp(context.script, 'main@head') # type: ignore[arg-type]
self.connection.commit()
+ def get_schema_version_profile(self) -> Optional[str]: # type: ignore[override]
+ """Return the schema version of the backend instance for this profile.
+
+ Note, the version will be None if the database is empty or is a legacy django database.
+ """
+ with self._migration_context() as context:
+ return context.get_current_revision()
+
+ @staticmethod
+ def _alembic_config():
+ """Return an instance of an Alembic `Config`."""
+ dirpath = pathlib.Path(__file__).resolve().parent
+ config = Config()
+ config.set_main_option('script_location', str(dirpath / ALEMBIC_REL_PATH))
+ return config
+
+ def validate_storage(self) -> None:
+ """Validate that the storage for this profile
+
+ 1. That the database schema is at the head version, i.e. is compatible with the code API.
+ 2. That the repository ID is equal to the UUID set in the database
+
+ :raises: :class:`aiida.common.exceptions.UnreachableStorage` if the storage cannot be connected to
+ :raises: :class:`aiida.common.exceptions.IncompatibleStorageSchema`
+ if the storage is not compatible with the code API.
+ :raises: :class:`aiida.common.exceptions.CorruptStorage`
+ if the repository ID is not equal to the UUID set in thedatabase.
+ """
+ # check there is an alembic_version table from which to get the schema version
+ if not inspect(self.connection).has_table(self.alembic_version_tbl_name):
+ raise exceptions.IncompatibleStorageSchema('The database has no known version.')
+
+ # now we can check that the alembic version is the latest
+ schema_version_code = self.get_schema_version_head()
+ schema_version_database = self.get_schema_version_profile()
+ if schema_version_database != schema_version_code:
+ raise exceptions.IncompatibleStorageSchema(
+ TEMPLATE_INVALID_SCHEMA_VERSION.format(
+ schema_version_database=schema_version_database,
+ schema_version_code=schema_version_code,
+ profile_name=self.profile.name,
+ )
+ )
+
+ # finally, we check that the ID set within the disk-objectstore is equal to the one saved in the database,
+ # i.e. this container is indeed the one associated with the db
+ repository_uuid = self.get_repository_uuid()
+ stmt = select(DbSetting.val).where(DbSetting.key == REPOSITORY_UUID_KEY)
+ database_repository_uuid = self.connection.execute(stmt).scalar_one_or_none()
+ if database_repository_uuid is None:
+ raise exceptions.CorruptStorage('The database has no repository UUID set.')
+ if database_repository_uuid != repository_uuid:
+ raise exceptions.CorruptStorage(
+ f'The database has a repository UUID configured to {database_repository_uuid} '
+ f"but the disk-objectstore's is {repository_uuid}."
+ )
+
+ @property
+ def is_database_initialised(self) -> bool:
+ """Return whether the database is initialised.
+
+ This is the case if it contains the table that holds the schema version for alembic.
+
+ :returns: ``True`` if the database is initialised, ``False`` otherwise.
+ """
+ return inspect(self.connection).has_table(self.alembic_version_tbl_name)
+
+ def migrate(self) -> None:
+ """Migrate the storage for this profile to the head version.
+
+ :raises: :class:`~aiida.common.exceptions.UnreachableStorage` if the storage cannot be accessed.
+ :raises: :class:`~aiida.common.exceptions.StorageMigrationError` if the storage is not initialised.
+ """
+ if not inspect(self.connection).has_table(self.alembic_version_tbl_name):
+ raise exceptions.StorageMigrationError('storage is uninitialised, cannot migrate.')
+
+ MIGRATE_LOGGER.report('Migrating to the head of the main branch')
+ self.migrate_up('main@head')
+ self.connection.commit()
+
class SqliteDosStorage(PsqlDosBackend):
"""A lightweight storage that is easy to install.
@@ -178,12 +274,9 @@ def get_repository(self) -> 'DiskObjectStoreRepositoryBackend':
return DiskObjectStoreRepositoryBackend(container=self.get_container())
@classmethod
- def version_head(cls) -> str:
- return get_schema_version_head()
-
- @classmethod
- def version_profile(cls, profile: Profile) -> str | None:
- return get_schema_version_head()
+ def version_profile(cls, profile: Profile) -> Optional[str]:
+ with cls.migrator_context(profile) as migrator:
+ return migrator.get_schema_version_profile()
def query(self) -> orm.SqliteQueryBuilder:
return orm.SqliteQueryBuilder(self)
diff --git a/src/aiida/storage/sqlite_dos/migrations/env.py b/src/aiida/storage/sqlite_dos/migrations/env.py
new file mode 100644
index 0000000000..e2beb1ad9f
--- /dev/null
+++ b/src/aiida/storage/sqlite_dos/migrations/env.py
@@ -0,0 +1,54 @@
+###########################################################################
+# Copyright (c), The AiiDA team. All rights reserved. #
+# This file is part of the AiiDA code. #
+# #
+# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
+# For further information on the license, see the LICENSE.txt file #
+# For further information please visit http://www.aiida.net #
+###########################################################################
+"""Environment configuration to be used by alembic to perform database migrations."""
+
+from alembic import context
+
+
+def run_migrations_online():
+ """Run migrations in 'online' mode.
+
+ The connection should have been passed to the config, which we use to configure the migration context.
+ """
+ from aiida.storage.sqlite_zip.models import SqliteBase
+
+ config = context.config
+
+ connection = config.attributes.get('connection', None)
+ aiida_profile = config.attributes.get('aiida_profile', None)
+ on_version_apply = config.attributes.get('on_version_apply', None)
+
+ if connection is None:
+ from aiida.common.exceptions import ConfigurationError
+
+ raise ConfigurationError('An initialized connection is expected for the AiiDA online migrations.')
+ if aiida_profile is None:
+ from aiida.common.exceptions import ConfigurationError
+
+ raise ConfigurationError('An aiida_profile is expected for the AiiDA online migrations.')
+
+ context.configure(
+ connection=connection,
+ target_metadata=SqliteBase.metadata,
+ transaction_per_migration=True,
+ aiida_profile=aiida_profile,
+ on_version_apply=on_version_apply,
+ )
+
+ context.run_migrations()
+
+
+try:
+ if context.is_offline_mode():
+ raise NotImplementedError('This feature is not currently supported.')
+
+ run_migrations_online()
+except NameError:
+ # This will occur in an environment that is just compiling the documentation
+ pass
diff --git a/src/aiida/storage/sqlite_dos/migrations/versions/main_0001_initial.py b/src/aiida/storage/sqlite_dos/migrations/versions/main_0001_initial.py
new file mode 100644
index 0000000000..6af0887766
--- /dev/null
+++ b/src/aiida/storage/sqlite_dos/migrations/versions/main_0001_initial.py
@@ -0,0 +1,198 @@
+###########################################################################
+# Copyright (c), The AiiDA team. All rights reserved. #
+# This file is part of the AiiDA code. #
+# #
+# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
+# For further information on the license, see the LICENSE.txt file #
+# For further information please visit http://www.aiida.net #
+###########################################################################
+"""Initial main branch schema
+
+This schema is mainly equivalent to the `main_0000_initial.py` schema of the `sqlite_zip` backend. Except that UUID
+columns use ``String(32)`` instead of ``CHAR(32)``.
+
+Revision ID: main_0001
+Revises:
+Create Date: 2024-05-29
+"""
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects.sqlite import JSON
+
+revision = 'main_0001'
+down_revision = None
+branch_labels = ('main',)
+depends_on = None
+
+
+def upgrade():
+ """Migrations for the upgrade."""
