lamindb_setup 1.3.0__py3-none-any.whl → 1.3.1__py3-none-any.whl

lamindb_setup/__init__.py

@@ -33,7 +33,7 @@ Modules & settings:
 
 """
 
-__version__ = "1.3.0"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "1.3.1"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os
 

lamindb_setup/_connect_instance.py

@@ -168,6 +168,7 @@ def _connect_instance(
                 schema_id=None
                 if (schema_id := instance_result["schema_id"]) is None
                 else UUID(schema_id),
+                fine_grained_access=instance_result.get("fine_grained_access", False),
             )
         else:
             if hub_result != "anonymous-user":
@@ -205,7 +206,6 @@ def connect(instance: str | None = None, **kwargs) -> str | tuple | None:
     for kwarg in kwargs:
         if kwarg not in valid_kwargs:
             raise TypeError(f"connect() got unexpected keyword argument '{kwarg}'")
-
     isettings: InstanceSettings = None  # type: ignore
     # _db is still needed because it is called in init
     _db: str | None = kwargs.get("_db", None)

lamindb_setup/_init_instance.py

@@ -6,6 +6,7 @@ import uuid
 from typing import TYPE_CHECKING, Literal
 from uuid import UUID
 
+import click
 from django.core.exceptions import FieldError
 from django.db.utils import OperationalError, ProgrammingError
 from lamin_utils import logger
@@ -25,6 +26,11 @@ if TYPE_CHECKING:
     from .core.types import UPathStr
 
 
+class InstanceNotCreated(click.ClickException):
+    def show(self, file=None):
+        pass
+
+
 def get_schema_module_name(module_name, raise_import_error: bool = True) -> str | None:
     import importlib.util
 
@@ -242,7 +248,7 @@ def init(
             raise CannotSwitchDefaultInstance(MESSAGE_CANNOT_SWITCH_DEFAULT_INSTANCE)
         elif _write_settings:
             close_instance(mute=True)
-        from .core._hub_core import init_instance as init_instance_hub
+        from .core._hub_core import init_instance_hub
 
         name_str, instance_id, instance_state, _ = validate_init_args(
             storage=storage,
@@ -284,6 +290,13 @@ def init(
             isettings.is_remote and instance_state != "instance-corrupted-or-deleted"
         )
         if register_on_hub:
+            # can't register the instance in the hub
+            # if storage is not in the hub
+            # raise the exception and initiate cleanups
+            if not isettings.storage.is_on_hub:
+                raise InstanceNotCreated(
+                    "Unable to create the instance because failed to register the storage."
+                )
             init_instance_hub(
                 isettings, account_id=user__uuid, access_token=access_token
             )

lamindb_setup/_migrate.py

@@ -23,25 +23,36 @@ def check_whether_migrations_in_sync(db_version_str: str):
         return None
     installed_version = version.parse(installed_version_str)
     db_version = version.parse(db_version_str)
-    if installed_version.major < db_version.major or (
+    if installed_version.major < db_version.major:
+        logger.warning(
+            f"the database ({db_version_str}) is far ahead of your installed lamindb package ({installed_version_str})"
+        )
+        logger.important(
+            f"please update lamindb: pip install lamindb>={db_version.major}"
+        )
+    elif (
         installed_version.major == db_version.major
         and installed_version.minor < db_version.minor
     ):
         db_version_lower = f"{db_version.major}.{db_version.minor}"
-        db_version_upper = f"{db_version.major}.{db_version.minor + 1}"
-        logger.warning(
+        logger.important(
             f"the database ({db_version_str}) is ahead of your installed lamindb"
             f" package ({installed_version_str})"
         )
         logger.important(
-            "please update lamindb: pip install"
-            f' "lamindb>={db_version_lower},<{db_version_upper}"'
+            f"consider updating lamindb: pip install lamindb>={db_version_lower}"
         )
-    elif installed_version.major > db_version.major or (
+    elif installed_version.major > db_version.major:
+        logger.warning(
+            f"the database ({db_version_str}) is far behind your installed lamindb package"
+            f" ({installed_version_str})"
+        )
+        logger.important("migrate your database: lamin migrate deploy")
+    elif (
         installed_version.major == db_version.major
         and installed_version.minor > db_version.minor
     ):
-        logger.warning(
+        logger.important(
             f"the database ({db_version_str}) is behind your installed lamindb package"
             f" ({installed_version_str})"
         )

