lamindb_setup 1.1.1__py3-none-any.whl → 1.3.0__py3-none-any.whl

lamindb_setup/__init__.py

@@ -33,7 +33,7 @@ Modules & settings:
 
 """
 
-__version__ = "1.1.1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "1.3.0"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os
 

lamindb_setup/_schema_metadata.py

@@ -148,6 +148,8 @@ class FieldMetadata(BaseModel):
     model_name: str
     schema_name: str
     is_link_table: bool
+    is_primary_key: bool
+    is_editable: bool
     relation_type: RelationType | None = None
     related_field_name: str | None = None
     related_model_name: str | None = None
@@ -156,6 +158,8 @@ class FieldMetadata(BaseModel):
 
 class _ModelHandler:
     def __init__(self, model, module_name: str, included_modules: list[str]) -> None:
+        from lamindb.models import LinkORM
+
         self.model = model
         self.class_name = model.__name__
         self.module_name = module_name
@@ -163,12 +167,14 @@ class _ModelHandler:
         self.table_name = model._meta.db_table
         self.included_modules = included_modules
         self.fields = self._get_fields_metadata(self.model)
+        self.is_link_table = issubclass(model, LinkORM)
 
     def to_dict(self, include_django_objects: bool = True):
         _dict = {
             "fields": self.fields.copy(),
             "class_name": self.class_name,
             "table_name": self.table_name,
+            "is_link_table": self.is_link_table,
         }
 
         for field_name in self.fields.keys():
@@ -242,13 +248,16 @@ class _ModelHandler:
             related_model_name = None
             related_schema_name = None
             related_field_name = None
-            field_name = field.name
+            is_editable = field.editable
         else:
             related_model_name = field.related_model._meta.model_name
             related_schema_name = field.related_model.__get_module_name__()
             schema_name = field.model.__get_module_name__()
             related_field_name = field.remote_field.name
-            field_name = field.name
+            is_editable = False
+
+        field_name = field.name
+        is_primary_key = getattr(field, "primary_key", False)
 
         if relation_type in ["one-to-many"]:
             # For a one-to-many relation, the field belong
@@ -278,6 +287,8 @@ class _ModelHandler:
             field_name=field_name,
             type=internal_type,
             is_link_table=issubclass(field.model, LinkORM),
+            is_primary_key=is_primary_key,
+            is_editable=is_editable,
             column_name=column,
             relation_type=relation_type,
             related_schema_name=related_schema_name

lamindb_setup/core/_aws_options.py

@@ -125,7 +125,13 @@ class AWSOptionsManager:
 
     def enrich_path(self, path: UPath, access_token: str | None = None) -> UPath:
         # ignore paths with non-lamin-managed endpoints
-        if path.storage_options.get("endpoint_url", None) not in LAMIN_ENDPOINTS:
+        if (
+            endpoint_url := path.storage_options.get("endpoint_url", None)
+        ) not in LAMIN_ENDPOINTS:
+            if "r2.cloudflarestorage.com" in endpoint_url:
+                # fixed_upload_size should always be True for R2
+                # this option is needed for correct uploads to R2
+                path = UPath(path, fixed_upload_size=True)
             return path
         # trailing slash is needed to avoid returning incorrect results
         # with .startswith

lamindb_setup/core/django.py

@@ -14,6 +14,31 @@ IS_MIGRATING = False
 CONN_MAX_AGE = 299
 
 
+def set_token(token: str | None, connection_name: str = "default"):
+    # None to reset
+    from django.db import connections
+    from django.db.backends.base.base import BaseDatabaseWrapper
+
+    connection = connections[connection_name]
+    assert connection.vendor == "postgresql"
+
+    if token is not None:
+
+        def connect(self):
+            BaseDatabaseWrapper.connect(self)
+            # now the connection should be set
+            # Use a psycopg cursor directly, bypassing Django's utilities.
+            with self.connection.cursor() as cursor:
+                cursor.execute("SELECT set_token(%s, false);", (token,))
+    else:
+        connect = BaseDatabaseWrapper.connect
+
+    connection.connect = connect.__get__(connection, connection.__class__)
+    # execute this to initially set or reset the token
+    connection.close()
+    connection.connect()
+
+
 def close_if_health_check_failed(self) -> None:
     if self.close_at is not None:
         if time.monotonic() >= self.close_at:

lamindb_setup/core/upath.py

@@ -517,7 +517,7 @@ def modified(self) -> datetime | None:
 
 
 def compute_file_tree(
-    path: Path,
+    path: UPath,
     *,
     level: int = -1,
     only_dirs: bool = False,
@@ -526,6 +526,11 @@ def compute_file_tree(
     include_paths: set[Any] | None = None,
     skip_suffixes: list[str] | None = None,
 ) -> tuple[str, int]:
+    # .exists() helps to separate files from folders for gcsfs
+    # otherwise sometimes it has is_dir() True and is_file() True
+    if path.protocol == "gs" and not path.exists():
+        raise FileNotFoundError
+
     space = "    "
     branch = "│   "
     tee = "├── "

