lamindb_setup 1.15.2__py3-none-any.whl → 1.16.0__py3-none-any.whl

lamindb_setup/__init__.py

@@ -35,7 +35,7 @@ Migration management
 
 """
 
-__version__ = "1.15.2"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "1.16.0"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os
 import warnings

lamindb_setup/_schema_metadata.py

@@ -172,7 +172,8 @@ 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, IsLink)
+        self.is_auto_created = bool(model._meta.auto_created)
+        self.is_link_table = issubclass(model, IsLink) or self.is_auto_created
         self.name_field = model._name_field if hasattr(model, "_name_field") else None
         self.ontology_id_field = (
             model._ontology_id_field if hasattr(model, "_ontology_id_field") else None
@@ -183,6 +184,7 @@ class _ModelHandler:
             "fields": self.fields.copy(),
             "class_name": self.class_name,
             "table_name": self.table_name,
+            "is_auto_created": self.is_auto_created,
             "is_link_table": self.is_link_table,
             "name_field": self.name_field,
             "ontology_id_field": self.ontology_id_field,
@@ -249,13 +251,13 @@ class _ModelHandler:
         return related_fields
 
     def _get_field_metadata(self, model, field: Field):
-        from lamindb.models import IsLink
+        from lamindb.models import IsLink, Registry
 
         internal_type = field.get_internal_type()
         model_name = field.model._meta.model_name
         relation_type = self._get_relation_type(model, field)
 
-        schema_name = field.model.__get_module_name__()
+        schema_name = Registry.__get_module_name__(field.model)
 
         if field.related_model is None:
             related_model_name = None
@@ -265,7 +267,7 @@ class _ModelHandler:
             max_length = field.max_length
         else:
             related_model_name = field.related_model._meta.model_name
-            related_schema_name = field.related_model.__get_module_name__()
+            related_schema_name = Registry.__get_module_name__(field.related_model)
             related_field_name = field.remote_field.name
             is_editable = False
             max_length = None
@@ -418,14 +420,10 @@ class _SchemaHandler:
         all_models = {module_name: {} for module_name in self.included_modules}
 
         # Iterate through all registered Django models
-        for model in apps.get_models():
+        for model in apps.get_models(include_auto_created=True):
             # Check if model meets the criteria
-            if (
-                model.__class__ is Registry
-                and model is not SQLRecord
-                and not model._meta.abstract
-            ):
-                module_name = model.__get_module_name__()
+            if model is not SQLRecord and not model._meta.abstract:
+                module_name = Registry.__get_module_name__(model)
                 # Only include if module is in our included list
                 if module_name in self.included_modules:
                     model_name = model._meta.model_name

lamindb_setup/_setup_user.py

@@ -43,6 +43,14 @@ def load_user(email: str | None = None, handle: str | None = None) -> UserSettin
     return user_settings
 
 
+def current_user_uid() -> str:
+    current_user_settings = current_user_settings_file()
+    if current_user_settings.exists():
+        return load_user_settings(current_user_settings).uid
+
+    return "00000000"  # anonymous
+
+
 def login(
     user: str | None = None, *, api_key: str | None = None, **kwargs
 ) -> UserSettings:
@@ -90,6 +98,9 @@ def login(
             "the legacy API key is deprecated and will likely be removed in a future version"
         )
 
+    # do this here because load_user overwrites current_user_settings_file
+    previous_user_uid = current_user_uid()
+
     if api_key is None:
         if "@" in user:  # type: ignore
             email, handle = user, None
@@ -144,8 +155,15 @@ def login(
     user_settings.api_key = api_key
     save_user_settings(user_settings)
 
-    if settings._instance_exists and _check_instance_setup():
-        register_user(user_settings)
+    if settings._instance_exists:
+        if (
+            isettings := settings.instance
+        ).is_on_hub and previous_user_uid != user_settings.uid:
+            logger.important_hint(
+                f"consider re-connecting to update permissions: lamin connect {isettings.slug}"
+            )
+        if _check_instance_setup():
+            register_user(user_settings)
 
     settings._user_settings = None
     # aws s3 credentials are scoped to the user

lamindb_setup/core/_clone.py

@@ -5,6 +5,7 @@
 
    init_local_sqlite
    connect_local_sqlite
+   connect_remote_sqlite
    upload_sqlite_clone
 """
 
