@nfdi4plants/arctrl 1.0.0-alpha6 → 1.0.0-alpha8

package/{ARCtrl.js → ARC.js}

@@ -14,13 +14,13 @@ import { tryISAReadContractFromPath } from "./Contracts/Contracts.ARCtrl.js";
 import { ArcTables__get_Tables, ArcTables_$ctor_Z18C2F36D, ArcTables_updateReferenceTablesBySheets_Z2EE88E97 } from "./ISA/ISA/ArcTypes/ArcTables.js";
 import { addToDict } from "./fable_modules/fable-library.4.1.4/MapUtil.js";
 import { ArcInvestigation } from "./ISA/ISA/ArcTypes/ArcTypes.js";
-import { printf, toConsole } from "./fable_modules/fable-library.4.1.4/String.js";
 import { Assay_fileNameFromIdentifier, Study_fileNameFromIdentifier } from "./ISA/ISA/Identifier.js";
 import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.4.1.0/Cells/FsCellsCollection.fs.js";
 import { Contract } from "./Contract/Contract.js";
 import { Clone_createCloneContract_5000466F, Init_createAddRemoteContract_Z721C83C5, gitignoreContract, Init_createInitContract_6DFDD678 } from "./Contracts/Contracts.Git.js";
 import { FSharpSet__Contains, ofSeq, unionMany } from "./fable_modules/fable-library.4.1.4/Set.js";
 import { comparePrimitives } from "./fable_modules/fable-library.4.1.4/Util.js";
+import { ofSeq as ofSeq_1 } from "./fable_modules/fable-library.4.1.4/Map.js";
 import { class_type } from "./fable_modules/fable-library.4.1.4/Reflection.js";
 
 export function ARCAux_getArcAssaysFromContracts(contracts) {
@@ -82,6 +82,7 @@ export class ARC {
     set ISA(newISA) {
         const this$ = this;
         this$._isa = newISA;
+        this$.UpdateFileSystem();
     }
     get CWL() {
         const this$ = this;
@@ -144,7 +145,6 @@ export class ARC {
         const matchValue = this$.ISA;
         if (matchValue == null) {
             addToDict(workbooks, "isa.investigation.xlsx", ["ISA_Investigation", toFsWorkbook(ArcInvestigation.create("MISSING_IDENTIFIER_"))]);
-            toConsole(printf("ARC contains no ISA part."));
         }
         else {
             const inv = matchValue;
@@ -245,6 +245,11 @@ export class ARC {
             }
         }, (tree = ((arg = ((array = FileSystemTree.toFilePaths()(this$._fs.Copy().Tree), array.filter((p) => !FSharpSet__Contains(registeredPayload, p)))), FileSystemTree.fromFilePaths(arg))), ignoreHidden ? FileSystemTree.filterFiles((n) => !(n.indexOf(".") === 0))(tree) : tree)), FileSystemTree.fromFilePaths([]));
     }
+    static get DefaultContracts() {
+        return ofSeq_1([[".gitignore", gitignoreContract]], {
+            Compare: comparePrimitives,
+        });
+    }
 }
 
