@nfdi4plants/arctrl 2.5.1 → 3.0.0-alpha.2

package/dist/ts/cjs/ts/Core/Conversion.js

@@ -0,0 +1,1131 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.Person_createAssayIdentifierKey = exports.Person_AssayIdentifierPrefix = exports.Person_orcidKey = void 0;
+exports.Person_setSourceAssayComment = Person_setSourceAssayComment;
+exports.Person_getSourceAssayIdentifiersFromComments = Person_getSourceAssayIdentifiersFromComments;
+exports.Person_removeSourceAssayComments = Person_removeSourceAssayComments;
+exports.Person_setOrcidFromComments = Person_setOrcidFromComments;
+exports.Person_setCommentFromORCID = Person_setCommentFromORCID;
+exports.JsonTypes_valueOfCell = JsonTypes_valueOfCell;
+exports.JsonTypes_composeComponent = JsonTypes_composeComponent;
+exports.JsonTypes_composeParameterValue = JsonTypes_composeParameterValue;
+exports.JsonTypes_composeFactorValue = JsonTypes_composeFactorValue;
+exports.JsonTypes_composeCharacteristicValue = JsonTypes_composeCharacteristicValue;
+exports.JsonTypes_composeFreetextMaterialName = JsonTypes_composeFreetextMaterialName;
+exports.JsonTypes_composeProcessInput = JsonTypes_composeProcessInput;
+exports.JsonTypes_composeProcessOutput = JsonTypes_composeProcessOutput;
+exports.JsonTypes_cellOfValue = JsonTypes_cellOfValue;
+exports.JsonTypes_decomposeComponent = JsonTypes_decomposeComponent;
+exports.JsonTypes_decomposeParameterValue = JsonTypes_decomposeParameterValue;
+exports.JsonTypes_decomposeFactorValue = JsonTypes_decomposeFactorValue;
+exports.JsonTypes_decomposeCharacteristicValue = JsonTypes_decomposeCharacteristicValue;
+exports.JsonTypes_decomposeProcessInput = JsonTypes_decomposeProcessInput;
+exports.JsonTypes_decomposeProcessOutput = JsonTypes_decomposeProcessOutput;
+exports.JsonTypes_composeTechnologyPlatform = JsonTypes_composeTechnologyPlatform;
+exports.JsonTypes_decomposeTechnologyPlatform = JsonTypes_decomposeTechnologyPlatform;
+exports.ProcessParsing_tryComponentGetter = ProcessParsing_tryComponentGetter;
+exports.ProcessParsing_tryParameterGetter = ProcessParsing_tryParameterGetter;
+exports.ProcessParsing_tryFactorGetter = ProcessParsing_tryFactorGetter;
+exports.ProcessParsing_tryCharacteristicGetter = ProcessParsing_tryCharacteristicGetter;
+exports.ProcessParsing_tryGetProtocolTypeGetter = ProcessParsing_tryGetProtocolTypeGetter;
+exports.ProcessParsing_tryGetProtocolREFGetter = ProcessParsing_tryGetProtocolREFGetter;
+exports.ProcessParsing_tryGetProtocolDescriptionGetter = ProcessParsing_tryGetProtocolDescriptionGetter;
+exports.ProcessParsing_tryGetProtocolURIGetter = ProcessParsing_tryGetProtocolURIGetter;
+exports.ProcessParsing_tryGetProtocolVersionGetter = ProcessParsing_tryGetProtocolVersionGetter;
+exports.ProcessParsing_tryGetInputGetter = ProcessParsing_tryGetInputGetter;
+exports.ProcessParsing_tryGetOutputGetter = ProcessParsing_tryGetOutputGetter;
+exports.ProcessParsing_tryGetCommentGetter = ProcessParsing_tryGetCommentGetter;
+exports.ProcessParsing_getProcessGetter = ProcessParsing_getProcessGetter;
+exports.ProcessParsing_groupProcesses = ProcessParsing_groupProcesses;
+exports.ProcessParsing_mergeIdenticalProcesses = ProcessParsing_mergeIdenticalProcesses;
+exports.ProcessParsing_processToRows = ProcessParsing_processToRows;
+exports.ARCtrl_CompositeHeader__CompositeHeader_TryParameter = ARCtrl_CompositeHeader__CompositeHeader_TryParameter;
+exports.ARCtrl_CompositeHeader__CompositeHeader_TryFactor = ARCtrl_CompositeHeader__CompositeHeader_TryFactor;
+exports.ARCtrl_CompositeHeader__CompositeHeader_TryCharacteristic = ARCtrl_CompositeHeader__CompositeHeader_TryCharacteristic;
+exports.ARCtrl_CompositeHeader__CompositeHeader_TryComponent = ARCtrl_CompositeHeader__CompositeHeader_TryComponent;
+exports.ARCtrl_CompositeCell__CompositeCell_fromValue_Static_Z6986DF18 = ARCtrl_CompositeCell__CompositeCell_fromValue_Static_Z6986DF18;
+exports.CompositeRow_toProtocol = CompositeRow_toProtocol;
+exports.ARCtrl_ArcTable__ArcTable_fromProtocol_Static_3BF20962 = ARCtrl_ArcTable__ArcTable_fromProtocol_Static_3BF20962;
+exports.ARCtrl_ArcTable__ArcTable_GetProtocols = ARCtrl_ArcTable__ArcTable_GetProtocols;
+exports.ARCtrl_ArcTable__ArcTable_GetProcesses = ARCtrl_ArcTable__ArcTable_GetProcesses;
+exports.ARCtrl_ArcTable__ArcTable_fromProcesses_Static = ARCtrl_ArcTable__ArcTable_fromProcesses_Static;
+exports.ARCtrl_ArcTables__ArcTables_GetProcesses = ARCtrl_ArcTables__ArcTables_GetProcesses;
+exports.ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D = ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D;
+const String_js_1 = require("@fable-org/fable-library-js/String.js");
+const Comment_js_1 = require("./Comment.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const Collections_js_1 = require("./Helper/Collections.js");
+const OntologyAnnotation_js_1 = require("./OntologyAnnotation.js");
+const Value_js_1 = require("./Value.js");
+const CompositeCell_js_1 = require("./Table/CompositeCell.js");
+const Component_js_1 = require("./Process/Component.js");
+const CompositeHeader_js_1 = require("./Table/CompositeHeader.js");
+const ProtocolParameter_js_1 = require("./Process/ProtocolParameter.js");
+const ProcessParameterValue_js_1 = require("./Process/ProcessParameterValue.js");
+const FactorValue_js_1 = require("./Process/FactorValue.js");
+const Factor_js_1 = require("./Process/Factor.js");
+const Types_js_1 = require("@fable-org/fable-library-js/Types.js");
+const MaterialAttributeValue_js_1 = require("./Process/MaterialAttributeValue.js");
+const MaterialAttribute_js_1 = require("./Process/MaterialAttribute.js");
+const ProcessInput_js_1 = require("./Process/ProcessInput.js");
+const ProcessOutput_js_1 = require("./Process/ProcessOutput.js");
+const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
+const Regex_js_1 = require("./Helper/Regex.js");
+const ColumnIndex_js_1 = require("./Process/ColumnIndex.js");
+const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
+const List_js_1 = require("@fable-org/fable-library-js/List.js");
+const Source_js_1 = require("./Process/Source.js");
+const Sample_js_1 = require("./Process/Sample.js");
+const Process_js_1 = require("./Process/Process.js");
+const Protocol_js_1 = require("./Process/Protocol.js");
+const Seq2_js_1 = require("@fable-org/fable-library-js/Seq2.js");
+const Identifier_js_1 = require("./Helper/Identifier.js");
+const HashCodes_js_1 = require("./Helper/HashCodes.js");
+const ArcTable_js_1 = require("./Table/ArcTable.js");
+const Array_js_1 = require("@fable-org/fable-library-js/Array.js");
+const Range_js_1 = require("@fable-org/fable-library-js/Range.js");
+const ArcTableAux_js_1 = require("./Table/ArcTableAux.js");
+const ArcTables_js_1 = require("./Table/ArcTables.js");
+exports.Person_orcidKey = "ORCID";
+exports.Person_AssayIdentifierPrefix = "performer (ARC:00000168)";
+exports.Person_createAssayIdentifierKey = (() => {
+    const clo_1 = (0, String_js_1.toText)((0, String_js_1.printf)("%s %s"))(exports.Person_AssayIdentifierPrefix);
+    return clo_1;
+})();
+function Person_setSourceAssayComment(person, assayIdentifier) {
+    const person_1 = person.Copy();
+    const comment = new Comment_js_1.Comment$((0, exports.Person_createAssayIdentifierKey)(assayIdentifier), assayIdentifier);
+    void (person_1.Comments.push(comment));
+    return person_1;
+}
+/**
+ * This functions helps encoding/decoding ISA-JSON. It returns a sequence of ArcAssay-Identifiers.
