def post_jdd_from_user(id_user=None, id_organism=None):
""" Post a jdd from the mtd XML"""
xml_jdd = None
xml_jdd = get_jdd_by_user_id(id_user)
if xml_jdd:
dataset_list = parse_jdd_xml(xml_jdd)
dataset_list_model = []
for ds in dataset_list:
new_af = post_acquisition_framework(
uuid=ds['uuid_acquisition_framework'],
id_user=id_user,
id_organism=id_organism
)
ds['id_acquisition_framework'] = new_af['id_acquisition_framework']
ds.pop('uuid_acquisition_framework')
# get the id of the dataset to check if exists
id_dataset = TDatasets.get_id(ds['unique_dataset_id'])
ds['id_dataset'] = id_dataset
dataset = TDatasets(**ds)
# id_role in cor_dataset_actor
actor = CorDatasetActor(
id_role=id_user,
id_nomenclature_actor_role=func.ref_nomenclatures.get_id_nomenclature('ROLE_ACTEUR', '1')
)
dataset.cor_dataset_actor.append(actor)
# id_organism in cor_dataset_actor
if id_organism:
actor = CorDatasetActor(
id_organism=id_organism,
id_nomenclature_actor_role=func.ref_nomenclatures.get_id_nomenclature('ROLE_ACTEUR', '1')
)
dataset.cor_dataset_actor.append(actor)
dataset_list_model.append(dataset)
try:
if id_dataset:
DB.session.merge(dataset)
else:
DB.session.add(dataset)
DB.session.commit()
DB.session.flush()
# TODO catch db error ?
except SQLAlchemyError as e:
DB.session.rollback()
error_msg = """
Error posting JDD {} \n\n Trace: \n {}
""".format(ds['unique_dataset_id'], e)
log.error(error_msg)
raise GeonatureApiError(error_msg)
return [d.as_dict() for d in dataset_list_model]
return {'message': 'Not found'}, 404
def import_all_dataset_af_and_actors(table_name):
file_handler = logging.FileHandler('/tmp/uuid_ca.txt')
file_handler.setLevel(logging.CRITICAL)
log.addHandler(file_handler)
datasets = DB.engine.execute(f"SELECT * FROM {table_name}")
for d in datasets:
xml_jdd = get_jdd_by_uuid(str(d.unique_dataset_id))
if xml_jdd:
ds_list = parse_jdd_xml(xml_jdd)
if ds_list:
ds = ds_list[0]
inpn_user = get_user_from_id_inpn_ws(ds['id_digitizer'])
# get user info from id_digitizer
if inpn_user:
# insert user id digitizer
insert_user_and_org(inpn_user)
actors = ds.pop("actors")
# prevent to not fetch, post or merge the same acquisition framework multiple times
new_af = post_acquisition_framework(
uuid=ds["uuid_acquisition_framework"], )
# get the id from the uuid
ds["id_acquisition_framework"] = new_af[
'id_acquisition_framework']
log.critical(str(new_af['id_acquisition_framework']) + ",")
ds.pop("uuid_acquisition_framework")
# get the id of the dataset to check if exists
id_dataset = TDatasets.get_id(ds["unique_dataset_id"])
ds["id_dataset"] = id_dataset
# search nomenclature
ds_copy = copy(ds)
for key, value in ds_copy.items():
if key.startswith("id_nomenclature"):
if value is not None:
ds[key] = func.ref_nomenclatures.get_id_nomenclature(
NOMENCLATURE_MAPPING.get(key), value)
else:
ds.pop(key)
# set validable = true
ds["validable"] = True
dataset = TDatasets(**ds)
# if the dataset already exist
if id_dataset:
# delete cor_ds_actor
dataset.id_dataset = id_dataset
delete_q = CorDatasetActor.__table__.delete().where(
CorDatasetActor.id_dataset == id_dataset)
DB.session.execute(delete_q)
DB.session.commit()
# create the correlation links
create_cor_object_actors(actors, dataset)
add_dataset_module(dataset)
DB.session.merge(dataset)
# its a new DS
else:
# set the dataset as activ
dataset.active = True
# create the correlation links
create_cor_object_actors(actors, dataset)
add_dataset_module(dataset)
# Add the new DS
DB.session.add(dataset)
# try to commit
try:
DB.session.commit()
# TODO catch db error ?
except SQLAlchemyError as e:
error_msg = "Error posting a dataset\nTrace:\n{} \n\n ".format(
e)
print(error_msg)
else:
print("NO USER FOUND")
else:
"NO JDD IN XML ????"
