feat: added AST for CWL (Part 2/n of CWL transpiler)

cmd/cwl2argo/transpiler/ast_cl.go

@@ -0,0 +1,321 @@
+// ________________________________________________________________________________
+//
+// Abstract Syntax Tree
+//
+// The AST for CWL  is represented in `ast_cl.go`
+// Note that a few modifications have been made to
+// the AST to make it more convenient to represent in Golang.
+//
+// Sum Types
+//
+// Sum Types (types of the form "ty | []ty") are represented by interfaces,
+// some extra type safety has been added by requiring the implementation of a dummy method in order to satisfy the interface.
+//
+// Normalisation
+//
+// Note how maps are not present in the AST
+// maps are to be represented by arrays.
+// This may incur a small performance hit for large arrays where lookup is required (but generally shouldn't since we will be traversing the entire data structure usually).
+//
+// Note how sum types of the form "ty | []ty" are represented in the AST.
+// This form is generally normalised to simply be "[]ty", the distinction between "ty | []ty" is made by examining the
+// length of the array.
+package transpiler
+
+type CWLRequirements interface {
+	isCWLRequirement()
+}
+
+type DockerRequirement struct {
+	Class                 string // constant DockerRequirement
+	DockerPull            *string
+	DockerLoad            *string
+	DockerFile            *string
+	DockerImport          *string
+	DockerImageId         *string
+	DockerOutputDirectory *string
+}
+
+type SoftwarePackage struct {
+	Package string
+	Version []string
+	Specs   []string
+}
+
+type SoftwareRequirement struct {
+	Class    string // constant SoftwareRequirement
+	Packages []SoftwarePackage
+}
+
+type LoadListingRequirement struct {
+	Class       string // constant LoadListingRequirement
+	LoadListing LoadListingEnum
+}
+
+type Dirent struct {
+	entry     CWLExpressionString
+	entryName CWLExpressionString
+	writeable *bool
+}
+
+type InitialWorkDirRequirementListing interface {
+	isInitialWorkDirRequirementListing()
+}
+
+type InitialWorkDirRequirement struct {
+	Class   string // constant InitialWorkDirRequirement
+	Listing InitialWorkDirRequirementListing
+}
+
+type InlineJavascriptRequirement struct {
+	Class         string // constant InlineJavascriptRequirement
+	ExpressionLib []string
+}
+
+type SchemaDefRequirementType interface {
+	isSchemaDefRequirementType()
+}
+
+type SchemaDefRequirement struct {
+	Class string // constant SchemaDefRequirement
+	Types []SchemaDefRequirementType
+}
+
+type EnvironmentDef struct {
+	EnvName  string
+	EnvValue CWLExpressionString
+}
+
+type EnvVarRequirement struct {
+	Class  string // constant EnvVarRequirement
+	EnvDef []EnvironmentDef
+}
+
+type ShellCommandRequirement struct {
+	Class string // constant ShellCommandRequirement
+}
+
+type WorkReuse struct {
+	Class       string // constant WorkReuse
+	enableReuse CWLExpressionBool
+}
+
+type NetworkAccess struct {
+	Class         string // constant NetworkAccess
+	NetworkAccess CWLExpressionBool
+}
+
+type InplaceUpdateRequirement struct {
+	Class         string // constant InplaceUpdateRequirement
+	InplaceUpdate Bool
+}
+
+type ToolTimeLimit struct {
+	Class     string // constant ToolTimeLimit
+	TimeLimit CWLExpressionInt
+}
+
+type ResourceRequirement struct {
+	Class     string // constand ResourceRequirement
+	CoresMin  *CWLExpressionNum
+	CoresMax  *CWLExpressionNum
+	RamMin    *CWLExpressionNum
+	RamMax    *CWLExpressionNum
+	TmpDirMin *CWLExpressionNum
+	TmpDirMax *CWLExpressionNum
+	OutdirMin *CWLExpressionNum
+	OutdirMax *CWLExpressionNum
+}
+
+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 CommandlineInputRecordFieldType interface {
+	isCommandlineInputRecordFieldType()
+}
+
+func (_ CWLNull) isCommandlineInputRecordFieldType()                      {}
+func (_ CWLBool) isCommandlineInputRecordFieldType()                      {}
+func (_ CWLInt) isCommandlineInputRecordFieldType()                       {}
+func (_ CWLLong) isCommandlineInputRecordFieldType()                      {}
+func (_ CWLFloat) isCommandlineInputRecordFieldType()                     {}
+func (_ CWLDouble) isCommandlineInputRecordFieldType()                    {}
+func (_ CWLString) isCommandlineInputRecordFieldType()                    {}
+func (_ CWLFile) isCommandlineInputRecordFieldType()                      {}
+func (_ CWLDirectory) isCommandlineInputRecordFieldType()                 {}
+func (_ CommandlineInputRecordSchema) isCommandlineInputRecordFieldType() {}
+func (_ CommandlineInputArraySchema) isCommandlineInputRecordFieldType()  {}
+func (_ CommandlineInputEnumSchema) isCommandlineInputRecordFieldType()   {}
+
+type CommandlineInputRecordField struct {
+	Name           string
+	Type           []CommandlineInputRecordFieldType // len(1) represents scalar len > 1 represents array
+	Doc            []string
+	Label          *string
+	SecondaryFiles []CWLSecondaryFileSchema
+	Streamable     *bool
+	Format         CWLFormat
+	LoadContents   *bool
