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(self, act_dir):
""" saves predicates to the
Open Context database, and / or reconciles these
items with previously saved items from the same project
"""
key = self.oc_config_relation_types
json_obj = self.fm.get_dict_from_file(key, act_dir)
if json_obj is None:
print('Need to 1st generate a oc-relation-types.json from the relns.xml!')
ok = False
else:
# we have JSON with dictionary for the attributes
ok = True
self.relation_types = json_obj
for faims_id_pred, rel_dict in json_obj.items():
if not isinstance(rel_dict['oc-equiv'], str):
# No equivalence, so reconcile the relation as a new predicate
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(rel_dict['label'],
rel_dict['predicate_type'],
rel_dict['data_type'])
if pred_obj is not False:
# we reconciled the predicate!
self.relation_types[faims_id_pred]['predicate_uuid'] = str(pred_obj.uuid)
# now save the results
self.fm.save_serialized_json(key,
act_dir,
self.relation_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_predicates(self, act_dir):
""" saves predicates to the
Open Context database, and / or reconciles these
items with previously saved items from the same project
"""
key = self.oc_config_relation_types
json_obj = self.fm.get_dict_from_file(key, act_dir)
if json_obj is None:
print(
'Need to 1st generate a oc-relation-types.json from the relns.xml!'
)
ok = False
else:
# we have JSON with dictionary for the attributes
ok = True
self.relation_types = json_obj
for faims_id_pred, rel_dict in json_obj.items():
if not isinstance(rel_dict['oc-equiv'], str):
# No equivalence, so reconcile the relation as a new predicate
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(
rel_dict['label'], rel_dict['predicate_type'],
rel_dict['data_type'])
if pred_obj is not False:
# we reconciled the predicate!
self.relation_types[faims_id_pred][
'predicate_uuid'] = str(pred_obj.uuid)
# now save the results
self.fm.save_serialized_json(key, act_dir, self.relation_types)
def add_description(self):
""" validates the value's data type
if the data type differs from the
predicate data type,
add it as a note
"""
# validate the faims record against its expected data type
# the validated_record will be None if not valid
if isinstance(self.subject_uuid, str) \
and isinstance(self.subject_type, str):
# we have subject information
ok_to_add = False
data_type = self.attrib_dict['data_type']
if isinstance(self.predicate_uuid, str):
predicate_uuid = self.predicate_uuid
elif 'predicate_uuid' in self.attrib_dict:
predicate_uuid = self.attrib_dict['predicate_uuid']
object_date = None
object_uuid = None
object_num = None
object_type = data_type
if data_type == 'id':
# we're processing a controlled vocab (oc-type) object
if isinstance(self.faims_record_id, str):
if self.faims_record_id in self.attrib_dict['objects']:
# we found the object for this item
obj_dict = self.attrib_dict['objects'][
self.faims_record_id]
object_uuid = obj_dict['type_uuid']
object_type = 'types'
ok_to_add = True
elif self.faims_record is not None:
# we're processing a literal value
ddt = DescriptionDataType()
validated_record = ddt.validate_literal_by_data_type(
data_type, self.faims_record)
if validated_record is not None:
# the record is valid for the data_type
ok_to_add = True
if data_type == 'xsd:date':
object_date = validated_record
elif data_type == 'xsd:string':
# we have a string, so add it to the database and get its uuid
str_man = StringManagement()
str_man.project_uuid = self.project_uuid
str_man.source_id = self.source_id
str_obj = str_man.get_make_string(validated_record)
object_uuid = str(str_obj.uuid)
else:
# we have numeric data, so add to numeric data
object_num = validated_record
else:
# the record is not valid for the data_type, so treat it as a string
# so first we need to make a predicate for it, that is for
# string values of this associated with this attribute
object_type = 'xsd:string'
sup_dict = LastUpdatedOrderedDict()
sup_dict[self.reconcile_key] = self.attrib_dict[
'id'] # the faims attribute 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.attrib_dict[
'id'] # the faims attribute id
pred_obj = pm.get_make_predicate(
self.attrib_dict['label'] + ' [Note]',
self.attrib_dict['predicate_type'], object_type)
if pred_obj is not False:
# we have a new predicate
predicate_uuid = pred_obj.uuid
