@nfdi4plants/arctrl 1.0.0-alpha6

package/ISA/ISA.Json/Study.js

@@ -0,0 +1,230 @@
+import { toString, nil, object as object_36 } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
+import { ofArray, choose } from "../../fable_modules/fable-library.4.1.4/List.js";
+import { uncurry2, equals } from "../../fable_modules/fable-library.4.1.4/Util.js";
+import { tryInclude } from "./GEncode.js";
+import { Sample_decoder, Source_decoder, Sample_encoder, Source_encoder } from "./Data.js";
+import { MaterialAttribute_decoder, MaterialAttribute_encoder, Material_decoder, Material_encoder } from "./Material.js";
+import { string, list as list_1, object as object_37 } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { StudyMaterials } from "../ISA/JsonTypes/StudyMaterials.js";
+import { replace } from "../../fable_modules/fable-library.4.1.4/String.js";
+import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
+import { empty, singleton, append, delay, toList } from "../../fable_modules/fable-library.4.1.4/Seq.js";
+import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
+import { decoder as decoder_10, encoder } from "./Publication.js";
+import { decoder as decoder_11, encoder as encoder_1 } from "./Person.js";
+import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./Ontology.js";
+import { Protocol_decoder, Protocol_encoder } from "./Protocol.js";
+import { Process_decoder, Process_encoder } from "./Process.js";
+import { Assay_decoder, Assay_encoder } from "./Assay.js";
+import { Factor_decoder, Factor_encoder } from "./Factor.js";
+import { decoder as decoder_12, encoder as encoder_2 } from "./Comment.js";
+import { fromString, uri } from "./Decode.js";
+import { Study } from "../ISA/JsonTypes/Study.js";
+import { ArcStudy } from "../ISA/ArcTypes/ArcTypes.js";
+
+export function StudyMaterials_encoder(options, oa) {
+    return object_36(choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, nil)) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, ofArray([tryInclude("sources", (oa_1) => Source_encoder(options, oa_1), oa["Sources"]), tryInclude("samples", (oa_2) => Sample_encoder(options, oa_2), oa["Samples"]), tryInclude("otherMaterials", (oa_3) => Material_encoder(options, oa_3), oa["OtherMaterials"])])));
+}
+
+export function StudyMaterials_decoder(options) {
+    return (path_3) => ((v) => object_37((get$) => {
+        let objectArg, objectArg_1, objectArg_2;
+        return new StudyMaterials((objectArg = get$.Optional, objectArg.Field("sources", (path, value) => list_1((s, json) => Source_decoder(options, s, json), path, value))), (objectArg_1 = get$.Optional, objectArg_1.Field("samples", (path_1, value_1) => list_1((s_1, json_1) => Sample_decoder(options, s_1, json_1), path_1, value_1))), (objectArg_2 = get$.Optional, objectArg_2.Field("otherMaterials", (path_2, value_2) => list_1((s_2, json_2) => Material_decoder(options, s_2, json_2), path_2, value_2))));
+    }, path_3, v));
+}
+
+export function Study_genID(s) {
+    const matchValue = s.ID;
+    if (matchValue == null) {
+        const matchValue_1 = s.FileName;
+        if (matchValue_1 == null) {
+            const matchValue_2 = s.Identifier;
+            if (matchValue_2 == null) {
+                const matchValue_3 = s.Title;
+                if (matchValue_3 == null) {
+                    return "#EmptyStudy";
+                }
+                else {
+                    return "#Study_" + replace(matchValue_3, " ", "_");
+                }
+            }
+            else {
+                return "#Study_" + replace(matchValue_2, " ", "_");
+            }
+        }
+        else {
+            return "#Study" + replace(matchValue_1, " ", "_");
+        }
+    }
+    else {
+        return URIModule_toString(matchValue);
+    }
+}
+
+export function Study_encoder(options, oa) {
+    return object_36(choose((tupledArg) => {
+        const v = tupledArg[1];
+        if (equals(v, nil)) {
+            return void 0;
+        }
+        else {
+            return [tupledArg[0], v];
+        }
+    }, toList(delay(() => {
+        let value, s_1;
+        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = Study_genID(oa), (typeof value === "string") ? ((s_1 = value, s_1)) : nil)]) : singleton(tryInclude("@id", (value_2) => {
+            let s_2;