 export function ARC_$reflection() {

package/ISA/ISA/ArcTypes/ArcTableAux.js

@@ -570,75 +570,39 @@ export function JsonTypes_composeProcessOutput(header, value) {
  */
 export function JsonTypes_cellOfValue(value, unit) {
     const value_2 = defaultArg(value, new Value(3, [""]));
-    let matchResult, oa, text, u, f, u_1, f_1, i, u_2, i_1;
     switch (value_2.tag) {
-        case 3: {
+        case 3:
             if (unit != null) {
-                if (value_2.fields[0] === "") {
-                    matchResult = 2;
-                    u = unit;
-                }
-                else {
-                    matchResult = 7;
-                }
+                const u = unit;
+                return new CompositeCell(2, [value_2.fields[0], u]);
             }
             else {
-                matchResult = 1;
-                text = value_2.fields[0];
+                return new CompositeCell(1, [value_2.fields[0]]);
             }
-            break;
-        }
-        case 2: {
+        case 2:
             if (unit == null) {
-                matchResult = 4;
-                f_1 = value_2.fields[0];
+                return new CompositeCell(1, [value_2.fields[0].toString()]);
             }
             else {
-                matchResult = 3;
-                f = value_2.fields[0];
-                u_1 = unit;
+                const u_1 = unit;
+                return new CompositeCell(2, [value_2.fields[0].toString(), u_1]);
             }
-            break;
-        }
-        case 1: {
+        case 1:
             if (unit == null) {
-                matchResult = 6;
-                i_1 = value_2.fields[0];
+                return new CompositeCell(1, [int32ToString(value_2.fields[0])]);
             }
             else {
-                matchResult = 5;
-                i = value_2.fields[0];
-                u_2 = unit;
+                const u_2 = unit;
+                return new CompositeCell(2, [int32ToString(value_2.fields[0]), u_2]);
             }
-            break;
-        }
         default:
             if (unit == null) {
-                matchResult = 0;
-                oa = value_2.fields[0];
+                return new CompositeCell(0, [value_2.fields[0]]);
             }
             else {
-                matchResult = 7;
+                return toFail(printf("Could not parse value %O with unit %O"))(value_2)(unit);
             }
     }
-    switch (matchResult) {
-        case 0:
-            return new CompositeCell(0, [oa]);
-        case 1:
-            return new CompositeCell(1, [text]);
-        case 2:
-            return new CompositeCell(2, ["", u]);
-        case 3:
-            return new CompositeCell(2, [f.toString(), u_1]);
-        case 4:
-            return new CompositeCell(1, [f_1.toString()]);
-        case 5:
-            return new CompositeCell(2, [int32ToString(i), u_2]);
-        case 6:
-            return new CompositeCell(1, [int32ToString(i_1)]);
-        default:
-            return toFail(printf("Could not parse value %O with unit %O"))(value_2)(unit);
-    }
 }
 
