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[GeoNature 2.14] Update to sqlalchemy1.4 #59

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merged 10 commits into from
May 27, 2024
Merged

[GeoNature 2.14] Update to sqlalchemy1.4 #59

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dd30051
feat: update to sqlalchemy1.4
Apr 3, 2024
318d78c
sqlalchemy update for hierarchy and river basins
Apr 5, 2024
f53ed6d
fix sqlalchemy update errors for river_basins
Apr 9, 2024
aa39485
fix duplicate results in cor_ch_status request
Apr 9, 2024
2d03683
sqlalchemy 1.4 review corrections
Apr 17, 2024
4447439
linter backend
Apr 17, 2024
0cd9291
fix getattr error
Apr 18, 2024
03ab4c5
lint: adjust to last lint updates
edelclaux May 21, 2024
d4f0864
fix: adjust scalars and execute
edelclaux May 27, 2024
ed71d7c
fix: update geometry
edelclaux May 27, 2024
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123 changes: 62 additions & 61 deletions backend/gn_module_zh/blueprint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
from geonature.utils.env import DB, ROOT_DIR, BACKEND_DIR
from pypnnomenclature.models import TNomenclatures
from pypnusershub.db.models import Organisme, User
from sqlalchemy import desc, func, text
from sqlalchemy import desc, func, text, select, update, delete
from sqlalchemy.orm import aliased
from utils_flask_sqla.generic import GenericQuery
from utils_flask_sqla.response import json_resp_accept_empty_list, json_resp
Expand Down Expand Up @@ -93,7 +93,7 @@ def get_zh(scope):
coauthor = aliased(User, name="coauthor")
coorganism = aliased(Organisme, name="coorganism")
q = (
DB.session.query(TZH)
select(TZH)
.join(TNomenclatures, TZH.sdage)
.join(User, TZH.authors)
.join(coauthor, TZH.coauthors)
Expand All @@ -109,6 +109,7 @@ def get_zh(scope):

if request.is_json:
q = main_search(q, request.json)
# q2 = main_search(q2, request.json)

return get_all_zh(
info_role=g.current_user,
Expand All @@ -123,7 +124,7 @@ def get_zh(scope):
def get_all_zh(info_role, query, limit, page, orderby=None, order="asc"):
# try:
# Pour obtenir le nombre de résultat de la requete sans le LIMIT
nb_results_without_limit = query.count()
nb_results_without_limit = DB.session.scalar(select(func.count()).select_from(query.subquery()))
user = info_role
user_cruved = get_user_cruved()

Expand Down Expand Up @@ -151,7 +152,7 @@ def get_all_zh(info_role, query, limit, page, orderby=None, order="asc"):

# Order by id because there can be ambiguity in order_by(col) depending
# on the column so add on order_by id makes it clearer
data = query.order_by(TZH.id_zh).limit(limit).offset(page * limit).all()
data = DB.session.scalars(query.order_by(TZH.id_zh).limit(limit).offset(page * limit)).all()
is_ref_geo = check_ref_geo_schema()

featureCollection = []
Expand Down Expand Up @@ -336,8 +337,7 @@ def get_pbf():
SELECT ST_AsGeobuf(q, 'geom') as pbf
FROM (SELECT id_zh, geom from pr_zh.t_zh tz) AS q;
"""
query = DB.session.execute(sql)
row = query.first()
row = DB.session.execute(text(sql)).first()
return Response(bytes(row["pbf"]) if row["pbf"] else bytes(), mimetype="application/protobuf")


Expand All @@ -364,8 +364,7 @@ def get_pbf_complete():
'bassin_versant', tz.bassin_versant) as json_arrays
FROM pr_zh.atlas_app tz) AS q;
"""
query = DB.session.execute(sql)
row = query.first()
row = DB.session.execute(text(sql)).first()
return Response(bytes(row["pbf"]) if row["pbf"] else bytes(), mimetype="application/protobuf")


Expand All @@ -385,8 +384,7 @@ def get_json():
) AS feature
FROM (SELECT * FROM pr_zh.atlas_app tz) inputs) features;
"""
query = DB.session.execute(sql)
row = query.first()
row = DB.session.execute(text(sql)).first()
return row["geojson"]


