class OccurrenceSchema(MA.SQLAlchemyAutoSchema):
class Meta:
model = TOccurrencesOccurrence
load_instance = True
include_fk = True
cor_counting_occtax = MA.Nested(CountingSchema, many=True)
taxref = MA.Nested(TaxrefSchema, dump_only=True)
class OccurrenceSchema(MA.SQLAlchemyAutoSchema):
class Meta:
model = TOccurrencesOccurrence
load_instance = True
include_fk = True
additional_fields = fields.Raw(allow_none=False, required=True)
# additional_fields = fields.Raw(load_only=True)
cor_counting_occtax = MA.Nested(CountingSchema, many=True)
taxref = MA.Nested(TaxrefSchema, dump_only=True)
pre_dump_fn = remove_additional_none_val
class DatasetActorSchema(MA.SQLAlchemyAutoSchema):
class Meta:
model = CorDatasetActor
load_instance = True
include_fk = True
role = MA.Nested(UserSchema, dump_only=True)
nomenclature_actor_role = MA.Nested(NomenclatureSchema, dump_only=True)
organism = MA.Nested(OrganismeSchema, dump_only=True)
@pre_load
def make_dataset_actor(self, data, **kwargs):
if data.get("id_cda") is None:
data.pop("id_cda", None)
return data
class AcquisitionFrameworkActorSchema(MA.SQLAlchemyAutoSchema):
class Meta:
model = CorAcquisitionFrameworkActor
load_instance = True
include_fk = True
role = MA.Nested(UserSchema, dump_only=True)
nomenclature_actor_role = MA.Nested(NomenclatureSchema, dump_only=True)
organism = MA.Nested(OrganismeSchema, dump_only=True)
cor_volets_sinp = MA.Nested(OrganismeSchema, dump_only=True)
@pre_load
def make_af_actor(self, data, **kwargs):
if data.get("id_cafa") is None:
data.pop("id_cafa", None)
return data
class AcquisitionFrameworkSchema(MetadataSchema):
class Meta:
model = TAcquisitionFramework
load_instance = True
include_fk = True
meta_create_date = fields.DateTime(dump_only=True)
meta_update_date = fields.DateTime(dump_only=True)
t_datasets = MA.Nested(
DatasetSchema(
exclude=(
"acquisition_framework",
"modules",
"nomenclature_dataset_objectif",
"nomenclature_collecting_method",
"nomenclature_data_origin",
"nomenclature_source_status",
"nomenclature_resource_type",
),
many=True,
),
many=True
)
bibliographical_references = MA.Nested(
BibliographicReferenceSchema(
exclude=(
"acquisition_framework",
),
many=True,
)
, many=True,
)
cor_af_actor = MA.Nested(
AcquisitionFrameworkActorSchema,
many=True
)
cor_volets_sinp = MA.Nested(
NomenclatureSchema,
many=True,
)
cor_objectifs = MA.Nested(
NomenclatureSchema,
many=True
)
cor_territories = MA.Nested(
NomenclatureSchema,
many=True
)
nomenclature_territorial_level = MA.Nested(NomenclatureSchema, dump_only=True)
nomenclature_financing_type = MA.Nested(NomenclatureSchema, dump_only=True)
creator = MA.Nested(UserSchema, dump_only=True)
class CountingSchema(MA.SQLAlchemyAutoSchema):
class Meta:
model = CorCountingOccurrence
load_instance = True
medias = MA.Nested(MediaSchema, many=True)
@pre_load
def make_counting(self, data, **kwargs):
if data.get("id_counting_occtax") is None:
data.pop("id_counting_occtax", None)
return data
class ReleveSchema(MA.SQLAlchemyAutoSchema):
class Meta:
model = TRelevesOccurrence
load_instance = True
include_fk = True
exclude = ("geom_local", )
date_min = fields.Date(format="%Y-%m-%d")
date_max = fields.Date(format="%Y-%m-%d")
hour_min = fields.Time(format="%H:%M", allow_none=True)
hour_max = fields.Time(format="%H:%M", allow_none=True)
geom_4326 = GeojsonSerializationField()
id_digitiser = MA.auto_field(dump_only=True)