+            const value_3 = value_2;
+            return (typeof value_3 === "string") ? ((s_2 = value_3, s_2)) : nil;
+        }, oa["ID"])), delay(() => {
+            let value_5, s_3;
+            return append(ConverterOptions__get_IncludeType(options) ? singleton(["@type", (value_5 = "Study", (typeof value_5 === "string") ? ((s_3 = value_5, s_3)) : nil)]) : empty(), delay(() => append(singleton(tryInclude("filename", (value_7) => {
+                let s_4;
+                const value_8 = value_7;
+                return (typeof value_8 === "string") ? ((s_4 = value_8, s_4)) : nil;
+            }, oa["FileName"])), delay(() => append(singleton(tryInclude("identifier", (value_10) => {
+                let s_5;
+                const value_11 = value_10;
+                return (typeof value_11 === "string") ? ((s_5 = value_11, s_5)) : nil;
+            }, oa["Identifier"])), delay(() => append(singleton(tryInclude("title", (value_13) => {
+                let s_6;
+                const value_14 = value_13;
+                return (typeof value_14 === "string") ? ((s_6 = value_14, s_6)) : nil;
+            }, oa["Title"])), delay(() => append(singleton(tryInclude("description", (value_16) => {
+                let s_7;
+                const value_17 = value_16;
+                return (typeof value_17 === "string") ? ((s_7 = value_17, s_7)) : nil;
+            }, oa["Description"])), delay(() => append(singleton(tryInclude("submissionDate", (value_19) => {
+                let s_8;
+                const value_20 = value_19;
+                return (typeof value_20 === "string") ? ((s_8 = value_20, s_8)) : nil;
+            }, oa["SubmissionDate"])), delay(() => append(singleton(tryInclude("publicReleaseDate", (value_22) => {
+                let s_9;
+                const value_23 = value_22;
+                return (typeof value_23 === "string") ? ((s_9 = value_23, s_9)) : nil;
+            }, oa["PublicReleaseDate"])), delay(() => append(singleton(tryInclude("publications", (oa_1) => encoder(options, oa_1), oa["Publications"])), delay(() => append(singleton(tryInclude("people", (oa_2) => encoder_1(options, oa_2), oa["Contacts"])), delay(() => append(singleton(tryInclude("studyDesignDescriptors", (oa_3) => OntologyAnnotation_encoder(options, oa_3), oa["StudyDesignDescriptors"])), delay(() => append(singleton(tryInclude("protocols", (oa_4) => Protocol_encoder(options, oa_4), oa["Protocols"])), delay(() => append(singleton(tryInclude("materials", (oa_5) => StudyMaterials_encoder(options, oa_5), oa["Materials"])), delay(() => append(singleton(tryInclude("processSequence", (oa_6) => Process_encoder(options, oa_6), oa["ProcessSequence"])), delay(() => append(singleton(tryInclude("assays", (oa_7) => Assay_encoder(options, oa_7), oa["Assays"])), delay(() => append(singleton(tryInclude("factors", (oa_8) => Factor_encoder(options, oa_8), oa["Factors"])), delay(() => append(singleton(tryInclude("characteristicCategories", (oa_9) => MaterialAttribute_encoder(options, oa_9), oa["CharacteristicCategories"])), delay(() => append(singleton(tryInclude("unitCategories", (oa_10) => OntologyAnnotation_encoder(options, oa_10), oa["UnitCategories"])), delay(() => singleton(tryInclude("comments", (comment) => encoder_2(options, comment), oa["Comments"]))))))))))))))))))))))))))))))))))));
+        }));
+    }))));
+}
+
+export function Study_decoder(options) {
+    return (path_16) => ((v) => object_37((get$) => {
+        let arg_33, decoder_8, objectArg_16, arg_35, decoder_9, objectArg_17;
+        let ID;
+        const objectArg = get$.Optional;
+        ID = objectArg.Field("@id", uri);
+        let FileName;
+        const objectArg_1 = get$.Optional;
+        FileName = objectArg_1.Field("filename", string);
+        let Identifier;
+        const objectArg_2 = get$.Optional;
+        Identifier = objectArg_2.Field("identifier", string);
+        let Title;
+        const objectArg_3 = get$.Optional;
+        Title = objectArg_3.Field("title", string);
+        let Description;
+        const objectArg_4 = get$.Optional;
+        Description = objectArg_4.Field("description", string);
+        let SubmissionDate;
+        const objectArg_5 = get$.Optional;
+        SubmissionDate = objectArg_5.Field("submissionDate", string);
+        let PublicReleaseDate;
