lamindb_setup 0.76.6__py2.py3-none-any.whl → 0.76.7__py2.py3-none-any.whl

lamindb_setup/_connect_instance.py

@@ -1,433 +1,433 @@
-from __future__ import annotations
-
-import os
-from typing import TYPE_CHECKING
-from uuid import UUID
-
-from lamin_utils import logger
-
-from ._check_setup import _check_instance_setup
-from ._close import close as close_instance
-from ._init_instance import MESSAGE_NO_MULTIPLE_INSTANCE, load_from_isettings
-from ._migrate import check_whether_migrations_in_sync
-from ._silence_loggers import silence_loggers
-from .core._hub_core import connect_instance as load_instance_from_hub
-from .core._hub_utils import (
-    LaminDsn,
-    LaminDsnModel,
-)
-from .core._settings import settings
-from .core._settings_instance import InstanceSettings
-from .core._settings_load import load_instance_settings
-from .core._settings_storage import StorageSettings
-from .core._settings_store import instance_settings_file, settings_dir
-from .core.cloud_sqlite_locker import unlock_cloud_sqlite_upon_exception
-
-if TYPE_CHECKING:
-    from pathlib import Path
-
-    from .core.types import UPathStr
-
-# this is for testing purposes only
-# set to True only to test failed load
-_TEST_FAILED_LOAD = False
-
-
-INSTANCE_NOT_FOUND_MESSAGE = (
-    "'{owner}/{name}' not found:"
-    " '{hub_result}'\nCheck your permissions:"
-    " https://lamin.ai/{owner}/{name}"
-)
-
-
-class InstanceNotFoundError(SystemExit):
-    pass
-
-
-def check_db_dsn_equal_up_to_credentials(db_dsn_hub, db_dsn_local):
-    return (
-        db_dsn_hub.scheme == db_dsn_local.scheme
-        and db_dsn_hub.host == db_dsn_local.host
-        and db_dsn_hub.database == db_dsn_local.database
-        and db_dsn_hub.port == db_dsn_local.port
-    )
-
-
-def update_db_using_local(
-    hub_instance_result: dict[str, str],
-    settings_file: Path,
-    db: str | None = None,
-    raise_permission_error=True,
-) -> str | None:
-    db_updated = None
-    # check if postgres
-    if hub_instance_result["db_scheme"] == "postgresql":
-        db_dsn_hub = LaminDsnModel(db=hub_instance_result["db"])
-        if db is not None:
-            db_dsn_local = LaminDsnModel(db=db)
-        else:
-            # read directly from the environment
-            if os.getenv("LAMINDB_INSTANCE_DB") is not None:
-                logger.important("loading db URL from env variable LAMINDB_INSTANCE_DB")
-                db_dsn_local = LaminDsnModel(db=os.getenv("LAMINDB_INSTANCE_DB"))
-            # read from a cached settings file in case the hub result is only
-            # read level or inexistent
-            elif settings_file.exists() and (
-                db_dsn_hub.db.user is None
-                or (db_dsn_hub.db.user is not None and "read" in db_dsn_hub.db.user)
-            ):
-                isettings = load_instance_settings(settings_file)
-                db_dsn_local = LaminDsnModel(db=isettings.db)
-            else:
-                # just take the default hub result and ensure there is actually a user
-                if (
-                    db_dsn_hub.db.user == "none"
-                    and db_dsn_hub.db.password == "none"
-                    and raise_permission_error
-                ):
-                    raise PermissionError(
-                        "No database access, please ask your admin to provide you with"
-                        " a DB URL and pass it via --db <db_url>"
-                    )
-                db_dsn_local = db_dsn_hub
-        if not check_db_dsn_equal_up_to_credentials(db_dsn_hub.db, db_dsn_local.db):
-            raise ValueError(
