Utils

linkml.utils.converter module

linkml.utils.datautils module

linkml.utils.datautils.get_dumper(fmt: str) → Loader

linkml.utils.datautils.get_loader(fmt: str) → Loader

linkml.utils.datautils.infer_index_slot(sv: SchemaView, root_class: ClassDefinitionName) → SlotDefinitionName | None

linkml.utils.datautils.infer_root_class(sv: SchemaView) → ClassDefinitionName | None

Infer the class that should be at the root of the object tree

(Note this is distinct from the root of the class hierarchy)

If a class is explicitly designated with tree_root, use this. Otherwise use the class that is not referenced as a range in any other class.

linkml.utils.datavalidator module

class linkml.utils.datavalidator.DataValidator(schema: str | SchemaDefinition | None = None)

Bases: object

Base class for all validators

schema: str | SchemaDefinition = None

LinkML Schema to validate against

validate_dict(data: dict, target_class: ClassDefinitionName | None = None, closed: bool = True) → None

linkml.utils.execute_tutorial module

class linkml.utils.execute_tutorial.Block(category: str = None, title: str = None, content: str = None, output: str = None, error: str = None, expected_fail: bool = None, prior_lines: List[str] = None, annotations: List[str] = None)

Bases: object

annotations: List[str] = None

category: str = None

content: str = None

error: str = None

expected_fail: bool = None

is_bash() → bool

is_file_block() → bool

is_stdout() → bool

output: str = None

prior_lines: List[str] = None

title: str = None

linkml.utils.execute_tutorial.execute_blocks(directory: str, blocks: List[Block]) → List[str]

Execute the code blocks embedded in a tutorial

Parameters:

• directory –

• blocks –

Returns:

errors

linkml.utils.execute_tutorial.parse_file_to_blocks(input) → List[Block]

Parses a markdown tutorial file to code blacks to be executed

Parameters:

input –

Returns:

linkml.utils.execute_tutorial.write_lines(lines: List[str]) → None

linkml.utils.generator module

Base class for all generators

Developer Notes

Subclasses of this class implement specific generators. Each generator is in one of two styles:

1. schemaloader-based, using a Visitor pattern (older)

2. schemaview-based, no visitor pattern (newer)

New generators should always using the latter approach

See: https://github.com/linkml/linkml/issues/923

class linkml.utils.generator.Generator(schema: str | ~typing.TextIO | ~linkml_runtime.linkml_model.meta.SchemaDefinition | ~linkml.utils.generator.Generator | ~pathlib.Path, schemaview: ~linkml_runtime.utils.schemaview.SchemaView | None = None, format: str | None = None, metadata: bool = True, useuris: bool | None = None, log_level: int | None = 30, mergeimports: bool | None = True, source_file_date: str | None = None, source_file_size: int | None = None, logger: ~logging.Logger | None = None, verbose: bool | None = None, output: str | None = None, namespaces: ~linkml_runtime.utils.namespaces.Namespaces | None = None, directory_output: bool = False, base_dir: str | None = None, metamodel_name_map: ~typing.Dict[str, str] | None = None, importmap: str | ~typing.Mapping[str, str] | None = None, emit_prefixes: ~typing.Set[str] = <factory>, metamodel: ~linkml.utils.schemaloader.SchemaLoader | None = None, stacktrace: bool = False, **_kwargs)

Bases: object

Base class for generators

For usage Generator Docs

add_id_prefixes(element: Element) → None

add_mappings(defn: Definition) → None

Process any mappings in defn, adding all of the mappings prefixes to the namespace map :param defn: Class or Slot Definition

add_prefix(ncname: str) → None

Add a prefix to the list of prefixes to emit

@param ncname: name to add

aliased_slot_name(slot: SlotDefinitionName | SlotDefinition) → SlotDefinitionName

Return the overloaded slot name – the alias if one exists otherwise the actual name

@param slot: either a slot name or a definition @return: overloaded name

all_slots(cls: ClassDefinitionName | ClassDefinition, *, cls_slots_first: bool = False, seen: Set[ClassDefinitionName] | None = None) → List[SlotDefinition]

