cwl

type Any interface {
	CWL_object
	String() string
}

type CWLType interface {
	// contains filtered or unexported methods
}

type CWLVersion interface{} // TODO

type CWL_collection struct {
	Workflows          map[string]*Workflow
	WorkflowStepInputs map[string]*WorkflowStepInput
	CommandLineTools   map[string]*CommandLineTool
	Files              map[string]*File
	Strings            map[string]*String
	Ints               map[string]*Int
	All                map[string]*CWL_object
}

type CWL_document_generic struct {
	CwlVersion string               `yaml:"cwlVersion"`
	Graph      []CWL_object_generic `yaml:"graph"`
}

type CWL_location interface {
	GetLocation() string
}

type CWL_object interface {
	GetClass() string
	GetId() string
	SetId(string)
}

type CWL_object_generic map[string]interface{}

type CommandInputParameter struct {
	Id             string             `yaml:"id"`
	SecondaryFiles []string           `yaml:"secondaryFiles"` // TODO string | Expression | array<string | Expression>
	Format         string             `yaml:"format"`
	Streamable     bool               `yaml:"streamable"`
	Type           string             `yaml:"type"` // TODO CWLType | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | string | array<CWLType | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | string>
	Label          string             `yaml:"label"`
	Description    string             `yaml:"description"`
	InputBinding   CommandLineBinding `yaml:"inputBinding"`
	Default        Any                `yaml:"default"`
}

type CommandLineBinding struct {
	LoadContents  bool   `yaml:"loadContents"`
	Position      int    `yaml:"position"`
	Prefix        string `yaml:"prefix"`
	Separate      string `yaml:"separate"`
	ItemSeparator string `yaml:"itemSeparator"`
	ValueFrom     string `yaml:"valueFrom"`
	ShellQuote    bool   `yaml:"shellQuote"`
}

type CommandLineTool struct {
	Id                 string                   `yaml:"id"`
	BaseCommand        string                   `yaml:"baseCommand"` // TODO also allow []string
	Inputs             []CommandInputParameter  `yaml:"inputs"`
	Outputs            []CommandOutputParameter `yaml:"outputs"`
	Hints              []Requirement            `yaml:"hints"` // TODO Any
	Label              string                   `yaml:"label"`
	Description        string                   `yaml:"description"`
	CwlVersion         CWLVersion               `yaml:"cwlVersion"`
	Arguments          []string                 `yaml:"arguments"` // TODO support CommandLineBinding
	Stdin              string                   `yaml:"stdin"`     // TODO support Expression
	Stdout             string                   `yaml:"stdout"`    // TODO support Expression
	SuccessCodes       []int                    `yaml:"successCodes"`
	TemporaryFailCodes []int                    `yaml:"temporaryFailCodes"`
	PermanentFailCodes []int                    `yaml:"permanentFailCodes"`
}

type CommandOutputBinding struct {
	Glob         []Expression `yaml:"glob"`
	LoadContents bool         `yaml:"loadContents"`
	OutputEval   Expression   `yaml:"outputEval"`
}

type CommandOutputParameter struct {
	Id             string               `yaml:"id"`
	SecondaryFiles []Expression         `yaml:"secondaryFiles"` // TODO string | Expression | array<string | Expression>
	Format         string               `yaml:"format"`
	Streamable     bool                 `yaml:"streamable"`
	Type           string               `yaml:"type"` // TODO CWLType | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | string | array<CWLType | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | string>
	Label          string               `yaml:"label"`
	Description    string               `yaml:"description"`
	OutputBinding  CommandOutputBinding `yaml:"outputBinding"`
}

type Directory struct {
	Id       string         `yaml:"id"`
	Location string         `yaml:"location"`
	Path     string         `yaml:"path"`
	Basename string         `yaml:"basename"`
	Listing  []CWL_location `yaml:"basename"`
}

type DockerRequirement struct {
	//Class         string `yaml:"class"`
	DockerPull    string `yaml:"dockerPull"`
	DockerLoad    string `yaml:"dockerLoad"`
	DockerFile    string `yaml:"dockerFile"`
	DockerImport  string `yaml:"dockerImport"`
	DockerImageId string `yaml:"dockerImageId"`
}

