cwl

package
v0.9.33 Latest Latest
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 Go to latest Published: Mar 27, 2017 License: BSD-2-Clause Imports: 15 Imported by: 6

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Index

Constants

This section is empty.

Variables

This section is empty.

Functions

func GetMapElement 

func GetMapElement(m map[interface{}]interface{}, key string) (value interface{}, err error)

func ParseJob 

func ParseJob(collection *CWL_collection, job_file string) (err error)

func Parse_cwl_document 

func Parse_cwl_document(collection *CWL_collection, yaml_str string) (err error)

func Unmarshal 

func Unmarshal(data []byte, v interface{}) (err error)

Types

type Any 

type Any interface {
	CWL_object
	String() string
}

type CWLType 

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

CWLType httpCWL_objectmonwl.org/v1.0/CommandLineTool.html#CWLType null, boolean, int, long, float, double, string, File, Directory

type CWLVersion 

type CWLVersion interface{} // TODO

type CWL_collection 

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
}

func NewCWL_collection 

func NewCWL_collection() (collection CWL_collection)

func (CWL_collection) Add 

func (c CWL_collection) Add(obj CWL_object) (err error)

func (CWL_collection) Evaluate 

func (c CWL_collection) Evaluate(raw string) (parsed string)

func (CWL_collection) Get 

func (c CWL_collection) Get(id string) (obj *CWL_object, err error)

func (CWL_collection) GetFile 

func (c CWL_collection) GetFile(id string) (obj *File, err error)

func (CWL_collection) GetInt 

func (c CWL_collection) GetInt(id string) (obj *Int, err error)

func (CWL_collection) GetString 

func (c CWL_collection) GetString(id string) (obj *String, err error)

func (CWL_collection) GetWorkflowStepInput 

func (c CWL_collection) GetWorkflowStepInput(id string) (obj *WorkflowStepInput, err error)

type CWL_document_generic 

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

this is used by YAML or JSON library for inital parsing

type CWL_location 

type CWL_location interface {
	GetLocation() string
}

generic class to represent Files and Directories

type CWL_object 

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

type CWL_object_generic 

type CWL_object_generic map[string]interface{}

type CommandInputParameter 

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"`
}

func CreateCommandInputArray 

func CreateCommandInputArray(original interface{}) (err error, new_array []CommandInputParameter)

keyname will be converted into 'Id'-field

type CommandLineBinding 

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"`
}

http://www.commonwl.org/v1.0/Workflow.html#CommandLineBinding

type CommandLineTool 

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"`
}

func (*CommandLineTool) GetClass 

func (c *CommandLineTool) GetClass() string

func (*CommandLineTool) GetId 

func (c *CommandLineTool) GetId() string

func (*CommandLineTool) SetId 

func (c *CommandLineTool) SetId(id string)

type CommandOutputBinding 

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

type CommandOutputParameter 

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"`
}

func CreateCommandOutputArray 

func CreateCommandOutputArray(original interface{}) (err error, new_array []CommandOutputParameter)

keyname will be converted into 'Id'-field

type Directory 

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

func (Directory) GetClass 

func (d Directory) GetClass() string

func (Directory) GetId 

func (d Directory) GetId() string

func (Directory) GetLocation 

func (d Directory) GetLocation() string

func (Directory) String 

func (d Directory) String() string

type DockerRequirement 

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"`
}

func (DockerRequirement) GetClass 

func (c DockerRequirement) GetClass() string

func (DockerRequirement) GetId 

func (c DockerRequirement) GetId() string

type Empty 

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

this is a generic CWL_object. Its only purpose is to retrieve the value of "class"

func (Empty) GetClass 

func (e Empty) GetClass() string

func (Empty) GetId 

func (e Empty) GetId() string

func (Empty) SetId 

func (e Empty) SetId(id string)