t_occurrences_occtax = MA.Nested(OccurrenceSchema, many=True)
observers = MA.Nested(
ObserverSchema,
many=True,
allow_none=current_app.config.get("OCCTAX",
{}).get("observers_txt", True),
)
digitiser = MA.Nested(ObserverSchema, dump_only=True)
dataset = MA.Nested(DatasetSchema, dump_only=True)
habitat = MA.Nested(HabrefSchema, dump_only=True)
@pre_load
def make_releve(self, data, **kwargs):
if data.get("observers") is None:
data["observers"] = []
if data.get("id_releve_occtax") is None:
data.pop("id_releve_occtax", None)
return data
class BibliographicReferenceSchema(MetadataSchema):
class Meta:
model = TBibliographicReference
load_instance = True
include_fk = True
acquisition_framework = MA.Nested("AcquisitionFrameworkSchema", exclude=("bibliographical_references",), dump_only=True)
@pre_load
def make_biblio_ref(self, data, **kwargs):
print(data)
if data.get("id_bibliographic_reference") is None:
data.pop("id_bibliographic_reference", None)
return data
class BibliographicReferenceSchema(CruvedSchemaMixin, SmartRelationshipsMixin,
MA.SQLAlchemyAutoSchema):
class Meta:
model = TBibliographicReference
load_instance = True
include_fk = True
acquisition_framework = MA.Nested("AcquisitionFrameworkSchema",
dump_only=True)
@pre_load
def make_biblio_ref(self, data, **kwargs):
if data.get("id_bibliographic_reference") is None:
data.pop("id_bibliographic_reference", None)
return data
class AcquisitionFrameworkSchema(CruvedSchemaMixin, SmartRelationshipsMixin,
MA.SQLAlchemyAutoSchema):
class Meta:
model = TAcquisitionFramework
load_instance = True
include_fk = True
meta_create_date = fields.DateTime(dump_only=True)
meta_update_date = fields.DateTime(dump_only=True)
t_datasets = MA.Nested(DatasetSchema, many=True)
bibliographical_references = MA.Nested(BibliographicReferenceSchema,
many=True)
cor_af_actor = MA.Nested(AcquisitionFrameworkActorSchema,
many=True,
unknown=EXCLUDE)
cor_volets_sinp = MA.Nested(NomenclatureSchema, many=True, unknown=EXCLUDE)
cor_objectifs = MA.Nested(NomenclatureSchema, many=True, unknown=EXCLUDE)
cor_territories = MA.Nested(NomenclatureSchema, many=True, unknown=EXCLUDE)
nomenclature_territorial_level = MA.Nested(NomenclatureSchema,
dump_only=True)
nomenclature_financing_type = MA.Nested(NomenclatureSchema, dump_only=True)
creator = MA.Nested(UserSchema, dump_only=True)
def get_app(config, _app=None, with_external_mods=True, with_flask_admin=True):
# Make sure app is a singleton
if _app is not None:
return _app
app = Flask(__name__)
app.config.update(config)
# Bind app to DB
DB.init_app(app)
# For deleting files on "delete" media
@before_models_committed.connect_via(app)
def on_before_models_committed(sender, changes):
for obj, change in changes:
if change == "delete" and hasattr(obj, "__before_commit_delete__"):
obj.__before_commit_delete__()
# Bind app to MA
MA.init_app(app)
# Pass parameters to the usershub authenfication sub-module, DONT CHANGE THIS
app.config["DB"] = DB
# Pass parameters to the submodules
app.config["MA"] = MA
# Pass the ID_APP to the submodule to avoid token conflict between app on the same server
app.config["ID_APP"] = app.config["ID_APPLICATION_GEONATURE"]
with app.app_context():
if app.config["MAIL_ON_ERROR"] and app.config["MAIL_CONFIG"]:
from geonature.utils.logs import mail_handler
logging.getLogger().addHandler(mail_handler)
# DB.create_all()
if with_flask_admin:
