feat : compatibility with SQLAlchemy 2.0

.github/workflows/install_taxhub.yml

@@ -3,59 +3,64 @@ name: Test the installation of TaxHub
 on: [pull_request]
 
 jobs:
-    setup:
-        runs-on: ubuntu-latest
-        steps:
-            - uses: actions/checkout@v4
-              with:
-                  submodules: true
-            - name: Set up Python 3.11
-              uses: actions/setup-python@v5
-              with:
-                  python-version: "3.11"
-                  cache: "pip"
-            - name: Install system dependencies
-              run: |
-                  sudo apt-get update
-                  sudo apt-get install -y apache2 libpq-dev libgdal-dev unzip gettext-base postgresql postgresql-postgis postgresql-contrib
-            - name: Start PostgreSQL
-              run: |
-                  sudo systemctl enable --now postgresql
-                  for i in $(seq 1 30); do
-                    sudo -u postgres pg_isready && break
-                    sleep 1
-                  done
-                  sudo -u postgres pg_isready
-            - name: Create PostgreSQL role
-              run: |
-                  sudo -u postgres psql -c "CREATE ROLE taxhubadmin LOGIN PASSWORD 'taxhubpwd';"
-            - name: Fill settings file
-              run: |
-                  cp settings.ini.sample settings.ini
-                  sed -i 's|db_name=.*|db_name=taxhub|' settings.ini
-                  sed -i 's|user_pg=.*|user_pg=taxhubadmin|' settings.ini
-                  sed -i 's|user_pg_pass=.*|user_pg_pass=taxhubpwd|' settings.ini
-                  sed -i 's|db_host=.*|db_host=localhost|' settings.ini
-                  sed -i 's|db_port=.*|db_port=5432|' settings.ini
-                  sed -i 's|insert_geonatureatlas_data=.*|insert_geonatureatlas_data=false|' settings.ini
-                  echo "users_schema=local" >> settings.ini
-                  cat settings.ini
-            - name: Install TaxHub application
-              run: |
-                  ./install_app.sh
-            - name: Install TaxHub database
-              run: |
-                  ./install_db.sh < /dev/null
-            - name: Run TaxHub
-              run: |
-                  sudo systemctl start taxhub
-                  sleep 5
-                  sudo systemctl status taxhub --no-pager
-            - name: Check if TaxHub is running
-              run: |
-                  CODE=$(curl -s -o /dev/null -w "%{http_code}" http://127.0.0.1:5000/bdc_statuts/status_types)
-                  if [ "$CODE" != "200" ]; then
-                    echo "Error: TaxHub is not running properly. Status code is $CODE"
-                    sudo journalctl -u taxhub --no-pager
-                    exit 1
-                  fi
+  setup:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y apache2 libpq-dev libgdal-dev unzip gettext-base postgresql postgresql-postgis postgresql-contrib
+      - name: Start PostgreSQL
+        run: |
+          sudo systemctl enable --now postgresql
+          for i in $(seq 1 30); do
+            sudo -u postgres pg_isready && break
+            sleep 1
+          done
+          sudo -u postgres pg_isready
+      - name: Create PostgreSQL role
+        run: |
+          sudo -u postgres psql -c "CREATE ROLE taxhubadmin LOGIN PASSWORD 'taxhubpwd';"
+      - name: Fill settings file
+        run: |
+          cp settings.ini.sample settings.ini
+          sed -i 's|db_name=.*|db_name=taxhub|' settings.ini
+          sed -i 's|user_pg=.*|user_pg=taxhubadmin|' settings.ini
+          sed -i 's|user_pg_pass=.*|user_pg_pass=taxhubpwd|' settings.ini
+          sed -i 's|db_host=.*|db_host=localhost|' settings.ini
+          sed -i 's|db_port=.*|db_port=5432|' settings.ini
+          sed -i 's|insert_geonatureatlas_data=.*|insert_geonatureatlas_data=false|' settings.ini
+          echo "users_schema=local" >> settings.ini
+          cat settings.ini
+      - name: Install TaxHub application
+        run: |
+          ./install_app.sh
+      - name: Setup python dev dependencies
+        if: github.base_ref != 'master'
+        run: |
+          source venv/bin/activate
+          pip install -r requirements-dev.txt
+      - name: Install TaxHub database
+        run: |
+          ./install_db.sh < /dev/null
+      - name: Run TaxHub
+        run: |
+          sudo systemctl start taxhub
+          sleep 5
+          sudo systemctl status taxhub --no-pager
+      - name: Check if TaxHub is running
+        run: |
+          CODE=$(curl -s -o /dev/null -w "%{http_code}" http://127.0.0.1:5000/bdc_statuts/status_types)
+          if [ "$CODE" != "200" ]; then
+            echo "Error: TaxHub is not running properly. Status code is $CODE"
+            sudo journalctl -u taxhub --no-pager
+            exit 1
+          fi

.github/workflows/pytest.yml

@@ -13,6 +13,7 @@ on:
       - master
       - hotfixes
       - develop
+      - chore/drop-py39
     paths-ignore:
       - "docs/**"
 
