bento_meta.mdb.mdb_tools

Imports functions from mdb_tools

Submodules

• bento_meta.mdb.mdb_tools.mdb_tools

Classes

EntityValidator	Entity validator that validate entities have all required attributes
ToolsMDB	Adds mdb-tools to WriteableMDB

Package Contents

class bento_meta.mdb.mdb_tools.EntityValidator

Entity validator that validate entities have all required attributes

required_attrs_by_entity_type: Dict[Type[bento_meta.entity.Entity], List[str]]

valid_attrs: Dict[Tuple[Type[bento_meta.entity.Entity], str], Set[str]]

exception MissingAttributeError

Bases: Exception

Raised when an entity doesn’t have the attributes required for unique identification

exception InvalidAttributeError

Bases: Exception

Raised when an entity attribute is invalid

static validate_entity_has_attribute(entity: bento_meta.entity.Entity, attr_name: str) → None

Validates the presence of an entity’s attribute

static _validate_entity_attribute(entity_type: Type[bento_meta.entity.Entity], attr_name: str) → None

Checks that an entity attribute is in a set of valid attributes

static validate_entity(entity: bento_meta.entity.Entity) → None

Checks if entity has all attributes required by MDB for its type, and that all of those attributes are valid themselves if they are entities or if they have a fixed set of possible values.

Verifies that bento-meta entity has all necesssary attributes before it is added to an MDB instance.

If looking for a unique identifier for the entity (i.e. nanoid), ensures entity has all the required attributes for unique identification.

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

Bases: bento_meta.mdb.writeable.WriteableMDB

Adds mdb-tools to WriteableMDB

exception EntityNotUniqueError

Bases: Exception

Raised when an entity’s attributes identify more than 1 property graph node in an MDB

exception EntityNotFoundError

Bases: Exception

Raised when an entity’s attributes fail to identify a property graph node in an MDB

exception PatternNotUniqueError

Bases: Exception

Raised when a match pattern’s attributes identify more than 1 property graph triple or set of overlapping triples in an MDB

exception PatternNotFoundError

Bases: Exception

Raised when a match pattern’s attributes fail to identify a property graph triple or set of overlapping triples in an MDB

_get_entity_count(entity: bento_meta.entity.Entity)

Returns count of given entity found in an MDB.

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

_get_pattern_count(pattern: minicypher.entities.T | minicypher.entities.G)

Returns count of given match pattern, which could be a triple like: (n)-[r]->(m), or a set of overlapping triples (Path) found in MDB.

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

validate_entity_unique(entity: bento_meta.entity.Entity) → None

Validates that the given entity occurs once (& only once) in an MDB

Raises EntityNotUniqueError if entity attributes match multiple property

graph nodes in the MDB.

Raises EntityNotFoundError if entity attributes don’t match any in the MDB.

Note: doesn’t validate the entity itself because not all entity attibutes

necessarily required to locate an entity in the MDB. (e.g. handle and model OR nanoid alone can identify a node)

validate_entities_unique(entities: Iterable[bento_meta.entity.Entity]) → None

Runs self.validate_entity_unique() over multiple entities

validate_pattern_unique(pattern: minicypher.entities.T | minicypher.entities.G) → None

Validates that the given match pattern occurs once (& only once) in an MDB

Raises PatternNotUniqueError if entity attributes match multiple property graph nodes in the MDB.

Raises PatternNotFoundError if entity attributes don’t match any in the MDB.

remove_entity_from_mdb(entity: bento_meta.entity.Entity)

Remove given Entity node from the database.

Accepts the following bento-meta Entities:

Concept, Node, Predicate, Property, Edge, Term

add_entity_to_mdb(entity: bento_meta.entity.Entity, _commit=None)

Adds given Entity node to MDB instance

get_concept_nanoids_linked_to_entity(entity: bento_meta.entity.Entity, mapping_source: str | None = None)

Returns list of concept nanoids linked to given entity by “represents” or “has_concept” relationships tagged with the given mapping source.

add_relationship_to_mdb(relationship_type: str, src_entity: bento_meta.entity.Entity, dst_entity: bento_meta.entity.Entity, _commit: str = '')

Adds relationship between given entities in MDB.

link_synonyms(entity_1: bento_meta.entity.Entity, entity_2: bento_meta.entity.Entity, mapping_source: str, _commit: str = '') → None

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.

Entities must both exist in the MDB instance and given entity attributes must uniquely identify property graph nodes in the MDB.

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

get_entity_nanoid(entity: bento_meta.entity.Entity)

Takes a unique entity in the MDB and returns its nanoid.

get_or_make_entity_nanoid(entity: bento_meta.entity.Entity) → str

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

get_term_nanoids(concept: bento_meta.objects.Concept, mapping_source: str = '')

Returns list of term nanoids representing given concept

get_predicate_nanoids(concept: bento_meta.objects.Concept, mapping_source: str = '')

Returns list of predicate nanoids with relationship to given concept

get_relationship_between_entities(src_entity: bento_meta.entity.Entity, dst_entity: bento_meta.entity.Entity)

Returns relationship type between given entities with (src)-[:rel_type]->(dst)

link_concepts_via_predicate(subject_concept: bento_meta.objects.Concept, object_concept: bento_meta.objects.Concept, predicate: bento_meta.objects.Predicate, _commit='') → None

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, mapping_source: str = '', _commit='') → 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()

Returns list of all terms in an MDB.

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

Returns list of dicts representing potential Term nodes synonymous to given Term in an MDB

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

link_term_synonyms_csv(term: bento_meta.objects.Term, csv_path: str, mapping_source: str, _commit: str = '') → None

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

get_property_synonyms_direct(entity: bento_meta.objects.Property, mapping_source: str = '')

Returns list of properties linked by concept to given property

_get_property_synonyms_direct_as_list(entity: bento_meta.objects.Property) → List[bento_meta.objects.Property]

Converts results of read_txn_data-wrapped function with one item to a simple list of bento_meta.objects.Property entities

get_property_synonyms_all(entity: bento_meta.objects.Property) → List[bento_meta.objects.Property]

Returns list of properties linked by concept to given property or to synonym of given property (and so on)

_get_property_parents_data(entity: bento_meta.objects.Property)

Get list of nodes/edges connected to given property via the “has_property” relationship

get_property_parents(entity: bento_meta.objects.Property) → List[bento_meta.objects.Node | bento_meta.objects.Edge]

Returns results of _get_property_parents_data as a list of bento_meta Nodes or Edges

add_tag_to_mdb_entity(tag: bento_meta.objects.Tag, entity: bento_meta.entity.Entity) → None

Adds a tag to an existing entity in an MDB.