@nfdi4plants/arctrl 1.0.0-alpha10

package/ISA/ISA/ArcTypes/CompositeHeader.js

@@ -0,0 +1,668 @@
+import { map } from "../../../fable_modules/fable-library.4.1.4/Array.js";
+import { union_type, string_type, getUnionCases, name } from "../../../fable_modules/fable-library.4.1.4/Reflection.js";
+import { Union, toString } from "../../../fable_modules/fable-library.4.1.4/Types.js";
+import { ActivePatterns_$007CTermColumn$007C_$007C, Pattern_OutputPattern, Pattern_InputPattern, ActivePatterns_$007CRegex$007C_$007C, tryParseIOTypeHeader } from "../Regex.js";
+import { equals } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.1.4/String.js";
+import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
+import { ProtocolParameter_create_Z6C54B221 } from "../JsonTypes/ProtocolParameter.js";
+import { Factor } from "../JsonTypes/Factor.js";
+import { MaterialAttribute_create_Z6C54B221 } from "../JsonTypes/MaterialAttribute.js";
+import { Component_create_61502994 } from "../JsonTypes/Component.js";
+
+export class IOType extends Union {
+    constructor(tag, fields) {
+        super();
+        this.tag = tag;
+        this.fields = fields;
+    }
+    cases() {
+        return ["Source", "Sample", "RawDataFile", "DerivedDataFile", "ImageFile", "Material", "FreeText"];
+    }
+    static get All() {
+        return [new IOType(0, []), new IOType(1, []), new IOType(2, []), new IOType(3, []), new IOType(4, []), new IOType(5, [])];
+    }
+    static get Cases() {
+        return map((x) => [x.tag, name(x)], getUnionCases(IOType_$reflection()));
+    }
+    get asInput() {
+        const this$ = this;
+        const stringCreate = (x) => {
+            let copyOfStruct;
+            return `Input [${(copyOfStruct = x, toString(copyOfStruct))}]`;
+        };
+        return (this$.tag === 6) ? stringCreate(this$.fields[0]) : stringCreate(this$);
+    }
+    get asOutput() {
+        const this$ = this;
+        const stringCreate = (x) => {
+            let copyOfStruct;
+            return `Output [${(copyOfStruct = x, toString(copyOfStruct))}]`;
+        };
+        return (this$.tag === 6) ? stringCreate(this$.fields[0]) : stringCreate(this$);
+    }
+    Merge(other) {
+        const this$ = this;
+        switch (this$.tag) {
+            case 4:
+                switch (other.tag) {
+                    case 0:
+                        return new IOType(4, []);
+                    case 2:
+                        return new IOType(4, []);
+                    case 3:
+                        return new IOType(4, []);
+                    case 4:
+                        return new IOType(4, []);
+                    default:
+                        throw new Error(`ImageFile IO column and ${other} can not be merged`);
+                }
+            case 3:
+                switch (other.tag) {
+                    case 0:
+                        return new IOType(3, []);
+                    case 2:
+                        return new IOType(3, []);
+                    case 3:
+                        return new IOType(3, []);
+                    case 4:
+                        return new IOType(4, []);
+                    default:
+                        throw new Error(`DerivedDataFile IO column and ${other} can not be merged`);
+                }
+            case 2:
+                switch (other.tag) {
+                    case 0:
+                        return new IOType(2, []);
+                    case 2:
+                        return new IOType(2, []);
+                    case 3:
+                        return new IOType(3, []);
+                    case 4:
+                        return new IOType(4, []);
+                    default:
+                        throw new Error(`RawDataFile IO column and ${other} can not be merged`);
+                }
+            case 1:
+                switch (other.tag) {
+                    case 0:
+                        return new IOType(1, []);
+                    case 1:
+                        return new IOType(1, []);
+                    default:
+                        throw new Error(`Sample IO column and ${other} can not be merged`);
+                }
+            case 0:
+                return (other.tag === 0) ? (new IOType(0, [])) : other;
+            case 5:
+                switch (other.tag) {
+                    case 0:
+                        return new IOType(5, []);