+ op.create_table(
+ 'db_dbcomputer',
+ sa.Column('id', sa.Integer(), nullable=False, primary_key=True),
+ sa.Column('uuid', sa.String(32), nullable=False, unique=True),
+ sa.Column('label', sa.String(length=255), nullable=False, unique=True),
+ sa.Column('hostname', sa.String(length=255), nullable=False),
+ sa.Column('description', sa.Text(), nullable=False),
+ sa.Column('scheduler_type', sa.String(length=255), nullable=False),
+ sa.Column('transport_type', sa.String(length=255), nullable=False),
+ sa.Column('metadata', JSON(), nullable=False),
+ )
+ op.create_table(
+ 'db_dbuser',
+ sa.Column('id', sa.Integer(), nullable=False, primary_key=True),
+ sa.Column('email', sa.String(length=254), nullable=False, unique=True),
+ sa.Column('first_name', sa.String(length=254), nullable=False),
+ sa.Column('last_name', sa.String(length=254), nullable=False),
+ sa.Column('institution', sa.String(length=254), nullable=False),
+ )
+ op.create_table(
+ 'db_dbauthinfo',
+ sa.Column('id', sa.Integer(), nullable=False, primary_key=True),
+ sa.Column('aiidauser_id', sa.Integer(), nullable=False, index=True),
+ sa.Column('dbcomputer_id', sa.Integer(), nullable=False, index=True),
+ sa.Column('metadata', JSON(), nullable=False),
+ sa.Column('auth_params', JSON(), nullable=False),
+ sa.Column('enabled', sa.Boolean(), nullable=False),
+ sa.ForeignKeyConstraint(
+ ['aiidauser_id'],
+ ['db_dbuser.id'],
+ ondelete='CASCADE',
+ initially='DEFERRED',
+ deferrable=True,
+ ),
+ sa.ForeignKeyConstraint(
+ ['dbcomputer_id'],
+ ['db_dbcomputer.id'],
+ ondelete='CASCADE',
+ initially='DEFERRED',
+ deferrable=True,
+ ),
+ sa.UniqueConstraint('aiidauser_id', 'dbcomputer_id'),
+ )
+ op.create_table(
+ 'db_dbgroup',
+ sa.Column('id', sa.Integer(), nullable=False, primary_key=True),
+ sa.Column('uuid', sa.String(32), nullable=False, unique=True),
+ sa.Column('label', sa.String(length=255), nullable=False, index=True),
+ sa.Column('type_string', sa.String(length=255), nullable=False, index=True),
+ sa.Column('time', sa.DateTime(timezone=True), nullable=False),
+ sa.Column('description', sa.Text(), nullable=False),
+ sa.Column('extras', JSON(), nullable=False),
+ sa.Column('user_id', sa.Integer(), nullable=False, index=True),
+ sa.ForeignKeyConstraint(
+ ['user_id'],
+ ['db_dbuser.id'],
+ ondelete='CASCADE',
+ initially='DEFERRED',
+ deferrable=True,
+ ),
+ sa.UniqueConstraint('label', 'type_string'),
+ )
+
+ op.create_table(
+ 'db_dbnode',
+ sa.Column('id', sa.Integer(), nullable=False, primary_key=True),
+ sa.Column('uuid', sa.String(32), nullable=False, unique=True),
+ sa.Column('node_type', sa.String(length=255), nullable=False, index=True),
+ sa.Column('process_type', sa.String(length=255), nullable=True, index=True),
+ sa.Column('label', sa.String(length=255), nullable=False, index=True),
+ sa.Column('description', sa.Text(), nullable=False),
+ sa.Column('ctime', sa.DateTime(timezone=True), nullable=False, index=True),
+ sa.Column('mtime', sa.DateTime(timezone=True), nullable=False, index=True),
+ sa.Column('attributes', JSON(), nullable=True),
+ sa.Column('extras', JSON(), nullable=True),
+ sa.Column('repository_metadata', JSON(), nullable=False),
+ sa.Column('dbcomputer_id', sa.Integer(), nullable=True, index=True),
+ sa.Column('user_id', sa.Integer(), nullable=False, index=True),
+ sa.ForeignKeyConstraint(
+ ['dbcomputer_id'],
+ ['db_dbcomputer.id'],
+ ondelete='RESTRICT',
+ initially='DEFERRED',
+ deferrable=True,
+ ),
+ sa.ForeignKeyConstraint(
+ ['user_id'],
+ ['db_dbuser.id'],
+ ondelete='restrict',
+ initially='DEFERRED',
+ deferrable=True,
+ ),
+ )
+
+ op.create_table(
+ 'db_dbcomment',
+ sa.Column('id', sa.Integer(), nullable=False, primary_key=True),
+ sa.Column('uuid', sa.String(32), nullable=False, unique=True),
+ sa.Column('dbnode_id', sa.Integer(), nullable=False, index=True),
+ sa.Column('ctime', sa.DateTime(timezone=True), nullable=False),
+ sa.Column('mtime', sa.DateTime(timezone=True), nullable=False),
+ sa.Column('user_id', sa.Integer(), nullable=False, index=True),
+ sa.Column('content', sa.Text(), nullable=False),
+ sa.ForeignKeyConstraint(
+ ['dbnode_id'],
+ ['db_dbnode.id'],
+ ondelete='CASCADE',
+ initially='DEFERRED',
+ deferrable=True,
+ ),
+ sa.ForeignKeyConstraint(
+ ['user_id'],
+ ['db_dbuser.id'],
+ ondelete='CASCADE',
+ initially='DEFERRED',
+ deferrable=True,
+ ),
+ )
+
+ op.create_table(
+ 'db_dbgroup_dbnodes',
+ sa.Column('id', sa.Integer(), nullable=False, primary_key=True),
+ sa.Column('dbnode_id', sa.Integer(), nullable=False, index=True),
+ sa.Column('dbgroup_id', sa.Integer(), nullable=False, index=True),
+ sa.ForeignKeyConstraint(['dbgroup_id'], ['db_dbgroup.id'], initially='DEFERRED', deferrable=True),
+ sa.ForeignKeyConstraint(['dbnode_id'], ['db_dbnode.id'], initially='DEFERRED', deferrable=True),
+ sa.UniqueConstraint('dbgroup_id', 'dbnode_id'),
+ )
+ op.create_table(
+ 'db_dblink',
+ sa.Column('id', sa.Integer(), nullable=False, primary_key=True),
+ sa.Column('input_id', sa.Integer(), nullable=False, index=True),
+ sa.Column('output_id', sa.Integer(), nullable=False, index=True),
+ sa.Column('label', sa.String(length=255), nullable=False, index=True),
+ sa.Column('type', sa.String(length=255), nullable=False, index=True),
+ sa.ForeignKeyConstraint(['input_id'], ['db_dbnode.id'], initially='DEFERRED', deferrable=True),
+ sa.ForeignKeyConstraint(
+ ['output_id'],
+ ['db_dbnode.id'],
+ ondelete='CASCADE',
+ initially='DEFERRED',
+ deferrable=True,
+ ),
+ )
+
+ op.create_table(
+ 'db_dblog',
+ sa.Column('id', sa.Integer(), nullable=False, primary_key=True),
+ sa.Column('uuid', sa.String(32), nullable=False, unique=True),
+ sa.Column('time', sa.DateTime(timezone=True), nullable=False),
+ sa.Column('loggername', sa.String(length=255), nullable=False, index=True),
+ sa.Column('levelname', sa.String(length=50), nullable=False, index=True),
+ sa.Column('dbnode_id', sa.Integer(), nullable=False, index=True),
+ sa.Column('message', sa.Text(), nullable=False),
+ sa.Column('metadata', JSON(), nullable=False),
+ sa.ForeignKeyConstraint(
+ ['dbnode_id'],
+ ['db_dbnode.id'],
+ ondelete='CASCADE',
+ initially='DEFERRED',
+ deferrable=True,
+ ),
+ )
+
+
+def downgrade():
+ """Migrations for the downgrade."""
+ raise NotImplementedError('Downgrade of main_0000.')
diff --git a/src/aiida/storage/sqlite_dos/migrations/versions/main_0002_recompute_hash_calc_job_node.py b/src/aiida/storage/sqlite_dos/migrations/versions/main_0002_recompute_hash_calc_job_node.py
new file mode 100644
index 0000000000..ae70c45c4c
--- /dev/null
+++ b/src/aiida/storage/sqlite_dos/migrations/versions/main_0002_recompute_hash_calc_job_node.py
@@ -0,0 +1,84 @@
+###########################################################################
+# Copyright (c), The AiiDA team. All rights reserved. #
+# This file is part of the AiiDA code. #
+# #
+# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
+# For further information on the license, see the LICENSE.txt file #
+# For further information please visit http://www.aiida.net #
+###########################################################################
+"""Drop the hashes for all ``CalcJobNode`` instances.