-                "The local differs from the hub database information:\n 1. did you"
-                " pass a wrong db URL with --db?\n 2. did your database get updated by"
-                " an admin?\nConsider deleting your cached database environment:\nrm"
-                f" {settings_file.as_posix()}"
-            )
-        db_updated = LaminDsn.build(
-            scheme=db_dsn_hub.db.scheme,
-            user=db_dsn_local.db.user,
-            password=db_dsn_local.db.password,
-            host=db_dsn_hub.db.host,  # type: ignore
-            port=db_dsn_hub.db.port,
-            database=db_dsn_hub.db.database,
-        )
-    return db_updated
-
-
-def _connect_instance(
-    owner: str,
-    name: str,
-    *,
-    db: str | None = None,
-    raise_permission_error: bool = True,
-) -> InstanceSettings:
-    settings_file = instance_settings_file(name, owner)
-    make_hub_request = True
-    if settings_file.exists():
-        isettings = load_instance_settings(settings_file)
-        # skip hub request for a purely local instance
-        make_hub_request = isettings.is_remote
-    if make_hub_request:
-        # the following will return a string if the instance does not exist
-        # on the hub
-        hub_result = load_instance_from_hub(owner=owner, name=name)
-        # if hub_result is not a string, it means it made a request
-        # that successfully returned metadata
-        if not isinstance(hub_result, str):
-            instance_result, storage_result = hub_result
-            db_updated = update_db_using_local(
-                instance_result,
-                settings_file,
-                db=db,
-                raise_permission_error=raise_permission_error,
-            )
-            ssettings = StorageSettings(
-                root=storage_result["root"],
-                region=storage_result["region"],
-                uid=storage_result["lnid"],
-                uuid=UUID(storage_result["id"]),
-                instance_id=UUID(instance_result["id"]),
-            )
-            isettings = InstanceSettings(
-                id=UUID(instance_result["id"]),
-                owner=owner,
-                name=name,
-                storage=ssettings,
-                db=db_updated,
-                schema=instance_result["schema_str"],
-                git_repo=instance_result["git_repo"],
-                keep_artifacts_local=bool(instance_result["keep_artifacts_local"]),
-                is_on_hub=True,
-            )
-            check_whether_migrations_in_sync(instance_result["lamindb_version"])
-        else:
-            message = INSTANCE_NOT_FOUND_MESSAGE.format(
-                owner=owner, name=name, hub_result=hub_result
-            )
-            if settings_file.exists():
-                isettings = load_instance_settings(settings_file)
-                if isettings.is_remote:
-                    raise InstanceNotFoundError(message)
-            else:
-                raise InstanceNotFoundError(message)
-    return isettings
-
-
-@unlock_cloud_sqlite_upon_exception(ignore_prev_locker=True)
-def connect(
-    slug: str,
-    *,
-    db: str | None = None,
-    storage: UPathStr | None = None,
-    _raise_not_found_error: bool = True,
-    _test: bool = False,
-) -> str | tuple | None:
-    """Connect to instance.
-
-    Args:
-        slug: The instance slug `account_handle/instance_name` or URL.
-            If the instance is owned by you, it suffices to pass the instance name.
-        db: Load the instance with an updated database URL.
-        storage: Load the instance with an updated default storage.