+        const objectArg_6 = get$.Optional;
+        PublicReleaseDate = objectArg_6.Field("publicReleaseDate", string);
+        let Publications;
+        let arg_15;
+        const decoder = decoder_10(options);
+        arg_15 = ((path_6) => ((value_6) => list_1(uncurry2(decoder), path_6, value_6)));
+        const objectArg_7 = get$.Optional;
+        Publications = objectArg_7.Field("publications", uncurry2(arg_15));
+        let Contacts;
+        let arg_17;
+        const decoder_1 = decoder_11(options);
+        arg_17 = ((path_7) => ((value_7) => list_1(uncurry2(decoder_1), path_7, value_7)));
+        const objectArg_8 = get$.Optional;
+        Contacts = objectArg_8.Field("people", uncurry2(arg_17));
+        let StudyDesignDescriptors;
+        let arg_19;
+        const decoder_2 = OntologyAnnotation_decoder(options);
+        arg_19 = ((path_8) => ((value_8) => list_1(uncurry2(decoder_2), path_8, value_8)));
+        const objectArg_9 = get$.Optional;
+        StudyDesignDescriptors = objectArg_9.Field("studyDesignDescriptors", uncurry2(arg_19));
+        let Protocols;
+        let arg_21;
+        const decoder_3 = Protocol_decoder(options);
+        arg_21 = ((path_9) => ((value_9) => list_1(uncurry2(decoder_3), path_9, value_9)));
+        const objectArg_10 = get$.Optional;
+        Protocols = objectArg_10.Field("protocols", uncurry2(arg_21));
+        let Materials;
+        const arg_23 = StudyMaterials_decoder(options);
+        const objectArg_11 = get$.Optional;
+        Materials = objectArg_11.Field("materials", uncurry2(arg_23));
+        let Assays;
+        let arg_25;
+        const decoder_4 = Assay_decoder(options);
+        arg_25 = ((path_10) => ((value_10) => list_1(uncurry2(decoder_4), path_10, value_10)));
+        const objectArg_12 = get$.Optional;
+        Assays = objectArg_12.Field("assays", uncurry2(arg_25));
+        let Factors;
+        let arg_27;
+        const decoder_5 = Factor_decoder(options);
+        arg_27 = ((path_11) => ((value_11) => list_1(uncurry2(decoder_5), path_11, value_11)));
+        const objectArg_13 = get$.Optional;
+        Factors = objectArg_13.Field("factors", uncurry2(arg_27));
+        let CharacteristicCategories;
+        let arg_29;
+        const decoder_6 = MaterialAttribute_decoder(options);
+        arg_29 = ((path_12) => ((value_12) => list_1(uncurry2(decoder_6), path_12, value_12)));
+        const objectArg_14 = get$.Optional;
+        CharacteristicCategories = objectArg_14.Field("characteristicCategories", uncurry2(arg_29));
+        let UnitCategories;
+        let arg_31;
+        const decoder_7 = OntologyAnnotation_decoder(options);
+        arg_31 = ((path_13) => ((value_13) => list_1(uncurry2(decoder_7), path_13, value_13)));
+        const objectArg_15 = get$.Optional;
+        UnitCategories = objectArg_15.Field("unitCategories", uncurry2(arg_31));
+        return new Study(ID, FileName, Identifier, Title, Description, SubmissionDate, PublicReleaseDate, Publications, Contacts, StudyDesignDescriptors, Protocols, Materials, (arg_33 = ((decoder_8 = Process_decoder(options), (path_14) => ((value_14) => list_1(uncurry2(decoder_8), path_14, value_14)))), (objectArg_16 = get$.Optional, objectArg_16.Field("processSequence", uncurry2(arg_33)))), Assays, Factors, CharacteristicCategories, UnitCategories, (arg_35 = ((decoder_9 = decoder_12(options), (path_15) => ((value_15) => list_1(uncurry2(decoder_9), path_15, value_15)))), (objectArg_17 = get$.Optional, objectArg_17.Field("comments", uncurry2(arg_35)))));
+    }, path_16, v));
+}
+
+export function Study_fromString(s) {
+    return fromString(uncurry2(Study_decoder(ConverterOptions_$ctor())), s);
+}
+
+export function Study_toString(p) {
+    return toString(2, Study_encoder(ConverterOptions_$ctor(), p));
+}
+
+/**
+ * exports in json-ld format
+ */
+export function Study_toStringLD(s) {
+    let returnVal;
+    return toString(2, Study_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), s));
+}
+
+export function ArcStudy_fromString(s) {
+    const arg = fromString(uncurry2(Study_decoder(ConverterOptions_$ctor())), s);
+    return ArcStudy.fromStudy(arg);
+}
+
+export function ArcStudy_toString(a, assays) {
+    return toString(2, Study_encoder(ConverterOptions_$ctor(), a.ToStudy(assays)));
+}
+
+/**
+ * exports in json-ld format