+
+The computed hash erroneously included the hash of the file repository. This was present as of v2.0 and so all nodes
+created with versions since then will have incorrect hashes.
+
+Revision ID: main_0002
+Revises: main_0001
+Create Date: 2024-05-29
+"""
+
+from __future__ import annotations
+
+from aiida.common.log import AIIDA_LOGGER
+from alembic import op
+
+LOGGER = AIIDA_LOGGER.getChild(__file__)
+
+revision = 'main_0002'
+down_revision = 'main_0001'
+branch_labels = None
+depends_on = None
+
+
+def drop_hashes(conn, hash_extra_key: str, entry_point_string: str | None = None) -> None:
+ """Drop hashes of nodes.
+
+ Print warning only if the DB actually contains nodes.
+
+ :param hash_extra_key: The key in the extras used to store the hash at the time of this migration.
+ :param entry_point_string: Optional entry point string of a node type to narrow the subset of nodes to reset. The
+ value should be a complete entry point string, e.g., ``aiida.node:process.calculation.calcjob`` to drop the hash
+ of all ``CalcJobNode`` rows.
+ """
+ from aiida.orm.utils.node import get_type_string_from_class
+ from aiida.plugins import load_entry_point_from_string
+ from sqlalchemy.sql import text
+
+ if entry_point_string is not None:
+ entry_point = load_entry_point_from_string(entry_point_string)
+ node_type = get_type_string_from_class(entry_point.__module__, entry_point.__name__)
+ else:
+ node_type = None
+
+ if node_type:
+ statement_count = text(f"SELECT count(*) FROM db_dbnode WHERE node_type = '{node_type}';")
+ statement_update = text(
+ f"UPDATE db_dbnode SET extras = json_remove(db_dbnode.extras, '$.{hash_extra_key}') WHERE node_type = '{node_type}';" # noqa: E501
+ )
+ else:
+ statement_count = text('SELECT count(*) FROM db_dbnode;')
+ statement_update = text(f"UPDATE db_dbnode SET extras = json_remove(db_dbnode.extras, '$.{hash_extra_key}');")
+
+ node_count = conn.execute(statement_count).fetchall()[0][0]
+
+ if node_count > 0:
+ if entry_point_string:
+ msg = f'Invalidating the hashes of certain nodes. Please run `verdi node rehash -e {entry_point_string}`.'
+ else:
+ msg = 'Invalidating the hashes of all nodes. Please run `verdi node rehash`.'
+ LOGGER.warning(msg)
+
+ conn.execute(statement_update)
+
+
+def upgrade():
+ """Migrations for the upgrade."""
+ drop_hashes(
+ op.get_bind(), hash_extra_key='_aiida_hash', entry_point_string='aiida.node:process.calculation.calcjob'
+ )
+
+
+def downgrade():
+ """Migrations for the downgrade."""
+ drop_hashes(
+ op.get_bind(), hash_extra_key='_aiida_hash', entry_point_string='aiida.node:process.calculation.calcjob'
+ )
diff --git a/src/aiida/storage/sqlite_zip/migrations/env.py b/src/aiida/storage/sqlite_zip/migrations/env.py
index 73abbd917b..5691a95568 100644
--- a/src/aiida/storage/sqlite_zip/migrations/env.py
+++ b/src/aiida/storage/sqlite_zip/migrations/env.py
@@ -6,7 +6,7 @@
# For further information on the license, see the LICENSE.txt file #
# For further information please visit http://www.aiida.net #
###########################################################################
-"""Upper level SQLAlchemy migration funcitons."""
+"""Upper level SQLAlchemy migration functions."""
from alembic import context
diff --git a/tests/cmdline/commands/test_status.py b/tests/cmdline/commands/test_status.py
index d02aff07d2..a4b81dbfc6 100644
--- a/tests/cmdline/commands/test_status.py
+++ b/tests/cmdline/commands/test_status.py
@@ -68,6 +68,7 @@ def test_storage_unable_to_connect(run_cli_command):
profile._attributes['storage']['config']['database_port'] = old_port
+@pytest.mark.requires_psql
def test_storage_incompatible(run_cli_command, monkeypatch):
"""Test `verdi status` when storage schema version is incompatible with that of the code."""
@@ -83,6 +84,7 @@ def storage_cls(*args, **kwargs):
assert result.exit_code is ExitCode.CRITICAL
+@pytest.mark.requires_psql
def test_storage_corrupted(run_cli_command, monkeypatch):
"""Test `verdi status` when the storage is found to be corrupt (e.g. non-matching repository UUIDs)."""
diff --git a/tests/storage/sqlite_dos/migrations/conftest.py b/tests/storage/sqlite_dos/migrations/conftest.py
new file mode 100644
index 0000000000..bba974705f
--- /dev/null
+++ b/tests/storage/sqlite_dos/migrations/conftest.py
@@ -0,0 +1,76 @@
+###########################################################################
+# Copyright (c), The AiiDA team. All rights reserved. #
+# This file is part of the AiiDA code. #
+# #
+# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
+# For further information on the license, see the LICENSE.txt file #
+# For further information please visit http://www.aiida.net #
+###########################################################################
+"""Tests for the migration engine (Alembic) as well as for the AiiDA migrations for SQLAlchemy."""
+
+import collections
+import pathlib
+
+import pytest
+from aiida.manage.configuration import Profile
+from aiida.storage.sqlite_zip.utils import create_sqla_engine
+from sqlalchemy import text
+
+
+@pytest.fixture
+def uninitialised_profile(tmp_path):
+ """Create a profile attached to an empty database and repository folder."""
+
+ yield Profile(
+ 'test_migrate',
+ {
+ 'test_profile': True,
+ 'storage': {
+ 'backend': 'core.sqlite_dos',
+ 'config': {
+ 'filepath': str(tmp_path),
+ },
+ },
+ 'process_control': {'backend': 'null', 'config': {}},
+ },
+ )
+
+
+def _generate_schema(profile: Profile) -> dict:
+ """Create a dict containing indexes of AiiDA tables."""
+ with create_sqla_engine(pathlib.Path(profile.storage_config['filepath']) / 'database.sqlite').connect() as conn:
+ data = collections.defaultdict(list)
+ for type_, name, tbl_name, rootpage, sql in conn.execute(text('SELECT * FROM sqlite_master;')):
+ lines_sql = sql.strip().split('\n') if sql else []
+
+ # For an unknown reason, the ``sql`` is not deterministic as the order of the ``CONSTRAINTS`` rules seem to
+ # be in random order. To make sure they are always in the same order, they have to be ordered manually.
+ if type_ == 'table':
+ lines_constraints = []
+ lines_other = []
+ for line in lines_sql:
+ stripped = line.strip().strip(',')
+
+ if 'CONSTRAINT' in stripped:
+ lines_constraints.append(stripped)
+ else:
+ lines_other.append(stripped)
+
+ lines_sql = lines_other + sorted(lines_constraints)
+ data[type_].append((name, tbl_name, lines_sql))
+
+ for key in data.keys():
+ data[key] = sorted(data[key], key=lambda v: v[0])
+
+ return dict(data)
+
+
+@pytest.fixture
+def reflect_schema():
+ """A fixture to generate the schema of AiiDA tables for a given profile."""
+
+ def factory(profile: Profile) -> dict:
+ """Create a dict containing all tables and fields of AiiDA tables."""
+ return _generate_schema(profile)
+
+ return factory
diff --git a/tests/storage/sqlite_dos/migrations/test_all_schema.py b/tests/storage/sqlite_dos/migrations/test_all_schema.py
new file mode 100644
index 0000000000..51351f918e
--- /dev/null
+++ b/tests/storage/sqlite_dos/migrations/test_all_schema.py
@@ -0,0 +1,49 @@
+###########################################################################
+# Copyright (c), The AiiDA team. All rights reserved. #
+# This file is part of the AiiDA code. #
+# #
+# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
+# For further information on the license, see the LICENSE.txt file #
+# For further information please visit http://www.aiida.net #
+###########################################################################
+"""Basic tests for all migrations"""
+
+import pytest
+from aiida.storage.sqlite_dos.backend import SqliteDosMigrator
+
+
+@pytest.mark.parametrize('version', list(v for v in SqliteDosMigrator.get_schema_versions() if v.startswith('main')))
+def test_main(version, uninitialised_profile, reflect_schema, data_regression):
+ """Test that the migrations produce the expected database schema."""