-    """
-    isettings: InstanceSettings = None  # type: ignore
-    try:
-        owner, name = get_owner_name_from_identifier(slug)
-
-        if _check_instance_setup() and not _test:
-            if (
-                settings._instance_exists
-                and f"{owner}/{name}" == settings.instance.slug
-            ):
-                logger.info(f"connected lamindb: {settings.instance.slug}")
-                return None
-            else:
-                raise RuntimeError(MESSAGE_NO_MULTIPLE_INSTANCE)
-        elif settings._instance_exists and f"{owner}/{name}" != settings.instance.slug:
-            close_instance(mute=True)
-
-        try:
-            isettings = _connect_instance(owner, name, db=db)
-        except InstanceNotFoundError as e:
-            if _raise_not_found_error:
-                raise e
-            else:
-                return "instance-not-found"
-        if isinstance(isettings, str):
-            return isettings
-        if storage is not None:
-            update_isettings_with_storage(isettings, storage)
-        isettings._persist()
-        if _test:
-            return None
-        silence_loggers()
-        check, msg = isettings._load_db()
-        if not check:
-            local_db = (
-                isettings._is_cloud_sqlite and isettings._sqlite_file_local.exists()
-            )
-            if local_db:
-                logger.warning(
-                    "SQLite file does not exist in the cloud, but exists locally:"
-                    f" {isettings._sqlite_file_local}\nTo push the file to the cloud,"
-                    " call: lamin close"
-                )
-            elif _raise_not_found_error:
-                raise SystemExit(msg)
-            else:
-                logger.warning(
-                    f"instance exists with id {isettings._id.hex}, but database is not"
-                    " loadable: re-initializing"
-                )
-                return "instance-corrupted-or-deleted"
-        # this is for testing purposes only
-        if _TEST_FAILED_LOAD:
-            raise RuntimeError("Technical testing error.")
-
-        if storage is not None and isettings.dialect == "sqlite":
-            update_root_field_in_default_storage(isettings)
-        # below is for backfilling the instance_uid value
-        # we'll enable it once more people migrated to 0.71.0
-        # ssettings_record = isettings.storage.record
-        # if ssettings_record.instance_uid is None:
-        #     ssettings_record.instance_uid = isettings.uid
-        #     # try saving if not read-only access
-        #     try:
-        #         ssettings_record.save()
-        #     # raised by django when the access is denied
-        #     except ProgrammingError:
-        #         pass
-        load_from_isettings(isettings)
-    except Exception as e:
-        if isettings is not None:
-            isettings._get_settings_file().unlink(missing_ok=True)  # type: ignore
-        raise e
-    # rename lnschema_bionty to bionty for sql tables
-    if "bionty" in isettings.schema:
-        no_lnschema_bionty_file = (
-            settings_dir / f"no_lnschema_bionty-{isettings.slug.replace('/', '')}"
-        )
-        if not no_lnschema_bionty_file.exists():
-            migrate_lnschema_bionty(isettings, no_lnschema_bionty_file)
-    return None
-
-
-def migrate_lnschema_bionty(isettings: InstanceSettings, no_lnschema_bionty_file: Path):
-    """Migrate lnschema_bionty tables to bionty tables if bionty_source doesn't exist.
-
-    :param db_uri: str, database URI (e.g., 'sqlite:///path/to/db.sqlite' or 'postgresql://user:password@host:port/dbname')
-    """
-    from urllib.parse import urlparse
-
-    parsed_uri = urlparse(isettings.db)
-    db_type = parsed_uri.scheme
-
-    if db_type == "sqlite":
-        import sqlite3
-
-        conn = sqlite3.connect(parsed_uri.path)
-    elif db_type in ["postgresql", "postgres"]:
-        import psycopg2
-
-        conn = psycopg2.connect(isettings.db)
-    else:
-        raise ValueError("Unsupported database type. Use 'sqlite' or 'postgresql' URI.")