+ */
+function Person_getSourceAssayIdentifiersFromComments(person) {
+    return (0, Seq_js_1.choose)((c) => {
+        if ((0, Option_js_1.defaultArg)((0, Option_js_1.map)((n) => n.startsWith(exports.Person_AssayIdentifierPrefix), c.Name), false)) {
+            return c.Value;
+        }
+        else {
+            return undefined;
+        }
+    }, person.Comments);
+}
+function Person_removeSourceAssayComments(person) {
+    return (0, Collections_js_1.ResizeArray_filter)((c) => {
+        if (c.Name != null) {
+            return !(0, Option_js_1.value)(c.Name).startsWith(exports.Person_AssayIdentifierPrefix);
+        }
+        else {
+            return false;
+        }
+    }, person.Comments);
+}
+function Person_setOrcidFromComments(person) {
+    const person_1 = person.Copy();
+    const isOrcidComment = (c) => {
+        if (c.Name != null) {
+            return (0, Option_js_1.value)(c.Name).toLocaleUpperCase().endsWith(exports.Person_orcidKey);
+        }
+        else {
+            return false;
+        }
+    };
+    const patternInput = [(0, Seq_js_1.tryPick)((c_1) => {
+            if (isOrcidComment(c_1)) {
+                return c_1.Value;
+            }
+            else {
+                return undefined;
+            }
+        }, person_1.Comments), (0, Collections_js_1.ResizeArray_filter)((arg) => !isOrcidComment(arg), person_1.Comments)];
+    person_1.ORCID = patternInput[0];
+    person_1.Comments = patternInput[1];
+    return person_1;
+}
+function Person_setCommentFromORCID(person) {
+    const person_1 = person.Copy();
+    const matchValue = person_1.ORCID;
+    if (matchValue == null) {
+    }
+    else {
+        const orcid = (0, Option_js_1.value)(matchValue);
+        const comment = Comment_js_1.Comment$.create(exports.Person_orcidKey, orcid);
+        void (person_1.Comments.push(comment));
+    }
+    return person_1;
+}
+/**
+ * Convert a CompositeCell to a ISA Value and Unit tuple.
+ */
+function JsonTypes_valueOfCell(value) {
+    let term;
+    switch (value.tag) {
+        case /* Term */ 0:
+            if ((term = value.fields[0], term.isEmpty())) {
+                const term_1 = value.fields[0];
+                return [undefined, undefined];
+            }
+            else {
+                const term_2 = value.fields[0];
+                return [(0, Value_js_1.Value_Ontology)(term_2), undefined];
+            }
+        case /* Unitized */ 2: {
+            const text_1 = value.fields[0];
+            const unit = value.fields[1];
+            return [(text_1 === "") ? undefined : Value_js_1.Value.fromString(text_1), unit.isEmpty() ? undefined : unit];
+        }
+        case /* Data */ 3: {
+            const data = value.fields[0];
+            throw new Error("Data cell should not be parsed to isa value");
+        }
+        default:
+            if (value.fields[0] === "") {
+                return [undefined, undefined];
+            }
+            else {
+                const text = value.fields[0];
+                return [Value_js_1.Value.fromString(text), undefined];
+            }
+    }
+}
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA Component
+ */
+function JsonTypes_composeComponent(header, value) {
+    const patternInput = JsonTypes_valueOfCell(value);
+    return (0, Component_js_1.Component_create_Z2F0B38C7)((0, Option_js_1.unwrap)(patternInput[0]), (0, Option_js_1.unwrap)(patternInput[1]), header.ToTerm());
+}
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA ProcessParameterValue
+ */
+function JsonTypes_composeParameterValue(header, value) {
+    const patternInput = JsonTypes_valueOfCell(value);
+    const p = ProtocolParameter_js_1.ProtocolParameter.create(undefined, header.ToTerm());
+    return ProcessParameterValue_js_1.ProcessParameterValue.create(p, (0, Option_js_1.unwrap)(patternInput[0]), (0, Option_js_1.unwrap)(patternInput[1]));
+}
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA FactorValue
+ */
+function JsonTypes_composeFactorValue(header, value) {
+    const patternInput = JsonTypes_valueOfCell(value);
+    return (0, FactorValue_js_1.FactorValue_create_30BDC49)(undefined, Factor_js_1.Factor.create((0, Types_js_1.toString)(header), header.ToTerm()), (0, Option_js_1.unwrap)(patternInput[0]), (0, Option_js_1.unwrap)(patternInput[1]));
+}
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA MaterialAttributeValue
+ */
+function JsonTypes_composeCharacteristicValue(header, value) {
+    const patternInput = JsonTypes_valueOfCell(value);
+    return (0, MaterialAttributeValue_js_1.MaterialAttributeValue_create_ZE1D108D)(undefined, (0, MaterialAttribute_js_1.MaterialAttribute_create_A220A8A)(undefined, header.ToTerm()), (0, Option_js_1.unwrap)(patternInput[0]), (0, Option_js_1.unwrap)(patternInput[1]));
+}
+function JsonTypes_composeFreetextMaterialName(headerFT, name) {
+    return `${headerFT}=${name}`;
+}
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA ProcessInput
+ */
+function JsonTypes_composeProcessInput(header, value) {
+    if (header.tag === /* Input */ 11) {
+        switch (header.fields[0].tag) {
+            case /* Sample */ 1:
+                return (0, ProcessInput_js_1.ProcessInput_createSample_Z598187B7)((0, Types_js_1.toString)(value));
+            case /* Material */ 3:
+                return (0, ProcessInput_js_1.ProcessInput_createMaterial_4452CB4C)((0, Types_js_1.toString)(value));
+            case /* Data */ 2:
+                return (0, ProcessInput_js_1.ProcessInput_createRawData_Z721C83C5)((0, Types_js_1.toString)(value));
+            case /* FreeText */ 4: {
+                const ft = header.fields[0].fields[0];
+                return (0, ProcessInput_js_1.ProcessInput_createMaterial_4452CB4C)(JsonTypes_composeFreetextMaterialName(ft, (0, Types_js_1.toString)(value)));
+            }
+            default:
+                return (0, ProcessInput_js_1.ProcessInput_createSource_Z5E00540E)((0, Types_js_1.toString)(value));
+        }
+    }
+    else {
+        return (0, String_js_1.toFail)((0, String_js_1.printf)("Could not parse input header %O"))(header);
+    }
+}
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA ProcessOutput
+ */
+function JsonTypes_composeProcessOutput(header, value) {
+    let matchResult, ft;
+    if (header.tag === /* Output */ 12) {
+        switch (header.fields[0].tag) {
+            case /* Material */ 3: {
+                matchResult = 1;
+                break;
+            }
+            case /* Data */ 2: {
+                matchResult = 2;
+                break;
+            }
+            case /* FreeText */ 4: {
+                matchResult = 3;
+                ft = header.fields[0].fields[0];
+                break;
+            }
+            default:
+                matchResult = 0;
+        }
+    }
+    else {
+        matchResult = 4;
+    }
+    switch (matchResult) {
+        case 0:
+            return (0, ProcessOutput_js_1.ProcessOutput_createSample_Z598187B7)((0, Types_js_1.toString)(value));
+        case 1:
+            return (0, ProcessOutput_js_1.ProcessOutput_createMaterial_4452CB4C)((0, Types_js_1.toString)(value));
+        case 2:
+            return (0, ProcessOutput_js_1.ProcessOutput_createRawData_Z721C83C5)((0, Types_js_1.toString)(value));
+        case 3:
+            return (0, ProcessOutput_js_1.ProcessOutput_createMaterial_4452CB4C)(JsonTypes_composeFreetextMaterialName(ft, (0, Types_js_1.toString)(value)));
+        default:
+            return (0, String_js_1.toFail)((0, String_js_1.printf)("Could not parse output header %O"))(header);
+    }
+}
+/**
+ * Convert an ISA Value and Unit tuple to a CompositeCell
+ */
+function JsonTypes_cellOfValue(value, unit) {