+ migrator = SqliteDosMigrator(uninitialised_profile)
+ migrator.migrate_up(f'main@{version}')
+ data_regression.check(reflect_schema(uninitialised_profile))
+
+
+def test_main_initialized(uninitialised_profile):
+ """Test that ``migrate`` properly stamps the new schema version when updating database with existing schema."""
+ migrator = SqliteDosMigrator(uninitialised_profile)
+
+ # Initialize database at first version of main branch
+ migrator.migrate_up('main@main_0001')
+ assert migrator.get_schema_version_profile() == 'main_0001'
+ migrator.close()
+
+ # Reinitialize the migrator to make sure we are fetching actual state of database and not in-memory state and then
+ # migrate to head schema version.
+ migrator = SqliteDosMigrator(uninitialised_profile)
+ migrator.migrate()
+ migrator.close()
+
+ # Reinitialize the migrator to make sure we are fetching actual state of database and not in-memory state and then
+ # assert that the database version is properly set to the head schema version
+ migrator = SqliteDosMigrator(uninitialised_profile)
+ assert migrator.get_schema_version_profile() == migrator.get_schema_version_head()
+
+
+def test_head_vs_orm(uninitialised_profile, reflect_schema, data_regression):
+ """Test that the migrations produce the same database schema as the models."""
+ migrator = SqliteDosMigrator(uninitialised_profile)
+ head_version = migrator.get_schema_version_head()
+ migrator.initialise()
+ data_regression.check(reflect_schema(uninitialised_profile), basename=f'test_head_vs_orm_{head_version}_')
diff --git a/tests/storage/sqlite_dos/migrations/test_all_schema/test_head_vs_orm_main_0002_.yml b/tests/storage/sqlite_dos/migrations/test_all_schema/test_head_vs_orm_main_0002_.yml
new file mode 100644
index 0000000000..b70a576550
--- /dev/null
+++ b/tests/storage/sqlite_dos/migrations/test_all_schema/test_head_vs_orm_main_0002_.yml
@@ -0,0 +1,269 @@
+index:
+- - ix_db_dbauthinfo_db_dbauthinfo_aiidauser_id
+ - db_dbauthinfo
+ - - CREATE INDEX ix_db_dbauthinfo_db_dbauthinfo_aiidauser_id ON db_dbauthinfo (aiidauser_id)
+- - ix_db_dbauthinfo_db_dbauthinfo_dbcomputer_id
+ - db_dbauthinfo
+ - - CREATE INDEX ix_db_dbauthinfo_db_dbauthinfo_dbcomputer_id ON db_dbauthinfo (dbcomputer_id)
+- - ix_db_dbcomment_db_dbcomment_dbnode_id
+ - db_dbcomment
+ - - CREATE INDEX ix_db_dbcomment_db_dbcomment_dbnode_id ON db_dbcomment (dbnode_id)
+- - ix_db_dbcomment_db_dbcomment_user_id
+ - db_dbcomment
+ - - CREATE INDEX ix_db_dbcomment_db_dbcomment_user_id ON db_dbcomment (user_id)
+- - ix_db_dbgroup_db_dbgroup_label
+ - db_dbgroup
+ - - CREATE INDEX ix_db_dbgroup_db_dbgroup_label ON db_dbgroup (label)
+- - ix_db_dbgroup_db_dbgroup_type_string
+ - db_dbgroup
+ - - CREATE INDEX ix_db_dbgroup_db_dbgroup_type_string ON db_dbgroup (type_string)
+- - ix_db_dbgroup_db_dbgroup_user_id
+ - db_dbgroup
+ - - CREATE INDEX ix_db_dbgroup_db_dbgroup_user_id ON db_dbgroup (user_id)
+- - ix_db_dbgroup_dbnodes_db_dbgroup_dbnodes_dbgroup_id
+ - db_dbgroup_dbnodes
+ - - CREATE INDEX ix_db_dbgroup_dbnodes_db_dbgroup_dbnodes_dbgroup_id ON db_dbgroup_dbnodes
+ (dbgroup_id)
+- - ix_db_dbgroup_dbnodes_db_dbgroup_dbnodes_dbnode_id
+ - db_dbgroup_dbnodes
+ - - CREATE INDEX ix_db_dbgroup_dbnodes_db_dbgroup_dbnodes_dbnode_id ON db_dbgroup_dbnodes
+ (dbnode_id)
+- - ix_db_dblink_db_dblink_input_id
+ - db_dblink
+ - - CREATE INDEX ix_db_dblink_db_dblink_input_id ON db_dblink (input_id)
+- - ix_db_dblink_db_dblink_label
+ - db_dblink
+ - - CREATE INDEX ix_db_dblink_db_dblink_label ON db_dblink (label)
+- - ix_db_dblink_db_dblink_output_id
+ - db_dblink
+ - - CREATE INDEX ix_db_dblink_db_dblink_output_id ON db_dblink (output_id)
+- - ix_db_dblink_db_dblink_type
+ - db_dblink
+ - - CREATE INDEX ix_db_dblink_db_dblink_type ON db_dblink (type)
+- - ix_db_dblog_db_dblog_dbnode_id
+ - db_dblog
+ - - CREATE INDEX ix_db_dblog_db_dblog_dbnode_id ON db_dblog (dbnode_id)
+- - ix_db_dblog_db_dblog_levelname
+ - db_dblog
+ - - CREATE INDEX ix_db_dblog_db_dblog_levelname ON db_dblog (levelname)
+- - ix_db_dblog_db_dblog_loggername
+ - db_dblog
+ - - CREATE INDEX ix_db_dblog_db_dblog_loggername ON db_dblog (loggername)
+- - ix_db_dbnode_db_dbnode_ctime
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_ctime ON db_dbnode (ctime)
+- - ix_db_dbnode_db_dbnode_dbcomputer_id
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_dbcomputer_id ON db_dbnode (dbcomputer_id)
+- - ix_db_dbnode_db_dbnode_label
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_label ON db_dbnode (label)
+- - ix_db_dbnode_db_dbnode_mtime
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_mtime ON db_dbnode (mtime)
+- - ix_db_dbnode_db_dbnode_node_type
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_node_type ON db_dbnode (node_type)
+- - ix_db_dbnode_db_dbnode_process_type
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_process_type ON db_dbnode (process_type)
+- - ix_db_dbnode_db_dbnode_user_id
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_user_id ON db_dbnode (user_id)
+- - sqlite_autoindex_alembic_version_1
+ - alembic_version
+ - []
+- - sqlite_autoindex_db_dbauthinfo_1
+ - db_dbauthinfo
+ - []
+- - sqlite_autoindex_db_dbcomment_1
+ - db_dbcomment
+ - []
+- - sqlite_autoindex_db_dbcomputer_1
+ - db_dbcomputer
+ - []
+- - sqlite_autoindex_db_dbcomputer_2
+ - db_dbcomputer
+ - []
+- - sqlite_autoindex_db_dbgroup_1
+ - db_dbgroup
+ - []
+- - sqlite_autoindex_db_dbgroup_2
+ - db_dbgroup
+ - []
+- - sqlite_autoindex_db_dbgroup_dbnodes_1
+ - db_dbgroup_dbnodes
+ - []
+- - sqlite_autoindex_db_dblog_1
+ - db_dblog
+ - []
+- - sqlite_autoindex_db_dbnode_1
+ - db_dbnode
+ - []
+- - sqlite_autoindex_db_dbsetting_1
+ - db_dbsetting
+ - []
+- - sqlite_autoindex_db_dbuser_1
+ - db_dbuser
+ - []
+table:
+- - alembic_version
+ - alembic_version
+ - - CREATE TABLE alembic_version (
+ - version_num VARCHAR(32) NOT NULL
+ - )
+ - CONSTRAINT alembic_version_pkc PRIMARY KEY (version_num)
+- - db_dbauthinfo
+ - db_dbauthinfo
+ - - CREATE TABLE db_dbauthinfo (
+ - id INTEGER NOT NULL
+ - aiidauser_id INTEGER NOT NULL
+ - dbcomputer_id INTEGER NOT NULL
+ - metadata JSON NOT NULL
