🎨 Use Field defaults (#2)

findrefs/__init__.py

@@ -31,5 +31,7 @@ def __getattr__(name):
 
 
 if _check_instance_setup():
+    import lamindb
+
     del __getattr__  # delete so that imports work out
     from .models import Reference

findrefs/migrations/0001_initial.py

@@ -132,7 +132,7 @@ class Migration(migrations.Migration):
             options={
                 "abstract": False,
             },
-            bases=(lnschema_core.models.CanValidate, models.Model),
+            bases=(lnschema_core.models.CanCurate, models.Model),
         ),
         migrations.AddField(
             model_name="artifactreference",

findrefs/migrations/0002_alter_artifactreference_artifact_and_more.py

@@ -0,0 +1,190 @@
+# Generated by Django 5.2 on 2024-11-15 12:53
+
+import django.core.validators
+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, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("findrefs", "0001_initial"),
+        (
+            "lnschema_core",
+            "0069_alter_artifact__accessor_alter_artifact__hash_type_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="artifactreference",
+            name="artifact",
+            field=lnschema_core.fields.ForeignKey(
+                blank=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="links_reference",
+                to="lnschema_core.artifact",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="artifactreference",
+            name="created_at",
+            field=lnschema_core.fields.DateTimeField(auto_now_add=True, db_index=True),
+        ),
+        migrations.AlterField(
+            model_name="artifactreference",
+            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="artifactreference",
+            name="feature",
+            field=lnschema_core.fields.ForeignKey(
+                blank=True,
+                default=None,
+                null=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="links_artifactreference",
+                to="lnschema_core.feature",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="artifactreference",
+            name="feature_ref_is_name",
+            field=lnschema_core.fields.BooleanField(
+                blank=True, default=None, null=True
+            ),
+        ),
+        migrations.AlterField(
+            model_name="artifactreference",
+            name="label_ref_is_name",
+            field=lnschema_core.fields.BooleanField(
+                blank=True, default=None, null=True
+            ),
+        ),
+        migrations.AlterField(
+            model_name="artifactreference",
+            name="reference",
+            field=lnschema_core.fields.ForeignKey(
+                blank=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="links_artifact",
+                to="findrefs.reference",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="artifactreference",
+            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="reference",
+            name="abbr",
+            field=lnschema_core.fields.CharField(
+                blank=True,
+                db_index=True,
+                default=None,
+                max_length=32,
+                null=True,
+                unique=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="reference",
+            name="created_at",
+            field=lnschema_core.fields.DateTimeField(auto_now_add=True, db_index=True),
+        ),
+        migrations.AlterField(
+            model_name="reference",
+            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="reference",
+            name="doi",
+            field=lnschema_core.fields.CharField(
+                blank=True,
+                db_index=True,
+                default=None,
+                max_length=255,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        message="Must be a DOI (e.g., 10.1000/xyz123 or https://doi.org/10.1000/xyz123)",
+                        regex="^(?:https?://(?:dx\\.)?doi\\.org/|doi:|DOI:)?10\\.\\d+/.*$",
+                    )
+                ],
+            ),
+        ),
+        migrations.AlterField(
+            model_name="reference",
+            name="name",
+            field=lnschema_core.fields.CharField(
+                blank=True, db_index=True, default=None, max_length=255
+            ),
+        ),
+        migrations.AlterField(
+            model_name="reference",
+            name="pubmed_id",
+            field=lnschema_core.fields.BigIntegerField(blank=True, null=True),
+        ),
+        migrations.AlterField(
+            model_name="reference",
+            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="reference",
+            name="text",
+            field=lnschema_core.fields.TextField(blank=True, default=None, null=True),
+        ),
+        migrations.AlterField(
+            model_name="reference",
+            name="uid",
+            field=lnschema_core.fields.CharField(
+                blank=True,
+                default=lnschema_core.ids.base62_12,
+                max_length=12,
+                unique=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="reference",
+            name="updated_at",
+            field=lnschema_core.fields.DateTimeField(auto_now=True, db_index=True),
+        ),
+        migrations.AlterField(
+            model_name="reference",
+            name="url",
+            field=models.URLField(blank=True, null=True),
+        ),
+    ]