+    const value_2 = (0, Option_js_1.defaultArg)(value, (0, Value_js_1.Value_Name)(""));
+    let matchResult, oa, text, name, u, f, u_1, f_1, i, u_2, i_1;
+    switch (value_2.tag) {
+        case /* Name */ 3: {
+            if (value_2.fields[0] === "") {
+                if (unit != null) {
+                    matchResult = 3;
+                    name = value_2.fields[0];
+                    u = (0, Option_js_1.value)(unit);
+                }
+                else {
+                    matchResult = 1;
+                }
+            }
+            else if (unit != null) {
+                matchResult = 3;
+                name = value_2.fields[0];
+                u = (0, Option_js_1.value)(unit);
+            }
+            else {
+                matchResult = 2;
+                text = value_2.fields[0];
+            }
+            break;
+        }
+        case /* Float */ 2: {
+            if (unit == null) {
+                matchResult = 5;
+                f_1 = value_2.fields[0];
+            }
+            else {
+                matchResult = 4;
+                f = value_2.fields[0];
+                u_1 = (0, Option_js_1.value)(unit);
+            }
+            break;
+        }
+        case /* Int */ 1: {
+            if (unit == null) {
+                matchResult = 7;
+                i_1 = value_2.fields[0];
+            }
+            else {
+                matchResult = 6;
+                i = value_2.fields[0];
+                u_2 = (0, Option_js_1.value)(unit);
+            }
+            break;
+        }
+        default:
+            if (unit == null) {
+                matchResult = 0;
+                oa = value_2.fields[0];
+            }
+            else {
+                matchResult = 8;
+            }
+    }
+    switch (matchResult) {
+        case 0:
+            return (0, CompositeCell_js_1.CompositeCell_Term)(oa);
+        case 1:
+            return (0, CompositeCell_js_1.CompositeCell_Term)(new OntologyAnnotation_js_1.OntologyAnnotation());
+        case 2:
+            return (0, CompositeCell_js_1.CompositeCell_Term)(new OntologyAnnotation_js_1.OntologyAnnotation(text));
+        case 3:
+            return (0, CompositeCell_js_1.CompositeCell_Unitized)(name, u);
+        case 4:
+            return (0, CompositeCell_js_1.CompositeCell_Unitized)(f.toString(), u_1);
+        case 5:
+            return (0, CompositeCell_js_1.CompositeCell_Unitized)(f_1.toString(), new OntologyAnnotation_js_1.OntologyAnnotation());
+        case 6:
+            return (0, CompositeCell_js_1.CompositeCell_Unitized)((0, Util_js_1.int32ToString)(i), u_2);
+        case 7:
+            return (0, CompositeCell_js_1.CompositeCell_Unitized)((0, Util_js_1.int32ToString)(i_1), new OntologyAnnotation_js_1.OntologyAnnotation());
+        default:
+            return (0, String_js_1.toFail)((0, String_js_1.printf)("Could not parse value %O with unit %O"))(value_2)(unit);
+    }
+}
+/**
+ * Convert an ISA Component to a CompositeHeader and Cell tuple
+ */
+function JsonTypes_decomposeComponent(c) {
+    return [(0, CompositeHeader_js_1.CompositeHeader_Component)((0, Option_js_1.value)(c.ComponentType)), JsonTypes_cellOfValue(c.ComponentValue, c.ComponentUnit)];
+}
+/**
+ * Convert an ISA ProcessParameterValue to a CompositeHeader and Cell tuple
+ */
+function JsonTypes_decomposeParameterValue(ppv) {
+    return [(0, CompositeHeader_js_1.CompositeHeader_Parameter)((0, Option_js_1.value)((0, Option_js_1.value)(ppv.Category).ParameterName)), JsonTypes_cellOfValue(ppv.Value, ppv.Unit)];
+}
+/**
+ * Convert an ISA FactorValue to a CompositeHeader and Cell tuple
+ */
+function JsonTypes_decomposeFactorValue(fv) {
+    return [(0, CompositeHeader_js_1.CompositeHeader_Factor)((0, Option_js_1.value)((0, Option_js_1.value)(fv.Category).FactorType)), JsonTypes_cellOfValue(fv.Value, fv.Unit)];
+}
+/**
+ * Convert an ISA MaterialAttributeValue to a CompositeHeader and Cell tuple
+ */
+function JsonTypes_decomposeCharacteristicValue(cv) {
+    return [(0, CompositeHeader_js_1.CompositeHeader_Characteristic)((0, Option_js_1.value)((0, Option_js_1.value)(cv.Category).CharacteristicType)), JsonTypes_cellOfValue(cv.Value, cv.Unit)];
+}
+/**
+ * Convert an ISA ProcessOutput to a CompositeHeader and Cell tuple
+ */
+function JsonTypes_decomposeProcessInput(pi) {
+    switch (pi.tag) {
+        case /* Sample */ 1:
+            return [(0, CompositeHeader_js_1.CompositeHeader_Input)((0, CompositeHeader_js_1.IOType_Sample)()), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.defaultArg)(pi.fields[0].Name, ""))];
+        case /* Material */ 3:
+            return [(0, CompositeHeader_js_1.CompositeHeader_Input)((0, CompositeHeader_js_1.IOType_Material)()), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.defaultArg)(pi.fields[0].Name, ""))];
+        case /* Data */ 2: {
+            const d = pi.fields[0];
+            const dataType = (0, Option_js_1.value)(d.DataType);
+            switch (dataType.tag) {
+                case /* RawDataFile */ 0:
+                    return [(0, CompositeHeader_js_1.CompositeHeader_Input)((0, CompositeHeader_js_1.IOType_Data)()), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.defaultArg)(d.Name, ""))];
+                case /* DerivedDataFile */ 1:
+                    return [(0, CompositeHeader_js_1.CompositeHeader_Input)((0, CompositeHeader_js_1.IOType_Data)()), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.defaultArg)(d.Name, ""))];
+                default:
+                    return [(0, CompositeHeader_js_1.CompositeHeader_Input)((0, CompositeHeader_js_1.IOType_Data)()), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.defaultArg)(d.Name, ""))];
+            }
+        }
+        default:
+            return [(0, CompositeHeader_js_1.CompositeHeader_Input)((0, CompositeHeader_js_1.IOType_Source)()), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.defaultArg)(pi.fields[0].Name, ""))];
+    }
+}
+/**
+ * Convert an ISA ProcessOutput to a CompositeHeader and Cell tuple
+ */
+function JsonTypes_decomposeProcessOutput(po) {
+    switch (po.tag) {
+        case /* Material */ 2:
+            return [(0, CompositeHeader_js_1.CompositeHeader_Output)((0, CompositeHeader_js_1.IOType_Material)()), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.defaultArg)(po.fields[0].Name, ""))];
+        case /* Data */ 1: {
+            const d = po.fields[0];
+            const dataType = (0, Option_js_1.value)(d.DataType);
+            switch (dataType.tag) {
+                case /* RawDataFile */ 0:
+                    return [(0, CompositeHeader_js_1.CompositeHeader_Output)((0, CompositeHeader_js_1.IOType_Data)()), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.defaultArg)(d.Name, ""))];
+                case /* DerivedDataFile */ 1:
+                    return [(0, CompositeHeader_js_1.CompositeHeader_Output)((0, CompositeHeader_js_1.IOType_Data)()), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.defaultArg)(d.Name, ""))];
+                default:
+                    return [(0, CompositeHeader_js_1.CompositeHeader_Output)((0, CompositeHeader_js_1.IOType_Data)()), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.defaultArg)(d.Name, ""))];
+            }
+        }
+        default:
+            return [(0, CompositeHeader_js_1.CompositeHeader_Output)((0, CompositeHeader_js_1.IOType_Sample)()), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.defaultArg)(po.fields[0].Name, ""))];
+    }
+}
+/**
+ * This function creates a string containing the name and the ontology short-string of the given ontology annotation term
+ *
+ * TechnologyPlatforms are plain strings in ISA-JSON.
