feat: add unmarshalling to AST (Part 3/n for transpiler implementation)

cmd/cwl2argo/transpiler/ast_cl.go

@@ -0,0 +1,303 @@
+package transpiler
+
+// interface due to large number of child types
+type CWLRequirements interface {
+	isCWLRequirement()
+}
+
+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"`
+	DockerOutputDirectory *string `yaml:"dockerOutputDirectory"`
+}
+
+type SoftwarePackage struct {
+	Package string  `yaml:"package"`
+	Version Strings `yaml:"version"`
+	Specs   Strings `yaml:"specs"`
+}
+
+type SoftwareRequirement struct {
+	Class    string            `yaml:"class"` // constant SoftwareRequirement
+	Packages []SoftwarePackage `yaml:"packages"`
+}
+
+type LoadListingRequirement struct {
+	Class       string           `yaml:"class"` // constant LoadListingRequirement
+	LoadListing *LoadListingEnum `yaml:"loadListing"`
+}
+
+type Dirent struct {
+	entry     CWLExpression  `yaml:"entry"`
+	entryName *CWLExpression `yaml:"entryName"`
+	writeable *bool          `yaml:"writeable"`
+}
+
+type InitialWorkDirRequirementListing interface {
+	isInitialWorkDirRequirementListing()
+}
+
+type InitialWorkDirRequirement struct {
+	Class   string                           `yaml:"class"` // constant InitialWorkDirRequirement
+	Listing InitialWorkDirRequirementListing `yaml:"listing"`
+}
+
+type InlineJavascriptRequirement struct {
+	Class         string  `yaml:"class"` // constant InlineJavascriptRequirement
+	ExpressionLib Strings `yaml:"expressionLib"`
+}
+
+type SchemaDefRequirementType interface {
+	isSchemaDefRequirementType()
+}
+
+type SchemaDefRequirement struct {
+	Class string                     `yaml:"class"` // constant SchemaDefRequirement
+	Types []SchemaDefRequirementType `yaml:"types"`
+}
+
+type EnvironmentDef struct {
+	EnvName  string        `yaml:"envName"`
+	EnvValue CWLExpression `yaml:"envValue"`
+}
+
+type EnvVarRequirement struct {
+	Class  string           `yaml:"class"` // constant EnvVarRequirement
+	EnvDef []EnvironmentDef `yaml:"envDef"`
+}
+
+type ShellCommandRequirement struct {
+	Class string `yaml:"class"` // constant ShellCommandRequirement
+}
+
+type WorkReuse struct {
+	Class       string        `yaml:"class"` // constant WorkReuse
+	EnableReuse CWLExpression `yaml:"enableReuse"`
+}
+
+type NetworkAccess struct {
+	Class         string // constant NetworkAccess
+	NetworkAccess CWLExpression
+}
+
+type InplaceUpdateRequirement struct {
+	Class         string `yaml:"class"` // constant InplaceUpdateRequirement
+	InplaceUpdate Bool   `yaml:"inplaceUpdate"`
+}
+
+type ToolTimeLimit struct {
+	Class     string        `yaml:"class"` // constant ToolTimeLimit
+	TimeLimit CWLExpression `yaml:"timeLimit"`
+}
+
+type ResourceRequirement struct {
+	Class     string         `yaml:"class"` // constand ResourceRequirement
+	CoresMin  *CWLExpression `yaml:"coresMin"`
+	CoresMax  *CWLExpression `yaml:"coresMax"`
+	RamMin    *CWLExpression `yaml:"ramMin"`
+	RamMax    *CWLExpression `yaml:"ramMax"`
+	TmpdirMin *CWLExpression `yaml:"tmpdirMin"`
+	TmpdirMax *CWLExpression `yaml:"tmpdirMin"`
+	OutdirMin *CWLExpression `yaml:"outdirMin"`
+	OutdirMax *CWLExpression `yaml:"outdirMax"`
+}
+
+func (_ InlineJavascriptRequirement) isCWLRequirement() {}
+func (_ SchemaDefRequirement) isCWLRequirement()        {}
+func (_ LoadListingRequirement) isCWLRequirement()      {}
+func (_ DockerRequirement) isCWLRequirement()           {}
+func (_ SoftwareRequirement) isCWLRequirement()         {}
+func (_ InitialWorkDirRequirement) isCWLRequirement()   {}
+func (_ EnvVarRequirement) isCWLRequirement()           {}
+func (_ ShellCommandRequirement) isCWLRequirement()     {}
+func (_ WorkReuse) isCWLRequirement()                   {}
+func (_ NetworkAccess) isCWLRequirement()               {}
+func (_ InplaceUpdateRequirement) isCWLRequirement()    {}
+func (_ ToolTimeLimit) isCWLRequirement()               {}
+
+func (_ CommandlineInputRecordSchema) isSchemaDefRequirementType() {}
+func (_ CommandlineInputEnumSchema) isSchemaDefRequirementType()   {}
+func (_ CommandlineInputArraySchema) isSchemaDefRequirementType()  {}
