Add script to build hierarchy from backend

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

+import logging
+
+from django.core.management.base import BaseCommand
+
+from metagenedb.apps.catalog.models import Taxonomy
+
+logging.basicConfig(format='[%(asctime)s] %(levelname)s:%(name)s:%(message)s')
+logger = logging.getLogger(__name__)
+
+SELECT_RELATED_PARENT = "parent{}".format("__parent" * 40)
+
+
+class HierarchyBuilder:
+
+    def __init__(self, queryset):
+        self.queryset = queryset
+        self.total_tax = queryset.count()
+        self.processed_tax = 0
+        self.hierarchy_built = 0
+        self.hierarchy_failed = 0
+
+    def build_all(self, chunk_size=8000):
+        logger.info("Building all hierarchy for all %s taxonomy items...", self.total_tax)
+        for taxonomy in self.queryset.iterator(chunk_size=chunk_size):
+            try:
+                hierarchy = taxonomy.parental_hierarchy  # noqa
+                self.hierarchy_built += 1
+            except Exception:
+                self.hierarchy_failed += 1
+            self.processed_tax += 1
+            if self.processed_tax % 10000 == 0:
+                logger.info("%s/%s Taxonomy processed so far...", self.processed_tax, self.total_tax)
+                break
+        logger.info("[DONE] %s/%s Hierarchy built.", self.hierarchy_built, self.total_tax)
+        logger.info("[DONE] %s/%s Hierarchy build skipped.", self.hierarchy_failed, self.total_tax)
+
+
+class Command(BaseCommand):
+    help = 'Build hierarchy for taxonomy entries.'
+
+    def set_logger_level(self, verbosity):
+        if verbosity > 2:
+            logger.setLevel(logging.DEBUG)
+        elif verbosity > 1:
+            logger.setLevel(logging.INFO)
+
+    def get_queryset(self):
+        return Taxonomy.objects.select_related(
+            SELECT_RELATED_PARENT, "superkingdom", "kingdom", "phylum", "class_rank",
+            "order", "family", "genus", "species"
+        ).all()
+
+    def handle(self, *args, **options):
+        self.set_logger_level(int(options['verbosity']))
+        hierarchy_builder = HierarchyBuilder(self.get_queryset())
+        hierarchy_builder.build_all()

ci/kubernetes/postgresql.yaml

@@ -54,10 +54,10 @@ spec:
           name: postgresql
         resources:
           requests:
-            memory: "256Mi"
+            memory: "512Mi"
             cpu: "100m"
           limits:
-            memory: "512Mi"
+            memory: "1024Mi"
             cpu: "500m"
         volumeMounts:
         - name: postgresql