bento_meta.mdb.mdb_tools.mdb_tools

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

EntityValidator: validates that entities have required attributes.

Attributes

log_ini_path
log_file_path
logger

Classes

ToolsMDB	bento_meta.mdb.writeable.WriteableMDB subclass with mdb-tools.
EntityValidator	Class to validate that bento-meta entities have all required attributes.

Functions

_get_nlp_model()

Install and import spacy & scispacy nlp model if any not already installed.

Module Contents

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

class bento_meta.mdb.mdb_tools.mdb_tools.ToolsMDB(uri: str | None, user: str | None, password: str | None)

Bases: bento_meta.mdb.writeable.WriteableMDB

bento_meta.mdb.writeable.WriteableMDB subclass with mdb-tools.

exception EntityNotUniqueError

Bases: Exception

Entity’s attributes identify more than 1 property graph node in an MDB.

exception EntityNotFoundError

Bases: Exception

Entity’s attributes fail to identify a property graph node in an MDB.

exception PatternNotUniqueError

Bases: Exception

Match pattern’s attributes identify more than 1 triple in an MDB.

exception PatternNotFoundError

Bases: Exception

Match pattern’s attributes fail to identify a triple in an MDB.

_get_entity_count(entity: bento_meta.entity.Entity) → list[neo4j.Record]

Return 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.

Parameters:

entity – The entity to count.

Returns:

List with count value.

_get_pattern_count(pattern: minicypher.entities.T | minicypher.entities.G) → list[neo4j.Record]

Return count of given match pattern (triple or path) found in an MDB.

Property graph triple: (n)-[r]->(m) Path: set of overlapping triples

• 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.

Parameters:

pattern – The pattern (triple or path) to count.

Returns:

List with count value.

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

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

Note: doesn’t validate the entity itself because not all entity attributes are necessarily required to locate an entity in the MDB. (e.g. handle and model OR nanoid alone can identify a node)

Parameters:

entity – The entity to validate.

Raises:

• EntityNotUniqueError – If entity attributes match multiple property graph nodes in the MDB.

• EntityNotFoundError – If entity attributes don’t match any in the MDB.

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

Run self.validate_entity_unique() over multiple entities.

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

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

Parameters:

pattern – The pattern to validate.

Raises:

• PatternNotUniqueError – If pattern attributes match multiple triples in the MDB.

• PatternNotFoundError – If pattern attributes don’t match any in the MDB.

remove_entity_from_mdb(entity: bento_meta.entity.Entity) → list[neo4j.Record]

Remove given Entity node from the database.

Accepts the following bento-meta Entities:

Concept, Node, Predicate, Property, Edge, Term

Parameters:

entity – The entity to remove.

Returns:

List of Records from the transaction.

add_entity_to_mdb(entity: bento_meta.entity.Entity, _commit: str | None = None) → list[neo4j.Record]

Add given Entity node to MDB instance.

Parameters:

• entity – The entity to add.

• _commit – Optional commit string to tag the entity.

Returns:

List of Records from the transaction.

get_concept_nanoids_linked_to_entity(entity: bento_meta.entity.Entity, mapping_source: str | None = None) → list[neo4j.Record]

Return list of concept nanoids linked to given entity.

The concept(s) have “represents” or “has_concept” relationships tagged with the given mapping source. If no mapping source is provided, return all.

Parameters:

• entity – The entity to get concepts for.

• mapping_source – Optional mapping source to filter by.

Returns:

List of concept nanoids.

add_relationship_to_mdb(relationship_type: str, src_entity: bento_meta.entity.Entity, dst_entity: bento_meta.entity.Entity, _commit: str = '') → list[neo4j.Record]

Add relationship between given entities in MDB.

Parameters:

• relationship_type – The type of relationship to create.

• src_entity – Source entity for the relationship.

• dst_entity – Destination entity for the relationship.

• _commit – Optional commit string to tag the relationship.

Returns:

List of Records from the transaction.

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.

Takes two synonymous Entities (as determined by user/SME) as bento-meta objects and 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.

Parameters:

• entity_1 – First entity to link.

• entity_2 – Second entity to link.

• mapping_source – Source of the mapping relationship.

• _commit – Optional commit string. If set, the _commit property of any node created is set to this value.

get_entity_nanoid(entity: bento_meta.entity.Entity) → list[neo4j.Record]

Take a unique entity in the MDB and return its nanoid.

