medkit.io._brat_utils ===================== .. py:module:: medkit.io._brat_utils Attributes ---------- .. autoapisummary:: medkit.io._brat_utils.GROUPING_ENTITIES medkit.io._brat_utils.GROUPING_RELATIONS medkit.io._brat_utils.logger Classes ------- .. autoapisummary:: medkit.io._brat_utils.BratEntity medkit.io._brat_utils.BratRelation medkit.io._brat_utils.BratAttribute medkit.io._brat_utils.BratNote medkit.io._brat_utils.Grouping medkit.io._brat_utils.BratAugmentedEntity medkit.io._brat_utils.BratDocument medkit.io._brat_utils.RelationConf medkit.io._brat_utils.AttributeConf medkit.io._brat_utils.BratAnnConfiguration Functions --------- .. autoapisummary:: medkit.io._brat_utils.ensure_attr_value medkit.io._brat_utils.parse_file medkit.io._brat_utils.parse_string medkit.io._brat_utils._parse_entity medkit.io._brat_utils._parse_relation medkit.io._brat_utils._parse_attribute medkit.io._brat_utils._parse_note Module Contents --------------- .. py:data:: GROUPING_ENTITIES .. py:data:: GROUPING_RELATIONS .. py:data:: logger .. py:class:: BratEntity A simple entity annotation data structure. .. !! processed by numpydoc !! .. py:attribute:: uid :type: str .. py:attribute:: type :type: str .. py:attribute:: span :type: list[tuple[int, int]] .. py:attribute:: text :type: str .. py:property:: start :type: int .. py:property:: end :type: int .. py:method:: to_str() -> str .. py:class:: BratRelation A simple relation data structure. .. !! processed by numpydoc !! .. py:attribute:: uid :type: str .. py:attribute:: type :type: str .. py:attribute:: subj :type: str .. py:attribute:: obj :type: str .. py:method:: to_str() -> str .. py:class:: BratAttribute A simple attribute data structure. .. !! processed by numpydoc !! .. py:attribute:: uid :type: str .. py:attribute:: type :type: str .. py:attribute:: target :type: str .. py:attribute:: value :type: str :value: None .. py:method:: to_str() -> str .. py:class:: BratNote A simple note data structure. .. !! processed by numpydoc !! .. py:attribute:: uid :type: str .. py:attribute:: target :type: str .. py:attribute:: value :type: str .. py:attribute:: type :type: str :value: 'AnnotatorNotes' .. py:method:: to_str() -> str .. py:function:: ensure_attr_value(attr_value: Any) -> str Ensure that the attribue value is a string. .. !! processed by numpydoc !! .. py:class:: Grouping A grouping data structure for entities of type And-Group and Or-Group. .. !! processed by numpydoc !! .. py:attribute:: uid :type: str .. py:attribute:: type :type: str .. py:attribute:: items :type: list[BratEntity] .. py:property:: text .. py:class:: BratAugmentedEntity An augmented entity data structure with its relations and attributes. .. !! processed by numpydoc !! .. py:attribute:: uid :type: str .. py:attribute:: type :type: str .. py:attribute:: span :type: tuple[tuple[int, int], Ellipsis] .. py:attribute:: text :type: str .. py:attribute:: relations_from_me :type: tuple[BratRelation, Ellipsis] .. py:attribute:: relations_to_me :type: tuple[BratRelation, Ellipsis] .. py:attribute:: attributes :type: tuple[BratAttribute, Ellipsis] .. py:property:: start :type: int .. py:property:: end :type: int .. py:class:: BratDocument .. py:attribute:: entities :type: dict[str, BratEntity] .. py:attribute:: relations :type: dict[str, BratRelation] .. py:attribute:: attributes :type: dict[str, BratAttribute] .. py:attribute:: notes :type: dict[str, BratNote] .. py:attribute:: groups :type: dict[str, Grouping] :value: None .. py:method:: get_augmented_entities() -> dict[str, BratAugmentedEntity] .. py:class:: RelationConf Bases: :py:obj:`NamedTuple` Configuration data structure of a BratRelation. .. !! processed by numpydoc !! .. py:attribute:: type :type: str .. py:attribute:: arg1 :type: str .. py:attribute:: arg2 :type: str .. py:class:: AttributeConf Bases: :py:obj:`NamedTuple` Configuration data structure of a BratAttribure. .. !! processed by numpydoc !! .. py:attribute:: from_entity :type: bool .. py:attribute:: type :type: str .. py:attribute:: value :type: str .. py:class:: BratAnnConfiguration(top_values_by_attr: int = 50) A data structure to represent 'annotation.conf' in brat documents. This is necessary to generate a valid annotation project in brat. An 'annotation.conf' has four