+ - auth_params JSON NOT NULL
+ - enabled BOOLEAN NOT NULL
+ - )
+ - CONSTRAINT db_dbauthinfo_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbauthinfo_aiidauser_id_db_dbuser FOREIGN KEY(aiidauser_id)
+ REFERENCES db_dbuser (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dbauthinfo_dbcomputer_id_db_dbcomputer FOREIGN KEY(dbcomputer_id)
+ REFERENCES db_dbcomputer (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbauthinfo_aiidauser_id_dbcomputer_id UNIQUE (aiidauser_id,
+ dbcomputer_id)
+- - db_dbcomment
+ - db_dbcomment
+ - - CREATE TABLE db_dbcomment (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - dbnode_id INTEGER NOT NULL
+ - ctime DATETIME NOT NULL
+ - mtime DATETIME NOT NULL
+ - user_id INTEGER NOT NULL
+ - content TEXT NOT NULL
+ - )
+ - CONSTRAINT db_dbcomment_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbcomment_dbnode_id_db_dbnode FOREIGN KEY(dbnode_id) REFERENCES
+ db_dbnode (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dbcomment_user_id_db_dbuser FOREIGN KEY(user_id) REFERENCES
+ db_dbuser (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbcomment_uuid UNIQUE (uuid)
+- - db_dbcomputer
+ - db_dbcomputer
+ - - CREATE TABLE db_dbcomputer (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - label VARCHAR(255) NOT NULL
+ - hostname VARCHAR(255) NOT NULL
+ - description TEXT NOT NULL
+ - scheduler_type VARCHAR(255) NOT NULL
+ - transport_type VARCHAR(255) NOT NULL
+ - metadata JSON NOT NULL
+ - )
+ - CONSTRAINT db_dbcomputer_pkey PRIMARY KEY (id)
+ - CONSTRAINT uq_db_dbcomputer_label UNIQUE (label)
+ - CONSTRAINT uq_db_dbcomputer_uuid UNIQUE (uuid)
+- - db_dbgroup
+ - db_dbgroup
+ - - CREATE TABLE db_dbgroup (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - label VARCHAR(255) NOT NULL
+ - type_string VARCHAR(255) NOT NULL
+ - time DATETIME NOT NULL
+ - description TEXT NOT NULL
+ - extras JSON NOT NULL
+ - user_id INTEGER NOT NULL
+ - )
+ - CONSTRAINT db_dbgroup_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbgroup_user_id_db_dbuser FOREIGN KEY(user_id) REFERENCES db_dbuser
+ (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbgroup_label_type_string UNIQUE (label, type_string)
+ - CONSTRAINT uq_db_dbgroup_uuid UNIQUE (uuid)
+- - db_dbgroup_dbnodes
+ - db_dbgroup_dbnodes
+ - - CREATE TABLE db_dbgroup_dbnodes (
+ - id INTEGER NOT NULL
+ - dbnode_id INTEGER NOT NULL
+ - dbgroup_id INTEGER NOT NULL
+ - )
+ - CONSTRAINT db_dbgroup_dbnodes_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbgroup_dbnodes_dbgroup_id_db_dbgroup FOREIGN KEY(dbgroup_id)
+ REFERENCES db_dbgroup (id) DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dbgroup_dbnodes_dbnode_id_db_dbnode FOREIGN KEY(dbnode_id)
+ REFERENCES db_dbnode (id) DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbgroup_dbnodes_dbgroup_id_dbnode_id UNIQUE (dbgroup_id, dbnode_id)
+- - db_dblink
+ - db_dblink
+ - - CREATE TABLE db_dblink (
+ - id INTEGER NOT NULL
+ - input_id INTEGER NOT NULL
+ - output_id INTEGER NOT NULL
+ - label VARCHAR(255) NOT NULL
+ - type VARCHAR(255) NOT NULL
+ - )
+ - CONSTRAINT db_dblink_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dblink_input_id_db_dbnode FOREIGN KEY(input_id) REFERENCES
+ db_dbnode (id) DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dblink_output_id_db_dbnode FOREIGN KEY(output_id) REFERENCES
+ db_dbnode (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+- - db_dblog
+ - db_dblog
+ - - CREATE TABLE db_dblog (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - time DATETIME NOT NULL
+ - loggername VARCHAR(255) NOT NULL
+ - levelname VARCHAR(50) NOT NULL
+ - dbnode_id INTEGER NOT NULL
+ - message TEXT NOT NULL
+ - metadata JSON NOT NULL
+ - )
+ - CONSTRAINT db_dblog_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dblog_dbnode_id_db_dbnode FOREIGN KEY(dbnode_id) REFERENCES
+ db_dbnode (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dblog_uuid UNIQUE (uuid)
+- - db_dbnode
+ - db_dbnode
+ - - CREATE TABLE db_dbnode (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - node_type VARCHAR(255) NOT NULL
+ - process_type VARCHAR(255)
+ - label VARCHAR(255) NOT NULL
+ - description TEXT NOT NULL
+ - ctime DATETIME NOT NULL
+ - mtime DATETIME NOT NULL
+ - attributes JSON
+ - extras JSON
+ - repository_metadata JSON NOT NULL
+ - dbcomputer_id INTEGER
+ - user_id INTEGER NOT NULL
+ - )
+ - CONSTRAINT db_dbnode_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbnode_dbcomputer_id_db_dbcomputer FOREIGN KEY(dbcomputer_id)
+ REFERENCES db_dbcomputer (id) ON DELETE RESTRICT DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dbnode_user_id_db_dbuser FOREIGN KEY(user_id) REFERENCES db_dbuser
+ (id) ON DELETE RESTRICT DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbnode_uuid UNIQUE (uuid)
+- - db_dbsetting
+ - db_dbsetting
+ - - CREATE TABLE db_dbsetting (
+ - id INTEGER NOT NULL
+ - '"key" VARCHAR(1024) NOT NULL'
+ - val JSON
+ - description TEXT NOT NULL
+ - time DATETIME NOT NULL
+ - )
+ - CONSTRAINT db_dbsetting_pkey PRIMARY KEY (id)
+ - CONSTRAINT uq_db_dbsetting_key UNIQUE ("key")
+- - db_dbuser
+ - db_dbuser
+ - - CREATE TABLE db_dbuser (
+ - id INTEGER NOT NULL
+ - email VARCHAR(254) NOT NULL
+ - first_name VARCHAR(254) NOT NULL
+ - last_name VARCHAR(254) NOT NULL
+ - institution VARCHAR(254) NOT NULL
+ - )
+ - CONSTRAINT db_dbuser_pkey PRIMARY KEY (id)
+ - CONSTRAINT uq_db_dbuser_email UNIQUE (email)
diff --git a/tests/storage/sqlite_dos/migrations/test_all_schema/test_main_main_0001_.yml b/tests/storage/sqlite_dos/migrations/test_all_schema/test_main_main_0001_.yml
new file mode 100644
index 0000000000..3b49696512
--- /dev/null
+++ b/tests/storage/sqlite_dos/migrations/test_all_schema/test_main_main_0001_.yml
@@ -0,0 +1,255 @@
+index:
+- - ix_db_dbauthinfo_db_dbauthinfo_aiidauser_id
+ - db_dbauthinfo
+ - - CREATE INDEX ix_db_dbauthinfo_db_dbauthinfo_aiidauser_id ON db_dbauthinfo (aiidauser_id)
+- - ix_db_dbauthinfo_db_dbauthinfo_dbcomputer_id
+ - db_dbauthinfo
+ - - CREATE INDEX ix_db_dbauthinfo_db_dbauthinfo_dbcomputer_id ON db_dbauthinfo (dbcomputer_id)
+- - ix_db_dbcomment_db_dbcomment_dbnode_id
+ - db_dbcomment
