lamindb_setup 0.71.0__py2.py3-none-any.whl → 0.71.2__py2.py3-none-any.whl

lamindb_setup/__init__.py

@@ -34,7 +34,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.71.0"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.71.2"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import sys
 from os import name as _os_name

lamindb_setup/_connect_instance.py

@@ -4,6 +4,7 @@ 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
@@ -106,7 +107,7 @@ def connect(
     *,
     db: str | None = None,
     storage: UPathStr | None = None,
-    _raise_not_reachable_error: bool = True,
+    _raise_not_found_error: bool = True,
     _test: bool = False,
 ) -> str | tuple | None:
     """Connect to instance.
@@ -158,6 +159,8 @@ def connect(
                     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"]),
@@ -178,12 +181,12 @@ def connect(
                 if settings_file.exists():
                     isettings = load_instance_settings(settings_file)
                     if isettings.is_remote:
-                        if _raise_not_reachable_error:
+                        if _raise_not_found_error:
                             raise InstanceNotFoundError(message)
                         return "instance-not-found"
 
                 else:
-                    if _raise_not_reachable_error:
+                    if _raise_not_found_error:
                         raise InstanceNotFoundError(message)
                     return "instance-not-found"
 
@@ -206,7 +209,7 @@ def connect(
                     f" {isettings._sqlite_file_local}\nTo push the file to the cloud,"
                     " call: lamin close"
                 )
-            elif _raise_not_reachable_error:
+            elif _raise_not_found_error:
                 raise SystemExit(msg)
             else:
                 logger.warning(
@@ -220,6 +223,17 @@ def connect(
 
         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:

lamindb_setup/_delete.py

@@ -6,7 +6,11 @@ from uuid import UUID
 
 from lamin_utils import logger
 
-from ._connect_instance import INSTANCE_NOT_FOUND_MESSAGE
+from ._connect_instance import (
+    INSTANCE_NOT_FOUND_MESSAGE,
+    InstanceNotFoundError,
+    get_owner_name_from_identifier,
+)
 from .core._hub_core import connect_instance as load_instance_from_hub
 from .core._hub_core import delete_instance as delete_instance_on_hub
 from .core._hub_core import get_storage_records_for_instance
@@ -54,55 +58,48 @@ def delete_by_isettings(isettings: InstanceSettings) -> None:
         settings._instance_settings = None
 
 
-def delete(
-    instance_name: str, force: bool = False, require_empty: bool = True
-) -> int | None:
+def delete(slug: str, force: bool = False, require_empty: bool = True) -> int | None:
     """Delete a LaminDB instance.
 
     Args:
-        instance_name (str): The name of the instance to delete.
-        force (bool): Whether to skip the confirmation prompt.
-        require_empty (bool): Whether to check if the instance is empty before deleting.
+        slug: The instance slug `account_handle/instance_name` or URL.
+            If the instance is owned by you, it suffices to pass the instance name.
+        force: Whether to skip the confirmation prompt.
+        require_empty: Whether to check if the instance is empty before deleting.
     """
-    if "/" in instance_name:
-        logger.warning(
-            "Deleting the instance of another user is currently not supported with the"
-            " CLI. Please provide only the instance name when deleting an instance ('/'"
-            " delimiter not allowed)."
-        )
-        raise ValueError("Invalid instance name: '/' delimiter not allowed.")
-    instance_slug = f"{settings.user.handle}/{instance_name}"
+    instance_owner, instance_name = get_owner_name_from_identifier(slug)
     if settings._instance_exists and settings.instance.name == instance_name:
         isettings = settings.instance
     else:
-        settings_file = instance_settings_file(instance_name, settings.user.handle)
+        settings_file = instance_settings_file(instance_name, instance_owner)
         if not settings_file.exists():
             hub_result = load_instance_from_hub(
-                owner=settings.user.handle, name=instance_name
+                owner=instance_owner, name=instance_name
             )
             if isinstance(hub_result, str):
                 message = INSTANCE_NOT_FOUND_MESSAGE.format(
-                    owner=settings.user.handle,
+                    owner=instance_owner,
                     name=instance_name,
                     hub_result=hub_result,
                 )
-                logger.warning(message)
-                return None
+                raise InstanceNotFoundError(message)
             instance_result, storage_result = hub_result
             ssettings = StorageSettings(
                 root=storage_result["root"],
                 region=storage_result["region"],
                 uid=storage_result["lnid"],
+                uuid=UUID(storage_result["id"]),
             )
             isettings = InstanceSettings(
                 id=UUID(instance_result["id"]),
-                owner=settings.user.handle,
+                owner=instance_owner,
                 name=instance_name,
                 storage=ssettings,
                 keep_artifacts_local=bool(instance_result["keep_artifacts_local"]),
                 db=instance_result["db"] if "db" in instance_result else None,
                 schema=instance_result["schema_str"],
                 git_repo=instance_result["git_repo"],
+                is_on_hub=True,
             )
         else:
             isettings = load_instance_settings(settings_file)
@@ -117,7 +114,7 @@ def delete(
     if not force:
         valid_responses = ["y", "yes"]
         user_input = (
-            input(f"Are you sure you want to delete instance {instance_slug}? (y/n) ")
+            input(f"Are you sure you want to delete instance {isettings.slug}? (y/n) ")
             .strip()
             .lower()
         )
@@ -161,10 +158,12 @@ def delete(
                 ssettings._mark_storage_root.unlink(
                     missing_ok=True  # this is totally weird, but needed on Py3.11
                 )
-    logger.info(f"deleting instance {instance_slug}")
+    logger.info(f"deleting instance {isettings.slug}")
     # below we can skip check_storage_is_empty() because we already called
     # it above
-    if settings.user.handle != "anonymous":
+    if settings.user.handle != "anonymous" and isettings.is_on_hub:
+        # start with deleting things on the hub
+        # this will error if the user doesn't have permission
         delete_instance_on_hub(isettings._id, require_empty=False)
     delete_by_isettings(isettings)
     # if .lndb file was delete, then we might count -1

