lamindb 1.0.5__py3-none-any.whl → 1.1.1__py3-none-any.whl

lamindb/curators/_cellxgene_schemas/__init__.py

@@ -0,0 +1,26 @@
+from pathlib import Path
+
+import pandas as pd
+import yaml  # type: ignore
+
+
+def _read_schema_versions(ontology_versions: Path) -> dict[str, pd.DataFrame]:
+    data = yaml.safe_load(open(ontology_versions))
+    schema_versions = data["schema-version"]
+
+    def _schema_to_df(schema_data):
+        return pd.DataFrame(
+            [
+                (entity, organism, ontology, version)
+                for entity, details in schema_data.items()
+                for ontology, values in details.items()
+                for organism, version in values.items()
+            ],
+            columns=["entity", "organism", "source", "version"],
+        ).set_index("entity")
+
+    schema_versions_df = {
+        version: _schema_to_df(details) for version, details in schema_versions.items()
+    }
+
+    return schema_versions_df

lamindb/curators/_cellxgene_schemas/schema_versions.yml

@@ -0,0 +1,104 @@
+schema-version:
+  4.0.0:
+    CellType:
+      cl:
+        all: "2023-08-24"
+    ExperimentalFactor:
+      efo:
+        all: "3.57.0"
+    Ethnicity:
+      hancestro:
+        human: "3.0"
+    DevelopmentalStage:
+      hsapdv:
+        human: "2020-03-10"
+      mmusdv:
+        mouse: "2020-03-10"
+    Disease:
+      mondo:
+        all: "2023-08-02"
+    Organism:
+      ncbitaxon:
+        all: "2023-06-20"
+    Phenotype:
+      pato:
+        all: "2023-05-18"
+    Tissue:
+      uberon:
+        all: "2023-09-05"
+    Gene:
+      genecode:
+        human: "v38"
+        mouse: "vM27"
+  5.0.0:
+    CellType:
+      cl:
+        all: "2024-01-04"
+    ExperimentalFactor:
+      efo:
+        all: "3.62.0"
+    Ethnicity:
+      hancestro:
+        human: "3.0"
+    DevelopmentalStage:
+      hsapdv:
+        human: "2020-03-10"
+      mmusdv:
+        mouse: "2020-03-10"
+    Disease:
+      mondo:
+        all: "2024-01-03"
+    Organism:
+      ncbitaxon:
+        all: "2023-06-20"
+      ensembl:
+        vertebrates: "release-110"
+    Phenotype:
+      pato:
+        all: "2023-05-18"
+    Tissue:
+      uberon:
+        all: "2024-01-18"
+    Gene:
+      genecode:
+        human: "v44"
+        mouse: "vM33"
+      ensembl:
+        human: "release-110"
+        mouse: "release-110"
+  5.1.0:
+    CellType:
+      cl:
+        all: "2024-04-05"
+    ExperimentalFactor:
+      efo:
+        all: "3.65.0"
+    Ethnicity:
+      hancestro:
+        human: "3.0"
+    DevelopmentalStage:
+      hsapdv:
+        human: "2020-03-10"
+      mmusdv:
+        mouse: "2020-03-10"
+    Disease:
+      mondo:
+        all: "2024-05-08"
+    Organism:
+      ncbitaxon:
+        all: "2023-06-20"
+      ensembl:
+        vertebrates: "release-110"
+    Phenotype:
+      pato:
+        all: "2023-05-18"
+    Tissue:
+      uberon:
+        all: "2024-03-22"
+    Gene:
+      genecode:
+        human: "v44"
+        mouse: "vM33"
+      ensembl:
+        human: "release-110"
+        mouse: "release-110"