-
-    cur = conn.cursor()
-
-    try:
-        # check if bionty_source table exists
-        if db_type == "sqlite":
-            cur.execute(
-                "SELECT name FROM sqlite_master WHERE type='table' AND name='bionty_source'"
-            )
-            migrated = cur.fetchone() is not None
-
-            # tables that need to be renamed
-            cur.execute(
-                "SELECT name FROM sqlite_master WHERE type='table' AND name LIKE 'lnschema_bionty_%'"
-            )
-            tables_to_rename = [
-                row[0][len("lnschema_bionty_") :] for row in cur.fetchall()
-            ]
-        else:  # postgres
-            cur.execute(
-                "SELECT EXISTS (SELECT FROM information_schema.tables WHERE table_name = 'bionty_source')"
-            )
-            migrated = cur.fetchone()[0]
-
-            # tables that need to be renamed
-            cur.execute(
-                "SELECT table_name FROM information_schema.tables WHERE table_name LIKE 'lnschema_bionty_%'"
-            )
-            tables_to_rename = [
-                row[0][len("lnschema_bionty_") :] for row in cur.fetchall()
-            ]
-
-        if migrated:
-            no_lnschema_bionty_file.touch(exist_ok=True)
-        else:
-            try:
-                # rename tables only if bionty_source doesn't exist and there are tables to rename
-                for table in tables_to_rename:
-                    if db_type == "sqlite":
-                        cur.execute(
-                            f"ALTER TABLE lnschema_bionty_{table} RENAME TO bionty_{table}"
-                        )
-                    else:  # postgres
-                        cur.execute(
-                            f"ALTER TABLE lnschema_bionty_{table} RENAME TO bionty_{table};"
-                        )
-
-                # update django_migrations table
-                cur.execute(
-                    "UPDATE django_migrations SET app = 'bionty' WHERE app = 'lnschema_bionty'"
-                )
-
-                logger.warning(
-                    "Please uninstall lnschema-bionty via `pip uninstall lnschema-bionty`!"
-                )
-
-                no_lnschema_bionty_file.touch(exist_ok=True)
-            except Exception:
-                # read-only users can't rename tables
-                pass
-
-        conn.commit()
-
-    except Exception as e:
-        print(f"An error occurred: {e}")
-        conn.rollback()
-
-    finally:
-        # close the cursor and connection
-        cur.close()
-        conn.close()
-
-
-def load(
-    slug: str,
-    *,
-    db: str | None = None,
-    storage: UPathStr | None = None,
-) -> str | tuple | None:
-    """Connect to instance and set ``auto-connect`` to true.
-
-    This is exactly the same as ``ln.connect()`` except for that
-    ``ln.connect()`` doesn't change the state of ``auto-connect``.
-    """
-    result = connect(slug, db=db, storage=storage)
-    settings.auto_connect = True
-    return result
-
-
-def get_owner_name_from_identifier(identifier: str):
-    if "/" in identifier:
-        if identifier.startswith("https://lamin.ai/"):
-            identifier = identifier.replace("https://lamin.ai/", "")
-        split = identifier.split("/")
-        if len(split) > 2:
-            raise ValueError(
-                "The instance identifier needs to be 'owner/name', the instance name"
-                " (owner is current user) or the URL: https://lamin.ai/owner/name."
-            )
-        owner, name = split
-    else:
-        owner = settings.user.handle
-        name = identifier
-    return owner, name
-
-
-def update_isettings_with_storage(
-    isettings: InstanceSettings, storage: UPathStr
-) -> None:
-    ssettings = StorageSettings(storage)
-    if ssettings.type_is_cloud:
-        try:  # triggering ssettings.id makes a lookup in the storage table
-            logger.success(f"loaded storage: {ssettings.id} / {ssettings.root_as_str}")
-        except RuntimeError as e:
-            logger.error(
-                "storage not registered!\n"
-                "load instance without the `storage` arg and register storage root: "
-                f"`lamin set storage --storage {storage}`"
-            )
-            raise e
-    else:
-        # local storage
-        # assumption is you want to merely update the storage location
-        isettings._storage = ssettings  # need this here already
-    # update isettings in place
-    isettings._storage = ssettings
-
-
-# this is different from register!
-# register registers a new storage location
-# update_root_field_in_default_storage updates the root
-# field in the default storage locations
-def update_root_field_in_default_storage(isettings: InstanceSettings):
-    from lnschema_core.models import Storage
-
-    storages = Storage.objects.all()
-    if len(storages) != 1:
-        raise RuntimeError(
-            "You have several storage locations: Can't identify in which storage"
-            " location the root column is to be updated!"
