@nfdi4plants/arctrl 2.1.0-alpha.4 → 2.2.0

package/CWL/Decode.js

@@ -0,0 +1,585 @@
+import { disposeSafe, getEnumerator } from "../fable_modules/fable-library-js.4.22.0/Util.js";
+import { setOptionalProperty, setProperty } from "../fable_modules/DynamicObj.4.0.3/DynObj.fs.js";
+import { DynamicObj } from "../fable_modules/DynamicObj.4.0.3/DynamicObj.fs.js";
+import { ofArray, tail, head, isEmpty, empty, map, iterate } from "../fable_modules/fable-library-js.4.22.0/List.js";
+import { read, int, float, resizearray, map as map_1, bool, string, object } from "../fable_modules/YAMLicious.0.0.3/Decode.fs.js";
+import { replace, toFail, printf, toText } from "../fable_modules/fable-library-js.4.22.0/String.js";
+import { CWLOutput, OutputBinding } from "./Outputs.js";
+import { SchemaDefRequirementType_$ctor_541DA560, SoftwarePackage, DirectoryInstance_$ctor, FileInstance_$ctor, CWLType, DirentInstance } from "./CWLTypes.js";
+import { length, item, singleton, empty as empty_1, append, collect, delay, toArray } from "../fable_modules/fable-library-js.4.22.0/Seq.js";
+import { getItemFromDict } from "../fable_modules/fable-library-js.4.22.0/MapUtil.js";
+import { Requirement, ResourceRequirementInstance_$ctor_D76FC00, EnvironmentDef, DockerRequirement } from "./Requirements.js";
+import { some } from "../fable_modules/fable-library-js.4.22.0/Option.js";
+import { FSharpMap__get_Values, FSharpMap__get_Keys } from "../fable_modules/fable-library-js.4.22.0/Map.js";
+import { CWLInput, InputBinding } from "./Inputs.js";
+import { WorkflowStep, StepOutput, StepInput } from "./WorkflowSteps.js";
+import { CWLToolDescription } from "./ToolDescription.js";
+import { CWLWorkflowDescription } from "./WorkflowDescription.js";
+
+export function ResizeArray_map(f, a) {
+    const b = [];
+    let enumerator = getEnumerator(a);
+    try {
+        while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+            const i = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+            void (b.push(f(i)));
+        }
+    }
+    finally {
+        disposeSafe(enumerator);
+    }
+    return b;
+}
+
+/**
+ * Decode key value pairs into a dynamic object, while preserving their tree structure
+ */
+export function Decode_overflowDecoder(dynObj, dict) {
+    let enumerator = getEnumerator(dict);
+    try {
+        while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+            const e = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+            const matchValue = e[1];
+            let matchResult, v, s;
+            if (matchValue.tag === 3) {
+                if (!isEmpty(matchValue.fields[0])) {
+                    switch (head(matchValue.fields[0]).tag) {
+                        case 1: {
+                            if (isEmpty(tail(matchValue.fields[0]))) {
+                                matchResult = 0;
+                                v = head(matchValue.fields[0]).fields[0];
+                            }
+                            else {
+                                matchResult = 2;
+                            }
+                            break;
+                        }
+                        case 2: {
+                            if (isEmpty(tail(matchValue.fields[0]))) {
+                                matchResult = 1;
+                                s = head(matchValue.fields[0]).fields[0];
+                            }
+                            else {
+                                matchResult = 2;
+                            }
+                            break;
+                        }
+                        default:
+                            matchResult = 2;
+                    }
+                }
+                else {
+                    matchResult = 2;
+                }
+            }
+            else {
+                matchResult = 2;
+            }
+            switch (matchResult) {