+ */
+export function ArcStudy_toStringLD(a, assays) {
+    let returnVal;
+    return toString(2, Study_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), a.ToStudy(assays)));
+}
+

package/ISA/ISA.Json/Validation/Fable.js

@@ -0,0 +1,69 @@
+import { Record } from "../../../fable_modules/fable-library.4.1.4/Types.js";
+import { bool_type, option_type, array_type, record_type, string_type, obj_type } from "../../../fable_modules/fable-library.4.1.4/Reflection.js";
+import { map } from "../../../fable_modules/fable-library.4.1.4/Array.js";
+import { singleton } from "../../../fable_modules/fable-library.4.1.4/AsyncBuilder.js";
+import { awaitPromise } from "../../../fable_modules/fable-library.4.1.4/Async.js";
+import * as JsonValidation from "../../../../../src/ISA/ISA.Json/Validation/JsonValidation.js";
+import { value } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+
+export class ValidationError extends Record {
+    constructor(path, property, message, schema, instance, name, argument, stack) {
+        super();
+        this.path = path;
+        this.property = property;
+        this.message = message;
+        this.schema = schema;
+        this.instance = instance;
+        this.name = name;
+        this.argument = argument;
+        this.stack = stack;
+    }
+}
+
+export function ValidationError_$reflection() {
+    return record_type("ARCtrl.ISA.Json.Fable.ValidationError", [], ValidationError, () => [["path", obj_type], ["property", string_type], ["message", string_type], ["schema", obj_type], ["instance", obj_type], ["name", string_type], ["argument", obj_type], ["stack", string_type]]);
+}
+
+export function ValidationError__ToErrorString(this$) {
+    return `Property ${this$.property} (${this$.instance}) ${this$.message}.`;
+}
+
+export class ValidatorResult extends Record {
+    constructor(instance, schema, options, path, propertyPath, errors, throwError, throFirst, throwAll, disableFormat) {
+        super();
+        this.instance = instance;
+        this.schema = schema;
+        this.options = options;
+        this.path = path;
+        this.propertyPath = propertyPath;
+        this.errors = errors;
+        this.throwError = throwError;
+        this.throFirst = throFirst;
+        this.throwAll = throwAll;
+        this.disableFormat = disableFormat;
+    }
+}
+
+export function ValidatorResult_$reflection() {
+    return record_type("ARCtrl.ISA.Json.Fable.ValidatorResult", [], ValidatorResult, () => [["instance", obj_type], ["schema", obj_type], ["options", obj_type], ["path", array_type(obj_type)], ["propertyPath", string_type], ["errors", array_type(ValidationError_$reflection())], ["throwError", option_type(obj_type)], ["throFirst", option_type(obj_type)], ["throwAll", option_type(obj_type)], ["disableFormat", bool_type]]);
+}
+
+export function ValidatorResult__ToValidationResult(this$) {
+    if (this$.errors.length === 0) {
+        return [true, []];
+    }
+    else {
+        return [false, map(ValidationError__ToErrorString, this$.errors)];
+    }
+}
+
+export function validate(schemaURL, objectString) {
+    let validationResult = void 0;
+    return singleton.Delay(() => singleton.Bind(awaitPromise(JsonValidation.validateAgainstSchema(objectString, schemaURL).then((o) => {
+        validationResult = o;
+    })), () => {
+        const output = ValidatorResult__ToValidationResult(value(validationResult));
+        return singleton.Return(output);
+    }));
+}
+

package/ISA/ISA.Json/Validation/JsonSchemaValidation.js

@@ -0,0 +1,88 @@
+import { singleton } from "../../../fable_modules/fable-library.4.1.4/AsyncBuilder.js";
+import { validate } from "./Fable.js";
+import { ValidationResult, ValidationResult_OfJSchemaOutput_Z6EC48F6B } from "./ValidationResult.js";
+
+export function Validation_validate(schemaURL, objectString) {
+    return singleton.Delay(() => singleton.TryWith(singleton.Delay(() => singleton.Bind(validate(schemaURL, objectString), (_arg) => singleton.Return(ValidationResult_OfJSchemaOutput_Z6EC48F6B([_arg[0], _arg[1]])))), (_arg_1) => singleton.Return(new ValidationResult(1, [[_arg_1.message]]))));
+}
+
+export function Validation_validateAssay(assayString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/assay_schema.json", assayString);
+}
+
