medkit.io._common

medkit.io._common#

Attributes#

logger

Classes#

`Entity`	Text entity referencing part of an `TextDocument`.
`Relation`	Relation between two text entities.
`Segment`	Text segment referencing part of an `TextDocument`.
`TextAnnotation`	Base abstract class for all text annotations.
`TextDocument`	Document holding text annotations.

Functions#

get_anns_by_type(→ dict[str, ...)

Filter annotations by labels and return a dictionary by type of annotation.

Module Contents#

class medkit.io._common.Entity(label: str, text: str, spans: list[medkit.core.text.span.AnySpan], attrs: list[medkit.core.attribute.Attribute] | None = None, metadata: dict[str, Any] | None = None, uid: str | None = None, store: medkit.core.store.Store | None = None, attr_container_class: type[medkit.core.text.entity_attribute_container.EntityAttributeContainer] = EntityAttributeContainer)#

Bases: Segment

Text entity referencing part of an TextDocument.

Attributes:

uidstr: The entity identifier.
labelstr: The label for this entity (e.g., DISEASE)
textstr: Text of the entity.
spanslist of AnySpan: List of spans indicating which parts of the entity text correspond to which part of the document’s full text.
attrsEntityAttributeContainer: Attributes of the entity. Stored in a :class:{~medkit.core.EntityAttributeContainer} but can be passed as a list at init.
metadatadict of str to Any: The metadata of the entity
keysset of str: Pipeline output keys to which the entity belongs to.

attrs: medkit.core.text.entity_attribute_container.EntityAttributeContainer#

class medkit.io._common.Relation(label: str, source_id: str, target_id: str, attrs: list[medkit.core.attribute.Attribute] | None = None, metadata: dict[str, Any] | None = None, uid: str | None = None, store: medkit.core.store.Store | None = None, attr_container_class: type[medkit.core.attribute_container.AttributeContainer] = AttributeContainer)#

Bases: TextAnnotation

Relation between two text entities.

Attributes:

uidstr: The identifier of the relation
labelstr: The relation label
source_idstr: The identifier of the entity from which the relation is defined
target_idstr: The identifier of the entity to which the relation is defined
attrsAttributeContainer: The attributes of the relation
metadatadict of str to Any: The metadata of the relation
keysset of str: Pipeline output keys to which the relation belongs to

source_id: str#

target_id: str#

to_dict() → dict[str, Any]#

classmethod from_dict(relation_dict: dict[str, Any]) → typing_extensions.Self#

Create a Relation from a dict.

Parameters:

relation_dictdict of str to Any: A dictionary from a serialized relation as generated by to_dict()

class medkit.io._common.Segment(label: str, text: str, spans: list[medkit.core.text.span.AnySpan], attrs: list[medkit.core.attribute.Attribute] | None = None, metadata: dict[str, Any] | None = None, uid: str | None = None, store: medkit.core.store.Store | None = None, attr_container_class: type[medkit.core.attribute_container.AttributeContainer] = AttributeContainer)#

Bases: TextAnnotation

Text segment referencing part of an TextDocument.

Attributes:

uidstr: The segment identifier.
labelstr: The label for this segment (e.g., SENTENCE)
textstr: Text of the segment.
spanslist of AnySpan: List of spans indicating which parts of the segment text correspond to which part of the document’s full text.
attrsAttributeContainer: Attributes of the segment. Stored in a :class:{~medkit.core.AttributeContainer} but can be passed as a list at init.
metadatadict of str to Any: The metadata of the segment
keysset of str: Pipeline output keys to which the segment belongs to.

spans: list[medkit.core.text.span.AnySpan]#

text: str#

to_dict() → dict[str, Any]#

classmethod from_dict(segment_dict: dict[str, Any]) → typing_extensions.Self#

Create a Segment from a dict.

Parameters:

segment_dictdict of str to Any: A dictionary from a serialized segment as generated by to_dict()

class medkit.io._common.TextAnnotation(label: str, attrs: list[medkit.core.attribute.Attribute] | None = None, metadata: dict[str, Any] | None = None, uid: str | None = None, attr_container_class: type[medkit.core.attribute_container.AttributeContainer] = AttributeContainer)#

Bases: abc.ABC, medkit.core.dict_conv.SubclassMapping

Base abstract class for all text annotations.

