optimize vm_taxref_tree

apptax/migrations/versions/3c4762751898_taxref_tree_v2.py

@@ -0,0 +1,90 @@
+"""create vm_taxref_tree v2
+
+Revision ID: 3c4762751898
+Revises: 83d7105edb76
+Create Date: 2024-12-03 13:30:26.521216
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "3c4762751898"
+down_revision = "83d7105edb76"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.execute("DROP MATERIALIZED VIEW IF EXISTS taxonomie.vm_taxref_tree")
+    op.execute(
+        """
+        CREATE MATERIALIZED VIEW taxonomie.vm_taxref_tree AS
+        WITH RECURSIVE
+        biota AS (
+                SELECT
+                    t.cd_nom,
+                    t.cd_ref::TEXT::ltree AS path
+                FROM
+                    taxonomie.taxref t
+                WHERE
+                    t.cd_nom = 349525
+            UNION ALL
+                SELECT
+                    child.cd_nom AS cd_nom,
+                    parent.path || child.cd_ref::TEXT AS path
+                FROM
+                    taxonomie.taxref child
+                JOIN
+                    taxonomie.taxref child_ref ON child.cd_ref = child_ref.cd_nom
+                JOIN
+                    biota parent ON parent.cd_nom = child_ref.cd_sup
+        ),
+        orphans AS (
+                SELECT
+                    t.cd_nom,
+                    t.cd_ref::TEXT::ltree AS path
+                FROM
+                    taxonomie.taxref t
+                JOIN
+                    taxonomie.taxref t_ref ON t.cd_ref = t_ref.cd_nom
+                LEFT JOIN
+                    taxonomie.taxref parent ON t_ref.cd_sup = parent.cd_nom AND parent.cd_nom != t_ref.cd_nom
+                WHERE
+                    parent.cd_nom IS NULL
+        )
+        SELECT
+            cd_nom,
+            path
+        FROM
+            biota
+        UNION DISTINCT -- do not include biota twice
+        SELECT
+            cd_nom,
+            path
+        FROM
+            orphans
+        WITH DATA;
+        """
+    )
+    op.create_index(
+        index_name="taxref_tree_cd_nom_idx",
+        schema="taxonomie",
+        table_name="vm_taxref_tree",
+        columns=["cd_nom"],
+        unique=True,
+    )
+    # required for these operators: <, <=, =, >=, >, @>, <@, @, ~, ?
+    op.create_index(
+        index_name="taxref_tree_path_idx",
+        schema="taxonomie",
+        table_name="vm_taxref_tree",
+        columns=["path"],
+        postgresql_using="gist",
+    )
+
+
+def downgrade():
+    op.execute("DROP MATERIALIZED VIEW taxonomie.vm_taxref_tree")

apptax/migrations/versions/83d7105edb76_taxref_tree_v1.py

@@ -0,0 +1,25 @@
+"""create vm_taxref_tree v1
+
+Revision ID: 83d7105edb76
+Revises: 44447746cacc
+Create Date: 2024-10-05 17:40:11.302423
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "83d7105edb76"
+down_revision = "6a20cd1055ec"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    pass
+
+
+def downgrade():
+    op.execute("DROP MATERIALIZED VIEW IF EXISTS taxonomie.vm_taxref_tree")

docs/changelog.md

@@ -1,5 +1,10 @@
 # CHANGELOG
 
+2.0.1 (unreleased)
+------------------
+
+- Optimisation de la VM `vm_taxref_tree` pour en améliorer les performances et gérer les cas où des taxons locaux ont été ajoutés à la table `taxref` (#587)
+
 2.0.0 (2024-10-29)
 ------------------