lamindb_setup 0.74.3__py2.py3-none-any.whl → 0.75.0__py2.py3-none-any.whl

lamindb_setup/__init__.py

@@ -34,7 +34,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.74.3"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.75.0"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import sys
 from os import name as _os_name

lamindb_setup/_close.py

@@ -24,8 +24,9 @@ def close(mute: bool = False) -> None:
                 logger.warning("did not upload cache file - not enough permissions")
             else:
                 raise e
+        if "bionty" in settings.instance.schema:
+            delete_bionty_sources_yaml()
         current_instance_settings_file().unlink()
-        delete_bionty_sources_yaml()
         clear_locker()
         if not mute:
             logger.success(f"closed instance: {instance}")

lamindb_setup/_connect_instance.py

@@ -4,7 +4,6 @@ import os
 from typing import TYPE_CHECKING
 from uuid import UUID
 
-from django.db import ProgrammingError
 from lamin_utils import logger
 
 from ._check_setup import _check_instance_setup
@@ -21,7 +20,7 @@ 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
+from .core._settings_store import instance_settings_file, settings_dir
 from .core.cloud_sqlite_locker import unlock_cloud_sqlite_upon_exception
 
 if TYPE_CHECKING:
@@ -257,9 +256,109 @@ def connect(
         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,
     *,

lamindb_setup/_register_instance.py

@@ -23,7 +23,10 @@ def register(_test: bool = False):
     if ssettings._uid is None and _test:
         # because django isn't up, we can't get it from the database
         ssettings._uid = base62(8)
-    init_storage_hub(ssettings)
+    # cannot yet populate the instance id here
+    ssettings._instance_id = None
+    # flag auto_populate_instance can be removed once FK migration is over
+    init_storage_hub(ssettings, auto_populate_instance=False)
     init_instance_hub(isettings)
     isettings._is_on_hub = True
     isettings._persist()

lamindb_setup/_schema_metadata.py

@@ -102,6 +102,8 @@ Type = Literal[
     "JSONField",
     "DateField",
     "FloatField",
+    "PositiveIntegerField",
+    "PositiveBigIntegerField",
 ]
 
 

lamindb_setup/core/_hub_core.py

@@ -118,11 +118,13 @@ def _select_storage(
 
 def init_storage(
     ssettings: StorageSettings,
+    auto_populate_instance: bool = True,
 ) -> None:
     if settings.user.handle != "anonymous":
         return call_with_fallback_auth(
             _init_storage,
             ssettings=ssettings,
+            auto_populate_instance=auto_populate_instance,
         )
     else:
         storage_exists = call_with_fallback(
@@ -134,7 +136,9 @@ def init_storage(
             raise ValueError("Log in to create a storage location on the hub.")
 
 
-def _init_storage(ssettings: StorageSettings, client: Client) -> None:
+def _init_storage(
+    ssettings: StorageSettings, auto_populate_instance: bool, client: Client
+) -> None:
     from lamindb_setup import settings
 
     # storage roots are always stored without the trailing slash in the SQL
@@ -146,7 +150,11 @@ def _init_storage(ssettings: StorageSettings, client: Client) -> None:
         id = uuid.uuid5(uuid.NAMESPACE_URL, root)
     else:
         id = uuid.uuid4()
-    if ssettings._instance_id is None and settings._instance_exists:
+    if (
+        ssettings._instance_id is None
+        and settings._instance_exists
+        and auto_populate_instance
+    ):
         logger.warning(
             f"will manage storage location {ssettings.root_as_str} with instance {settings.instance.slug}"
         )

lamindb_setup/core/_setup_bionty_sources.py

@@ -14,9 +14,9 @@ def write_bionty_sources(isettings: InstanceSettings) -> None:
         return None
     import shutil
 
-    import bionty_base
-    from bionty_base.dev._handle_sources import parse_sources_yaml
-    from lnschema_bionty.models import Source
+    import bionty.base as bionty_base
+    from bionty.base.dev._handle_sources import parse_sources_yaml
+    from bionty.models import Source
 
     shutil.copy(
         bionty_base.settings.current_sources, bionty_base.settings.lamindb_sources
@@ -58,10 +58,10 @@ def load_bionty_sources(isettings: InstanceSettings):
     if "bionty" not in isettings.schema:
         return None
 
-    import bionty_base
-    from bionty_base.dev._handle_sources import parse_currently_used_sources
-    from bionty_base.dev._io import write_yaml
-    from lnschema_bionty.models import Source
+    import bionty.base as bionty_base
+    from bionty.base.dev._handle_sources import parse_currently_used_sources
+    from bionty.base.dev._io import write_yaml
+    from bionty.models import Source
 
     try:
         # need try except because of integer primary key migration
@@ -77,7 +77,7 @@ def load_bionty_sources(isettings: InstanceSettings):
 def delete_bionty_sources_yaml():
     """Delete LAMINDB_SOURCES_PATH in bionty."""
     try:
-        import bionty_base
+        import bionty.base as bionty_base
 
         bionty_base.settings.lamindb_sources.unlink(missing_ok=True)
     except ModuleNotFoundError:

{lamindb_setup-0.74.3.dist-info → lamindb_setup-0.75.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb_setup
-Version: 0.74.3
+Version: 0.75.0
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Description-Content-Type: text/markdown

{lamindb_setup-0.74.3.dist-info → lamindb_setup-0.75.0.dist-info}/RECORD

@@ -1,18 +1,18 @@
-lamindb_setup/__init__.py,sha256=FLoipEAQXtUmcK_Dwo1brKCnl2kfCxuCwN6GTe1FgxU,1542
+lamindb_setup/__init__.py,sha256=h484xhWUuDVBkjDLj8nu5IKkNELvscWtoABYLZIU7dU,1542
 lamindb_setup/_cache.py,sha256=wA7mbysANwe8hPNbjDo9bOmXJ0xIyaS5iyxIpxSWji4,846
 lamindb_setup/_check.py,sha256=28PcG8Kp6OpjSLSi1r2boL2Ryeh6xkaCL87HFbjs6GA,129
 lamindb_setup/_check_setup.py,sha256=cNEL9Q4yPpmEkGKHH8JgullWl1VUZwALJ4RHn9wZypY,2613
-lamindb_setup/_close.py,sha256=1QS9p2SCacgovYn6xqWU4zFvwHN1RgIccvzwJgFvKgU,1186
-lamindb_setup/_connect_instance.py,sha256=dWqvNBBxqCG6xOiY_fI-P5ccyzno_ePGP3Rp1rgNq3g,12512
+lamindb_setup/_close.py,sha256=cXNwK7QTTyNFt2XTpLnO3KHljJ7ShOcISk95np_dltE,1239
+lamindb_setup/_connect_instance.py,sha256=kAZMTP3w5Vgw-pgZDX9RhYl3TKHaxBuTczTVIsy8Xms,16069
 lamindb_setup/_delete.py,sha256=Y8KSFYgY0UHAvjd7cCL6hZ_XiLeJwx50BguVATcj_Xo,5524
 lamindb_setup/_django.py,sha256=EoyWvFzH0i9wxjy4JZhcoXCTckztP_Mrl6FbYQnMmLE,1534
 lamindb_setup/_exportdb.py,sha256=43g77-tH-vAlTn8ig1mMD9-KXLKvxUeDLaq0gVu3l-c,2114
 lamindb_setup/_importdb.py,sha256=yYYShzUajTsR-cTW4CZ-UNDWZY2uE5PAgNbp-wn8Ogc,1874
 lamindb_setup/_init_instance.py,sha256=jcKtXLOwkoq7bC-0j0xnNU4_up9nPl0iKQPNoJbBts8,12078
 lamindb_setup/_migrate.py,sha256=P4n3x0SYzO9szjF2-JMa7z4mQadtWjHv5ow4HbCDZLI,8864
-lamindb_setup/_register_instance.py,sha256=LlD2n44Gmh8OXrAkL9iL9NiML8QDKnk4d869MhXoOWI,1083
+lamindb_setup/_register_instance.py,sha256=alQuYp2f8Ct8xvRC1gt8p_HZ0tqCd3gZD3kiPBLPpsI,1269
 lamindb_setup/_schema.py,sha256=b3uzhhWpV5mQtDwhMINc2MabGCnGLESy51ito3yl6Wc,679
-lamindb_setup/_schema_metadata.py,sha256=fXqXmKOp81DSOFOem_aE7u5QENRfcNWU-OS7PmSP7qU,12901
+lamindb_setup/_schema_metadata.py,sha256=L0QjUsRmL63txvqptj4t_wh4ZamQ15mKSYsSMrHB1ME,12960
 lamindb_setup/_set_managed_storage.py,sha256=mNZrANn-9rwZ0oGWxxg0wS0T0VOQCWyo4nSSyNAE15Q,1419
 lamindb_setup/_setup_user.py,sha256=6Oc7Rke-yRQSZbuntdUAz8QbJ6UuPzYHI9FnYlf_q-A,3670
 lamindb_setup/_silence_loggers.py,sha256=AKF_YcHvX32eGXdsYK8MJlxEaZ-Uo2f6QDRzjKFCtws,1568
@@ -22,7 +22,7 @@ lamindb_setup/core/_aws_storage.py,sha256=nEjeUv4xUVpoV0Lx-zjjmyb9w804bDyaeiM-Oq