+export function Validation_validateComment(commentString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/comment_schema.json", commentString);
+}
+
+export function Validation_validateData(dataString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/data_schema.json", dataString);
+}
+
+export function Validation_validateFactor(factorString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/factor_schema.json", factorString);
+}
+
+export function Validation_validateFactorValue(factorValueString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/factor_value_schema.json", factorValueString);
+}
+
+export function Validation_validateInvestigation(investigationString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/investigation_schema.json", investigationString);
+}
+
+export function Validation_validateMaterialAttribute(materialAttributeString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/material_attribute_schema.json", materialAttributeString);
+}
+
+export function Validation_validateMaterialAttributeValue(materialAttributeValueString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/material_attribute_value_schema.json", materialAttributeValueString);
+}
+
+export function Validation_validateMaterial(materialString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/material_schema.json", materialString);
+}
+
+export function Validation_validateOntologyAnnotation(ontologyAnnotationString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/ontology_annotation_schema.json", ontologyAnnotationString);
+}
+
+export function Validation_validateOntologySourceReference(ontologySourceReferenceString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/ontology_source_reference_schema.json", ontologySourceReferenceString);
+}
+
+export function Validation_validatePerson(personString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/person_schema.json", personString);
+}
+
+export function Validation_validateProcessParameterValue(processParameterValueString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/process_parameter_value_schema.json", processParameterValueString);
+}
+
+export function Validation_validateProcess(processString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/process_schema.json", processString);
+}
+
+export function Validation_validateProtocolParameter(protocolParameterString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/protocol_parameter_schema.json", protocolParameterString);
+}
+
+export function Validation_validateProtocol(protocolString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/protocol_schema.json", protocolString);
+}
+
+export function Validation_validatePublication(publicationString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/publication_schema.json", publicationString);
+}
+
+export function Validation_validateSample(sampleString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/sample_schema.json", sampleString);
+}
+
+export function Validation_validateSource(sourceString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/source_schema.json", sourceString);
+}
+
+export function Validation_validateStudy(studyString) {
+    return Validation_validate("https://raw.githubusercontent.com/HLWeil/isa-specs/anyof/source/_static/isajson/study_schema.json", studyString);
+}
+

package/ISA/ISA.Json/Validation/ValidationResult.js

@@ -0,0 +1,45 @@
+import { Union } from "../../../fable_modules/fable-library.4.1.4/Types.js";
+import { union_type, array_type, string_type } from "../../../fable_modules/fable-library.4.1.4/Reflection.js";
+
+export class ValidationResult extends Union {
+    constructor(tag, fields) {
+        super();
+        this.tag = tag;
+        this.fields = fields;
+    }
+    cases() {
+        return ["Ok", "Failed"];
+    }
+}
+
+export function ValidationResult_$reflection() {
+    return union_type("ARCtrl.ISA.Json.ValidationTypes.ValidationResult", [], ValidationResult, () => [[], [["Item", array_type(string_type)]]]);
+}
+
+export function ValidationResult__get_Success(this$) {
+    if (this$.tag === 0) {
+        return true;
+    }
+    else {
+        return false;
+    }
+}
+
+export function ValidationResult__GetErrors(this$) {
+    if (this$.tag === 1) {
+        return this$.fields[0];
+    }
+    else {
+        return [];
+    }
+}
+
