add property to Taxonomy to retrieve one line taxonomy description

backend/metagenedb/apps/catalog/factory/taxonomy.py

@@ -40,6 +40,8 @@ class DbGenerator:
                     rank=rank,
                     parent=getattr(self, "last_tax", None)
                 )
+            else:
+                self.last_tax = models.Taxonomy.objects.get(tax_id=desc['tax_id'])
             self.created_ids.add(desc['tax_id'])
         self.last_tax.build_hierarchy()
 

backend/metagenedb/apps/catalog/management/commands/create_light_db.py

@@ -11,6 +11,7 @@ from metagenedb.apps.catalog.models import (
 from metagenedb.apps.catalog.management.commands.compute_stats import (
     ComputeStatistics, ComputeCounts, ComputeGeneLength, ComputeTaxonomyRepartition, ComputeTaxonomyPresence
 )
+from metagenedb.apps.catalog.management.commands.compute_stats import clean_db as clean_db_stats
 
 logging.basicConfig(format='[%(asctime)s] %(levelname)s:%(name)s:%(message)s')
 logger = logging.getLogger()
@@ -37,7 +38,7 @@ def create_genes_db():
 
 
 def compute_stats():
-    ComputeStatistics('all').clean_db()
+    clean_db_stats()
     for gene_source in ['all', 'virgo', 'igc']:
         ComputeCounts(gene_source).all()
         ComputeGeneLength(gene_source).all()

backend/metagenedb/apps/catalog/models/statistics.py

 from django.db import models
-from django.contrib.postgres.fields import JSONField
 
 
 class Statistics(models.Model):
@@ -8,7 +7,7 @@ class Statistics(models.Model):
     """
 
     stats_id = models.SlugField(max_length=400, db_index=True, unique=True)
-    body = JSONField()
+    body = models.JSONField()
 
     class Meta:
         verbose_name_plural = "Statistics"

backend/metagenedb/apps/catalog/models/taxonomy.py

 from django.db import models
-from django.contrib.postgres.fields import JSONField
 
 
 class Taxonomy(models.Model):
@@ -52,7 +51,7 @@ class Taxonomy(models.Model):
         on_delete=models.SET_NULL,
         null=True, blank=True,
     )
-    hierarchy = JSONField(null=True)
+    hierarchy = models.JSONField(null=True)
 
     def __str__(self):
         return f"{self.name}"
@@ -73,6 +72,32 @@ class Taxonomy(models.Model):
         self.save()
         return hierarchy
 
+    def _compute_one_line_detailed_taxonomy(self) -> str:
+        default_item = {
+            'name': ''
+        }
+        if self.hierarchy is None:
+            self.build_hierarchy()
+        if self.hierarchy.get('species', None) is None:
+            s = ''
+        else:
+            s = self.hierarchy.get('species')['name'].split()[-1]
+        return "k__{k}; p__{p}; c__{c}; o__{o}; f__{f}; g__{g}; s__{s}".format(
+            k=self.hierarchy.get('kingdom', self.hierarchy.get('superkingdom', default_item))['name'],
+            p=self.hierarchy.get('phylum', default_item)['name'],
+            c=self.hierarchy.get('class', default_item)['name'],
+            o=self.hierarchy.get('order', default_item)['name'],
+            f=self.hierarchy.get('family', default_item)['name'],
+            g=self.hierarchy.get('genus', default_item)['name'],
+            s=s
+        )
+
+    @property
+    def one_line_detailed_taxonomy(self) -> str:
+        if getattr(self, '_one_line_detailed_taxonomy', None) is None:
+            self._one_line_detailed_taxonomy = self._compute_one_line_detailed_taxonomy()
+        return self._one_line_detailed_taxonomy
+
     class Meta:
         verbose_name_plural = "Taxonomy"
         ordering = ['-tax_id']