mmif.serialize module

mmif.serialize.model module

The model module contains the classes used to represent an abstract MMIF object as a live Python object.

The MmifObject class or one of its derivatives is subclassed by all other classes defined in this SDK, except for MmifObjectEncoder.

These objects are generally instantiated from JSON, either as a string or as an already-loaded Python dictionary. This base class provides the core functionality for deserializing MMIF JSON data into live objects and serializing live objects into MMIF JSON data. Specialized behavior for the different components of MMIF is added in the subclasses.

class mmif.serialize.model.DataDict(*args, **kwds)[source]

Bases: mmif.serialize.model.MmifObject, typing.Generic

get(key: str) → Optional[T][source]
items()[source]
keys()[source]
update(other, overwrite)[source]
values()[source]
class mmif.serialize.model.DataList(*args, **kwds)[source]

Bases: mmif.serialize.model.MmifObject, typing.Generic

The DataList class is an abstraction that represents the various lists found in a MMIF file, such as documents, subdocuments, views, and annotations.

Parameters

list] mmif_obj (Union[str,) – the data that the list contains

append(value, overwrite)[source]
deserialize(mmif_json: Union[str, list]) → None[source]

Passes the input data into the internal deserializer.

get(key: str) → Optional[T][source]

Standard dictionary-style get() method, albeit with no default parameter. Relies on the implementation of __getitem__.

Will return None if the key is not found.

Parameters

key – the key to search for

Returns

the value matching that key

class mmif.serialize.model.FreezableDataDict(*args, **kwds)[source]

Bases: mmif.serialize.model.FreezableMmifObject, mmif.serialize.model.DataDict

deep_freeze(*args, **kwargs) → bool[source]

Deeply freezes this FreezableMmifObject, calling deep_freeze on all FreezableMmifObjects contained as attributes or members of iterable attributes.

Note: in general, this makes no promises about the mutability of non-FreezableMmifObject state within the object. However, if all attributes and members of iterable attributes are either Freezable or hashable, this method will return True. Note that whether an object is hashable is not a contract of immutability but merely a suggestion, as anyone can implement __hash__.

Parameters

additional_containers – any names of attributes in the object that should have their contents frozen but not themselves. This is only used for FreezableDataList and FreezableDataDict classes to freeze their contents.

Returns

True if all state is either Freezable or Hashable

class mmif.serialize.model.FreezableDataList(*args, **kwds)[source]

Bases: mmif.serialize.model.FreezableMmifObject, mmif.serialize.model.DataList

deep_freeze(*args, **kwargs) → bool[source]

Deeply freezes this FreezableMmifObject, calling deep_freeze on all FreezableMmifObjects contained as attributes or members of iterable attributes.

Note: in general, this makes no promises about the mutability of non-FreezableMmifObject state within the object. However, if all attributes and members of iterable attributes are either Freezable or hashable, this method will return True. Note that whether an object is hashable is not a contract of immutability but merely a suggestion, as anyone can implement __hash__.

Parameters

additional_containers – any names of attributes in the object that should have their contents frozen but not themselves. This is only used for FreezableDataList and FreezableDataDict classes to freeze their contents.

Returns

True if all state is either Freezable or Hashable

class mmif.serialize.model.FreezableMmifObject(*args, **kwargs)[source]

Bases: mmif.serialize.model.MmifObject

deep_freeze(*additional_containers: str) → bool[source]

Deeply freezes this FreezableMmifObject, calling deep_freeze on all FreezableMmifObjects contained as attributes or members of iterable attributes.

Note: in general, this makes no promises about the mutability of non-FreezableMmifObject state within the object. However, if all attributes and members of iterable attributes are either Freezable or hashable, this method will return True. Note that whether an object is hashable is not a contract of immutability but merely a suggestion, as anyone can implement __hash__.

Parameters

additional_containers – any names of attributes in the object that should have their contents frozen but not themselves. This is only used for FreezableDataList and FreezableDataDict classes to freeze their contents.

Returns

True if all state is either Freezable or Hashable

freeze() → None[source]

Shallowly freezes this FreezableMmifObject, preventing attribute assignments with =. Makes no promises about the mutability of state within the object, only the references to that state.

Returns

asdf

is_frozen()[source]
class mmif.serialize.model.MmifObject(mmif_obj: Union[bytes, str, dict] = None)[source]

Bases: object

Abstract superclass for MMIF related key-value pair objects.

Any MMIF object can be initialized as an empty placeholder or an actual representation with a JSON formatted string or equivalent dict object argument.

This superclass has three specially designed instance variables, and these variable names cannot be used as attribute names for MMIF objects.