+                    case 5:
+                        return new IOType(5, []);
+                    default:
+                        throw new Error(`Material IO column and ${other} can not be merged`);
+                }
+            default:
+                if (other.tag === 6) {
+                    if (this$.fields[0] === other.fields[0]) {
+                        return new IOType(6, [this$.fields[0]]);
+                    }
+                    else {
+                        throw new Error(`FreeText IO column names ${this$.fields[0]} and ${other.fields[0]} do differ`);
+                    }
+                }
+                else {
+                    throw new Error(`FreeText IO column and ${other} can not be merged`);
+                }
+        }
+    }
+    toString() {
+        const this$ = this;
+        return (this$.tag === 1) ? "Sample Name" : ((this$.tag === 2) ? "Raw Data File" : ((this$.tag === 3) ? "Derived Data File" : ((this$.tag === 4) ? "Image File" : ((this$.tag === 5) ? "Material" : ((this$.tag === 6) ? this$.fields[0] : "Source Name")))));
+    }
+    static ofString(str) {
+        return (str === "Source") ? (new IOType(0, [])) : ((str === "Source Name") ? (new IOType(0, [])) : ((str === "Sample") ? (new IOType(1, [])) : ((str === "Sample Name") ? (new IOType(1, [])) : ((str === "RawDataFile") ? (new IOType(2, [])) : ((str === "Raw Data File") ? (new IOType(2, [])) : ((str === "DerivedDataFile") ? (new IOType(3, [])) : ((str === "Derived Data File") ? (new IOType(3, [])) : ((str === "ImageFile") ? (new IOType(4, [])) : ((str === "Image File") ? (new IOType(4, [])) : ((str === "Material") ? (new IOType(5, [])) : (new IOType(6, [str]))))))))))));
+    }
+    static tryOfHeaderString(str) {
+        const matchValue = tryParseIOTypeHeader(str);
+        if (matchValue == null) {
+            return void 0;
+        }
+        else {
+            const s = matchValue;
+            return IOType.ofString(s);
+        }
+    }
+    GetUITooltip() {
+        const this$ = this;
+        return IOType.getUITooltip(this$);
+    }
+    static getUITooltip(iotype) {
+        let matchResult;
+        if (typeof iotype === "string") {
+            if (equals(iotype, "Source")) {
+                matchResult = 0;
+            }
+            else if (equals(iotype, "Sample")) {
+                matchResult = 1;
+            }
+            else if (equals(iotype, "RawDataFile")) {
+                matchResult = 2;
+            }
+            else if (equals(iotype, "DerivedDataFile")) {
+                matchResult = 3;
+            }
+            else if (equals(iotype, "ImageFile")) {
+                matchResult = 4;
+            }
+            else if (equals(iotype, "Material")) {
+                matchResult = 5;
+            }
+            else if (equals(iotype, "FreeText")) {
+                matchResult = 6;
+            }
+            else {
+                matchResult = 7;
+            }
+        }
+        else {
+            switch (iotype.tag) {
+                case 1: {
+                    matchResult = 1;
+                    break;
+                }
+                case 2: {
+                    matchResult = 2;
+                    break;
+                }
+                case 3: {
+                    matchResult = 3;
+                    break;
+                }
+                case 4: {
+                    matchResult = 4;
+                    break;
+                }
+                case 5: {
+                    matchResult = 5;
+                    break;
+                }
+                case 6: {
+                    matchResult = 6;
+                    break;
+                }
+                default:
+                    matchResult = 0;
+            }
+        }
+        switch (matchResult) {
+            case 0:
+                return "The source value must be a unique identifier for an organism or a sample.";
+            case 1:
+                return "The Sample Name column describes specifc laboratory samples with a unique identifier.";
+            case 2:
+                return "The Raw Data File column defines untransformed and unprocessed data files.";
+            case 3:
+                return "The Derived Data File column defines transformed and/or processed data files.";
+            case 4:
+                return "Placeholder";
+            case 5:
+                return "Placeholder";
+            case 6:
+                return "Placeholder";
+            default:
+                throw new Error(`Unable to parse combination to existing IOType: \`${iotype}\``);
+        }
+    }
+}
+
+export function IOType_$reflection() {
+    return union_type("ARCtrl.ISA.IOType", [], IOType, () => [[], [], [], [], [], [], [["Item", string_type]]]);
+}
+
+export class CompositeHeader extends Union {
+    constructor(tag, fields) {
+        super();
+        this.tag = tag;
+        this.fields = fields;
+    }
+    cases() {
+        return ["Component", "Characteristic", "Factor", "Parameter", "ProtocolType", "ProtocolDescription", "ProtocolUri", "ProtocolVersion", "ProtocolREF", "Performer", "Date", "Input", "Output", "FreeText"];
+    }
+    static get Cases() {
+        return map((x) => [x.tag, name(x)], getUnionCases(CompositeHeader_$reflection()));
+    }
+    static jsGetColumnMetaType(inp) {
+        return (inp === 0) ? 1 : ((inp === 1) ? 1 : ((inp === 2) ? 1 : ((inp === 3) ? 1 : ((inp === 4) ? 0 : ((inp === 5) ? 0 : ((inp === 6) ? 0 : ((inp === 7) ? 0 : ((inp === 8) ? 0 : ((inp === 9) ? 0 : ((inp === 10) ? 0 : ((inp === 11) ? 2 : ((inp === 12) ? 2 : ((inp === 13) ? 3 : toFail(printf("Cannot assign input `Tag` (%i) to `CompositeHeader`"))(inp))))))))))))));
+    }
+    toString() {
+        const this$ = this;
+        return (this$.tag === 2) ? (`Factor [${this$.fields[0].NameText}]`) : ((this$.tag === 1) ? (`Characteristic [${this$.fields[0].NameText}]`) : ((this$.tag === 0) ? (`Component [${this$.fields[0].NameText}]`) : ((this$.tag === 4) ? "Protocol Type" : ((this$.tag === 8) ? "Protocol REF" : ((this$.tag === 5) ? "Protocol Description" : ((this$.tag === 6) ? "Protocol Uri" : ((this$.tag === 7) ? "Protocol Version" : ((this$.tag === 9) ? "Performer" : ((this$.tag === 10) ? "Date" : ((this$.tag === 11) ? this$.fields[0].asInput : ((this$.tag === 12) ? this$.fields[0].asOutput : ((this$.tag === 13) ? this$.fields[0] : (`Parameter [${this$.fields[0].NameText}]`)))))))))))));
+    }
+    ToTerm() {
+        const this$ = this;
+        return (this$.tag === 2) ? this$.fields[0] : ((this$.tag === 1) ? this$.fields[0] : ((this$.tag === 0) ? this$.fields[0] : ((this$.tag === 4) ? OntologyAnnotation.fromString("Protocol Type") : ((this$.tag === 8) ? OntologyAnnotation.fromString("Protocol REF") : ((this$.tag === 5) ? OntologyAnnotation.fromString("Protocol Description") : ((this$.tag === 6) ? OntologyAnnotation.fromString("Protocol Uri") : ((this$.tag === 7) ? OntologyAnnotation.fromString("Protocol Version") : ((this$.tag === 9) ? OntologyAnnotation.fromString("Performer") : ((this$.tag === 10) ? OntologyAnnotation.fromString("Date") : ((this$.tag === 11) ? OntologyAnnotation.fromString(this$.fields[0].asInput) : ((this$.tag === 12) ? OntologyAnnotation.fromString(this$.fields[0].asOutput) : ((this$.tag === 13) ? OntologyAnnotation.fromString(this$.fields[0]) : this$.fields[0]))))))))))));
+    }
+    static OfHeaderString(str) {
+        const matchValue = str.trim();
+        const activePatternResult = ActivePatterns_$007CRegex$007C_$007C(Pattern_InputPattern, matchValue);
+        if (activePatternResult != null) {
+            const r = activePatternResult;
+            const iotype = (r.groups && r.groups.iotype) || "";
+            return new CompositeHeader(11, [IOType.ofString(iotype)]);
+        }
+        else {
+            const activePatternResult_1 = ActivePatterns_$007CRegex$007C_$007C(Pattern_OutputPattern, matchValue);
+            if (activePatternResult_1 != null) {
+                const r_1 = activePatternResult_1;
+                const iotype_1 = (r_1.groups && r_1.groups.iotype) || "";
+                return new CompositeHeader(12, [IOType.ofString(iotype_1)]);
+            }
+            else {
+                const activePatternResult_2 = ActivePatterns_$007CTermColumn$007C_$007C(matchValue);
+                if (activePatternResult_2 != null) {
+                    const r_2 = activePatternResult_2;
+                    const matchValue_1 = r_2.TermColumnType;
+                    switch (matchValue_1) {
+                        case "Parameter":
+                        case "Parameter Value":
+                            return new CompositeHeader(3, [OntologyAnnotation.fromString(r_2.TermName)]);
+                        case "Factor":
+                        case "Factor Value":