+	LoadListing    LoadListingEnum
+	InputBinding   *CommandlineBinding
+}
+
+type CommandlineInputArraySchemaType interface {
+	isCommandlineInputArraySchemaType()
+}
+
+func (_ CWLNull) isCommandlineInputArraySchemaType()                      {}
+func (_ CWLBool) isCommandlineInputArraySchemaType()                      {}
+func (_ CWLInt) isCommandlineInputArraySchemaType()                       {}
+func (_ CWLLong) isCommandlineInputArraySchemaType()                      {}
+func (_ CWLFloat) isCommandlineInputArraySchemaType()                     {}
+func (_ CWLDouble) isCommandlineInputArraySchemaType()                    {}
+func (_ CWLString) isCommandlineInputArraySchemaType()                    {}
+func (_ CWLFile) isCommandlineInputArraySchemaType()                      {}
+func (_ CWLDirectory) isCommandlineInputArraySchemaType()                 {}
+func (_ CommandlineInputRecordSchema) isCommandlineInputArraySchemaType() {}
+func (_ CommandlineInputArraySchema) isCommandlineInputArraySchemaType()  {}
+func (_ CommandlineInputEnumSchema) isCommandlineInputArraySchemaType()   {}
+
+type CommandlineInputArraySchema struct {
+	Items        CommandlineInputArraySchemaType
+	Type         string // MUST be array
+	Label        *string
+	Doc          []string
+	Name         *string
+	InputBinding *CommandlineBinding
+}
+
+type CommandlineInputEnumSchema struct {
+	Symbols      []string
+	Type         string // MUST BE enum, only a placeholder for type verification purposes
+	Label        *string
+	Doc          []string
+	Name         *string
+	InputBinding *CommandlineBinding
+}
+
+type CommandlineInputRecordSchema struct {
+	Type         string // MUST BE "record"
+	Fields       []CommandlineInputRecordField
+	Label        *string
+	Doc          *[]string
+	Name         *string
+	inputBinding *CommandlineBinding
+}
+
+type CommandlineInputParameterType interface {
+	isCLIParamType()
+}
+
+func (_ CWLNull) isCLIParamType()                      {}
+func (_ CWLBool) isCLIParamType()                      {}
+func (_ CWLInt) isCLIParamType()                       {}
+func (_ CWLLong) isCLIParamType()                      {}
+func (_ CWLFloat) isCLIParamType()                     {}
+func (_ CWLDouble) isCLIParamType()                    {}
+func (_ CWLString) isCLIParamType()                    {}
+func (_ CWLFile) isCLIParamType()                      {}
+func (_ CWLDirectory) isCLIParamType()                 {}
+func (_ CWLStdin) isCLIParamType()                     {}
+func (_ CommandlineInputRecordSchema) isCLIParamType() {}
+func (_ CommandlineInputEnumSchema) isCLIParamType()   {}
+func (_ CommandlineInputArraySchema) isCLIParamType()  {}
+func (_ String) isCLIParamType()                       {}
+
+type CommandlineBinding struct {
+	LoadContents  *bool
+	Position      *int
+	Prefix        *string
+	Seperate      *bool
+	ItemSeperator *string
+	ValueFrom     CWLExpressionString
+	ShellQuote    *bool
+}
+
+type CommandlineInputParameter struct {
+	Type           []CommandlineInputParameterType // len(1) == scalar while len > 1 == array
+	Label          *string
+	SecondaryFiles []CWLSecondaryFileSchema // len(1) == scalar while len > 1 == array
+	Streamable     *bool
+	Doc            []string
+	Id             *string
+	Format         CWLFormat
+	LoadContents   *bool
+	LoadListing    LoadListingEnum
+	Default        interface{}
+	InputBinding   *CommandlineBinding
+}
+
+type CommandlineOutputBindingGlob interface {
+	isCommandlineOutputBindingGlob()
+}
+
+func (_ String) isCommandlineOutputBindingGlob()        {}
+func (_ Strings) isCommandlineOutputBindingGlob()       {}
+func (_ CWLExpression) isCommandlineOutputBindingGlob() {}
+
+type CommandlineOutputBinding struct {
+	LoadContents *bool
+	LoadListing  LoadListingEnum
+	Glob         CommandlineOutputBindingGlob
+	OutputEval   CWLExpression
+}
+
+type CommandlineOutputParameterType interface {
+	isCommandlineOutputParameterType()
+}
+
+type CommandlineOutputParameter struct {
+	Type           []CommandlineOutputParameterType
+	Label          *string
+	SecondaryFiles []CWLSecondaryFileSchema
+	Streamable     *bool
+	Doc            []string
+	Id             *string
+	Format         CWLFormat
+	OutputBinding  *CommandlineOutputBinding
+}
+
+type CommandlineArgument interface {
+	isCommandlineArguement()
+}
+
+func (_ String) isCommandlineArguement()             {}
+func (_ CWLExpression) isCommandlineArguement()      {}
+func (_ CommandlineBinding) isCommandlineArguement() {}
+
+type CommandlineTool struct {
+	Inputs       []CommandlineInputParameter
+	Outputs      []CommandlineOutputParameter
+	Class        string // Must be "CommandLineTool"
+	Id           *string
+	Label        *string
+	Doc          []string
+	Requirements []CWLRequirements
+	Hints        []interface{}
+	CWLVersion   *string
+	Intent       []string
+	BaseCommand  []string
+	Arguments    []CommandlineArgument
+	Stdin        CWLExpressionString
+	Stderr       CWLExpressionString
+	Stdout       CWLExpressionString
+}