# now make an object_uuid for the original faims record
str_man = StringManagement()
str_man.project_uuid = self.project_uuid
str_man.source_id = self.source_id
str_obj = str_man.get_make_string(self.faims_record)
object_uuid = str(str_obj.uuid)
ok_to_add = True
else:
# not valid data, don't add
ok_to_add = False
if ok_to_add:
# now we're OK to add the descrpitive assertion
new_ass = Assertion()
new_ass.uuid = self.subject_uuid
new_ass.subject_type = self.subject_type
new_ass.project_uuid = self.project_uuid
new_ass.source_id = self.source_id
new_ass.obs_node = '#obs-' + str(self.obs_num)
new_ass.obs_num = self.obs_num
new_ass.sort = self.sort_num
new_ass.visibility = 1
new_ass.predicate_uuid = predicate_uuid
new_ass.object_type = object_type
if object_num is not None:
new_ass.data_num = object_num
if object_date is not None:
new_ass.data_date = object_date
if object_uuid is not None:
new_ass.object_uuid = object_uuid
try:
new_ass.save()
except:
# probably already imported
pass
def add_description(self):
""" validates the value's data type
if the data type differs from the
predicate data type,
add it as a note
"""
# validate the faims record against its expected data type
# the validated_record will be None if not valid
if isinstance(self.subject_uuid, str) \
and isinstance(self.subject_type, str):
# we have subject information
ok_to_add = False
data_type = self.attrib_dict['data_type']
if isinstance(self.predicate_uuid, str):
predicate_uuid = self.predicate_uuid
elif 'predicate_uuid' in self.attrib_dict:
predicate_uuid = self.attrib_dict['predicate_uuid']
object_date = None
object_uuid = None
object_num = None
object_type = data_type
if data_type == 'id':
# we're processing a controlled vocab (oc-type) object
if isinstance(self.faims_record_id, str):
if self.faims_record_id in self.attrib_dict['objects']:
# we found the object for this item
obj_dict = self.attrib_dict['objects'][self.faims_record_id]
object_uuid = obj_dict['type_uuid']
object_type = 'types'
ok_to_add = True
elif self.faims_record is not None:
# we're processing a literal value
ddt = DescriptionDataType()
validated_record = ddt.validate_literal_by_data_type(data_type,
self.faims_record)
if validated_record is not None:
# the record is valid for the data_type
ok_to_add = True
if data_type == 'xsd:date':
object_date = validated_record
elif data_type == 'xsd:string':
# we have a string, so add it to the database and get its uuid
str_man = StringManagement()
str_man.project_uuid = self.project_uuid
str_man.source_id = self.source_id
str_obj = str_man.get_make_string(validated_record)
object_uuid = str(str_obj.uuid)
else:
# we have numeric data, so add to numeric data
object_num = validated_record
else:
# the record is not valid for the data_type, so treat it as a string
# so first we need to make a predicate for it, that is for
# string values of this associated with this attribute
object_type = 'xsd:string'
sup_dict = LastUpdatedOrderedDict()
sup_dict[self.reconcile_key] = self.attrib_dict['id'] # the faims attribute 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.attrib_dict['id'] # the faims attribute id
pred_obj = pm.get_make_predicate(self.attrib_dict['label'] + ' [Note]',
self.attrib_dict['predicate_type'],
object_type)
if pred_obj is not False:
# we have a new predicate
predicate_uuid = pred_obj.uuid
# now make an object_uuid for the original faims record
str_man = StringManagement()
str_man.project_uuid = self.project_uuid
str_man.source_id = self.source_id
str_obj = str_man.get_make_string(self.faims_record)
object_uuid = str(str_obj.uuid)
ok_to_add = True
else:
# not valid data, don't add
ok_to_add = False
if ok_to_add:
# now we're OK to add the descrpitive assertion
new_ass = Assertion()
new_ass.uuid = self.subject_uuid
new_ass.subject_type = self.subject_type
new_ass.project_uuid = self.project_uuid
new_ass.source_id = self.source_id
new_ass.obs_node = '#obs-' + str(self.obs_num)
new_ass.obs_num = self.obs_num
new_ass.sort = self.sort_num
new_ass.visibility = 1
new_ass.predicate_uuid = predicate_uuid
new_ass.object_type = object_type
if object_num is not None:
new_ass.data_num = object_num
if object_date is not None:
new_ass.data_date = object_date
if object_uuid is not None:
new_ass.object_uuid = object_uuid
try:
new_ass.save()
except:
# probably already imported
pass
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)