+ *
+ * This function allows us, to parse them as an ontology term.
+ */
+function JsonTypes_composeTechnologyPlatform(tp) {
+    const matchValue = tp.TANInfo;
+    if (matchValue == null) {
+        return `${tp.NameText}`;
+    }
+    else {
+        return `${tp.NameText} (${tp.TermAccessionShort})`;
+    }
+}
+/**
+ * This function parses the given string containing the name and the ontology short-string of the given ontology annotation term
+ *
+ * TechnologyPlatforms are plain strings in ISA-JSON.
+ *
+ * This function allows us, to parse them as an ontology term.
+ */
+function JsonTypes_decomposeTechnologyPlatform(name) {
+    const activePatternResult = (0, Regex_js_1.ActivePatterns_$007CRegex$007C_$007C)("^(?<value>.+) \\((?<ontology>[^(]*:[^)]*)\\)$", name);
+    if (activePatternResult != null) {
+        const r = (0, Option_js_1.value)(activePatternResult);
+        let oa;
+        const tan = (r.groups && r.groups.ontology) || "";
+        oa = OntologyAnnotation_js_1.OntologyAnnotation.fromTermAnnotation(tan);
+        const v = (r.groups && r.groups.value) || "";
+        return OntologyAnnotation_js_1.OntologyAnnotation.create(v, (0, Option_js_1.unwrap)(oa.TermSourceREF), (0, Option_js_1.unwrap)(oa.TermAccessionNumber));
+    }
+    else {
+        return OntologyAnnotation_js_1.OntologyAnnotation.create(name);
+    }
+}
+/**
+ * If the given headers depict a component, returns a function for parsing the values of the matrix to the values of this component
+ */
+function ProcessParsing_tryComponentGetter(generalI, valueI, valueHeader) {
+    if (valueHeader.tag === /* Component */ 0) {
+        const oa = valueHeader.fields[0];
+        const newOA = oa.Copy();
+        (0, ColumnIndex_js_1.ARCtrl_OntologyAnnotation__OntologyAnnotation_SetColumnIndex_Z524259A4)(newOA, valueI);
+        return (matrix) => ((i) => JsonTypes_composeComponent((0, CompositeHeader_js_1.CompositeHeader_Component)(newOA), (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i])));
+    }
+    else {
+        return undefined;
+    }
+}
+/**
+ * If the given headers depict a parameter, returns a function for parsing the values of the matrix to the values of this type
+ */
+function ProcessParsing_tryParameterGetter(generalI, valueI, valueHeader) {
+    if (valueHeader.tag === /* Parameter */ 3) {
+        const cat = (0, CompositeHeader_js_1.CompositeHeader_Parameter)((0, ColumnIndex_js_1.ARCtrl_OntologyAnnotation__OntologyAnnotation_setColumnIndex_Static)(valueI, valueHeader.fields[0]));
+        return (matrix) => ((i_1) => JsonTypes_composeParameterValue(cat, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i_1])));
+    }
+    else {
+        return undefined;
+    }
+}
+/**
+ * If the given headers depict a factor, returns a function for parsing the values of the matrix to the values of this type
+ */
+function ProcessParsing_tryFactorGetter(generalI, valueI, valueHeader) {
+    if (valueHeader.tag === /* Factor */ 2) {
+        const cat = (0, CompositeHeader_js_1.CompositeHeader_Factor)((0, ColumnIndex_js_1.ARCtrl_OntologyAnnotation__OntologyAnnotation_setColumnIndex_Static)(valueI, valueHeader.fields[0]));
+        return (matrix) => ((i_1) => JsonTypes_composeFactorValue(cat, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i_1])));
+    }
+    else {
+        return undefined;
+    }
+}
+/**
+ * If the given headers depict a protocolType, returns a function for parsing the values of the matrix to the values of this type
+ */
+function ProcessParsing_tryCharacteristicGetter(generalI, valueI, valueHeader) {
+    if (valueHeader.tag === /* Characteristic */ 1) {
+        const cat = (0, CompositeHeader_js_1.CompositeHeader_Characteristic)((0, ColumnIndex_js_1.ARCtrl_OntologyAnnotation__OntologyAnnotation_setColumnIndex_Static)(valueI, valueHeader.fields[0]));
+        return (matrix) => ((i_1) => JsonTypes_composeCharacteristicValue(cat, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i_1])));
+    }
+    else {
+        return undefined;
+    }
+}
+/**
+ * If the given headers depict a protocolType, returns a function for parsing the values of the matrix to the values of this type
+ */
+function ProcessParsing_tryGetProtocolTypeGetter(generalI, header) {
+    if (header.tag === /* ProtocolType */ 4) {
+        return (matrix) => ((i) => (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsTerm);
+    }
+    else {
+        return undefined;
+    }
+}
+/**
+ * If the given headers depict a protocolREF, returns a function for parsing the values of the matrix to the values of this type
+ */
+function ProcessParsing_tryGetProtocolREFGetter(generalI, header) {
+    if (header.tag === /* ProtocolREF */ 8) {
+        return (matrix) => ((i) => (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsFreeText);
+    }
+    else {
+        return undefined;
+    }
+}
+/**
+ * If the given headers depict a protocolDescription, returns a function for parsing the values of the matrix to the values of this type
+ */
+function ProcessParsing_tryGetProtocolDescriptionGetter(generalI, header) {
+    if (header.tag === /* ProtocolDescription */ 5) {
+        return (matrix) => ((i) => (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsFreeText);
+    }
+    else {
+        return undefined;
+    }
+}
+/**
+ * If the given headers depict a protocolURI, returns a function for parsing the values of the matrix to the values of this type
+ */
+function ProcessParsing_tryGetProtocolURIGetter(generalI, header) {
+    if (header.tag === /* ProtocolUri */ 6) {
+        return (matrix) => ((i) => (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsFreeText);
+    }
+    else {
+        return undefined;
+    }
+}
+/**
+ * If the given headers depict a protocolVersion, returns a function for parsing the values of the matrix to the values of this type
+ */
+function ProcessParsing_tryGetProtocolVersionGetter(generalI, header) {
+    if (header.tag === /* ProtocolVersion */ 7) {
+        return (matrix) => ((i) => (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsFreeText);
+    }
+    else {
+        return undefined;
+    }
+}
+/**
+ * If the given headers depict an input, returns a function for parsing the values of the matrix to the values of this type
+ */
+function ProcessParsing_tryGetInputGetter(generalI, header) {
+    if (header.tag === /* Input */ 11) {
+        const io = header.fields[0];
+        return (matrix) => ((i) => JsonTypes_composeProcessInput(header, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i])));
+    }
+    else {
+        return undefined;
+    }
+}
+/**
+ * If the given headers depict an output, returns a function for parsing the values of the matrix to the values of this type
+ */
+function ProcessParsing_tryGetOutputGetter(generalI, header) {
+    if (header.tag === /* Output */ 12) {
+        const io = header.fields[0];
+        return (matrix) => ((i) => JsonTypes_composeProcessOutput(header, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i])));
+    }
+    else {
+        return undefined;
+    }
+}
+/**
+ * If the given headers depict a comment, returns a function for parsing the values of the matrix to the values of this type
+ */
+function ProcessParsing_tryGetCommentGetter(generalI, header) {
+    if (header.tag === /* Comment */ 14) {
+        const c = header.fields[0];
+        return (matrix) => ((i) => (new Comment_js_1.Comment$(c, (0, MapUtil_js_1.getItemFromDict)(matrix, [generalI, i]).AsFreeText)));
+    }
+    else {
+        return undefined;
+    }
+}
+/**
+ * Given the header sequence of an ArcTable, returns a function for parsing each row of the table to a process
+ */
+function ProcessParsing_getProcessGetter(processNameRoot, headers) {
+    const headers_1 = (0, Seq_js_1.indexed)(headers);