lamindb_setup/_register_instance.py

@@ -10,8 +10,7 @@ from .core.django import setup_django
 def register(_test: bool = False):
     """Register an instance on the hub."""
     from ._check_setup import _check_instance_setup
-    from .core._hub_core import init_instance as init_instance_hub
-    from .core._hub_core import init_storage as init_storage_hub
+    from .core._hub_core import init_instance_hub, init_storage_hub
 
     logger.warning("""lamin register will be removed soon""")
 

lamindb_setup/core/_hub_client.py

@@ -180,3 +180,37 @@ def call_with_fallback(
             except NameError:
                 pass
     return result
+
+
+def requests_client():
+    # local is used in tests
+    if os.environ.get("LAMIN_ENV", "prod") == "local":
+        from fastapi.testclient import TestClient
+        from laminhub_rest.main import app
+
+        return TestClient(app)
+
+    import requests  # type: ignore
+
+    return requests
+
+
+def request_get_auth(url: str, access_token: str, renew_token: bool = True):
+    requests = requests_client()
+
+    response = requests.get(url, headers={"Authorization": f"Bearer {access_token}"})
+    # upate access_token and try again if failed
+    if response.status_code != 200 and renew_token:
+        from lamindb_setup import settings
+
+        access_token = get_access_token(
+            settings.user.email, settings.user.password, settings.user.api_key
+        )
+
+        settings.user.access_token = access_token
+        save_user_settings(settings.user)
+
+        response = requests.get(
+            url, headers={"Authorization": f"Bearer {access_token}"}
+        )
+    return response

lamindb_setup/core/_hub_core.py

@@ -16,6 +16,7 @@ from ._hub_client import (
     call_with_fallback,
     call_with_fallback_auth,
     connect_hub,
+    request_get_auth,
 )
 from ._hub_crud import (
     _delete_instance_record,
@@ -115,7 +116,7 @@ def _select_storage(
         return True
 
 
-def init_storage(
+def init_storage_hub(
     ssettings: StorageSettings,
     auto_populate_instance: bool = True,
     created_by: UUID | None = None,
@@ -123,7 +124,7 @@ def init_storage(
 ) -> Literal["hub-record-retireved", "hub-record-created"]:
     if settings.user.handle != "anonymous" or access_token is not None:
         return call_with_fallback_auth(
-            _init_storage,
+            _init_storage_hub,
             ssettings=ssettings,
             auto_populate_instance=auto_populate_instance,
             created_by=created_by,
@@ -139,7 +140,7 @@ def init_storage(
             raise ValueError("Log in to create a storage location on the hub.")
 
 
-def _init_storage(
+def _init_storage_hub(
     client: Client,
     ssettings: StorageSettings,
     auto_populate_instance: bool,
@@ -269,20 +270,20 @@ def delete_instance_record(instance_id: UUID, access_token: str | None = None) -
     )
 
 
-def init_instance(
+def init_instance_hub(
     isettings: InstanceSettings,
     account_id: UUID | None = None,
     access_token: str | None = None,
 ) -> None:
     return call_with_fallback_auth(
-        _init_instance,
+        _init_instance_hub,
         isettings=isettings,
         account_id=account_id,
         access_token=access_token,
     )
 
 
-def _init_instance(
+def _init_instance_hub(
     client: Client, isettings: InstanceSettings, account_id: UUID | None = None
 ) -> None:
     from ._settings import settings
@@ -437,6 +438,38 @@ def _access_aws(*, storage_root: str, client: Client) -> dict[str, dict]:
     return storage_root_info
 