lamindb/errors.py

@@ -0,0 +1,96 @@
+"""Exceptions.
+
+.. autosummary::
+   :toctree: .
+
+   ValidationError
+   InvalidArgument
+   DoesNotExist
+   NotebookNotSaved
+   MissingContextUID
+   UpdateContext
+   IntegrityError
+   RecordNameChangeIntegrityError
+
+"""
+
+# inheriting from SystemExit has the sole purpose of suppressing
+# the traceback - this isn't optimal but the current best solution
+# https://laminlabs.slack.com/archives/C04A0RMA0SC/p1726856875597489
+
+
+class ValidationError(Exception):
+    """Validation error."""
+
+    pass
+
+
+class InvalidArgument(Exception):
+    """Invalid method or function argument."""
+
+    pass
+
+
+class TrackNotCalled(Exception):
+    """`ln.track()` wasn't called."""
+
+    pass
+
+
+class NotebookNotSaved(Exception):
+    """Notebook wasn't saved."""
+
+    pass
+
+
+# equivalent to Django's DoesNotExist
+# and SQLAlchemy's NoResultFound
+class DoesNotExist(Exception):
+    """No record found."""
+
+    pass
+
+
+class InconsistentKey(Exception):
+    """Inconsistent transform or artifact `key`."""
+
+    pass
+
+
+class RecordNameChangeIntegrityError(Exception):
+    """Custom exception for name change errors."""
+
+    pass
+
+
+class FieldValidationError(Exception):
+    """Field validation error."""
+
+    pass
+
+
+# -------------------------------------------------------------------------------------
+# run context
+# -------------------------------------------------------------------------------------
+
+
+class IntegrityError(Exception):
+    """Integrity error.
+
+    For instance, it's not allowed to delete artifacts outside managed storage
+    locations.
+    """
+
+    pass
+
+
+class MissingContextUID(SystemExit):
+    """User didn't define transform settings."""
+
+    pass
+
+
+class UpdateContext(SystemExit):
+    """Transform settings require update."""
+
+    pass

lamindb/integrations/_vitessce.py

@@ -31,7 +31,7 @@ def save_vitessce_config(
     Args:
         vitessce_config: A `VitessceConfig` object.
         description: A description for the `VitessceConfig` object. Is used as
-            `name` for a `Collection` in case the `VitessceConfig` object
+            `key` for a `Collection` in case the `VitessceConfig` object
             references multiple artifacts.
 
     .. versionchanged:: 0.76.12
@@ -58,7 +58,7 @@ def save_vitessce_config(
     assert len(dataset_artifacts) > 0  # noqa: S101
 
     # the below will be replaced with a `ln.tracked()` decorator soon
-    transform = Transform(
+    transform = Transform(  # type: ignore
         uid="kup03MJBsIVa0002",
         key="save_vitessce_config",
         type="function",
@@ -70,7 +70,7 @@ def save_vitessce_config(
     if len(dataset_artifacts) > 1:
         # if we have more datasets, we should create a collection
         # and attach an action to the collection
-        collection = Collection(dataset_artifacts, name=description).save()
+        collection = Collection(dataset_artifacts, key=description).save()
 