else:
print("JDD NOT FOUND")
def post_jdd_from_user(id_user=None):
""" Post a jdd from the mtd XML"""
xml_jdd = None
xml_jdd = get_jdd_by_user_id(id_user)
if xml_jdd:
dataset_list = parse_jdd_xml(xml_jdd)
posted_af_uuid = {}
for ds in dataset_list:
actors = ds.pop("actors")
# prevent to not fetch, post or merge the same acquisition framework multiple times
if ds["uuid_acquisition_framework"] not in posted_af_uuid:
new_af = post_acquisition_framework(
uuid=ds["uuid_acquisition_framework"], )
# build a cached dict like {'<uuid>': 'id_acquisition_framework}
posted_af_uuid[ds["uuid_acquisition_framework"]] = new_af[
"id_acquisition_framework"]
# get the id from the uuid
ds["id_acquisition_framework"] = posted_af_uuid.get(
ds["uuid_acquisition_framework"])
ds.pop("uuid_acquisition_framework")
# get the id of the dataset to check if exists
id_dataset = TDatasets.get_id(ds["unique_dataset_id"])
ds["id_dataset"] = id_dataset
# search nomenclature
ds_copy = copy(ds)
for key, value in ds_copy.items():
if key.startswith("id_nomenclature"):
response = DB.session.query(
func.ref_nomenclatures.get_id_nomenclature(
NOMENCLATURE_MAPPING.get(key),
value)).one_or_none()
if response and response[0]:
ds[key] = response[0]
else:
ds.pop(key)
# set validable = true
ds["validable"] = True
dataset = TDatasets(**ds)
# if the dataset already exist
if id_dataset:
# delete cor_ds_actor
dataset.id_dataset = id_dataset
delete_q = CorDatasetActor.__table__.delete().where(
CorDatasetActor.id_dataset == id_dataset)
DB.session.execute(delete_q)
DB.session.commit()
# create the correlation links
create_cor_object_actors(actors, dataset)
add_dataset_module(dataset)
DB.session.merge(dataset)
# its a new DS
else:
# set the dataset as activ
dataset.active = True
# create the correlation links
create_cor_object_actors(actors, dataset)
add_dataset_module(dataset)
# Add the new DS
DB.session.add(dataset)
# try to commit
try:
DB.session.commit()
# TODO catch db error ?
except SQLAlchemyError as e:
error_msg = "Error posting a dataset\nTrace:\n{} \n\n ".format(
e)
log.error(error_msg)
def post_jdd_from_user(id_user=None, id_organism=None):
""" Post a jdd from the mtd XML"""
xml_jdd = None
xml_jdd = get_jdd_by_user_id(id_user)
dataset_list_model = []
if xml_jdd:
dataset_list = parse_jdd_xml(xml_jdd)
posted_af_uuid = {}
for ds in dataset_list:
# prevent to not fetch, post or merge the same acquisition framework multiple times
if ds['uuid_acquisition_framework'] not in posted_af_uuid:
new_af = post_acquisition_framework(
uuid=ds['uuid_acquisition_framework'],
id_user=id_user,
id_organism=id_organism)
# build a cached dict like {'<uuid>': 'id_acquisition_framework}
posted_af_uuid[ds['uuid_acquisition_framework']] = new_af[
'id_acquisition_framework']
# get the id from the uuid
ds['id_acquisition_framework'] = posted_af_uuid.get(
ds['uuid_acquisition_framework'])
ds.pop('uuid_acquisition_framework')
# get the id of the dataset to check if exists
id_dataset = TDatasets.get_id(ds['unique_dataset_id'])
ds['id_dataset'] = id_dataset
dataset = TDatasets(**ds)
# if the dataset already exist
if id_dataset:
#check if actor exist:
actor_role = CorDatasetActor.get_actor(
id_dataset=id_dataset,
id_nomenclature_actor_role=func.ref_nomenclatures.