Expand All @@ -396,7 +394,7 @@ def get_json():
def get_geometries():
"""Get list of all zh geometries (contours)"""
try:
if not DB.session.query(TZH).all():
if not DB.session.execute(select(TZH)).all():
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raise ZHApiError(
message="no_geometry",
details="Empty list of zh returned from get_zh_list db request",
Expand All @@ -406,7 +404,7 @@ def get_geometries():
"geometry": zh.get_geofeature()["geometry"],
"id_zh": zh.get_geofeature()["properties"]["id_zh"],
}
for zh in DB.session.query(TZH).all()
for zh in DB.session.scalars(select(TZH)).all()
]
except Exception as e:
if e.__class__.__name__ == "ZHApiError":
Expand All @@ -428,17 +426,14 @@ def get_ref_autocomplete():
params = request.args
search_title = params.get("search_title")
# search_title = 'MCD'
q = DB.session.query(
TReferences,
func.similarity(TReferences.title, search_title).label("idx_trgm"),
)
q = select(TReferences, func.similarity(TReferences.title, search_title).label("idx_trgm"))

search_title = search_title.replace(" ", "%")
q = q.filter(TReferences.title.ilike("%" + search_title + "%")).order_by(desc("idx_trgm"))
q = q.where(TReferences.title.ilike("%" + search_title + "%")).order_by(desc("idx_trgm"))

limit = request.args.get("limit", 20)

data = q.limit(limit).all()
data = DB.session.execute(q.limit(limit)).all()
if data:
return [d[0].as_dict() for d in data]
else:
Expand All @@ -462,17 +457,16 @@ def get_file_list(id_zh):
"""get a list of the zh files contained in static repo"""
try:
# FIXME: to optimize... See relationships and lazy join with sqlalchemy
zh_uuid = DB.session.query(TZH).filter(TZH.id_zh == id_zh).one().zh_uuid
q_medias = (
DB.session.query(TMedias, TNomenclatures.label_default)
.filter(TMedias.unique_id_media == zh_uuid)
zh_uuid = DB.session.scalar(select(TZH.zh_uuid).where(TZH.id_zh == id_zh))
q_medias = DB.session.execute(
select(TMedias, TNomenclatures.label_default)
.join(
TNomenclatures,
TNomenclatures.id_nomenclature == TMedias.id_nomenclature_media_type,
)
.where(TMedias.unique_id_media == zh_uuid)
.order_by(TMedias.meta_update_date.desc())
.all()
)
).all()
res_media, image_medias = [], []
for media, media_type in q_medias:
res_media.append(media)
Expand Down Expand Up @@ -528,9 +522,12 @@ def post_main_pict(id_zh, id_media):
"""post main picture id in tzh"""
try:
# FIXME: after insert+after update on t_zh => update_date=dt.now()
DB.session.query(TZH).filter(TZH.id_zh == id_zh).update(
{TZH.main_pict_id: id_media, TZH.update_date: dt.now()}
stmt = (
update(TZH)
.where(TZH.id_zh == id_zh)
.values(main_pict_id=id_media, update_date=dt.now())
)
DB.session.execute(stmt)
DB.session.commit()
return ("", 204)
except Exception as e:
Expand All @@ -553,18 +550,16 @@ def post_main_pict(id_zh, id_media):
@blueprint.route("<int:id_zh>/photos", methods=["GET"])
@json_resp
def get_all_photos(id_zh: int):
q_medias = (
DB.session.query(TZH.main_pict_id, TMedias.id_media, TMedias.media_path)
q_medias = DB.session.execute(
select(TZH.main_pict_id, TMedias.id_media, TMedias.media_path)
.join(TZH, TZH.zh_uuid == TMedias.unique_id_media)
.join(
TNomenclatures,
TNomenclatures.id_nomenclature == TMedias.id_nomenclature_media_type,
)
.order_by(TMedias.meta_update_date.desc())
.filter(TNomenclatures.label_default == "Photo")
.filter(TZH.id_zh == id_zh)
.all()
)
.where(TNomenclatures.label_default == "Photo", TZH.id_zh == id_zh)
).all()
api_uri = urljoin(
f"{config['API_ENDPOINT']}/",
f"{blueprint.config['MODULE_CODE'].lower()}/{blueprint.config['file_path']}/",
Expand Down Expand Up @@ -767,18 +762,18 @@ def deleteOneZh(id_zh):
zhRepository = ZhRepository(TZH)

# delete references
DB.session.query(CorZhRef).filter(CorZhRef.id_zh == id_zh).delete()
DB.session.execute(delete(CorZhRef).where(CorZhRef.id_zh == id_zh))

# delete criteres delim
id_lim_list = DB.session.query(TZH).filter(TZH.id_zh == id_zh).one().id_lim_list
DB.session.query(CorLimList).filter(CorLimList.id_lim_list == id_lim_list).delete()
id_lim_list = DB.session.execute(select(TZH.id_lim_list).where(TZH.id_zh == id_zh)).scalar_one()
DB.session.execute(delete(CorLimList).where(CorLimList.id_lim_list == id_lim_list))

# delete cor_zh_area
DB.session.query(CorZhArea).filter(CorZhArea.id_zh == id_zh).delete()
DB.session.execute(delete(CorZhArea).where(CorZhArea.id_zh == id_zh))

# delete files in TMedias and repos
zh_uuid = DB.session.query(TZH).filter(TZH.id_zh == id_zh).one().zh_uuid
q_medias = DB.session.query(TMedias).filter(TMedias.unique_id_media == zh_uuid).all()
zh_uuid = DB.session.execute(select(TZH.zh_uuid).where(TZH.id_zh == id_zh)).scalar_one()
q_medias = DB.session.scalars(select(TMedias).where(TMedias.unique_id_media == zh_uuid)).all()
for media in q_medias:
delete_file(media.id_media)