lamindb_setup/_init_instance.py

@@ -184,7 +184,7 @@ def validate_init_args(
     name_str = infer_instance_name(storage=storage, name=name, db=db)
     # test whether instance exists by trying to load it
     instance_slug = f"{settings.user.handle}/{name_str}"
-    response = connect(instance_slug, _raise_not_reachable_error=False, _test=_test)
+    response = connect(instance_slug, db=db, _raise_not_found_error=False, _test=_test)
     instance_state: Literal[
         "connected",
         "instance-corrupted-or-deleted",
@@ -277,10 +277,14 @@ def init(
 
         if isettings is not None:
             delete_by_isettings(isettings)
-            if settings.user.handle != "anonymous":
+            if settings.user.handle != "anonymous" and isettings.is_on_hub:
                 delete_instance_record(isettings._id)
             isettings._get_settings_file().unlink(missing_ok=True)  # type: ignore
-        if ssettings is not None and settings.user.handle != "anonymous":
+        if (
+            ssettings is not None
+            and settings.user.handle != "anonymous"
+            and ssettings.is_on_hub
+        ):
             delete_storage_record(ssettings._uuid)  # type: ignore
         raise e
     return None

lamindb_setup/{_add_remote_storage.py → _set_managed_storage.py}

@@ -12,10 +12,8 @@ if TYPE_CHECKING:
     from lamindb_setup.core.types import UPathStr
 
 
-def add_managed_storage(root: UPathStr, **fs_kwargs):
-    """Add a remote default storage location to a local instance.
-
-    This can be used to selectively share data.
+def set_managed_storage(root: UPathStr, **fs_kwargs):
+    """Add or switch to another managed storage location.
 
     Args:
         root: `UPathStr` - The new storage root, e.g., an S3 bucket.

lamindb_setup/core/_hub_core.py

@@ -53,6 +53,11 @@ def _delete_storage_record(storage_uuid: UUID, client: Client) -> None:
     response = client.table("storage").delete().eq("id", storage_uuid.hex).execute()
     if response.data:
         logger.important(f"deleted storage record on hub {storage_uuid.hex}")
+    else:
+        raise PermissionError(
+            f"Deleting of storage with {storage_uuid.hex} was not successful. Probably, you"
+            " don't have sufficient permissions."
+        )
 
 
 def update_instance_record(instance_uuid: UUID, fields: dict) -> None:
@@ -285,7 +290,7 @@ def _init_instance(isettings: InstanceSettings, client: Client) -> None:
     client.table("storage").update(
         {"instance_id": isettings._id.hex, "is_default": True}
     ).eq("id", isettings.storage._uuid.hex).execute()  # type: ignore
-    logger.save(f"browse to: https://lamin.ai/{isettings.owner}/{isettings.name}")
+    logger.important(f"go to: https://lamin.ai/{isettings.owner}/{isettings.name}")
 