  1. _unnamed_attributes: Only can be either None or an empty dictionary. If it’s set to None, it means the class won’t take any Additional Attributes in the JSON schema sense. If it’s a dict, users can throw any k-v pairs to the class, EXCEPT for the reserved two key names.

  2. _attribute_classes: This is a dict from a key name to a specific python class to use for deserialize the value. Note that a key name in this dict does NOT have to be a named attribute, but is recommended to be one.

  3. _required_attributes: This is a simple list of names of attributes that are required in the object. When serialize, an object will skip its empty (e.g. zero-length, or None) attributes unless they are in this list. Otherwise, the serialized JSON string would have empty representations (e.g. "", []).

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now developers should be careful to add types to hints as well as to this dict.

Also note that those two special attributes MUST be set in the __init__() before calling super method, otherwise deserialization will not work.

And also, a subclass that has one or more named attributes, it must set those attributes in the __init__() before calling super method. When serializing a MmifObject, all empty attributes will be ignored, so for optional named attributes, you must leave leave the values empty, but NOT None. Any None-valued named attributes will cause issues with current implementation.

Parameters

mmif_obj – JSON string or dict to initialize an object. If not given, an empty object will be initialized, sometimes with an ID value automatically generated, based on its parent object.

deserialize(mmif_json: Union[str, dict]) → None[source]

Takes a JSON-formatted string or a simple dict that’s json-loaded from such a string as an input and populates object’s fields with the values specified in the input.

Parameters

mmif_json – JSON-formatted string or dict from such a string that represents a MMIF object

disallow_additional_properties() → None[source]

Call this method in __init__() to prevent the insertion of unnamed attributes after initialization.

static is_empty(obj) → bool[source]

return True if the obj is None or “emtpy”. The emptiness first defined as having zero length. But for objects that lack __len__ method, we need additional check.

reserved_names: pyrsistent._pset.PSet = pset(['_frozen', '_parent_view_id', '_attribute_classes', '_unnamed_attributes', 'reserved_names', '_required_attributes'])[source]
serialize(pretty: bool = False) → str[source]

Generates JSON representation of an object.

Parameters

pretty – If True, returns string representation with indentation.

Returns

JSON string of the object.

set_additional_property(key: str, value: Any) → None[source]

Method to set values in _unnamed_attributes.

Parameters
  • key – the attribute name

  • value – the desired value

Returns

None

Raise

AttributeError if additional properties are disallowed by disallow_additional_properties()

class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]

Bases: json.encoder.JSONEncoder

Encoder class to define behaviors of de-/serialization

default(obj: mmif.serialize.model.MmifObject)[source]

Overrides default encoding behavior to prioritize MmifObject.serialize().

mmif.serialize.mmif module

The mmif module contains the classes used to represent a full MMIF file as a live Python object.

See the specification docs and the JSON Schema file for more information.

class mmif.serialize.mmif.Mmif(mmif_obj: Union[bytes, str, dict] = None, *, validate: bool = True, frozen: bool = True)[source]

Bases: mmif.serialize.model.MmifObject

MmifObject that represents a full MMIF file.

Parameters
  • mmif_obj – the JSON data

  • validate – whether to validate the data against the MMIF JSON schema.

add_document(document: mmif.serialize.annotation.Document, overwrite=False) → None[source]

Appends a Document object to the documents list.

Fails if there is already a document with the same ID in the MMIF object.

Parameters
  • document – the Document object to add

  • overwrite – if set to True, will overwrite an existing view with the same ID

Returns

None

add_view(view: mmif.serialize.view.View, overwrite=False) → None[source]

Appends a View object to the views list.

Fails if there is already a view with the same ID in the MMIF object.

Parameters
  • view – the Document object to add

  • overwrite – if set to True, will overwrite an existing view with the same ID

Returns

None

freeze_documents() → bool[source]

Deeply freezes the list of documents. Returns the result of the deep_freeze() call, signifying whether everything was fully frozen or not.

freeze_views() → bool[source]

Deeply freezes all of the existing views without freezing the list of views itself. Returns the conjunct of the returns of all of the deep_freeze() calls, signifying whether everything was fully frozen or not.

get_alignments(at_type1: Union[str, mmif.vocabulary.thing_types.ThingTypesBase], at_type2: Union[str, mmif.vocabulary.thing_types.ThingTypesBase]) → Dict[str, List[mmif.serialize.annotation.Annotation]][source]

Finds views where alignments between two given annotation types occurred.

Returns

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

get_all_views_contain(at_types: Union[mmif.vocabulary.thing_types.ThingTypesBase, str, List[Union[str, mmif.vocabulary.thing_types.ThingTypesBase]]]) → List[mmif.serialize.view.View][source]

Returns the list of all views in the MMIF if given types are present in that view’s ‘contains’ metadata.