+                case 0: {
+                    setProperty(e[0], v.Value, dynObj);
+                    break;
+                }
+                case 1: {
+                    const newDynObj = new DynamicObj();
+                    iterate((x) => {
+                        setProperty(e[0], x, dynObj);
+                    }, map((arg) => Decode_overflowDecoder(newDynObj, object((get$) => get$.Overflow.FieldList(empty()), arg)), s));
+                    break;
+                }
+                case 2: {
+                    setProperty(e[0], e[1], dynObj);
+                    break;
+                }
+            }
+        }
+    }
+    finally {
+        disposeSafe(enumerator);
+    }
+    return dynObj;
+}
+
+/**
+ * Decode a YAMLElement which is either a string or expression into a string
+ */
+export function Decode_decodeStringOrExpression(yEle) {
+    let matchResult, v, c, v_1;
+    switch (yEle.tag) {
+        case 1: {
+            matchResult = 0;
+            v = yEle.fields[0];
+            break;
+        }
+        case 3: {
+            if (!isEmpty(yEle.fields[0])) {
+                switch (head(yEle.fields[0]).tag) {
+                    case 1: {
+                        if (isEmpty(tail(yEle.fields[0]))) {
+                            matchResult = 0;
+                            v = head(yEle.fields[0]).fields[0];
+                        }
+                        else {
+                            matchResult = 2;
+                        }
+                        break;
+                    }
+                    case 0: {
+                        if (head(yEle.fields[0]).fields[1].tag === 3) {
+                            if (!isEmpty(head(yEle.fields[0]).fields[1].fields[0])) {
+                                if (head(head(yEle.fields[0]).fields[1].fields[0]).tag === 1) {
+                                    if (isEmpty(tail(head(yEle.fields[0]).fields[1].fields[0]))) {
+                                        if (isEmpty(tail(yEle.fields[0]))) {
+                                            matchResult = 1;
+                                            c = head(yEle.fields[0]).fields[0];
+                                            v_1 = head(head(yEle.fields[0]).fields[1].fields[0]).fields[0];
+                                        }
+                                        else {
+                                            matchResult = 2;
+                                        }
+                                    }
+                                    else {
+                                        matchResult = 2;
+                                    }
+                                }
+                                else {
+                                    matchResult = 2;
+                                }
+                            }
+                            else {
+                                matchResult = 2;
+                            }
+                        }
+                        else {
+                            matchResult = 2;
+                        }
+                        break;
+                    }
+                    default:
+                        matchResult = 2;
+                }
+            }
+            else {
+                matchResult = 2;
+            }
+            break;
+        }
+        default:
+            matchResult = 2;
+    }
+    switch (matchResult) {
+        case 0:
+            return v.Value;
+        case 1:
+            return toText(printf("%s: %s"))(c.Value)(v_1.Value);
+        default:
+            return toFail(printf("%A"))(yEle);
+    }
+}
+
+export const Decode_outputBindingGlobDecoder = (value_1) => object((get$) => {
+    let objectArg;
+    return new OutputBinding((objectArg = get$.Optional, objectArg.Field("glob", string)));
+}, value_1);
+
+export const Decode_outputBindingDecoder = (value) => object((get$) => {
