def db_save_reconcile_entity_predicates_types(self, act_dir):
""" saves predicates and type items to the
Open Context database, and / or reconciles these
items with previously saved items from the same project
"""
key = self.oc_config_entity_types
json_obj = self.fm.get_dict_from_file(key, act_dir)
if json_obj is None:
print('Need to 1st generate an attributes file from the ArchEnts!')
ok = False
else:
# we have JSON with dictionary for the entity_types
self.entity_types = json_obj
make_entity_types_assertions = False
for faims_ent_type_id, ent_dict in json_obj.items():
if isinstance(ent_dict['item_type'], str) \
and ent_dict['add_type_as_attribute']:
# OK we have some items that need entity types made as
# a descriptive attribute
make_entity_types_assertions = True
break
if make_entity_types_assertions:
# we have entity_types that need to have a descriptive
# predicate, so create a new predicate in Open Context
# to describe entity_types for this project
sup_dict = LastUpdatedOrderedDict()
sup_dict[self.reconcile_key] = self.ent_type_pred_sup_id
pm = PredicateManagement()
pm.project_uuid = self.project_uuid
pm.source_id = self.source_id
pm.sup_dict = sup_dict
pm.sup_reconcile_key = self.reconcile_key
pm.sup_reconcile_value = self.ent_type_pred_sup_id
pred_obj = pm.get_make_predicate(
self.FAIMS_ENTITY_TYPE_PREDICATE_LABEL, 'variable', 'id')
if pred_obj is not False:
# we reconciled or created the predicate!
# now we mint oc_types for all the entity_types
predicate_uuid = str(pred_obj.uuid)
for faims_ent_type_id, ent_dict in json_obj.items():
if isinstance(ent_dict['item_type'], str) \
and ent_dict['add_type_as_attribute']:
# OK, we have an item entity type to be used as a description
sup_dict = LastUpdatedOrderedDict()
sup_dict[self.reconcile_key] = faims_ent_type_id
tm = TypeManagement()
tm.project_uuid = self.project_uuid
tm.source_id = self.source_id
tm.sup_dict = sup_dict
tm.sup_reconcile_key = self.reconcile_key
tm.sup_reconcile_value = faims_ent_type_id
type_obj = tm.get_make_type_within_pred_uuid(
predicate_uuid, ent_dict['label'])
if type_obj is not False:
# we have reconciled the type!
ent_dict['type_uuid'] = str(type_obj.uuid)
ent_dict['predicate_uuid'] = predicate_uuid
self.entity_types[faims_ent_type_id] = ent_dict
# now save the results
self.fm.save_serialized_json(key, act_dir, self.entity_types)
def db_save_reconcile_predicates_types(self, act_dir):
""" saves predicates and type items to the
Open Context database, and / or reconciles these
items with previously saved items from the same project
"""
key = self.oc_config_attributes
json_obj = self.fm.get_dict_from_file(key, act_dir)
if json_obj is None:
print('Need to 1st generate an attributes file from the ArchEnts!')
ok = False
else:
# we have JSON with dictionary for the attributes
ok = True
self.attributes = json_obj
for faims_id_pred, attrib_dict in json_obj.items():
# default to always making a predicate and a type for attributes
sup_dict = LastUpdatedOrderedDict()
sup_dict[self.reconcile_key] = faims_id_pred
pm = PredicateManagement()
pm.project_uuid = self.project_uuid
pm.source_id = self.source_id
pm.sup_dict = sup_dict
pm.sup_reconcile_key = self.reconcile_key
pm.sup_reconcile_value = faims_id_pred
pred_obj = pm.get_make_predicate(attrib_dict['label'],
attrib_dict['predicate_type'],
attrib_dict['data_type'])
if pred_obj is not False:
# we reconciled the predicate!
self.attributes[faims_id_pred]['predicate_uuid'] = str(
pred_obj.uuid)
if 'objects' in attrib_dict:
for faims_id_type, type_dict in attrib_dict[
'objects'].items():
sup_dict = LastUpdatedOrderedDict()
sup_dict[self.reconcile_key] = faims_id_type
tm = TypeManagement()
tm.project_uuid = self.project_uuid
tm.source_id = self.source_id
tm.sup_dict = sup_dict
tm.sup_reconcile_key = self.reconcile_key
tm.sup_reconcile_value = faims_id_type
type_obj = tm.get_make_type_within_pred_uuid(
pred_obj.uuid, type_dict['label'])
if type_obj is not False:
# we have reconciled the type!
type_dict['type_uuid'] = str(type_obj.uuid)
type_dict['predicate_uuid'] = str(
pred_obj.uuid)
self.attributes[faims_id_pred]['objects'][
faims_id_type] = type_dict
# now save the results
self.fm.save_serialized_json(key, act_dir, self.attributes)
def db_save_reconcile_predicates_types(self, act_dir):
""" saves predicates and type items to the
Open Context database, and / or reconciles these
items with previously saved items from the same project
"""
key = self.oc_config_attributes
json_obj = self.fm.get_dict_from_file(key, act_dir)
if json_obj is None:
print('Need to 1st generate an attributes file from the ArchEnts!')