 /**

package/ISA/ISA/ArcTypes/ArcTypes.js

@@ -1,6 +1,6 @@
 import { map as map_1, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.1.4/Option.js";
 import { ArcTables_updateReferenceTablesBySheets_Z2EE88E97, ArcTables_fromProcesses_134EBDED, ArcTables__get_Tables, ArcTables__GetProcesses, ArcTables__GetRow_Z18115A39, ArcTables__GetRowAt_Z37302880, ArcTables__UpdateRow_1BFE2CFB, ArcTables__UpdateRowAt_1CF7B5DC, ArcTables__RemoveRow_Z18115A39, ArcTables__RemoveRowAt_Z37302880, ArcTables__AddRow_Z16315DE5, ArcTables__AddRowAt_Z12CDB784, ArcTables__GetColumn_Z18115A39, ArcTables__GetColumnAt_Z37302880, ArcTables__UpdateColumn_Z6083042A, ArcTables__UpdateColumnAt_21300791, ArcTables__RemoveColumn_Z18115A39, ArcTables__RemoveColumnAt_Z37302880, ArcTables__AddColumn_1FF50D3C, ArcTables__AddColumnAt_6A9784DB, ArcTables__RenameTable_Z384F8060, ArcTables__RenameTableAt_Z176EF219, ArcTables__MapTable_27DD7B1B, ArcTables__MapTableAt_8FC095C, ArcTables__RemoveTable_Z721C83C5, ArcTables__RemoveTableAt_Z524259A4, ArcTables__SetTable_51766571, ArcTables__SetTableAt_7E571736, ArcTables__UpdateTable_51766571, ArcTables__UpdateTableAt_7E571736, ArcTables__GetTable_Z721C83C5, ArcTables__GetTableAt_Z524259A4, ArcTables__InitTables_7B28792B, ArcTables__InitTable_3B406CA4, ArcTables__AddTables_Z2D453886, ArcTables__AddTable_EC12B15, ArcTables__get_TableNames, ArcTables_$ctor_Z18C2F36D, ArcTables__get_Count } from "./ArcTables.js";
-import { concat, toList, tryFind, removeAt, tryFindIndex, map as map_2, contains, filter, toArray } from "../../../fable_modules/fable-library.4.1.4/Seq.js";
+import { concat, tryFind, removeAt, tryFindIndex, item, map as map_2, delay, toList, fold, length, forAll, contains, filter, toArray } from "../../../fable_modules/fable-library.4.1.4/Seq.js";
 import { defaultOf, safeHash, equals, disposeSafe, getEnumerator, stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
 import { tryFind as tryFind_1, removeInPlace, equalsWith, append as append_3, contains as contains_1, map } from "../../../fable_modules/fable-library.4.1.4/Array.js";
 import { distinctBy, Array_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
@@ -15,6 +15,7 @@ import { unzip, ofSeq, map as map_3, toArray as toArray_1, ofArray, empty } from
 import { getSources, getProtocols, getUnits, getCharacteristics, getData, getMaterials, getSamples } from "../JsonTypes/ProcessSequence.js";
 import { Assay_create_3D372A24 } from "../JsonTypes/Assay.js";
 import { Study_identifierFromFileName, Study_fileNameFromIdentifier, Assay_identifierFromFileName, createMissingIdentifier, Assay_fileNameFromIdentifier, isMissingIdentifier } from "../Identifier.js";
+import { rangeDouble } from "../../../fable_modules/fable-library.4.1.4/Range.js";
 import { class_type } from "../../../fable_modules/fable-library.4.1.4/Reflection.js";
 import { StudyMaterials_get_empty, StudyMaterials_create_1BE9FA55 } from "../JsonTypes/StudyMaterials.js";
 import { Study_create_Z2D28E954 } from "../JsonTypes/Study.js";
@@ -637,6 +638,41 @@ export class ArcAssay {
         identifer = ((matchValue == null) ? createMissingIdentifier() : Assay_identifierFromFileName(matchValue));
         return ArcAssay.create(identifer, unwrap(map_1((x) => x.Copy(), a.MeasurementType)), unwrap(map_1((x_1) => x_1.Copy(), a.TechnologyType)), unwrap(map_1((arg_2) => ArcAssay.decomposeTechnologyPlatform(arg_2), a.TechnologyPlatform)), unwrap(tables), void 0, unwrap(map_1(toArray_1, a.Comments)));
     }
+    StructurallyEquals(other) {
+        let a, b, a_1, b_1, a_2, b_2;
+        const this$ = this;
+        return forAll((x) => (x === true), [this$.Identifier === other.Identifier, equals(this$.MeasurementType, other.MeasurementType), equals(this$.TechnologyType, other.TechnologyType), equals(this$.TechnologyPlatform, other.TechnologyPlatform), (a = this$.Tables, (b = other.Tables, (length(a) === length(b)) && fold((acc, e) => {
+            if (acc) {
+                return e;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_1) => equals(item(i_1, a), item(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Performers, (b_1 = other.Performers, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
+            if (acc_1) {
+                return e_1;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_2) => equals(item(i_2, a_1), item(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.Comments, (b_2 = other.Comments, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
+            if (acc_2) {
+                return e_2;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_3) => equals(item(i_3, a_2), item(i_3, b_2)), rangeDouble(0, 1, length(a_2) - 1)))))))]);
+    }
+    ReferenceEquals(other) {
+        const this$ = this;
+        return this$ === other;
+    }
+    Equals(other) {
+        let assay;
+        const this$ = this;
+        return (other instanceof ArcAssay) && ((assay = other, this$.StructurallyEquals(assay)));
+    }
 }
 
