Schema

---
id: https://w3id.org/p2p_ld/nwb-schema-language
name: nwb-schema-language
title: nwb-schema-language
description: |-
  Translation of the nwb-schema-language to LinkML
license: GNU GPL v3.0
see_also:
  - https://p2p_ld.github.io/nwb-schema-language

prefixes:
  nwb_schema_language: https://w3id.org/p2p_ld/nwb-schema-language/
  linkml: https://w3id.org/linkml/
  schema: http://schema.org/

default_prefix: nwb_schema_language
default_range: string

imports:
  - linkml:types

settings:
  email: "\\S+@\\S+{\\.\\w}+"
  protected_string: "^[A-Za-z_][A-Za-z0-9_]*$"

classes:
  Namespace:
    slots:
      - doc
      - name
      - full_name
      - version
      - date
      - author
      - contact
      - schema
    slot_usage:
      name:
        required: true

  Namespaces:
    slots:
      - namespaces

  Schema:
    slots:
      - source
      - namespace
      - title
      - neurodata_types
    attributes:
      doc:
        required: false
    rules:
      - preconditions: {slot_conditions: { namespace: { value_presence: ABSENT }}}
        postconditions: {slot_conditions: { source: {required: true }}}
        description: If namespace is absent, source is required
      - preconditions: {slot_conditions: { source: { value_presence: ABSENT }}}
        postconditions: {slot_conditions: { namespace: {required: true }}}
        description: If source is absent, namespace is required.
      - preconditions: { slot_conditions: { namespace: { value_presence: PRESENT }}}
        postconditions: { slot_conditions: { source: { value_presence: ABSENT }}}
        description: If namespace is present, source is cannot be
      - preconditions: { slot_conditions: { source: { value_presence: PRESENT }}}
        postconditions: { slot_conditions: { namespace: { value_presence: ABSENT }}}
        description: If source is present, namespace cannot be.

  Group:
    slots:
      - neurodata_type_def
      - neurodata_type_inc
      - name
      - default_name
      - doc
      - quantity
      - linkable
      - attributes
      - datasets
      - groups
      - links
      - parent

  Groups:
    slots:
      - groups

  Attribute:
    mixins:
      - DtypeMixin
    slots:
      - name
      - dims
      - shape
      - value
      - default_value
      - doc
      - required
      - parent
    slot_usage:
      name:
        required: true
      parent:
        any_of:
          - range: Group
          - range: Dataset

  Link:
    slots:
      - name
      - doc
      - target_type
      - quantity

  Dataset:
    mixins:
      - DtypeMixin
    slots:
      - neurodata_type_def
      - neurodata_type_inc
      - name
      - default_name
      - dims
      - shape
      - value
      - default_value
      - doc
      - quantity
      - linkable
      - attributes
      - parent

  Datasets:
    slots:
      - datasets

  ReferenceDtype:
    slots:
      - target_type
      - reftype

  CompoundDtype:
    slots:
      - name
      - doc
      - dtype
    slot_usage:
      name:
        required: true
      dtype:
        required: true
        any_of:
          - range: ReferenceDtype
          - range: FlatDtype
        multivalued: false

  DtypeMixin:
    mixin: true
    slots:
      - dtype
    rules:
      - preconditions:
          slot_conditions:
            dtype:
              range: FlatDtype
        postconditions:
          slot_conditions:
            dtype:
              multivalued: false

  AnyType:
    class_uri: linkml:Any


slots:
  # namespaces
  doc:
    required: true
    description: Description of corresponding object.
  name:
    structured_pattern:
      syntax: "{protected_string}"
      interpolated: true
  full_name:
    description: Optional string with extended full name for the namespace.
  version:
    required: true
#    pattern: "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$"
  date:
    range: datetime
    slot_uri: schema:dateModified
    description: Date that a namespace was last modified or released
    examples:
      - value: 2017-04-25 17:14:13
  author:
    multivalued: true
    required: true
    slot_uri: schema:author
    description: List of strings with the names of the authors of the namespace.
  contact:
    multivalued: true
    required: true
    slot_uri: schema:email
    structured_pattern:
      syntax: "{email}"
      interpolated: true
    description: List of strings with the contact information for the authors. Ordering of the contacts should match the ordering of the authors.
  schema:
    multivalued: true
    range: Schema
    description: List of the schema to be included in this namespace.
    inlined_as_list: true
    alias: schema_

  # schema
  source:
    description: describes the name of the YAML (or JSON) file with the schema specification. The schema files should be located in the same folder as the namespace file.
  namespace:
    description: describes a named reference to another namespace. In contrast to source, this is a reference by name to a known namespace (i.e., the namespace is resolved during the build and must point to an already existing namespace). This mechanism is used to allow, e.g., extension of a core namespace (here the NWB core namespace) without requiring hard paths to the files describing the core namespace. Either source or namespace must be specified, but not both.
  namespaces:
    multivalued: true
    range: Namespace
    inlined_as_list: true
  neurodata_types:
    multivalued: true
    any_of:
      - range: Dataset
      - range: Group
    description: an optional list of strings indicating which data types should be included from the given specification source or namespace. The default is null indicating that all data types should be included.
  title:
    description: a descriptive title for a file for documentation purposes.

