🎨 Fix model relationships (#83)

* 🎨 Fix model relationships

* 💚 Fix migration

* 💚 Fix migration

* 💚 Fix guide

docs/guide/modeling_perturbations.ipynb

@@ -242,9 +242,9 @@
     "combination_perturbation = wl.CombinationPerturbation(\n",
     "    name=\"gefitinib and EGFR/KRAS knockdown combination perturbation subject to smoking\"\n",
     ").save()\n",
-    "combination_perturbation.genetics.set([EGFR_kd, KRAS_kd])\n",
-    "combination_perturbation.compounds.add(gefitinib)\n",
-    "combination_perturbation.environmentals.add(smoking)"
+    "combination_perturbation.genetic_perturbations.set([EGFR_kd, KRAS_kd])\n",
+    "combination_perturbation.compound_perturbations.add(gefitinib)\n",
+    "combination_perturbation.environmental_perturbations.add(smoking)"
    ]
   },
   {
@@ -259,7 +259,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "lamindb",
+   "display_name": "py310",
    "language": "python",
    "name": "python3"
   },
@@ -273,7 +273,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

wetlab/migrations/0028_remove_combinationperturbation_compounds_and_more.py

@@ -0,0 +1,83 @@
+# Generated by Django 5.2 on 2024-12-12 16:23
+
+import django.db.models.deletion
+import lnschema_core.fields
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("wetlab", "0027_rename_treatment_add_donor"),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name="compoundperturbation",
+            name="compounds",
+        ),
+        migrations.AddField(
+            model_name="compoundperturbation",
+            name="compound",
+            field=lnschema_core.fields.ForeignKey(
+                blank=True,
+                default=None,
+                null=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                to="wetlab.compound",
+            ),
+        ),
+        migrations.RenameField(
+            model_name="combinationperturbation",
+            old_name="environmentals",
+            new_name="environmental_perturbations",
+        ),
+        migrations.AlterField(
+            model_name="combinationperturbation",
+            name="environmental_perturbations",
+            field=models.ManyToManyField(
+                related_name="combination_perturbations",
+                to="wetlab.environmentalperturbation",
+            ),
+        ),
+        migrations.RenameField(
+            model_name="combinationperturbation",
+            old_name="genetics",
+            new_name="genetic_perturbations",
+        ),
+        migrations.AlterField(
+            model_name="combinationperturbation",
+            name="genetic_perturbations",
+            field=models.ManyToManyField(
+                related_name="combination_perturbations",
+                to="wetlab.geneticperturbation",
+            ),
+        ),
+        migrations.RenameField(
+            model_name="combinationperturbation",
+            old_name="compounds",
+            new_name="compound_perturbations",
+        ),
+        migrations.AlterField(
+            model_name="combinationperturbation",
+            name="compound_perturbations",
+            field=models.ManyToManyField(
+                related_name="combination_perturbations",
+                to="wetlab.compoundperturbation",
+            ),
+        ),
+        migrations.AddField(
+            model_name="compoundperturbation",
+            name="description",
+            field=lnschema_core.fields.TextField(blank=True, default=None, null=True),
+        ),
+        migrations.AddField(
+            model_name="environmentalperturbation",
+            name="description",
+            field=lnschema_core.fields.TextField(blank=True, default=None, null=True),
+        ),
+        migrations.AddField(
+            model_name="geneticperturbation",
+            name="description",
+            field=lnschema_core.fields.TextField(blank=True, default=None, null=True),
+        ),
+    ]

wetlab/models.py

@@ -339,6 +339,8 @@ class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):
         db_index=True,
     )
     """:class:`~wetlab.GeneticPerturbationSystem` used for the genetic perturbation."""
+    description: str | None = TextField(null=True, default=None)
+    """Description of the genetic perturbation."""
     sequence: str | None = models.TextField(null=True, default=None, db_index=True)
     """Sequence of the perturbation."""
     on_target_score: float | None = FloatField(
@@ -408,6 +410,8 @@ class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):
     """Universal id, valid across DB instances."""
     name: str = CharField(max_length=255, default=None, db_index=True)
     """Name of the compound perturbation."""
+    description: str | None = TextField(null=True, default=None)
+    """Description of the compound perturbation."""
     concentration: float = FloatField(null=True, default=None, blank=True)
     """Concentration of the compound."""
     concentration_unit: str = CharField(max_length=32, null=True, default=None)
@@ -418,7 +422,7 @@ class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):
         PerturbationTarget, related_name="compound_targets"
     )
     """Targets of the perturbation."""
-    compounds: Compound = models.ManyToManyField(Compound, related_name="compounds")
+    compound: Compound | None = ForeignKey("Compound", PROTECT, null=True, default=None)
     """Compounds linked to the perturbation."""
     artifacts: Artifact = models.ManyToManyField(
         Artifact,
@@ -484,6 +488,8 @@ class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):
     """Name of the environmental perturbation."""
     ontology_id = CharField(max_length=32, db_index=True, null=True, default=None)
     """Ontology ID (EFO) of the environmental perturbation."""
+    description: str | None = TextField(null=True, default=None)
+    """Description of the environmental perturbation."""
     value: float | None = FloatField(null=True, default=None, blank=True)
     """The value of the environmental perturbation such as a temperature."""
     unit: str | None = CharField(max_length=32, null=True, default=None)
@@ -579,16 +585,16 @@ class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):
         max_length=32, db_index=True, null=True, default=None
     )
     """Ontology ID of the perturbation."""
-    genetics: GeneticPerturbation = models.ManyToManyField(
-        GeneticPerturbation, related_name="genetic_perturbations"
+    genetic_perturbations: GeneticPerturbation = models.ManyToManyField(
+        GeneticPerturbation, related_name="combination_perturbations"
     )
     """:class:`wetlab.GeneticPerturbation` perturbations."""
-    compounds: CompoundPerturbation = models.ManyToManyField(
-        CompoundPerturbation, related_name="compound_perturbations"
+    compound_perturbations: CompoundPerturbation = models.ManyToManyField(
+        CompoundPerturbation, related_name="combination_perturbations"
     )
     """:class:`wetlab.CompoundPerturbation` perturbations."""
-    environmentals: EnvironmentalPerturbation = models.ManyToManyField(
-        EnvironmentalPerturbation, related_name="environmental_perturbations"
+    environmental_perturbations: EnvironmentalPerturbation = models.ManyToManyField(
+        EnvironmentalPerturbation, related_name="combination_perturbations"
     )
     """:class:`wetlab.EnvironmentalPerturbation` perturbations."""
     artifacts: Artifact = models.ManyToManyField(