 export function ArcAssay_$reflection() {
@@ -656,7 +692,7 @@ export class ArcStudy {
         const registeredAssayIdentifiers_1 = defaultArg(registeredAssayIdentifiers, []);
         const factors_1 = defaultArg(factors, []);
         const comments_1 = defaultArg(comments, []);
-        this["identifier@615"] = identifier;
+        this["identifier@641"] = identifier;
         this.investigation = void 0;
         this["Title@"] = title;
         this["Description@"] = description;
@@ -672,11 +708,11 @@ export class ArcStudy {
     }
     get Identifier() {
         const this$ = this;
-        return this$["identifier@615"];
+        return this$["identifier@641"];
     }
     set Identifier(i) {
         const this$ = this;
-        this$["identifier@615"] = i;
+        this$["identifier@641"] = i;
     }
     get Investigation() {
         const this$ = this;
@@ -1379,6 +1415,69 @@ export class ArcStudy {
         assaysIdentifiers = Array.from(arg_5);
         return [ArcStudy.create(identifer, unwrap(s.Title), unwrap(s.Description), unwrap(s.SubmissionDate), unwrap(s.PublicReleaseDate), unwrap(map_1(toArray_1, s.Publications)), unwrap(map_1(toArray_1, s.Contacts)), unwrap(map_1(toArray_1, s.StudyDesignDescriptors)), unwrap(tables), assaysIdentifiers, unwrap(map_1(toArray_1, s.Factors)), unwrap(map_1(toArray_1, s.Comments))), assays];
     }
+    StructurallyEquals(other) {
+        let a, b, a_1, b_1, a_2, b_2, a_3, b_3, a_4, b_4, a_5, b_5, a_6, b_6;
+        const this$ = this;
+        return forAll((x) => (x === true), [this$.Identifier === other.Identifier, equals(this$.Title, other.Title), equals(this$.Description, other.Description), equals(this$.SubmissionDate, other.SubmissionDate), equals(this$.PublicReleaseDate, other.PublicReleaseDate), (a = this$.Publications, (b = other.Publications, (length(a) === length(b)) && fold((acc, e) => {
+            if (acc) {
+                return e;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_1) => equals(item(i_1, a), item(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Contacts, (b_1 = other.Contacts, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
+            if (acc_1) {
+                return e_1;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_2) => equals(item(i_2, a_1), item(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.StudyDesignDescriptors, (b_2 = other.StudyDesignDescriptors, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
+            if (acc_2) {
+                return e_2;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_3) => equals(item(i_3, a_2), item(i_3, b_2)), rangeDouble(0, 1, length(a_2) - 1))))))), (a_3 = this$.Tables, (b_3 = other.Tables, (length(a_3) === length(b_3)) && fold((acc_3, e_3) => {
+            if (acc_3) {
+                return e_3;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_4) => equals(item(i_4, a_3), item(i_4, b_3)), rangeDouble(0, 1, length(a_3) - 1))))))), (a_4 = this$.RegisteredAssayIdentifiers, (b_4 = other.RegisteredAssayIdentifiers, (length(a_4) === length(b_4)) && fold((acc_4, e_4) => {
+            if (acc_4) {
+                return e_4;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_5) => (item(i_5, a_4) === item(i_5, b_4)), rangeDouble(0, 1, length(a_4) - 1))))))), (a_5 = this$.Factors, (b_5 = other.Factors, (length(a_5) === length(b_5)) && fold((acc_5, e_5) => {
+            if (acc_5) {
+                return e_5;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_6) => equals(item(i_6, a_5), item(i_6, b_5)), rangeDouble(0, 1, length(a_5) - 1))))))), (a_6 = this$.Comments, (b_6 = other.Comments, (length(a_6) === length(b_6)) && fold((acc_6, e_6) => {
+            if (acc_6) {
+                return e_6;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_7) => equals(item(i_7, a_6), item(i_7, b_6)), rangeDouble(0, 1, length(a_6) - 1)))))))]);
+    }
+    ReferenceEquals(other) {
+        const this$ = this;
+        return this$ === other;
+    }
+    Equals(other) {
+        let s;
+        const this$ = this;
+        return (other instanceof ArcStudy) && ((s = other, this$.StructurallyEquals(s)));
+    }
 }
 