+func (_ DockerRequirement) isSchemaDefRequirementType()            {}
+func (_ SoftwareRequirement) isSchemaDefRequirementType()          {}
+func (_ InitialWorkDirRequirement) isSchemaDefRequirementType()    {}
+
+type CommandlineInputRecordField struct {
+	Name           string              `yaml:"name"`
+	Type           CommandlineTypes    `yaml:"type"` // len(1) represents scalar len > 1 represents array
+	Doc            Strings             `yaml:"doc"`
+	Label          *string             `yaml:"label"`
+	SecondaryFiles SecondaryFiles      `yaml:"secondaryFiles"`
+	Streamable     *bool               `yaml:"streamable"`
+	Format         CWLFormat           `yaml:"format"`
+	LoadContents   *bool               `yaml:"loadContents"`
+	LoadListing    LoadListingEnum     `yaml:"loadListing"`
+	InputBinding   *CommandlineBinding `yaml:"inputBinding"`
+}
+
+type CommandlineInputArraySchema struct {
+	Items        CommandlineTypes    `yaml:"items"`
+	Type         string              `yaml:"type"` // MUST be array
+	Label        *string             `yaml:"label"`
+	Doc          Strings             `yaml:"doc"`
+	Name         *string             `yaml:"name"`
+	InputBinding *CommandlineBinding `yaml:"inputBinding"`
+}
+
+type CommandlineInputEnumSchema struct {
+	Symbols      Strings `yaml:"symbols"`
+	Type         string  `yaml:"type"` // MUST BE enum, only a placeholder for type verification purposes
+	Label        *string `yaml:"label"`
+	Doc          Strings `yaml:"doc"`
+	Name         *string `yaml:"name"`
+	InputBinding *CommandlineBinding
+}
+
+type CommandlineInputRecordSchema struct {
+	Type         string                         `yaml:"type"` // MUST BE "record"
+	Fields       *[]CommandlineInputRecordField `yaml:"fields"`
+	Label        *string                        `yaml:"label"`
+	Doc          *Strings                       `yaml:"doc"`
+	Name         *string                        `yaml:"name"`
+	inputBinding *CommandlineBinding            `yaml:"inputBinding"`
+}
+
+func (_ CWLNull) isFlat()                    {}
+func (_ CWLBool) isFlat()                    {}
+func (_ CWLInt) isFlat()                     {}
+func (_ CWLLong) isFlat()                    {}
+func (_ CWLFloat) isFlat()                   {}
+func (_ CWLDouble) isFlat()                  {}
+func (_ CWLFile) isFlat()                    {}
+func (_ CWLDirectory) isFlat()               {}
+func (_ CWLStdin) isFlat()                   {}
+func (_ String) isFlat()                     {}
+func (_ CommandlineInputEnumSchema) isFlat() {}
+
+type Type int32
+
+const (
+	CWLNullKind Type = iota
+	CWLBoolKind
+	CWLIntKind
+	CWLLongKind
+	CWLFloatKind
+	CWLDoubleKind
+	CWLFileKind
+	CWLDirectoryKind
+	CWLStdinKind
+	CWLStringKind
+	CWLRecordKind
+	CWLRecordFieldKind
+	CWLEnumKind
+	CWLArrayKind
+)
+
+type CommandlineType struct {
+	Kind   Type
+	Record *CommandlineInputRecordSchema
+	Enum   *CommandlineInputEnumSchema
+	Array  *CommandlineInputArraySchema
+}
+
+type CommandlineTypes []CommandlineType
+
+type CommandlineBinding struct {
+	LoadContents  *bool         `yaml:"loadContents"`
+	Position      *int          `yaml:"position"`
+	Prefix        *string       `yaml:"prefix"`
+	Seperate      *bool         `yaml:"seperate"`
+	ItemSeperator *string       `yaml:"itemSeperator"`
+	ValueFrom     CWLExpression `yaml:"valueFrom"`
+	ShellQuote    *bool         `yaml:"bool"`
+}
+
+type CommandlineInputParameter struct {
+	Type           CommandlineTypes    `yaml:"type"` // len(1) == scalar while len > 1 == array
+	Label          *string             `yaml:"label"`
+	SecondaryFiles SecondaryFiles      `yaml:"secondaryFiles"` // len(1) == scalar while len > 1 == array
+	Streamable     *bool               `yaml:"streamable"`
+	Doc            Strings             `yaml:"doc"`
+	Id             *string             `yaml:"id"`
+	Format         CWLFormat           `yaml:"format"`
+	LoadContents   *bool               `yaml:"loadContents"`
+	LoadListing    LoadListingEnum     `yaml:"loadListing"`
+	Default        interface{}         `yaml:"default"`
+	InputBinding   *CommandlineBinding `yaml:"inputBinding"`
+}
+
