Process.yml

$base: "https://w3id.org/cwl/cwl#"

$namespaces:
  cwl: "https://w3id.org/cwl/cwl#"
  sld: "https://w3id.org/cwl/salad#"
  rdfs: "http://www.w3.org/2000/01/rdf-schema#"

$graph:

- name: "Common Workflow Language, v1.1.0-dev1"
  type: documentation
  doc: {$include: concepts.md}

- $import: "salad/schema_salad/metaschema/metaschema_base.yml"

- name: BaseTypesDoc
  type: documentation
  doc: |
    ## Base types
  docChild:
    - "#CWLType"
    - "#Process"

- type: enum
  name: CWLVersion
  doc: "Version symbols for published CWL document versions."
  symbols:
    - cwl:draft-2
    - cwl:draft-3.dev1
    - cwl:draft-3.dev2
    - cwl:draft-3.dev3
    - cwl:draft-3.dev4
    - cwl:draft-3.dev5
    - cwl:draft-3
    - cwl:draft-4.dev1
    - cwl:draft-4.dev2
    - cwl:draft-4.dev3
    - cwl:v1.0.dev4
    - cwl:v1.0
    - cwl:v1.1.0-dev1 # a dash is required by the semver 2.0 rules

- name: CWLType
  type: enum
  extends: "sld:PrimitiveType"
  symbols:
    - cwl:File
    - cwl:Directory
  doc:
    - "Extends primitive types with the concept of a file and directory as a builtin type."
    - "File: A File object"
    - "Directory: A Directory object"

- name: File
  type: record
  docParent: "#CWLType"
  doc: |
    Represents a file (or group of files if `secondaryFiles` is specified) that
    must be accessible by tools using standard POSIX file system call API such as
    open(2) and read(2).
  fields:
    - name: class
      type:
        type: enum
        name: File_class
        symbols:
          - cwl:File
      jsonldPredicate:
        _id: "@type"
        _type: "@vocab"
      doc: Must be `File` to indicate this object describes a file.
    - name: location
      type: string?
      doc: |
        An IRI that identifies the file resource.  This may be a relative
        reference, in which case it must be resolved using the base IRI of the
        document.  The location may refer to a local or remote resource; the
        implementation must use the IRI to retrieve file content.  If an
        implementation is unable to retrieve the file content stored at a
        remote resource (due to unsupported protocol, access denied, or other
        issue) it must signal an error.

        If the `location` field is not provided, the `contents` field must be
        provided.  The implementation must assign a unique identifier for
        the `location` field.

        If the `path` field is provided but the `location` field is not, an
        implementation may assign the value of the `path` field to `location`,
        then follow the rules above.
      jsonldPredicate:
        _id: "@id"
        _type: "@id"
    - name: path
      type: string?
      doc: |
        The local host path where the File is available when a CommandLineTool is
        executed.  This field must be set by the implementation.  The final
        path component must match the value of `basename`.  This field
        must not be used in any other context.  The command line tool being
        executed must be able to to access the file at `path` using the POSIX
        `open(2)` syscall.

        As a special case, if the `path` field is provided but the `location`
        field is not, an implementation may assign the value of the `path`
        field to `location`, and remove the `path` field.

        If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
        (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
        `<space>`, `<tab>`, and `<newline>`) or characters
        [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
        for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
        then implementations may terminate the process with a
        `permanentFailure`.
      jsonldPredicate:
        "_id": "cwl:path"
        "_type": "@id"
    - name: basename
      type: string?
      doc: |
        The base name of the file, that is, the name of the file without any
        leading directory path.  The base name must not contain a slash `/`.

        If not provided, the implementation must set this field based on the
        `location` field by taking the final path component after parsing
        `location` as an IRI.  If `basename` is provided, it is not required to
        match the value from `location`.

        When this file is made available to a CommandLineTool, it must be named
        with `basename`, i.e. the final component of the `path` field must match
        `basename`.
      jsonldPredicate: "cwl:basename"
    - name: dirname
      type: string?
      doc: |
        The name of the directory containing file, that is, the path leading up
        to the final slash in the path such that `dirname + '/' + basename ==
        path`.