+                            return new CompositeHeader(2, [OntologyAnnotation.fromString(r_2.TermName)]);
+                        case "Characteristic":
+                        case "Characteristics":
+                        case "Characteristics Value":
+                            return new CompositeHeader(1, [OntologyAnnotation.fromString(r_2.TermName)]);
+                        case "Component":
+                            return new CompositeHeader(0, [OntologyAnnotation.fromString(r_2.TermName)]);
+                        default:
+                            return new CompositeHeader(13, [str]);
+                    }
+                }
+                else {
+                    return (matchValue === "Date") ? (new CompositeHeader(10, [])) : ((matchValue === "Performer") ? (new CompositeHeader(9, [])) : ((matchValue === "Protocol Description") ? (new CompositeHeader(5, [])) : ((matchValue === "Protocol Uri") ? (new CompositeHeader(6, [])) : ((matchValue === "Protocol Version") ? (new CompositeHeader(7, [])) : ((matchValue === "Protocol Type") ? (new CompositeHeader(4, [])) : ((matchValue === "Protocol REF") ? (new CompositeHeader(8, [])) : (new CompositeHeader(13, [matchValue]))))))));
+                }
+            }
+        }
+    }
+    get IsDeprecated() {
+        const this$ = this;
+        let matchResult, s_4, s_5, s_6, s_7;
+        if (this$.tag === 13) {
+            if (this$.fields[0].toLocaleLowerCase() === "sample name") {
+                matchResult = 0;
+                s_4 = this$.fields[0];
+            }
+            else if (this$.fields[0].toLocaleLowerCase() === "source name") {
+                matchResult = 1;
+                s_5 = this$.fields[0];
+            }
+            else if (this$.fields[0].toLocaleLowerCase() === "data file name") {
+                matchResult = 2;
+                s_6 = this$.fields[0];
+            }
+            else if (this$.fields[0].toLocaleLowerCase() === "derived data file") {
+                matchResult = 3;
+                s_7 = this$.fields[0];
+            }
+            else {
+                matchResult = 4;
+            }
+        }
+        else {
+            matchResult = 4;
+        }
+        switch (matchResult) {
+            case 0:
+                return true;
+            case 1:
+                return true;
+            case 2:
+                return true;
+            case 3:
+                return true;
+            default:
+                return false;
+        }
+    }
+    get IsCvParamColumn() {
+        const this$ = this;
+        switch (this$.tag) {
+            case 3:
+            case 2:
+            case 1:
+            case 0:
+                return true;
+            default:
+                return false;
+        }
+    }
+    get IsTermColumn() {
+        const this$ = this;
+        switch (this$.tag) {
+            case 3:
+            case 2:
+            case 1:
+            case 0:
+            case 4:
+                return true;
+            default:
+                return false;
+        }
+    }
+    get IsFeaturedColumn() {
+        const this$ = this;
+        return this$.tag === 4;
+    }
+    get GetFeaturedColumnAccession() {
+        const this$ = this;
+        if (this$.tag === 4) {
+            return "DPBO:1000161";
+        }
+        else {
+            throw new Error(`Tried matching ${this$} in getFeaturedColumnAccession, but is not a featured column.`);
+        }
+    }
+    get GetColumnAccessionShort() {
+        const this$ = this;
+        switch (this$.tag) {
+            case 4:
+                return this$.GetFeaturedColumnAccession;
+            case 3:
+                return this$.fields[0].TermAccessionShort;
+            case 2:
+                return this$.fields[0].TermAccessionShort;
+            case 1:
+                return this$.fields[0].TermAccessionShort;
+            case 0:
+                return this$.fields[0].TermAccessionShort;
+            default:
+                throw new Error(`Tried matching ${this$}, but is not a column with an accession.`);
+        }
+    }
+    get IsSingleColumn() {
+        const this$ = this;
+        switch (this$.tag) {
+            case 13:
+            case 11:
+            case 12:
+            case 8:
+            case 5:
+            case 6:
+            case 7:
+            case 9:
+            case 10:
+                return true;