+    const objectArg = get$.Optional;
+    return objectArg.Field("outputBinding", Decode_outputBindingGlobDecoder);
+}, value);
+
+export const Decode_direntDecoder = (value_1) => object((get$) => {
+    let objectArg, objectArg_1, objectArg_2;
+    return new CWLType(2, [new DirentInstance((objectArg = get$.Required, objectArg.Field("entry", Decode_decodeStringOrExpression)), (objectArg_1 = get$.Optional, objectArg_1.Field("entryname", Decode_decodeStringOrExpression)), (objectArg_2 = get$.Optional, objectArg_2.Field("writable", bool)))]);
+}, value_1);
+
+export const Decode_cwlArrayTypeDecoder = (value_1) => object((get$) => {
+    let objectArg_1;
+    let items;
+    const objectArg = get$.Required;
+    items = objectArg.Field("items", string);
+    switch (items) {
+        case "File":
+            return new CWLType(11, [new CWLType(0, [FileInstance_$ctor()])]);
+        case "Directory":
+            return new CWLType(11, [new CWLType(1, [DirectoryInstance_$ctor()])]);
+        case "Dirent":
+            return new CWLType(11, [(objectArg_1 = get$.Required, objectArg_1.Field("listing", Decode_direntDecoder))]);
+        case "string":
+            return new CWLType(11, [new CWLType(3, [])]);
+        case "int":
+            return new CWLType(11, [new CWLType(4, [])]);
+        case "long":
+            return new CWLType(11, [new CWLType(5, [])]);
+        case "float":
+            return new CWLType(11, [new CWLType(6, [])]);
+        case "double":
+            return new CWLType(11, [new CWLType(7, [])]);
+        case "boolean":
+            return new CWLType(11, [new CWLType(8, [])]);
+        default:
+            throw new Error("Invalid CWL type");
+    }
+}, value_1);
+
+/**
+ * Match the input string to the possible CWL types and checks if it is optional
+ */
+export function Decode_cwlTypeStringMatcher(t, get$) {
+    let objectArg, objectArg_1;
+    const patternInput = t.endsWith("?") ? [true, replace(t, "?", "")] : [false, t];
+    const newT = patternInput[1];
+    return [(newT === "File") ? (new CWLType(0, [FileInstance_$ctor()])) : ((newT === "Directory") ? (new CWLType(1, [DirectoryInstance_$ctor()])) : ((newT === "Dirent") ? ((objectArg = get$.Required, objectArg.Field("listing", Decode_direntDecoder))) : ((newT === "string") ? (new CWLType(3, [])) : ((newT === "int") ? (new CWLType(4, [])) : ((newT === "long") ? (new CWLType(5, [])) : ((newT === "float") ? (new CWLType(6, [])) : ((newT === "double") ? (new CWLType(7, [])) : ((newT === "boolean") ? (new CWLType(8, [])) : ((newT === "File[]") ? (new CWLType(11, [new CWLType(0, [FileInstance_$ctor()])])) : ((newT === "Directory[]") ? (new CWLType(11, [new CWLType(1, [DirectoryInstance_$ctor()])])) : ((newT === "Dirent[]") ? (new CWLType(11, [(objectArg_1 = get$.Required, objectArg_1.Field("listing", Decode_direntDecoder))])) : ((newT === "string[]") ? (new CWLType(11, [new CWLType(3, [])])) : ((newT === "int[]") ? (new CWLType(11, [new CWLType(4, [])])) : ((newT === "long[]") ? (new CWLType(11, [new CWLType(5, [])])) : ((newT === "float[]") ? (new CWLType(11, [new CWLType(6, [])])) : ((newT === "double[]") ? (new CWLType(11, [new CWLType(7, [])])) : ((newT === "boolean[]") ? (new CWLType(11, [new CWLType(8, [])])) : ((newT === "stdout") ? (new CWLType(9, [])) : ((newT === "null") ? (new CWLType(10, [])) : (() => {
+        throw new Error("Invalid CWL type");
+    })()))))))))))))))))))), patternInput[0]];
+}
+
+export const Decode_cwlTypeDecoder = (value_1) => object((get$) => {
+    let objectArg_1;
+    let cwlType;
+    const objectArg = get$.Required;
+    cwlType = objectArg.Field("type", (value) => {
+        let matchResult, v, o;
+        switch (value.tag) {
+            case 1: {
+                matchResult = 0;
+                v = value.fields[0];
+                break;
+            }
+            case 3: {