# from geonature.core.admin import flask_admin
from geonature.core.admin.admin import flask_admin
from pypnusershub.routes import routes
app.register_blueprint(routes, url_prefix="/auth")
from pypn_habref_api.routes import routes
app.register_blueprint(routes, url_prefix="/habref")
from pypnusershub import routes_register
app.register_blueprint(routes_register.bp, url_prefix="/pypn/register")
from pypnnomenclature.routes import routes
app.register_blueprint(routes, url_prefix="/nomenclatures")
from geonature.core.gn_permissions.routes import routes
app.register_blueprint(routes, url_prefix="/permissions")
from geonature.core.gn_permissions.backoffice.views import routes
app.register_blueprint(routes, url_prefix="/permissions_backoffice")
from geonature.core.routes import routes
app.register_blueprint(routes, url_prefix="")
from geonature.core.users.routes import routes
app.register_blueprint(routes, url_prefix="/users")
from geonature.core.gn_synthese.routes import routes
app.register_blueprint(routes, url_prefix="/synthese")
from geonature.core.gn_meta.routes import routes
app.register_blueprint(routes, url_prefix="/meta")
from geonature.core.ref_geo.routes import routes
app.register_blueprint(routes, url_prefix="/geo")
from geonature.core.gn_exports.routes import routes
app.register_blueprint(routes, url_prefix="/exports")
from geonature.core.auth.routes import routes
app.register_blueprint(routes, url_prefix="/gn_auth")
from geonature.core.gn_monitoring.routes import routes
app.register_blueprint(routes, url_prefix="/gn_monitoring")
from geonature.core.gn_commons.routes import routes
app.register_blueprint(routes, url_prefix="/gn_commons")
# Errors
from geonature.core.errors import routes
app.wsgi_app = ReverseProxied(app.wsgi_app,
script_name=config["API_ENDPOINT"])
CORS(app, supports_credentials=True)
# Emails configuration
if app.config["MAIL_CONFIG"]:
conf = app.config.copy()
conf.update(app.config["MAIL_CONFIG"])
app.config = conf
MAIL.init_app(app)
# Loading third-party modules
if with_external_mods:
for conf, manifest, module in list_and_import_gn_modules(app):
app.register_blueprint(module.backend.blueprint.blueprint,
url_prefix=conf["MODULE_URL"])
_app = app
return app
class Meta:
model = TValidations
load_instance = True
include_fk = True
validation_label = fields.Nested(NomenclatureSchema, dump_only=True)
validator_role = MA.Nested(UserSchema, dump_only=True)
class DatasetSchema(MetadataSchema):
class Meta:
model = TDatasets
load_instance = True
include_fk = True
meta_create_date = fields.DateTime(dump_only=True)
meta_update_date = fields.DateTime(dump_only=True)
cor_dataset_actor = MA.Nested(
DatasetActorSchema,
many=True
)
modules = MA.Nested(
ModuleSchema,
many=True,
exclude=("meta_create_date", "meta_update_date")
)
creator = MA.Nested(UserSchema, dump_only=True)
nomenclature_data_type = MA.Nested(NomenclatureSchema, dump_only=True)
nomenclature_dataset_objectif = MA.Nested(NomenclatureSchema, dump_only=True)
nomenclature_collecting_method = MA.Nested(NomenclatureSchema, dump_only=True)
nomenclature_data_origin = MA.Nested(NomenclatureSchema, dump_only=True)
nomenclature_source_status = MA.Nested(NomenclatureSchema, dump_only=True)
nomenclature_resource_type = MA.Nested(NomenclatureSchema, dump_only=True)
cor_territories = MA.Nested(
NomenclatureSchema,
many=True
)