Expand All @@ -803,17 +798,19 @@ def write_csv(id_zh):
names = []
FILE_PATH = blueprint.config["file_path"]
MODULE_NAME = blueprint.config["MODULE_CODE"].lower()
zh_code = DB.session.query(TZH).filter(TZH.id_zh == id_zh).one().code
zh_code = DB.session.scalar(select(TZH.code).where(TZH.id_zh == id_zh))
# author name
user = DB.session.query(User).filter(User.id_role == g.current_user.id_role).one()
user = DB.session.execute(
select(User).where(User.id_role == g.current_user.id_role)
).scalar_one()
author = user.prenom_role + " " + user.nom_role
for i in ["vertebrates_view_name", "invertebrates_view_name", "flora_view_name"]:
query = GenericQuery(
DB=DB,
tableName=blueprint.config[i]["table_name"],
schemaName=blueprint.config[i]["schema_name"],
filters={"id_zh": id_zh, "orderby": "id_zh"},
limit=-1,
limit=100,
)
results = query.return_query().get("items", [])
current_date = dt.now()
Expand Down Expand Up @@ -864,8 +861,10 @@ def write_csv(id_zh):
DB.session.flush()

# update TMedias.media_path with media_filename
DB.session.query(TMedias).filter(TMedias.id_media == id_media).update(
{"media_path": str(media_path)}
DB.session.execute(
update(TMedias)
.where(TMedias.id_media == id_media)
.values(media_path=str(media_path))
)

DB.session.commit()
Expand Down Expand Up @@ -924,41 +923,43 @@ def download(id_zh: int):
@json_resp
def departments():
query = (
DB.session.query(LAreas)
.with_entities(LAreas.area_name, LAreas.area_code, LAreas.id_type, BibAreasTypes.type_code)
select(LAreas)
.with_only_columns(
LAreas.area_name, LAreas.area_code, LAreas.id_type, BibAreasTypes.type_code
)
.join(BibAreasTypes, LAreas.id_type == BibAreasTypes.id_type)
.filter(BibAreasTypes.type_code == "DEP")
.filter(LAreas.enable)
.where(BibAreasTypes.type_code == "DEP")
.where(LAreas.enable)
.order_by(LAreas.area_code)
)
resp = query.all()
resp = DB.session.execute(query).all()
return [{"code": r.area_code, "name": r.area_name} for r in resp]


@blueprint.route("/communes", methods=["POST"])
@json_resp
def get_area_from_department() -> dict:
# route utilisée ?
code = request.json.get("code")
if code:
query = (
DB.session.query(LiMunicipalities)
.with_entities(LiMunicipalities.id_area, LAreas.area_name, LAreas.area_code)
select(LiMunicipalities)
.with_only_columns(LiMunicipalities.id_area, LAreas.area_name, LAreas.area_code)
.join(LAreas, LiMunicipalities.id_area == LAreas.id_area)
.filter(LiMunicipalities.insee_com.like("{}%".format(code)))
.filter(LAreas.enable)
.where(LiMunicipalities.insee_com.like("{}%".format(code)))
.where(LAreas.enable)
.order_by(LAreas.area_code)
)
query = query.order_by(LAreas.area_code)
resp = query.all()
resp = DB.session.execute(query).all()
return [{"code": r.area_code, "name": r.area_name} for r in resp]

return []


@blueprint.route("/bassins", methods=["GET"])
@json_resp
def bassins():
query = DB.session.query(TRiverBasin).with_entities(TRiverBasin.id_rb, TRiverBasin.name)
resp = query.order_by(TRiverBasin.name).all()
query = select(TRiverBasin.id_rb, TRiverBasin.name).order_by(TRiverBasin.name)
resp = DB.session.execute(query).all()
return [{"code": r.id_rb, "name": r.name} for r in resp]


Expand All @@ -968,19 +969,19 @@ def get_hydro_zones_from_bassin() -> dict:
code = request.json.get("code")
if code:
query = (
DB.session.query(THydroArea)
.with_entities(THydroArea.id_hydro, THydroArea.name, TRiverBasin.id_rb)
.filter(TRiverBasin.id_rb == code)
select(THydroArea.id_hydro, THydroArea.name, TRiverBasin.id_rb)
.where(TRiverBasin.id_rb == code)
.join(
TRiverBasin,
func.ST_Contains(
func.ST_SetSRID(TRiverBasin.geom, 4326),
func.ST_SetSRID(THydroArea.geom, 4326),
),
)
.order_by(THydroArea.name)
)

resp = query.order_by(THydroArea.name).all()
resp = DB.session.execute(query).all()
return [{"code": r.id_hydro, "name": r.name} for r in resp]

return []
Expand Down
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