Return all slots that are part of the class definition. This includes all is_a, mixin and apply_to slots but does NOT include slot_usage targets. If class B has a slot_usage entry for slot “s”, only the slot definition for the redefined slot will be included, not its base. Slots are added in the order they appear in classes, with recursive is_a’s being added first followed by mixins and finally apply_tos

@param cls: class definition or class definition name @param cls_slots_first: True means return own slots at the top of the list @param seen: List of slots already recorded. Used for internal recursion @return: ordered list of slots in the class with slot usages removed

ancestors(element: ClassDefinition | SlotDefinition) → List[ElementName]

Return an ordered list of ancestor names for the supplied slot or class

@param element: Slot or class name or definition @return: Ordered list of ancestor names

base_dir: str = None

Working directory or base URL of sources. Setting this is necessary for correct retrieval of relative imports.

class_identifier(def_or_name: str | ClassDefinition | TypeDefinition) → SlotDefinitionName | None

Return the class identifier if any

Parameters:

def_or_name – class name or definition

Returns:

name of class key (or identifier) if one exists

class_identifier_path(cls_or_clsname: str | ClassDefinition, force_non_key: bool) → List[str]

Return the path closure to a class identifier if the class has a key and force_non_key is false otherwise return a dictionary closure.

Parameters:

• cls_or_clsname – class definition

• force_non_key – True means inlined even if the class has a key

Returns:

path

class_or_type_for(name: str) → Element | None

Return the corresponding class or type for name

class_or_type_name(name: str) → str

Return the camelcase representation of clsname if it is a valid class or type. Prepend “Unknown” if the name isn’t valid

default_prefix() → str | None

Return the default prefix for the schema

@return: URI or NCNAME of default prefix

directory_output: bool = False

True means output is to a directory, False is to stdout

domain_slots(cls: ClassDefinition) → List[SlotDefinition]

Return all slots in the class definition that are owned by the class

emit_prefixes: Set[str]

Prefixes to emit, for RDF-based generators

end_class(cls: ClassDefinition) → str | None

Visited after visit_class_slots (if visit_class returned true)

@param cls: class being visited

end_schema(**kwargs) → str | None

Visited once at the end of generation

@param kwargs: Arguments passed through from CLI – implementation dependent

static enum_identifier_path(enum_or_enumname: str | EnumDefinition) → List[str]

Return an enum_identifier path

file_extension: ClassVar[str] = None

format: str | None = None

expected output format

formatted_element_name(el_or_elname: ElementName | Element, is_range_name: bool = False) → str | None

Return the default format for the name or the referenced element. Slots are under_scored, all others are CamelCased. Slot names are the alias, not the actual name

Parameters:

• el_or_elname – element or name to map

• is_range_name – True means that we’re looking for a class or type. False means Slot or Subset. Only applies if el_or_elname is an ElementName (otherwise we know what we’ve got

Returns:

Formatted name if type can be known else None

generatorname: ClassVar[str] = None

Name of the generator. Override with os.path.basename(__file__)

generatorversion: ClassVar[str] = None

Version of the generator. Consider deprecating and instead use overall linkml version

get_metamodel_slot_name(slot_name: str) → str

Allows for localization of some generators, such as markdown generator

The client can control how metamodel elements are displayed; e.g. mapping the metamodel slot “slot” to “field”

This method also takes care of pluralization; e.g. if “slot” is mapped to “field”, then “slots” will be mapped to “fields”

Parameters:

slot_name –

Returns:

importmap: str | Mapping[str, str] | None = None

File name of import mapping file – maps import name/uri to target

static is_class_unconstrained(cls: ClassDefinition)