 
+def access_db(isettings: InstanceSettings, access_token: str | None = None) -> str:
+    if access_token is None:
+        if settings.user.handle == "anonymous":
+            raise RuntimeError(
+                f"Can only get fine-grained access to {isettings.slug} if authenticated."
+            )
+        else:
+            access_token = settings.user.access_token
+            renew_token = True
+    else:
+        renew_token = False
+    # local is used in tests
+    url = f"/access_v2/instances/{isettings._id}/db_token"
+    if os.environ.get("LAMIN_ENV", "prod") != "local":
+        api_url = isettings._api_url
+        if api_url is None:
+            raise RuntimeError(
+                f"Can only get fine-grained access to {isettings.slug} if api_url is present."
+            )
+        url = api_url + url
+
+    response = request_get_auth(url, access_token, renew_token)  # type: ignore
+    response_json = response.json()
+    if response.status_code != 200:
+        raise PermissionError(
+            f"Fine-grained access to {isettings.slug} failed: {response_json}"
+        )
+    if "token" not in response_json:
+        raise RuntimeError("The response of access_db does not contain a db token.")
+    return response_json["token"]
+
+
 def get_lamin_site_base_url():
     if "LAMIN_ENV" in os.environ:
         if os.environ["LAMIN_ENV"] == "local":

lamindb_setup/core/_settings_instance.py

@@ -59,6 +59,7 @@ class InstanceSettings:
         is_on_hub: bool | None = None,  # initialized from hub
         api_url: str | None = None,
         schema_id: UUID | None = None,
+        fine_grained_access: bool = False,
         _locker_user: UserSettings | None = None,  # user to lock for if cloud sqlite
     ):
         from ._hub_utils import validate_db_arg
@@ -76,9 +77,12 @@ class InstanceSettings:
         self._keep_artifacts_local = keep_artifacts_local
         self._storage_local: StorageSettings | None = None
         self._is_on_hub = is_on_hub
-        # private, needed for writing instance settings
+        # private, needed for api requests
         self._api_url = api_url
         self._schema_id = schema_id
+        # private, whether fine grained access is used
+        # needed to be set to request jwt etc
+        self._fine_grained_access = fine_grained_access
         # if None then settings.user is used
         self._locker_user = _locker_user
 

lamindb_setup/core/_settings_load.py

@@ -101,6 +101,9 @@ def setup_instance_from_store(store: InstanceSettingsStore) -> InstanceSettings:
         modules=_null_to_value(store.schema_str),
         git_repo=_null_to_value(store.git_repo),
         keep_artifacts_local=store.keep_artifacts_local,  # type: ignore
+        api_url=_null_to_value(store.api_url),
+        schema_id=None if store.schema_id == "null" else UUID(store.schema_id),
+        fine_grained_access=store.fine_grained_access,
     )
 
 

lamindb_setup/core/_settings_save.py

@@ -60,6 +60,7 @@ def save_settings(
                         "id",
                         "api_url",
                         "schema_id",
+                        "fine_grained_access",
                     }:
                         settings_key = f"_{store_key.rstrip('_')}"
                     else:

lamindb_setup/core/_settings_storage.py

@@ -150,8 +150,7 @@ def init_storage(
     # the below might update the uid with one that's already taken on the hub
     if not prevent_register_hub:
         if ssettings.type_is_cloud or register_hub:
-            from ._hub_core import delete_storage_record
-            from ._hub_core import init_storage as init_storage_hub
+            from ._hub_core import delete_storage_record, init_storage_hub
 
             hub_record_status = init_storage_hub(
                 ssettings,
@@ -175,6 +174,7 @@ def init_storage(
         # only newly created
         if hub_record_status == "hub-record-created" and ssettings._uuid is not None:
             delete_storage_record(ssettings._uuid, access_token=access_token)  # type: ignore
+            ssettings._uuid_ = None
             hub_record_status = "hub-record-not-created"
         ssettings._instance_id = None
     return ssettings, hub_record_status

lamindb_setup/core/_settings_store.py

@@ -57,6 +57,7 @@ class InstanceSettingsStore(BaseSettings):
     db: Optional[str]  # doesn't like new types on 3.9 even with future annotations
     schema_str: Optional[str]
     schema_id: Optional[str] = None
+    fine_grained_access: bool = False
     id: str
     git_repo: Optional[str]
     keep_artifacts_local: Optional[bool]

lamindb_setup/core/django.py

@@ -14,7 +14,7 @@ IS_MIGRATING = False
 CONN_MAX_AGE = 299
 
 
-def set_token(token: str | None, connection_name: str = "default"):
+def set_db_token(token: str | None, connection_name: str = "default"):
     # None to reset
     from django.db import connections
     from django.db.backends.base.base import BaseDatabaseWrapper
@@ -125,6 +125,11 @@ def setup_django(
 
