bento_meta.mdb.mdb_tools.mdb_tools

ToolsMDB: subclass of ‘WriteableMDB’ to support interactions with the MDB.

Module Contents

Classes

ToolsMDB

Adds mdb-tools to WriteableMDB

Functions

get_entity_type(entity)

returns type of entity

Attributes

log_ini_path

log_file_path

logger

bento_meta.mdb.mdb_tools.mdb_tools.log_ini_path
bento_meta.mdb.mdb_tools.mdb_tools.log_file_path
bento_meta.mdb.mdb_tools.mdb_tools.logger
exception bento_meta.mdb.mdb_tools.mdb_tools.EntNotFoundError

Bases: Exception

Raised when an entity is not found and shouldn’t be created

bento_meta.mdb.mdb_tools.mdb_tools.get_entity_type(entity: bento_meta.entity.Entity)

returns type of entity

class bento_meta.mdb.mdb_tools.mdb_tools.ToolsMDB(uri, user, password)

Bases: bento_meta.mdb.writeable.WriteableMDB

Adds mdb-tools to WriteableMDB

get_entity_attrs(entity: bento_meta.entity.Entity, output_str: bool = True)

Returns attributes as str or dict for given entity.

Param output_as_str parm defaults to True and returns a string that is usable in Cypher query as node properties.

If output_as_str = False, return dict of attributes instead, which is used as params of function with write_txn decorator.

detach_delete_entity(entity: bento_meta.entity.Entity) → tuple

Remove given Entity node from the database.

Accepts the following bento-meta Entities:

Concept, Node, Predicate, Property, Edge, Term

get_entity_count(entity: bento_meta.entity.Entity) → tuple

Returns count of given entity (w/ its properties) found in MDB.

If count = 0, entity with given properties not found in MDB. If count = 1, entity with given properties is unique in MDB If count > 1, more properties needed to uniquely id entity in MDB.

get_triple_count(src_entity: bento_meta.entity.Entity, dst_entity: bento_meta.entity.Entity, relationship: str) → tuple

Returns count of given triple, (src)-[rel]->(dst), found in MDB.

If count = 0, triple with given properties not found in MDB. If count = 1, triple with given properties is unique in MDB If count > 1, more properties needed to uniquely id triple in MDB.

create_entity(entity: bento_meta.entity.Entity, _commit=None) → tuple

Adds given Entity node to database

get_concepts(entity: bento_meta.entity.Entity)

Returns list of concepts represented by given entity

create_relationship(src_entity: bento_meta.entity.Entity, dst_entity: bento_meta.entity.Entity, relationship: str, _commit=None)

Adds relationship between given entities in MDB

Link two synonymous entities in the MDB via a Concept node.

This function takes two synonymous Entities (as determined by user/SME) as bento-meta objects connects them to a Concept node via a ‘represents’ relationship.

If one or both doesn’t exist in the MDB and add_missing_ent is True they will be added.

If one or both doesn’t uniquely identify a node in the MDB will give error.

If _commit is set (to a string), the _commit property of any node created is set to this value.

make_nano()

Generates valid nanoid

_get_prop_nano(prop: bento_meta.entity.Entity, node_handle: str)

Takes Property and Node entities and returns Property nanoid.

This is used to help uniquely identify a property node in the MDB, which requires a node connected via the has_property relationship.

_get_edge_nano(edge: bento_meta.entity.Entity, src_handle: str, dst_handle: str)

Takes Edge, src node handle, and dst Node handle and returns Edge nanoid.

This is used to help uniquely identify an edge node in the MDB, which requires nodes connected via the has_src and has_dst relationships.

get_entity_nano(entity: bento_meta.entity.Entity, extra_handle_1: str = '', extra_handle_2: str = '') → tuple

Takes an entity and returns its nanoid. If entity requires handles of connected nodes for unique identification (Property or Edge), extra_handle_1 and _2 hold these as str.

Note: If an entity exists in the MDB with the given properties, but doesn’t have an assigned nanoid for some reason, returns [None] instead of [].

get_or_make_nano(entity: bento_meta.entity.Entity, extra_handle_1: str = '', extra_handle_2: str = '') → str

Obtains existing entity’s nanoid or creates one for new entity.

get_term_nanos(concept: bento_meta.objects.Concept)

Returns list of term nanoids representing given concept

get_predicate_nanos(concept: bento_meta.objects.Concept)

Returns list of predicate nanoids with relationship to given concept

get_predicate_relationship(concept: bento_meta.objects.Concept, predicate: bento_meta.objects.Predicate)

Returns relationship type between given concept and predicate

Links two synonymous Concepts via a Predicate

This function takes two synonymous Concepts as objects and links them via a Predicate node and has_subject and has_object relationships.

merge_two_concepts(concept_1: bento_meta.objects.Concept, concept_2: bento_meta.objects.Concept, _commit=None) → None

Combine two synonymous Concepts into a single Concept.

This function takes two synonymous Concept as bento-meta objects and merges them into a single Concept along with any connected Terms and Predicates.

_get_all_terms()

Gets value, origin_name, and nanoid for all terms in database.

get_term_synonyms(term: bento_meta.objects.Term, threshhold: float = 0.8) → List[dict]

Returns list of dicts representing Term nodes synonymous to given Term

potential_synonyms_to_csv(input_data: List[dict], output_path: str) → None

Given a list of synonymous Terms as dicts, outputs to CSV file at given output path

Given a CSV of syonymous Terms, links each via a Concept node to given Term

get_property_synonyms(prop: bento_meta.objects.Property)

Returns list of properties linked by concept to given property or to synonym of given property