WIP: ajustements pour upgrade SQLAlchemy

app/__init__.py

@@ -3,6 +3,7 @@
 
 import base64
 import datetime
+import json
 import os
 import socket
 import sys
@@ -12,12 +13,13 @@ import traceback
 import logging
 from logging.handlers import SMTPHandler, WatchedFileHandler
 from threading import Thread
+import warnings
 
-import flask
 from flask import current_app, g, request
 from flask import Flask
 from flask import abort, flash, has_request_context, jsonify
 from flask import render_template
+from flask.json import JSONEncoder
 from flask.logging import default_handler
 
 from flask_bootstrap import Bootstrap
@@ -42,6 +44,8 @@ from app.scodoc.sco_exceptions import (
     ScoValueError,
     APIInvalidParams,
 )
+from app.scodoc.sco_vdi import ApoEtapeVDI
+
 from config import DevConfig
 import sco_version
 
@@ -140,12 +144,14 @@ def handle_invalid_usage(error):
 
 
 # JSON ENCODING
-class ScoDocJSONEncoder(flask.json.provider.DefaultJSONProvider):
+class ScoDocJSONEncoder(JSONEncoder):
-    def default(self, o):
+    def default(self, o):  # pylint: disable=E0202
-        if isinstance(o, (datetime.datetime, datetime.date)):
+        if isinstance(o, (datetime.date, datetime.datetime)):
             return o.isoformat()
-
+        elif isinstance(o, ApoEtapeVDI):
-        return super().default(o)
+            return str(o)
+        else:
+            return json.JSONEncoder.default(self, o)
 
 
 def render_raw_html(template_filename: str, **args) -> str:
@@ -258,6 +264,10 @@ def create_app(config_class=DevConfig):
     # Evite de logguer toutes les requetes dans notre log
     logging.getLogger("werkzeug").disabled = True
     app.logger.setLevel(app.config["LOG_LEVEL"])
+    if app.config["TESTING"] or app.config["DEBUG"]:
+        # S'arrête sur tous les warnings, sauf
+        #  flask_sqlalchemy/query (pb deprecation du model.get())
+        warnings.filterwarnings("error", module="flask_sqlalchemy/query")
 
     # Vérifie/crée lien sym pour les URL statiques
     link_filename = f"{app.root_path}/static/links/{sco_version.SCOVERSION}"

app/comp/inscr_mod.py

@@ -4,6 +4,7 @@
 """Matrices d'inscription aux modules d'un semestre
 """
 import pandas as pd
+import sqlalchemy as sa
 
 from app import db
 
@@ -12,6 +13,13 @@ from app import db
 # sur test debug 116 etuds, 18 modules, on est autour de 250ms.
 # On a testé trois approches, ci-dessous (et retenu la 1ere)
 #
+_load_modimpl_inscr_q = sa.text(
+    """SELECT etudid, 1 AS ":moduleimpl_id"
+    FROM notes_moduleimpl_inscription
+    WHERE moduleimpl_id=:moduleimpl_id"""
+)
+
+
 def df_load_modimpl_inscr(formsemestre) -> pd.DataFrame:
     """Charge la matrice des inscriptions aux modules du semestre
     rows: etudid (inscrits au semestre, avec DEM et DEF)
@@ -22,17 +30,16 @@ def df_load_modimpl_inscr(formsemestre) -> pd.DataFrame:
     moduleimpl_ids = [m.id for m in formsemestre.modimpls_sorted]
     etudids = [inscr.etudid for inscr in formsemestre.inscriptions]
     df = pd.DataFrame(index=etudids, dtype=int)
-    for moduleimpl_id in moduleimpl_ids:
+    with db.engine.begin() as connection:
-        ins_df = pd.read_sql_query(
+        for moduleimpl_id in moduleimpl_ids:
-            """SELECT etudid, 1 AS "%(moduleimpl_id)s"
+            ins_df = pd.read_sql_query(
-                FROM notes_moduleimpl_inscription
+                _load_modimpl_inscr_q,
-                WHERE moduleimpl_id=%(moduleimpl_id)s""",
+                connection,
-            db.engine,
+                params={"moduleimpl_id": moduleimpl_id},
-            params={"moduleimpl_id": moduleimpl_id},
+                index_col="etudid",
-            index_col="etudid",
+                dtype=int,
-            dtype=int,
+            )
-        )
+            df = df.merge(ins_df, how="left", left_index=True, right_index=True)
-        df = df.merge(ins_df, how="left", left_index=True, right_index=True)
     # Force columns names to integers (moduleimpl ids)
     df.columns = pd.Index([int(x) for x in df.columns], dtype=int)
     # les colonnes de df sont en float (Nan) quand il n'y a

