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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,185 @@ | ||
| namespace ARCtrl.CWL | ||
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| open YAMLicious | ||
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| module Decode = | ||
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| let outputBindingGlobDecoder: (YAMLiciousTypes.YAMLElement -> OutputBinding) = | ||
| Decode.object (fun get -> | ||
| let glob = get.Optional.Field "glob" Decode.string | ||
| { Glob = glob } | ||
| ) | ||
|
|
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| let outputBindingDecoder: (YAMLiciousTypes.YAMLElement -> OutputBinding) = | ||
| Decode.object(fun get -> | ||
| let outputBinding = get.Required.Field "outputBinding" outputBindingGlobDecoder | ||
| outputBinding | ||
| ) | ||
|
|
||
| let cwlArrayTypeDecoder: (YAMLiciousTypes.YAMLElement -> CWLType) = | ||
| Decode.object (fun get -> | ||
| let items = get.Required.Field "items" Decode.string | ||
| match items with | ||
| | "File" -> Array (File (FileInstance ())) | ||
| | "Directory" -> Array (Directory (DirectoryInstance ())) | ||
| | "Dirent" -> Array (Dirent { Entry = ""; Entryname = None; Writable = None }) | ||
| | "string" -> Array String | ||
| | "int" -> Array Int | ||
| | "long" -> Array Long | ||
| | "float" -> Array Float | ||
| | "double" -> Array Double | ||
| | "boolean" -> Array Boolean | ||
| | _ -> failwith "Invalid CWL type" | ||
| ) | ||
|
|
||
| let cwlTypeDecoder: (YAMLiciousTypes.YAMLElement -> CWLType) = | ||
| Decode.object (fun get -> | ||
| let cwlType = | ||
| get.Required.Field | ||
| "type" | ||
| ( | ||
| fun value -> | ||
| match value with | ||
| | YAMLElement.Value v | YAMLElement.Object [YAMLElement.Value v] -> Some v.Value | ||
| | YAMLElement.Object o -> None | ||
| | _ -> failwith "Unexpected YAMLElement" | ||
| ) | ||
| match cwlType with | ||
| | Some t -> | ||
| match t with | ||
| | "File" -> File (FileInstance ()) | ||
| | "Directory" -> Directory (DirectoryInstance ()) | ||
| | "Dirent" -> Dirent { Entry = ""; Entryname = None; Writable = None } | ||
| | "string" -> String | ||
| | "int" -> Int | ||
| | "long" -> Long | ||
| | "float" -> Float | ||
| | "double" -> Double | ||
| | "boolean" -> Boolean | ||
| | "File[]" -> Array (File (FileInstance ())) | ||
| | "Directory[]" -> Array (Directory (DirectoryInstance ())) | ||
| | "Dirent[]" -> Array (Dirent { Entry = ""; Entryname = None; Writable = None }) | ||
| | "string[]" -> Array String | ||
| | "int[]" -> Array Int | ||
| | "long[]" -> Array Long | ||
| | "float[]" -> Array Float | ||
| | "double[]" -> Array Double | ||
| | "boolean[]" -> Array Boolean | ||
| | "stdout" -> Stdout | ||
| | "null" -> Null | ||
| | _ -> failwith "Invalid CWL type" | ||
| | None -> | ||
| let cwlTypeArray = get.Required.Field "type" cwlArrayTypeDecoder | ||
| cwlTypeArray | ||
| ) | ||
|
|
||
| let outputArrayDecoder: (YAMLiciousTypes.YAMLElement -> Output[]) = | ||
| Decode.object (fun get -> | ||
| let dict = get.Overflow.FieldList [] | ||
| [| | ||
| for key in dict.Keys do | ||
| let value = dict.[key] | ||
| let outputBinding = outputBindingDecoder value | ||
| let cwlType = cwlTypeDecoder value | ||
| { Name = key; Type = cwlType; OutputBinding = Some outputBinding } | ||
| |] | ||
| ) | ||
|
|
||
| let outputsDecoder: (YAMLiciousTypes.YAMLElement -> Output[]) = | ||
| Decode.object (fun get -> | ||
| let outputs = get.Required.Field "outputs" outputArrayDecoder | ||
| outputs | ||
| ) | ||
|
|
||
| let requirementArrayDecoder: (YAMLiciousTypes.YAMLElement -> Requirement[]) = | ||