+ - - CREATE INDEX ix_db_dbcomment_db_dbcomment_dbnode_id ON db_dbcomment (dbnode_id)
+- - ix_db_dbcomment_db_dbcomment_user_id
+ - db_dbcomment
+ - - CREATE INDEX ix_db_dbcomment_db_dbcomment_user_id ON db_dbcomment (user_id)
+- - ix_db_dbgroup_db_dbgroup_label
+ - db_dbgroup
+ - - CREATE INDEX ix_db_dbgroup_db_dbgroup_label ON db_dbgroup (label)
+- - ix_db_dbgroup_db_dbgroup_type_string
+ - db_dbgroup
+ - - CREATE INDEX ix_db_dbgroup_db_dbgroup_type_string ON db_dbgroup (type_string)
+- - ix_db_dbgroup_db_dbgroup_user_id
+ - db_dbgroup
+ - - CREATE INDEX ix_db_dbgroup_db_dbgroup_user_id ON db_dbgroup (user_id)
+- - ix_db_dbgroup_dbnodes_db_dbgroup_dbnodes_dbgroup_id
+ - db_dbgroup_dbnodes
+ - - CREATE INDEX ix_db_dbgroup_dbnodes_db_dbgroup_dbnodes_dbgroup_id ON db_dbgroup_dbnodes
+ (dbgroup_id)
+- - ix_db_dbgroup_dbnodes_db_dbgroup_dbnodes_dbnode_id
+ - db_dbgroup_dbnodes
+ - - CREATE INDEX ix_db_dbgroup_dbnodes_db_dbgroup_dbnodes_dbnode_id ON db_dbgroup_dbnodes
+ (dbnode_id)
+- - ix_db_dblink_db_dblink_input_id
+ - db_dblink
+ - - CREATE INDEX ix_db_dblink_db_dblink_input_id ON db_dblink (input_id)
+- - ix_db_dblink_db_dblink_label
+ - db_dblink
+ - - CREATE INDEX ix_db_dblink_db_dblink_label ON db_dblink (label)
+- - ix_db_dblink_db_dblink_output_id
+ - db_dblink
+ - - CREATE INDEX ix_db_dblink_db_dblink_output_id ON db_dblink (output_id)
+- - ix_db_dblink_db_dblink_type
+ - db_dblink
+ - - CREATE INDEX ix_db_dblink_db_dblink_type ON db_dblink (type)
+- - ix_db_dblog_db_dblog_dbnode_id
+ - db_dblog
+ - - CREATE INDEX ix_db_dblog_db_dblog_dbnode_id ON db_dblog (dbnode_id)
+- - ix_db_dblog_db_dblog_levelname
+ - db_dblog
+ - - CREATE INDEX ix_db_dblog_db_dblog_levelname ON db_dblog (levelname)
+- - ix_db_dblog_db_dblog_loggername
+ - db_dblog
+ - - CREATE INDEX ix_db_dblog_db_dblog_loggername ON db_dblog (loggername)
+- - ix_db_dbnode_db_dbnode_ctime
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_ctime ON db_dbnode (ctime)
+- - ix_db_dbnode_db_dbnode_dbcomputer_id
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_dbcomputer_id ON db_dbnode (dbcomputer_id)
+- - ix_db_dbnode_db_dbnode_label
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_label ON db_dbnode (label)
+- - ix_db_dbnode_db_dbnode_mtime
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_mtime ON db_dbnode (mtime)
+- - ix_db_dbnode_db_dbnode_node_type
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_node_type ON db_dbnode (node_type)
+- - ix_db_dbnode_db_dbnode_process_type
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_process_type ON db_dbnode (process_type)
+- - ix_db_dbnode_db_dbnode_user_id
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_user_id ON db_dbnode (user_id)
+- - sqlite_autoindex_alembic_version_1
+ - alembic_version
+ - []
+- - sqlite_autoindex_db_dbauthinfo_1
+ - db_dbauthinfo
+ - []
+- - sqlite_autoindex_db_dbcomment_1
+ - db_dbcomment
+ - []
+- - sqlite_autoindex_db_dbcomputer_1
+ - db_dbcomputer
+ - []
+- - sqlite_autoindex_db_dbcomputer_2
+ - db_dbcomputer
+ - []
+- - sqlite_autoindex_db_dbgroup_1
+ - db_dbgroup
+ - []
+- - sqlite_autoindex_db_dbgroup_2
+ - db_dbgroup
+ - []
+- - sqlite_autoindex_db_dbgroup_dbnodes_1
+ - db_dbgroup_dbnodes
+ - []
+- - sqlite_autoindex_db_dblog_1
+ - db_dblog
+ - []
+- - sqlite_autoindex_db_dbnode_1
+ - db_dbnode
+ - []
+- - sqlite_autoindex_db_dbuser_1
+ - db_dbuser
+ - []
+table:
+- - alembic_version
+ - alembic_version
+ - - CREATE TABLE alembic_version (
+ - version_num VARCHAR(32) NOT NULL
+ - )
+ - CONSTRAINT alembic_version_pkc PRIMARY KEY (version_num)
+- - db_dbauthinfo
+ - db_dbauthinfo
+ - - CREATE TABLE db_dbauthinfo (
+ - id INTEGER NOT NULL
+ - aiidauser_id INTEGER NOT NULL
+ - dbcomputer_id INTEGER NOT NULL
+ - metadata JSON NOT NULL
+ - auth_params JSON NOT NULL
+ - enabled BOOLEAN NOT NULL
+ - )
+ - CONSTRAINT db_dbauthinfo_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbauthinfo_aiidauser_id_db_dbuser FOREIGN KEY(aiidauser_id)
+ REFERENCES db_dbuser (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dbauthinfo_dbcomputer_id_db_dbcomputer FOREIGN KEY(dbcomputer_id)
+ REFERENCES db_dbcomputer (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbauthinfo_aiidauser_id_dbcomputer_id UNIQUE (aiidauser_id,
+ dbcomputer_id)
+- - db_dbcomment
+ - db_dbcomment
+ - - CREATE TABLE db_dbcomment (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - dbnode_id INTEGER NOT NULL
+ - ctime DATETIME NOT NULL
+ - mtime DATETIME NOT NULL
+ - user_id INTEGER NOT NULL
+ - content TEXT NOT NULL
+ - )
+ - CONSTRAINT db_dbcomment_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbcomment_dbnode_id_db_dbnode FOREIGN KEY(dbnode_id) REFERENCES
+ db_dbnode (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dbcomment_user_id_db_dbuser FOREIGN KEY(user_id) REFERENCES
+ db_dbuser (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbcomment_uuid UNIQUE (uuid)
+- - db_dbcomputer
+ - db_dbcomputer
+ - - CREATE TABLE db_dbcomputer (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - label VARCHAR(255) NOT NULL
+ - hostname VARCHAR(255) NOT NULL
+ - description TEXT NOT NULL
+ - scheduler_type VARCHAR(255) NOT NULL
+ - transport_type VARCHAR(255) NOT NULL
+ - metadata JSON NOT NULL
+ - )
+ - CONSTRAINT db_dbcomputer_pkey PRIMARY KEY (id)
+ - CONSTRAINT uq_db_dbcomputer_label UNIQUE (label)
+ - CONSTRAINT uq_db_dbcomputer_uuid UNIQUE (uuid)
+- - db_dbgroup
+ - db_dbgroup
+ - - CREATE TABLE db_dbgroup (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - label VARCHAR(255) NOT NULL
+ - type_string VARCHAR(255) NOT NULL
+ - time DATETIME NOT NULL
+ - description TEXT NOT NULL
+ - extras JSON NOT NULL
+ - user_id INTEGER NOT NULL
+ - )
+ - CONSTRAINT db_dbgroup_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbgroup_user_id_db_dbuser FOREIGN KEY(user_id) REFERENCES db_dbuser
+ (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbgroup_label_type_string UNIQUE (label, type_string)
+ - CONSTRAINT uq_db_dbgroup_uuid UNIQUE (uuid)
+- - db_dbgroup_dbnodes
+ - db_dbgroup_dbnodes
+ - - CREATE TABLE db_dbgroup_dbnodes (
+ - id INTEGER NOT NULL
+ - dbnode_id INTEGER NOT NULL
+ - dbgroup_id INTEGER NOT NULL