     # create a JSON export
     config_file_local_path = ln_setup.settings.cache_dir / "config.vitessce.json"

lamindb/migrations/0069_squashed.py

@@ -10,81 +10,82 @@ import lamindb.models
 
 
 class Migration(migrations.Migration):
-    replaces = [
-        (
-            "lamindb",
-            "0037_rename_dataset_to_collection",
-        ),
-        (
-            "lamindb",
-            "0038_alter_collection_artifact_alter_collection_artifacts_and_more",
-        ),
-        (
-            "lamindb",
-            "0039_remove_collection_artifacts_collectionartifact_and_more",
-        ),
-        ("lamindb", "0040_alter_transform_type"),
-        (
-            "lamindb",
-            "0041_remove_transform_short_name_transform_description_and_more",
-        ),
-        ("lamindb", "0042_rename_run_at_run_started_at_run_finished_at"),
-        ("lamindb", "0043_run_json"),
-        ("lamindb", "0044_run_replicated_outputs_transform_ulabels_and_more"),
-        (
-            "lamindb",
-            "0045_rename_replicated_outputs_run_replicated_output_artifacts_and_more",
-        ),
-        ("lamindb", "0046_storage_instance_uid"),
-        ("lamindb", "0047_featurevalue_artifactfeaturevalue_and_more"),
-        ("lamindb", "0048_alter_artifactulabel_feature_and_more"),
-        ("lamindb", "0049_rename_type_feature_dtype_and_more"),
-        ("lamindb", "0050_artifactfeatureset_feature_ref_is_semantic_and_more"),
-        (
-            "lamindb",
-            "0051_remove_feature_feature_sets_featuresetfeature_and_more",
-        ),
-        (
-            "lamindb",
-            "0052_rename_feature_value_artifactfeaturevalue_featurevalue_and_more",
-        ),
-        ("lamindb", "0052_squashed"),
-        (
-            "lamindb",
-            "0053_alter_featureset_hash_alter_paramvalue_created_by_and_more",
-        ),
-        ("lamindb", "0054_alter_feature_previous_runs_and_more"),
-        ("lamindb", "0055_artifact_type_artifactparamvalue_and_more"),
-        (
-            "lamindb",
-            "0056_rename_ulabel_ref_is_name_artifactulabel_label_ref_is_name_and_more",
-        ),
-        ("lamindb", "0057_link_models_latest_report_and_others"),
-        ("lamindb", "0058_artifact__actions_collection__actions"),
-        (
-            "lamindb",
-            "0059_alter_artifact__accessor_alter_artifact__hash_type_and_more",
-        ),
-        ("lamindb", "0060_alter_artifact__actions"),
-        (
-            "lamindb",
-            "0061_alter_collection_meta_artifact_alter_run_environment_and_more",
-        ),
-        ("lamindb", "0062_add_is_latest_field"),
-        ("lamindb", "0063_populate_latest_field"),
-        (
-            "lamindb",
-            "0064_alter_artifact_version_alter_collection_version_and_more",
-        ),
-        ("lamindb", "0065_remove_collection_feature_sets_and_more"),
-        ("lamindb", "0066_alter_artifact__feature_values_and_more"),
-        ("lamindb", "0067_alter_featurevalue_unique_together_and_more"),
-        ("lamindb", "0068_alter_artifactulabel_unique_together_and_more"),
-        (
-            "lamindb",
-            "0069_alter_artifact__accessor_alter_artifact__hash_type_and_more",
-        ),
-    ]
+    initial = True
+    # replaces = [
+    #     (
+    #         "lamindb",
+    #         "0037_rename_dataset_to_collection",
+    #     ),
+    #     (
+    #         "lamindb",
+    #         "0038_alter_collection_artifact_alter_collection_artifacts_and_more",
+    #     ),
+    #     (
+    #         "lamindb",
+    #         "0039_remove_collection_artifacts_collectionartifact_and_more",
+    #     ),
+    #     ("lamindb", "0040_alter_transform_type"),
+    #     (
+    #         "lamindb",
+    #         "0041_remove_transform_short_name_transform_description_and_more",
+    #     ),
+    #     ("lamindb", "0042_rename_run_at_run_started_at_run_finished_at"),
+    #     ("lamindb", "0043_run_json"),
+    #     ("lamindb", "0044_run_replicated_outputs_transform_ulabels_and_more"),
+    #     (
+    #         "lamindb",
+    #         "0045_rename_replicated_outputs_run_replicated_output_artifacts_and_more",
+    #     ),
+    #     ("lamindb", "0046_storage_instance_uid"),
+    #     ("lamindb", "0047_featurevalue_artifactfeaturevalue_and_more"),
+    #     ("lamindb", "0048_alter_artifactulabel_feature_and_more"),
+    #     ("lamindb", "0049_rename_type_feature_dtype_and_more"),
+    #     ("lamindb", "0050_artifactfeatureset_feature_ref_is_semantic_and_more"),
+    #     (
+    #         "lamindb",
+    #         "0051_remove_feature_feature_sets_featuresetfeature_and_more",
+    #     ),
+    #     (
+    #         "lamindb",
+    #         "0052_rename_feature_value_artifactfeaturevalue_featurevalue_and_more",
+    #     ),
+    #     ("lamindb", "0052_squashed"),
+    #     (
+    #         "lamindb",
+    #         "0053_alter_featureset_hash_alter_paramvalue_created_by_and_more",
+    #     ),
+    #     ("lamindb", "0054_alter_feature_previous_runs_and_more"),
+    #     ("lamindb", "0055_artifact_type_artifactparamvalue_and_more"),
+    #     (
+    #         "lamindb",
+    #         "0056_rename_ulabel_ref_is_name_artifactulabel_label_ref_is_name_and_more",
+    #     ),
+    #     ("lamindb", "0057_link_models_latest_report_and_others"),
+    #     ("lamindb", "0058_artifact__actions_collection__actions"),
+    #     (
+    #         "lamindb",
+    #         "0059_alter_artifact__accessor_alter_artifact__hash_type_and_more",
+    #     ),
+    #     ("lamindb", "0060_alter_artifact__actions"),
+    #     (
+    #         "lamindb",
+    #         "0061_alter_collection_meta_artifact_alter_run_environment_and_more",
+    #     ),
+    #     ("lamindb", "0062_add_is_latest_field"),
+    #     ("lamindb", "0063_populate_latest_field"),
+    #     (
+    #         "lamindb",
+    #         "0064_alter_artifact_version_alter_collection_version_and_more",
+    #     ),
+    #     ("lamindb", "0065_remove_collection_feature_sets_and_more"),
+    #     ("lamindb", "0066_alter_artifact__feature_values_and_more"),
+    #     ("lamindb", "0067_alter_featurevalue_unique_together_and_more"),
+    #     ("lamindb", "0068_alter_artifactulabel_unique_together_and_more"),
+    #     (
+    #         "lamindb",
+    #         "0069_alter_artifact__accessor_alter_artifact__hash_type_and_more",
+    #     ),
+    # ]
 