+    const valueHeaders = (0, Seq_js_1.toList)((0, Seq_js_1.indexed)((0, Seq_js_1.filter)((arg) => arg[1].IsCvParamColumn, headers_1)));
+    const charGetters = (0, List_js_1.choose)((tupledArg) => {
+        const _arg = tupledArg[1];
+        return ProcessParsing_tryCharacteristicGetter(_arg[0], tupledArg[0], _arg[1]);
+    }, valueHeaders);
+    const factorValueGetters = (0, List_js_1.choose)((tupledArg_1) => {
+        const _arg_1 = tupledArg_1[1];
+        return ProcessParsing_tryFactorGetter(_arg_1[0], tupledArg_1[0], _arg_1[1]);
+    }, valueHeaders);
+    const parameterValueGetters = (0, List_js_1.choose)((tupledArg_2) => {
+        const _arg_2 = tupledArg_2[1];
+        return ProcessParsing_tryParameterGetter(_arg_2[0], tupledArg_2[0], _arg_2[1]);
+    }, valueHeaders);
+    const componentGetters = (0, List_js_1.choose)((tupledArg_3) => {
+        const _arg_3 = tupledArg_3[1];
+        return ProcessParsing_tryComponentGetter(_arg_3[0], tupledArg_3[0], _arg_3[1]);
+    }, valueHeaders);
+    const protocolTypeGetter = (0, Seq_js_1.tryPick)((tupledArg_4) => ProcessParsing_tryGetProtocolTypeGetter(tupledArg_4[0], tupledArg_4[1]), headers_1);
+    const protocolREFGetter = (0, Seq_js_1.tryPick)((tupledArg_5) => ProcessParsing_tryGetProtocolREFGetter(tupledArg_5[0], tupledArg_5[1]), headers_1);
+    const protocolDescriptionGetter = (0, Seq_js_1.tryPick)((tupledArg_6) => ProcessParsing_tryGetProtocolDescriptionGetter(tupledArg_6[0], tupledArg_6[1]), headers_1);
+    const protocolURIGetter = (0, Seq_js_1.tryPick)((tupledArg_7) => ProcessParsing_tryGetProtocolURIGetter(tupledArg_7[0], tupledArg_7[1]), headers_1);
+    const protocolVersionGetter = (0, Seq_js_1.tryPick)((tupledArg_8) => ProcessParsing_tryGetProtocolVersionGetter(tupledArg_8[0], tupledArg_8[1]), headers_1);
+    const commentGetters = (0, Seq_js_1.toList)((0, Seq_js_1.choose)((tupledArg_9) => ProcessParsing_tryGetCommentGetter(tupledArg_9[0], tupledArg_9[1]), headers_1));
+    let inputGetter_1;
+    const matchValue = (0, Seq_js_1.tryPick)((tupledArg_10) => ProcessParsing_tryGetInputGetter(tupledArg_10[0], tupledArg_10[1]), headers_1);
+    if (matchValue == null) {
+        inputGetter_1 = ((matrix_1) => ((i_1) => (0, List_js_1.singleton)((0, ProcessInput_js_1.ProcessInput_Source)((0, Source_js_1.Source_create_Z5CA08497)(undefined, `${processNameRoot}_Input_${i_1}`, (0, Seq_js_1.toList)((0, Seq_js_1.map)((f_1) => f_1(matrix_1)(i_1), charGetters)))))));
+    }
+    else {
+        const inputGetter = (0, Option_js_1.value)(matchValue);
+        inputGetter_1 = ((matrix) => ((i) => {
+            const chars = (0, Seq_js_1.toList)((0, Seq_js_1.map)((f) => f(matrix)(i), charGetters));
+            const input = inputGetter(matrix)(i);
+            return (!((0, ProcessInput_js_1.ProcessInput__isSample)(input) ? true : (0, ProcessInput_js_1.ProcessInput__isSource)(input)) && !(0, List_js_1.isEmpty)(chars)) ? (0, List_js_1.ofArray)([input, (0, ProcessInput_js_1.ProcessInput_createSample_Z598187B7)((0, ProcessInput_js_1.ProcessInput__get_Name)(input), chars)]) : (0, List_js_1.singleton)(((0, List_js_1.length)(chars) > 0) ? (0, ProcessInput_js_1.ProcessInput_setCharacteristicValues)(chars, input) : input);
+        }));
+    }
+    let outputGetter_1;
+    const matchValue_1 = (0, Seq_js_1.tryPick)((tupledArg_11) => ProcessParsing_tryGetOutputGetter(tupledArg_11[0], tupledArg_11[1]), headers_1);
+    if (matchValue_1 == null) {
+        outputGetter_1 = ((matrix_3) => ((i_3) => (0, List_js_1.singleton)((0, ProcessOutput_js_1.ProcessOutput_Sample)((0, Sample_js_1.Sample_create_62424AD2)(undefined, `${processNameRoot}_Output_${i_3}`, undefined, (0, Seq_js_1.toList)((0, Seq_js_1.map)((f_3) => f_3(matrix_3)(i_3), factorValueGetters)))))));
+    }
+    else {
+        const outputGetter = (0, Option_js_1.value)(matchValue_1);
+        outputGetter_1 = ((matrix_2) => ((i_2) => {
+            const factors = (0, Seq_js_1.toList)((0, Seq_js_1.map)((f_2) => f_2(matrix_2)(i_2), factorValueGetters));
+            const output = outputGetter(matrix_2)(i_2);
+            return (!(0, ProcessOutput_js_1.ProcessOutput__isSample)(output) && !(0, List_js_1.isEmpty)(factors)) ? (0, List_js_1.ofArray)([output, (0, ProcessOutput_js_1.ProcessOutput_createSample_Z598187B7)((0, ProcessOutput_js_1.ProcessOutput__get_Name)(output), undefined, factors)]) : (0, List_js_1.singleton)(((0, List_js_1.length)(factors) > 0) ? (0, ProcessOutput_js_1.ProcessOutput_setFactorValues)(factors, output) : output);
+        }));
+    }
+    return (matrix_4) => ((i_4) => {
+        const pn = (0, Option_js_1.map)((p) => (0, Process_js_1.Process_composeName)(p, i_4), (0, Collections_js_1.Option_fromValueWithDefault)("", processNameRoot));
+        const paramvalues = (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_4) => f_4(matrix_4)(i_4), parameterValueGetters));
+        const parameters = (0, Option_js_1.map)((list_5) => (0, List_js_1.map)((pv) => (0, Option_js_1.value)(pv.Category), list_5), paramvalues);
+        const comments = (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_5) => f_5(matrix_4)(i_4), commentGetters));
+        let protocol;
+        const p_1 = (0, Protocol_js_1.Protocol_make)(undefined, (0, Option_js_1.map)((f_6) => f_6(matrix_4)(i_4), protocolREFGetter), (0, Option_js_1.map)((f_7) => f_7(matrix_4)(i_4), protocolTypeGetter), (0, Option_js_1.map)((f_8) => f_8(matrix_4)(i_4), protocolDescriptionGetter), (0, Option_js_1.map)((f_9) => f_9(matrix_4)(i_4), protocolURIGetter), (0, Option_js_1.map)((f_10) => f_10(matrix_4)(i_4), protocolVersionGetter), parameters, (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_11) => f_11(matrix_4)(i_4), componentGetters)), undefined);
+        let matchResult;
+        if (p_1.Name == null) {
+            if (p_1.ProtocolType == null) {
+                if (p_1.Description == null) {
+                    if (p_1.Uri == null) {
+                        if (p_1.Version == null) {
+                            if (p_1.Components == null) {
+                                matchResult = 0;
+                            }
+                            else {
+                                matchResult = 1;
+                            }
+                        }
+                        else {
+                            matchResult = 1;
+                        }
+                    }
+                    else {
+                        matchResult = 1;
+                    }
+                }
+                else {
+                    matchResult = 1;
+                }
+            }
+            else {
+                matchResult = 1;
+            }
+        }
+        else {
+            matchResult = 1;
+        }
+        switch (matchResult) {
+            case 0: {
+                protocol = undefined;
+                break;
+            }
+            default:
+                protocol = p_1;
+        }
+        let patternInput;
+        const inputs = inputGetter_1(matrix_4)(i_4);
+        const outputs = outputGetter_1(matrix_4)(i_4);
+        patternInput = ((((0, List_js_1.length)(inputs) === 1) && ((0, List_js_1.length)(outputs) === 2)) ? [(0, List_js_1.ofArray)([(0, List_js_1.item)(0, inputs), (0, List_js_1.item)(0, inputs)]), outputs] : ((((0, List_js_1.length)(inputs) === 2) && ((0, List_js_1.length)(outputs) === 1)) ? [inputs, (0, List_js_1.ofArray)([(0, List_js_1.item)(0, outputs), (0, List_js_1.item)(0, outputs)])] : [inputs, outputs]));
+        return (0, Process_js_1.Process_make)(undefined, pn, protocol, paramvalues, undefined, undefined, undefined, undefined, patternInput[0], patternInput[1], comments);
+    });
+}
+/**
+ * Groups processes by their name, or by the name of the protocol they execute
+ *
+ * Process names are taken from the Worksheet name and numbered: SheetName_1, SheetName_2, etc.