+                if (!isEmpty(value.fields[0])) {
+                    if (head(value.fields[0]).tag === 1) {
+                        if (isEmpty(tail(value.fields[0]))) {
+                            matchResult = 0;
+                            v = head(value.fields[0]).fields[0];
+                        }
+                        else {
+                            matchResult = 1;
+                            o = value.fields[0];
+                        }
+                    }
+                    else {
+                        matchResult = 1;
+                        o = value.fields[0];
+                    }
+                }
+                else {
+                    matchResult = 1;
+                    o = value.fields[0];
+                }
+                break;
+            }
+            default:
+                matchResult = 2;
+        }
+        switch (matchResult) {
+            case 0:
+                return v.Value;
+            case 1:
+                return undefined;
+            default:
+                throw new Error("Unexpected YAMLElement");
+        }
+    });
+    if (cwlType == null) {
+        return [(objectArg_1 = get$.Required, objectArg_1.Field("type", Decode_cwlArrayTypeDecoder)), false];
+    }
+    else {
+        return Decode_cwlTypeStringMatcher(cwlType, get$);
+    }
+}, value_1);
+
+export const Decode_outputArrayDecoder = (value_2) => object((get$) => {
+    const dict = get$.Overflow.FieldList(empty());
+    const collection = toArray(delay(() => collect((key) => {
+        const value = getItemFromDict(dict, key);
+        const outputBinding = Decode_outputBindingDecoder(value);
+        let outputSource;
+        const objectArg = get$.Optional;
+        outputSource = objectArg.Field("outputSource", string);
+        const output = new CWLOutput(key, (value.tag === 3) ? (!isEmpty(value.fields[0]) ? ((head(value.fields[0]).tag === 1) ? (isEmpty(tail(value.fields[0])) ? Decode_cwlTypeStringMatcher(head(value.fields[0]).fields[0].Value, get$)[0] : Decode_cwlTypeDecoder(value)[0]) : Decode_cwlTypeDecoder(value)[0]) : Decode_cwlTypeDecoder(value)[0]) : Decode_cwlTypeDecoder(value)[0]);
+        return append((outputBinding != null) ? ((setOptionalProperty("outputBinding", outputBinding, output), empty_1())) : empty_1(), delay(() => append((outputSource != null) ? ((setOptionalProperty("outputSource", outputSource, output), empty_1())) : empty_1(), delay(() => singleton(output)))));
+    }, dict.keys())));
+    return Array.from(collection);
+}, value_2);
+
+export const Decode_outputsDecoder = (value) => object((get$) => {
+    const objectArg = get$.Required;
+    return objectArg.Field("outputs", Decode_outputArrayDecoder);
+}, value);
+
+/**
+ * Decode a YAMLElement into a DockerRequirement
+ */
+export function Decode_dockerRequirementDecoder(get$) {
+    let objectArg, objectArg_1, objectArg_2;
+    return new DockerRequirement((objectArg = get$.Optional, objectArg.Field("dockerPull", string)), (objectArg_1 = get$.Optional, objectArg_1.Field("dockerFile", (value_1) => map_1((x) => x, string, value_1))), (objectArg_2 = get$.Optional, objectArg_2.Field("dockerImageId", string)));
+}
+
+/**
+ * Decode a YAMLElement into an EnvVarRequirement array
+ */
+export function Decode_envVarRequirementDecoder(get$) {
+    const objectArg = get$.Required;
+    return objectArg.Field("envDef", (value_3) => resizearray((value_2) => object((get2) => {
+        let objectArg_1, objectArg_2;
+        return new EnvironmentDef((objectArg_1 = get2.Required, objectArg_1.Field("envName", string)), (objectArg_2 = get2.Required, objectArg_2.Field("envValue", string)));
+    }, value_2), value_3));
+}
+
+/**
+ * Decode a YAMLElement into a SoftwareRequirement array
+ */
+export function Decode_softwareRequirementDecoder(get$) {
+    const objectArg = get$.Required;
+    return objectArg.Field("packages", (value_6) => resizearray((value_5) => object((get2) => {
