New genome fields and _metadata_yaml

apollo_portal/tracks/migrations/0010_remove_genome__metadata_remove_track__metadata_and_more.py

@@ -0,0 +1,46 @@
+# Generated by Django 4.2 on 2023-12-07 19:22
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('tracks', '0009_genome_group'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='genome',
+            name='_metadata',
+        ),
+        migrations.RemoveField(
+            model_name='track',
+            name='_metadata',
+        ),
+        migrations.AddField(
+            model_name='genome',
+            name='_metadata_yaml',
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='genome',
+            name='description',
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='genome',
+            name='doi',
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+        migrations.AddField(
+            model_name='genome',
+            name='ncbi_bioproject',
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='genome',
+            name='reference',
+            field=models.TextField(blank=True, null=True),
+        ),
+    ]

apollo_portal/tracks/models.py

@@ -1,6 +1,6 @@
 """Models for managing Apollo instances and their genome tracks."""
 
-import json
+import yaml
 from django.db import models
 from django.conf import settings
 from django.contrib.auth.models import Group
@@ -76,7 +76,11 @@ class Genome(models.Model):
     condition = models.CharField(max_length=255, null=True, blank=True)
     thumbnail = models.ImageField(null=True, blank=True, upload_to="genomes")
     apollo_url = models.URLField(null=True, blank=True)
-    _metadata = models.TextField(default="{}")
+    description = models.TextField(null=True, blank=True)
+    reference = models.TextField(null=True, blank=True)
+    ncbi_bioproject = models.TextField(null=True, blank=True)
+    doi = models.CharField(max_length=255, null=True, blank=True)
+    _metadata_yaml = models.TextField(null=True, blank=True)
 
     def __str__(self):
         """Return string representation."""
@@ -85,14 +89,16 @@ def __str__(self):
     @property
     def metadata(self):
         """Return metadata as a dictionary."""
-        return json.loads(self._metadata)
+        if not self._metadata_yaml:
+            return {}
+        return yaml.safe_load(self._metadata_yaml)
 
     @property
     def set_metadata(self, k, v):
         """Set metadata key to given value."""
-        data = json.loads(self._metadata)
+        data = self.metadata
         data[k] = v
-        self._metadata = json.dumps(data)
+        self._metadata_yaml = yaml.safe_dump(data)
 
     def as_json(self):
         """Serialize model for JSON encoding."""
@@ -137,20 +143,7 @@ class Track(models.Model):
     name = models.CharField(max_length=255)
     accession_id = models.CharField(max_length=255, null=True, blank=True)
     track_type = models.CharField(max_length=255)
-    _metadata = models.TextField(null=True, blank=True)
 
     def __str__(self):
         """Return string representation."""
         return f"{self.genome.lab.name}: {self.genome.name}: {self.name}"
-
-    @property
-    def metadata(self):
-        """Return metadata as a dictionary."""
-        return json.loads(self._metadata)
-
-    @property
-    def set_metadata(self, k, v):
-        """Set metadata key to given value."""
-        data = json.loads(self._metadata)
-        data[k] = v
-        self._metadata = json.dumps(data)

requirements.txt

@@ -9,3 +9,4 @@ Pillow==10.0
 factory_boy==3.3
 requests
 psycopg2-binary
+pyyaml