 export function ArcStudy_$reflection() {
@@ -1425,7 +1524,7 @@ export class ArcInvestigation {
         const registeredStudyIdentifiers_1 = defaultArg(registeredStudyIdentifiers, []);
         const comments_1 = defaultArg(comments, []);
         const remarks_1 = defaultArg(remarks, []);
-        this["identifier@1235"] = identifier;
+        this["identifier@1292"] = identifier;
         this["Title@"] = title;
         this["Description@"] = description;
         this["SubmissionDate@"] = submissionDate;
@@ -1438,15 +1537,15 @@ export class ArcInvestigation {
         this["RegisteredStudyIdentifiers@"] = registeredStudyIdentifiers_1;
         this["Comments@"] = comments_1;
         this["Remarks@"] = remarks_1;
-        this["init@1216"] = 1;
+        this["init@1273"] = 1;
     }
     get Identifier() {
         const this$ = this;
-        return this$["identifier@1235"];
+        return this$["identifier@1292"];
     }
     set Identifier(i) {
         const this$ = this;
-        this$["identifier@1235"] = i;
+        this$["identifier@1292"] = i;
     }
     get Title() {
         const __ = this;
@@ -2006,6 +2105,76 @@ export class ArcInvestigation {
         assays = Array.from(arg_2);
         return ArcInvestigation.create(identifer, i.Title, i.Description, i.SubmissionDate, i.PublicReleaseDate, void 0, map_1(toArray_1, i.Publications), map_1(toArray_1, i.Contacts), assays, studies, studyIdentifiers, map_1(toArray_1, i.Comments));
     }
+    StructurallyEquals(other) {
+        let a, b, a_1, b_1, a_2, b_2, a_3, b_3, a_4, b_4, a_5, b_5, a_6, b_6, a_7, b_7;
+        const this$ = this;
+        return forAll((x) => (x === true), [this$.Identifier === other.Identifier, equals(this$.Title, other.Title), equals(this$.Description, other.Description), equals(this$.SubmissionDate, other.SubmissionDate), equals(this$.PublicReleaseDate, other.PublicReleaseDate), (a = this$.Publications, (b = other.Publications, (length(a) === length(b)) && fold((acc, e) => {
+            if (acc) {
+                return e;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_1) => equals(item(i_1, a), item(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Contacts, (b_1 = other.Contacts, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
+            if (acc_1) {
+                return e_1;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_2) => equals(item(i_2, a_1), item(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.OntologySourceReferences, (b_2 = other.OntologySourceReferences, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
+            if (acc_2) {
+                return e_2;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_3) => equals(item(i_3, a_2), item(i_3, b_2)), rangeDouble(0, 1, length(a_2) - 1))))))), (a_3 = this$.Assays, (b_3 = other.Assays, (length(a_3) === length(b_3)) && fold((acc_3, e_3) => {
+            if (acc_3) {
+                return e_3;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_4) => equals(item(i_4, a_3), item(i_4, b_3)), rangeDouble(0, 1, length(a_3) - 1))))))), (a_4 = this$.Studies, (b_4 = other.Studies, (length(a_4) === length(b_4)) && fold((acc_4, e_4) => {
+            if (acc_4) {
+                return e_4;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_5) => equals(item(i_5, a_4), item(i_5, b_4)), rangeDouble(0, 1, length(a_4) - 1))))))), (a_5 = this$.RegisteredStudyIdentifiers, (b_5 = other.RegisteredStudyIdentifiers, (length(a_5) === length(b_5)) && fold((acc_5, e_5) => {
+            if (acc_5) {
+                return e_5;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_6) => (item(i_6, a_5) === item(i_6, b_5)), rangeDouble(0, 1, length(a_5) - 1))))))), (a_6 = this$.Comments, (b_6 = other.Comments, (length(a_6) === length(b_6)) && fold((acc_6, e_6) => {
+            if (acc_6) {
+                return e_6;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_7) => equals(item(i_7, a_6), item(i_7, b_6)), rangeDouble(0, 1, length(a_6) - 1))))))), (a_7 = this$.Remarks, (b_7 = other.Remarks, (length(a_7) === length(b_7)) && fold((acc_7, e_7) => {
+            if (acc_7) {
+                return e_7;
+            }
+            else {
+                return false;
+            }
+        }, true, toList(delay(() => map_2((i_8) => equals(item(i_8, a_7), item(i_8, b_7)), rangeDouble(0, 1, length(a_7) - 1)))))))]);
+    }
+    ReferenceEquals(other) {
+        const this$ = this;
+        return this$ === other;
+    }
+    Equals(other) {
+        let i;
+        const this$ = this;
+        return (other instanceof ArcInvestigation) && ((i = other, this$.StructurallyEquals(i)));
+    }
 }
 