+        let objectArg_1, objectArg_2, objectArg_3;
+        return new SoftwarePackage((objectArg_1 = get2.Required, objectArg_1.Field("package", string)), (objectArg_2 = get2.Optional, objectArg_2.Field("version", (value_1) => resizearray(string, value_1))), (objectArg_3 = get2.Optional, objectArg_3.Field("specs", (value_3) => resizearray(string, value_3))));
+    }, value_5), value_6));
+}
+
+/**
+ * Decode a YAMLElement into a InitialWorkDirRequirement array
+ */
+export function Decode_initialWorkDirRequirementDecoder(get$) {
+    const objectArg = get$.Required;
+    return objectArg.Field("listing", (value) => resizearray(Decode_direntDecoder, value));
+}
+
+/**
+ * Decode a YAMLElement into a ResourceRequirementInstance
+ */
+export function Decode_resourceRequirementDecoder(get$) {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, objectArg_7;
+    return ResourceRequirementInstance_$ctor_D76FC00(some((objectArg = get$.Optional, objectArg.Field("coresMin", (x) => x))), some((objectArg_1 = get$.Optional, objectArg_1.Field("coresMax", (x_1) => x_1))), some((objectArg_2 = get$.Optional, objectArg_2.Field("ramMin", (x_2) => x_2))), some((objectArg_3 = get$.Optional, objectArg_3.Field("ramMax", (x_3) => x_3))), some((objectArg_4 = get$.Optional, objectArg_4.Field("tmpdirMin", (x_4) => x_4))), some((objectArg_5 = get$.Optional, objectArg_5.Field("tmpdirMax", (x_5) => x_5))), some((objectArg_6 = get$.Optional, objectArg_6.Field("outdirMin", (x_6) => x_6))), some((objectArg_7 = get$.Optional, objectArg_7.Field("outdirMax", (x_7) => x_7))));
+}
+
+/**
+ * Decode a YAMLElement into a SchemaDefRequirementType array
+ */
+export function Decode_schemaDefRequirementDecoder(get$) {
+    let objectArg;
+    return ResizeArray_map((m) => SchemaDefRequirementType_$ctor_541DA560(item(0, FSharpMap__get_Keys(m)), item(0, FSharpMap__get_Values(m))), (objectArg = get$.Required, objectArg.Field("types", (value_2) => resizearray((value) => map_1((x) => x, string, value), value_2))));
+}
+
+/**
+ * Decode a YAMLElement into a ToolTimeLimitRequirement
+ */
+export function Decode_toolTimeLimitRequirementDecoder(get$) {
+    const objectArg = get$.Required;
+    return objectArg.Field("timelimit", float);
+}
+
+export const Decode_requirementArrayDecoder = (value_2) => resizearray((value_1) => object((get$) => {
+    let cls;
+    const objectArg = get$.Required;
+    cls = objectArg.Field("class", string);
+    switch (cls) {
+        case "InlineJavascriptRequirement":
+            return new Requirement(0, []);
+        case "SchemaDefRequirement":
+            return new Requirement(1, [Decode_schemaDefRequirementDecoder(get$)]);
+        case "DockerRequirement":
+            return new Requirement(2, [Decode_dockerRequirementDecoder(get$)]);
+        case "SoftwareRequirement":
+            return new Requirement(3, [Decode_softwareRequirementDecoder(get$)]);
+        case "InitialWorkDirRequirement":
+            return new Requirement(4, [Decode_initialWorkDirRequirementDecoder(get$)]);
+        case "EnvVarRequirement":
+            return new Requirement(5, [Decode_envVarRequirementDecoder(get$)]);
+        case "ShellCommandRequirement":
+            return new Requirement(6, []);
+        case "ResourceRequirement":
+            return new Requirement(7, [Decode_resourceRequirementDecoder(get$)]);
+        case "WorkReuse":
+            return new Requirement(8, []);
+        case "NetworkAccess":
+            return new Requirement(9, []);
+        case "InplaceUpdateRequirement":
+            return new Requirement(10, []);
+        case "ToolTimeLimit":
+            return new Requirement(11, [Decode_toolTimeLimitRequirementDecoder(get$)]);
+        case "SubworkflowFeatureRequirement":
+            return new Requirement(12, []);
+        case "ScatterFeatureRequirement":
+            return new Requirement(13, []);