@@ -13,7 +14,6 @@ import os
 import shutil
 from pathlib import Path
 
-from lamindb_setup.core._settings_instance import InstanceSettings
 from lamindb_setup.core._settings_load import load_instance_settings
 from lamindb_setup.core._settings_store import instance_settings_file
 from lamindb_setup.core.django import reset_django

lamindb_setup/core/_private_django_api.py

@@ -37,7 +37,6 @@ def private_django_api(reverse=False):
         "MultipleObjectsReturned",
         "add_to_class",
         "adelete",
-        "refresh_from_db",
         "asave",
         "clean",
         "clean_fields",

lamindb_setup/core/_settings_storage.py

@@ -122,6 +122,7 @@ def init_storage(
     access_token: str | None = None,
     region: str | None = None,
     space_uuid: UUID | None = None,
+    skip_mark_storage_root: bool = False,
 ) -> tuple[
     StorageSettings,
     Literal["hub-record-not-created", "hub-record-retrieved", "hub-record-created"],
@@ -181,7 +182,8 @@ def init_storage(
         space_id=space_uuid,
     )
     # we check the write access here if the storage record has not been retrieved from the hub
-    if hub_record_status != "hub-record-retrieved":
+    # Sergei: should it in fact still go through if hub_record_status == "hub-record-not-created"?
+    if hub_record_status != "hub-record-retrieved" and not skip_mark_storage_root:
         try:
             # (federated) credentials for AWS access are provisioned under-the-hood
             # discussion: https://laminlabs.slack.com/archives/C04FPE8V01W/p1719260587167489

lamindb_setup/core/django.py

@@ -238,6 +238,8 @@ def setup_django(
         if view_schema:
             installed_apps = installed_apps[::-1]  # to fix how apps appear
             installed_apps += ["schema_graph", "django.contrib.staticfiles"]
+        if isettings.dialect == "postgresql":
+            installed_apps.insert(0, "pgtrigger")
 
         kwargs = dict(
             INSTALLED_APPS=installed_apps,

lamindb_setup/core/upath.py

@@ -93,10 +93,12 @@ def extract_suffix_from_path(path: Path, arg_name: str | None = None) -> str:
         else:
             return suffix
 
-    if len(path.suffixes) <= 1:
+    suffixes = path.suffixes
+
+    if len(suffixes) <= 1:
         return process_digits(path.suffix)
 
-    total_suffix = "".join(path.suffixes)
+    total_suffix = "".join(suffixes)
     if total_suffix in VALID_SIMPLE_SUFFIXES:
         return total_suffix
     elif total_suffix.endswith(tuple(VALID_COMPOSITE_SUFFIXES)):
@@ -115,14 +117,24 @@ def extract_suffix_from_path(path: Path, arg_name: str | None = None) -> str:
         # in COMPRESSION_SUFFIXES to detect something like .random.gz and then
         # add ".random.gz" but concluded it's too dangerous it's safer to just
         # use ".gz" in such a case
-        if path.suffixes[-2] in VALID_SIMPLE_SUFFIXES:
-            suffix = "".join(path.suffixes[-2:])
-            msg += f"inferring: '{suffix}'"
+        if suffixes[-2] in VALID_SIMPLE_SUFFIXES:
+            suffix = "".join(suffixes[-2:])
+            # if the suffix preceding the compression suffixes is a valid suffix,
+            # we account for it; otherwise we don't.
+            # i.e. we should have .h5ad.tar.gz or .csv.tar.gz, not just .tar.gz
+            if (
+                suffix == ".tar.gz"
+                and len(suffixes) > 2
+                and (suffix_3 := suffixes[-3]) in VALID_SIMPLE_SUFFIXES
+            ):
+                suffix = suffix_3 + suffix
             # do not print a warning for things like .tar.gz, .fastq.gz
-            if path.suffixes[-1] == ".gz":
+            if suffixes[-1] == ".gz":
                 print_hint = False
+            else:
+                msg += f"inferring: '{suffix}'"
         else:
-            suffix = path.suffixes[-1]  # this is equivalent to path.suffix
+            suffix = suffixes[-1]  # this is equivalent to path.suffix
             msg += (
                 f"using only last suffix: '{suffix}' - if you want your composite"
                 " suffix to be recognized add it to"

