Merge pull request #515 from xchem/m2ms-1277-tags

Site observation tags (1277)

viewer/managers.py

@@ -13,8 +13,10 @@ def filter_qs(self):
             "experiment",
             "experiment__experiment_upload",
             "experiment__experiment_upload__target",
+            "cmpd",
         ).annotate(
             target=F("experiment__experiment_upload__target"),
+            compound_code=F("cmpd__compound_code"),
         )
 
         return qs

viewer/migrations/0038_auto_20240202_1030.py

@@ -0,0 +1,39 @@
+# Generated by Django 3.2.23 on 2024-02-02 10:30
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ('viewer', '0037_rename_event_map_info_experiment_map_info'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='historicalsiteobservation',
+            name='longcode',
+            field=models.TextField(null=True),
+        ),
+        migrations.AddField(
+            model_name='siteobservation',
+            name='longcode',
+            field=models.TextField(null=True),
+        ),
+        migrations.AddField(
+            model_name='xtalformsite',
+            name='xtalform_site_num',
+            field=models.IntegerField(
+                help_text='numeric xtalform site id (enumerated on creation)', null=True
+            ),
+        ),
+        migrations.AlterField(
+            model_name='historicalsiteobservation',
+            name='code',
+            field=models.TextField(null=True),
+        ),
+        migrations.AlterField(
+            model_name='siteobservation',
+            name='code',
+            field=models.TextField(null=True),
+        ),
+    ]

viewer/migrations/0039_canonsite_canon_site_num.py

@@ -0,0 +1,19 @@
+# Generated by Django 3.2.23 on 2024-02-02 11:35
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ('viewer', '0038_auto_20240202_1030'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='canonsite',
+            name='canon_site_num',
+            field=models.IntegerField(
+                help_text='numeric canon site id (enumerated on creation)', null=True
+            ),
+        ),
+    ]

viewer/migrations/0040_quatassembly_assembly_num.py

@@ -0,0 +1,19 @@
+# Generated by Django 3.2.23 on 2024-02-02 11:47
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ('viewer', '0039_canonsite_canon_site_num'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='quatassembly',
+            name='assembly_num',
+            field=models.IntegerField(
+                help_text='numeric assembly id (enumerated on creation)', null=True
+            ),
+        ),
+    ]

viewer/migrations/0041_xtalform_xtalform_num.py

@@ -0,0 +1,19 @@
+# Generated by Django 3.2.23 on 2024-02-05 11:27
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ('viewer', '0040_quatassembly_assembly_num'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='xtalform',
+            name='xtalform_num',
+            field=models.IntegerField(
+                help_text='numeric xtalform id (enumerated on creation)', null=True
+            ),
+        ),
+    ]

viewer/migrations/0042_alter_xtalformsite_xtalform_site_num.py

@@ -0,0 +1,20 @@
+# Generated by Django 3.2.23 on 2024-02-05 12:02
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ('viewer', '0041_xtalform_xtalform_num'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='xtalformsite',
+            name='xtalform_site_num',
+            field=models.TextField(
+                help_text='alphabetic xtalform site id (enumerated on creation)',
+                null=True,
+            ),
+        ),
+    ]

viewer/models.py

@@ -281,6 +281,9 @@ class Meta:
 class QuatAssembly(models.Model):
     chains = models.TextField()
     name = models.TextField()
+    assembly_num = models.IntegerField(
+        null=True, help_text="numeric assembly id (enumerated on creation)"
+    )
 
     objects = models.Manager()
     filter_manager = QuatAssemblyDataManager()
@@ -301,6 +304,9 @@ class Xtalform(models.Model):
         through="XtalformQuatAssembly",
         through_fields=("xtalform", "quat_assembly"),
     )
+    xtalform_num = models.IntegerField(
+        null=True, help_text="numeric xtalform id (enumerated on creation)"
+    )
 
     objects = models.Manager()
     filter_manager = XtalformDataManager()
@@ -360,6 +366,9 @@ class CanonSite(models.Model):
     ref_conf_site = models.OneToOneField(
         "CanonSiteConf", null=True, on_delete=models.CASCADE
     )
+    canon_site_num = models.IntegerField(
+        null=True, help_text="numeric canon site id (enumerated on creation)"
+    )
 
     objects = models.Manager()
     filter_manager = CanonSiteDataManager()
@@ -379,6 +388,10 @@ class XtalformSite(models.Model):
     xtalform_site_id = models.TextField(
         null=False, help_text="xtalform site id from YAML"
     )
+    # unused, remove when certain
+    xtalform_site_num = models.TextField(
+        null=True, help_text="alphabetic xtalform site id (enumerated on creation)"
+    )
 
     objects = models.Manager()
     filter_manager = XtalformSiteDataManager()
@@ -414,7 +427,8 @@ def __repr__(self) -> str:
 
 
 class SiteObservation(models.Model):
-    code = models.TextField()
+    code = models.TextField(null=True)
+    longcode = models.TextField(null=True)
     experiment = models.ForeignKey(Experiment, on_delete=models.CASCADE)
     cmpd = models.ForeignKey(Compound, null=True, on_delete=models.CASCADE)
     xtalform_site = models.ForeignKey(XtalformSite, on_delete=models.CASCADE)

viewer/serializers.py

@@ -950,6 +950,8 @@ class Meta:
 
 
 class SiteObservationReadSerializer(serializers.ModelSerializer):
+    compound_code = serializers.StringRelatedField()
+
     class Meta:
         model = models.SiteObservation
         fields = '__all__'