type Empty struct {
	Id    string `yaml:"id"`
	Class string `yaml:"class"`
}

type Expression string

type File struct {
	Id             string         `yaml:"id"`
	Location       string         `yaml:"location"` // An IRI that identifies the file resource.
	Path           string         `yaml:"path"`     // dirname + '/' + basename == path This field must be set by the implementation.
	Basename       string         `yaml:"basename"` // dirname + '/' + basename == path // if not defined, take from location
	Dirname        string         `yaml:"dirname"`  // dirname + '/' + basename == path
	Nameroot       string         `yaml:"nameroot"`
	Nameext        string         `yaml:"nameext"`
	Checksum       string         `yaml:"checksum"`
	Size           int32          `yaml:"size"`
	SecondaryFiles []CWL_location `yaml:"secondaryFiles"`
	Format         string         `yaml:"format"`
	Contents       string         `yaml:"contents"`
	// Shock node
	Host   string
	Node   string
	Bearer string
	Token  string
}

type InputParameter struct {
	Id             string             `yaml:"id"`
	Label          string             `yaml:"label"`
	SecondaryFiles []string           `yaml:"secondaryFiles"` // TODO string | Expression | array<string | Expression>
	Format         string             `yaml:"format"`
	Streamable     bool               `yaml:"streamable"`
	Doc            string             `yaml:"doc"`
	InputBinding   CommandLineBinding `yaml:"inputBinding"` //TODO
	Default        Any                `yaml:"default"`
	Type           string             `yaml:"type"` // TODO CWLType | InputRecordSchema | InputEnumSchema | InputArraySchema | string | array<CWLType | InputRecordSchema | InputEnumSchema | InputArraySchema | string>
}

type Int struct {
	Id    string `yaml:"id"`
	Value int    `yaml:"value"`
}

type Job_document map[string]interface{}

type LinkMergeMethod string // merge_nested or merge_flattened

type Requirement interface {
	GetClass() string
}

type ShockRequirement struct {
	Host string `yaml:"host"`
}

type StepInputExpressionRequirement struct {
}

type String struct {
	Id    string `yaml:"id"`
	Value string `yaml:"value"`
}

type Workflow struct {
	Inputs       []InputParameter          `yaml:"inputs"`
	Outputs      []WorkflowOutputParameter `yaml:"outputs"`
	Id           string                    `yaml:"id"`
	Steps        []WorkflowStep            `yaml:"steps"`
	Requirements []Requirement             `yaml:"requirements"`
	Hints        []Requirement             `yaml:"hints"` // TODO Hints may contain non-requirement objects. Give warning in those cases.
	Label        string                    `yaml:"label"`
	Doc          string                    `yaml:"doc"`
	CwlVersion   CWLVersion                `yaml:"cwlVersion"`
	Metadata     map[string]interface{}    `yaml:"metadata"`
}

type WorkflowOutputParameter struct {
	Id             string               `yaml:"id"`
	Label          string               `yaml:"label"`
	SecondaryFiles []Expression         `yaml:"secondaryFiles"` // TODO string | Expression | array<string | Expression>
	Format         []Expression         `yaml:"format"`
	Streamable     bool                 `yaml:"streamable"`
	Doc            string               `yaml:"doc"`
	OutputBinding  CommandOutputBinding `yaml:"outputBinding"` //TODO
	OutputSource   []string             `yaml:"outputSource"`
	LinkMerge      LinkMergeMethod      `yaml:"linkMerge"`
	Type           string               `yaml:"type"` // TODO CWLType | OutputRecordSchema | OutputEnumSchema | OutputArraySchema | string | array<CWLType | OutputRecordSchema | OutputEnumSchema | OutputArraySchema | string>
}

type WorkflowStep struct {
	Id            string               `yaml:"id"`
	In            []WorkflowStepInput  `yaml:"in"` // array<WorkflowStepInput> | map<WorkflowStepInput.id, WorkflowStepInput.source> | map<WorkflowStepInput.id, WorkflowStepInput>
	Out           []WorkflowStepOutput `yaml:"out"`
	Run           string               `yaml:"run"` // Specification unclear: string | CommandLineTool | ExpressionTool | Workflow
	Requirements  []Requirement        `yaml:"requirements"`
	Hints         []Requirement        `yaml:"hints"`
	Label         string               `yaml:"label"`
	Doc           string               `yaml:"doc"`
	Scatter       string               `yaml:"scatter"`       // ScatterFeatureRequirement
	ScatterMethod string               `yaml:"scatterMethod"` // ScatterFeatureRequirement
}

type WorkflowStepInput struct {
	Id        string          `yaml:"id"`
	Source    []string        `yaml:"source"` // MultipleInputFeatureRequirement
	LinkMerge LinkMergeMethod `yaml:"linkMerge"`
	Default   Any             `yaml:"default"`   // type Any does not make sense
	ValueFrom Expression      `yaml:"valueFrom"` // StepInputExpressionRequirement
}

type WorkflowStepOutput struct {
	Id string `yaml:"id"`
}