Usernames and full names in quality status API response (issue 1408)

viewer/managers.py

@@ -465,3 +465,26 @@ def annotated_qs(self):
                 'upload_version',
             )
         )
+
+
+class SiteObservationQualityStatusQueryset(QuerySet):
+    def annotated_qs(self):
+        SiteObservationQualityStatus = apps.get_model(
+            "viewer",
+            "SiteObservationQualityStatus",
+        )
+        qs = SiteObservationQualityStatus.objects.annotate(
+            username=F("user__username"),
+            first_name=F("user__first_name"),
+            last_name=F("user__last_name"),
+        )
+
+        return qs
+
+
+class SiteObservationQualityStatusDataManager(Manager):
+    def get_queryset(self):
+        return SiteObservationQualityStatusQueryset(self.model, using=self._db)
+
+    def annotated_qs(self):
+        return self.get_queryset().annotated_qs()

viewer/migrations/0101_auto_20250226_1139.py

@@ -0,0 +1,32 @@
+# Generated by Django 3.2.25 on 2025-02-26 11:39
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('viewer', '0100_auto_20250213_1039'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='RefinementStatusType',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('code', models.IntegerField(blank=True)),
+                ('description', models.TextField(blank=True)),
+                ('default_quality_status', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='viewer.qualitystatustype')),
+            ],
+        ),
+        migrations.AddField(
+            model_name='experiment',
+            name='refinement_outcome',
+            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='viewer.refinementstatustype'),
+        ),
+        migrations.AddConstraint(
+            model_name='refinementstatustype',
+            constraint=models.UniqueConstraint(fields=('code',), name='unique_refinement_code'),
+        ),
+    ]

viewer/migrations/0102_auto_20250226_1146.py

@@ -0,0 +1,41 @@
+# Generated by Django 3.2.25 on 2025-02-26 11:46
+
+from django.db import migrations
+
+
+
+refinement_status = (
+    (0, "All Datasets"),
+    (1, "Analysis Pending"),
+    (2, "PANDDA model"),
+    (3, "In Refinement"),
+    (4, "CompChem Ready"),
+    (5, "Deposition Ready"),
+    (6, "Deposited"),
+    (7, "Analysed & Rejected"),
+)
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('viewer', '0101_auto_20250226_1139'),
+    ]
+
+    def populate_refinements(apps, schema_editor):
+        RefinementStatusType = apps.get_model("viewer", "RefinementStatusType")
+        for code, description in refinement_status:
+            RefinementStatusType(
+                code=code,
+                description=description,
+            )
+
+
+
+    def depopulate_refinements(apps, schema_editor):
+        RefinementStatusType = apps.get_model("viewer", "RefinementStatusType")
+        RefinementStatusType.objects.all().delete()
+
+
+    operations = [
+        migrations.RunPython(populate_refinements, depopulate_refinements)
+    ]

viewer/migrations/0103_remove_refinementstatustype_default_quality_status.py

@@ -0,0 +1,17 @@
+# Generated by Django 3.2.25 on 2025-02-26 12:04
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('viewer', '0102_auto_20250226_1146'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='refinementstatustype',
+            name='default_quality_status',
+        ),
+    ]

viewer/models.py

@@ -26,6 +26,7 @@
     QuatAssemblyDataManager,
     SessionActionsDataManager,
     SiteObservationDataManager,
+    SiteObservationQualityStatusDataManager,
     SnapshotActionsDataManager,
     SnapshotDataManager,
     XtalformDataManager,
@@ -227,6 +228,32 @@ def get_download_path(self):
         )
 
 
+class QualityStatusType(models.Model):
+    status = models.TextField(primary_key=True)
+
+
+class RefinementStatusType(models.Model):
+    code = models.IntegerField(blank=True)
+    description = models.TextField(blank=True)
+
+    class Meta:
+        constraints = [
+            models.UniqueConstraint(
+                fields=[
+                    "code",
+                ],
+                name="unique_refinement_code",
+            ),
+        ]
+
+    def __repr__(self) -> str:
+        return "<RefinementStatusType %r %r %r>" % (
+            self.id,
+            self.code,
+            self.description,
+        )
+
+
 class Experiment(models.Model):
     experiment_upload = models.ForeignKey(ExperimentUpload, on_delete=models.CASCADE)
     code = models.TextField(null=True)
@@ -256,6 +283,11 @@ class Experiment(models.Model):
     )
     # need to set null=True due to the data saving order
     xtalform = models.ForeignKey("Xtalform", null=True, on_delete=models.CASCADE)
+    refinement_outcome = models.ForeignKey(
+        RefinementStatusType,
+        on_delete=models.SET_NULL,
+        null=True,
+    )
 
     objects = models.Manager()
     filter_manager = ExperimentDataManager()
@@ -594,10 +626,6 @@ def get_ligand_mol_file(self):
         return contents
 