+        case "MultipleInputFeatureRequirement":
+            return new Requirement(14, []);
+        case "StepInputExpressionRequirement":
+            return new Requirement(15, []);
+        default:
+            throw new Error("Invalid requirement");
+    }
+}, value_1), value_2);
+
+export const Decode_requirementsDecoder = (value) => object((get$) => {
+    const objectArg = get$.Optional;
+    return objectArg.Field("requirements", Decode_requirementArrayDecoder);
+}, value);
+
+export const Decode_hintsDecoder = (value) => object((get$) => {
+    const objectArg = get$.Optional;
+    return objectArg.Field("hints", Decode_requirementArrayDecoder);
+}, value);
+
+export const Decode_inputBindingDecoder = (value_5) => object((get$) => {
+    const objectArg = get$.Optional;
+    return objectArg.Field("inputBinding", (value_4) => object((get$0027) => {
+        let objectArg_1, objectArg_2, objectArg_3, objectArg_4;
+        return new InputBinding((objectArg_1 = get$0027.Optional, objectArg_1.Field("prefix", string)), (objectArg_2 = get$0027.Optional, objectArg_2.Field("position", int)), (objectArg_3 = get$0027.Optional, objectArg_3.Field("itemSeparator", string)), (objectArg_4 = get$0027.Optional, objectArg_4.Field("separate", bool)));
+    }, value_4));
+}, value_5);
+
+export const Decode_inputArrayDecoder = (value_1) => object((get$) => {
+    const dict = get$.Overflow.FieldList(empty());
+    const collection = toArray(delay(() => collect((key) => {
+        const value = getItemFromDict(dict, key);
+        const inputBinding = Decode_inputBindingDecoder(value);
+        const patternInput = (value.tag === 3) ? (!isEmpty(value.fields[0]) ? ((head(value.fields[0]).tag === 1) ? (isEmpty(tail(value.fields[0])) ? Decode_cwlTypeStringMatcher(head(value.fields[0]).fields[0].Value, get$) : Decode_cwlTypeDecoder(value)) : Decode_cwlTypeDecoder(value)) : Decode_cwlTypeDecoder(value)) : Decode_cwlTypeDecoder(value);
+        const input = new CWLInput(key, patternInput[0]);
+        return append((inputBinding != null) ? ((setOptionalProperty("inputBinding", inputBinding, input), empty_1())) : empty_1(), delay(() => append(patternInput[1] ? ((setOptionalProperty("optional", true, input), empty_1())) : empty_1(), delay(() => singleton(input)))));
+    }, dict.keys())));
+    return Array.from(collection);
+}, value_1);
+
+export const Decode_inputsDecoder = (value) => object((get$) => {
+    const objectArg = get$.Optional;
+    return objectArg.Field("inputs", Decode_inputArrayDecoder);
+}, value);
+
+export const Decode_baseCommandDecoder = (value_2) => object((get$) => {
+    const objectArg = get$.Optional;
+    return objectArg.Field("baseCommand", (value) => resizearray(string, value));
+}, value_2);
+
+export const Decode_versionDecoder = (value_1) => object((get$) => {
+    const objectArg = get$.Required;
+    return objectArg.Field("cwlVersion", string);
+}, value_1);
+
+export const Decode_classDecoder = (value_1) => object((get$) => {
+    const objectArg = get$.Required;
+    return objectArg.Field("class", string);
+}, value_1);
+
+export function Decode_stringOptionFieldDecoder(field) {
+    return (value_1) => object((get$) => {
+        const objectArg = get$.Optional;
+        return objectArg.Field(field, string);
+    }, value_1);
+}
+
+export function Decode_stringFieldDecoder(field) {
+    return (value_1) => object((get$) => {
+        const objectArg = get$.Required;
+        return objectArg.Field(field, string);
+    }, value_1);
+}
+
+export const Decode_inputStepDecoder = (value_1) => object((get$) => {
+    const dict = get$.Overflow.FieldList(empty());
+    const collection = toArray(delay(() => collect((key) => {
+        let s1, s2;
+        const value = getItemFromDict(dict, key);