 lamindb_setup/core/_deprecated.py,sha256=3qxUI1dnDlSeR0BYrv7ucjqRBEojbqotPgpShXs4KF8,2520
 lamindb_setup/core/_docs.py,sha256=3k-YY-oVaJd_9UIY-LfBg_u8raKOCNfkZQPA73KsUhs,276
 lamindb_setup/core/_hub_client.py,sha256=Gpt3TmxWQMVenKugCu1agUb-xGN9YFsQOKmrHuFiiDs,5605
-lamindb_setup/core/_hub_core.py,sha256=VToaY2uUHpP5ETkNeuMO4gUeuAfj6ap8uFSndCN1fGk,16592
+lamindb_setup/core/_hub_core.py,sha256=L9rQXM5eVIFOR6oP5uSqHpkYy4y3Bx0w_6acy-_hEVk,16787
 lamindb_setup/core/_hub_crud.py,sha256=b1XF7AJpM9Q-ttm9nPG-r3OTRWHQaGzAGIyvmb83NTo,4859
 lamindb_setup/core/_hub_utils.py,sha256=w5IRtrxZcvxmGSJslzuZF89ewkzXV4cCUmZUVrqmAfo,3026
 lamindb_setup/core/_private_django_api.py,sha256=KIn43HOhiRjkbTbddyJqv-WNTTa1bAizbM1tWXoXPBg,2869
@@ -33,14 +33,14 @@ lamindb_setup/core/_settings_save.py,sha256=n_tYfb9EBSxwm4LHyPRHJptE5uB8lmHhcRkz
 lamindb_setup/core/_settings_storage.py,sha256=65aobewYX6VfOeYZjZQOOI7ZD_3b4QA9TDmrduU0m4c,13262
 lamindb_setup/core/_settings_store.py,sha256=VEE8Ff2A7y4j8ksOaa7g48jNaOqe1PBnBjb1PKKGUKU,2115
 lamindb_setup/core/_settings_user.py,sha256=P2lC4WDRAFfT-Xq3MlXJ-wMKIHCoGNhMTQfRGIAyUNQ,1344
-lamindb_setup/core/_setup_bionty_sources.py,sha256=i_fVCnoh38ouTKKeM-MUXQbkkxMcrSz5dTM_mOCHUcU,2732
+lamindb_setup/core/_setup_bionty_sources.py,sha256=Y6_DiIj1RS8HsUewWtfjIDchYkL1GE98bf75hHN-j5A,2759
 lamindb_setup/core/cloud_sqlite_locker.py,sha256=reu02M4aE2BT_A5AFqwhv48l91mOMyQ4zTd-hh-wtuU,6922
 lamindb_setup/core/django.py,sha256=QUQm3zt5QIiD8uv6o9vbSm_bshqiSWzKSkgD3z2eJCg,3542
 lamindb_setup/core/exceptions.py,sha256=eoI7AXgATgDVzgArtN7CUvpaMUC067vsBg5LHCsWzDM,305
 lamindb_setup/core/hashing.py,sha256=_JliYeCcjT_foOUJ5ck1rvcCo9q7r4b4SaSclQ_w4Qo,3071
 lamindb_setup/core/types.py,sha256=bcYnZ0uM_2NXKJCl94Mmc-uYrQlRUUVKG3sK2N-F-N4,532
 lamindb_setup/core/upath.py,sha256=dwudkTVsXuyjS-2xR16WomcWtXJAEfRZ0ZzFq8_EDhE,27157
-lamindb_setup-0.74.3.dist-info/LICENSE,sha256=UOZ1F5fFDe3XXvG4oNnkL1-Ecun7zpHzRxjp-XsMeAo,11324
-lamindb_setup-0.74.3.dist-info/WHEEL,sha256=Sgu64hAMa6g5FdzHxXv9Xdse9yxpGGMeagVtPMWpJQY,99
-lamindb_setup-0.74.3.dist-info/METADATA,sha256=dqS1Dfpqk1G-BoZzexMF8b1wv_MxWPuqKwKMM1rvWx8,1638
-lamindb_setup-0.74.3.dist-info/RECORD,,
+lamindb_setup-0.75.0.dist-info/LICENSE,sha256=UOZ1F5fFDe3XXvG4oNnkL1-Ecun7zpHzRxjp-XsMeAo,11324
+lamindb_setup-0.75.0.dist-info/WHEEL,sha256=Sgu64hAMa6g5FdzHxXv9Xdse9yxpGGMeagVtPMWpJQY,99
+lamindb_setup-0.75.0.dist-info/METADATA,sha256=tpmMZNwLSmNudPk6PE-n6mRXDk7DSjAvfEMbtGeU9uA,1638
+lamindb_setup-0.75.0.dist-info/RECORD,,