 export function ArcInvestigation_$reflection() {

package/ISA/ISA/Regex.js

@@ -49,7 +49,7 @@ export function ActivePatterns_$007CReferenceColumnHeader$007C_$007C(input) {
  * Matches any column header starting with some text, followed by one whitespace and a term name inside squared brackets.
  */
 export function ActivePatterns_$007CTermColumn$007C_$007C(input) {
-    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("(?<termcolumntype>.+)\\s\\[(?<termname>.+)\\]", input);
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("(?<termcolumntype>.+?)\\s\\[(?<termname>.+)\\]", input);
     if (activePatternResult != null) {
         const r = activePatternResult;
         return {

package/ISA/ISA.Json/Assay.js

@@ -12,7 +12,7 @@ import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetI
 import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./Ontology.js";
 import { Process_decoder, Process_encoder } from "./Process.js";
 import { decoder as decoder_5, encoder } from "./Comment.js";
-import { fromString, uri } from "./Decode.js";
+import { fromJsonString, uri } from "./Decode.js";
 import { Assay } from "../ISA/JsonTypes/Assay.js";
 import { ArcAssay } from "../ISA/ArcTypes/ArcTypes.js";
 
@@ -88,11 +88,11 @@ export function Assay_decoder(options) {
     }, path_7, v));
 }
 
-export function Assay_fromString(s) {
-    return fromString(uncurry2(Assay_decoder(ConverterOptions_$ctor())), s);
+export function Assay_fromJsonString(s) {
+    return fromJsonString(uncurry2(Assay_decoder(ConverterOptions_$ctor())), s);
 }
 
-export function Assay_toString(p) {
+export function Assay_toJsonString(p) {
     return toString(2, Assay_encoder(ConverterOptions_$ctor(), p));
 }
 
@@ -104,12 +104,12 @@ export function Assay_toStringLD(a) {
     return toString(2, Assay_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), a));
 }
 
-export function ArcAssay_fromString(s) {
-    const arg = fromString(uncurry2(Assay_decoder(ConverterOptions_$ctor())), s);
+export function ArcAssay_fromJsonString(s) {
+    const arg = fromJsonString(uncurry2(Assay_decoder(ConverterOptions_$ctor())), s);
     return ArcAssay.fromAssay(arg);
 }
 
-export function ArcAssay_toString(a) {
+export function ArcAssay_toJsonString(a) {
     return toString(2, Assay_encoder(ConverterOptions_$ctor(), a.ToAssay()));
 }
 

package/ISA/ISA.Json/Comment.js

@@ -1,14 +1,14 @@
 import { replace } from "../../fable_modules/fable-library.4.1.4/String.js";
 import { value as value_13 } from "../../fable_modules/fable-library.4.1.4/Option.js";
 import { URIModule_toString } from "../ISA/JsonTypes/URI.js";
-import { toString as toString_1, nil, object as object_6 } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
+import { toString, nil, object as object_6 } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
 import { 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 { 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_$ctor, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
 import { tryInclude } from "./GEncode.js";
 import { string, object as object_7 } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
-import { fromString as fromString_1, uri } from "./Decode.js";
+import { fromJsonString as fromJsonString_1, uri } from "./Decode.js";
 import { Comment$ } from "../ISA/JsonTypes/Comment.js";
 
 export function genID(c) {
@@ -66,12 +66,12 @@ export function decoder(options) {
     }, path_2, v));
 }
 
-export function fromString(s) {
-    return fromString_1(uncurry2(decoder(ConverterOptions_$ctor())), s);
+export function fromJsonString(s) {
+    return fromJsonString_1(uncurry2(decoder(ConverterOptions_$ctor())), s);
 }
 
-export function toString(c) {
-    return toString_1(2, encoder(ConverterOptions_$ctor(), c));
+export function toJsonString(c) {
+    return toString(2, encoder(ConverterOptions_$ctor(), c));
 }
 