 
 def connect_instance(

lamindb_setup/core/_hub_crud.py

@@ -100,7 +100,7 @@ def update_instance(instance_id: str, instance_fields: dict, client: Client):
         client.table("instance").update(instance_fields).eq("id", instance_id).execute()
     )
     if len(response.data) == 0:
-        raise RuntimeError(
+        raise PermissionError(
             f"Update of instance with {instance_id} was not successful. Probably, you"
             " don't have sufficient permissions."
         )
@@ -187,3 +187,8 @@ def _delete_instance_record(instance_id: UUID, client: Client) -> None:
     response = client.table("instance").delete().eq("id", instance_id.hex).execute()
     if response.data:
         logger.important(f"deleted instance record on hub {instance_id.hex}")
+    else:
+        raise PermissionError(
+            f"Deleting of instance with {instance_id.hex} was not successful. Probably, you"
+            " don't have sufficient permissions."
+        )

lamindb_setup/core/_settings_load.py

@@ -89,6 +89,7 @@ def setup_instance_from_store(store: InstanceSettingsStore) -> InstanceSettings:
         db=store.db if store.db != "null" else None,  # type: ignore
         schema=store.schema_str if store.schema_str != "null" else None,
         git_repo=store.git_repo if store.git_repo != "null" else None,
+        keep_artifacts_local=store.keep_artifacts_local,  # type: ignore
     )
 
 

lamindb_setup/core/_settings_save.py

@@ -41,6 +41,8 @@ def save_settings(
         for store_key, type in type_hints.items():
             if type == Optional[str]:
                 type = str
+            if type == Optional[bool]:
+                type = bool
             if "__" not in store_key:
                 if store_key == "storage_root":
                     value = settings.storage.root_as_str

lamindb_setup/core/_settings_storage.py

@@ -177,7 +177,6 @@ class StorageSettings:
         # local storage
         self._has_local = False
         self._local = None
-        self._is_on_hub: bool | None = None
 
     @property
     def id(self) -> int:
@@ -320,16 +319,10 @@ class StorageSettings:
 
         Only works if user has access to the instance.
         """
-        if self._is_on_hub is None:
-            from ._hub_client import call_with_fallback_auth
-            from ._hub_crud import select_storage
-
-            response = call_with_fallback_auth(select_storage, id=self._uuid.hex)  # type: ignore
-            if response is None:
-                self._is_on_hub = False
-            else:
-                self._is_on_hub = True
-        return self._is_on_hub
+        if self._uuid is None:
+            return False
+        else:
+            return True
 
     def key_to_filepath(self, filekey: Path | UPath | str) -> UPath:
         """Cloud or local filepath from filekey."""

lamindb_setup/core/_settings_store.py

@@ -57,6 +57,7 @@ class InstanceSettingsStore(BaseSettings):
     schema_str: Optional[str]
     id: str
     git_repo: Optional[str]
+    keep_artifacts_local: Optional[bool]
 
     class Config:
         env_prefix = "lamindb_instance_"

lamindb_setup/core/_settings_user.py

@@ -46,6 +46,10 @@ class UserSettings:
     @property
     def id(self):
         """Integer id valid in current intance."""
-        from lnschema_core.users import current_user_id
+        # do NOT use the function below because this
+        # doesn't error - it needs to be this way to have
+        # a user id available in migrations
+        # from lnschema_core.users import current_user_id
+        from lnschema_core.models import User
 
-        return current_user_id()
+        return User.objects.get(uid=self.uid).id

lamindb_setup/core/upath.py

@@ -56,7 +56,10 @@ VALID_SUFFIXES = {
     ".zarr",
     ".json",
 }
-
+VALID_COMPOSITE_SUFFIXES = {
+    ".anndata.zarr",
+    ".spatialdata.zarr",
+}
 
 TRAILING_SEP = (os.sep, os.altsep) if os.altsep is not None else os.sep
 
@@ -74,6 +77,12 @@ def extract_suffix_from_path(path: Path, arg_name: str | None = None) -> str:
     total_suffix = "".join(path.suffixes)
     if total_suffix in VALID_SUFFIXES:
         return total_suffix
+    elif total_suffix.endswith(tuple(VALID_COMPOSITE_SUFFIXES)):
+        # below seems slow but OK for now
+        for suffix in VALID_COMPOSITE_SUFFIXES:
+            if total_suffix.endswith(suffix):
+                break
+        return suffix
     else:
         print_hint = True
         arg_name = "file" if arg_name is None else arg_name  # for the warning
@@ -462,7 +471,8 @@ def compute_file_tree(
             contents = [d for d in contents if d.is_dir()]
         pointers = [tee] * (len(contents) - 1) + [last]
         n_files_per_dir_and_type = defaultdict(lambda: 0)  # type: ignore
-        for pointer, child_path in zip(pointers, contents, strict=False):  # type: ignore
+        # TODO: pass strict=False to zip with python > 3.9
+        for pointer, child_path in zip(pointers, contents):  # type: ignore
             if child_path.is_dir():
                 if include_dirs and child_path not in include_dirs:
                     continue
@@ -495,8 +505,8 @@ def compute_file_tree(
     display_suffixes = ", ".join([f"{suffix!r}" for suffix in suffixes])
     suffix_message = f" with suffixes {display_suffixes}" if n_objects > 0 else ""
     message = (
-        f"{path.name} ({n_directories} sub-{directory_info} &"
-        f" {n_objects} files{suffix_message}): {folder_tree}"
+        f"{n_directories} sub-{directory_info} &"
+        f" {n_objects} files{suffix_message}\n{path.resolve()}{folder_tree}"
     )
     return message, n_objects
 