     dependencies = []  # type: ignore
     operations = [

lamindb/migrations/0075_lamindbv1_part5.py

@@ -1,7 +1,6 @@
 # Generated by Django 5.2 on 2025-01-13 14:10
 
 import django.db.models.deletion
-import lamindb_setup
 from django.db import migrations, models
 
 import lamindb.base.fields
@@ -270,7 +269,7 @@ class Migration(migrations.Migration):
     ]
 
 
-if "bionty" in lamindb_setup.settings.instance.modules:
-    Migration.dependencies += [
-        ("bionty", "0046_alter_cellline__aux_alter_cellmarker__aux_and_more"),
-    ]
+# if "bionty" in lamindb_setup.settings.instance.modules:
+#     Migration.dependencies += [
+#         ("bionty", "0046_alter_cellline__aux_alter_cellmarker__aux_and_more"),
+#     ]

lamindb/migrations/0082_alter_feature_dtype.py

@@ -0,0 +1,21 @@
+# Generated by Django 5.2 on 2025-01-25 08:26
+
+from django.db import migrations
+
+import lamindb.base.fields
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("lamindb", "0081_revert_textfield_collection"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="feature",
+            name="dtype",
+            field=lamindb.base.fields.CharField(
+                blank=True, db_index=True, default=None, max_length=255, null=True
+            ),
+        ),
+    ]

lamindb/migrations/0083_alter_feature_is_type_alter_flextable_is_type_and_more.py