+            default:
+                return false;
+        }
+    }
+    get IsIOType() {
+        const this$ = this;
+        let matchResult, io;
+        switch (this$.tag) {
+            case 11: {
+                matchResult = 0;
+                io = this$.fields[0];
+                break;
+            }
+            case 12: {
+                matchResult = 0;
+                io = this$.fields[0];
+                break;
+            }
+            default:
+                matchResult = 1;
+        }
+        switch (matchResult) {
+            case 0:
+                return true;
+            default:
+                return false;
+        }
+    }
+    get isInput() {
+        const this$ = this;
+        return this$.tag === 11;
+    }
+    get isOutput() {
+        const this$ = this;
+        return this$.tag === 12;
+    }
+    get isParameter() {
+        const this$ = this;
+        return this$.tag === 3;
+    }
+    get isFactor() {
+        const this$ = this;
+        return this$.tag === 2;
+    }
+    get isCharacteristic() {
+        const this$ = this;
+        return this$.tag === 1;
+    }
+    get isComponent() {
+        const this$ = this;
+        return this$.tag === 0;
+    }
+    get isProtocolType() {
+        const this$ = this;
+        return this$.tag === 4;
+    }
+    get isProtocolREF() {
+        const this$ = this;
+        return this$.tag === 8;
+    }
+    get isProtocolDescription() {
+        const this$ = this;
+        return this$.tag === 5;
+    }
+    get isProtocolUri() {
+        const this$ = this;
+        return this$.tag === 6;
+    }
+    get isProtocolVersion() {
+        const this$ = this;
+        return this$.tag === 7;
+    }
+    get isProtocolColumn() {
+        const this$ = this;
+        switch (this$.tag) {
+            case 8:
+            case 5:
+            case 6:
+            case 7:
+            case 4:
+                return true;
+            default:
+                return false;
+        }
+    }
+    get isPerformer() {
+        const this$ = this;
+        return this$.tag === 9;
+    }
+    get isDate() {
+        const this$ = this;
+        return this$.tag === 10;
+    }
+    get isFreeText() {
+        const this$ = this;
+        return this$.tag === 13;
+    }
+    tryInput() {
+        const this$ = this;
+        return (this$.tag === 11) ? this$.fields[0] : void 0;
+    }
+    tryOutput() {
+        const this$ = this;
+        return (this$.tag === 12) ? this$.fields[0] : void 0;
+    }
+    TryParameter() {
+        const this$ = this;
+        return (this$.tag === 3) ? ProtocolParameter_create_Z6C54B221(void 0, this$.fields[0]) : void 0;
+    }
+    TryFactor() {
+        const this$ = this;
+        return (this$.tag === 2) ? Factor.create(void 0, void 0, this$.fields[0]) : void 0;
+    }
+    TryCharacteristic() {
+        const this$ = this;
+        return (this$.tag === 1) ? MaterialAttribute_create_Z6C54B221(void 0, this$.fields[0]) : void 0;
+    }
+    TryComponent() {
+        const this$ = this;
+        return (this$.tag === 0) ? Component_create_61502994(void 0, void 0, void 0, this$.fields[0]) : void 0;
+    }
+    GetUITooltip() {
+        const this$ = this;
+        return CompositeHeader.getUITooltip(this$);
+    }
+    static getUITooltip(header) {
+        let matchResult;
+        if (typeof header === "string") {
+            if (equals(header, "Component")) {
+                matchResult = 0;
+            }
+            else if (equals(header, "Characteristic")) {
+                matchResult = 1;
+            }
+            else if (equals(header, "Factor")) {
+                matchResult = 2;
+            }
+            else if (equals(header, "Parameter")) {
+                matchResult = 3;
+            }
+            else if (equals(header, "ProtocolType")) {
+                matchResult = 4;
+            }
+            else if (equals(header, "ProtocolDescription")) {
+                matchResult = 5;
+            }
+            else if (equals(header, "ProtocolUri")) {
+                matchResult = 6;
+            }
+            else if (equals(header, "ProtocolVersion")) {
+                matchResult = 7;
+            }
+            else if (equals(header, "ProtocolREF")) {
+                matchResult = 8;
+            }
+            else if (equals(header, "Performer")) {
+                matchResult = 9;