Parameters

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

Returns

the list of views that contain the type

get_document_by_id(doc_id: str)mmif.serialize.annotation.Document[source]

Finds a Document object with the given ID.

Parameters

doc_id – the ID to search for

Returns

a reference to the corresponding document, if it exists

Raises

Exception – if there is no corresponding document

get_document_location(m_type: Union[mmif.vocabulary.document_types.DocumentTypes, str]) → str[source]

Method to get the location of first document of given type.

Parameters

m_type – the type to search for

Returns

the value of the location field in the corresponding document

get_documents_by_app(app_id: str) → List[mmif.serialize.annotation.Document][source]

Method to get all documents object queries by its originated app name.

Parameters

app_id – the app name to search for

Returns

a list of documents matching the requested app name, or an empty list if the app not found

get_documents_by_property(prop_key: str, prop_value: str) → List[mmif.serialize.annotation.Document][source]

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

Parameters
  • prop_key – the metadata key to search for

  • prop_value – the metadata value to match

Returns

a list of documents matching the requested metadata key-value pair

get_documents_by_type(doc_type: Union[str, mmif.vocabulary.document_types.DocumentTypes]) → List[mmif.serialize.annotation.Document][source]

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

Parameters

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

Returns

a list of documents matching the requested type, or an empty list if none found.

get_documents_in_view(vid: str = None) → List[mmif.serialize.annotation.Document][source]

Method to get all documents object queries by a view id.

Parameters

vid – the source view ID to search for

Returns

a list of documents matching the requested source view ID, or an empty list if the view not found

get_documents_locations(m_type: Union[mmif.vocabulary.document_types.DocumentTypes, str]) → List[str][source]

This method returns the file paths of documents of given type. Only top-level documents have locations, so we only check them.

Parameters

m_type – the type to search for

Returns

a list of the values of the location fields in the corresponding documents

get_view_by_id(req_view_id: str)mmif.serialize.view.View[source]

Finds a View object with the given ID.

Parameters

req_view_id – the ID to search for

Returns

a reference to the corresponding view, if it exists

Raises

Exception – if there is no corresponding view

get_view_contains(at_types: Union[mmif.vocabulary.thing_types.ThingTypesBase, str, List[Union[str, mmif.vocabulary.thing_types.ThingTypesBase]]]) → Optional[mmif.serialize.view.View][source]

Returns the last view appended that contains the given types in its ‘contains’ metadata.

Parameters

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

Returns

the view, or None if the type is not found

get_views_contain(at_types: Union[mmif.vocabulary.thing_types.ThingTypesBase, str, List[Union[str, mmif.vocabulary.thing_types.ThingTypesBase]]]) → List[mmif.serialize.view.View][source]

An alias to get_all_views_contain method.

get_views_for_document(doc_id: str)[source]

Returns the list of all views that have annotations anchored on a particular document. Note that when the document is insids a view (generated during the pipeline’s running), doc_id must be prefixed with the view_id.

new_view()mmif.serialize.view.View[source]

Creates an empty view with a new ID and appends it to the views list.

Returns

a reference to the new View object

new_view_id() → str[source]

Fetches an ID for a new view.

Returns

the ID

static validate(json_str: Union[bytes, str, dict]) → None[source]

Validates a MMIF JSON object against the MMIF Schema. Note that this method operates before processing by MmifObject._load_str, so it expects @ and not _ for the JSON-LD @-keys.

Raises

jsonschema.exceptions.ValidationError – if the input fails validation

Parameters

json_str – a MMIF JSON dict or string

Returns

None

view_prefix: ClassVar[str] = 'v_'[source]

mmif.serialize.view module

The view module contains the classes used to represent a MMIF view as a live Python object.

In MMIF, views are created by apps in a pipeline that are annotating data that was previously present in the MMIF file.

class mmif.serialize.view.Contain(contain_obj: Union[bytes, str, dict] = None)[source]

Bases: mmif.serialize.model.FreezableMmifObject

Contain object that represents the metadata of a single annotation type in the contains metadata of a MMIF view.

Parameters

contain_obj – the metadata that defines this object

class mmif.serialize.view.View(view_obj: Union[bytes, str, dict] = None)[source]

Bases: mmif.serialize.model.FreezableMmifObject

View object that represents a single view in a MMIF file.

A view is identified by an ID, and contains certain metadata, a list of annotations, and potentially a JSON-LD @context IRI.

If view_obj is not provided, an empty View will be generated.

Parameters

view_obj – the JSON data that defines the view

add_annotation(annotation: mmif.serialize.annotation.Annotation, overwrite=False)mmif.serialize.annotation.Annotation[source]

Adds an annotation to the current view.

Fails if there is already an annotation with the same ID in the view, unless overwrite is set to True.