-        )
-    storage = storages[0]
-    storage.root = isettings.storage.root_as_str
-    storage.save()
-    logger.save(f"updated storage root {storage.id} to {isettings.storage.root_as_str}")
+from __future__ import annotations
+
+import os
+from typing import TYPE_CHECKING
+from uuid import UUID
+
+from lamin_utils import logger
+
+from ._check_setup import _check_instance_setup
+from ._close import close as close_instance
+from ._init_instance import MESSAGE_NO_MULTIPLE_INSTANCE, load_from_isettings
+from ._migrate import check_whether_migrations_in_sync
+from ._silence_loggers import silence_loggers
+from .core._hub_core import connect_instance as load_instance_from_hub
+from .core._hub_utils import (
+    LaminDsn,
+    LaminDsnModel,
+)
+from .core._settings import settings
+from .core._settings_instance import InstanceSettings
+from .core._settings_load import load_instance_settings
+from .core._settings_storage import StorageSettings
+from .core._settings_store import instance_settings_file, settings_dir
+from .core.cloud_sqlite_locker import unlock_cloud_sqlite_upon_exception
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+    from .core.types import UPathStr
+
+# this is for testing purposes only
+# set to True only to test failed load
+_TEST_FAILED_LOAD = False
+
+
+INSTANCE_NOT_FOUND_MESSAGE = (
+    "'{owner}/{name}' not found:"
+    " '{hub_result}'\nCheck your permissions:"
+    " https://lamin.ai/{owner}/{name}"
+)
+
+
+class InstanceNotFoundError(SystemExit):
+    pass
+
+
+def check_db_dsn_equal_up_to_credentials(db_dsn_hub, db_dsn_local):
+    return (
+        db_dsn_hub.scheme == db_dsn_local.scheme
+        and db_dsn_hub.host == db_dsn_local.host
+        and db_dsn_hub.database == db_dsn_local.database
+        and db_dsn_hub.port == db_dsn_local.port
+    )
+
+
+def update_db_using_local(
+    hub_instance_result: dict[str, str],
+    settings_file: Path,
+    db: str | None = None,
+    raise_permission_error=True,
+) -> str | None:
+    db_updated = None
+    # check if postgres
+    if hub_instance_result["db_scheme"] == "postgresql":
+        db_dsn_hub = LaminDsnModel(db=hub_instance_result["db"])
+        if db is not None:
+            db_dsn_local = LaminDsnModel(db=db)
+        else:
+            # read directly from the environment
+            if os.getenv("LAMINDB_INSTANCE_DB") is not None:
+                logger.important("loading db URL from env variable LAMINDB_INSTANCE_DB")
+                db_dsn_local = LaminDsnModel(db=os.getenv("LAMINDB_INSTANCE_DB"))
+            # read from a cached settings file in case the hub result is only
+            # read level or inexistent
+            elif settings_file.exists() and (
+                db_dsn_hub.db.user is None
+                or (db_dsn_hub.db.user is not None and "read" in db_dsn_hub.db.user)
+            ):
+                isettings = load_instance_settings(settings_file)
+                db_dsn_local = LaminDsnModel(db=isettings.db)
+            else:
+                # just take the default hub result and ensure there is actually a user
+                if (
+                    db_dsn_hub.db.user == "none"
+                    and db_dsn_hub.db.password == "none"
+                    and raise_permission_error
+                ):
+                    raise PermissionError(
+                        "No database access, please ask your admin to provide you with"
+                        " a DB URL and pass it via --db <db_url>"
+                    )
+                db_dsn_local = db_dsn_hub
+        if not check_db_dsn_equal_up_to_credentials(db_dsn_hub.db, db_dsn_local.db):