sections. The section 'events' is not supported in medkit, so the section is empty. .. !! processed by numpydoc !! .. py:attribute:: _entity_types :type: set[str] .. py:attribute:: _rel_types_arg_1 :type: dict[str, set[str]] .. py:attribute:: _rel_types_arg_2 :type: dict[str, set[str]] .. py:attribute:: _attr_entity_values :type: dict[str, list[str]] .. py:attribute:: _attr_relation_values :type: dict[str, list[str]] .. py:attribute:: top_values_by_attr :value: 50 .. py:property:: entity_types :type: list[str] .. py:property:: rel_types_arg_1 :type: dict[str, list[str]] .. py:property:: rel_types_arg_2 :type: dict[str, list[str]] .. py:property:: attr_relation_values :type: dict[str, list[str]] .. py:property:: attr_entity_values :type: dict[str, list[str]] .. py:method:: add_entity_type(type: str) .. py:method:: add_relation_type(relation_conf: RelationConf) .. py:method:: add_attribute_type(attr_conf: AttributeConf) .. py:method:: to_str() -> str .. py:method:: _attribute_to_str(type: str, values: list[str], from_entity: bool) -> str :staticmethod: .. py:method:: _relation_to_str(type: str, arg_1_types: list[str], arg_2_types: list[str]) -> str :staticmethod: .. py:function:: parse_file(ann_path: str | pathlib.Path, detect_groups: bool = False) -> BratDocument Read an annotation file to get the Entities, Relations and Attributes in it. All other lines are ignored. :Parameters: **ann_path** : str or Path The path to the annotation file to be processed. **detect_groups** : bool, default=False If set to True, the function will also parse the group of entities according to some specific keywords. By default, it is set to False. :Returns: Document The dataclass object containing entities, relations and attributes .. !! processed by numpydoc !! .. py:function:: parse_string(ann_string: str, detect_groups: bool = False) -> BratDocument Read a string containing all annotations and extract Entities, Relations and Attributes. All other lines are ignored. :Parameters: **ann_string** : str The string containing all brat annotations **detect_groups** : bool, default=False If set to True, the function will also parse the group of entities according to some specific keywords. By default, it is set to False. :Returns: Document The dataclass object containing entities, relations and attributes .. !! processed by numpydoc !! .. py:function:: _parse_entity(entity_id: str, entity_content: str) -> BratEntity Parse the brat entity string into an Entity structure. :Parameters: **entity_id** : str The ID defined in the brat annotation (e.g., 'T12') **entity_content** : str The string content for this ID to parse (e.g., 'Temporal-Modifier 116 126\thistory of') :Returns: BratEntity The dataclass object representing the entity :Raises: ValueError Raises when the entity can't be parsed .. !! processed by numpydoc !! .. py:function:: _parse_relation(relation_id: str, relation_content: str) -> BratRelation Parse the annotation string into a Relation structure. :Parameters: **relation_id** : str The ID defined in the brat annotation (e.g., 'R12') **relation_content** : str The relation text content. (e.g., 'Modified-By Arg1:T8 Arg2:T6\t') :Returns: BratRelation The dataclass object representing the relation :Raises: ValueError Raises when the relation can't be parsed .. !! processed by numpydoc !! .. py:function:: _parse_attribute(attribute_id: str, attribute_content: str) -> BratAttribute Parse the annotation string into an Attribute structure. :Parameters: **attribute_id** : str The attribute ID defined in the annotation. (e.g., 'A1') **attribute_content** : str The attribute text content. (e.g., 'Tense T19 Past-Ended') :Returns: BratAttribute The dataclass object representing the attribute :Raises: ValueError Raises when the attribute can't be parsed .. !! processed by numpydoc !! .. py:function:: _parse_note(note_id: str, note_content: str) -> BratNote Parse the annotation string into an Note structure. :Parameters: **note_id** : str The note ID defined in the annotation. (e.g., '#1') **note_content** : str The note text content. (e.g., 'AnnotatorNotes T10 C0011849') :Returns: BratNote The dataclass object representing the note :Raises: ValueError Raises when the note can't be parsed .. !! processed by numpydoc !!