+type OutputBindingGlobKind int32
+
+const (
+	GlobStringKind OutputBindingGlobKind = iota
+	GlobStringsKind
+	GlobExpressionKind
+)
+
+type CommandlineOutputBindingGlob struct {
+	Kind       OutputBindingGlobKind
+	String     String
+	Strings    Strings
+	Expression CWLExpression
+}
+
+type CommandlineOutputBinding struct {
+	LoadContents *bool                        `yaml:"loadContents"`
+	LoadListing  LoadListingEnum              `yaml:"loadListing"`
+	Glob         CommandlineOutputBindingGlob `yaml:"glob"`
+	OutputEval   CWLExpression                `yaml:"outputEval"`
+}
+
+type CommandlineOutputParameter struct {
+	Type           CommandlineTypes          `yaml:"type"`
+	Label          *string                   `yaml:"label"`
+	SecondaryFiles SecondaryFiles            `yaml:"secondaryFiles"`
+	Streamable     *bool                     `yaml:"streamable"`
+	Doc            Strings                   `yaml:"doc"`
+	Id             *string                   `yaml:"id"`
+	Format         CWLFormat                 `yaml:"format"`
+	OutputBinding  *CommandlineOutputBinding `yaml:"outputBinding"`
+}
+
+type CommandlineArgumentKind int32
+
+const (
+	ArguementStringKind CommandlineArgumentKind = iota
+	ArguementExpressionKind
+	ArguementCLIBindingKind
+)
+
+type CommandlineArgument struct {
+	Kind               CommandlineArgumentKind
+	String             String
+	Expression         CWLExpression
+	CommandlineBinding CommandlineBinding
+}
+
+type Inputs []CommandlineInputParameter
+type Outputs []CommandlineOutputParameter
+type Requirements []CWLRequirements
+type Hints []interface{}
+type Arguments []CommandlineArgument
+
+type CommandlineTool struct {
+	Inputs       Inputs        `yaml:"inputs"`
+	Outputs      Outputs       `yaml:"outputs"`
+	Class        string        `yaml:"class"` // Must be "CommandLineTool"
+	Id           *string       `yaml:"id"`
+	Label        *string       `yaml:"label"`
+	Doc          Strings       `yaml:"doc"`
+	Requirements Requirements  `yaml:"requirements"`
+	Hints        Hints         `yaml:"hints"`
+	CWLVersion   *string       `yaml:"cwlVersion"`
+	Intent       Strings       `yaml:"intent"`
+	BaseCommand  Strings       `yaml:"baseCommand"`
+	Arguments    Arguments     `yaml:"arguments"`
+	Stdin        CWLExpression `yaml:"stdin"`
+	Stderr       CWLExpression `yaml:"stderr"`
+	Stdout       CWLExpression `yaml:"stdout"`
+}

cmd/cwl2argo/transpiler/ast_common.go

@@ -0,0 +1,89 @@
+package transpiler
+
+type (
+	String         string
+	Bool           bool
+	Int            int
+	Float          float32
+	Strings        []string
+	SecondaryFiles []CWLSecondaryFileSchema
+)
+
+type CWLFormatKind int32
+
+const (
+	FormatStringKind CWLFormatKind = iota
+	FormatStringsKind
+	FormatExpressionKind
+)
+
+type CWLFormat struct {
+	Kind       CWLFormatKind
+	String     String
+	Strings    Strings
+	Expression CWLExpression
+}
+
+type (
+	CWLNull      struct{}
+	CWLBool      struct{}
+	CWLInt       struct{}
+	CWLLong      struct{}
+	CWLFloat     struct{}
+	CWLDouble    struct{}
+	CWLString    struct{}
+	CWLFile      struct{}
+	CWLDirectory struct{}
+)
+
+func (_ CWLNull) isCWLType()      {}
+func (_ CWLBool) isCWLType()      {}
+func (_ CWLInt) isCWLType()       {}
+func (_ CWLLong) isCWLType()      {}
+func (_ CWLFloat) isCWLType()     {}
+func (_ CWLDouble) isCWLType()    {}
+func (_ CWLString) isCWLType()    {}
+func (_ CWLFile) isCWLType()      {}
+func (_ CWLDirectory) isCWLType() {}
+
+type CWLStdin struct{}
+
+type CWLType interface {
+	isCWLType()
+}
+
+type LoadListingKind int32
+
+const (
+	ShallowListingKind LoadListingKind = iota
+	DeepListingKind
+	NoListingKind
+)
+
+type LoadListingEnum struct {
+	Kind LoadListingKind
+}
+
+type CWLExpressionKind int32
+
+const (
+	RawKind CWLExpressionKind = iota
+	ExpressionKind
+	BoolKind
+	IntKind
+	FloatKind
+)
+
+type CWLExpression struct {
+	Kind       CWLExpressionKind
+	Raw        string
+	Expression string
+	Bool       bool
+	Int        int
+	Float      float64
+}
+
+type CWLSecondaryFileSchema struct {
+	Pattern  CWLExpression `yaml:"pattern"`
+	Required CWLExpression `yaml:"required"`
+}