+            raise ValueError(
+                "The local differs from the hub database information:\n 1. did you"
+                " pass a wrong db URL with --db?\n 2. did your database get updated by"
+                " an admin?\nConsider deleting your cached database environment:\nrm"
+                f" {settings_file.as_posix()}"
+            )
+        db_updated = LaminDsn.build(
+            scheme=db_dsn_hub.db.scheme,
+            user=db_dsn_local.db.user,
+            password=db_dsn_local.db.password,
+            host=db_dsn_hub.db.host,  # type: ignore
+            port=db_dsn_hub.db.port,
+            database=db_dsn_hub.db.database,
+        )
+    return db_updated
+
+
+def _connect_instance(
+    owner: str,
+    name: str,
+    *,
+    db: str | None = None,
+    raise_permission_error: bool = True,
+) -> InstanceSettings:
+    settings_file = instance_settings_file(name, owner)
+    make_hub_request = True
+    if settings_file.exists():
+        isettings = load_instance_settings(settings_file)
+        # skip hub request for a purely local instance
+        make_hub_request = isettings.is_remote
+    if make_hub_request:
+        # the following will return a string if the instance does not exist
+        # on the hub
+        hub_result = load_instance_from_hub(owner=owner, name=name)
+        # if hub_result is not a string, it means it made a request
+        # that successfully returned metadata
+        if not isinstance(hub_result, str):
+            instance_result, storage_result = hub_result
+            db_updated = update_db_using_local(
+                instance_result,
+                settings_file,
+                db=db,
+                raise_permission_error=raise_permission_error,
+            )
+            ssettings = StorageSettings(
+                root=storage_result["root"],
+                region=storage_result["region"],
+                uid=storage_result["lnid"],
+                uuid=UUID(storage_result["id"]),
+                instance_id=UUID(instance_result["id"]),
+            )
+            isettings = InstanceSettings(
+                id=UUID(instance_result["id"]),
+                owner=owner,
+                name=name,
+                storage=ssettings,
+                db=db_updated,
+                schema=instance_result["schema_str"],
+                git_repo=instance_result["git_repo"],
+                keep_artifacts_local=bool(instance_result["keep_artifacts_local"]),
+                is_on_hub=True,
+            )
+            check_whether_migrations_in_sync(instance_result["lamindb_version"])
+        else:
+            message = INSTANCE_NOT_FOUND_MESSAGE.format(
+                owner=owner, name=name, hub_result=hub_result
+            )
+            if settings_file.exists():
+                isettings = load_instance_settings(settings_file)
+                if isettings.is_remote:
+                    raise InstanceNotFoundError(message)
+            else:
+                raise InstanceNotFoundError(message)
+    return isettings
+
+
+@unlock_cloud_sqlite_upon_exception(ignore_prev_locker=True)
+def connect(
+    slug: str,
+    *,
+    db: str | None = None,
+    storage: UPathStr | None = None,
+    _raise_not_found_error: bool = True,
+    _test: bool = False,
+) -> str | tuple | None:
+    """Connect to instance.
+
+    Args:
+        slug: The instance slug `account_handle/instance_name` or URL.
+            If the instance is owned by you, it suffices to pass the instance name.
+        db: Load the instance with an updated database URL.
+        storage: Load the instance with an updated default storage.
