Merge pull request #2 from laminlabs/field-defaults

🎨 Add blank=True

cellregistry/__init__.py

@@ -29,5 +29,7 @@ def __getattr__(name):
 
 
 if _check_instance_setup():
+    import lamindb
+
     del __getattr__  # delete so that imports work out
     from .models import Cell

cellregistry/migrations/0001_initial.py

@@ -66,7 +66,7 @@ class Migration(migrations.Migration):
             options={
                 "abstract": False,
             },
-            bases=(lnschema_core.models.CanValidate, models.Model),
+            bases=(lnschema_core.models.CanCurate, models.Model),
         ),
         migrations.CreateModel(
             name="ArtifactCell",

cellregistry/migrations/0002_alter_artifactcell_artifact_alter_artifactcell_cell_and_more.py

@@ -0,0 +1,126 @@
+# Generated by Django 5.2 on 2024-11-15 14:16
+
+import django.db.models.deletion
+import lnschema_core.fields
+import lnschema_core.ids
+import lnschema_core.models
+import lnschema_core.users
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("cellregistry", "0001_initial"),
+        (
+            "lnschema_core",
+            "0069_alter_artifact__accessor_alter_artifact__hash_type_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="artifactcell",
+            name="artifact",
+            field=lnschema_core.fields.ForeignKey(
+                blank=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="links_cell",
+                to="lnschema_core.artifact",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="artifactcell",
+            name="cell",
+            field=lnschema_core.fields.ForeignKey(
+                blank=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="links_artifact",
+                to="cellregistry.cell",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="artifactcell",
+            name="created_at",
+            field=lnschema_core.fields.DateTimeField(auto_now_add=True, db_index=True),
+        ),
+        migrations.AlterField(
+            model_name="artifactcell",
+            name="created_by",
+            field=lnschema_core.fields.ForeignKey(
+                blank=True,
+                default=lnschema_core.users.current_user_id,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="+",
+                to="lnschema_core.user",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="artifactcell",
+            name="run",
+            field=lnschema_core.fields.ForeignKey(
+                blank=True,
+                default=lnschema_core.models.current_run,
+                null=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="+",
+                to="lnschema_core.run",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="cell",
+            name="created_at",
+            field=lnschema_core.fields.DateTimeField(auto_now_add=True, db_index=True),
+        ),
+        migrations.AlterField(
+            model_name="cell",
+            name="created_by",
+            field=lnschema_core.fields.ForeignKey(
+                blank=True,
+                default=lnschema_core.users.current_user_id,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="+",
+                to="lnschema_core.user",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="cell",
+            name="description",
+            field=lnschema_core.fields.CharField(
+                blank=True, db_index=True, default=None, max_length=255, null=True
+            ),
+        ),
+        migrations.AlterField(
+            model_name="cell",
+            name="name",
+            field=lnschema_core.fields.CharField(
+                blank=True, db_index=True, default=None, max_length=255, unique=True
+            ),
+        ),
+        migrations.AlterField(
+            model_name="cell",
+            name="run",
+            field=lnschema_core.fields.ForeignKey(
+                blank=True,
+                default=lnschema_core.models.current_run,
+                null=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="+",
+                to="lnschema_core.run",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="cell",
+            name="uid",
+            field=lnschema_core.fields.CharField(
+                blank=True,
+                default=lnschema_core.ids.base62_20,
+                max_length=20,
+                unique=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="cell",
+            name="updated_at",
+            field=lnschema_core.fields.DateTimeField(auto_now=True, db_index=True),
+        ),
+    ]

cellregistry/models.py

@@ -4,9 +4,10 @@
 from django.db import models
 from django.db.models import CASCADE, PROTECT
 from lnschema_core import ids
+from lnschema_core.fields import CharField, ForeignKey
 from lnschema_core.models import (
     Artifact,
-    CanValidate,
+    CanCurate,
     Feature,
     LinkORM,
     Record,
@@ -16,7 +17,7 @@
 )
 
 
-class Cell(Record, CanValidate, TracksRun, TracksUpdates):
+class Cell(Record, CanCurate, TracksRun, TracksUpdates):
     """Single cells.
 
     Example:
@@ -30,11 +31,9 @@ class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):
 
     id: int = models.BigAutoField(primary_key=True)
     """Internal id, valid only in one DB instance."""
-    uid: str = models.CharField(unique=True, max_length=20, default=ids.base62_20)
+    uid: str = CharField(unique=True, max_length=20, default=ids.base62_20)
     """Universal id, valid across DB instances."""
-    name: str = models.CharField(
-        max_length=255, default=None, unique=True, db_index=True
-    )
+    name: str = CharField(max_length=255, default=None, unique=True, db_index=True)
     """A unique name for the cell.
 
     It's typically the barcode combined with an identifier for the dataset that
@@ -47,9 +46,7 @@ class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):
         Pan_T7935494_ATCATGGTCTACCTGC
 
     """
-    description: str = models.CharField(
-        max_length=255, db_index=True, null=True, default=None
-    )
+    description: str = CharField(max_length=255, db_index=True, null=True, default=None)
     """A description."""
     # ulabels: ULabel = models.ManyToManyField(
     #     ULabel, through="CellULabel", related_name="cells"
@@ -67,24 +64,24 @@ class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):
 
 class ArtifactCell(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
-    artifact: Artifact = models.ForeignKey(Artifact, CASCADE, related_name="links_cell")
-    cell: Cell = models.ForeignKey(Cell, CASCADE, related_name="links_artifact")
+    artifact: Artifact = ForeignKey(Artifact, CASCADE, related_name="links_cell")
+    cell: Cell = ForeignKey(Cell, CASCADE, related_name="links_artifact")
 
 
 class CellCellType:
     id: int = models.BigAutoField(primary_key=True)
-    cell: Cell = models.ForeignKey(Cell, CASCADE, related_name="links_cell_type")
+    cell: Cell = ForeignKey(Cell, CASCADE, related_name="links_cell_type")
     # follow the .lower() convention in link models
-    celltype: CellType = models.ForeignKey(CellType, PROTECT, related_name="links_cell")
-    feature: Feature = models.ForeignKey(
+    celltype: CellType = ForeignKey(CellType, PROTECT, related_name="links_cell")
+    feature: Feature = ForeignKey(
         Feature, PROTECT, null=True, default=None, related_name="links_cellcelltype"
     )
 
 
 class CellULabel:
     id: int = models.BigAutoField(primary_key=True)
-    cell: Cell = models.ForeignKey(Cell, CASCADE, related_name="links_ulabel")
-    ulabel: ULabel = models.ForeignKey(ULabel, PROTECT, related_name="links_cell")
-    feature: Feature = models.ForeignKey(
+    cell: Cell = ForeignKey(Cell, CASCADE, related_name="links_ulabel")
+    ulabel: ULabel = ForeignKey(ULabel, PROTECT, related_name="links_cell")
+    feature: Feature = ForeignKey(
         Feature, PROTECT, null=True, default=None, related_name="links_cellulabel"
     )