lamindb_setup/io.py

@@ -3,7 +3,7 @@ from __future__ import annotations
 import io
 import json
 import warnings
-from concurrent.futures import ProcessPoolExecutor, as_completed
+from concurrent.futures import ThreadPoolExecutor, as_completed
 from importlib import import_module
 from pathlib import Path
 from typing import TYPE_CHECKING
@@ -14,24 +14,13 @@ from django.db import models, transaction
 from rich.progress import Progress
 
 if TYPE_CHECKING:
-    from collections.abc import Sequence
+    from collections.abc import Iterable, Sequence
     from typing import Literal
 
 
 def _get_registries(module_name: str) -> list[str]:
     """Get registry class names from a module."""
     schema_module = import_module(module_name)
-    exclude = {"SQLRecord", "BaseSQLRecord"}
-
-    if module_name == "lamindb":
-        module_filter = lambda cls, name: cls.__module__.startswith(
-            f"{module_name}.models."
-        ) and name in dir(schema_module)
-    else:
-        module_filter = (
-            lambda cls, name: cls.__module__ == f"{module_name}.models"
-            and name in dir(schema_module)
-        )
 
     return [
         name
@@ -40,8 +29,8 @@ def _get_registries(module_name: str) -> list[str]:
             name[0].isupper()
             and isinstance(cls := getattr(schema_module.models, name, None), type)
             and issubclass(cls, models.Model)
-            and module_filter(cls, name)
-            and name not in exclude
+            # Table names starting with `None_` are abstract base classes or Django mixins
+            and not cls._meta.db_table.startswith("None_")  # type: ignore
         )
     ]
 
@@ -59,7 +48,7 @@ def _export_full_table(
     For SQLite with large tables, reads in chunks to avoid memory issues when tables exceed available RAM.
 
     Args:
-        registry_info: Tuple of (module_name, model_name, field_name) where field_name
+        registry_info: Tuple of (module_name, model_name, field_name) where `field_name`
             is None for regular tables or the field name for M2M link tables.
         directory: Output directory for parquet files.
         chunk_size: Maximum rows per chunk for SQLite large tables.
@@ -73,7 +62,7 @@ def _export_full_table(
 
     module_name, model_name, field_name = registry_info
     schema_module = import_module(module_name)
-    registry = getattr(schema_module, model_name)
+    registry = getattr(schema_module.models, model_name)
 
     if field_name:
         registry = getattr(registry, field_name).through
@@ -84,12 +73,19 @@ def _export_full_table(
         if ln_setup.settings.instance.dialect == "postgresql":
             buffer = io.StringIO()
             with connection.cursor() as cursor:
+                cursor.execute("SET statement_timeout = 0")
                 cursor.copy_expert(
                     f'COPY "{table_name}" TO STDOUT WITH (FORMAT CSV, HEADER TRUE)',
                     buffer,
                 )
             buffer.seek(0)
-            df = pd.read_csv(buffer)
+            # Prevent pandas from converting empty strings to float NaN (which PyArrow rejects)
+            df = pd.read_csv(buffer, keep_default_na=False)
+            # Convert object columns to string to handle mixed types from data corruption,
+            # schema migrations, or manual SQL inserts. PyArrow rejects mixed-type objects.
+            df = df.astype(
+                {col: str for col in df.columns if df[col].dtype == "object"}
+            )
             df.to_parquet(directory / f"{table_name}.parquet", compression=None)
             return (
                 f"{module_name}.{model_name}.{field_name}"
@@ -118,11 +114,21 @@ def _export_full_table(
                         chunk_file = (
                             directory / f"{table_name}_chunk_{chunk_id}.parquet"
                         )
+                        df = df.astype(
+                            {
+                                col: str
+                                for col in df.columns
+                                if df[col].dtype == "object"
+                            }
+                        )
                         df.to_parquet(chunk_file, compression=None)
                         chunk_files.append((table_name, chunk_file))
                     return chunk_files
                 else:
                     df = pd.read_sql_table(table_name, ln_setup.settings.instance.db)
+                    df = df.astype(
+                        {col: str for col in df.columns if df[col].dtype == "object"}
+                    )
                     df.to_parquet(directory / f"{table_name}.parquet", compression=None)
                     return (
                         f"{module_name}.{model_name}.{field_name}"
@@ -163,7 +169,7 @@ def export_db(
     for module_name, model_names in modules.items():
         schema_module = import_module(module_name)
         for model_name in model_names:
-            registry = getattr(schema_module, model_name)
+            registry = getattr(schema_module.models, model_name)
             tasks.append((module_name, model_name, None))
             for field in registry._meta.many_to_many:
                 tasks.append((module_name, model_name, field.name))
@@ -173,13 +179,8 @@ def export_db(
     with Progress() as progress:
         task_id = progress.add_task("Exporting", total=len(tasks))
 