+ *
+ * This function decomposes this name into a root name and a number, and groups processes by root name.
+ */
+function ProcessParsing_groupProcesses(ps) {
+    return (0, Seq2_js_1.List_groupBy)((x) => {
+        if ((x.Name != null) && ((0, Process_js_1.Process_decomposeName_Z721C83C5)((0, Option_js_1.value)(x.Name))[1] != null)) {
+            return (0, Process_js_1.Process_decomposeName_Z721C83C5)((0, Option_js_1.value)(x.Name))[0];
+        }
+        else if ((x.ExecutesProtocol != null) && ((0, Option_js_1.value)(x.ExecutesProtocol).Name != null)) {
+            return (0, Option_js_1.value)((0, Option_js_1.value)(x.ExecutesProtocol).Name);
+        }
+        else if ((x.Name != null) && ((0, Option_js_1.value)(x.Name).indexOf("_") >= 0)) {
+            const lastUnderScoreIndex = (0, Option_js_1.value)(x.Name).lastIndexOf("_") | 0;
+            return (0, String_js_1.remove)((0, Option_js_1.value)(x.Name), lastUnderScoreIndex);
+        }
+        else if (x.Name != null) {
+            return (0, Option_js_1.value)(x.Name);
+        }
+        else if ((x.ExecutesProtocol != null) && ((0, Option_js_1.value)(x.ExecutesProtocol).ID != null)) {
+            return (0, Option_js_1.value)((0, Option_js_1.value)(x.ExecutesProtocol).ID);
+        }
+        else {
+            return (0, Identifier_js_1.createMissingIdentifier)();
+        }
+    }, ps, {
+        Equals: (x_1, y) => (x_1 === y),
+        GetHashCode: Util_js_1.stringHash,
+    });
+}
+/**
+ * Merges processes with the same name, protocol and param values
+ */
+function ProcessParsing_mergeIdenticalProcesses(processes) {
+    const l = (0, Seq2_js_1.List_groupBy)((x) => {
+        if ((x.Name != null) && ((0, Process_js_1.Process_decomposeName_Z721C83C5)((0, Option_js_1.value)(x.Name))[1] != null)) {
+            return [(0, Process_js_1.Process_decomposeName_Z721C83C5)((0, Option_js_1.value)(x.Name))[0], (0, HashCodes_js_1.boxHashOption)(x.ExecutesProtocol), (0, Option_js_1.map)(HashCodes_js_1.boxHashSeq, x.ParameterValues), (0, Option_js_1.map)(HashCodes_js_1.boxHashSeq, x.Comments)];
+        }
+        else if ((x.ExecutesProtocol != null) && ((0, Option_js_1.value)(x.ExecutesProtocol).Name != null)) {
+            return [(0, Option_js_1.value)((0, Option_js_1.value)(x.ExecutesProtocol).Name), (0, HashCodes_js_1.boxHashOption)(x.ExecutesProtocol), (0, Option_js_1.map)(HashCodes_js_1.boxHashSeq, x.ParameterValues), (0, Option_js_1.map)(HashCodes_js_1.boxHashSeq, x.Comments)];
+        }
+        else {
+            return [(0, Identifier_js_1.createMissingIdentifier)(), (0, HashCodes_js_1.boxHashOption)(x.ExecutesProtocol), (0, Option_js_1.map)(HashCodes_js_1.boxHashSeq, x.ParameterValues), (0, Option_js_1.map)(HashCodes_js_1.boxHashSeq, x.Comments)];
+        }
+    }, processes, {
+        Equals: Util_js_1.equalArrays,
+        GetHashCode: Util_js_1.arrayHash,
+    });
+    return (0, List_js_1.mapIndexed)((i, tupledArg) => {
+        const processes_1 = tupledArg[1];
+        const n = tupledArg[0][0];
+        const pVs = (0, List_js_1.item)(0, processes_1).ParameterValues;
+        const inputs = (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.collect)((p) => (0, Option_js_1.defaultArg)(p.Inputs, (0, List_js_1.empty)()), processes_1));
+        const outputs = (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.collect)((p_1) => (0, Option_js_1.defaultArg)(p_1.Outputs, (0, List_js_1.empty)()), processes_1));
+        return (0, Process_js_1.Process_create_Z7C1F7FA9)(undefined, ((0, List_js_1.length)(l) > 1) ? (0, Process_js_1.Process_composeName)(n, i) : n, (0, Option_js_1.unwrap)((0, List_js_1.item)(0, processes_1).ExecutesProtocol), (0, Option_js_1.unwrap)(pVs), undefined, undefined, undefined, undefined, (0, Option_js_1.unwrap)(inputs), (0, Option_js_1.unwrap)(outputs), (0, Option_js_1.unwrap)((0, List_js_1.item)(0, processes_1).Comments));
+    }, l);
+}
+function ProcessParsing_processToRows(p) {
+    let list_4;
+    const pvs = (0, List_js_1.map)((ppv) => [JsonTypes_decomposeParameterValue(ppv), (0, ColumnIndex_js_1.tryGetParameterColumnIndex)(ppv)], (0, Option_js_1.defaultArg)(p.ParameterValues, (0, List_js_1.empty)()));
+    let components;
+    const matchValue = p.ExecutesProtocol;
+    components = ((matchValue == null) ? (0, List_js_1.empty)() : (0, List_js_1.map)((ppv_1) => [JsonTypes_decomposeComponent(ppv_1), (0, ColumnIndex_js_1.tryGetComponentIndex)(ppv_1)], (0, Option_js_1.defaultArg)((0, Option_js_1.value)(matchValue).Components, (0, List_js_1.empty)())));
+    let protVals;
+    const matchValue_1 = p.ExecutesProtocol;
+    if (matchValue_1 == null) {
+        protVals = (0, List_js_1.empty)();
+    }
+    else {
+        const prot_1 = (0, Option_js_1.value)(matchValue_1);
+        protVals = (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((prot_1.Name != null) ? (0, Seq_js_1.singleton)([(0, CompositeHeader_js_1.CompositeHeader_ProtocolREF)(), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.value)(prot_1.Name))]) : (0, Seq_js_1.empty)(), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((prot_1.ProtocolType != null) ? (0, Seq_js_1.singleton)([(0, CompositeHeader_js_1.CompositeHeader_ProtocolType)(), (0, CompositeCell_js_1.CompositeCell_Term)((0, Option_js_1.value)(prot_1.ProtocolType))]) : (0, Seq_js_1.empty)(), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((prot_1.Description != null) ? (0, Seq_js_1.singleton)([(0, CompositeHeader_js_1.CompositeHeader_ProtocolDescription)(), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.value)(prot_1.Description))]) : (0, Seq_js_1.empty)(), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((prot_1.Uri != null) ? (0, Seq_js_1.singleton)([(0, CompositeHeader_js_1.CompositeHeader_ProtocolUri)(), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.value)(prot_1.Uri))]) : (0, Seq_js_1.empty)(), (0, Seq_js_1.delay)(() => ((prot_1.Version != null) ? (0, Seq_js_1.singleton)([(0, CompositeHeader_js_1.CompositeHeader_ProtocolVersion)(), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.value)(prot_1.Version))]) : (0, Seq_js_1.empty)())))))))))));
+    }
+    const comments = (0, List_js_1.map)((c) => [(0, CompositeHeader_js_1.CompositeHeader_Comment)((0, Option_js_1.defaultArg)(c.Name, "")), (0, CompositeCell_js_1.CompositeCell_FreeText)((0, Option_js_1.defaultArg)(c.Value, ""))], (0, Option_js_1.defaultArg)(p.Comments, (0, List_js_1.empty)()));
+    return (0, List_js_1.map)((tupledArg_1) => {
+        const ios = tupledArg_1[1];
+        const inputForCharas = (0, Option_js_1.defaultArg)((0, List_js_1.tryPick)((tupledArg_2) => {
+            const i_2 = tupledArg_2[0];
+            if ((0, ProcessInput_js_1.ProcessInput__isSource)(i_2) ? true : (0, ProcessInput_js_1.ProcessInput__isSample)(i_2)) {
+                return i_2;
+            }
+            else {
+                return undefined;
+            }
+        }, ios), (0, List_js_1.head)(ios)[0]);
+        const inputForType = (0, Option_js_1.defaultArg)((0, List_js_1.tryPick)((tupledArg_3) => {
+            const i_3 = tupledArg_3[0];
+            if ((0, ProcessInput_js_1.ProcessInput__isData)(i_3) ? true : (0, ProcessInput_js_1.ProcessInput__isMaterial)(i_3)) {
+                return i_3;
+            }
+            else {
+                return undefined;
+            }
+        }, ios), (0, List_js_1.head)(ios)[0]);
+        const chars = (0, List_js_1.map)((cv) => [JsonTypes_decomposeCharacteristicValue(cv), (0, ColumnIndex_js_1.tryGetCharacteristicColumnIndex)(cv)], (0, ProcessInput_js_1.ProcessInput_getCharacteristicValues_5B3D5BA9)(inputForCharas));