+ - )
+ - CONSTRAINT db_dbgroup_dbnodes_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbgroup_dbnodes_dbgroup_id_db_dbgroup FOREIGN KEY(dbgroup_id)
+ REFERENCES db_dbgroup (id) DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dbgroup_dbnodes_dbnode_id_db_dbnode FOREIGN KEY(dbnode_id)
+ REFERENCES db_dbnode (id) DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbgroup_dbnodes_dbgroup_id_dbnode_id UNIQUE (dbgroup_id, dbnode_id)
+- - db_dblink
+ - db_dblink
+ - - CREATE TABLE db_dblink (
+ - id INTEGER NOT NULL
+ - input_id INTEGER NOT NULL
+ - output_id INTEGER NOT NULL
+ - label VARCHAR(255) NOT NULL
+ - type VARCHAR(255) NOT NULL
+ - )
+ - CONSTRAINT db_dblink_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dblink_input_id_db_dbnode FOREIGN KEY(input_id) REFERENCES
+ db_dbnode (id) DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dblink_output_id_db_dbnode FOREIGN KEY(output_id) REFERENCES
+ db_dbnode (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+- - db_dblog
+ - db_dblog
+ - - CREATE TABLE db_dblog (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - time DATETIME NOT NULL
+ - loggername VARCHAR(255) NOT NULL
+ - levelname VARCHAR(50) NOT NULL
+ - dbnode_id INTEGER NOT NULL
+ - message TEXT NOT NULL
+ - metadata JSON NOT NULL
+ - )
+ - CONSTRAINT db_dblog_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dblog_dbnode_id_db_dbnode FOREIGN KEY(dbnode_id) REFERENCES
+ db_dbnode (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dblog_uuid UNIQUE (uuid)
+- - db_dbnode
+ - db_dbnode
+ - - CREATE TABLE db_dbnode (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - node_type VARCHAR(255) NOT NULL
+ - process_type VARCHAR(255)
+ - label VARCHAR(255) NOT NULL
+ - description TEXT NOT NULL
+ - ctime DATETIME NOT NULL
+ - mtime DATETIME NOT NULL
+ - attributes JSON
+ - extras JSON
+ - repository_metadata JSON NOT NULL
+ - dbcomputer_id INTEGER
+ - user_id INTEGER NOT NULL
+ - )
+ - CONSTRAINT db_dbnode_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbnode_dbcomputer_id_db_dbcomputer FOREIGN KEY(dbcomputer_id)
+ REFERENCES db_dbcomputer (id) ON DELETE RESTRICT DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dbnode_user_id_db_dbuser FOREIGN KEY(user_id) REFERENCES db_dbuser
+ (id) ON DELETE restrict DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbnode_uuid UNIQUE (uuid)
+- - db_dbuser
+ - db_dbuser
+ - - CREATE TABLE db_dbuser (
+ - id INTEGER NOT NULL
+ - email VARCHAR(254) NOT NULL
+ - first_name VARCHAR(254) NOT NULL
+ - last_name VARCHAR(254) NOT NULL
+ - institution VARCHAR(254) NOT NULL
+ - )
+ - CONSTRAINT db_dbuser_pkey PRIMARY KEY (id)
+ - CONSTRAINT uq_db_dbuser_email UNIQUE (email)
diff --git a/tests/storage/sqlite_dos/migrations/test_all_schema/test_main_main_0002_.yml b/tests/storage/sqlite_dos/migrations/test_all_schema/test_main_main_0002_.yml
new file mode 100644
index 0000000000..3b49696512
--- /dev/null
+++ b/tests/storage/sqlite_dos/migrations/test_all_schema/test_main_main_0002_.yml
@@ -0,0 +1,255 @@
+index:
+- - ix_db_dbauthinfo_db_dbauthinfo_aiidauser_id
+ - db_dbauthinfo
+ - - CREATE INDEX ix_db_dbauthinfo_db_dbauthinfo_aiidauser_id ON db_dbauthinfo (aiidauser_id)
+- - ix_db_dbauthinfo_db_dbauthinfo_dbcomputer_id
+ - db_dbauthinfo
+ - - CREATE INDEX ix_db_dbauthinfo_db_dbauthinfo_dbcomputer_id ON db_dbauthinfo (dbcomputer_id)
+- - ix_db_dbcomment_db_dbcomment_dbnode_id
+ - db_dbcomment
+ - - CREATE INDEX ix_db_dbcomment_db_dbcomment_dbnode_id ON db_dbcomment (dbnode_id)
+- - ix_db_dbcomment_db_dbcomment_user_id
+ - db_dbcomment
+ - - CREATE INDEX ix_db_dbcomment_db_dbcomment_user_id ON db_dbcomment (user_id)
+- - ix_db_dbgroup_db_dbgroup_label
+ - db_dbgroup
+ - - CREATE INDEX ix_db_dbgroup_db_dbgroup_label ON db_dbgroup (label)
+- - ix_db_dbgroup_db_dbgroup_type_string
+ - db_dbgroup
+ - - CREATE INDEX ix_db_dbgroup_db_dbgroup_type_string ON db_dbgroup (type_string)
+- - ix_db_dbgroup_db_dbgroup_user_id
+ - db_dbgroup
+ - - CREATE INDEX ix_db_dbgroup_db_dbgroup_user_id ON db_dbgroup (user_id)
+- - ix_db_dbgroup_dbnodes_db_dbgroup_dbnodes_dbgroup_id
+ - db_dbgroup_dbnodes
+ - - CREATE INDEX ix_db_dbgroup_dbnodes_db_dbgroup_dbnodes_dbgroup_id ON db_dbgroup_dbnodes
+ (dbgroup_id)
+- - ix_db_dbgroup_dbnodes_db_dbgroup_dbnodes_dbnode_id
+ - db_dbgroup_dbnodes
+ - - CREATE INDEX ix_db_dbgroup_dbnodes_db_dbgroup_dbnodes_dbnode_id ON db_dbgroup_dbnodes
+ (dbnode_id)
+- - ix_db_dblink_db_dblink_input_id
+ - db_dblink
+ - - CREATE INDEX ix_db_dblink_db_dblink_input_id ON db_dblink (input_id)
+- - ix_db_dblink_db_dblink_label
+ - db_dblink
+ - - CREATE INDEX ix_db_dblink_db_dblink_label ON db_dblink (label)
+- - ix_db_dblink_db_dblink_output_id
+ - db_dblink
+ - - CREATE INDEX ix_db_dblink_db_dblink_output_id ON db_dblink (output_id)
+- - ix_db_dblink_db_dblink_type
+ - db_dblink
+ - - CREATE INDEX ix_db_dblink_db_dblink_type ON db_dblink (type)
+- - ix_db_dblog_db_dblog_dbnode_id
+ - db_dblog
+ - - CREATE INDEX ix_db_dblog_db_dblog_dbnode_id ON db_dblog (dbnode_id)
+- - ix_db_dblog_db_dblog_levelname
+ - db_dblog
+ - - CREATE INDEX ix_db_dblog_db_dblog_levelname ON db_dblog (levelname)
+- - ix_db_dblog_db_dblog_loggername
+ - db_dblog
+ - - CREATE INDEX ix_db_dblog_db_dblog_loggername ON db_dblog (loggername)
+- - ix_db_dbnode_db_dbnode_ctime
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_ctime ON db_dbnode (ctime)
+- - ix_db_dbnode_db_dbnode_dbcomputer_id
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_dbcomputer_id ON db_dbnode (dbcomputer_id)
+- - ix_db_dbnode_db_dbnode_label
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_label ON db_dbnode (label)
+- - ix_db_dbnode_db_dbnode_mtime
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_mtime ON db_dbnode (mtime)
+- - ix_db_dbnode_db_dbnode_node_type
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_node_type ON db_dbnode (node_type)
+- - ix_db_dbnode_db_dbnode_process_type
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_process_type ON db_dbnode (process_type)
+- - ix_db_dbnode_db_dbnode_user_id
+ - db_dbnode
+ - - CREATE INDEX ix_db_dbnode_db_dbnode_user_id ON db_dbnode (user_id)