ok = False
else:
# we have JSON with dictionary for the attributes
ok = True
self.attributes = json_obj
for faims_id_pred, attrib_dict in json_obj.items():
# default to always making a predicate and a type for attributes
sup_dict = LastUpdatedOrderedDict()
sup_dict[self.reconcile_key] = faims_id_pred
pm = PredicateManagement()
pm.project_uuid = self.project_uuid
pm.source_id = self.source_id
pm.sup_dict = sup_dict
pm.sup_reconcile_key = self.reconcile_key
pm.sup_reconcile_value = faims_id_pred
pred_obj = pm.get_make_predicate(attrib_dict['label'],
attrib_dict['predicate_type'],
attrib_dict['data_type'])
if pred_obj is not False:
# we reconciled the predicate!
self.attributes[faims_id_pred]['predicate_uuid'] = str(pred_obj.uuid)
if 'objects' in attrib_dict:
for faims_id_type, type_dict in attrib_dict['objects'].items():
sup_dict = LastUpdatedOrderedDict()
sup_dict[self.reconcile_key] = faims_id_type
tm = TypeManagement()
tm.project_uuid = self.project_uuid
tm.source_id = self.source_id
tm.sup_dict = sup_dict
tm.sup_reconcile_key = self.reconcile_key
tm.sup_reconcile_value = faims_id_type
type_obj = tm.get_make_type_within_pred_uuid(pred_obj.uuid,
type_dict['label'])
if type_obj is not False:
# we have reconciled the type!
type_dict['type_uuid'] = str(type_obj.uuid)
type_dict['predicate_uuid'] = str(pred_obj.uuid)
self.attributes[faims_id_pred]['objects'][faims_id_type] = type_dict
# now save the results
self.fm.save_serialized_json(key,
act_dir,
self.attributes)
def db_save_reconcile_entity_predicates_types(self, act_dir):
""" saves predicates and type items to the
Open Context database, and / or reconciles these
items with previously saved items from the same project
"""
key = self.oc_config_entity_types
json_obj = self.fm.get_dict_from_file(key, act_dir)
if json_obj is None:
print('Need to 1st generate an attributes file from the ArchEnts!')
ok = False
else:
# we have JSON with dictionary for the entity_types
self.entity_types = json_obj
make_entity_types_assertions = False
for faims_ent_type_id, ent_dict in json_obj.items():
if isinstance(ent_dict['item_type'], str) \
and ent_dict['add_type_as_attribute']:
# OK we have some items that need entity types made as
# a descriptive attribute
make_entity_types_assertions = True
break
if make_entity_types_assertions:
# we have entity_types that need to have a descriptive
# predicate, so create a new predicate in Open Context
# to describe entity_types for this project
sup_dict = LastUpdatedOrderedDict()
sup_dict[self.reconcile_key] = self.ent_type_pred_sup_id
pm = PredicateManagement()
pm.project_uuid = self.project_uuid
pm.source_id = self.source_id
pm.sup_dict = sup_dict
pm.sup_reconcile_key = self.reconcile_key
pm.sup_reconcile_value = self.ent_type_pred_sup_id
pred_obj = pm.get_make_predicate(self.FAIMS_ENTITY_TYPE_PREDICATE_LABEL,
'variable',
'id')
if pred_obj is not False:
# we reconciled or created the predicate!
# now we mint oc_types for all the entity_types
predicate_uuid = str(pred_obj.uuid)
for faims_ent_type_id, ent_dict in json_obj.items():
if isinstance(ent_dict['item_type'], str) \
and ent_dict['add_type_as_attribute']:
# OK, we have an item entity type to be used as a description
sup_dict = LastUpdatedOrderedDict()
sup_dict[self.reconcile_key] = faims_ent_type_id
tm = TypeManagement()
tm.project_uuid = self.project_uuid
tm.source_id = self.source_id
tm.sup_dict = sup_dict
tm.sup_reconcile_key = self.reconcile_key
tm.sup_reconcile_value = faims_ent_type_id
type_obj = tm.get_make_type_within_pred_uuid(predicate_uuid,
ent_dict['label'])
if type_obj is not False:
# we have reconciled the type!
ent_dict['type_uuid'] = str(type_obj.uuid)
ent_dict['predicate_uuid'] = predicate_uuid
self.entity_types[faims_ent_type_id] = ent_dict
# now save the results
self.fm.save_serialized_json(key,
act_dir,
self.entity_types)