-        import multiprocessing
-
-        mp_context = multiprocessing.get_context("spawn")
-
-        with ProcessPoolExecutor(
-            max_workers=max_workers, mp_context=mp_context
-        ) as executor:
+        # This must be a ThreadPoolExecutor and not a ProcessPoolExecutor to inherit JWTs
+        with ThreadPoolExecutor(max_workers=max_workers) as executor:
             futures = {
                 executor.submit(_export_full_table, task, directory, chunk_size): task
                 for task in tasks
@@ -229,7 +230,6 @@ def _import_registry(
     parquet_file = directory / f"{table_name}.parquet"
 
     if not parquet_file.exists():
-        print(f"Skipped {table_name} (file not found)")
         return
 
     df = pd.read_parquet(parquet_file)
@@ -244,12 +244,37 @@ def _import_registry(
             if mask.any():
                 df.loc[mask, col] = df.loc[mask, col].map(_serialize_value)
 
+    for field in registry._meta.fields:
+        # Convert PostgreSQL boolean string literals ('t'/'f') to Python booleans for SQLite compatibility
+        if field.get_internal_type() == "BooleanField" and field.column in df.columns:
+            df[field.column] = df[field.column].map(
+                {"t": True, "f": False, True: True, False: False, None: None}
+            )
+
+        # PostgreSQL CSV export writes NULL as empty string; convert back to None for nullable fields
+        if field.null and field.column in df.columns:
+            df[field.column] = df[field.column].replace("", None)
+
+        # Convert numeric fields from strings to proper types for SQLite
+        if (
+            field.get_internal_type()
+            in (
+                "IntegerField",
+                "BigIntegerField",
+                "PositiveIntegerField",
+                "FloatField",
+                "DecimalField",
+            )
+            and field.column in df.columns
+        ):
+            df[field.column] = pd.to_numeric(df[field.column], errors="coerce")
+
     if if_exists == "append":
         # Fill NULL values in NOT NULL columns to handle schema mismatches between postgres source and SQLite target
         # This allows importing data where fields were nullable
         for field in registry._meta.fields:
             if field.column in df.columns and not field.null:
-                df[field.column] = df[field.column].fillna("")
+                df[field.column] = df[field.column].fillna("").infer_objects(copy=False)
 
     if df.empty:
         return
@@ -297,7 +322,7 @@ def _import_registry(
 
 
 def import_db(
-    module_names: Sequence[str] | None = None,
+    module_names: Iterable[str] | None = None,
     *,
     input_dir: str | Path = "./lamindb_export/",
     if_exists: Literal["fail", "replace", "append"] = "replace",
@@ -362,7 +387,7 @@ def import_db(
                         progress.update(
                             task, description=f"[cyan]{module_name}.{model_name}"
                         )
-                        registry = getattr(schema_module, model_name)
+                        registry = getattr(schema_module.models, model_name)
                         _import_registry(registry, directory, if_exists=if_exists)
                         for field in registry._meta.many_to_many:
                             link_orm = getattr(registry, field.name).through