get_id_nomenclature('ROLE_ACTEUR', '1'),
id_role=id_user)
if actor_role is None:
actor = CorDatasetActor(
id_role=id_user,
id_nomenclature_actor_role=func.ref_nomenclatures.
get_id_nomenclature('ROLE_ACTEUR', '1'))
dataset.cor_dataset_actor.append(actor)
organism_role = None
if id_organism:
organism_role = CorDatasetActor.get_actor(
id_dataset=id_dataset,
id_nomenclature_actor_role=func.ref_nomenclatures.
get_id_nomenclature('ROLE_ACTEUR', '1'),
id_organism=id_organism)
if organism_role is None:
actor = CorDatasetActor(
id_organism=id_organism,
id_nomenclature_actor_role=func.ref_nomenclatures.
get_id_nomenclature('ROLE_ACTEUR', '1'))
dataset.cor_dataset_actor.append(actor)
# finnaly merge
DB.session.merge(dataset)
# if not dataset already in database
else:
actor = CorDatasetActor(id_role=id_user,
id_nomenclature_actor_role=func.
ref_nomenclatures.get_id_nomenclature(
'ROLE_ACTEUR', '1'))
dataset.cor_dataset_actor.append(actor)
# id_organism in cor_dataset_actor
if id_organism:
actor = CorDatasetActor(
id_organism=id_organism,
id_nomenclature_actor_role=func.ref_nomenclatures.
get_id_nomenclature('ROLE_ACTEUR', '1'))
dataset.cor_dataset_actor.append(actor)
DB.session.add(dataset)
try:
DB.session.commit()
dataset_list_model.append(dataset)
except SQLAlchemyError as e:
DB.session.commit()
DB.session.flush()
error_msg = """
Error posting JDD {} \n\n Trace: \n {}
""".format(ds['unique_dataset_id'], e)
log.error(error_msg)
raise GeonatureApiError(error_msg)
return [d.as_dict() for d in dataset_list_model]
return {'message': 'Not found'}, 404
def export_sinp(info_role):
""" Return the data (CSV) at SINP
from pr_occtax.export_occtax_sinp view
If no paramater return all the dataset allowed of the user
params:
- id_dataset : integer
- uuid_dataset: uuid
"""
viewSINP = GenericTable('export_occtax_dlb', 'pr_occtax', None)
q = DB.session.query(viewSINP.tableDef)
params = request.args
allowed_datasets = TDatasets.get_user_datasets(info_role)
# if params in empty and user not admin,
# get the data off all dataset allowed
if not params.get('id_dataset') and not params.get('uuid_dataset'):
if info_role.tag_object_code != '3':
allowed_uuid = (str(TDatasets.get_uuid(id_dataset))
for id_dataset in allowed_datasets)
q = q.filter(viewSINP.tableDef.columns.jddId.in_(allowed_uuid))
# filter by dataset id or uuid
else:
if 'id_dataset' in params:
id_dataset = int(params['id_dataset'])
uuid_dataset = TDatasets.get_uuid(id_dataset)
elif 'uuid_dataset' in params:
id_dataset = TDatasets.get_id(params['uuid_dataset'])
uuid_dataset = params['uuid_dataset']
# if data_scope 1 or 2, check if the dataset requested is allorws
if (info_role.tag_object_code == '1'
or info_role.tag_object_code == '2'):
if id_dataset not in allowed_datasets:
raise InsufficientRightsError(
('User "{}" cannot export dataset no "{}').format(
info_role.id_role, id_dataset), 403)
elif info_role.tag_object_code == '1':
# join on TCounting, TOccurrence, Treleve and corRoleOccurrence
# to get users
q = q.outerjoin(
CorCountingOccurrence, viewSINP.tableDef.columns.permId ==
CorCountingOccurrence.unique_id_sinp_occtax
).join(
TOccurrencesOccurrence,
CorCountingOccurrence.id_occurrence_occtax ==
TOccurrencesOccurrence.id_occurrence_occtax).join(
