✨ "same as" relationship support

TODO.md

@@ -10,15 +10,6 @@ InjectTool TODO
   - if needed, should be implemented using [django-rest-framework](https://www.django-rest-framework.org/)
 
 * Regarding data submissions
-  - implement the sameAs key for already submitted biosamples:
-    ```
-    "sampleRelationships": [
-      {
-        "relationshipNature": "same as",
-        "alias": "502-W-133-4FE274B"
-      }
-    ]
-    ```
   - Supposing a submission has issues in USI validation. Shuold I track it in
     validation tables? should I have tables for USI errors, since if the
     data is validated using `image_validation` is not a user error?

django-data/image/uid/admin.py

@@ -98,7 +98,7 @@ class SampleAdmin(admin.ModelAdmin):
         'animal_age_at_collection', 'animal_age_at_collection_units',
         'availability', 'storage', 'storage_processing',
         'preparation_interval', 'preparation_interval_units',
-        'description', 'publication', 'owner'
+        'description', 'publication', 'owner', "same_as",
         )
 
     # To tell Django we want to perform a join instead of fetching the names of
@@ -112,7 +112,7 @@ class SampleAdmin(admin.ModelAdmin):
     list_filter = ('owner', 'status')
 
     fields = (
-        ('name', 'alternative_id', 'biosample_id'),
+        ('name', 'alternative_id', 'biosample_id', "same_as"),
         ('submission', 'owner', 'status'),
         ('description', 'publication'),
         ('animal', 'protocol', 'organism_part'),
@@ -140,7 +140,7 @@ class AnimalAdmin(admin.ModelAdmin):
         'last_submitted', 'alternative_id', 'breed', 'sex', 'father', 'mother',
         'birth_date', 'birth_location', 'birth_location_latitude',
         'birth_location_longitude', 'birth_location_accuracy', 'description',
-        'publication', 'owner'
+        'publication', 'owner', "same_as",
         )
 
     list_filter = ('owner', 'status')
@@ -149,7 +149,7 @@ class AnimalAdmin(admin.ModelAdmin):
     readonly_fields = ("owner",)
 
     fields = (
-        ('name', 'alternative_id', 'biosample_id'),
+        ('name', 'alternative_id', 'biosample_id', "same_as"),
         ('submission', 'owner', 'status'),
         ('description', 'publication'),
         ('breed', 'sex'),

django-data/image/uid/fixtures/uid/animal.json

@@ -7,6 +7,7 @@
     "submission": 1,
     "biosample_id": null,
     "publication": 1,
+    "same_as": "SAMEA4450079",
     "alternative_id": "11",
     "description": "a 4-year old pig organic fed",
     "material": "Organism",

django-data/image/uid/migrations/0004_auto_20200131_1622.py

@@ -0,0 +1,23 @@
+# Generated by Django 2.2.9 on 2020-01-31 15:22
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('uid', '0003_auto_20200129_1630'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='animal',
+            name='same_as',
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+        migrations.AddField(
+            model_name='sample',
+            name='same_as',
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+    ]

django-data/image/uid/mixins.py

@@ -234,6 +234,16 @@ def to_biosample(self, release_date=None):
         # define attributes that will be customized in Animal and sample
         result['attributes'] = self.get_attributes()
 
+        # define an empty relationship array
+        result['sampleRelationships'] = []
+
+        # test for same as relationship
+        if self.same_as and self.same_as != '':
+            result['sampleRelationships'].append({
+                "relationshipNature": "same as",
+                "accession": self.same_as
+            })
+
         return result
 
     def __status_not_in(self, statuses):

django-data/image/uid/models.py

@@ -140,6 +140,12 @@ class Name(BaseMixin, models.Model):
         null=True,
         unique=True)
 
+    # model a same as relationship
+    same_as = models.CharField(
+        max_length=255,
+        blank=True,
+        null=True)
+
     # '+' instructs Django that we don’t need this reverse relationship
     owner = models.ForeignKey(
         User,
@@ -669,9 +675,6 @@ def to_biosample(self, release_date=None):
         # with USI mandatory keys and attributes
         result = super().to_biosample(release_date)
 
-        # define relationship with mother and father (if possible)
-        result['sampleRelationships'] = []
-
         father_relationship = self.get_father_relationship()
 
         if father_relationship is not None:
@@ -869,7 +872,7 @@ def to_biosample(self, release_date=None):
         result = super().to_biosample(release_date)
 
         # define relationship to the animal where this sample come from
-        result['sampleRelationships'] = [self.animal.get_relationship()]
+        result['sampleRelationships'].append(self.animal.get_relationship())
 
         return result
 

django-data/image/uid/tests/biosample_animal.json

@@ -192,5 +192,10 @@
       }
     ]
   },
-  "sampleRelationships": []
+  "sampleRelationships": [
+    {
+      "relationshipNature": "same as",
+      "accession": "SAMEA4450079"
+    }
+  ]
 }