+export function ValidationResult_OfJSchemaOutput_Z6EC48F6B(output) {
+    if (output[0]) {
+        return new ValidationResult(0, []);
+    }
+    else {
+        return new ValidationResult(1, [output[1]]);
+    }
+}
+

package/ISA/ISA.Spreadsheet/AnnotationTable/ArcTable.js

@@ -0,0 +1,137 @@
+import { iterateIndexed, length, sortBy, collect, toArray, empty, tail, head, isEmpty, cons, singleton, fold, map, reverse } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { tryParseReferenceColumnHeader } from "../../ISA/Regex.js";
+import { map as map_1, toList, tryFind } from "../../../fable_modules/fable-library.4.1.4/Seq.js";
+import { toFsColumns, fixDeprecatedIOHeader, fromFsColumns } from "./CompositeColumn.js";
+import { ArcTable } from "../../ISA/ArcTypes/ArcTable.js";
+import { FsWorksheet } from "../../../fable_modules/FsSpreadsheet.4.1.0/FsWorksheet.fs.js";
+import { comparePrimitives } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+import { FsRangeAddress_$ctor_7E77A4A0 } from "../../../fable_modules/FsSpreadsheet.4.1.0/Ranges/FsRangeAddress.fs.js";
+import { FsAddress_$ctor_Z37302880 } from "../../../fable_modules/FsSpreadsheet.4.1.0/FsAddress.fs.js";
+import { Dictionary_tryGet } from "../../../fable_modules/FsSpreadsheet.4.1.0/Cells/FsCellsCollection.fs.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
+import { FsRangeBase__Cell_Z3407A44B } from "../../../fable_modules/FsSpreadsheet.4.1.0/Ranges/FsRangeBase.fs.js";
+
+/**
+ * Iterates over elements of the input list and groups adjacent elements.
+ * A new group is started when the specified predicate holds about the element
+ * of the list (and at the beginning of the iteration).
+ * 
+ * For example:
+ * List.groupWhen isOdd [3;3;2;4;1;2] = [[3]; [3; 2; 4]; [1; 2]]
+ */
+export function Aux_List_groupWhen(f, list) {
+    return reverse(map(reverse, fold((acc, e) => {
+        const matchValue = f(e);
+        if (matchValue) {
+            return cons(singleton(e), acc);
+        }
+        else if (!isEmpty(acc)) {
+            return cons(cons(e, head(acc)), tail(acc));
+        }
+        else {
+            return singleton(singleton(e));
+        }
+    }, empty(), list)));
+}
+
+export function classifyHeaderOrder(header) {
+    switch (header.tag) {
+        case 4:
+        case 5:
+        case 6:
+        case 7:
+        case 8:
+        case 9:
+        case 10:
+            return 2;
+        case 0:
+        case 1:
+        case 2:
+        case 3:
+        case 13:
+            return 3;
+        case 12:
+            return 4;
+        default:
+            return 1;
+    }
+}
+
+export function classifyColumnOrder(column) {
+    return classifyHeaderOrder(column.Header);
+}
+
+export function groupColumnsByHeader(columns) {
+    return Aux_List_groupWhen((c) => {
+        if (tryParseReferenceColumnHeader(c.Item(1).Value) == null) {
+            return !(c.Item(1).Value.indexOf("Unit") === 0);
+        }
+        else {
+            return false;
+        }
+    }, columns);
+}
+
+/**
+ * Returns the annotation table of the worksheet if it exists, else returns None
+ */
+export function tryAnnotationTable(sheet) {
+    return tryFind((t) => (t.Name.indexOf("annotationTable") === 0), sheet.Tables);
+}
+
+/**
+ * Groups and parses a collection of single columns into the according ISA composite columns
+ */
+export function composeColumns(columns) {
+    return toArray(map(fromFsColumns, groupColumnsByHeader(toList(columns))));
+}
+
+/**
+ * Returns the protocol described by the headers and a function for parsing the values of the matrix to the processes of this protocol
+ */
+export function tryFromFsWorksheet(sheet) {
+    const matchValue = tryAnnotationTable(sheet);
+    if (matchValue == null) {
+        return void 0;
+    }
+    else {
+        const t = matchValue;
+        const compositeColumns = composeColumns(map_1(fixDeprecatedIOHeader, t.GetColumns(sheet.CellCollection)));
+        return ArcTable.addColumns(compositeColumns)(ArcTable.init(sheet.Name));
+    }
+}
+
+export function toFsWorksheet(table) {
+    const stringCount = new Map([]);
+    const ws = new FsWorksheet(table.Name);
+    const columns = collect(toFsColumns, sortBy(classifyColumnOrder, table.Columns, {
+        Compare: comparePrimitives,
+    }));
+    const maxRow = length(head(columns)) | 0;
