🚚 Add unique constraints and fix gene_ref_is_symbol to label_ref_is_s…

…ymbol

bionty/migrations/0040_rename_gene_ref_is_symbol_artifactgene_label_ref_is_symbol_and_more.py

@@ -0,0 +1,86 @@
+# Generated by Django 5.1.1 on 2024-10-18 14:12
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("bionty", "0039_alter_cellline_source_alter_cellmarker_source_and_more"),
+        ("lnschema_core", "0067_alter_featurevalue_unique_together_and_more"),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="artifactgene",
+            old_name="gene_ref_is_symbol",
+            new_name="label_ref_is_symbol",
+        ),
+        migrations.AlterUniqueTogether(
+            name="artifactcellline",
+            unique_together={("artifact", "cellline", "feature")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="artifactcellmarker",
+            unique_together={("artifact", "cellmarker", "feature")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="artifactcelltype",
+            unique_together={("artifact", "celltype", "feature")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="artifactdevelopmentalstage",
+            unique_together={("artifact", "developmentalstage", "feature")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="artifactdisease",
+            unique_together={("artifact", "disease", "feature")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="artifactethnicity",
+            unique_together={("artifact", "ethnicity", "feature")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="artifactexperimentalfactor",
+            unique_together={("artifact", "experimentalfactor", "feature")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="artifactgene",
+            unique_together={("artifact", "gene", "feature")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="artifactorganism",
+            unique_together={("artifact", "organism", "feature")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="artifactpathway",
+            unique_together={("artifact", "pathway", "feature")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="artifactphenotype",
+            unique_together={("artifact", "phenotype", "feature")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="artifactprotein",
+            unique_together={("artifact", "protein", "feature")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="artifacttissue",
+            unique_together={("artifact", "tissue", "feature")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="featuresetcellmarker",
+            unique_together={("featureset", "cellmarker")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="featuresetgene",
+            unique_together={("featureset", "gene")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="featuresetpathway",
+            unique_together={("featureset", "pathway")},
+        ),
+        migrations.AlterUniqueTogether(
+            name="featuresetprotein",
+            unique_together={("featureset", "protein")},
+        ),
+    ]

bionty/models.py

@@ -1479,6 +1479,9 @@ class FeatureSetGene(Record, LinkORM):
     )
     gene: Gene = models.ForeignKey("Gene", PROTECT, related_name="+")
 
+    class Meta:
+        unique_together = ("featureset", "gene")
+
 
 class FeatureSetProtein(Record, LinkORM):
     id: int = models.BigAutoField(primary_key=True)
@@ -1488,6 +1491,9 @@ class FeatureSetProtein(Record, LinkORM):
     )
     protein: Protein = models.ForeignKey("Protein", PROTECT, related_name="+")
 
+    class Meta:
+        unique_together = ("featureset", "protein")
+
 
 class FeatureSetCellMarker(Record, LinkORM):
     id: int = models.BigAutoField(primary_key=True)
@@ -1498,6 +1504,9 @@ class FeatureSetCellMarker(Record, LinkORM):
     # follow the .lower() convention in link models
     cellmarker: CellMarker = models.ForeignKey("CellMarker", PROTECT, related_name="+")
 
+    class Meta:
+        unique_together = ("featureset", "cellmarker")
+
 
 class FeatureSetPathway(Record, LinkORM):
     id: int = models.BigAutoField(primary_key=True)
@@ -1507,6 +1516,9 @@ class FeatureSetPathway(Record, LinkORM):
     )
     pathway: Pathway = models.ForeignKey("Pathway", PROTECT, related_name="+")
 
+    class Meta:
+        unique_together = ("featureset", "pathway")
+
 
 class ArtifactOrganism(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
@@ -1522,6 +1534,9 @@ class ArtifactOrganism(Record, LinkORM, TracksRun):
     label_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
     feature_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
 