         BaseDatabaseWrapper.close_if_health_check_failed = close_if_health_check_failed
 
+        if isettings._fine_grained_access:
+            from ._hub_core import access_db
+
+            set_db_token(access_db(isettings))
+
     if configure_only:
         return None
 

{lamindb_setup-1.3.0.dist-info → lamindb_setup-1.3.1.dist-info}/METADATA

@@ -1,12 +1,12 @@
 Metadata-Version: 2.3
 Name: lamindb_setup
-Version: 1.3.0
+Version: 1.3.1
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 Requires-Dist: lamin_utils>=0.3.3
-Requires-Dist: django>=5,<5.2
+Requires-Dist: django>=5.1,<5.2
 Requires-Dist: dj_database_url>=1.3.0,<3.0.0
 Requires-Dist: pydantic-settings
 Requires-Dist: appdirs<2.0.0

{lamindb_setup-1.3.0.dist-info → lamindb_setup-1.3.1.dist-info}/RECORD

@@ -1,17 +1,17 @@
-lamindb_setup/__init__.py,sha256=B7IVjz1M1qrpfYuPg4mQ66YiIyfAcYtmSfjLULXKpII,2692
+lamindb_setup/__init__.py,sha256=ufOB1lSTRTPp-RZONLCcBSPomaQdlpnxW9U__2ODvcQ,2692
 lamindb_setup/_cache.py,sha256=aszT-zk3S5dTLKp5g1W-S_FPh2E5YVCALwWSGPJLWBM,1493
 lamindb_setup/_check.py,sha256=28PcG8Kp6OpjSLSi1r2boL2Ryeh6xkaCL87HFbjs6GA,129
 lamindb_setup/_check_setup.py,sha256=d1GS1Csy2G9AysfjoyVcNVY0lhHiWSwSLpfgdIQf35s,5477
 lamindb_setup/_close.py,sha256=pf8PHrtRBC6TycBtVAXzD9EZSGufoyp5M82o6zLHmt4,1240
-lamindb_setup/_connect_instance.py,sha256=eMiAjuMDuZ_x8N5LLHwz5O4VXv0nH6AzYW0tnnjUSug,18190
+lamindb_setup/_connect_instance.py,sha256=IXpU43DO-DWm9twDeuQJeBbKj-oB4SzEqsCjIX4AZMo,18276
 lamindb_setup/_delete.py,sha256=4NqJkEA812VWRxTBW1o1h1YX0fF7sQwn08hj1BmvCPs,5673
 lamindb_setup/_django.py,sha256=uIQflpkp8l3axyPaKURlk3kacgpElVP5KOKmFxYSMGk,1454
 lamindb_setup/_entry_points.py,sha256=sKwXPX9xjOotoAjvgkU5LBwjjHLWVkh0ZGdiSsrch9k,522
 lamindb_setup/_exportdb.py,sha256=QLjoH4dEwqa01A12naKaDPglCCzl2_VLKWFfJRE_uSg,2113
 lamindb_setup/_importdb.py,sha256=fKv9ev5OOj_-bmzC8XZ1GxOcjIjI486yrHSHDWQrJeI,1874
-lamindb_setup/_init_instance.py,sha256=nZkqGqJQ_sF1-oQmnbpIjP1ExWUow5I5N7lsyX9m-io,13811
-lamindb_setup/_migrate.py,sha256=drf7Lsa8oDXBPBWMWMge0n5VyNPvsrCFAhcXlN91OxM,9165
-lamindb_setup/_register_instance.py,sha256=alQuYp2f8Ct8xvRC1gt8p_HZ0tqCd3gZD3kiPBLPpsI,1269
+lamindb_setup/_init_instance.py,sha256=wZ1yEnbogduQOXkEbcip9Jm8mys1NtJy2W5RRWJy1lQ,14253
+lamindb_setup/_migrate.py,sha256=gqWfXgixiD4dpQOq1ePVPfCj88iMCQSx4vxg_QKvFGc,9586
+lamindb_setup/_register_instance.py,sha256=X7ZGlCVOZKq4zTpi3bxML4jzo6hgN9UYmdTxxf6JLmc,1205