        The implementation must set this field based on the value of `path`
        prior to evaluating parameter references or expressions in a
        CommandLineTool document.  This field must not be used in any other
        context.
    - name: nameroot
      type: string?
      doc: |
        The basename root such that `nameroot + nameext == basename`, and
        `nameext` is empty or begins with a period and contains at most one
        period.  For the purposess of path splitting leading periods on the
        basename are ignored; a basename of `.cshrc` will have a nameroot of
        `.cshrc`.

        The implementation must set this field automatically based on the value
        of `basename` prior to evaluating parameter references or expressions.
    - name: nameext
      type: string?
      doc: |
        The basename extension such that `nameroot + nameext == basename`, and
        `nameext` is empty or begins with a period and contains at most one
        period.  Leading periods on the basename are ignored; a basename of
        `.cshrc` will have an empty `nameext`.

        The implementation must set this field automatically based on the value
        of `basename` prior to evaluating parameter references or expressions.
    - name: checksum
      type: string?
      doc: |
        Optional hash code for validating file integrity.  Currently must be in the form
        "sha1$ + hexadecimal string" using the SHA-1 algorithm.
    - name: size
      type: long?
      doc: Optional file size
    - name: "secondaryFiles"
      type:
        - "null"
        - type: array
          items: [File, Directory]
      jsonldPredicate: "cwl:secondaryFiles"
      doc: |
        A list of additional files that are associated with the primary file
        and must be transferred alongside the primary file.  Examples include
        indexes of the primary file, or external references which must be
        included when loading primary document.  A file object listed in
        `secondaryFiles` may itself include `secondaryFiles` for which the same
        rules apply.
    - name: format
      type: string?
      jsonldPredicate:
        _id: cwl:format
        _type: "@id"
        identity: true
      doc: |
        The format of the file: this must be an IRI of a concept node that
        represents the file format, preferrably defined within an ontology.
        If no ontology is available, file formats may be tested by exact match.

        Reasoning about format compatability must be done by checking that an
        input file format is the same, `owl:equivalentClass` or
        `rdfs:subClassOf` the format required by the input parameter.
        `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if
        `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer
        `<C> owl:subclassOf <A>`.

        File format ontologies may be provided in the "$schema" metadata at the
        root of the document.  If no ontologies are specified in `$schema`, the
        runtime may perform exact file format matches.
    - name: contents
      type: string?
      doc: |
        File contents literal.  Maximum of 64 KiB.

        If neither `location` nor `path` is provided, `contents` must be
        non-null.  The implementation must assign a unique identifier for the
        `location` field.  When the file is staged as input to CommandLineTool,
        the value of `contents` must be written to a file.

        If `loadContents` of `inputBinding` or `outputBinding` is true and
        `location` is valid, the implementation must read up to the first 64
        KiB of text from the file and place it in the "contents" field.


- name: Directory
  type: record
  docAfter: "#File"
  doc: |
    Represents a directory to present to a command line tool.
  fields:
    - name: class
      type:
        type: enum
        name: Directory_class
        symbols:
          - cwl:Directory
      jsonldPredicate:
        _id: "@type"
        _type: "@vocab"
      doc: Must be `Directory` to indicate this object describes a Directory.
    - name: location
      type: string?
      doc: |
        An IRI that identifies the directory resource.  This may be a relative
        reference, in which case it must be resolved using the base IRI of the
        document.  The location may refer to a local or remote resource.  If
        the `listing` field is not set, the implementation must use the
        location IRI to retrieve directory listing.  If an implementation is
        unable to retrieve the directory listing stored at a remote resource (due to
        unsupported protocol, access denied, or other issue) it must signal an
        error.

        If the `location` field is not provided, the `listing` field must be
        provided.  The implementation must assign a unique identifier for
        the `location` field.

        If the `path` field is provided but the `location` field is not, an
        implementation may assign the value of the `path` field to `location`,
        then follow the rules above.
      jsonldPredicate:
        _id: "@id"
        _type: "@id"
    - name: path
      type: string?
      doc: |
        The local path where the Directory is made available prior to executing a
        CommandLineTool.  This must be set by the implementation.  This field
        must not be used in any other context.  The command line tool being
        executed must be able to to access the directory at `path` using the POSIX
        `opendir(2)` syscall.

        If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
        (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
        `<space>`, `<tab>`, and `<newline>`) or characters
        [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
        for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
        then implementations may terminate the process with a
        `permanentFailure`.
      jsonldPredicate:
        _id: "cwl:path"
        _type: "@id"
    - name: basename
      type: string?
      doc: |
        The base name of the directory, that is, the name of the file without any
        leading directory path.  The base name must not contain a slash `/`.

