omni_schema.yaml

---
id: https://w3id.org/omnibenchmark/omni-schema
name: omni-schema
title: omni-schema
description: |-
  Data model for omnibenchmark.
license: Apache Software License 2.0
see_also:
  - https://omnibenchmark.github.io/omni-schema

prefixes:
  omni_schema: https://w3id.org/omnibenchmark/omni-schema/
  linkml: https://w3id.org/linkml/
  schema: http://schema.org/
  example: https://example.org/
default_prefix: omni_schema
default_range: string

imports:
  - linkml:types

enums:
  StorageAPIEnum:
    permissible_values:
      S3:
        text: S3
  SoftwareBackendEnum:
    permissible_values:
      apptainer:
        text: apptainer
      envmodules:
        text: envmodules
      conda:
        text: conda
      docker:
        text: docker
      host:
        text: host

classes:
  IdentifiableEntity:
    abstract: true
    description: >-
      A generic grouping for any identifiable entity
    slots:
      - id
      - name
      - description
    class_uri: schema:Thing

  Benchmark:
    is_a: IdentifiableEntity
    tree_root: true
    description: >-
      A multi-stage workflow to evaluate processing stage for a specific task.
    slots:
      - version
      - benchmarker
      - software_backend
      - storage
      - storage_api
      - storage_bucket_name
      - software_environments
      - benchmark_yaml_spec
      - metric_collectors
      - stages

  Stage:
    is_a: IdentifiableEntity
    description: >-
      A benchmark subtask with equivalent and independent modules.
    slots:
      - modules
      - inputs
      - outputs

  Module:
    is_a: IdentifiableEntity
    description: >-
      A single benchmark component assigned to a specific stage.
    slots:
      - software_environment
      - repository
      - exclude
      - parameters

  IOFile:
    is_a: IdentifiableEntity
    description: >-
      Represents an input / output file.
    slots:
      - path

  InputCollection:
    description: >-
      A holder for valid input combinations.
    slots:
      - entries

  Repository:
    description: >-
      A reference to code repository containing the module's executable code.
    slots:
      - url
      - commit

  Parameter:
    description: >-
      A parameter and its scope.
    slots:
      - values

  SoftwareEnvironment:
    is_a: IdentifiableEntity
    description: >-
      Contains snapshots of the software environment required for the modules to run.
    slots:
      - easyconfig
      - envmodule
      - conda
      - apptainer

  MetricCollector:
    is_a: IdentifiableEntity
    description: >-
      Describes a module collecting/gathering multiple metrics and generating (potentially single) aggregated files collecting these metrics.
    slots:
      - software_environment
      - repository
      - inputs
      - outputs

slots:
  id:
    identifier: true
    slot_uri: schema:identifier
    range: uriorcurie
    description: A unique identifier for a thing
    required: true

  name:
    slot_uri: schema:name
    description: A human-readable name for a thing

  description:
    slot_uri: schema:description
    description: A human-readable description for a thing

  version:
    range: string
    description: The version of the benchmark.
    required: true

  benchmarker:
    range: string
    description: The name and contact details of the person responsible for this benchmark.
    required: true

  software_backend:
    range: SoftwareBackendEnum
    description: The software backend used to run the benchmark, e.g. whether apptainer, envmodules, or conda.
    required: true
    
  storage:
    range: string
    description: The place hosting all benchmark data.
    required: true

  storage_api:
    range: StorageAPIEnum
    description: The type of the storage API, i.e. S3.
    required: true
    
  storage_bucket_name:
    range: string 
    description: The name of the bucket (i.e. for S3)
    required: true

  stages:
    range: Stage
    multivalued: true
    inlined: true
    inlined_as_list: true
    required: true

  modules:
    range: Module
    multivalued: true
    inlined: true
    inlined_as_list: true
    required: true

  inputs:
    range: InputCollection
    multivalued: true
    inlined: true
    inlined_as_list: true

  outputs:
    range: IOFile
    multivalued: true
    inlined: true
    inlined_as_list: true

  exclude:
    range: Module
    multivalued: true
    description: Ignore these module's outputs as input.

  repository:
    range: Repository
    description: The code repository hosting the module.
    required: true

  parameters:
    range: Parameter
    multivalued: true

  metric_collectors:
    range: MetricCollector
    description: "Metric collecting/gathering module(s)"
    multivalued: true
    inlined: true
    inlined_as_list: true
    required: false

  software_environments:
    range: SoftwareEnvironment
    description: "Dictionary of software environments keyed by their identifiers"
    multivalued: true
    inlined: true
    inlined_as_list: true
    required: false

  software_environment:
    range: SoftwareEnvironment
    description: Reference to a software environment by key.
    required: true

  path:
    range: string
    description: The output path pattern for the IO file.

  url:
    range: string
    description: The git compatible url.
    required: true

  commit:
    range: string
    description: The commit hash.
    required: true

  values:
    range: string
    multivalued: true

  entries:
    range: IOFile
    multivalued: true

  easyconfig:
    range: string
    description: Easybuild configuration file.

  envmodule:
    range: string
    description: Environment module name.

  conda:
    range: string
    description: Conda environment file.

  apptainer:
    range: string
    description: Apptainer image static ORAS url, including name:tag.

  benchmark_yaml_spec:
    range: string
    description: Benchmark Specification version.