 lamindb_setup/_schema.py,sha256=b3uzhhWpV5mQtDwhMINc2MabGCnGLESy51ito3yl6Wc,679
 lamindb_setup/_schema_metadata.py,sha256=cDkNHyFTFZq879UGY6i-rJEXfeBN59AN3Wz86caKnYI,14358
 lamindb_setup/_set_managed_storage.py,sha256=4tDxXQMt8Gw028uY3vIQxZQ7qBNXhQMc8saarNK_Z-s,2043
@@ -22,26 +22,26 @@ lamindb_setup/core/_aws_options.py,sha256=Umxu_1AYd-0LJUElZxowvE9vNA7Z8kh_63g3pp
 lamindb_setup/core/_aws_storage.py,sha256=nEjeUv4xUVpoV0Lx-zjjmyb9w804bDyaeiM-OqbfwM0,1799
 lamindb_setup/core/_deprecated.py,sha256=HN7iUBdEgahw5e4NHCd1VJooUfieNb6GRzS5x8jU-q8,2549
 lamindb_setup/core/_docs.py,sha256=3k-YY-oVaJd_9UIY-LfBg_u8raKOCNfkZQPA73KsUhs,276
-lamindb_setup/core/_hub_client.py,sha256=ywJ_HpGqwui6t_vsj-my80gYgSSgAiSFyZoRj03sBWk,6464
-lamindb_setup/core/_hub_core.py,sha256=OPByE76h6MQaCToT7AzbeH9Tr5-BbpIAh__oIiEl1VE,20021
+lamindb_setup/core/_hub_client.py,sha256=Wy3QRJ1mySSu7xHjLZkcQvZpBX03g8oKbxiqxRIpPgo,7456
+lamindb_setup/core/_hub_core.py,sha256=8ZdekUtJMPdWLUqiHeT2nZ_F7FV0GJkQ7ixaIOSaAr4,21309
 lamindb_setup/core/_hub_crud.py,sha256=IAuPZes1am8OFwtcf5jSRQPGG1eKwVTEsp9Li-uq0cQ,5377
 lamindb_setup/core/_hub_utils.py,sha256=6dyDGyzYFgVfR_lE3VN3CP1jGp98gxPtr-T91PAP05U,2687
 lamindb_setup/core/_private_django_api.py,sha256=By63l3vIEtK1pq246FhHq3tslxsaTJGKm5VakYluWp4,2656
 lamindb_setup/core/_settings.py,sha256=eslFO84vb5uRRfJ3r_uu4O8677l8lU5BbpZJMSAYw6A,8244
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 lamindb_setup/core/_settings_user.py,sha256=lWqV3HmZCsEq2UsU_iVNW0p9ddsNg7-B6xOaMNH1aw0,1475
 lamindb_setup/core/_setup_bionty_sources.py,sha256=qTPMV5TEbNiTB81QqG2rSs6W8j8kQ7kVQMLOXRzAxBI,4004
 lamindb_setup/core/cloud_sqlite_locker.py,sha256=i6TrT7HG0lqliPvZTlsZ_uplPaqhPBbabyfeR32SkA8,7107
-lamindb_setup/core/django.py,sha256=vmrGDiqX2FSmMII_YLcQtwO8SRzm6zKayjeNJLGhuiU,4697
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 lamindb_setup/core/exceptions.py,sha256=4NpLUNUIfXYVTFX2FvLZF8RW34exk2Vn2X3G4YhnTRg,276
 lamindb_setup/core/hashing.py,sha256=M3Q1-ywnqh4Uy5zojbQfLju19HU0ySp8Oi7FGIJXfFI,3667
 lamindb_setup/core/types.py,sha256=zJii2le38BJUmsNVvzDrbzGYr0yaeb-9Rw9IKmsBr3k,523
 lamindb_setup/core/upath.py,sha256=AvRmICPBxQx-2iQYsXDFsrJS-AAUNuw6IymLcVmkWvo,33550
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-lamindb_setup-1.3.0.dist-info/RECORD,,
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