lamindb_setup 0.74.3__tar.gz → 0.75.0__tar.gz

{lamindb_setup-0.74.3 → lamindb_setup-0.75.0}/PKG-INFO

@@ -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 → lamindb_setup-0.75.0}/docs/hub-cloud/04-test-bionty.ipynb

@@ -49,7 +49,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from lnschema_bionty import Source"
+    "from bionty import Source"
    ]
   },
   {
@@ -70,7 +70,7 @@
    },
    "outputs": [],
    "source": [
-    "from bionty_base import settings as bionty_base_settings\n",
+    "from bionty.base import settings as bionty_base_settings\n",
     "\n",
     "assert sources_df.shape[0] > 0\n",
     "assert bionty_base_settings.lamindb_sources.exists()"

{lamindb_setup-0.74.3 → lamindb_setup-0.75.0}/docs/hub-cloud/05-init-hosted-instance.ipynb

@@ -125,7 +125,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.17"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

{lamindb_setup-0.74.3 → lamindb_setup-0.75.0}/docs/hub-cloud/06-connect-hosted-instance.ipynb

@@ -170,7 +170,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.17"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

{lamindb_setup-0.74.3 → lamindb_setup-0.75.0}/docs/hub-prod/test-sqlite-lock.ipynb

@@ -272,7 +272,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.17"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

{lamindb_setup-0.74.3 → lamindb_setup-0.75.0}/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-0.74.3 → lamindb_setup-0.75.0}/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-0.74.3 → lamindb_setup-0.75.0}/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-0.74.3 → lamindb_setup-0.75.0}/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-0.74.3 → lamindb_setup-0.75.0}/lamindb_setup/_schema_metadata.py

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

{lamindb_setup-0.74.3 → lamindb_setup-0.75.0}/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-0.74.3 → lamindb_setup-0.75.0}/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 → lamindb_setup-0.75.0}/noxfile.py

@@ -27,8 +27,8 @@ def lint(session: nox.Session) -> None:
     ["hub-local", "hub-prod", "hub-cloud", "storage", "docs"],
 )
 def install(session: nox.Session, group: str) -> None:
-    no_deps_packages = "git+https://github.com/laminlabs/lnschema-bionty git+https://github.com/laminlabs/lnschema-core git+https://github.com/laminlabs/wetlab lamin-cli"
-    schema_deps = f"""uv pip install --system bionty git+https://github.com/laminlabs/bionty-base
+    no_deps_packages = "git+https://github.com/laminlabs/lnschema-core git+https://github.com/laminlabs/wetlab@single-bionty-repo lamin-cli"
+    schema_deps = f"""uv pip install --system git+https://github.com/laminlabs/bionty git+https://github.com/laminlabs/lamindb@single-bionty-repo
 uv pip install --system --no-deps {no_deps_packages}
 """
     if group == "hub-cloud":

lamindb_setup-0.75.0/tests/hub-local/conftest.py

@@ -0,0 +1,29 @@
+from __future__ import annotations
+
+import os
+
+from laminhub_rest.dev._seed import seed_local_test
+from laminhub_rest.dev._supabase import SupabaseResources
+from laminhub_rest.dev._utils import remove_lamin_local_settings
+
+supabase_resources = SupabaseResources()
+
+
+pytest_plugins = [
+    "laminhub_rest.core.account.user.test.fixtures",
+    "laminhub_rest.test.fixtures.run_id",
+]
+
+
+def pytest_configure():
+    os.environ["LAMIN_ENV"] = "local"
+    remove_lamin_local_settings()
+    supabase_resources.start_local()
+    supabase_resources.reset_local()
+    supabase_resources.migrate()
+    seed_local_test()
+
+
+def pytest_unconfigure():
+    if supabase_resources.edge_function_process:
+        supabase_resources.stop_local_edge_functions()

{lamindb_setup-0.74.3 → lamindb_setup-0.75.0}/tests/hub-local/test_update_schema_in_hub.py

@@ -79,7 +79,7 @@ def test_update_schema_in_hub(setup_instance):
         "through": {
             "left_key": "gene_id",
             "right_key": "pathway_id",
-            "link_table_name": "lnschema_bionty_pathway_genes",
+            "link_table_name": "bionty_pathway_genes",
         },
         "field_name": "pathways",
         "model_name": "gene",

lamindb_setup-0.74.3/tests/hub-local/conftest.py

@@ -1,23 +0,0 @@
-from __future__ import annotations
-
-import os
-
-from lamin_utils import logger
-from laminhub_rest.dev._setup_laminapp_rest import setup_local
-
-pytest_plugins = [
-    "laminhub_rest.core.account.user.test.fixtures",
-    "laminhub_rest.test.fixtures.run_id",
-]
-
-local_setup_state = setup_local()
-
-
-def pytest_configure():
-    assert os.environ["LAMIN_ENV"] == "local"
-    local_setup_state.__enter__()
-
-
-def pytest_unconfigure():
-    if os.environ["LAMIN_ENV"] == "local":
-        local_setup_state.__exit__(None, None, None)