+- - sqlite_autoindex_alembic_version_1
+ - alembic_version
+ - []
+- - sqlite_autoindex_db_dbauthinfo_1
+ - db_dbauthinfo
+ - []
+- - sqlite_autoindex_db_dbcomment_1
+ - db_dbcomment
+ - []
+- - sqlite_autoindex_db_dbcomputer_1
+ - db_dbcomputer
+ - []
+- - sqlite_autoindex_db_dbcomputer_2
+ - db_dbcomputer
+ - []
+- - sqlite_autoindex_db_dbgroup_1
+ - db_dbgroup
+ - []
+- - sqlite_autoindex_db_dbgroup_2
+ - db_dbgroup
+ - []
+- - sqlite_autoindex_db_dbgroup_dbnodes_1
+ - db_dbgroup_dbnodes
+ - []
+- - sqlite_autoindex_db_dblog_1
+ - db_dblog
+ - []
+- - sqlite_autoindex_db_dbnode_1
+ - db_dbnode
+ - []
+- - sqlite_autoindex_db_dbuser_1
+ - db_dbuser
+ - []
+table:
+- - alembic_version
+ - alembic_version
+ - - CREATE TABLE alembic_version (
+ - version_num VARCHAR(32) NOT NULL
+ - )
+ - CONSTRAINT alembic_version_pkc PRIMARY KEY (version_num)
+- - db_dbauthinfo
+ - db_dbauthinfo
+ - - CREATE TABLE db_dbauthinfo (
+ - id INTEGER NOT NULL
+ - aiidauser_id INTEGER NOT NULL
+ - dbcomputer_id INTEGER NOT NULL
+ - metadata JSON NOT NULL
+ - auth_params JSON NOT NULL
+ - enabled BOOLEAN NOT NULL
+ - )
+ - CONSTRAINT db_dbauthinfo_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbauthinfo_aiidauser_id_db_dbuser FOREIGN KEY(aiidauser_id)
+ REFERENCES db_dbuser (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dbauthinfo_dbcomputer_id_db_dbcomputer FOREIGN KEY(dbcomputer_id)
+ REFERENCES db_dbcomputer (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbauthinfo_aiidauser_id_dbcomputer_id UNIQUE (aiidauser_id,
+ dbcomputer_id)
+- - db_dbcomment
+ - db_dbcomment
+ - - CREATE TABLE db_dbcomment (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - dbnode_id INTEGER NOT NULL
+ - ctime DATETIME NOT NULL
+ - mtime DATETIME NOT NULL
+ - user_id INTEGER NOT NULL
+ - content TEXT NOT NULL
+ - )
+ - CONSTRAINT db_dbcomment_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbcomment_dbnode_id_db_dbnode FOREIGN KEY(dbnode_id) REFERENCES
+ db_dbnode (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dbcomment_user_id_db_dbuser FOREIGN KEY(user_id) REFERENCES
+ db_dbuser (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbcomment_uuid UNIQUE (uuid)
+- - db_dbcomputer
+ - db_dbcomputer
+ - - CREATE TABLE db_dbcomputer (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - label VARCHAR(255) NOT NULL
+ - hostname VARCHAR(255) NOT NULL
+ - description TEXT NOT NULL
+ - scheduler_type VARCHAR(255) NOT NULL
+ - transport_type VARCHAR(255) NOT NULL
+ - metadata JSON NOT NULL
+ - )
+ - CONSTRAINT db_dbcomputer_pkey PRIMARY KEY (id)
+ - CONSTRAINT uq_db_dbcomputer_label UNIQUE (label)
+ - CONSTRAINT uq_db_dbcomputer_uuid UNIQUE (uuid)
+- - db_dbgroup
+ - db_dbgroup
+ - - CREATE TABLE db_dbgroup (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - label VARCHAR(255) NOT NULL
+ - type_string VARCHAR(255) NOT NULL
+ - time DATETIME NOT NULL
+ - description TEXT NOT NULL
+ - extras JSON NOT NULL
+ - user_id INTEGER NOT NULL
+ - )
+ - CONSTRAINT db_dbgroup_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbgroup_user_id_db_dbuser FOREIGN KEY(user_id) REFERENCES db_dbuser
+ (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbgroup_label_type_string UNIQUE (label, type_string)
+ - CONSTRAINT uq_db_dbgroup_uuid UNIQUE (uuid)
+- - db_dbgroup_dbnodes
+ - db_dbgroup_dbnodes
+ - - CREATE TABLE db_dbgroup_dbnodes (
+ - id INTEGER NOT NULL
+ - dbnode_id INTEGER NOT NULL
+ - dbgroup_id INTEGER NOT NULL
+ - )
+ - CONSTRAINT db_dbgroup_dbnodes_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbgroup_dbnodes_dbgroup_id_db_dbgroup FOREIGN KEY(dbgroup_id)
+ REFERENCES db_dbgroup (id) DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dbgroup_dbnodes_dbnode_id_db_dbnode FOREIGN KEY(dbnode_id)
+ REFERENCES db_dbnode (id) DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbgroup_dbnodes_dbgroup_id_dbnode_id UNIQUE (dbgroup_id, dbnode_id)
+- - db_dblink
+ - db_dblink
+ - - CREATE TABLE db_dblink (
+ - id INTEGER NOT NULL
+ - input_id INTEGER NOT NULL
+ - output_id INTEGER NOT NULL
+ - label VARCHAR(255) NOT NULL
+ - type VARCHAR(255) NOT NULL
+ - )
+ - CONSTRAINT db_dblink_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dblink_input_id_db_dbnode FOREIGN KEY(input_id) REFERENCES
+ db_dbnode (id) DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dblink_output_id_db_dbnode FOREIGN KEY(output_id) REFERENCES
+ db_dbnode (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+- - db_dblog
+ - db_dblog
+ - - CREATE TABLE db_dblog (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - time DATETIME NOT NULL
+ - loggername VARCHAR(255) NOT NULL
+ - levelname VARCHAR(50) NOT NULL
+ - dbnode_id INTEGER NOT NULL
+ - message TEXT NOT NULL
+ - metadata JSON NOT NULL
+ - )
+ - CONSTRAINT db_dblog_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dblog_dbnode_id_db_dbnode FOREIGN KEY(dbnode_id) REFERENCES
+ db_dbnode (id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dblog_uuid UNIQUE (uuid)
+- - db_dbnode
+ - db_dbnode
+ - - CREATE TABLE db_dbnode (
+ - id INTEGER NOT NULL
+ - uuid VARCHAR(32) NOT NULL
+ - node_type VARCHAR(255) NOT NULL
+ - process_type VARCHAR(255)
+ - label VARCHAR(255) NOT NULL
+ - description TEXT NOT NULL
+ - ctime DATETIME NOT NULL
+ - mtime DATETIME NOT NULL
+ - attributes JSON
+ - extras JSON
+ - repository_metadata JSON NOT NULL
+ - dbcomputer_id INTEGER
+ - user_id INTEGER NOT NULL
+ - )
+ - CONSTRAINT db_dbnode_pkey PRIMARY KEY (id)
+ - CONSTRAINT fk_db_dbnode_dbcomputer_id_db_dbcomputer FOREIGN KEY(dbcomputer_id)
+ REFERENCES db_dbcomputer (id) ON DELETE RESTRICT DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT fk_db_dbnode_user_id_db_dbuser FOREIGN KEY(user_id) REFERENCES db_dbuser
+ (id) ON DELETE restrict DEFERRABLE INITIALLY DEFERRED
+ - CONSTRAINT uq_db_dbnode_uuid UNIQUE (uuid)
+- - db_dbuser
+ - db_dbuser
+ - - CREATE TABLE db_dbuser (
+ - id INTEGER NOT NULL
+ - email VARCHAR(254) NOT NULL
+ - first_name VARCHAR(254) NOT NULL
+ - last_name VARCHAR(254) NOT NULL
+ - institution VARCHAR(254) NOT NULL
+ - )
+ - CONSTRAINT db_dbuser_pkey PRIMARY KEY (id)
+ - CONSTRAINT uq_db_dbuser_email UNIQUE (email)