@@ -0,0 +1,94 @@
+# Generated by Django 5.2 on 2025-01-25 13:29
+
+from django.db import migrations
+
+import lamindb.base.fields
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("lamindb", "0082_alter_feature_dtype"),
+    ]
+
+    operations = [
+        migrations.RunSQL(
+            sql="""
+                UPDATE lamindb_feature
+                SET is_type = FALSE
+                WHERE is_type IS NULL;
+
+                UPDATE lamindb_flextable
+                SET is_type = FALSE
+                WHERE is_type IS NULL;
+
+                UPDATE lamindb_param
+                SET is_type = FALSE
+                WHERE is_type IS NULL;
+
+                UPDATE lamindb_project
+                SET is_type = FALSE
+                WHERE is_type IS NULL;
+
+                UPDATE lamindb_reference
+                SET is_type = FALSE
+                WHERE is_type IS NULL;
+
+                UPDATE lamindb_schema
+                SET is_type = FALSE
+                WHERE is_type IS NULL;
+
+                UPDATE lamindb_ulabel
+                SET is_type = FALSE
+                WHERE is_type IS NULL;
+            """
+        ),
+        migrations.AlterField(
+            model_name="feature",
+            name="is_type",
+            field=lamindb.base.fields.BooleanField(
+                blank=True, db_index=True, default=False
+            ),
+        ),
+        migrations.AlterField(
+            model_name="flextable",
+            name="is_type",
+            field=lamindb.base.fields.BooleanField(
+                blank=True, db_index=True, default=False
+            ),
+        ),
+        migrations.AlterField(
+            model_name="param",
+            name="is_type",
+            field=lamindb.base.fields.BooleanField(
+                blank=True, db_index=True, default=False
+            ),
+        ),
+        migrations.AlterField(
+            model_name="project",
+            name="is_type",
+            field=lamindb.base.fields.BooleanField(
+                blank=True, db_index=True, default=False
+            ),
+        ),
+        migrations.AlterField(
+            model_name="reference",
+            name="is_type",
+            field=lamindb.base.fields.BooleanField(
+                blank=True, db_index=True, default=False
+            ),
+        ),
+        migrations.AlterField(
+            model_name="schema",
+            name="is_type",
+            field=lamindb.base.fields.BooleanField(
+                blank=True, db_index=True, default=False
+            ),
+        ),
+        migrations.AlterField(
+            model_name="ulabel",
+            name="is_type",
+            field=lamindb.base.fields.BooleanField(
+                blank=True, db_index=True, default=False
+            ),
+        ),
+    ]

lamindb/migrations/0084_alter_schemafeature_feature_and_more.py

@@ -0,0 +1,35 @@
+# Generated by Django 5.2 on 2025-01-27 07:22
+
+import django.db.models.deletion
+from django.db import migrations
+
+import lamindb.base.fields
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("lamindb", "0083_alter_feature_is_type_alter_flextable_is_type_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="schemafeature",
+            name="feature",
+            field=lamindb.base.fields.ForeignKey(
+                blank=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="links_schema",
+                to="lamindb.feature",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="schemafeature",
+            name="schema",
+            field=lamindb.base.fields.ForeignKey(
+                blank=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="links_feature",
+                to="lamindb.schema",
+            ),
+        ),
+    ]

lamindb/migrations/0085_alter_feature_is_type_alter_flextable_is_type_and_more.py

@@ -0,0 +1,63 @@
+# Generated by Django 5.2 on 2025-01-27 13:48
+
+from django.db import migrations
+
+import lamindb.base.fields
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("lamindb", "0084_alter_schemafeature_feature_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="feature",
+            name="is_type",
+            field=lamindb.base.fields.BooleanField(
+                blank=True, db_index=True, default=False, null=True
+            ),
+        ),
+        migrations.AlterField(
+            model_name="flextable",
+            name="is_type",
+            field=lamindb.base.fields.BooleanField(
+                blank=True, db_index=True, default=False, null=True
+            ),
+        ),
+        migrations.AlterField(
+            model_name="param",
+            name="is_type",
+            field=lamindb.base.fields.BooleanField(
+                blank=True, db_index=True, default=False, null=True
+            ),
+        ),
+        migrations.AlterField(
+            model_name="project",
+            name="is_type",
+            field=lamindb.base.fields.BooleanField(
+                blank=True, db_index=True, default=False, null=True
+            ),
+        ),
+        migrations.AlterField(
+            model_name="reference",
+            name="is_type",
+            field=lamindb.base.fields.BooleanField(
+                blank=True, db_index=True, default=False, null=True
+            ),
+        ),
+        migrations.AlterField(
+            model_name="schema",
+            name="is_type",
+            field=lamindb.base.fields.BooleanField(
+                blank=True, db_index=True, default=False, null=True
+            ),
+        ),
+        migrations.AlterField(
+            model_name="ulabel",
+            name="is_type",
+            field=lamindb.base.fields.BooleanField(
+                blank=True, db_index=True, default=False, null=True
+            ),
+        ),
+    ]