| Decode.array | ||
| ( | ||
| Decode.object (fun get -> | ||
| let cls = get.Required.Field "class" Decode.string | ||
| match cls with | ||
| | "InlineJavascriptRequirement" -> InlineJavascriptRequirement | ||
| | "SchemaDefRequirement" -> SchemaDefRequirement [||] | ||
| | "DockerRequirement" -> | ||
| let dockerReq = { | ||
| DockerPull = get.Optional.Field "dockerPull" Decode.string | ||
| DockerFile = Some "" | ||
| DockerImageId = get.Optional.Field "dockerImageId" Decode.string | ||
| } | ||
| DockerRequirement dockerReq | ||
| | "SoftwareRequirement" -> SoftwareRequirement [||] | ||
| | "InitialWorkDirRequirement" -> InitialWorkDirRequirement [||] | ||
| | "EnvVarRequirement" -> EnvVarRequirement {EnvName = ""; EnvValue = ""} | ||
| | "ShellCommandRequirement" -> ShellCommandRequirement | ||
| | "ResourceRequirement" -> ResourceRequirement (ResourceRequirementInstance()) | ||
| | "NetworkAccess" -> NetworkAccessRequirement | ||
|
|
||
| ) | ||
| ) | ||
|
|
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| let requirementsDecoder: (YAMLiciousTypes.YAMLElement -> Requirement[]) = | ||
| Decode.object (fun get -> | ||
| let requirements = get.Required.Field "requirements" requirementArrayDecoder | ||
| requirements | ||
| ) | ||
|
|
||
| let hintsDecoder: (YAMLiciousTypes.YAMLElement -> Requirement[]) = | ||
| Decode.object (fun get -> | ||
| let requirements = get.Required.Field "hints" requirementArrayDecoder | ||
| requirements | ||
| ) | ||
|
|
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| let inputBindingDecoder: (YAMLiciousTypes.YAMLElement -> InputBinding option) = | ||
| Decode.object(fun get -> | ||
| let outputBinding = | ||
| get.Optional.Field | ||
| "inputBinding" | ||
| ( | ||
| Decode.object (fun get' -> | ||
| { | ||
| Prefix = get'.Optional.Field "prefix" Decode.string | ||
| Position = get'.Optional.Field "position" Decode.int | ||
| ItemSeparator = get'.Optional.Field "itemSeparator" Decode.string | ||
| Separate = get'.Optional.Field "separate" Decode.bool | ||
| } | ||
| ) | ||
| ) | ||
| outputBinding | ||
| ) | ||
|
|
||
| let inputArrayDecoder: (YAMLiciousTypes.YAMLElement -> Input[]) = | ||
| Decode.object (fun get -> | ||
| let dict = get.Overflow.FieldList [] | ||
| [| | ||
| for key in dict.Keys do | ||
| let value = dict.[key] | ||
| let inputBinding = inputBindingDecoder value | ||
| let cwlType = cwlTypeDecoder value | ||
| { Name = key; Type = cwlType; InputBinding = inputBinding } | ||
| |] | ||
| ) | ||
|
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| let inputsDecoder: (YAMLiciousTypes.YAMLElement -> Input[]) = | ||
| Decode.object (fun get -> | ||
| let outputs = get.Required.Field "inputs" inputArrayDecoder | ||
| outputs | ||
| ) | ||
|
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||
| let decodeAll = | ||
| let yamlCWL = Decode.read exampleCWL | ||
| CWL( | ||
| cwlVersion = Decode.object (fun get -> get.Required.Field "cwlVersion" Decode.string) yamlCWL, | ||
| cls = | ||
| Decode.object (fun get -> | ||
| match get.Required.Field "class" Decode.string with | ||
| | "Workflow" -> Workflow | ||
| | "CommandLineTool" -> CommandLineTool | ||
| | "ExpressionTool" -> ExpressionTool | ||
| | _ -> failwith "Invalid class" | ||
| ) yamlCWL | ||
| , | ||
| outputs = outputsDecoder yamlCWL, | ||
| inputs = inputsDecoder yamlCWL, | ||
| //baseCommand = Decode.object (fun get -> get.Optional.Field "baseCommand" (Decode.array Decode.string)) yamlCWL, | ||
| requirements = requirementsDecoder yamlCWL, | ||
| hints = hintsDecoder yamlCWL | ||
| ) |
Empty file.