Determine if the class is mapped to typing.Any, i.e the unconstrained class

Parameters:

cls – class definition

Returns:

true if the class is unconstrained

log_level: int | None = 30

Logging level, 0 is minimum

logger: Logger | None = None

Logger to use for logging messages

mergeimports: bool | None = True

True means merge non-linkml sources into importing package. False means separate packages

metadata: bool = True

True means include date, generator, etc. information in source header if appropriate

metamodel: SchemaLoader = None

A SchemaLoader instance that points to the LinkML metamodel (meta.yaml)

metamodel_name_map: Dict[str, str] = None

Allows mapping of names of metamodel elements such as slot, etc

namespaces: Namespaces | None = None

All prefix expansions used

neighborhood(elements: str | ElementName | List[ElementName]) → References

Return a list of all slots, classes and types that touch any element in elements, including the element itself

@param elements: Element names to do proximity with @return: All slots and classes that touch element

obj_for(el_or_elname: str, is_range_name: bool = False) → Element | None

output: str | None = None

Path to output file. Note all generators may not implement this uniformly, see https://github.com/linkml/linkml/issues/923

own_slot_names(cls: ClassDefinitionName | ClassDefinition) → List[SlotDefinitionName]

own_slots(cls: ClassDefinitionName | ClassDefinition) → List[SlotDefinition]

Return the list of slots owned the class definition. An “own slot” is any cls slot that does not appear in the class is_a parent. Own_slots include:

• any slot whose domain is cls

• slot_usage entries

• slots from mixins entries

• slots from apply_to entries

@param cls: class name or class definition name @return: list of owned slots. List is sorted if sort_class_slots is true, otherwise in class order

parent(element: ClassDefinition | SlotDefinition) → ClassDefinition | SlotDefinition | None

Return the parent of element, if any

range_type_path(typ: TypeDefinition) → List[str]

Return a formatted list of range types from the base up

Parameters:

typ – type definition whose name is to be formatted

Returns:

List of possible types with base at the leftmost

requires_metamodel: ClassVar[bool] = True

Generator queries an instance of the metamodel

schema: str | TextIO | SchemaDefinition | Generator | Path

metamodel compliant schema. Can be URI, file name, actual schema, another generator, an open file or a pre-parsed schema

schemaview: SchemaView | None = None

A wrapper onto the schema object

serialize(**kwargs) → str

Generate output in the required format

Parameters:

kwargs – Generator specific parameters

Returns:

Generated output

slot_for(name: str) → Element | None

slot_name(name: str) → str

Return the underscored version of the aliased slot name if name is a slot. Prepend unknown_ if the name isn’t valid.

slot_range_path(slot_or_name: str | SlotDefinition) → List[str]

Return an ordered list of slot ranges from distal to proximal

Parameters:

slot_or_name – slot whose range is being typed

Returns:

ordered list of types from base type forward

sort_class_slots: ClassVar[bool] = False

True means visit class slots in alphabetical order

Type:

Visitor ClassVar

source_file_date: str | None = None

Modification date of input source file

source_file_size: int | None = None

Size of the source file in bytes

stacktrace: bool = False

True means print stack trace, false just error message

subset_for(name: str) → Element | None

subset_name(name: str) → str

uses_schemaloader: ClassVar[bool] = True

Old-style generator that uses the SchemaLoader and visitor pattern

useuris: bool | None = None

True means declared class slot uri’s are used. False means use model uris

valid_formats: ClassVar[List[str]] = []

Allowed formats - first format is default

verbose: bool | None = None

Verbosity

visit_all_class_slots: ClassVar[bool] = False

False means only visit own slots, True means visit all slots

Type:

Visitor ClassVar

visit_class(cls: ClassDefinition) → str | bool | None

Visited once per schema class

@param cls: class being visited @return: Visit slots and end class. False means skip and go on

visit_class_slot(cls: ClassDefinition, aliased_slot_name: str, slot: SlotDefinition) → str | None

Visited for each slot in a class. If class level visit_all_slots is true, this is visited once for any class that is inherited (class itself, is_a, mixin, apply_to). Otherwise, just the own slots.

