Merge pull request #3425 from AlexsLemonade/ark/3306-sample-developme…

…ntal-stage

Add Sample::developmental_stage field support

api/data_refinery_api/views/sample.py

@@ -88,6 +88,7 @@ class Meta:
             "age",
             "specimen_part",
             "genetic_information",
+            "developmental_stage",
             "disease",
             "disease_stage",
             "cell_line",
@@ -159,6 +160,7 @@ class SampleListView(generics.ListAPIView):
         "age",
         "specimen_part",
         "genetic_information",
+        "developmental_stage",
         "disease",
         "disease_stage",
         "cell_line",

common/data_refinery_common/migrations/0074_sample_developmental_stage.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.2.18 on 2023-10-17 22:53
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("data_refinery_common", "0073_rename_genotype_sample_genetic_information"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="sample",
+            name="developmental_stage",
+            field=models.CharField(blank=True, max_length=255),
+        ),
+    ]

common/data_refinery_common/models/sample.py

@@ -60,6 +60,7 @@ def __str__(self):
     age = models.DecimalField(max_length=255, blank=True, max_digits=8, decimal_places=3, null=True)
     specimen_part = models.CharField(max_length=255, blank=True)
     genetic_information = models.CharField(max_length=255, blank=True)
+    developmental_stage = models.CharField(max_length=255, blank=True)
     disease = models.CharField(max_length=255, blank=True)
     disease_stage = models.CharField(max_length=255, blank=True)
     cell_line = models.CharField(max_length=255, blank=True)
@@ -126,6 +127,7 @@ def to_metadata_dict(self, computed_file=None):
         metadata["refinebio_annotations"] = [
             data for data in self.sampleannotation_set.all().values_list("data", flat=True)
         ]
+        metadata["refinebio_developmental_stage"] = self.developmental_stage
 
         if computed_file and computed_file.result and computed_file.result.processor:
             metadata["refinebio_processor_id"] = computed_file.result.processor.id

common/tests/models/test_sample.py

@@ -17,6 +17,7 @@ def test_to_metadata_dict(self):
                 "refinebio_annotations",
                 "refinebio_cell_line",
                 "refinebio_compound",
+                "refinebio_developmental_stage",
                 "refinebio_disease",
                 "refinebio_disease_stage",
                 "refinebio_genetic_information",

foreman/data_refinery_foreman/surveyor/harmony.py

@@ -6,6 +6,7 @@
   `age`,
   `specimen_part`,
   `genetic_information`,
+  `developmental_stage`,
   `disease`,
   `disease_stage`,
   `cell_line`,