TRelevesOccurrence,
TOccurrencesOccurrence.id_releve_occtax ==
TRelevesOccurrence.id_releve_occtax).outerjoin(
corRoleRelevesOccurrence,
TRelevesOccurrence.id_releve_occtax ==
corRoleRelevesOccurrence.columns.id_releve_occtax)
q = q.filter(
or_(
corRoleRelevesOccurrence.columns.id_role ==
info_role.id_role,
TRelevesOccurrence.id_digitiser == info_role.id_role))
q = q.filter(viewSINP.tableDef.columns.jddId == str(uuid_dataset))
data = q.all()
export_columns = blueprint.config['export_columns']
file_name = datetime.datetime.now().strftime('%Y-%m-%d-%Hh%Mm%S')
return (filemanager.removeDisallowedFilenameChars(file_name),
[viewSINP.as_dict(d) for d in data], export_columns, ';')
def post_jdd_from_user(id_user=None, id_organism=None):
""" Post a jdd from the mtd XML"""
xml_jdd = None
xml_jdd = get_jdd_by_user_id(id_user)
dataset_list_model = []
if xml_jdd:
dataset_list = parse_jdd_xml(xml_jdd)
posted_af_uuid = {}
for ds in dataset_list:
# prevent to not fetch, post or merge the same acquisition framework multiple times
if ds["uuid_acquisition_framework"] not in posted_af_uuid:
new_af = post_acquisition_framework(
uuid=ds["uuid_acquisition_framework"],
id_user=id_user,
id_organism=id_organism,
)
# build a cached dict like {'<uuid>': 'id_acquisition_framework}
posted_af_uuid[ds["uuid_acquisition_framework"]] = new_af[
"id_acquisition_framework"]
# get the id from the uuid
ds["id_acquisition_framework"] = posted_af_uuid.get(
ds["uuid_acquisition_framework"])
ds.pop("uuid_acquisition_framework")
# get the id of the dataset to check if exists
id_dataset = TDatasets.get_id(ds["unique_dataset_id"])
ds["id_dataset"] = id_dataset
# search nomenclature
for key, value in ds.items():
if key.startswith("id_nomenclature"):
ds[key] = func.ref_nomenclatures.get_id_nomenclature(
NOMENCLATURE_MAPPING.get(key), value)
# set validable = true
ds["validable"] = True
dataset = TDatasets(**ds)
# if the dataset already exist
if id_dataset:
# check if actor exist:
actor_role = CorDatasetActor.get_actor(
id_dataset=id_dataset,
id_nomenclature_actor_role=func.ref_nomenclatures.
get_id_nomenclature("ROLE_ACTEUR", "1"),
id_role=id_user,
)
if actor_role is None:
actor = CorDatasetActor(
id_role=id_user,
id_nomenclature_actor_role=func.ref_nomenclatures.
get_id_nomenclature("ROLE_ACTEUR", "1"),
)
dataset.cor_dataset_actor.append(actor)
organism_role = None
if id_organism:
organism_role = CorDatasetActor.get_actor(
id_dataset=id_dataset,
id_nomenclature_actor_role=func.ref_nomenclatures.
get_id_nomenclature("ROLE_ACTEUR", "1"),
id_organism=id_organism,
)
if organism_role is None:
actor = CorDatasetActor(
id_organism=id_organism,
id_nomenclature_actor_role=func.ref_nomenclatures.
get_id_nomenclature("ROLE_ACTEUR", "1"),
)
dataset.cor_dataset_actor.append(actor)
add_dataset_module(dataset)
# finnaly merge
DB.session.merge(dataset)
# if not dataset already in database
else:
actor = CorDatasetActor(
id_role=id_user,
id_nomenclature_actor_role=func.ref_nomenclatures.
get_id_nomenclature("ROLE_ACTEUR", "1"),
)
dataset.cor_dataset_actor.append(actor)
# id_organism in cor_dataset_actor
if id_organism:
actor = CorDatasetActor(
id_organism=id_organism,
id_nomenclature_actor_role=func.ref_nomenclatures.