app/comp/jury.py

@@ -7,6 +7,7 @@
 """Stockage des décisions de jury
 """
 import pandas as pd
+import sqlalchemy as sa
 
 from app import db
 from app.models import FormSemestre, Identite, ScolarFormSemestreValidation, UniteEns
@@ -132,7 +133,8 @@ def formsemestre_get_ue_capitalisees(formsemestre: FormSemestre) -> pd.DataFrame
     # Note: pour récupérer aussi les UE validées en CMp ou ADJ, changer une ligne
     #   and ( SFV.code = 'ADM' or SFV.code = 'ADJ' or SFV.code = 'CMP' )
 
-    query = """
+    query = sa.text(
+        """
     SELECT DISTINCT SFV.*, ue.ue_code
     FROM 
     notes_ue ue, 
@@ -144,21 +146,22 @@ def formsemestre_get_ue_capitalisees(formsemestre: FormSemestre) -> pd.DataFrame
 
     WHERE ue.formation_id = nf.id
     and nf.formation_code = nf2.formation_code
-    and nf2.id=%(formation_id)s
+    and nf2.id=:formation_id
     and ins.etudid = SFV.etudid
-    and ins.formsemestre_id = %(formsemestre_id)s
+    and ins.formsemestre_id = :formsemestre_id
 
     and SFV.ue_id = ue.id
     and SFV.code = 'ADM'
 
     and ( (sem.id = SFV.formsemestre_id
-        and sem.date_debut < %(date_debut)s
+        and sem.date_debut < :date_debut
-        and sem.semestre_id = %(semestre_id)s )
+        and sem.semestre_id = :semestre_id )
         or (
             ((SFV.formsemestre_id is NULL) OR (SFV.is_external)) -- les UE externes ou "anterieures"
-            AND (SFV.semestre_id is NULL OR SFV.semestre_id=%(semestre_id)s)
+            AND (SFV.semestre_id is NULL OR SFV.semestre_id=:semestre_id)
            ) )
     """
+    )
     params = {
         "formation_id": formsemestre.formation.id,
         "formsemestre_id": formsemestre.id,
@@ -166,5 +169,6 @@ def formsemestre_get_ue_capitalisees(formsemestre: FormSemestre) -> pd.DataFrame
         "date_debut": formsemestre.date_debut,
     }
 
-    df = pd.read_sql_query(query, db.engine, params=params, index_col="etudid")
+    with db.engine.begin() as connection:
+        df = pd.read_sql_query(query, connection, params=params, index_col="etudid")
     return df

app/comp/moy_mod.py

@@ -38,6 +38,7 @@ from dataclasses import dataclass
 
 import numpy as np
 import pandas as pd
+import sqlalchemy as sa
 
 import app
 from app import db
@@ -192,24 +193,29 @@ class ModuleImplResults:
         evals_notes.columns = pd.Index([int(x) for x in evals_notes.columns], dtype=int)
         self.evals_notes = evals_notes
 
