Add p_value column for the peaks

server/api/migrations/0060_peak_p_value.py

+# Generated by Django 3.2.7 on 2022-03-14 12:21
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('api', '0059_alter_galaxyworkflow_version'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='peak',
+            name='p_value',
+            field=models.FloatField(null=True),
+        ),
+    ]

server/api/models.py

@@ -239,7 +239,8 @@ class Experiment(models.Model):
                 raise RessourceAlreadyExists()
                 # Add reader role to the team the current user belongs
 
-    def generate_experiment_file(self, name, phenotype_type_name):
+    def generate_experiment_file(self, name, phenotype_type_name, galaxy_workflow_id):
+        galaxy_workflow_excel = {"657f009ad32a3f27", "bd6cadfea4e7afba"}
         phenotypes = (
             Phenotype.objects.filter(experiment_cc_line__experiment=self)
             .values(
@@ -278,10 +279,16 @@ class Experiment(models.Model):
             columns = ["CC_ID", "Line_M", "Line_F", "Sex"] + [phenotype_type_name]
             pivoted.reset_index(inplace=True)
             dirpath = tempfile.mkdtemp(prefix="cc-qtl-", dir="/tmp-exp-files")
-            experiment_file_path = f"{dirpath}/{name}.xls"
-            pivoted.to_excel(
-                experiment_file_path, index=False, columns=columns,
-            )
+            if galaxy_workflow_id in galaxy_workflow_excel:
+                experiment_file_path = f"{dirpath}/{name}.xls"
+                pivoted.to_excel(
+                    experiment_file_path, index=False, columns=columns,
+                )
+            else:
+                experiment_file_path = f"{dirpath}/{name}.csv"
+                pivoted.to_csv(
+                    experiment_file_path, index=False, columns=columns,
+                )
             return experiment_file_path
         else:
             raise NameError(f"No phenotype type defined for {phenotype_type_name}")
@@ -984,6 +991,7 @@ class Peak(models.Model):
     lod = models.FloatField()
     ci_lo = models.FloatField()
     ci_hi = models.FloatField()
+    p_value = models.FloatField(null=True)
 
     objects = PeakManager()