@param cls: containing class @param aliased_slot_name: Aliased slot name. May not be unique across all class slots @param slot: being visited

visit_enum(enum: EnumDefinition) → str | None

Visited once for every enum definition in the schema

@param enum: Enum definition

visit_schema(**kwargs) → str | None

Visited once at the beginning of generation

@param kwargs: Arguments passed through from CLI – implementation dependent

visit_slot(aliased_slot_name: str, slot: SlotDefinition) → str | None

Visited once for every slot definition in the schema.

@param aliased_slot_name: Aliased name of the slot. May not be unique @param slot: visited slot

visit_subset(subset: SubsetDefinition) → str | None

Visited once for every subset definition in the schema

#param subset: Subset definition

visit_type(typ: TypeDefinition) → str | None

Visited once for every type definition in the schema

@param typ: Type definition

visits_are_sorted: ClassVar[bool] = True

True means visit basic types in alphabetial order, false in entry

Type:

Visitor ClassVar

linkml.utils.generator.shared_arguments(g: Type[Generator]) → Callable[[Command], Command]

linkml.utils.helpers module

linkml.utils.helpers.convert_to_snake_case(str)

linkml.utils.helpers.remove_duplicates(lst)

Remove duplicate tuples from a list of tuples.

linkml.utils.helpers.write_to_file(file_path, data, mode='w', encoding='utf-8')

linkml.utils.ifabsent_functions module

linkml.utils.ifabsent_functions.curie_for(loader: SchemaLoader, is_class: bool) → str | None

Return the Curie for the schema in loader. Return None if there is no curie form

linkml.utils.ifabsent_functions.default_curie_or_uri(loader: SchemaLoader) → str

linkml.utils.ifabsent_functions.default_ns_for(loader: SchemaLoader, cls: ClassDefinition) → str

Return code to produce the default namespace for the supplied class

linkml.utils.ifabsent_functions.default_uri_for(loader: SchemaLoader) → str

linkml.utils.ifabsent_functions.ifabsent_postinit_declaration(txt: str, loader, cls, slot) → str | None

linkml.utils.ifabsent_functions.ifabsent_value_declaration(txt: str, loader, cls, slot) → str | None

linkml.utils.ifabsent_functions.isabsent_match(txt: str) → Tuple[Match[str], bool, Callable[[Match[str], SchemaLoader, ClassDefinition, SlotDefinition], str]] | Tuple[None, None, None]

linkml.utils.ifabsent_functions.strval(txt: str) → str

linkml.utils.ifabsent_functions.uri_for(s: str, loader: SchemaLoader) → str

linkml.utils.mergeutils module

linkml.utils.mergeutils.alias_root(schema: SchemaDefinition, slotname: SlotDefinitionName) → SlotDefinitionName | None

Return the ultimate alias of a slot

linkml.utils.mergeutils.merge_classes(schema: SchemaDefinition, target: ClassDefinition, source: ClassDefinition, at_end: bool = False) → None

Merge the slots in source into target

Parameters:

• schema – Containing schema

• target – mergee

• source – class to merge

• at_end – True means add mergee to the end. False to the front

linkml.utils.mergeutils.merge_dicts(target: Dict[str, Element], source: Dict[str, Element], imported_from: str, imported_from_uri: str, merge_imports: bool) → None

linkml.utils.mergeutils.merge_enums(schema: SchemaDefinition, target: EnumDefinition, source: EnumDefinition, at_end: bool = False) → None

Merge the slots in source into target

Parameters:

• schema – Containing schema

• target – mergee

• source – enum to merge

• at_end – True means add mergee to the end. False to the front

linkml.utils.mergeutils.merge_namespaces(target: SchemaDefinition, mergee: SchemaDefinition, namespaces) → None

Add the mergee namespace definitions to target

Parameters:

• target –

• mergee –

• namespaces –

Returns:

linkml.utils.mergeutils.merge_schemas(target: SchemaDefinition, mergee: SchemaDefinition, imported_from: str | None = None, namespaces: Namespaces | None = None, merge_imports: bool = True) → None

Merge mergee into target

linkml.utils.mergeutils.merge_slots(target: SlotDefinition | TypeDefinition, source: SlotDefinition | TypeDefinition, skip: List[SlotDefinitionName | TypeDefinitionName] | None = None, inheriting: bool = True) → None