+    _load_evaluation_notes_q = sa.text(
+        """SELECT n.etudid, n.value AS ":evaluation_id"
+                FROM notes_notes n, notes_moduleimpl_inscription i
+                WHERE evaluation_id=:evaluation_id
+                AND n.etudid = i.etudid
+                AND i.moduleimpl_id = :moduleimpl_id
+            """
+    )
+
     def _load_evaluation_notes(self, evaluation: Evaluation) -> pd.DataFrame:
         """Charge les notes de l'évaluation
         Resultat: dataframe, index: etudid ayant une note, valeur: note brute.
         """
-        eval_df = pd.read_sql_query(
+        with db.engine.begin() as connection:
-            """SELECT n.etudid, n.value AS "%(evaluation_id)s"
+            eval_df = pd.read_sql_query(
-            FROM notes_notes n, notes_moduleimpl_inscription i
+                self._load_evaluation_notes_q,
-            WHERE evaluation_id=%(evaluation_id)s
+                connection,
-            AND n.etudid = i.etudid
+                params={
-            AND i.moduleimpl_id = %(moduleimpl_id)s
+                    "evaluation_id": evaluation.id,
-            """,
+                    "moduleimpl_id": evaluation.moduleimpl.id,
-            db.engine,
+                },
-            params={
+                index_col="etudid",
-                "evaluation_id": evaluation.id,
+            )
-                "moduleimpl_id": evaluation.moduleimpl.id,
-            },
-            index_col="etudid",
-        )
         eval_df[str(evaluation.id)] = pd.to_numeric(eval_df[str(evaluation.id)])
         return eval_df
 

app/models/ues.py

@@ -206,20 +206,14 @@ class UniteEns(db.Model):
 
         Si niveau est None, désassocie.
         """
-        if niveau is not None:
+        if niveau.id == self.niveau_competence_id:
-            self._check_apc_conflict(niveau.id, self.parcour_id)
+            return True  # nothing to do
-            # Le niveau est-il dans le parcours ? Sinon, erreur
+        if (niveau is not None) and (self.niveau_competence_id is not None):
-            if self.parcour and niveau.id not in (
+            ok, error_message = self.check_niveau_unique_dans_parcours(
-                n.id
+                niveau, self.parcours
-                for n in niveau.niveaux_annee_de_parcours(
+            )
-                    self.parcour, self.annee(), self.formation.referentiel_competence
+            if not ok:
-                )
+                return ok, error_message
-            ):
-                log(
-                    f"set_niveau_competence: niveau {niveau} hors parcours {self.parcour}"
-                )
-                return
-
         self.niveau_competence = niveau
 
         db.session.add(self)

app/scodoc/gen_tables.py

@@ -40,7 +40,6 @@ Par exemple, la clé '_css_row_class' spécifie le style CSS de la ligne.
 
 """
 
-from __future__ import print_function
 import random
 from collections import OrderedDict
 from xml.etree import ElementTree
@@ -60,7 +59,7 @@ from app.scodoc import sco_pdf
 from app.scodoc import sco_xml
 from app.scodoc.sco_exceptions import ScoPDFFormatError
 from app.scodoc.sco_pdf import SU
-from app import log
+from app import log, ScoDocJSONEncoder
 
 
 def mark_paras(L, tags) -> list[str]:
@@ -647,7 +646,7 @@ class GenTable(object):
                 #    v = str(v)
                 r[cid] = v
             d.append(r)
-        return json.dumps(d, cls=scu.ScoDocJSONEncoder)
+        return json.dumps(d, cls=ScoDocJSONEncoder)
 
     def make_page(
         self,

app/scodoc/sco_archives.py

@@ -64,7 +64,7 @@ from flask import flash, g, request, url_for
 
 import app.scodoc.sco_utils as scu
 from config import Config
-from app import log
+from app import log, ScoDocJSONEncoder
 from app.but import jury_but_pv
 from app.comp import res_sem
 from app.comp.res_compat import NotesTableCompat
@@ -365,7 +365,7 @@ def do_formsemestre_archive(
 
     # Bulletins en JSON
     data = gen_formsemestre_recapcomplet_json(formsemestre_id, xml_with_decisions=True)
-    data_js = json.dumps(data, indent=1, cls=scu.ScoDocJSONEncoder)
+    data_js = json.dumps(data, indent=1, cls=ScoDocJSONEncoder)
     if data:
         PVArchive.store(archive_id, "Bulletins.json", data_js)
     # Décisions de jury, en XLS

app/scodoc/sco_bulletins_json.py

@@ -33,6 +33,7 @@ import json
 
 from flask import abort
 
+from app import ScoDocJSONEncoder
 from app.comp import res_sem
 from app.comp.res_compat import NotesTableCompat
 from app.models import but_validations
@@ -74,7 +75,7 @@ def make_json_formsemestre_bulletinetud(
         version=version,
     )
 