@@ -801,12 +811,12 @@ def check_storage_is_empty(
         if raise_error
         else "consider deleting them"
     )
-    hint = "'./lamindb/_is_initialized' "
+    hint = "'_is_initialized'"
     if n_offset_objects == 2:
-        hint += "& SQLite file"
+        hint += " & SQLite file"
     hint += " ignored"
     message = (
-        f"Storage {directory_string} contains {n_objects} objects "
+        f"Storage {directory_string} contains {n_objects - n_offset_objects} objects "
         f"({hint}) - {ask_for_deletion}\n{objects}"
     )
     if n_diff > 0:

{lamindb_setup-0.71.0.dist-info → lamindb_setup-0.71.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb_setup
-Version: 0.71.0
+Version: 0.71.2
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <laminlabs@gmail.com>
 Description-Content-Type: text/markdown

{lamindb_setup-0.71.0.dist-info → lamindb_setup-0.71.2.dist-info}/RECORD

@@ -1,18 +1,18 @@
-lamindb_setup/__init__.py,sha256=6a3FROJtySXqU0zXTq1xIniLLPzc7_JufrXPqKJ11eI,1542
-lamindb_setup/_add_remote_storage.py,sha256=j-p29pxrr_07Ns5X2tm6yKxa3VESPkjyt35X4Cvr-nk,1325
+lamindb_setup/__init__.py,sha256=Z6OThfuMvv_NukKBoTOjxZV5sex6PgniejgS9LiuODs,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=ElpbjSaAI9vq3OfmPM8TxvsqfrZyytTZSRyYUDfiv3E,11944
-lamindb_setup/_delete.py,sha256=tOEb8N7Ga9hrMpup2zBugtl0wN_Xxv0MqqKP2CpHArQ,7267
+lamindb_setup/_connect_instance.py,sha256=6DiKFpw0k_gcWlZxI8ZJoqHungW-el3JbaWcmV9wGIg,12600
+lamindb_setup/_delete.py,sha256=hf8zfVJfW74QR7eK4xJNQ6HbkkZBsl5eTqj-Ni5jPo0,7232
 lamindb_setup/_django.py,sha256=EoyWvFzH0i9wxjy4JZhcoXCTckztP_Mrl6FbYQnMmLE,1534
 lamindb_setup/_exportdb.py,sha256=uTIZjKKTB7arzEr1j0O6lONiT2pRBKeOFdLvOV8ZwzE,2120
 lamindb_setup/_importdb.py,sha256=yYYShzUajTsR-cTW4CZ-UNDWZY2uE5PAgNbp-wn8Ogc,1874
-lamindb_setup/_init_instance.py,sha256=XLf-xkF_YBwvT_sGyW1wFJFbOWpTFABPRt2oeIICQNI,11825
+lamindb_setup/_init_instance.py,sha256=2NT4ERk0RFrcgpnH5O-sAwkd7E1QLIOaFavyFzdAZbc,11924
 lamindb_setup/_migrate.py,sha256=4nBTFg5-BK4A2gH-D3_tcFf8EtvMnIo5Mq0e_C6_9-U,8815
 lamindb_setup/_register_instance.py,sha256=Jeu0wyvJVSVQ_n-A_7yn7xOZIP0ncJD92DRABqzPIjA,940
 lamindb_setup/_schema.py,sha256=b3uzhhWpV5mQtDwhMINc2MabGCnGLESy51ito3yl6Wc,679
+lamindb_setup/_set_managed_storage.py,sha256=BUUJzKNWNEA5KnKnFZsas0ANU6w-LBZL-CKRu-sNLPE,1268
 lamindb_setup/_setup_user.py,sha256=6Oc7Rke-yRQSZbuntdUAz8QbJ6UuPzYHI9FnYlf_q-A,3670