+        const outputForFactors = (0, Option_js_1.defaultArg)((0, List_js_1.tryPick)((tupledArg_4) => {
+            const o_4 = tupledArg_4[1];
+            if ((0, ProcessOutput_js_1.ProcessOutput__isSample)(o_4)) {
+                return o_4;
+            }
+            else {
+                return undefined;
+            }
+        }, ios), (0, List_js_1.head)(ios)[1]);
+        const outputForType = (0, Option_js_1.defaultArg)((0, List_js_1.tryPick)((tupledArg_5) => {
+            const o_5 = tupledArg_5[1];
+            if ((0, ProcessOutput_js_1.ProcessOutput__isData)(o_5) ? true : (0, ProcessOutput_js_1.ProcessOutput__isMaterial)(o_5)) {
+                return o_5;
+            }
+            else {
+                return undefined;
+            }
+        }, ios), (0, List_js_1.head)(ios)[1]);
+        const vals = (0, List_js_1.map)((tuple_5) => tuple_5[0], (0, List_js_1.sortBy)((arg) => (0, Option_js_1.defaultArg)(arg[1], 10000), (0, List_js_1.append)(chars, (0, List_js_1.append)(components, (0, List_js_1.append)(pvs, (0, List_js_1.map)((fv) => [JsonTypes_decomposeFactorValue(fv), (0, ColumnIndex_js_1.tryGetFactorColumnIndex)(fv)], (0, ProcessOutput_js_1.ProcessOutput_getFactorValues_Z42C11600)(outputForFactors))))), {
+            Compare: Util_js_1.comparePrimitives,
+        }));
+        return (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.append)((0, Seq_js_1.singleton)(JsonTypes_decomposeProcessInput(inputForType)), (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)(protVals, (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)(vals, (0, Seq_js_1.delay)(() => (0, Seq_js_1.append)(comments, (0, Seq_js_1.delay)(() => (0, Seq_js_1.singleton)(JsonTypes_decomposeProcessOutput(outputForType))))))))))));
+    }, (0, Seq2_js_1.List_groupBy)((tupledArg) => [(0, ProcessInput_js_1.ProcessInput__get_Name)(tupledArg[0]), (0, ProcessOutput_js_1.ProcessOutput__get_Name)(tupledArg[1])], (list_4 = (0, Option_js_1.defaultArg)(p.Outputs, (0, List_js_1.empty)()), (0, List_js_1.zip)((0, Option_js_1.defaultArg)(p.Inputs, (0, List_js_1.empty)()), list_4)), {
+        Equals: Util_js_1.equalArrays,
+        GetHashCode: Util_js_1.arrayHash,
+    }));
+}
+function ARCtrl_CompositeHeader__CompositeHeader_TryParameter(this$) {
+    if (this$.tag === /* Parameter */ 3) {
+        const oa = this$.fields[0];
+        return ProtocolParameter_js_1.ProtocolParameter.create(undefined, oa);
+    }
+    else {
+        return undefined;
+    }
+}
+function ARCtrl_CompositeHeader__CompositeHeader_TryFactor(this$) {
+    if (this$.tag === /* Factor */ 2) {
+        const oa = this$.fields[0];
+        return Factor_js_1.Factor.create(undefined, oa);
+    }
+    else {
+        return undefined;
+    }
+}
+function ARCtrl_CompositeHeader__CompositeHeader_TryCharacteristic(this$) {
+    if (this$.tag === /* Characteristic */ 1) {
+        return (0, MaterialAttribute_js_1.MaterialAttribute_create_A220A8A)(undefined, this$.fields[0]);
+    }
+    else {
+        return undefined;
+    }
+}
+function ARCtrl_CompositeHeader__CompositeHeader_TryComponent(this$) {
+    if (this$.tag === /* Component */ 0) {
+        return (0, Component_js_1.Component_create_Z2F0B38C7)(undefined, undefined, this$.fields[0]);
+    }
+    else {
+        return undefined;
+    }
+}
+/**
+ * This function is used to improve interoperability with ISA-JSON types. It is not recommended for default ARCtrl usage.
+ */
+function ARCtrl_CompositeCell__CompositeCell_fromValue_Static_Z6986DF18(value, unit) {
+    return JsonTypes_cellOfValue(value, unit);
+}
+function CompositeRow_toProtocol(tableName, row) {
+    return (0, Seq_js_1.fold)((p, hc) => {
+        let matchResult, oa, v, v_1, v_2, v_3, oa_1, oa_2, unit, v_4, oa_3, t;
+        switch (hc[0].tag) {
+            case /* ProtocolType */ 4: {
+                if (hc[1].tag === /* Term */ 0) {
+                    matchResult = 0;
+                    oa = hc[1].fields[0];
+                }
+                else {
+                    matchResult = 8;
+                }
+                break;
+            }
+            case /* ProtocolVersion */ 7: {
+                if (hc[1].tag === /* FreeText */ 1) {
+                    matchResult = 1;
+                    v = hc[1].fields[0];
+                }
+                else {
+                    matchResult = 8;
+                }
+                break;
+            }
+            case /* ProtocolUri */ 6: {
+                if (hc[1].tag === /* FreeText */ 1) {
+                    matchResult = 2;
+                    v_1 = hc[1].fields[0];
+                }
+                else {
+                    matchResult = 8;
+                }
+                break;
+            }
+            case /* ProtocolDescription */ 5: {
+                if (hc[1].tag === /* FreeText */ 1) {
+                    matchResult = 3;
+                    v_2 = hc[1].fields[0];
+                }
+                else {
+                    matchResult = 8;
+                }
+                break;
+            }
+            case /* ProtocolREF */ 8: {
+                if (hc[1].tag === /* FreeText */ 1) {
+                    matchResult = 4;
+                    v_3 = hc[1].fields[0];
+                }
+                else {
+                    matchResult = 8;
+                }
+                break;
+            }
+            case /* Parameter */ 3: {
+                matchResult = 5;
+                oa_1 = hc[0].fields[0];
+                break;
+            }
+            case /* Component */ 0: {
+                switch (hc[1].tag) {
+                    case /* Unitized */ 2: {
+                        matchResult = 6;
+                        oa_2 = hc[0].fields[0];
+                        unit = hc[1].fields[1];
+                        v_4 = hc[1].fields[0];
+                        break;
+                    }
+                    case /* Term */ 0: {
+                        matchResult = 7;
+                        oa_3 = hc[0].fields[0];
+                        t = hc[1].fields[0];
+                        break;
+                    }
+                    default:
+                        matchResult = 8;
+                }
+                break;
+            }
+            default:
+                matchResult = 8;
+        }
+        switch (matchResult) {
+            case 0:
+                return (0, Protocol_js_1.Protocol_setProtocolType)(p, oa);
+            case 1:
+                return (0, Protocol_js_1.Protocol_setVersion)(p, v);
+            case 2:
+                return (0, Protocol_js_1.Protocol_setUri)(p, v_1);
+            case 3:
+                return (0, Protocol_js_1.Protocol_setDescription)(p, v_2);
+            case 4:
+                return (0, Protocol_js_1.Protocol_setName)(p, v_3);
+            case 5:
+                return (0, Protocol_js_1.Protocol_addParameter)(ProtocolParameter_js_1.ProtocolParameter.create(undefined, oa_1), p);
+            case 6:
+                return (0, Protocol_js_1.Protocol_addComponent)((0, Component_js_1.Component_create_Z2F0B38C7)(Value_js_1.Value.fromString(v_4), unit, oa_2), p);
+            case 7:
+                return (0, Protocol_js_1.Protocol_addComponent)((0, Component_js_1.Component_create_Z2F0B38C7)((0, Value_js_1.Value_Ontology)(t), undefined, oa_3), p);
+            default:
+                return p;
+        }
+    }, (0, Protocol_js_1.Protocol_create_Z414665E7)(undefined, tableName), row);
+}
+/**
+ * Create a new table from an ISA protocol.