Attributes:

uidstr: Unique identifier of the annotation.
labelstr: The label for this annotation (e.g., SENTENCE)
attrsAttributeContainer: Attributes of the annotation. Stored in a :class:{~medkit.core.AttributeContainer} but can be passed as a list at init.
metadatadict of str to Any: The metadata of the annotation
keysset of str: Pipeline output keys to which the annotation belongs to.

uid: str#

label: str#

attrs: medkit.core.attribute_container.AttributeContainer#

metadata: dict[str, Any]#

keys: set[str]#

classmethod __init_subclass__()#

classmethod from_dict(ann_dict: dict[str, Any]) → typing_extensions.Self#

abstract to_dict() → dict[str, Any]#

class medkit.io._common.TextDocument(text: str, anns: Sequence[medkit.core.text.annotation.TextAnnotation] | None = None, attrs: Sequence[medkit.core.Attribute] | None = None, metadata: dict[str, Any] | None = None, uid: str | None = None)#

Bases: medkit.core.dict_conv.SubclassMapping

Document holding text annotations.

Annotations must be subclasses of TextAnnotation.

Examples

>>> doc = TextDocument(text="hello")
>>> raw_text = doc.anns.get(label=TextDocument.RAW_LABEL)[0]

Attributes:

uidstr: Unique identifier of the document.
textstr: Full document text.
annsTextAnnotationContainer: Annotations of the document. Stored in an TextAnnotationContainer but can be passed as a list at init.
attrsAttributeContainer: Attributes of the document. Stored in an AttributeContainer but can be passed as a list at init
metadatadict of str to Any: Document metadata.
raw_segmentSegment: Auto-generated segment containing the full unprocessed document text. To get the raw text as an annotation to pass to processing operations:

RAW_LABEL: ClassVar[str] = 'RAW_TEXT'#

uid: str#

anns: medkit.core.text.annotation_container.TextAnnotationContainer#

attrs: medkit.core.AttributeContainer#

metadata: dict[str, Any]#

raw_segment: medkit.core.text.annotation.Segment#

classmethod _generate_raw_segment(text: str, doc_id: str) → medkit.core.text.annotation.Segment#

property text: str#

classmethod __init_subclass__()#

to_dict(with_anns: bool = True) → dict[str, Any]#

classmethod from_dict(doc_dict: dict[str, Any]) → typing_extensions.Self#

Create a TextDocument from a dict.

Parameters:

doc_dictdict of str to Any: A dictionary from a serialized TextDocument as generated by to_dict()

classmethod from_file(path: os.PathLike, encoding: str = 'utf-8') → typing_extensions.Self#

Create a document from a text file.

Parameters:

pathPath: Path of the text file
encodingstr, default=”utf-8”: Text encoding to use

Returns:

TextDocument: Text document with contents of path as text. The file path is included in the document metadata.

classmethod from_dir(path: os.PathLike, pattern: str = '*.txt', encoding: str = 'utf-8') → list[typing_extensions.Self]#

Create documents from text files in a directory.

Parameters:

pathPath: Path of the directory containing text files
patternstr: Glob pattern to match text files in path
encodingstr: Text encoding to use

Returns:

list of TextDocument: Text documents with contents of each file as text

get_snippet(segment: medkit.core.text.annotation.Segment, max_extend_length: int) → str#

Return a portion of the original text containing the annotation.

Parameters:

segmentSegment: The annotation
max_extend_lengthint: Maximum number of characters to use around the annotation

Returns:

str: A portion of the text around the annotation

medkit.io._common.logger#

medkit.io._common.get_anns_by_type(medkit_doc: medkit.core.text.TextDocument, anns_labels: list[str] | None = None) → dict[str, medkit.core.text.TextAnnotation]#

Filter annotations by labels and return a dictionary by type of annotation.

Parameters:

medkit_docTextDocument: Text document with annotations
anns_labelslist of str, optional: Labels to filter annotations. If not provided, all annotations will be in the dictionary

Returns:

Dict[str, TextAnnotation]: Annotations by type: ‘entities’, ‘relations’, and ‘segments’.