+    """
+    isettings: InstanceSettings = None  # type: ignore
+    try:
+        owner, name = get_owner_name_from_identifier(slug)
+
+        if _check_instance_setup() and not _test:
+            if (
+                settings._instance_exists
+                and f"{owner}/{name}" == settings.instance.slug
+            ):
+                logger.info(f"connected lamindb: {settings.instance.slug}")
+                return None
+            else:
+                raise RuntimeError(MESSAGE_NO_MULTIPLE_INSTANCE)
+        elif settings._instance_exists and f"{owner}/{name}" != settings.instance.slug:
+            close_instance(mute=True)
+
+        try:
+            isettings = _connect_instance(owner, name, db=db)
+        except InstanceNotFoundError as e:
+            if _raise_not_found_error:
+                raise e
+            else:
+                return "instance-not-found"
+        if isinstance(isettings, str):
+            return isettings
+        if storage is not None:
+            update_isettings_with_storage(isettings, storage)
+        isettings._persist()
+        if _test:
+            return None
+        silence_loggers()
+        check, msg = isettings._load_db()
+        if not check:
+            local_db = (
+                isettings._is_cloud_sqlite and isettings._sqlite_file_local.exists()
+            )
+            if local_db:
+                logger.warning(
+                    "SQLite file does not exist in the cloud, but exists locally:"
+                    f" {isettings._sqlite_file_local}\nTo push the file to the cloud,"
+                    " call: lamin close"
+                )
+            elif _raise_not_found_error:
+                raise SystemExit(msg)
+            else:
+                logger.warning(
+                    f"instance exists with id {isettings._id.hex}, but database is not"
+                    " loadable: re-initializing"
+                )
+                return "instance-corrupted-or-deleted"
+        # this is for testing purposes only
+        if _TEST_FAILED_LOAD:
+            raise RuntimeError("Technical testing error.")
+
+        if storage is not None and isettings.dialect == "sqlite":
+            update_root_field_in_default_storage(isettings)
+        # below is for backfilling the instance_uid value
+        # we'll enable it once more people migrated to 0.71.0
+        # ssettings_record = isettings.storage.record
+        # if ssettings_record.instance_uid is None:
+        #     ssettings_record.instance_uid = isettings.uid
+        #     # try saving if not read-only access
+        #     try:
+        #         ssettings_record.save()
+        #     # raised by django when the access is denied
+        #     except ProgrammingError:
+        #         pass
+        load_from_isettings(isettings)
+    except Exception as e:
+        if isettings is not None:
+            isettings._get_settings_file().unlink(missing_ok=True)  # type: ignore
+        raise e
+    # rename lnschema_bionty to bionty for sql tables
+    if "bionty" in isettings.schema:
+        no_lnschema_bionty_file = (
+            settings_dir / f"no_lnschema_bionty-{isettings.slug.replace('/', '')}"
+        )
+        if not no_lnschema_bionty_file.exists():
+            migrate_lnschema_bionty(isettings, no_lnschema_bionty_file)
+    return None
+
+
+def migrate_lnschema_bionty(isettings: InstanceSettings, no_lnschema_bionty_file: Path):
+    """Migrate lnschema_bionty tables to bionty tables if bionty_source doesn't exist.
+
+    :param db_uri: str, database URI (e.g., 'sqlite:///path/to/db.sqlite' or 'postgresql://user:password@host:port/dbname')
+    """
+    from urllib.parse import urlparse
+
+    parsed_uri = urlparse(isettings.db)
+    db_type = parsed_uri.scheme
+
+    if db_type == "sqlite":
+        import sqlite3
+
+        conn = sqlite3.connect(parsed_uri.path)
+    elif db_type in ["postgresql", "postgres"]:
+        import psycopg2
+
+        conn = psycopg2.connect(isettings.db)
+    else:
+        raise ValueError("Unsupported database type. Use 'sqlite' or 'postgresql' URI.")