  # groups
  neurodata_type_def:
    description: Used alongside neurodata_type_inc to indicate inheritance, naming, and mixins
    structured_pattern:
      syntax: "{protected_string}"
      interpolated: true
  neurodata_type_inc:
    description: Used alongside neurodata_type_def to indicate inheritance, naming, and mixins
    structured_pattern:
      syntax: "{protected_string}"
      interpolated: true
  default_name:
    structured_pattern:
      syntax: "{protected_string}"
      interpolated: true
  quantity:
    any_of:
      - range: integer
        minimum_value: 1
      - range: QuantityEnum
    ifabsent: int(1)
    todos:
      - logic to check that the corresponding class can only be implemented quantity times.
  linkable:
    range: boolean

  # Recursive properties
  attributes:
    range: Attribute
    multivalued: true
  datasets:
    range: Dataset
    multivalued: true
    inlined_as_list: true
  groups:
    range: Group
    multivalued: true
    inlined_as_list: true
  links:
    range: Link
    multivalued: true

  # attributes
  dtype:
    any_of:
      - range: FlatDtype
      - range: CompoundDtype
      - range: ReferenceDtype
    multivalued: true
  dims:
    multivalued: true
    any_of:
      - range: string
      - range: AnyType
    todos:
      - Can't quite figure out how to allow an array of arrays - see https://github.com/linkml/linkml/issues/895
  shape:
    multivalued: true
    any_of:
      - range: integer
        minimum_value: 1
      - equals_string: "null"
        range: string
      - range: AnyType
    todos:
      - Can't quite figure out how to allow an array of arrays - see https://github.com/linkml/linkml/issues/895
  value:
    range: AnyType
    description: Optional constant, fixed value for the attribute.
  default_value:
    range: AnyType
    description: Optional default value for variable-valued attributes.
  required:
    range: boolean
    description: Optional boolean key describing whether the attribute is required. Default value is True.
    ifabsent: "true"

  # links
  target_type:
    description: Describes the neurodata_type of the target that the reference points
      to
    required: true
#    any_of:
#      - range: Dataset
#      - range: Group
  reftype:
    description: describes the kind of reference
    range: reftype_options

  # extra - not defined in nwb-schema-language but useful when working with class objects
  parent:
    description: The parent group that contains this dataset or group
    range: Group
    required: false


enums:
  reftype_options:
    permissible_values:
      ref: { description: Reference to another group or dataset of the given target_type }
      reference: { description: Reference to another group or dataset of the given target_type }
      object: { description: Reference to another group or dataset of the given target_type }
      region: { description: Reference to a region (i.e. subset) of another dataset of the given target_type}
  QuantityEnum:
    permissible_values:
      "*":
        description: Zero or more instances, equivalent to zero_or_many
      "?":
        description: Zero or one instances, equivalent to zero_or_one
      "+":
        description: One or more instances, equivalent to one_or_many
      "zero_or_many":
        description: Zero or more instances, equivalent to *
      "one_or_many":
        description: One or more instances, equivalent to +
      "zero_or_one":
        description: Zero or one instances, equivalent to ?
  FlatDtype:
    permissible_values:
      "float":
        description: single precision floating point (32 bit)
      "float32":
        description: single precision floating point (32 bit)
      "double":
        description: double precision floating point (64 bit)
      "float64":
        description: double precision floating point (64 bit)
      "long":
        description: signed 64 bit integer
      "int64":
        description: signed 64 bit integer
      "int":
        description: signed 32 bit integer
      "int32":
        description: signed 32 bit integer
      "int16":
        description: signed 16 bit integer
      "short":
        description: signed 16 bit integer
      "int8":
        description: signed 8 bit integer
      "uint":
        description: unsigned 32 bit integer
      "uint32":
        description: unsigned 32 bit integer
      "uint16":
        description: unsigned 16 bit integer
      "uint8":
        description: unsigned 8 bit integer
      "uint64":
        description: unsigned 64 bit integer
      "numeric":
        description: any numeric type (i.e., any int, uint, float)
      "text":
        description: 8-bit Unicode
      "utf":
        description: 8-bit Unicode
      "utf8":
        description: 8-bit Unicode
      "utf-8":
        description: 8-bit Unicode
      "ascii":
        description: ASCII text
      "bool":
        description: 8 bit integer with valid values 0 or 1
      "isodatetime":
        description: ISO 8601 datetime string
        examples:
          - value: 2018-09-28T14:43:54.123+02:00