        If not provided, the implementation must set this field based on the
        `location` field by taking the final path component after parsing
        `location` as an IRI.  If `basename` is provided, it is not required to
        match the value from `location`.

        When this file is made available to a CommandLineTool, it must be named
        with `basename`, i.e. the final component of the `path` field must match
        `basename`.
      jsonldPredicate: "cwl:basename"
    - name: listing
      type:
        - "null"
        - type: array
          items: [File, Directory]
      doc: |
        List of files or subdirectories contained in this directory.  The name
        of each file or subdirectory is determined by the `basename` field of
        each `File` or `Directory` object.  It is an error if a `File` shares a
        `basename` with any other entry in `listing`.  If two or more
        `Directory` object share the same `basename`, this must be treated as
        equivalent to a single subdirectory with the listings recursively
        merged.
      jsonldPredicate:
        _id: "cwl:listing"

- name: SchemaBase
  type: record
  abstract: true
  fields:
    - name: label
      type:
        - "null"
        - string
      jsonldPredicate: "rdfs:label"
      doc: "A short, human-readable label of this object."


- name: Parameter
  type: record
  extends: SchemaBase
  abstract: true
  doc: |
    Define an input or output parameter to a process.

  fields:
    - name: secondaryFiles
      type:
        - "null"
        - string
        - Expression
        - type: array
          items: [string, Expression]
      jsonldPredicate: "cwl:secondaryFiles"
      doc: |
        Only valid when `type: File` or is an array of `items: File`.

        Describes files that must be included alongside the primary file(s).

        If the value is an expression, the value of `self` in the expression
        must be the primary input or output File to which this binding applies.

        If the value is a string, it specifies that the following pattern
        should be applied to the primary file:

          1. If string begins with one or more caret `^` characters, for each
            caret, remove the last file extension from the path (the last
            period `.` and all following characters).  If there are no file
            extensions, the path is unchanged.
          2. Append the remainder of the string to the end of the file path.

    - name: format
      type:
        - "null"
        - string
        - type: array
          items: string
        - Expression
      jsonldPredicate:
        _id: cwl:format
        _type: "@id"
        identity: true
      doc: |
        Only valid when `type: File` or is an array of `items: File`.

        For input parameters, this must be one or more IRIs of concept nodes
        that represents file formats which are allowed as input to this
        parameter, preferrably defined within an ontology.  If no ontology is
        available, file formats may be tested by exact match.

        For output parameters, this is the file format that will be assigned to
        the output parameter.

    - name: streamable
      type: boolean?
      doc: |
        Only valid when `type: File` or is an array of `items: File`.

        A value of `true` indicates that the file is read or written
        sequentially without seeking.  An implementation may use this flag to
        indicate whether it is valid to stream file contents using a named
        pipe.  Default: `false`.

    - name: doc
      type:
        - string?
        - string[]?
      doc: "A documentation string for this type, or an array of strings which should be concatenated."
      jsonldPredicate: "rdfs:comment"


- type: enum
  name: Expression
  doc: |
    'Expression' is not a real type.  It indicates that a field must allow
    runtime parameter references.  If [InlineJavascriptRequirement](#InlineJavascriptRequirement)
    is declared and supported by the platform, the field must also allow
    Javascript expressions.
  symbols:
    - cwl:ExpressionPlaceholder


- name: InputBinding
  type: record
  abstract: true
  fields:
    - name: loadContents
      type:
        - "null"
        - boolean
      jsonldPredicate: "cwl:loadContents"
      doc: |
        Only valid when `type: File` or is an array of `items: File`.

        Read up to the first 64 KiB of text from the file and place it in the
        "contents" field of the file object for use by expressions.


- name: OutputBinding
  type: record
  abstract: true


- name: InputSchema
  extends: SchemaBase
  type: record
  abstract: true


- name: OutputSchema
  extends: SchemaBase
  type: record
  abstract: true


- name: InputRecordField
  type: record
  extends: "sld:RecordField"
  specialize:
    - specializeFrom: "sld:RecordSchema"
      specializeTo: InputRecordSchema
    - specializeFrom: "sld:EnumSchema"
      specializeTo: InputEnumSchema
    - specializeFrom: "sld:ArraySchema"
      specializeTo: InputArraySchema
    - specializeFrom: "sld:PrimitiveType"
      specializeTo: CWLType
  fields:
    - name: inputBinding
      type: InputBinding?
      jsonldPredicate: "cwl:inputBinding"
    - name: label
      type: string?
      jsonldPredicate: "rdfs:label"
      doc: "A short, human-readable label of this process object."