Merge slot source into target

Parameters:

• target – slot to merge into

• source – slot to be merged from

• skip – Properties to not merge (used to prevent provenance such as ‘inherited from’ from propagating)

• inheriting – True means source is the parent. False means that everything gets copied

linkml.utils.mergeutils.set_from_schema(schema: SchemaDefinition) → None

linkml.utils.mergeutils.slot_usage_name(usage_name: SlotDefinitionName, owning_class: ClassDefinition) → SlotDefinitionName

Synthesize a unique name for an overridden slot

Parameters:

• usage_name –

• owning_class –

Returns:

Synthesized name

linkml.utils.rawloader module

linkml.utils.rawloader.load_raw_schema(data: str | dict | TextIO | Path, source_file: str | None = None, source_file_date: str | None = None, source_file_size: int | None = None, base_dir: str | None = None, merge_modules: bool | None = True, emit_metadata: bool | None = True) → SchemaDefinition

Load and flatten SchemaDefinition from a file name, a URL or a block of text

@param data: URL, file name or block of text YAML Object or open file handle @param source_file: Source file name for the schema if data is type TextIO @param source_file_date: timestamp of source file if data is type TextIO @param source_file_size: size of source file if data is type TextIO @param base_dir: Working directory or base URL of sources @param merge_modules: True means combine modules into one source, false means keep separate @param emit_metadata: True means add source file info to the output @return: Un-processed Schema Definition object

linkml.utils.rawloader.mrf(self, field_name: str) → None

linkml.utils.schemaloader module

class linkml.utils.schemaloader.SchemaLoader(data: str | TextIO | SchemaDefinition | dict | Path, base_dir: str | None = None, namespaces: Namespaces | None = None, useuris: bool | None = None, importmap: Mapping[str, str] | None = None, logger: Logger | None = None, mergeimports: bool | None = True, emit_metadata: bool | None = True, source_file_date: str | None = None, source_file_size: int | None = None)

Bases: object

check_prefix(prefix_or_curie_or_uri: str) → None

check_prefixes() → None

Iterate over the entire schema checking all prefixes

logger_warning(warning: str, loc_str: str | TypedNode | Iterator[TypedNode] | None) → None

merge_class(cls: ClassDefinition, merged_classes: List[ClassDefinitionName]) → None

Merge parent class information into target class

Parameters:

• cls – target class

• merged_classes – list of class names that have been merged. Used to do distal ancestor resolution

merge_enum(enum: EnumDefinition, merged_enums: List[EnumDefinitionName]) → None

Merge parent enumeration information into target enum

Parameters:

• enum – target enumeration

• merged_enums – list of enum names that have been merged. Used to do distal ancestor resolution

merge_slot(slot: SlotDefinition, merged_slots: List[SlotDefinitionName]) → None

Merge parent slot information into target slot

Parameters:

• slot – target slot

• merged_slots – list of slot names that have been merged. Used to do a distal ancestor resolution

merge_type(typ: TypeDefinition, merged_types: List[TypeDefinitionName]) → None

Merge parent type information into target type :param typ: target type :param merged_types: list of type names that have bee merged.

process_slot_usage_definitions()

Slot usages can be used to completely define slots. Iterate over the class hierarchy finding all slot definitions that are introduced strictly as usages and add them to the slots component

process_slot_usages(cls: ClassDefinition) → None

Connect any slot usage items

Parameters:

cls – class to process

Returns:

usage item

static raise_value_error(error: str, loc_str: TypedNode | str | None = None) → None

static raise_value_errors(error: str, loc_str: str | TypedNode | Iterator[TypedNode] | None) → None

resolve() → SchemaDefinition

Reconcile a loaded schema, applying is_a, mixins, apply_to’s and other such things. Also validate the content and load a SchemaSynopsis entry

Returns:

Fully resolved definition

schema_errors() → List[str]

slot_definition_for(slotname: SlotDefinitionName, cls: ClassDefinition) → SlotDefinition | None