 /**
@@ -79,6 +79,6 @@ export function toString(c) {
  */
 export function toStringLD(c) {
     let returnVal;
-    return toString_1(2, encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), c));
+    return toString(2, encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), c));
 }
 

package/ISA/ISA.Json/Data.js

@@ -10,7 +10,7 @@ import { empty, singleton, append, delay, toList } from "../../fable_modules/fab
 import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID } from "./ConverterOptions.js";
 import { tryInclude } from "./GEncode.js";
 import { decoder as decoder_3, encoder } from "./Comment.js";
-import { fromString, uri, hasUnknownFields } from "./Decode.js";
+import { fromJsonString, uri, hasUnknownFields } from "./Decode.js";
 import { Data } from "../ISA/JsonTypes/Data.js";
 import { replace } from "../../fable_modules/fable-library.4.1.4/String.js";
 import { MaterialAttributeValue_decoder, MaterialAttributeValue_encoder } from "./Material.js";
@@ -110,12 +110,12 @@ export function Data_decoder(options, s, json) {
     }
 }
 
-export function Data_fromString(s) {
+export function Data_fromJsonString(s) {
     let options;
-    return fromString(uncurry2((options = ConverterOptions_$ctor(), (s_1) => ((json) => Data_decoder(options, s_1, json)))), s);
+    return fromJsonString(uncurry2((options = ConverterOptions_$ctor(), (s_1) => ((json) => Data_decoder(options, s_1, json)))), s);
 }
 
-export function Data_toString(m) {
+export function Data_toJsonString(m) {
     return toString(2, Data_encoder(ConverterOptions_$ctor(), m));
 }
 
@@ -181,12 +181,12 @@ export function Source_decoder(options, s, json) {
     }
 }
 
-export function Source_fromString(s) {
+export function Source_fromJsonString(s) {
     let options;
-    return fromString(uncurry2((options = ConverterOptions_$ctor(), (s_1) => ((json) => Source_decoder(options, s_1, json)))), s);
+    return fromJsonString(uncurry2((options = ConverterOptions_$ctor(), (s_1) => ((json) => Source_decoder(options, s_1, json)))), s);
 }
 
-export function Source_toString(m) {
+export function Source_toJsonString(m) {
     return toString(2, Source_encoder(ConverterOptions_$ctor(), m));
 }
 
@@ -252,12 +252,12 @@ export function Sample_decoder(options, s, json) {
     }
 }
 
-export function Sample_fromString(s) {
+export function Sample_fromJsonString(s) {
     let options;
-    return fromString(uncurry2((options = ConverterOptions_$ctor(), (s_1) => ((json) => Sample_decoder(options, s_1, json)))), s);
+    return fromJsonString(uncurry2((options = ConverterOptions_$ctor(), (s_1) => ((json) => Sample_decoder(options, s_1, json)))), s);
 }
 
-export function Sample_toString(m) {
+export function Sample_toJsonString(m) {
     return toString(2, Sample_encoder(ConverterOptions_$ctor(), m));
 }
 

package/ISA/ISA.Json/Decode.js

@@ -1,4 +1,4 @@
-import { fromString as fromString_1, string } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { fromString, string } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
 import { FSharpResult$2 } from "../../fable_modules/fable-library.4.1.4/Choice.js";
 import { printf, toText } from "../../fable_modules/fable-library.4.1.4/String.js";
 import { ErrorReason } from "../../fable_modules/Thoth.Json.10.1.0/Types.fs.js";
@@ -23,8 +23,8 @@ export function uri(s, json) {
     }
 }
 
-export function fromString(decoder, s) {
-    const matchValue = fromString_1(decoder, s);
+export function fromJsonString(decoder, s) {
+    const matchValue = fromString(decoder, s);
     if (matchValue.tag === 1) {
         throw new Error(toText(printf("Error decoding string: %s"))(matchValue.fields[0]));
     }

package/ISA/ISA.Json/Factor.js

@@ -3,7 +3,7 @@ import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./Ontolo
 import { object as object_8, toString, nil } from "../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
 import { array, object as object_9, string, float, int } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
 import { FSharpResult$2 } from "../../fable_modules/fable-library.4.1.4/Choice.js";
-import { uri, fromString } from "./Decode.js";
+import { uri, fromJsonString } from "./Decode.js";
 import { equals, uncurry2 } from "../../fable_modules/fable-library.4.1.4/Util.js";
 import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions__get_IncludeType, ConverterOptions__get_SetID, ConverterOptions_$ctor } from "./ConverterOptions.js";
 import { replace } from "../../fable_modules/fable-library.4.1.4/String.js";
@@ -63,12 +63,12 @@ export function Value_decoder(options, s, json) {
     }
 }
 