- name: InputRecordSchema
  type: record
  extends: ["sld:RecordSchema", InputSchema]
  specialize:
    - specializeFrom: "sld:RecordField"
      specializeTo: InputRecordField


- name: InputEnumSchema
  type: record
  extends: ["sld:EnumSchema", InputSchema]
  fields:
    - name: inputBinding
      type: InputBinding?
      jsonldPredicate: "cwl:inputBinding"


- name: InputArraySchema
  type: record
  extends: ["sld:ArraySchema", InputSchema]
  specialize:
    - specializeFrom: "sld:RecordSchema"
      specializeTo: InputRecordSchema
    - specializeFrom: "sld:EnumSchema"
      specializeTo: InputEnumSchema
    - specializeFrom: "sld:ArraySchema"
      specializeTo: InputArraySchema
    - specializeFrom: "sld:PrimitiveType"
      specializeTo: CWLType
  fields:
    - name: inputBinding
      type: InputBinding?
      jsonldPredicate: "cwl:inputBinding"


- name: OutputRecordField
  type: record
  extends: "sld:RecordField"
  specialize:
    - specializeFrom: "sld:RecordSchema"
      specializeTo: OutputRecordSchema
    - specializeFrom: "sld:EnumSchema"
      specializeTo: OutputEnumSchema
    - specializeFrom: "sld:ArraySchema"
      specializeTo: OutputArraySchema
    - specializeFrom: "sld:PrimitiveType"
      specializeTo: CWLType
  fields:
    - name: outputBinding
      type: OutputBinding?
      jsonldPredicate: "cwl:outputBinding"


- name: OutputRecordSchema
  type: record
  extends: ["sld:RecordSchema", "#OutputSchema"]
  docParent: "#OutputParameter"
  specialize:
    - specializeFrom: "sld:RecordField"
      specializeTo: OutputRecordField


- name: OutputEnumSchema
  type: record
  extends: ["sld:EnumSchema", OutputSchema]
  docParent: "#OutputParameter"
  fields:
    - name: outputBinding
      type: OutputBinding?
      jsonldPredicate: "cwl:outputBinding"

- name: OutputArraySchema
  type: record
  extends: ["sld:ArraySchema", OutputSchema]
  docParent: "#OutputParameter"
  specialize:
    - specializeFrom: "sld:RecordSchema"
      specializeTo: OutputRecordSchema
    - specializeFrom: "sld:EnumSchema"
      specializeTo: OutputEnumSchema
    - specializeFrom: "sld:ArraySchema"
      specializeTo: OutputArraySchema
    - specializeFrom: "sld:PrimitiveType"
      specializeTo: CWLType
  fields:
    - name: outputBinding
      type: OutputBinding?
      jsonldPredicate: "cwl:outputBinding"


- name: InputParameter
  type: record
  extends: Parameter
  fields:
    - name: id
      type: string
      jsonldPredicate: "@id"
      doc: "The unique identifier for this parameter object."

    - name: inputBinding
      type: InputBinding?
      jsonldPredicate: "cwl:inputBinding"
      doc: |
        Describes how to handle the inputs of a process and convert them
        into a concrete form for execution, such as command line parameters.

    - name: default
      type: Any?
      jsonldPredicate: "cwl:default"
      doc: |
        The default value for this parameter if not provided in the input
        object.

- name: RegularInputParameter
  type: record
  extends: InputParameter
  fields:
    - name: type
      type:
        - "null"
        - CWLType
        - InputRecordSchema
        - InputEnumSchema
        - InputArraySchema
        - string
        - type: array
          items:
            - CWLType
            - InputRecordSchema
            - InputEnumSchema
            - InputArraySchema
            - string
      jsonldPredicate:
        "_id": "sld:type"
        "_type": "@vocab"
        refScope: 2
        typeDSL: True
      doc: |
        Specify valid types of data that may be assigned to this parameter.