acquisition_framework = MA.Nested("AcquisitionFrameworkSchema", exclude=("t_datasets",), dump_only=True)
class DatasetSchema(CruvedSchemaMixin, SmartRelationshipsMixin,
MA.SQLAlchemyAutoSchema):
class Meta:
model = TDatasets
load_instance = True
include_fk = True
meta_create_date = fields.DateTime(dump_only=True)
meta_update_date = fields.DateTime(dump_only=True)
cor_dataset_actor = MA.Nested(DatasetActorSchema,
many=True,
unknown=EXCLUDE)
modules = MA.Nested(ModuleSchema,
many=True,
exclude=("meta_create_date", "meta_update_date"),
unknown=EXCLUDE)
creator = MA.Nested(UserSchema, dump_only=True)
nomenclature_data_type = MA.Nested(NomenclatureSchema, dump_only=True)
nomenclature_dataset_objectif = MA.Nested(NomenclatureSchema,
dump_only=True)
nomenclature_collecting_method = MA.Nested(NomenclatureSchema,
dump_only=True)
nomenclature_data_origin = MA.Nested(NomenclatureSchema, dump_only=True)
nomenclature_source_status = MA.Nested(NomenclatureSchema, dump_only=True)
nomenclature_resource_type = MA.Nested(NomenclatureSchema, dump_only=True)
cor_territories = MA.Nested(NomenclatureSchema, many=True, unknown=EXCLUDE)
acquisition_framework = MA.Nested("AcquisitionFrameworkSchema",
dump_only=True)
def create_app(with_external_mods=True):
app = Flask(__name__.split('.')[0], static_folder="../static")
app.config.update(config)
api_uri = urlsplit(app.config['API_ENDPOINT'])
app.config['APPLICATION_ROOT'] = api_uri.path
app.config['PREFERRED_URL_SCHEME'] = api_uri.scheme
if 'SCRIPT_NAME' not in os.environ:
os.environ['SCRIPT_NAME'] = app.config['APPLICATION_ROOT'].rstrip('/')
app.config['TEMPLATES_AUTO_RELOAD'] = True
# disable cache for downloaded files (PDF file stat for ex)
app.config['SEND_FILE_MAX_AGE_DEFAULT'] = 0
if len(app.config['SECRET_KEY']) < 20:
raise Exception("The SECRET_KEY config option must have a length "
"greater or equals to 20 characters.")
# set from headers HTTP_HOST, SERVER_NAME, and SERVER_PORT
app.wsgi_app = ProxyFix(app.wsgi_app, x_host=1)
app.json_encoder = MyJSONEncoder
# set logging config
config_loggers(app.config)
db.init_app(app)
migrate.init_app(app,
DB,
directory=BACKEND_DIR / 'geonature' / 'migrations')
MA.init_app(app)
CORS(app, supports_credentials=True)
# Emails configuration
if app.config["MAIL_CONFIG"]:
conf = app.config.copy()
conf.update(app.config["MAIL_CONFIG"])
app.config = conf
MAIL.init_app(app)
# Pass parameters to the usershub authenfication sub-module, DONT CHANGE THIS
app.config["DB"] = DB
# Pass parameters to the submodules
app.config["MA"] = MA
# For deleting files on "delete" media
@before_models_committed.connect_via(app)
def on_before_models_committed(sender, changes):
for obj, change in changes:
if change == "delete" and hasattr(obj, "__before_commit_delete__"):
obj.__before_commit_delete__()
# setting g.current_user on each request
@app.before_request
def load_current_user():
try:
g.current_user = user_from_token(request.cookies['token']).role
except (KeyError, UnreadableAccessRightsError,
AccessRightsExpiredError):
g.current_user = None
admin.init_app(app)
# Pass the ID_APP to the submodule to avoid token conflict between app on the same server
with app.app_context():
try:
gn_app = Application.query.filter_by(
code_application=config['CODE_APPLICATION']).one()
except (ProgrammingError, NoResultFound):
logging.warning(
"Warning: unable to find GeoNature application, database not yet initialized?"