{lamindb_setup-1.15.2.dist-info → lamindb_setup-1.16.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb_setup
-Version: 1.15.2
+Version: 1.16.0
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10
@@ -8,6 +8,7 @@ Description-Content-Type: text/markdown
 Requires-Dist: lamin_utils>=0.3.3
 Requires-Dist: django>=5.2,<5.3
 Requires-Dist: dj_database_url>=1.3.0,<3.0.0
+Requires-Dist: django-pgtrigger
 Requires-Dist: pydantic-settings
 Requires-Dist: platformdirs<5.0.0
 Requires-Dist: httpx_retries<1.0.0

{lamindb_setup-1.15.2.dist-info → lamindb_setup-1.16.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-lamindb_setup/__init__.py,sha256=T0CRWMhViQuKtrYM_foGZnApH3-uh0ta8YyS7rd9Fj0,3215
+lamindb_setup/__init__.py,sha256=zAgDC8o3cyH4eXcM60mbulFPECs5XZbqFRxLfGpgpc8,3215
 lamindb_setup/_cache.py,sha256=pGvDNVHGx4HWr_6w5ajqEJOdysmaGc6F221qFnXkT-k,2747
 lamindb_setup/_check.py,sha256=28PcG8Kp6OpjSLSi1r2boL2Ryeh6xkaCL87HFbjs6GA,129
 lamindb_setup/_check_setup.py,sha256=ToKMxsUq8dQBQh8baOrNVlSb1iC8h4zTg5dV8wMu0W4,6760
@@ -11,40 +11,40 @@ lamindb_setup/_init_instance.py,sha256=zNXmZPUHYda1CfLGtsvo4gNhHprK9QVPfffUIfBlT
 lamindb_setup/_migrate.py,sha256=SN8uphuQX-8XShH5odLyzV8-eyXATDxB5hWoxwxmgBU,11264
 lamindb_setup/_register_instance.py,sha256=RdUZxZWHLdbvdNZWpF8e0UWROb_T0cStWbzc5yUw34I,1047
 lamindb_setup/_schema.py,sha256=b3uzhhWpV5mQtDwhMINc2MabGCnGLESy51ito3yl6Wc,679
-lamindb_setup/_schema_metadata.py,sha256=af1Es7qFKGPRdNmk48384HiB2r-cDTdBPu0wB9qrga4,15526
+lamindb_setup/_schema_metadata.py,sha256=Whs-e4ZMnA1niZ2l5Eu8il-33IxI4Hr5ylGEgPxx8wk,15628
 lamindb_setup/_set_managed_storage.py,sha256=xQe5DXCRiQ5VseAjVC2Bki0wB0n0tSTchvVKSx9I6eo,3094
-lamindb_setup/_setup_user.py,sha256=ojq7UP2Aia8GTCr6m8fylFx9VSuvGu0HmvIJ8RzymE0,6108
+lamindb_setup/_setup_user.py,sha256=cjQ-Md-FkP04PnBxocbHW6wCsZsNtD2T2NB52vAOnHI,6730
 lamindb_setup/_silence_loggers.py,sha256=AKF_YcHvX32eGXdsYK8MJlxEaZ-Uo2f6QDRzjKFCtws,1568
 lamindb_setup/errors.py,sha256=lccF3X3M2mcbHVG_0HxfuJRFFpUE-42paccIxFOfefQ,1958
-lamindb_setup/io.py,sha256=jLJ3WbWWDctXmzl6XTES6_CutX3TsvG1BSW-Jd5UITo,15081
+lamindb_setup/io.py,sha256=9s4Itt4rrHzsUATY79r4nhGp9zVAm-9uBhiQgg60l6U,16708
 lamindb_setup/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 lamindb_setup/types.py,sha256=fuQxZJnrGYe7a_Ju9n1RqO-HhkOAr1l1xjpAg9dmBu8,605
 lamindb_setup/core/__init__.py,sha256=adZtacDwG2C0tgx-ypp9yOAqw9qaR-IRWkgLurKpXVE,668