+
+    cur = conn.cursor()
+
+    try:
+        # check if bionty_source table exists
+        if db_type == "sqlite":
+            cur.execute(
+                "SELECT name FROM sqlite_master WHERE type='table' AND name='bionty_source'"
+            )
+            migrated = cur.fetchone() is not None
+
+            # tables that need to be renamed
+            cur.execute(
+                "SELECT name FROM sqlite_master WHERE type='table' AND name LIKE 'lnschema_bionty_%'"
+            )
+            tables_to_rename = [
+                row[0][len("lnschema_bionty_") :] for row in cur.fetchall()
+            ]
+        else:  # postgres
+            cur.execute(
+                "SELECT EXISTS (SELECT FROM information_schema.tables WHERE table_name = 'bionty_source')"
+            )
+            migrated = cur.fetchone()[0]
+
+            # tables that need to be renamed
+            cur.execute(
+                "SELECT table_name FROM information_schema.tables WHERE table_name LIKE 'lnschema_bionty_%'"
+            )
+            tables_to_rename = [
+                row[0][len("lnschema_bionty_") :] for row in cur.fetchall()
+            ]
+
+        if migrated:
+            no_lnschema_bionty_file.touch(exist_ok=True)
+        else:
+            try:
+                # rename tables only if bionty_source doesn't exist and there are tables to rename
+                for table in tables_to_rename:
+                    if db_type == "sqlite":
+                        cur.execute(
+                            f"ALTER TABLE lnschema_bionty_{table} RENAME TO bionty_{table}"
+                        )
+                    else:  # postgres
+                        cur.execute(
+                            f"ALTER TABLE lnschema_bionty_{table} RENAME TO bionty_{table};"
+                        )
+
+                # update django_migrations table
+                cur.execute(
+                    "UPDATE django_migrations SET app = 'bionty' WHERE app = 'lnschema_bionty'"
+                )
+
+                logger.warning(
+                    "Please uninstall lnschema-bionty via `pip uninstall lnschema-bionty`!"
+                )
+
+                no_lnschema_bionty_file.touch(exist_ok=True)
+            except Exception:
+                # read-only users can't rename tables
+                pass
+
+        conn.commit()
+
+    except Exception as e:
+        print(f"An error occurred: {e}")
+        conn.rollback()
+
+    finally:
+        # close the cursor and connection
+        cur.close()
+        conn.close()
+
+
+def load(
+    slug: str,
+    *,
+    db: str | None = None,
+    storage: UPathStr | None = None,
+) -> str | tuple | None:
+    """Connect to instance and set ``auto-connect`` to true.
+
+    This is exactly the same as ``ln.connect()`` except for that
+    ``ln.connect()`` doesn't change the state of ``auto-connect``.
+    """
+    result = connect(slug, db=db, storage=storage)
+    settings.auto_connect = True
+    return result
+
+
+def get_owner_name_from_identifier(identifier: str):
+    if "/" in identifier:
+        if identifier.startswith("https://lamin.ai/"):
+            identifier = identifier.replace("https://lamin.ai/", "")
+        split = identifier.split("/")
+        if len(split) > 2:
+            raise ValueError(
+                "The instance identifier needs to be 'owner/name', the instance name"
+                " (owner is current user) or the URL: https://lamin.ai/owner/name."
+            )
+        owner, name = split
+    else:
+        owner = settings.user.handle
+        name = identifier
+    return owner, name
+
+
+def update_isettings_with_storage(
+    isettings: InstanceSettings, storage: UPathStr
+) -> None:
+    ssettings = StorageSettings(storage)
+    if ssettings.type_is_cloud:
+        try:  # triggering ssettings.id makes a lookup in the storage table
+            logger.success(f"loaded storage: {ssettings.id} / {ssettings.root_as_str}")
+        except RuntimeError as e:
+            logger.error(
+                "storage not registered!\n"
+                "load instance without the `storage` arg and register storage root: "
+                f"`lamin set storage --storage {storage}`"
+            )
+            raise e
+    else:
+        # local storage
+        # assumption is you want to merely update the storage location
+        isettings._storage = ssettings  # need this here already
+    # update isettings in place
+    isettings._storage = ssettings
+
+
+# this is different from register!
+# register registers a new storage location
+# update_root_field_in_default_storage updates the root
+# field in the default storage locations
+def update_root_field_in_default_storage(isettings: InstanceSettings):
+    from lnschema_core.models import Storage
+
+    storages = Storage.objects.all()
+    if len(storages) != 1:
+        raise RuntimeError(
+            "You have several storage locations: Can't identify in which storage"
+            " location the root column is to be updated!"
+        )
+    storage = storages[0]
+    storage.root = isettings.storage.root_as_str
+    storage.save()
+    logger.save(f"updated storage root {storage.id} to {isettings.storage.root_as_str}")