 
-class QualityStatusType(models.Model):
-    status = models.TextField(primary_key=True)
-
-
 class SiteObservationQualityStatus(models.Model):
     site_observation = models.ForeignKey(SiteObservation, on_delete=models.CASCADE)
     status = models.ForeignKey(QualityStatusType, on_delete=models.CASCADE)
@@ -607,6 +635,9 @@ class SiteObservationQualityStatus(models.Model):
     main_status = models.BooleanField(default=False)
     comment = models.TextField()
 
+    objects = models.Manager()
+    filter_manager = SiteObservationQualityStatusDataManager()
+
 
 class CompoundIdentifierType(models.Model):
     name = models.TextField(primary_key=True)

viewer/serializers.py

@@ -1236,13 +1236,20 @@ class MetadataUploadSerializer(serializers.Serializer):
 
 
 class SiteObservationQualityStatusSerializer(serializers.ModelSerializer):
+    username = serializers.CharField(read_only=True)
+    first_name = serializers.CharField(read_only=True)
+    last_name = serializers.CharField(read_only=True)
+
     class Meta:
         model = models.SiteObservationQualityStatus
         fields = '__all__'
         extra_kwargs = {
             "auto_assigned": {"read_only": True},
             "timestamp": {"read_only": True},
             "user": {"read_only": True},
+            "username": {"read_only": True},
+            "first_name": {"read_only": True},
+            "last_name": {"read_only": True},
         }
 
     def create(self, validated_data):

viewer/target_loader.py

@@ -4,7 +4,8 @@
 import logging
 import math
 import os
-import random
+
+# import random
 import shutil
 import tarfile
 from collections.abc import Callable
@@ -1533,17 +1534,17 @@ def process_site_observation(
             "smiles": smiles,
         }
 
-        index_data = {
-            "auto_build_score": random.random(),
-        }
+        # index_data = {
+        #     "auto_build_score": random.random(),
+        # }
 
         return ProcessedObject(
             model_class=SiteObservation,
             fields=fields,
             defaults=defaults,
             key=key,
             versioned_key=v_key,
-            index_data=index_data,
+            index_data={},
         )
 
     def process_bundle(self):
@@ -2238,7 +2239,7 @@ def process_bundle(self):
             if val.new:
                 self._assign_observation_quality_status(
                     val.instance,
-                    val.index_data["auto_build_score"],
+                    # val.index_data["auto_build_score"],
                 )
 
     def import_compound_identifiers(self, alias_file_path):
@@ -2608,13 +2609,8 @@ def _get_final_path(self, path: str | None) -> Path | None:
             # received invalid path
             return None
 
-    def _assign_observation_quality_status(self, site_observation, score) -> None:
-        if score > 0.7:
-            status = QualityStatusType.objects.get(status="GOOD")
-        elif score <= 0.7 and score > 0.4:
-            status = QualityStatusType.objects.get(status="MEDIOCRE")
-        else:
-            status = QualityStatusType.objects.get(status="BAD")
+    def _assign_observation_quality_status(self, site_observation) -> None:
+        status = QualityStatusType.objects.get(status="NONE")
 
         SiteObservationQualityStatus(
             site_observation=site_observation,

viewer/views.py

@@ -2839,7 +2839,7 @@ class SiteObservationQualityStatusView(
     mixins.UpdateModelMixin,
     ISPyBSafeQuerySet,
 ):
-    queryset = models.SiteObservationQualityStatus.objects.all()
+    queryset = models.SiteObservationQualityStatus.filter_manager.annotated_qs()
     serializer_class = serializers.SiteObservationQualityStatusSerializer
     filterset_class = filters.SiteObservationQualityStatusFilter
     filter_permissions = "site_observation__experiment__experiment_upload__project"