+    const maxCol = length(columns) | 0;
+    const fsTable = ws.Table("annotationTable", FsRangeAddress_$ctor_7E77A4A0(FsAddress_$ctor_Z37302880(1, 1), FsAddress_$ctor_Z37302880(maxRow, maxCol)));
+    iterateIndexed((colI, col) => {
+        iterateIndexed((rowI, cell) => {
+            let value;
+            if (rowI === 0) {
+                const matchValue = Dictionary_tryGet(cell.Value, stringCount);
+                if (matchValue == null) {
+                    addToDict(stringCount, cell.Value, "");
+                    value = cell.Value;
+                }
+                else {
+                    const spaces = matchValue;
+                    stringCount.set(cell.Value, spaces + " ");
+                    value = ((cell.Value + " ") + spaces);
+                }
+            }
+            else {
+                value = cell.Value;
+            }
+            const address = FsAddress_$ctor_Z37302880(rowI + 1, colI + 1);
+            FsRangeBase__Cell_Z3407A44B(fsTable, address, ws.CellCollection).SetValueAs(value);
+        }, col);
+    }, columns);
+    return ws;
+}
+

package/ISA/ISA.Spreadsheet/AnnotationTable/CompositeCell.js

@@ -0,0 +1,78 @@
+import { singleton, ofArray, head, tail, isEmpty, map } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { CompositeCell } from "../../ISA/ArcTypes/CompositeCell.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.1.4/String.js";
+import { FsCell } from "../../../fable_modules/FsSpreadsheet.4.1.0/Cells/FsCell.fs.js";
+
+export function fromFsCells(cells) {
+    const cellValues = map((c) => c.Value, cells);
+    let matchResult, v, v1, v2, v3, v1_1, v2_1, v3_1, v4;
+    if (!isEmpty(cellValues)) {
+        if (!isEmpty(tail(cellValues))) {
+            if (!isEmpty(tail(tail(cellValues)))) {
+                if (!isEmpty(tail(tail(tail(cellValues))))) {
+                    if (isEmpty(tail(tail(tail(tail(cellValues)))))) {
+                        matchResult = 2;
+                        v1_1 = head(cellValues);
+                        v2_1 = head(tail(cellValues));
+                        v3_1 = head(tail(tail(cellValues)));
+                        v4 = head(tail(tail(tail(cellValues))));
+                    }
+                    else {
+                        matchResult = 3;
+                    }
+                }
+                else {
+                    matchResult = 1;
+                    v1 = head(cellValues);
+                    v2 = head(tail(cellValues));
+                    v3 = head(tail(tail(cellValues)));
+                }
+            }
+            else {
+                matchResult = 3;
+            }
+        }
+        else {
+            matchResult = 0;
+            v = head(cellValues);
+        }
+    }
+    else {
+        matchResult = 3;
+    }
+    switch (matchResult) {
+        case 0:
+            return CompositeCell.createFreeText(v);
+        case 1:
+            return CompositeCell.createTermFromString(v1, v2, v3);
+        case 2:
+            return CompositeCell.createUnitizedFromString(v1_1, v2_1, v3_1, v4);
+        default:
+            return toFail(printf("Dafuq"));
+    }
+}
+
+export function toFsCells(isTerm, hasUnit, cell) {
+    switch (cell.tag) {
+        case 0:
+            if (hasUnit) {
+                return ofArray([new FsCell(cell.fields[0].NameText), new FsCell(""), new FsCell(cell.fields[0].TermSourceREFString), new FsCell(cell.fields[0].TermAccessionOntobeeUrl)]);
+            }
+            else {
+                return ofArray([new FsCell(cell.fields[0].NameText), new FsCell(cell.fields[0].TermSourceREFString), new FsCell(cell.fields[0].TermAccessionOntobeeUrl)]);
+            }
+        case 2:
+            return ofArray([new FsCell(cell.fields[0]), new FsCell(cell.fields[1].NameText), new FsCell(cell.fields[1].TermSourceREFString), new FsCell(cell.fields[1].TermAccessionOntobeeUrl)]);
+        default:
+            if (hasUnit) {
+                return ofArray([new FsCell(cell.fields[0]), new FsCell(""), new FsCell(""), new FsCell("")]);
+            }
+            else if (isTerm) {
+                return ofArray([new FsCell(cell.fields[0]), new FsCell(""), new FsCell("")]);
+            }
+            else {
+                return singleton(new FsCell(cell.fields[0]));
+            }
+    }
+}
+