-export function Value_fromString(s) {
+export function Value_fromJsonString(s) {
     let options;
-    return fromString(uncurry2((options = ConverterOptions_$ctor(), (s_1) => ((json) => Value_decoder(options, s_1, json)))), s);
+    return fromJsonString(uncurry2((options = ConverterOptions_$ctor(), (s_1) => ((json) => Value_decoder(options, s_1, json)))), s);
 }
 
-export function Value_toString(v) {
+export function Value_toJsonString(v) {
     return toString(2, Value_encoder(ConverterOptions_$ctor(), v));
 }
 
@@ -121,11 +121,11 @@ export function Factor_decoder(options) {
     }, path_2, v));
 }
 
-export function Factor_fromString(s) {
-    return fromString(uncurry2(Factor_decoder(ConverterOptions_$ctor())), s);
+export function Factor_fromJsonString(s) {
+    return fromJsonString(uncurry2(Factor_decoder(ConverterOptions_$ctor())), s);
 }
 
-export function Factor_toString(f) {
+export function Factor_toJsonString(f) {
     return toString(2, Factor_encoder(ConverterOptions_$ctor(), f));
 }
 
@@ -176,11 +176,11 @@ export function FactorValue_decoder(options) {
     }, path, v));
 }
 
-export function FactorValue_fromString(s) {
-    return fromString(uncurry2(FactorValue_decoder(ConverterOptions_$ctor())), s);
+export function FactorValue_fromJsonString(s) {
+    return fromJsonString(uncurry2(FactorValue_decoder(ConverterOptions_$ctor())), s);
 }
 
-export function FactorValue_toString(f) {
+export function FactorValue_toJsonString(f) {
     return toString(2, FactorValue_encoder(ConverterOptions_$ctor(), f));
 }
 

package/ISA/ISA.Json/Investigation.js

@@ -13,7 +13,7 @@ import { Study_decoder, Study_encoder } from "./Study.js";
 import { decoder as decoder_7, encoder as encoder_2 } from "./Comment.js";
 import { list as list_1, string, object as object_25 } from "../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
 import { Investigation } from "../ISA/JsonTypes/Investigation.js";
-import { fromString } from "./Decode.js";
+import { fromJsonString } from "./Decode.js";
 import { ArcInvestigation } from "../ISA/ArcTypes/ArcTypes.js";
 
 export function Investigation_genID(i) {
@@ -97,11 +97,11 @@ export function Investigation_decoder(options) {
     }, path_12, v));
 }
 
-export function Investigation_fromString(s) {
-    return fromString(uncurry2(Investigation_decoder(ConverterOptions_$ctor())), s);
+export function Investigation_fromJsonString(s) {
+    return fromJsonString(uncurry2(Investigation_decoder(ConverterOptions_$ctor())), s);
 }
 
-export function Investigation_toString(p) {
+export function Investigation_toJsonString(p) {
     return toString(2, Investigation_encoder(ConverterOptions_$ctor(), p));
 }
 
@@ -113,12 +113,12 @@ export function Investigation_toStringLD(i) {
     return toString(2, Investigation_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), i));
 }
 
-export function ArcInvestigation_fromString(s) {
-    const arg = fromString(uncurry2(Investigation_decoder(ConverterOptions_$ctor())), s);
+export function ArcInvestigation_fromJsonString(s) {
+    const arg = fromJsonString(uncurry2(Investigation_decoder(ConverterOptions_$ctor())), s);
     return ArcInvestigation.fromInvestigation(arg);
 }
 
-export function ArcInvestigation_toString(a) {
+export function ArcInvestigation_toJsonString(a) {
     return toString(2, Investigation_encoder(ConverterOptions_$ctor(), a.ToInvestigation()));
 }