+            }
+            else if (equals(header, "Date")) {
+                matchResult = 10;
+            }
+            else if (equals(header, "Input")) {
+                matchResult = 11;
+            }
+            else if (equals(header, "Output")) {
+                matchResult = 12;
+            }
+            else if (equals(header, "FreeText")) {
+                matchResult = 13;
+            }
+            else {
+                matchResult = 14;
+            }
+        }
+        else {
+            switch (header.tag) {
+                case 1: {
+                    matchResult = 1;
+                    break;
+                }
+                case 2: {
+                    matchResult = 2;
+                    break;
+                }
+                case 3: {
+                    matchResult = 3;
+                    break;
+                }
+                case 4: {
+                    matchResult = 4;
+                    break;
+                }
+                case 5: {
+                    matchResult = 5;
+                    break;
+                }
+                case 6: {
+                    matchResult = 6;
+                    break;
+                }
+                case 7: {
+                    matchResult = 7;
+                    break;
+                }
+                case 8: {
+                    matchResult = 8;
+                    break;
+                }
+                case 9: {
+                    matchResult = 9;
+                    break;
+                }
+                case 10: {
+                    matchResult = 10;
+                    break;
+                }
+                case 11: {
+                    matchResult = 11;
+                    break;
+                }
+                case 12: {
+                    matchResult = 12;
+                    break;
+                }
+                case 13: {
+                    matchResult = 13;
+                    break;
+                }
+                default:
+                    matchResult = 0;
+            }
+        }
+        switch (matchResult) {
+            case 0:
+                return "Component columns are used to describe physical components of a experiment, e.g. instrument names, software names, and reagents names.";
+            case 1:
+                return "Characteristic columns are used for study descriptions and describe inherent properties of the source material, e.g. a certain strain or organism part.";
+            case 2:
+                return "Use Factor columns to describe independent variables that result in a specific output of your experiment, e.g. the light intensity under which an organism was grown.";
+            case 3:
+                return "Parameter columns describe steps in your experimental workflow, e.g. the centrifugation time or the temperature used for your assay.";
+            case 4:
+                return "Defines the protocol type according to your preferred endpoint repository.";
+            case 5:
+                return "Describe the protocol in free text.";
+            case 6:
+                return "Web or local address where the in-depth protocol is stored.";
+            case 7:
+                return "Defines the protocol version.";
+            case 8:
+                return "Defines the protocol name.";
+            case 9:
+                return "Defines the protocol performer.";
+            case 10:
+                return "Defines the date the protocol was performed.";
+            case 11:
+                return "Only one input column per table. E.g. experimental samples or files.";
+            case 12:
+                return "Only one output column per table. E.g. experimental samples or files.";
+            case 13:
+                return "Placeholder";
+            default:
+                throw new Error(`Unable to parse combination to existing CompositeHeader: \`${header}\``);
+        }
+    }
+}
+
+export function CompositeHeader_$reflection() {
+    return union_type("ARCtrl.ISA.CompositeHeader", [], CompositeHeader, () => [[["Item", OntologyAnnotation_$reflection()]], [["Item", OntologyAnnotation_$reflection()]], [["Item", OntologyAnnotation_$reflection()]], [["Item", OntologyAnnotation_$reflection()]], [], [], [], [], [], [], [], [["Item", IOType_$reflection()]], [["Item", IOType_$reflection()]], [["Item", string_type]]]);
+}
+