-    return json.dumps(d, cls=scu.ScoDocJSONEncoder)
+    return json.dumps(d, cls=ScoDocJSONEncoder)
 
 
 # (fonction séparée: n'utilise pas formsemestre_bulletinetud_dict()

app/scodoc/sco_preferences.py

@@ -111,7 +111,7 @@ get_base_preferences(formsemestre_id)
 
 """
 import flask
-from flask import g, request, url_for
+from flask import current_app, g, request, url_for
 
 # from flask_login import current_user
 
@@ -2000,7 +2000,8 @@ class BasePreferences(object):
                 value = _get_pref_default_value_from_config(name, pref[1])
                 self.default[name] = value
                 self.prefs[None][name] = value
-                log(f"creating missing preference for {name}={value}")
+                if not current_app.testing:
+                    log(f"creating missing preference for {name}={value}")
                 # add to db table
                 self._editor.create(
                     cnx, {"dept_id": self.dept_id, "name": name, "value": value}

app/scodoc/sco_saisie_notes.py

@@ -152,7 +152,7 @@ def _check_notes(notes: list[(int, float)], evaluation: dict, mod: dict):
     absents = []  # etudid absents
     tosuppress = []  # etudids avec ancienne note à supprimer
 
-    for (etudid, note) in notes:
+    for etudid, note in notes:
         note = str(note).strip().upper()
         try:
             etudid = int(etudid)  #
@@ -536,7 +536,7 @@ def notes_add(
             evaluation_id, getallstudents=True, include_demdef=True
         )
     }
-    for (etudid, value) in notes:
+    for etudid, value in notes:
         if check_inscription and (etudid not in inscrits):
             raise NoteProcessError(f"etudiant {etudid} non inscrit dans ce module")
         if (value is not None) and not isinstance(value, float):
@@ -556,7 +556,7 @@ def notes_add(
         []
     )  # etudids pour lesquels il y a une decision de jury et que la note change
     try:
-        for (etudid, value) in notes:
+        for etudid, value in notes:
             changed = False
             if etudid not in notes_db:
                 # nouvelle note
@@ -657,6 +657,7 @@ def notes_add(
                 formsemestre_id=M["formsemestre_id"]
             )  # > modif notes (exception)
             sco_cache.EvaluationCache.delete(evaluation_id)
+        raise  # XXX
         raise ScoGenError("Erreur enregistrement note: merci de ré-essayer") from exc
     if do_it:
         cnx.commit()

app/scodoc/sco_utils.py

@@ -61,8 +61,8 @@ from flask import flash, url_for, make_response, jsonify
 from werkzeug.http import HTTP_STATUS_CODES
 
 from config import Config
-from app import log
+from app import log, ScoDocJSONEncoder
-from app.scodoc.sco_vdi import ApoEtapeVDI
+
 from app.scodoc.codes_cursus import NOTES_TOLERANCE, CODES_EXPL
 from app.scodoc import sco_xml
 import sco_version
@@ -855,16 +855,6 @@ def sendPDFFile(data, filename):  # DEPRECATED  utiliser send_file
     return send_file(data, filename=filename, mime=PDF_MIMETYPE, attached=True)
 
 
-class ScoDocJSONEncoder(flask.json.provider.DefaultJSONProvider):
-    def default(self, o):  # pylint: disable=E0202
-        if isinstance(o, (datetime.date, datetime.datetime)):
-            return o.isoformat()
-        elif isinstance(o, ApoEtapeVDI):
-            return str(o)
-        else:
-            return json.JSONEncoder.default(self, o)
-
-
 def sendJSON(data, attached=False, filename=None):
     js = json.dumps(data, indent=1, cls=ScoDocJSONEncoder)
     return send_file(

migrations/env.py

@@ -1,9 +1,10 @@
-from __future__ import with_statement
+# Copied 2023-04-03 from
-
+# https://raw.githubusercontent.com/miguelgrinberg/Flask-Migrate/main/src/flask_migrate/templates/flask/env.py
 import logging
 from logging.config import fileConfig
 