)
else:
app.config["ID_APP"] = app.config[
"ID_APPLICATION_GEONATURE"] = gn_app.id_application
for blueprint_path, url_prefix in [
('pypnusershub.routes:routes', '/auth'),
('pypn_habref_api.routes:routes', '/habref'),
('pypnusershub.routes_register:bp', '/pypn/register'),
('pypnnomenclature.routes:routes', '/nomenclatures'),
('geonature.core.gn_commons.routes:routes', '/gn_commons'),
('geonature.core.gn_permissions.routes:routes', '/permissions'),
('geonature.core.gn_permissions.backoffice.views:routes',
'/permissions_backoffice'),
('geonature.core.routes:routes', '/'),
('geonature.core.users.routes:routes', '/users'),
('geonature.core.gn_synthese.routes:routes', '/synthese'),
('geonature.core.gn_meta.routes:routes', '/meta'),
('geonature.core.ref_geo.routes:routes', '/geo'),
('geonature.core.auth.routes:routes', '/gn_auth'),
('geonature.core.gn_monitoring.routes:routes', '/gn_monitoring'),
('geonature.core.gn_profiles.routes:routes', '/gn_profiles'),
]:
module_name, blueprint_name = blueprint_path.split(':')
blueprint = getattr(import_module(module_name), blueprint_name)
app.register_blueprint(blueprint, url_prefix=url_prefix)
with app.app_context():
# register errors handlers
import geonature.core.errors
# Loading third-party modules
if with_external_mods:
try:
for module_object, module_config, module_blueprint in import_backend_enabled_modules(
):
app.config[module_config['MODULE_CODE']] = module_config
app.register_blueprint(
module_blueprint,
url_prefix=module_config['MODULE_URL'])
except ProgrammingError as sqla_error:
if isinstance(sqla_error.orig, UndefinedTable):
logging.warning(
"Warning: database not yet initialized, skipping loading of external modules"
)
else:
raise
return app
def create_app(with_external_mods=True, with_flask_admin=True):
app = Flask(__name__)
app.config.update(config)
# Bind app to DB
DB.init_app(app)
MAIL.init_app(app)
# For deleting files on "delete" media
@before_models_committed.connect_via(app)
def on_before_models_committed(sender, changes):
for obj, change in changes:
if change == "delete" and hasattr(obj, "__before_commit_delete__"):
obj.__before_commit_delete__()
# Bind app to MA
MA.init_app(app)
# Pass parameters to the usershub authenfication sub-module, DONT CHANGE THIS
app.config["DB"] = DB
# Pass parameters to the submodules
app.config["MA"] = MA
# Pass the ID_APP to the submodule to avoid token conflict between app on the same server
app.config["ID_APP"] = app.config["ID_APPLICATION_GEONATURE"]
if with_flask_admin:
from geonature.core.admin.admin import admin
admin.init_app(app)
with app.app_context():
if app.config["MAIL_ON_ERROR"] and app.config["MAIL_CONFIG"]:
from geonature.utils.logs import mail_handler
logging.getLogger().addHandler(mail_handler)
from pypnusershub.routes import routes
app.register_blueprint(routes, url_prefix="/auth")
from pypn_habref_api.routes import routes
app.register_blueprint(routes, url_prefix="/habref")
from pypnusershub import routes_register
app.register_blueprint(routes_register.bp, url_prefix="/pypn/register")
from pypnnomenclature.routes import routes
app.register_blueprint(routes, url_prefix="/nomenclatures")
from geonature.core.gn_permissions.routes import routes
app.register_blueprint(routes, url_prefix="/permissions")
from geonature.core.gn_permissions.backoffice.views import routes
app.register_blueprint(routes, url_prefix="/permissions_backoffice")
from geonature.core.routes import routes
app.register_blueprint(routes, url_prefix="")
from geonature.core.users.routes import routes
app.register_blueprint(routes, url_prefix="/users")
from geonature.core.gn_synthese.routes import routes
app.register_blueprint(routes, url_prefix="/synthese")
from geonature.core.gn_meta.routes import routes
app.register_blueprint(routes, url_prefix="/meta")
from geonature.core.ref_geo.routes import routes
app.register_blueprint(routes, url_prefix="/geo")
from geonature.core.gn_exports.routes import routes
app.register_blueprint(routes, url_prefix="/exports")
from geonature.core.auth.routes import routes
app.register_blueprint(routes, url_prefix="/gn_auth")
from geonature.core.gn_monitoring.routes import routes
app.register_blueprint(routes, url_prefix="/gn_monitoring")
from geonature.core.gn_commons.routes import routes
app.register_blueprint(routes, url_prefix="/gn_commons")
# Errors
from geonature.core.errors import routes
CORS(app, supports_credentials=True)
# Emails configuration
if app.config["MAIL_CONFIG"]:
conf = app.config.copy()
conf.update(app.config["MAIL_CONFIG"])
app.config = conf
MAIL.init_app(app)
app.config['TEMPLATES_AUTO_RELOAD'] = True
# disable cache for downloaded files (PDF file stat for ex)
app.config['SEND_FILE_MAX_AGE_DEFAULT'] = 0
# Loading third-party modules
if with_external_mods:
for module, blueprint in import_backend_enabled_modules():
app.config[blueprint.config['MODULE_CODE']] = blueprint.config
app.register_blueprint(
blueprint, url_prefix=blueprint.config['MODULE_URL'])
_app = app
return app