func (Empty) String 

func (e Empty) String() string

type Expression 

type Expression string

func (Expression) Evaluate 

func (e Expression) Evaluate(collection *CWL_collection) string

func (Expression) String 

func (e Expression) String() string

type File 

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
}

http://www.commonwl.org/v1.0/Workflow.html#File

func MakeFile 

func MakeFile(id string, obj interface{}) (file File, err error)

func (*File) GetClass 

func (f *File) GetClass() string

func (*File) GetId 

func (f *File) GetId() string

func (*File) GetLocation 

func (f *File) GetLocation() string

func (*File) SetId 

func (f *File) SetId(id string)

func (*File) String 

func (f *File) String() string

type InputParameter 

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>
}

func CreateInputParameterArray 

func CreateInputParameterArray(original interface{}) (err error, new_array []InputParameter)

InputParameter

func (InputParameter) GetClass 

func (i InputParameter) GetClass() string

func (InputParameter) GetId 

func (i InputParameter) GetId() string

func (InputParameter) SetId 

func (i InputParameter) SetId(id string)

type Int 

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

func (*Int) GetClass 

func (i *Int) GetClass() string

func (*Int) GetId 

func (i *Int) GetId() string

func (*Int) SetId 

func (i *Int) SetId(id string)

func (*Int) String 

func (i *Int) String() string

type Job_document 

type Job_document map[string]interface{}

type LinkMergeMethod 

type LinkMergeMethod string // merge_nested or merge_flattened

type Requirement 

type Requirement interface {
	GetClass() string
}

func CreateRequirementArray 

func CreateRequirementArray(original interface{}) (err error, new_array []Requirement)

[]Requirement

func NewRequirement 

func NewRequirement(class string, obj interface{}) (r Requirement, err error)

type ShockRequirement 

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

func (ShockRequirement) GetClass 

func (s ShockRequirement) GetClass() string

func (ShockRequirement) GetId 

func (s ShockRequirement) GetId() string

type StepInputExpressionRequirement 

type StepInputExpressionRequirement struct {
}

func (StepInputExpressionRequirement) GetClass 

func (c StepInputExpressionRequirement) GetClass() string

func (StepInputExpressionRequirement) GetId 

func (c StepInputExpressionRequirement) GetId() string

type String 

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

func (*String) GetClass 

func (s *String) GetClass() string

func (*String) GetId 

func (s *String) GetId() string

func (*String) SetId 

func (s *String) SetId(id string)

func (*String) String 

func (s *String) String() string

type Workflow 

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"`
}

func (*Workflow) GetClass 

func (w *Workflow) GetClass() string

func (*Workflow) GetId 

func (w *Workflow) GetId() string

func (*Workflow) SetId 

func (w *Workflow) SetId(id string)

type WorkflowOutputParameter 

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>
}

func CreateWorkflowOutputParameterArray 

func CreateWorkflowOutputParameterArray(original interface{}) (err error, new_array []WorkflowOutputParameter)

WorkflowOutputParameter

type WorkflowStep 

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
}

func CreateWorkflowStepsArray 

func CreateWorkflowStepsArray(original interface{}) (err error, new_array []WorkflowStep)

CreateWorkflowStepsArray

func (WorkflowStep) GetOutput 

func (w WorkflowStep) GetOutput(id string) (output *WorkflowStepOutput, err error)

type WorkflowStepInput 

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
}

http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput

func CreateWorkflowStepInputArray 

func CreateWorkflowStepInputArray(original interface{}) (err error, new_array []WorkflowStepInput)

func (WorkflowStepInput) GetClass 

func (w WorkflowStepInput) GetClass() string

func (WorkflowStepInput) GetId 

func (w WorkflowStepInput) GetId() string

func (WorkflowStepInput) GetObject 

func (input WorkflowStepInput) GetObject(c *CWL_collection) (obj *CWL_object, err error)

func (WorkflowStepInput) SetId 

func (w WorkflowStepInput) SetId(id string)

type WorkflowStepOutput 

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

func CreateWorkflowStepOutputArray 

func CreateWorkflowStepOutputArray(original interface{}) (err error, new_array []WorkflowStepOutput)

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