- name: OutputParameter
  type: record
  extends: Parameter
  fields:
    - name: id
      type: string
      jsonldPredicate: "@id"
      doc: "The unique identifier for this parameter object."
    - name: outputBinding
      type: OutputBinding?
      jsonldPredicate: "cwl:outputBinding"
      doc: |
        Describes how to handle the outputs of a process.


- type: record
  name: ProcessRequirement
  abstract: true
  doc: |
    A process requirement declares a prerequisite that may or must be fulfilled
    before executing a process.  See [`Process.hints`](#process) and
    [`Process.requirements`](#process).

    Process requirements are the primary mechanism for specifying extensions to
    the CWL core specification.


- type: record
  name: Process
  abstract: true
  doc: |

    The base executable type in CWL is the `Process` object defined by the
    document.  Note that the `Process` object is abstract and cannot be
    directly executed.

  fields:
    - name: id
      type: string?
      jsonldPredicate: "@id"
      doc: "The unique identifier for this process object."
    - name: inputs
      type:
        type: array
        items: InputParameter
      jsonldPredicate:
        _id: "cwl:inputs"
        mapSubject: id
        mapPredicate: type
      doc: |
        Defines the input parameters of the process.  The process is ready to
        run when all required input parameters are associated with concrete
        values.  Input parameters include a schema for each parameter which is
        used to validate the input object.  It may also be used to build a user
        interface for constructing the input object.
    - name: outputs
      type:
        type: array
        items: OutputParameter
      jsonldPredicate:
        _id: "cwl:outputs"
        mapSubject: id
        mapPredicate: type
      doc: |
        Defines the parameters representing the output of the process.  May be
        used to generate and/or validate the output object.
    - name: requirements
      type: ProcessRequirement[]?
      jsonldPredicate:
        _id: "cwl:requirements"
        mapSubject: class
      doc: |
        Declares requirements that apply to either the runtime environment or the
        workflow engine that must be met in order to execute this process.  If
        an implementation cannot satisfy all requirements, or a requirement is
        listed which is not recognized by the implementation, it is a fatal
        error and the implementation must not attempt to run the process,
        unless overridden at user option.
    - name: hints
      type: Any[]?
      doc: |
        Declares hints applying to either the runtime environment or the
        workflow engine that may be helpful in executing this process.  It is
        not an error if an implementation cannot satisfy all hints, however
        the implementation may report a warning.
      jsonldPredicate:
        _id: cwl:hints
        noLinkCheck: true
        mapSubject: class
    - name: label
      type: string?
      jsonldPredicate: "rdfs:label"
      doc: "A short, human-readable label of this process object."
    - name: doc
      type: string?
      jsonldPredicate: "rdfs:comment"
      doc: "A long, human-readable description of this process object."
    - name: cwlVersion
      type: CWLVersion?
      doc: |
        CWL document version. Always required at the document root. Not
        required for a Process embedded inside another Process.
      jsonldPredicate:
        "_id": "cwl:cwlVersion"
        "_type": "@vocab"

- name: InlineJavascriptRequirement
  type: record
  extends: ProcessRequirement
  doc: |
    Indicates that the workflow platform must support inline Javascript expressions.
    If this requirement is not present, the workflow platform must not perform expression
    interpolatation.
  fields:
    - name: class
      type: string
      doc: "Always 'InlineJavascriptRequirement'"
      jsonldPredicate:
        "_id": "@type"
        "_type": "@vocab"
    - name: expressionLib
      type: string[]?
      doc: |
        Additional code fragments that will also be inserted
        before executing the expression code.  Allows for function definitions that may
        be called from CWL expressions.


- name: SchemaDefRequirement
  type: record
  extends: ProcessRequirement
  doc: |
    This field consists of an array of type definitions which must be used when
    interpreting the `inputs` and `outputs` fields.  When a `type` field
    contain a IRI, the implementation must check if the type is defined in
    `schemaDefs` and use that definition.  If the type is not found in
    `schemaDefs`, it is an error.  The entries in `schemaDefs` must be
    processed in the order listed such that later schema definitions may refer
    to earlier schema definitions.
  fields:
    - name: class
      type: string
      doc: "Always 'SchemaDefRequirement'"
      jsonldPredicate:
        "_id": "@type"
        "_type": "@vocab"
    - name: types
      type:
        type: array
        items: InputSchema
      doc: The list of type definitions.