+ *
+ * The table will have at most one row, with the protocol information and the component values
+ */
+function ARCtrl_ArcTable__ArcTable_fromProtocol_Static_3BF20962(p) {
+    const t = ArcTable_js_1.ArcTable.init((0, Option_js_1.defaultArg)(p.Name, (0, Identifier_js_1.createMissingIdentifier)()));
+    const enumerator = (0, Util_js_1.getEnumerator)((0, Option_js_1.defaultArg)(p.Parameters, (0, List_js_1.empty)()));
+    try {
+        while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+            const pp = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+            t.AddColumn((0, CompositeHeader_js_1.CompositeHeader_Parameter)((0, Option_js_1.value)(pp.ParameterName)), undefined, (0, Option_js_1.unwrap)((0, ColumnIndex_js_1.ARCtrl_Process_ProtocolParameter__ProtocolParameter_TryGetColumnIndex)(pp)));
+        }
+    }
+    finally {
+        (0, Util_js_1.disposeSafe)(enumerator);
+    }
+    const enumerator_1 = (0, Util_js_1.getEnumerator)((0, Option_js_1.defaultArg)(p.Components, (0, List_js_1.empty)()));
+    try {
+        while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
+            const c = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
+            const v_1 = (0, Option_js_1.map)((arg) => (0, Array_js_1.singleton)(ARCtrl_CompositeCell__CompositeCell_fromValue_Static_Z6986DF18(arg, (0, Option_js_1.unwrap)(c.ComponentUnit))), c.ComponentValue);
+            t.AddColumn((0, CompositeHeader_js_1.CompositeHeader_Parameter)((0, Option_js_1.value)(c.ComponentType)), (0, Option_js_1.unwrap)(v_1), (0, Option_js_1.unwrap)((0, ColumnIndex_js_1.ARCtrl_Process_Component__Component_TryGetColumnIndex)(c)));
+        }
+    }
+    finally {
+        (0, Util_js_1.disposeSafe)(enumerator_1);
+    }
+    (0, Option_js_1.map)((d) => {
+        t.AddProtocolDescriptionColumn([d]);
+    }, p.Description);
+    (0, Option_js_1.map)((d_1) => {
+        t.AddProtocolVersionColumn([d_1]);
+    }, p.Version);
+    (0, Option_js_1.map)((d_2) => {
+        t.AddProtocolTypeColumn([d_2]);
+    }, p.ProtocolType);
+    (0, Option_js_1.map)((d_3) => {
+        t.AddProtocolUriColumn([d_3]);
+    }, p.Uri);
+    (0, Option_js_1.map)((d_4) => {
+        t.AddProtocolNameColumn([d_4]);
+    }, p.Name);
+    return t;
+}
+/**
+ * Returns the list of protocols executed in this ArcTable
+ */
+function ARCtrl_ArcTable__ArcTable_GetProtocols(this$) {
+    let source;
+    if (this$.RowCount === 0) {
+        return (0, List_js_1.singleton)((source = this$.Headers, (0, Seq_js_1.fold)((p, h) => {
+            switch (h.tag) {
+                case /* ProtocolType */ 4:
+                    return (0, Protocol_js_1.Protocol_setProtocolType)(p, new OntologyAnnotation_js_1.OntologyAnnotation());
+                case /* ProtocolVersion */ 7:
+                    return (0, Protocol_js_1.Protocol_setVersion)(p, "");
+                case /* ProtocolUri */ 6:
+                    return (0, Protocol_js_1.Protocol_setUri)(p, "");
+                case /* ProtocolDescription */ 5:
+                    return (0, Protocol_js_1.Protocol_setDescription)(p, "");
+                case /* ProtocolREF */ 8:
+                    return (0, Protocol_js_1.Protocol_setName)(p, "");
+                case /* Parameter */ 3: {
+                    const oa = h.fields[0];
+                    return (0, Protocol_js_1.Protocol_addParameter)(ProtocolParameter_js_1.ProtocolParameter.create(undefined, oa), p);
+                }
+                case /* Component */ 0:
+                    return (0, Protocol_js_1.Protocol_addComponent)((0, Component_js_1.Component_create_Z2F0B38C7)(undefined, undefined, h.fields[0]), p);
+                default:
+                    return p;
+            }
+        }, (0, Protocol_js_1.Protocol_create_Z414665E7)(undefined, this$.Name), source)));
+    }
+    else {
+        return (0, Seq2_js_1.List_distinct)((0, List_js_1.initialize)(this$.RowCount, (i) => {
+            let row;
+            const source_2 = this$.GetRow(i, true);
+            row = (0, Seq_js_1.zip)(this$.Headers, source_2);
+            return CompositeRow_toProtocol(this$.Name, row);
+        }), {
+            Equals: Util_js_1.equals,
+            GetHashCode: Util_js_1.safeHash,
+        });
+    }
+}
+/**
+ * Returns the list of processes specidified in this ArcTable
+ */
+function ARCtrl_ArcTable__ArcTable_GetProcesses(this$) {
+    if (this$.RowCount === 0) {
+        return (0, List_js_1.singleton)((0, Process_js_1.Process_create_Z7C1F7FA9)(undefined, this$.Name));
+    }
+    else {
+        let getter;
+        const clo = ProcessParsing_getProcessGetter(this$.Name, this$.Headers);
+        getter = ((arg) => {
+            const clo_1 = clo(arg);
+            return clo_1;
+        });
+        return ProcessParsing_mergeIdenticalProcesses((0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i) => getter(this$.Values)(i), (0, Range_js_1.rangeDouble)(0, 1, this$.RowCount - 1)))));
+    }
+}
+/**
+ * Create a new table from a list of processes
+ *
+ * The name will be used as the sheet name
+ *
+ * The processes SHOULD have the same headers, or even execute the same protocol
+ */
+function ARCtrl_ArcTable__ArcTable_fromProcesses_Static(name, ps) {
+    const tupledArg = (0, ArcTableAux_js_1.Unchecked_alignByHeaders)(true, (0, List_js_1.collect)(ProcessParsing_processToRows, ps));
+    return ArcTable_js_1.ArcTable.create(name, tupledArg[0], tupledArg[1]);
+}
+/**
+ * Return a list of all the processes in all the tables.
+ */
+function ARCtrl_ArcTables__ArcTables_GetProcesses(this$) {
+    return (0, List_js_1.collect)(ARCtrl_ArcTable__ArcTable_GetProcesses, (0, Seq_js_1.toList)(this$.Tables));
+}
+/**
+ * Create a collection of tables from a list of processes.
+ *
+ * For this, the processes are grouped by nameroot ("nameroot_1", "nameroot_2" ...) or exectued protocol if no name exists
+ *
+ * Then each group is converted to a table with this nameroot as sheetname
+ */
+function ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(ps) {
+    let collection;
+    return new ArcTables_js_1.ArcTables((collection = (0, List_js_1.map)((tupledArg) => {
+        const tupledArg_1 = (0, ArcTableAux_js_1.Unchecked_alignByHeaders)(true, (0, List_js_1.collect)(ProcessParsing_processToRows, tupledArg[1]));
+        return ArcTable_js_1.ArcTable.create(tupledArg[0], tupledArg_1[0], tupledArg_1[1]);
+    }, ProcessParsing_groupProcesses(ps)), Array.from(collection)));
+}