@@ -24,7 +25,7 @@ jobs:
       fail-fast: false
       matrix:
         debian-version: ["12", "13"]
-        sqlalchemy-version: ["1.4"]
+        sqlalchemy-version: ["2.0"]
         include:
           - debian-version: "12"
             python-version: "3.11"
@@ -35,7 +36,8 @@ jobs:
             postgres-version: "17"
             postgis-version: "3.5"
 
-    name: Debian ${{ matrix.debian-version }} - SQLAlchemy ${{ matrix.sqlalchemy-version }}
+    name: Debian ${{ matrix.debian-version }} - SQLAlchemy ${{
+      matrix.sqlalchemy-version }}
 
     services:
       postgres:
@@ -47,9 +49,7 @@ jobs:
         ports:
           - 5432:5432
         options: >-
-          --health-cmd pg_isready
-          --health-interval 10s
-          --health-timeout 5s
+          --health-cmd pg_isready --health-interval 10s --health-timeout 5s
           --health-retries 5
 
     steps:
@@ -79,7 +79,6 @@ jobs:
           sudo apt update
           sudo apt install -y libgdal-dev
       - name: Install dependencies
-        if: ${{ matrix.sqlalchemy-version == '1.4' }}
         run: |
           python -m pip install --upgrade pip
           python -m pip install \

VERSION

@@ -1 +1 @@
-2.3.1
+2.4.0

apptax/admin/admin_view.py

@@ -430,20 +430,23 @@ def _apply_search(self, query, count_query, joins, count_joins, search):
 
     def _get_theme_attributes(self, taxon):
         return (
-            db.session.query(BibThemes)
-            .join(
-                BibAttributs,
-                and_(
-                    BibAttributs.id_theme == BibThemes.id_theme,
-                    or_(BibAttributs.regne == taxon.regne, BibAttributs.regne == None),
-                    or_(
-                        BibAttributs.group2_inpn == taxon.group2_inpn,
-                        BibAttributs.group2_inpn == None,
+            db.session.scalars(
+                select(BibThemes)
+                .join(
+                    BibAttributs,
+                    and_(
+                        BibAttributs.id_theme == BibThemes.id_theme,
+                        or_(BibAttributs.regne == taxon.regne, BibAttributs.regne == None),
+                        or_(
+                            BibAttributs.group2_inpn == taxon.group2_inpn,
+                            BibAttributs.group2_inpn == None,
+                        ),
                     ),
-                ),
+                )
+                .options(contains_eager(BibThemes.attributs))
+                .order_by(BibAttributs.ordre)
             )
-            .options(contains_eager(BibThemes.attributs))
-            .order_by(BibAttributs.ordre)
+            .unique()
             .all()
         )
 
@@ -497,9 +500,9 @@ def render(self, template, **kwargs):
     @expose("/details/", methods=("GET",))
     def details_view(self):
         id = get_mdict_item_or_list(request.args, "id")
-        taxon_name = db.session.query(Taxref).get(id)
+        taxon_name = db.session.get(Taxref, id)
         if not taxon_name.cd_nom == taxon_name.cd_ref:
-            taxon_valid = db.session.query(Taxref).get(taxon_name.cd_ref)
+            taxon_valid = db.session.get(Taxref, taxon_name.cd_ref)
         else:
             taxon_valid = taxon_name
 
@@ -536,14 +539,8 @@ def edit_form(self, obj=None):
     def edit_view(self):
         # Get Taxon data
         id = get_mdict_item_or_list(request.args, "id")
-        taxon_name = db.session.query(Taxref).get(id)
-
-        # Get attributes only if cd_nom is cd_ref
+        taxon_name = db.session.get(Taxref, id)
         if taxon_name.cd_nom == taxon_name.cd_ref:
-            theme_attributs_def = self._get_theme_attributes(taxon_name)
-            attributes_val = self._get_attributes_value(taxon_name, theme_attributs_def)
-            self._template_args["theme_attributs_def"] = theme_attributs_def
-            self._template_args["attributes_val"] = attributes_val
             if request.method == "POST":
                 for f in request.form:
                     if request.form.getlist(f) and f.startswith("attr."):
@@ -569,6 +566,10 @@ def edit_view(self):
                             )
                             db.session.add(model)
                         db.session.commit()
+            theme_attributs_def = self._get_theme_attributes(taxon_name)
+            attributes_val = self._get_attributes_value(taxon_name, theme_attributs_def)
+            self._template_args["theme_attributs_def"] = theme_attributs_def
+            self._template_args["attributes_val"] = attributes_val
         self._template_args["url_cancel"] = request.referrer or url_for("taxons.index_view")
 
         return super(TaxrefView, self).edit_view()
@@ -584,15 +585,12 @@ def format(self, model):
         return None
 
     def get_one(self, pk):
-        return Taxref.query.filter(Taxref.cd_nom == pk).first()
+        return db.session.scalars(select(Taxref).where(Taxref.cd_nom == pk)).first()
 
     def get_list(self, query, offset=0, limit=DEFAULT_PAGE_SIZE):
-        results = (
-            Taxref.query.filter(Taxref.nom_complet.ilike(f"{query}%"))
-            .limit(limit)
-            .offset(offset)
-            .all()
-        )
+        results = db.session.scalars(
+            select(Taxref).where(Taxref.nom_complet.ilike(f"{query}%")).limit(limit).offset(offset)
+        ).all()
         return results
 