findrefs/models.py

@@ -1,20 +1,29 @@
 from __future__ import annotations
 
+from django.core.validators import RegexValidator
 from django.db import models
 from django.db.models import CASCADE, PROTECT
 from lnschema_core import ids
+from lnschema_core.fields import (
+    BigIntegerField,
+    BooleanField,
+    CharField,
+    ForeignKey,
+    TextField,
+)
 from lnschema_core.models import (
     Artifact,
-    CanValidate,
+    CanCurate,
     Feature,
     LinkORM,
     Record,
     TracksRun,
     TracksUpdates,
+    ValidateFields,
 )
 
 
-class Reference(Record, CanValidate, TracksRun, TracksUpdates):
+class Reference(Record, CanCurate, TracksRun, TracksUpdates, ValidateFields):
     """References such as a publication or document, with unique identifiers and metadata.
 
     Example:
@@ -29,23 +38,33 @@ class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):
 
     id: int = models.AutoField(primary_key=True)
     """Internal id, valid only in one DB instance."""
-    uid: str = models.CharField(unique=True, max_length=12, default=ids.base62_12)
+    uid: str = CharField(max_length=12, unique=True, default=ids.base62_12)
     """Universal id, valid across DB instances."""
-    name: str = models.CharField(max_length=255, default=None, db_index=True)
+    name: str = CharField(db_index=True)
     """Title or name of the reference document."""
-    abbr: str | None = models.CharField(
-        max_length=32, db_index=True, unique=True, null=True, default=None
+    abbr: str | None = CharField(
+        max_length=32,
+        db_index=True,
+        unique=True,
+        null=True,
     )
     """A unique abbreviation for the reference."""
-    url: str | None = models.URLField(max_length=255, null=True, default=None)
+    url: str | None = models.URLField(null=True, blank=True)
     """URL linking to the reference."""
-    pubmed_id: int | None = models.BigIntegerField(null=True, default=None)
+    pubmed_id: int | None = BigIntegerField(null=True)
     """A PudMmed ID."""
-    doi: int | None = models.CharField(
-        max_length=255, null=True, default=None, db_index=True
+    doi: int | None = CharField(
+        null=True,
+        db_index=True,
+        validators=[
+            RegexValidator(
+                regex=r"^(?:https?://(?:dx\.)?doi\.org/|doi:|DOI:)?10\.\d+/.*$",
+                message="Must be a DOI (e.g., 10.1000/xyz123 or https://doi.org/10.1000/xyz123)",
+            )
+        ],
     )
     """Digital Object Identifier (DOI) for the reference."""
-    text: str | None = models.TextField(null=True, default=None)
+    text: str | None = TextField(null=True)
     """Text of the reference such as the abstract or the full-text to enable search."""
     artifacts: Artifact = models.ManyToManyField(
         Artifact, through="ArtifactReference", related_name="references"
@@ -55,18 +74,14 @@ class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):
 
 class ArtifactReference(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
-    artifact: Artifact = models.ForeignKey(
-        Artifact, CASCADE, related_name="links_reference"
-    )
-    reference: Reference = models.ForeignKey(
-        Reference, PROTECT, related_name="links_artifact"
-    )
-    feature: Feature = models.ForeignKey(
+    artifact: Artifact = ForeignKey(Artifact, CASCADE, related_name="links_reference")
+    reference: Reference = ForeignKey(Reference, PROTECT, related_name="links_artifact")
+    feature: Feature = ForeignKey(
         Feature,
         PROTECT,
         null=True,
         default=None,
         related_name="links_artifactreference",
     )
-    label_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
-    feature_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
+    label_ref_is_name: bool | None = BooleanField(null=True, default=None)
+    feature_ref_is_name: bool | None = BooleanField(null=True, default=None)

pyproject.toml

@@ -8,7 +8,7 @@ authors = [{name = "Lamin Labs", email = "[email protected]"}]
 readme = "README.md"
 dynamic = ["version", "description"]
 dependencies = [
-    "lamindb"
+    "lamindb>=0.76.16"
 ]
 
 [project.urls]