+        return singleton(new StepInput(key, (s1 = ((value.tag === 3) ? (!isEmpty(value.fields[0]) ? ((head(value.fields[0]).tag === 1) ? (isEmpty(tail(value.fields[0])) ? head(value.fields[0]).fields[0].Value : undefined) : undefined) : undefined) : undefined), (s2 = Decode_stringOptionFieldDecoder("source")(value), (s1 != null) ? s1 : ((s2 != null) ? s2 : undefined))), Decode_stringOptionFieldDecoder("default")(value), Decode_stringOptionFieldDecoder("valueFrom")(value)));
+    }, dict.keys())));
+    return Array.from(collection);
+}, value_1);
+
+export const Decode_outputStepsDecoder = (value_2) => object((get$) => {
+    const objectArg = get$.Required;
+    return objectArg.Field("out", (value) => resizearray(string, value));
+}, value_2);
+
+export const Decode_stepArrayDecoder = (value_1) => object((get$) => {
+    const dict = get$.Overflow.FieldList(empty());
+    const collection = toArray(delay(() => collect((key) => {
+        const value = getItemFromDict(dict, key);
+        const run = Decode_stringFieldDecoder("run")(value);
+        const inputs = object((get$_1) => {
+            const objectArg = get$_1.Required;
+            return objectArg.Field("in", Decode_inputStepDecoder);
+        }, value);
+        const outputs = new StepOutput(Decode_outputStepsDecoder(value));
+        const requirements = Decode_requirementsDecoder(value);
+        const hints = Decode_hintsDecoder(value);
+        const wfStep = new WorkflowStep(key, inputs, outputs, run);
+        return append((requirements != null) ? ((wfStep.Requirements = requirements, empty_1())) : empty_1(), delay(() => append((hints != null) ? ((wfStep.Hints = hints, empty_1())) : empty_1(), delay(() => singleton(wfStep)))));
+    }, dict.keys())));
+    return Array.from(collection);
+}, value_1);
+
+export const Decode_stepsDecoder = (value) => object((get$) => {
+    const objectArg = get$.Required;
+    return objectArg.Field("steps", Decode_stepArrayDecoder);
+}, value);
+
+/**
+ * Decode a CWL file string written in the YAML format into a CWLToolDescription
+ */
+export function Decode_decodeCommandLineTool(cwl) {
+    const yamlCWL = read(cwl);
+    const cwlVersion = Decode_versionDecoder(yamlCWL);
+    const outputs = Decode_outputsDecoder(yamlCWL);
+    const inputs = Decode_inputsDecoder(yamlCWL);
+    const requirements = Decode_requirementsDecoder(yamlCWL);
+    const hints = Decode_hintsDecoder(yamlCWL);
+    const baseCommand = Decode_baseCommandDecoder(yamlCWL);
+    const description = new CWLToolDescription(outputs, cwlVersion);
+    let metadata;
+    const md = new DynamicObj();
+    object((get$) => Decode_overflowDecoder(md, get$.Overflow.FieldList(ofArray(["inputs", "outputs", "class", "id", "label", "doc", "requirements", "hints", "cwlVersion", "baseCommand", "arguments", "stdin", "stderr", "stdout", "successCodes", "temporaryFailCodes", "permanentFailCodes"]))), yamlCWL);
+    metadata = md;
+    object((get$_1) => Decode_overflowDecoder(description, get$_1.MultipleOptional.FieldList(ofArray(["id", "label", "doc", "arguments", "stdin", "stderr", "stdout", "successCodes", "temporaryFailCodes", "permanentFailCodes"]))), yamlCWL);
+    if (inputs != null) {
+        description.Inputs = inputs;
+    }
+    if (requirements != null) {
+        description.Requirements = requirements;
+    }
+    if (hints != null) {
+        description.Hints = hints;
+    }
+    if (baseCommand != null) {
+        description.BaseCommand = baseCommand;
+    }
+    if (length(metadata.GetProperties(false)) > 0) {
+        description.Metadata = metadata;
+    }
+    return description;
+}
+
+/**
+ * Decode a CWL file string written in the YAML format into a CWLWorkflowDescription
+ */
+export function Decode_decodeWorkflow(cwl) {
+    const yamlCWL = read(cwl);
+    const cwlVersion = Decode_versionDecoder(yamlCWL);
+    const outputs = Decode_outputsDecoder(yamlCWL);
+    let inputs;
+    const matchValue = Decode_inputsDecoder(yamlCWL);
+    if (matchValue == null) {