 lamindb_setup/_silence_loggers.py,sha256=AKF_YcHvX32eGXdsYK8MJlxEaZ-Uo2f6QDRzjKFCtws,1568
 lamindb_setup/core/__init__.py,sha256=dV9S-rQpNK9JcBn4hiEmiLnmNqfpPFJD9pqagMCaIew,416
@@ -20,24 +20,24 @@ 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=V0qKDsCdRn-tQy2YIk4VgXcpJFmuum6N3gcavAC7gBQ,5504
-lamindb_setup/core/_hub_core.py,sha256=88EZA5G2JLlEZP6ol_km3Cv0dEpV2U2Z6X5vQOorGrs,15776
-lamindb_setup/core/_hub_crud.py,sha256=m8DgbWIBZBLWB-PV_UNBldUebqnxABfJfrqvzgr3t5s,4662
+lamindb_setup/core/_hub_core.py,sha256=Cp8w0QY3DNOGWOhzzWmElj-pUm6tAkrQCLikbq_ksq8,15971
+lamindb_setup/core/_hub_crud.py,sha256=b1XF7AJpM9Q-ttm9nPG-r3OTRWHQaGzAGIyvmb83NTo,4859
 lamindb_setup/core/_hub_utils.py,sha256=b_M1LkdCjiMWm1EOlSb9GuPdLijwVgQDtATTpeZuXI0,1875
 lamindb_setup/core/_settings.py,sha256=jjZ_AxRXB3Y3UP6m04BAw_dhFbJbdg2-nZWmEv2LNZ8,3141
 lamindb_setup/core/_settings_instance.py,sha256=RFUcnBBUp303dbVEHcAaIm_q7lzlWg56OrKLwdam8Pg,16588
-lamindb_setup/core/_settings_load.py,sha256=0MkFvZa0fVrMt087GL8Y-mHH44RUDQYybKqqj-c8flU,3849
-lamindb_setup/core/_settings_save.py,sha256=sLVNEMsrEO238Px8P8PsQjl4_RxGSKwRqB9Cffg2TrY,2637
-lamindb_setup/core/_settings_storage.py,sha256=yN2KNd6lq1RDNYbnkaCIfoYc3uKqkSU70otUr4qALPM,12739
-lamindb_setup/core/_settings_store.py,sha256=OMBn396BFkMXGg3came1pToBqnBUwpyqBFv2G8GARiM,2043
-lamindb_setup/core/_settings_user.py,sha256=P2lC4WDRAFfT-Xq3MlXJ-wMKIHCoGNhMTQfRGIAyUNQ,1344
+lamindb_setup/core/_settings_load.py,sha256=NGgCDpN85j1EqoKlrYFIlZBMlBJm33gx2-wc96CP_ZQ,3922
+lamindb_setup/core/_settings_save.py,sha256=d1A-Ex-7H08mb8l7I0Oe0j0GilrfaDuprh_NMxhQAsQ,2704
+lamindb_setup/core/_settings_storage.py,sha256=VgsqdIImQRfOZ6FGNY6DLVohaSxerj_F-sWtjD9hzcs,12382
+lamindb_setup/core/_settings_store.py,sha256=dagS5c7wAMRnuZTRfCU4sKaIOyF_HwAP5Fnnn8vphno,2084
+lamindb_setup/core/_settings_user.py,sha256=IOOd3E3YN5xPEYy7fkWQDB6X06OcY4FkBqWT-XGxrjM,1563
 lamindb_setup/core/_setup_bionty_sources.py,sha256=OgPpZxN2_Wffy-ogEBz_97c_k8d2bD-DDVt89-u9GLY,3002
 lamindb_setup/core/cloud_sqlite_locker.py,sha256=NIBNAGq7TTRrip9OzMdiQKj8QOuwhL9esyM0aehUqBA,6893
 lamindb_setup/core/django.py,sha256=m0AKg2lJ1EYCtEtZ8frFFJbAR9qX0gnFcgqp7aeC2k0,3450
 lamindb_setup/core/exceptions.py,sha256=eoI7AXgATgDVzgArtN7CUvpaMUC067vsBg5LHCsWzDM,305
 lamindb_setup/core/hashing.py,sha256=mv9UCvAsSrdHYQAv3Kz7UOvjd5tIjvDTIYv_ettBuVY,2218
 lamindb_setup/core/types.py,sha256=bcYnZ0uM_2NXKJCl94Mmc-uYrQlRUUVKG3sK2N-F-N4,532
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