get_id_nomenclature("ROLE_ACTEUR", "1"),
)
dataset.cor_dataset_actor.append(actor)
add_dataset_module(dataset)
DB.session.add(dataset)
try:
DB.session.commit()
DB.session.flush()
dataset_list_model.append(dataset)
except SQLAlchemyError as e:
DB.session.rollback()
error_msg = """
Error posting JDD {} \n\n Trace: \n {}
""".format(ds["unique_dataset_id"], e)
log.error(error_msg)
raise GeonatureApiError(error_msg)
return [d.as_dict() for d in dataset_list_model]
return {"message": "Not found"}, 404
def post_jdd_from_user(id_user=None, id_organism=None):
""" Post a jdd from the mtd XML"""
xml_jdd = None
xml_jdd = get_jdd_by_user_id(id_user)
dataset_list_model = []
if xml_jdd:
dataset_list = parse_jdd_xml(xml_jdd)
posted_af_uuid = {}
for ds in dataset_list:
# prevent to not fetch, post or merge the same acquisition framework multiple times
if ds['uuid_acquisition_framework'] not in posted_af_uuid:
new_af = post_acquisition_framework(
uuid=ds['uuid_acquisition_framework'],
id_user=id_user,
id_organism=id_organism
)
# build a cached dict like {'<uuid>': 'id_acquisition_framework}
posted_af_uuid[ds['uuid_acquisition_framework']] = new_af['id_acquisition_framework']
# get the id from the uuid
ds['id_acquisition_framework'] = posted_af_uuid.get(ds['uuid_acquisition_framework'])
ds.pop('uuid_acquisition_framework')
# get the id of the dataset to check if exists
id_dataset = TDatasets.get_id(ds['unique_dataset_id'])
ds['id_dataset'] = id_dataset
dataset = TDatasets(**ds)
# if the dataset already exist
if id_dataset:
#check if actor exist:
actor_role = CorDatasetActor.get_actor(
id_dataset=id_dataset,
id_nomenclature_actor_role=func.ref_nomenclatures.get_id_nomenclature('ROLE_ACTEUR', '1'),
id_role=id_user
)
if actor_role is None:
actor = CorDatasetActor(
id_role=id_user,
id_nomenclature_actor_role=func.ref_nomenclatures.get_id_nomenclature('ROLE_ACTEUR', '1')
)
dataset.cor_dataset_actor.append(actor)
organism_role = None
if id_organism:
organism_role = CorDatasetActor.get_actor(
id_dataset=id_dataset,
id_nomenclature_actor_role=func.ref_nomenclatures.get_id_nomenclature('ROLE_ACTEUR', '1'),
id_organism=id_organism
)
if organism_role is None:
actor = CorDatasetActor(
id_organism=id_organism,
id_nomenclature_actor_role=func.ref_nomenclatures.get_id_nomenclature('ROLE_ACTEUR', '1')
)
dataset.cor_dataset_actor.append(actor)
# finnaly merge
DB.session.merge(dataset)
# if not dataset already in database
else:
actor = CorDatasetActor(
id_role=id_user,
id_nomenclature_actor_role=func.ref_nomenclatures.get_id_nomenclature('ROLE_ACTEUR', '1')
)
dataset.cor_dataset_actor.append(actor)
# id_organism in cor_dataset_actor
if id_organism:
actor = CorDatasetActor(
id_organism=id_organism,
id_nomenclature_actor_role=func.ref_nomenclatures.get_id_nomenclature('ROLE_ACTEUR', '1')
)
dataset.cor_dataset_actor.append(actor)
DB.session.add(dataset)
try:
DB.session.commit()
dataset_list_model.append(dataset)
except SQLAlchemyError as e:
DB.session.commit()
DB.session.flush()
error_msg = """
Error posting JDD {} \n\n Trace: \n {}
""".format(ds['unique_dataset_id'], e)
log.error(error_msg)
raise GeonatureApiError(error_msg)
return [d.as_dict() for d in dataset_list_model]
return {'message': 'Not found'}, 404
