Merge branch 'develop'

VERSION

@@ -1 +1 @@
-2.0.0
+2.1.0

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")

apptax/taxonomie/models.py

@@ -216,7 +216,14 @@ def where_id_liste(cls, id_liste, *, query):
     def where_params(cls, filters=None, *, query):
 
         for filter in filters:
-            if hasattr(Taxref, filter) and filters[filter] != "":
+            # Test empty values
+            if not filters[filter]:
+                continue
+
+            if hasattr(Taxref, filter) and isinstance(filters[filter], list):
+                col = getattr(Taxref, filter)
+                query = query.filter(col.in_(tuple(filters[filter])))
+            elif hasattr(Taxref, filter) and filters[filter] != "":
                 col = getattr(Taxref, filter)
                 query = query.filter(col == filters[filter])
             elif filter == "is_ref" and filters[filter] == "true":
@@ -261,13 +268,17 @@ class BibListes(db.Model):
 
     @hybrid_property
     def nb_taxons(self):
-        return len(self.noms)
+        return db.session.scalar(
+            select([db.func.count(cor_nom_liste.c.cd_nom)]).where(
+                cor_nom_liste.c.id_liste == self.id_liste
+            )
+        )
 
     @nb_taxons.expression
     def nb_taxons(cls):
         return (
-            db.select([db.func.count(cor_nom_liste.id_liste)])
-            .where(BibListes.id_liste == cls.id_liste)
+            db.select([db.func.count(cor_nom_liste.c.cd_nom)])
+            .where(cor_nom_liste.c.id_liste == cls.id_liste)
             .label("nb_taxons")
         )
 

apptax/taxonomie/routesbiblistes.py

@@ -3,16 +3,13 @@
 import os
 import logging
 
-from flask import Blueprint, request, current_app
-from sqlalchemy import func, or_
-from sqlalchemy.orm import joinedload
+from flask import Blueprint
+from sqlalchemy import select
 
-from pypnusershub import routes as fnauth
 from utils_flask_sqla.response import json_resp
 
-from . import filemanager
 from . import db
-from .models import BibListes, Taxref
+from .models import BibListes
 from apptax.taxonomie.schemas import BibListesSchema
 
 adresses = Blueprint("bib_listes", __name__)
@@ -24,26 +21,38 @@
 
 @adresses.route("/", methods=["GET"])
 @json_resp
-def get_biblistes(id=None):
+def get_biblistes():
     """
     retourne les contenu de bib_listes dans "data"
     et le nombre d'enregistrements dans "count"
     """
-    data = db.session.query(BibListes).all()
+    biblistes_records = db.session.execute(
+        select(
+            BibListes.id_liste,
+            BibListes.code_liste,
+            BibListes.nom_liste,
+            BibListes.desc_liste,
+            BibListes.nb_taxons,
+            BibListes.regne,
+            BibListes.group2_inpn,
+        )
+    ).all()
     biblistes_schema = BibListesSchema()
-    maliste = {"data": [], "count": 0}
-    maliste["count"] = len(data)
-    maliste["data"] = biblistes_schema.dump(data, many=True)
-    return maliste
+    biblistes_infos = {
+        "data": biblistes_schema.dump(biblistes_records, many=True),
+        "count": len(biblistes_records),
+    }
+
+    return biblistes_infos
 
 
 @adresses.route("/<regne>", methods=["GET"], defaults={"group2_inpn": None})
 @adresses.route("/<regne>/<group2_inpn>", methods=["GET"])
 def get_biblistesbyTaxref(regne, group2_inpn):
-    q = db.session.query(BibListes)
+    q = select(BibListes)
     if regne:
         q = q.where(BibListes.regne == regne)
     if group2_inpn:
         q = q.where(BibListes.group2_inpn == group2_inpn)
-    results = q.all()
+    results = db.session.scalars(q).all()
     return BibListesSchema().dump(results, many=True)

apptax/taxonomie/routestaxref.py

@@ -162,10 +162,18 @@ def get_taxref_list():
     limit = request.values.get("limit", 20, int)
     page = request.values.get("page", 1, int)
     id_liste = None
+    cd_nom = None
+
     if "id_liste" in request.values:
-        id_liste = request.values.get("id_liste").split(",")
+        id_liste = (
+            request.values.get("id_liste").split(",") if request.values.get("id_liste") else None
+        )
+    if "cd_nom" in request.values:
+        cd_nom = request.values.get("cd_nom").split(",") if request.values.get("cd_nom") else None
+
     fields = request.values.get("fields", type=str, default=[])
     parameters = request.values.to_dict()
+    parameters["cd_nom"] = cd_nom
 
     dump_options = {}
     if fields:
@@ -178,10 +186,10 @@ def get_taxref_list():
 
     joinedload_when_attributs = get_joinedload_when_attributs(fields=fields)
     query = Taxref.joined_load(fields).options(*joinedload_when_attributs)
+    query = Taxref.where_params(parameters, query=query)
 
     if id_liste and "-1" not in id_liste:
         query = Taxref.where_id_liste(id_liste, query=query)
-
     count_filter = db.session.scalar(
         db.select(func.count()).select_from(
             Taxref.where_params(parameters, query=query),

apptax/taxonomie/routestmedias.py

@@ -5,8 +5,8 @@
 from flask import json, Blueprint, request, current_app, send_file, abort
 
 
-from .models import TMedias
-from .schemas import TMediasSchema
+from .models import TMedias, BibTypesMedia
+from .schemas import TMediasSchema, BibTypesMediaSchema
 
 from .filemanager import FILEMANAGER
 
@@ -29,6 +29,19 @@ def get_tmedias(id=None):
     return TMediasSchema().dump(medias, many=True)
 
 
+@adresses.route("/types", methods=["GET"])
+@adresses.route("/types/<int:id>", methods=["GET"])
+def get_type_tmedias(id=None):
+    """
+    Liste des types de médias
+    """
+    if id:
+        type_media = BibTypesMedia.query.get(id)
+        return BibTypesMediaSchema().dump(type_media)
+    types_media = BibTypesMedia.query.all()
+    return BibTypesMediaSchema().dump(types_media, many=True)
+
+
 @adresses.route("/bycdref/<cd_ref>", methods=["GET"])
 def get_tmediasbyTaxon(cd_ref):
     """

apptax/tests/fixtures.py

@@ -95,7 +95,14 @@ def liste():
         "code_liste": "TEST_LIST_Plantae",
         "nom_liste": "Liste test Plantae",
         "desc_liste": "Liste description",
-        "regne": "Plantea",
+        "regne": "Plantae",
+    },
+    {
+        "code_liste": "TEST_LIST_Mousses",
+        "nom_liste": "Liste test Mousses",
+        "desc_liste": "Liste description",
+        "regne": "Plantae",
+        "group2_inpn": "Mousses",
     },
 ]