+        throw new Error("Inputs are required for a workflow");
+    }
+    else {
+        inputs = matchValue;
+    }
+    const requirements = Decode_requirementsDecoder(yamlCWL);
+    const hints = Decode_hintsDecoder(yamlCWL);
+    const description = new CWLWorkflowDescription(Decode_stepsDecoder(yamlCWL), inputs, outputs, cwlVersion);
+    let metadata;
+    const md = new DynamicObj();
+    object((get$) => Decode_overflowDecoder(md, get$.Overflow.FieldList(ofArray(["inputs", "outputs", "class", "steps", "id", "label", "doc", "requirements", "hints", "cwlVersion"]))), yamlCWL);
+    metadata = md;
+    object((get$_1) => Decode_overflowDecoder(description, get$_1.MultipleOptional.FieldList(ofArray(["id", "label", "doc"]))), yamlCWL);
+    if (requirements != null) {
+        description.Requirements = requirements;
+    }
+    if (hints != null) {
+        description.Hints = hints;
+    }
+    if (length(metadata.GetProperties(false)) > 0) {
+        description.Metadata = metadata;
+    }
+    return description;
+}
+

package/CWL/Inputs.js

@@ -0,0 +1,62 @@
+import { FSharpRef, Record } from "../fable_modules/fable-library-js.4.22.0/Types.js";
+import { class_type, record_type, bool_type, int32_type, option_type, string_type } from "../fable_modules/fable-library-js.4.22.0/Reflection.js";
+import { value, unwrap } from "../fable_modules/fable-library-js.4.22.0/Option.js";
+import { CWLType } from "./CWLTypes.js";
+import { defaultOf } from "../fable_modules/fable-library-js.4.22.0/Util.js";
+import { setOptionalProperty } from "../fable_modules/DynamicObj.4.0.3/DynObj.fs.js";
+import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.4.0.3/DynamicObj.fs.js";
+
+export class InputBinding extends Record {
+    constructor(Prefix, Position, ItemSeparator, Separate) {
+        super();
+        this.Prefix = Prefix;
+        this.Position = Position;
+        this.ItemSeparator = ItemSeparator;
+        this.Separate = Separate;
+    }
+}
+
+export function InputBinding_$reflection() {
+    return record_type("ARCtrl.CWL.InputBinding", [], InputBinding, () => [["Prefix", option_type(string_type)], ["Position", option_type(int32_type)], ["ItemSeparator", option_type(string_type)], ["Separate", option_type(bool_type)]]);
+}
+
+export class CWLInput extends DynamicObj {
+    constructor(name, type_, inputBinding, optional) {
+        super();
+        const this$ = new FSharpRef(defaultOf());
+        this.name = name;
+        this$.contents = this;
+        this["init@14"] = 1;
+        setOptionalProperty("type", type_, this$.contents);
+        setOptionalProperty("inputBinding", inputBinding, this$.contents);
+        setOptionalProperty("optional", optional, this$.contents);
+    }
+    get Name() {
+        const this$ = this;
+        return this$.name;
+    }
+    get Type_() {
+        let matchValue, o;
+        const this$ = this;
+        return unwrap((matchValue = this$.TryGetPropertyValue("type"), (matchValue != null) ? ((o = value(matchValue), (o instanceof CWLType) ? o : undefined)) : undefined));
+    }
+    get InputBinding() {
+        let matchValue, o;
+        const this$ = this;
+        return unwrap((matchValue = this$.TryGetPropertyValue("inputBinding"), (matchValue != null) ? ((o = value(matchValue), (o instanceof InputBinding) ? o : undefined)) : undefined));
+    }
+    get Optional() {
+        let matchValue, o;
+        const this$ = this;
+        return unwrap((matchValue = this$.TryGetPropertyValue("optional"), (matchValue != null) ? ((o = value(matchValue), (typeof o === "boolean") ? o : undefined)) : undefined));
+    }
+}
+
+export function CWLInput_$reflection() {
+    return class_type("ARCtrl.CWL.CWLInput", undefined, CWLInput, DynamicObj_$reflection());
+}
+
+export function CWLInput_$ctor_Z3A15BEDB(name, type_, inputBinding, optional) {
+    return new CWLInput(name, type_, inputBinding, optional);
+}
+