Parameters
Raises

KeyError – if overwrite is set to False and an annotation with the same ID exists in the view

Returns

the same Annotation object passed in as annotation

add_document(document: mmif.serialize.annotation.Document, overwrite=False)mmif.serialize.annotation.Annotation[source]

Appends a Document object to the annotations list.

Fails if there is already a document with the same ID in the annotations list.

Parameters
  • document – the Document object to add

  • overwrite – if set to True, will overwrite an existing view with the same ID

Returns

None

get_annotations(at_type: Union[str, mmif.vocabulary.thing_types.ThingTypesBase] = None, **properties) → Generator[mmif.serialize.annotation.Annotation, None, None][source]

Look for certain annotations in this view, specified by parameters

Parameters
  • at_type – @type of the annotations to look for. When this is None, any @type will match.

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that some annotation properties (annotation type medata) are specified in the contains view metadata

get_document_by_id(doc_id)mmif.serialize.annotation.Document[source]
get_documents()[source]
new_annotation(aid: str, at_type: Union[str, mmif.vocabulary.thing_types.ThingTypesBase], overwrite=False)mmif.serialize.annotation.Annotation[source]

Generates a new mmif.serialize.annotation.Annotation object and adds it to the current view.

Fails if there is already an annotation with the same ID in the view, unless overwrite is set to True.

Parameters
  • aid – the desired ID of the annotation

  • at_type – the desired @type of the annotation

  • overwrite – if set to True, will overwrite an existing annotation with the same ID

Raises

KeyError – if overwrite is set to False and an annotation with the same ID exists in the view

Returns

the generated mmif.serialize.annotation.Annotation

new_contain(at_type: Union[str, mmif.vocabulary.thing_types.ThingTypesBase], contain_dict: dict = None) → Optional[mmif.serialize.view.Contain][source]

Adds a new element to the contains metadata.

Parameters
  • at_type – the @type of the annotation type being added

  • contain_dict – any metadata associated with the annotation type

Returns

the generated Contain object

class mmif.serialize.view.ViewMetadata(viewmetadata_obj: Union[bytes, str, dict] = None)[source]

Bases: mmif.serialize.model.FreezableMmifObject

ViewMetadata object that represents the metadata object within a MMIF view.

Parameters

viewmetadata_obj – the JSON data that defines the metadata

new_contain(at_type: Union[str, mmif.vocabulary.thing_types.ThingTypesBase], contain_dict: dict = None) → Optional[mmif.serialize.view.Contain][source]

Adds a new element to the contains dictionary.

Parameters
  • at_type – the @type of the annotation type being added

  • contain_dict – any metadata associated with the annotation type

Returns

the generated Contain object

mmif.serialize.annotation module

The annotation module contains the classes used to represent a MMIF annotation as a live Python object.

In MMIF, annotations are created by apps in a pipeline as a part of a view. For documentation on how views are represented, see mmif.serialize.view.

class mmif.serialize.annotation.Annotation(anno_obj: Union[bytes, str, dict] = None)[source]

Bases: mmif.serialize.model.FreezableMmifObject

MmifObject that represents an annotation in a MMIF view.

add_property(name: str, value: str) → None[source]

Adds a property to the annotation’s properties. :param name: the name of the property :param value: the property’s desired value :return: None

property at_type[source]
property id[source]
is_document()[source]
is_type(type: Union[str, mmif.vocabulary.thing_types.ThingTypesBase]) → bool[source]

Check if the @type of this object matches.

class mmif.serialize.annotation.AnnotationProperties(mmif_obj: Union[bytes, str, dict] = None)[source]

Bases: mmif.serialize.model.FreezableMmifObject

AnnotationProperties object that represents the properties object within a MMIF annotation.

Parameters

mmif_obj – the JSON data that defines the properties

class mmif.serialize.annotation.Document(doc_obj: Union[bytes, str, dict] = None)[source]

Bases: mmif.serialize.annotation.Annotation

Document object that represents a single document in a MMIF file.

A document is identified by an ID, and contains certain attributes and potentially contains the contents of the document itself, metadata about how the document was created, and/or a list of subdocuments grouped together logically.

If document_obj is not provided, an empty Document will be generated.

Parameters

document_obj – the JSON data that defines the document

property location[source]
property parent[source]
class mmif.serialize.annotation.DocumentProperties(mmif_obj: Union[bytes, str, dict] = None)[source]

Bases: mmif.serialize.annotation.AnnotationProperties

DocumentProperties object that represents the properties object within a MMIF document.

Parameters

mmif_obj – the JSON data that defines the properties

property text_language[source]
property text_value[source]
class mmif.serialize.annotation.Text(text_obj: Union[bytes, str, dict] = None)[source]

Bases: mmif.serialize.model.FreezableMmifObject

property lang[source]
property value[source]