Find the most proximal definition for slotname in the context of cls

static slot_name_for(slot: SlotDefinition) → str

validate_item_names(typ: str, names: List[str]) → None

linkml.utils.schemasynopsis module

class linkml.utils.schemasynopsis.SchemaSynopsis(schema: linkml_runtime.linkml_model.meta.SchemaDefinition, typerefs: Dict[linkml_runtime.linkml_model.meta.TypeDefinitionName, linkml.utils.typereferences.References] = <factory>, slotrefs: Dict[linkml_runtime.linkml_model.meta.SlotDefinitionName, linkml.utils.typereferences.References] = <factory>, classrefs: Dict[linkml_runtime.linkml_model.meta.ClassDefinitionName, linkml.utils.typereferences.References] = <factory>, subsetrefs: Dict[linkml_runtime.linkml_model.meta.SubsetDefinitionName, linkml.utils.typereferences.References] = <factory>, enumrefs: Dict[linkml_runtime.linkml_model.meta.EnumDefinitionName, linkml.utils.typereferences.References] = <factory>, typebases: Dict[str, Set[linkml_runtime.linkml_model.meta.TypeDefinitionName]] = <factory>, typeofs: Dict[linkml_runtime.linkml_model.meta.TypeDefinitionName, linkml_runtime.linkml_model.meta.TypeDefinitionName] = <factory>, slotclasses: Dict[linkml_runtime.linkml_model.meta.SlotDefinitionName, Set[linkml_runtime.linkml_model.meta.ClassDefinitionName]] = <factory>, definingslots: Dict[linkml_runtime.linkml_model.meta.SlotDefinitionName, Set[linkml_runtime.linkml_model.meta.ClassDefinitionName]] = <factory>, slotusages: Dict[linkml_runtime.linkml_model.meta.SlotDefinitionName, Set[linkml_runtime.linkml_model.meta.ClassDefinitionName]] = <factory>, owners: Dict[linkml_runtime.linkml_model.meta.SlotDefinitionName, Set[linkml_runtime.linkml_model.meta.ClassDefinitionName]] = <factory>, inverses: Dict[str, Set[str]] = <factory>, ownslots: Dict[linkml_runtime.linkml_model.meta.ClassDefinitionName, Set[linkml_runtime.linkml_model.meta.SlotDefinitionName]] = <factory>, codesets: Dict[rdflib.term.URIRef, Set[linkml_runtime.linkml_model.meta.EnumDefinitionName]] = <factory>, roots: linkml.utils.typereferences.References = <factory>, isarefs: Dict[linkml_runtime.linkml_model.meta.DefinitionName, linkml.utils.typereferences.References] = <factory>, mixinrefs: Dict[linkml_runtime.linkml_model.meta.DefinitionName, linkml.utils.typereferences.References] = <factory>, mixins: linkml.utils.typereferences.References = <factory>, abstracts: linkml.utils.typereferences.References = <factory>, applytos: linkml.utils.typereferences.References = <factory>, applytorefs: Dict[linkml_runtime.linkml_model.meta.DefinitionName, linkml.utils.typereferences.References] = <factory>, rangerefs: Dict[linkml_runtime.linkml_model.meta.ElementName, Set[linkml_runtime.linkml_model.meta.SlotDefinitionName]] = <factory>, inschema: Dict[str, linkml.utils.typereferences.References] = <factory>, **_kwargs)

Bases: object

abstracts: References

add_ref(fromtype: RefType, fromname: ElementName, totype: RefType, toname: ElementName) → None

Add an inverse reference, indicating that to type/name is referenced by from type/name

Parameters:

• fromtype – Referencer type

• fromname – Referencer name

• totype – Referencee type

• toname – Referencee name

Returns:

applytorefs: Dict[DefinitionName, References]

applytos: References

classrefs: Dict[ClassDefinitionName, References]

codesets: Dict[URIRef, Set[EnumDefinitionName]]

definingslots: Dict[SlotDefinitionName, Set[ClassDefinitionName]]

enumrefs: Dict[EnumDefinitionName, References]

errors() → List[str]

inschema: Dict[str, References]

inverses: Dict[str, Set[str]]

isarefs: Dict[DefinitionName, References]

mixinrefs: Dict[DefinitionName, References]

mixins: References

owners: Dict[SlotDefinitionName, Set[ClassDefinitionName]]

ownslots: Dict[ClassDefinitionName, Set[SlotDefinitionName]]

rangerefs: Dict[ElementName, Set[SlotDefinitionName]]

roots: References

schema: SchemaDefinition

slotclasses: Dict[SlotDefinitionName, Set[ClassDefinitionName]]

slotrefs: Dict[SlotDefinitionName, References]

slotusages: Dict[SlotDefinitionName, Set[ClassDefinitionName]]

subsetrefs: Dict[SubsetDefinitionName, References]

summarize_class_definition(k: ClassDefinitionName, v: ClassDefinition) → None

Summarize class definition element

Parameters:

• k – Class name

• v – Class definition

Returns:

summarize_definition(typ: RefType, k: DefinitionName, v: Definition) → None

Summarize slot and class definitions

Parameters:

• typ – type (slot or class)

• k – name

• v – definition

Returns:

summarize_element(typ: RefType, k: ElementName, v: Element) → None

Summarize element level items

Parameters:

• typ – element type

• k – element name

• v – element definition

Returns:

summarize_enum_definition(k: EnumDefinitionName, v: EnumDefinition)

Summarize enum definition

Parameters:

• k – Enum name

• v – Enum definition

Returns:

summarize_slot_definition(k: SlotDefinitionName, v: SlotDefinition) → None

Summarize a slot definition :param k: slot name :param v: slot definition :return:

summarize_type_definition(k: TypeDefinitionName, v: TypeDefinition)

Summarize type definition

Parameters:

• k – Type name

• v – Type definition

Returns:

summary() → str

typebases: Dict[str, Set[TypeDefinitionName]]

typeofs: Dict[TypeDefinitionName, TypeDefinitionName]

typerefs: Dict[TypeDefinitionName, References]

linkml.utils.schemasynopsis.empty_references() → field

linkml.utils.typereferences module

class linkml.utils.typereferences.RefType(name: str)

Bases: object

name: str

class linkml.utils.typereferences.References(classrefs: ~typing.Set[~linkml_runtime.linkml_model.meta.ClassDefinitionName] = <factory>, slotrefs: ~typing.Set[~linkml_runtime.linkml_model.meta.SlotDefinitionName] = <factory>, typerefs: ~typing.Set[~linkml_runtime.linkml_model.meta.TypeDefinitionName] = <factory>, subsetrefs: ~typing.Set[~linkml_runtime.linkml_model.meta.SubsetDefinitionName] = <factory>, enumrefs: ~typing.Set[~linkml_runtime.linkml_model.meta.EnumDefinitionName] = <factory>)

Bases: object

Summary of references to a given class. The reference class is the key to the dictionary carrying classrefs

addref(fromtype: RefType, fromname: ElementName) → None

classrefs: Set[ClassDefinitionName]

enumrefs: Set[EnumDefinitionName]

slotrefs: Set[SlotDefinitionName]

subsetrefs: Set[SubsetDefinitionName]

typerefs: Set[TypeDefinitionName]

update(other: References) → None

linkml.utils.validation module

linkml.utils.validation.validate_object(data: YAMLRoot, schema: str | TextIO | SchemaDefinition, target_class: Type[YAMLRoot] | None = None, closed: bool = True)

validates instance data against a schema

Parameters:

• data – LinkML instance to be validates

• schema – LinkML schema

• target_class – class in schema to validate against

• closed –

Returns:

Module contents

linkml.utils.deprecation_warning(name: str)

Call this with the name of the deprecation object wherever the deprecated functionality will be used

This function will

• emit a warning if the current version is greater than deprecated_in

• log that the deprecated feature was accessed in EMITTED for testing deprecations and muting warnings