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

Obtain existing entity’s nanoid or create one for new entity.

get_term_nanoids(concept: bento_meta.objects.Concept, mapping_source: str = '') → list[neo4j.Record]

Return list of term nanoids representing given concept.

get_predicate_nanoids(concept: bento_meta.objects.Concept, mapping_source: str = '') → list[neo4j.Record]

Return 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) → list[neo4j.Record]

Return relationship type between given entities.

Relationship pattern: (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: str = '') → None

Link two synonymous Concepts via a Predicate.

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

Parameters:

• subject_concept – The subject concept.

• object_concept – The object concept.

• predicate – The predicate linking them.

• _commit – Optional commit string to tag created nodes.

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

Combine two synonymous Concepts into a single Concept.

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

Parameters:

• concept_1 – First concept (will remain after merge).

• concept_2 – Second concept (will be deleted after merge).

• mapping_source – Source of the mapping relationship.

• _commit – Optional commit string to tag relationships.

_get_all_terms() → list[neo4j.Record]

Return list of all terms in an MDB.

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

Return list of dicts representing potential synonymous Term nodes.

Parameters:

• term – The term to find synonyms for.

• threshhold – Similarity threshold (0-1) for considering terms synonymous.

Returns:

List of dicts with value, origin_name, nanoid, similarity, valid_synonym.

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

Write CSV with list of synonymous Terms as dicts to given output path.

Parameters:

• input_data – List of dicts representing potential synonyms.

• output_path – Path to write CSV file to.

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

Link Terms in a CSV of synonymous Terms to given Term via a Concept node.

Parameters:

• term – The term to link synonyms to.

• csv_path – Path to CSV file containing potential synonyms.

• mapping_source – Source of the mapping relationship.

• _commit – Optional commit string to tag relationships.

get_property_synonyms_direct(entity: bento_meta.objects.Property, mapping_source: str = '') → list[neo4j.Record]

Return list of properties linked by concept to given property.

Parameters:

• entity – The property to get synonyms for.

• mapping_source – Optional mapping source to filter by.

Returns:

List of Records with property synonyms.

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

Convert results of read_txn_data-wrapped function with one Property to a list.

Parameters:

entity – The property to get synonyms for.

Returns:

List of bento_meta.objects.Property entities.

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

Return list of properties linked by concept to given property or its synonyms.

Chains through synonyms of given property (and so on).

Parameters:

entity – The property to get all synonyms for.

Returns:

List of Property entities that are synonyms.

_get_property_parents_data(entity: bento_meta.objects.Property) → list[neo4j.Record]

Get list of nodes/edges connected to given property.

Parents are Nodes or Edges via the “has_property” relationship.

Parameters:

entity – The property to get parents for.

Returns:

List of Records with nodes and edges.

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

Get parents of a property as a list of bento_meta Nodes or Edges.

Parameters:

entity – The property to get parents for.

Returns:

List of Node or Edge entities.

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

Add a tag to an existing entity in an MDB.

Parameters:

• tag – The tag to add.

• entity – The entity to tag.

class bento_meta.mdb.mdb_tools.mdb_tools.EntityValidator

Class to validate that bento-meta entities have all required attributes.

required_attrs_by_entity_type: ClassVar[dict[type[bento_meta.entity.Entity], list[str]]]

valid_attrs: ClassVar[dict[tuple[type[bento_meta.entity.Entity], str], set[str]]]

exception MissingAttributeError

Bases: Exception

An entity doesn’t have the attributes required for unique identification.

exception InvalidAttributeError

Bases: Exception

An entity attribute is invalid.

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

Validate the presence of an entity’s attribute.

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

Check that an entity attribute is in a set of valid attributes.

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

Check if entity has all attributes required by MDB for its type.

Also checks validates all of those attributes are valid themselves if they are entities or if they have a fixed set of possible values.

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

Parameters:

entity – The entity to validate.

Raises:

• ValueError – If entity type not supported.

• MissingAttributeError – If required attribute missing.

• InvalidAttributeError – If attribute value invalid.

bento_meta.mdb.mdb_tools.mdb_tools._get_nlp_model()

Install and import spacy & scispacy nlp model if any not already installed.