 from flask import current_app
+import flask_sqlalchemy
 
 from alembic import context
 
@@ -14,17 +15,31 @@ config = context.config
 # Interpret the config file for Python logging.
 # This line sets up loggers basically.
 fileConfig(config.config_file_name)
-logger = logging.getLogger('alembic.env')
+logger = logging.getLogger("alembic.env")
+
+
+def get_engine():
+    if int(flask_sqlalchemy.__version__[0]) < 3:  # <--------- MODIFIED By EMMANUEL
+        # this works with Flask-SQLAlchemy<3 and Alchemical
+        return current_app.extensions["migrate"].db.get_engine()
+    else:
+        # this works with Flask-SQLAlchemy>=3
+        return current_app.extensions["migrate"].db.engine
+
+
+def get_engine_url():
+    try:
+        return get_engine().url.render_as_string(hide_password=False).replace("%", "%%")
+    except AttributeError:
+        return str(get_engine().url).replace("%", "%%")
+
 
 # add your model's MetaData object here
 # for 'autogenerate' support
 # from myapp import mymodel
 # target_metadata = mymodel.Base.metadata
-config.set_main_option(
+config.set_main_option("sqlalchemy.url", get_engine_url())
-    'sqlalchemy.url',
+target_db = current_app.extensions["migrate"].db
-    str(current_app.extensions['migrate'].db.get_engine().url).replace(
-        '%', '%%'))
-target_metadata = current_app.extensions['migrate'].db.metadata
 
 # other values from the config, defined by the needs of env.py,
 # can be acquired:
@@ -32,6 +47,12 @@ target_metadata = current_app.extensions['migrate'].db.metadata
 # ... etc.
 
 
+def get_metadata():
+    if hasattr(target_db, "metadatas"):
+        return target_db.metadatas[None]
+    return target_db.metadata
+
+
 def run_migrations_offline():
     """Run migrations in 'offline' mode.
 
@@ -45,9 +66,7 @@ def run_migrations_offline():
 
     """
     url = config.get_main_option("sqlalchemy.url")
-    context.configure(
+    context.configure(url=url, target_metadata=get_metadata(), literal_binds=True)
-        url=url, target_metadata=target_metadata, literal_binds=True
-    )
 
     with context.begin_transaction():
         context.run_migrations()
@@ -65,20 +84,20 @@ def run_migrations_online():
     # when there are no changes to the schema
     # reference: http://alembic.zzzcomputing.com/en/latest/cookbook.html
     def process_revision_directives(context, revision, directives):
-        if getattr(config.cmd_opts, 'autogenerate', False):
+        if getattr(config.cmd_opts, "autogenerate", False):
             script = directives[0]
             if script.upgrade_ops.is_empty():
                 directives[:] = []
-                logger.info('No changes in schema detected.')
+                logger.info("No changes in schema detected.")
 
-    connectable = current_app.extensions['migrate'].db.get_engine()
+    connectable = get_engine()
 
     with connectable.connect() as connection:
         context.configure(
             connection=connection,
-            target_metadata=target_metadata,
+            target_metadata=get_metadata(),
             process_revision_directives=process_revision_directives,
-            **current_app.extensions['migrate'].configure_args
+            **current_app.extensions["migrate"].configure_args
         )
 
         with context.begin_transaction():

tests/unit/sco_fake_gen.py

@@ -178,7 +178,7 @@ class ScoFake(object):
         self,
         formation_id=None,
         acronyme=None,
-        numero=None,
+        numero=0,
         titre="",
         type=None,
         ue_code=None,
@@ -200,7 +200,7 @@ class ScoFake(object):
         return oid
 
     @logging_meth
-    def create_matiere(self, ue_id=None, titre=None, numero=None) -> int:
+    def create_matiere(self, ue_id=None, titre=None, numero=0) -> int:
         oid = sco_edit_matiere.do_matiere_create(locals())
         oids = sco_edit_matiere.matiere_list(args={"matiere_id": oid})
         if not oids:
@@ -218,7 +218,7 @@ class ScoFake(object):
         coefficient=None,
         matiere_id=None,
         semestre_id=1,
-        numero=None,
+        numero=0,
         abbrev=None,
         ects=None,
         code_apogee=None,