+    class Meta:
+        unique_together = ("artifact", "organism", "feature")
+
 
 class ArtifactGene(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
@@ -1530,9 +1545,12 @@ class ArtifactGene(Record, LinkORM, TracksRun):
     feature: Feature = models.ForeignKey(
         Feature, PROTECT, null=True, default=None, related_name="links_artifactgene"
     )
-    gene_ref_is_symbol: bool | None = models.BooleanField(null=True, default=None)
+    label_ref_is_symbol: bool | None = models.BooleanField(null=True, default=None)
     feature_ref_is_symbol: bool | None = models.BooleanField(null=True, default=None)
 
+    class Meta:
+        unique_together = ("artifact", "gene", "feature")
+
 
 class ArtifactProtein(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
@@ -1548,6 +1566,9 @@ class ArtifactProtein(Record, LinkORM, TracksRun):
     label_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
     feature_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
 
+    class Meta:
+        unique_together = ("artifact", "protein", "feature")
+
 
 class ArtifactCellMarker(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
@@ -1568,6 +1589,9 @@ class ArtifactCellMarker(Record, LinkORM, TracksRun):
     label_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
     feature_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
 
+    class Meta:
+        unique_together = ("artifact", "cellmarker", "feature")
+
 
 class ArtifactTissue(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
@@ -1581,6 +1605,9 @@ class ArtifactTissue(Record, LinkORM, TracksRun):
     label_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
     feature_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
 
+    class Meta:
+        unique_together = ("artifact", "tissue", "feature")
+
 
 class ArtifactCellType(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
@@ -1597,6 +1624,9 @@ class ArtifactCellType(Record, LinkORM, TracksRun):
     label_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
     feature_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
 
+    class Meta:
+        unique_together = ("artifact", "celltype", "feature")
+
 
 class ArtifactDisease(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
@@ -1612,6 +1642,9 @@ class ArtifactDisease(Record, LinkORM, TracksRun):
     label_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
     feature_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
 
+    class Meta:
+        unique_together = ("artifact", "disease", "feature")
+
 
 class ArtifactCellLine(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
@@ -1628,6 +1661,9 @@ class ArtifactCellLine(Record, LinkORM, TracksRun):
     label_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
     feature_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
 
+    class Meta:
+        unique_together = ("artifact", "cellline", "feature")
+
 
 class ArtifactPhenotype(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
@@ -1647,6 +1683,9 @@ class ArtifactPhenotype(Record, LinkORM, TracksRun):
     label_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
     feature_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
 
+    class Meta:
+        unique_together = ("artifact", "phenotype", "feature")
+
 
 class ArtifactPathway(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
@@ -1662,6 +1701,9 @@ class ArtifactPathway(Record, LinkORM, TracksRun):
     label_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
     feature_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
 
+    class Meta:
+        unique_together = ("artifact", "pathway", "feature")
+
 
 class ArtifactExperimentalFactor(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
@@ -1681,6 +1723,9 @@ class ArtifactExperimentalFactor(Record, LinkORM, TracksRun):
     label_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
     feature_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
 
+    class Meta:
+        unique_together = ("artifact", "experimentalfactor", "feature")
+
 
 class ArtifactDevelopmentalStage(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
@@ -1701,6 +1746,9 @@ class ArtifactDevelopmentalStage(Record, LinkORM, TracksRun):
     label_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
     feature_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
 
+    class Meta:
+        unique_together = ("artifact", "developmentalstage", "feature")
+
 
 class ArtifactEthnicity(Record, LinkORM, TracksRun):
     id: int = models.BigAutoField(primary_key=True)
@@ -1720,6 +1768,9 @@ class ArtifactEthnicity(Record, LinkORM, TracksRun):
     label_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
     feature_ref_is_name: bool | None = models.BooleanField(null=True, default=None)
 
+    class Meta:
+        unique_together = ("artifact", "ethnicity", "feature")
+
 
 # backward compat
 Species = Organism