{lamindb_setup-1.1.1.dist-info → lamindb_setup-1.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb_setup
-Version: 1.1.1
+Version: 1.3.0
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10
@@ -40,7 +40,7 @@ Provides-Extra: gcp
 
 [![codecov](https://codecov.io/gh/laminlabs/lamindb-setup/branch/main/graph/badge.svg)](https://codecov.io/gh/laminlabs/lamindb-setup)
 
-# lamindb-setup: Setup LaminDB
+# lamindb-setup: Setting up `lamindb`
 
 - User [docs](https://lamin.ai/docs)
 - Developer [docs](https://lamindb-setup-htry.netlify.app/)

{lamindb_setup-1.1.1.dist-info → lamindb_setup-1.3.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-lamindb_setup/__init__.py,sha256=6TuxQ39LS6eQzygoAXTY6B7NyqslymPPePkClF5BLss,2692
+lamindb_setup/__init__.py,sha256=B7IVjz1M1qrpfYuPg4mQ66YiIyfAcYtmSfjLULXKpII,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
@@ -13,12 +13,12 @@ lamindb_setup/_init_instance.py,sha256=nZkqGqJQ_sF1-oQmnbpIjP1ExWUow5I5N7lsyX9m-
 lamindb_setup/_migrate.py,sha256=drf7Lsa8oDXBPBWMWMge0n5VyNPvsrCFAhcXlN91OxM,9165
 lamindb_setup/_register_instance.py,sha256=alQuYp2f8Ct8xvRC1gt8p_HZ0tqCd3gZD3kiPBLPpsI,1269
 lamindb_setup/_schema.py,sha256=b3uzhhWpV5mQtDwhMINc2MabGCnGLESy51ito3yl6Wc,679
-lamindb_setup/_schema_metadata.py,sha256=7ITlzIK32GHdhMq9e0GtPM3QbzJWhUvzPutiHrjjPk0,13986
+lamindb_setup/_schema_metadata.py,sha256=cDkNHyFTFZq879UGY6i-rJEXfeBN59AN3Wz86caKnYI,14358
 lamindb_setup/_set_managed_storage.py,sha256=4tDxXQMt8Gw028uY3vIQxZQ7qBNXhQMc8saarNK_Z-s,2043
 lamindb_setup/_setup_user.py,sha256=-g7Xj6510BDyM8kuqAsVBZFwehlhBa_uWBSV1rPeuM8,4586
 lamindb_setup/_silence_loggers.py,sha256=AKF_YcHvX32eGXdsYK8MJlxEaZ-Uo2f6QDRzjKFCtws,1568
 lamindb_setup/core/__init__.py,sha256=BxIVMX5HQq8oZ1OuY_saUEJz5Tdd7gaCPngxVu5iou4,417
-lamindb_setup/core/_aws_options.py,sha256=Evu8W9Xcr1_vYKo3Vfsv03dmD4x3itaPyWY8fBOrYcE,6954
+lamindb_setup/core/_aws_options.py,sha256=Umxu_1AYd-0LJUElZxowvE9vNA7Z8kh_63g3pp1gfd8,7243
 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
@@ -36,12 +36,12 @@ lamindb_setup/core/_settings_store.py,sha256=WcsgOmgnu9gztcrhp-N4OONNZyxICHV8M0H
 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=jSbckc_R39BhnANGhO5YFzKA8BHNANJDDgS5rwkDWmU,3828
+lamindb_setup/core/django.py,sha256=vmrGDiqX2FSmMII_YLcQtwO8SRzm6zKayjeNJLGhuiU,4697
 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=FUCBicCTAUPq-3lFwcDPngRLrNGfqQEn7l9ZCLjkz3Y,33335
-lamindb_setup-1.1.1.dist-info/LICENSE,sha256=UOZ1F5fFDe3XXvG4oNnkL1-Ecun7zpHzRxjp-XsMeAo,11324
-lamindb_setup-1.1.1.dist-info/WHEEL,sha256=CpUCUxeHQbRN5UGRQHYRJorO5Af-Qy_fHMctcQ8DSGI,82
-lamindb_setup-1.1.1.dist-info/METADATA,sha256=dn4Sbq-u6AoTsN06Sfa0jlbWPt41MBMsBqqdEnVS13U,1770
-lamindb_setup-1.1.1.dist-info/RECORD,,
+lamindb_setup/core/upath.py,sha256=AvRmICPBxQx-2iQYsXDFsrJS-AAUNuw6IymLcVmkWvo,33550
+lamindb_setup-1.3.0.dist-info/LICENSE,sha256=UOZ1F5fFDe3XXvG4oNnkL1-Ecun7zpHzRxjp-XsMeAo,11324
+lamindb_setup-1.3.0.dist-info/WHEEL,sha256=CpUCUxeHQbRN5UGRQHYRJorO5Af-Qy_fHMctcQ8DSGI,82
+lamindb_setup-1.3.0.dist-info/METADATA,sha256=jGAuIu11oaJ-YYGXR4iXnh99vurdfu1vaJuEPL756gc,1777
+lamindb_setup-1.3.0.dist-info/RECORD,,