Merge pull request #3415 from AlexsLemonade/ark/3408-change-sample-ge…

…notype-field Rename Sample::genotype to Sample::genetic_information
AlexsLemonade · Oct 17, 2023 · f5d4b39 · f5d4b39
2 parents 06511fa + 548dc82
commit f5d4b39
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Showing 7 changed files with 65 additions and 10 deletions.
diff --git a/api/data_refinery_api/views/sample.py b/api/data_refinery_api/views/sample.py
@@ -87,7 +87,7 @@ class Meta:
             "sex",
             "age",
             "specimen_part",
-            "genotype",
+            "genetic_information",
             "disease",
             "disease_stage",
             "cell_line",
@@ -158,7 +158,7 @@ class SampleListView(generics.ListAPIView):
         "sex",
         "age",
         "specimen_part",
-        "genotype",
+        "genetic_information",
         "disease",
         "disease_stage",
         "cell_line",
@@ -217,7 +217,7 @@ def get_queryset(self):
                 | Q(sex__icontains=filter_by)
                 | Q(age__icontains=filter_by)
                 | Q(specimen_part__icontains=filter_by)
-                | Q(genotype__icontains=filter_by)
+                | Q(genetic_information__icontains=filter_by)
                 | Q(disease__icontains=filter_by)
                 | Q(disease_stage__icontains=filter_by)
                 | Q(cell_line__icontains=filter_by)

diff --git a/common/data_refinery_common/migrations/0073_rename_genotype_sample_genetic_information.py b/common/data_refinery_common/migrations/0073_rename_genotype_sample_genetic_information.py
@@ -0,0 +1,18 @@
+# Generated by Django 3.2.18 on 2023-10-12 16:07
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("data_refinery_common", "0072_auto_20220927_2235"),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="sample",
+            old_name="genotype",
+            new_name="genetic_information",
+        ),
+    ]
diff --git a/common/data_refinery_common/models/experiment.py b/common/data_refinery_common/models/experiment.py
@@ -148,7 +148,7 @@ def get_sample_metadata_fields(self):
             "sex",
             "age",
             "specimen_part",
-            "genotype",
+            "genetic_information",
             "disease",
             "disease_stage",
             "cell_line",

diff --git a/common/data_refinery_common/models/sample.py b/common/data_refinery_common/models/sample.py
@@ -59,7 +59,7 @@ def __str__(self):
     sex = models.CharField(max_length=255, blank=True)
     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)
-    genotype = models.CharField(max_length=255, blank=True)
+    genetic_information = 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)
@@ -112,7 +112,7 @@ def to_metadata_dict(self, computed_file=None):
         metadata["refinebio_sex"] = self.sex
         metadata["refinebio_age"] = self.age or ""
         metadata["refinebio_specimen_part"] = self.specimen_part
-        metadata["refinebio_genetic_information"] = self.genotype
+        metadata["refinebio_genetic_information"] = self.genetic_information
         metadata["refinebio_disease"] = self.disease
         metadata["refinebio_disease_stage"] = self.disease_stage
         metadata["refinebio_cell_line"] = self.cell_line

diff --git a/common/tests/models/test_sample.py b/common/tests/models/test_sample.py
@@ -0,0 +1,36 @@
+from django.test import TestCase
+
+from data_refinery_common.models import Sample
+
+
+class TestSample(TestCase):
+    def setUp(self):
+        self.sample = Sample()
+        self.sample.save()
+
+    def test_to_metadata_dict(self):
+        self.assertListEqual(
+            sorted(self.sample.to_metadata_dict().keys()),
+            [
+                "refinebio_accession_code",
+                "refinebio_age",
+                "refinebio_annotations",
+                "refinebio_cell_line",
+                "refinebio_compound",
+                "refinebio_disease",
+                "refinebio_disease_stage",
+                "refinebio_genetic_information",
+                "refinebio_organism",
+                "refinebio_platform",
+                "refinebio_processed",
+                "refinebio_race",
+                "refinebio_sex",
+                "refinebio_source_archive_url",
+                "refinebio_source_database",
+                "refinebio_specimen_part",
+                "refinebio_subject",
+                "refinebio_time",
+                "refinebio_title",
+                "refinebio_treatment",
+            ],
+        )
diff --git a/foreman/data_refinery_foreman/surveyor/harmony.py b/foreman/data_refinery_foreman/surveyor/harmony.py
@@ -5,7 +5,7 @@
   `sex`,
   `age`,
   `specimen_part`,
-  `genotype`,
+  `genetic_information`,
   `disease`,
   `disease_stage`,
   `cell_line`,
@@ -626,7 +626,7 @@ def __init__(self):
         ]
         self.specimen_part_fields = create_variants(specimen_part_fields)
 
-        genotype_fields = [
+        genetic_information_fields = [
             "strain/background",
             "strain",
             "strain or line",
@@ -639,7 +639,7 @@ def __init__(self):
             "cultivar",
             "strain/genotype",
         ]
-        self.genotype_fields = create_variants(genotype_fields)
+        self.genetic_information_fields = create_variants(genetic_information_fields)
 
         disease_fields = [
             "disease",
@@ -797,7 +797,7 @@ def harmonize_sample(self, sample_metadata: Dict, title_field: str = None) -> Di
             "sex_fields",
             "age_fields",
             "specimen_part_fields",
-            "genotype_fields",
+            "genetic_information_fields",
             "disease_fields",
             "disease_stage_fields",
             "cell_line_fields",

diff --git a/scripts/make_migrations.sh b/scripts/make_migrations.sh
@@ -14,6 +14,7 @@ script_directory="$(
 )"
 cd "$script_directory" || exit
 
+./prepare_image.sh -i base -s common
 ./prepare_image.sh -i migrations -s common
 
 . ./common.sh