 lamindb_setup/core/_aws_options.py,sha256=9kQ5BB-cuJQrlJRGNqMRe1m48dP67xMbefOJP2c9OQw,9674
 lamindb_setup/core/_aws_storage.py,sha256=QEtV-riQrwfivcwqHnXBbkJ-9YyNEXL4fLoCmOHZ1BI,2003
-lamindb_setup/core/_clone.py,sha256=Vikc0LckB7fWTS06ei5enErWqe1mx6XvP7Ikkj-fzdg,6493
+lamindb_setup/core/_clone.py,sha256=oLTMItGxRQB1THSDP-RG2eH1qPTVcuZ7_-eElttJ518,6451
 lamindb_setup/core/_deprecated.py,sha256=M3vpM4fZPOncxY2qsXQAPeaEph28xWdv7tYaueaUyAA,2554
 lamindb_setup/core/_docs.py,sha256=3k-YY-oVaJd_9UIY-LfBg_u8raKOCNfkZQPA73KsUhs,276
 lamindb_setup/core/_hub_client.py,sha256=vem145S5ppRPcWob7iclGhos8k-BfwJi9AI-l5PteDs,10481
 lamindb_setup/core/_hub_core.py,sha256=GAQK5XkHROIuqA-H8sOQZVlxvN4QIH_cmHY0TENnq2U,29090
 lamindb_setup/core/_hub_crud.py,sha256=j6516H82kLjFUNPqFGUINbDw9YbofMgjxadGzYb0OS4,6362
 lamindb_setup/core/_hub_utils.py,sha256=6dyDGyzYFgVfR_lE3VN3CP1jGp98gxPtr-T91PAP05U,2687
-lamindb_setup/core/_private_django_api.py,sha256=By63l3vIEtK1pq246FhHq3tslxsaTJGKm5VakYluWp4,2656
+lamindb_setup/core/_private_django_api.py,sha256=Z9uGL4CK0OX58rc8R_qarg9rIBp1DgjsjfP9Vj2vJHI,2629
 lamindb_setup/core/_settings.py,sha256=QbTrSkkdx0u685NJ4neNtWzhdHoaGMKcIvrfFnctTQ4,15450
 lamindb_setup/core/_settings_instance.py,sha256=eDkueLK5JZOGFhZRbGa-OffS9iBFlxMp47vF_MfmCYI,24301
 lamindb_setup/core/_settings_load.py,sha256=NQDOln8e3qyGphk8ucU7mm3HVkCv4QV4rDZro3TIwfo,5183
 lamindb_setup/core/_settings_save.py,sha256=96mWdYLyfvbnG_ok_vK4x7jm-rtqcWCD1OHEt2QSAms,3328
-lamindb_setup/core/_settings_storage.py,sha256=mO5WVlybloyizKILGpbJf_Fe5yp32D-fYERURcncQ3o,15505
+lamindb_setup/core/_settings_storage.py,sha256=22EBagIr5qOZr9pqVkJsTcQtgE14en-Wh0y9rgF4FEQ,15677
 lamindb_setup/core/_settings_store.py,sha256=auZssUBb6qE5oSqdGiHhqI2B46qSpegX89VwObPQksk,2601
 lamindb_setup/core/_settings_user.py,sha256=gFfyMf-738onbh1Mf4wsmLlenQJPtjQfpUgKnOlqc2o,1453
 lamindb_setup/core/_setup_bionty_sources.py,sha256=ox3X-SHiHa2lNPSWjwZhINypbLacX6kGwH6hVVrSFZc,1505
 lamindb_setup/core/cloud_sqlite_locker.py,sha256=H_CTUCjURFXwD1cCtV_Jn0_60iztZTkaesLLXIBgIxc,7204
-lamindb_setup/core/django.py,sha256=2HwhtfUEX4peSkczc0VSfA-CpfCGL4vNgkPe9Pwu5kw,12429
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 lamindb_setup/core/types.py,sha256=T7NwspfRHgIIpYsXDcApks8jkOlGeGRW-YbVLB7jNIo,67
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