 
@@ -657,10 +655,14 @@ def format(self, model):
         return None
 
     def get_one(self, pk):
-        return Taxref.query.with_entities(Taxref.regne).filter(Taxref.regne == pk).distinct().one()
+        from apptax.taxonomie import db
+
+        return db.session.execute(select(Taxref.regne).where(Taxref.regne == pk).distinct()).one()
 
     def get_list(self, query, offset=0, limit=DEFAULT_PAGE_SIZE):
-        return Taxref.query.with_entities(Taxref.regne).distinct().all()
+        from apptax.taxonomie import db
+
+        return db.session.execute(select(Taxref.regne).distinct()).all()
 
 
 class BibAttributsView(FlaskAdminProtectedMixin, RegneAndGroupFormMixin, ModelView):

apptax/admin/filters.py

@@ -6,8 +6,11 @@
 from flask_admin.contrib.sqla.filters import FilterEqual
 from flask_admin.babel import lazy_gettext
 
+from sqlalchemy import select
 from sqlalchemy.orm import aliased
 
+from apptax.database import db
+
 from apptax.taxonomie.models import (
     Taxref,
     BibAttributs,
@@ -39,8 +42,10 @@ class TaxrefDistinctFilter(DynamicOptionsMixin, FilterEqual):
     def get_dynamic_options(self, view):
         if has_app_context():
             yield from [
-                (getattr(row, self.column.key), getattr(row, self.column.key))
-                for row in Taxref.query.distinct(self.column).order_by(self.column).all()
+                (row[0], row[0])
+                for row in db.session.execute(
+                    select(self.column).distinct().order_by(self.column)
+                ).all()
             ]
 
 
@@ -53,9 +58,9 @@ def operation(self):
 
     def get_dynamic_options(self, view):
         if has_app_context():
-            yield from [
-                (attr.id_attribut, attr.label_attribut) for attr in BibAttributs.query.all()
-            ]
+            yield from db.session.execute(
+                select(BibAttributs.id_attribut, BibAttributs.label_attribut)
+            ).all()
 
 
 class FilterBiblist(DynamicOptionsMixin, BaseFilter):
@@ -67,7 +72,7 @@ def operation(self):
 
     def get_dynamic_options(self, view):
         if has_app_context():
-            yield from [(list.id_liste, list.nom_liste) for list in BibListes.query.all()]
+            yield from db.session.execute(select(BibListes.id_liste, BibListes.nom_liste)).all()
 
 
 class FilterIsValidName(BaseFilter):

apptax/migrations/env.py

@@ -24,7 +24,10 @@
 from flask import current_app
 
 config.set_main_option(
-    "sqlalchemy.url", str(current_app.extensions["migrate"].db.engine.url).replace("%", "%%")
+    "sqlalchemy.url",
+    current_app.extensions["migrate"]
+    .db.engine.url.render_as_string(hide_password=False)
+    .replace("%", "%%"),
 )
 target_metadata = current_app.extensions["migrate"].db.metadata
 

apptax/migrations/versions/44447746cacc_drop_t_medias_supprime_column.py

@@ -24,9 +24,9 @@
 def upgrade():
     # Suppression des fichiers médias
     conn = op.get_bind()
-    res = conn.execute("""SELECT id_media, chemin 
+    res = conn.execute(sa.text("""SELECT id_media, chemin 
         FROM taxonomie.t_medias
-        WHERE NOT NULLIF(chemin , '') IS NULL AND  supprime = TRUE;""")
+        WHERE NOT NULLIF(chemin , '') IS NULL AND  supprime = TRUE;"""))
 
     if "MEDIA_FOLDER" in current_app.config:
         media_path = Path(current_app.config["MEDIA_FOLDER"], "taxhub").absolute()

apptax/taxonomie/commands/taxref.py

@@ -2,7 +2,7 @@
 import csv
 
 from flask.cli import with_appcontext
-from sqlalchemy import select, func
+from sqlalchemy import select, func, text
 from sqlalchemy.orm.exc import NoResultFound
 
 
@@ -81,7 +81,7 @@ def delete():
     ) as bar:
         for i, table in enumerate(tables):
             bar.update(n_steps=i, current_item=table)
-            db.session.execute(f"DELETE FROM {table}")
+            db.session.execute(text(f"DELETE FROM {table}"))
 
     db.session.commit()
 
@@ -118,7 +118,7 @@ def import_inpn_media(file):
 
             # Get Taxon
             try:
-                taxon = Taxref.query.get(int(value))
+                taxon = db.session.get(Taxref, int(value))
             except (NoResultFound, ValueError):
                 logger.error(f"{value} is not a valid cd_ref")
                 continue