@nfdi4plants/arctrl 1.0.0-beta.9 → 1.0.0

package/ISA/ISA/ArcTypes/ArcTable.js

@@ -9,7 +9,7 @@ import { sortBy, indexed, mapIndexed, singleton as singleton_1, initialize, sort
 import { append, collect as collect_1, initialize as initialize_1, singleton as singleton_2, empty as empty_1, iterate, isEmpty } from "../../../fable_modules/fable-library.4.5.0/List.js";
 import { StringBuilder__AppendLine_Z721C83C5, StringBuilder_$ctor } from "../../../fable_modules/fable-library.4.5.0/System.Text.js";
 import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
-import { join, toConsole, printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { join, printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
 import { CompositeCell } from "./CompositeCell.js";
 import { CompositeHeader } from "./CompositeHeader.js";
 import { createMissingIdentifier } from "../Identifier.js";
@@ -739,18 +739,15 @@ export class ArcTable {
     GetProcesses() {
         const this$ = this;
         if (this$.RowCount === 0) {
-            toConsole(printf("GetProcesses xddd"));
             return singleton_2(Process_create_Z42860F3E(void 0, this$.Name));
         }
         else {
-            toConsole(printf("GetProcesses rofl"));
             let getter;
             const clo = ProcessParsing_getProcessGetter(this$.Name, this$.Headers);
             getter = ((arg) => {
                 const clo_1 = clo(arg);
                 return clo_1;
             });
-            toConsole(printf("GetProcesses roflcopter"));
             return ProcessParsing_mergeIdenticalProcesses(toList(delay(() => map((i) => getter(this$.Values)(i), rangeDouble(0, 1, this$.RowCount - 1)))));
         }
     }

package/ISA/ISA/ArcTypes/ArcTableAux.js

@@ -17,7 +17,7 @@ import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
 import { MaterialAttributeValue_create_7F714043 } from "../JsonTypes/MaterialAttributeValue.js";
 import { MaterialAttribute_create_Z6C54B221 } from "../JsonTypes/MaterialAttribute.js";
 import { ProcessInput_getCharacteristicValues_102B6859, ProcessInput__isMaterial, ProcessInput__isData, ProcessInput_setCharacteristicValues, ProcessInput__get_Name, ProcessInput__isSource, ProcessInput__isSample, ProcessInput, ProcessInput_createDerivedData_Z721C83C5, ProcessInput_createRawData_Z721C83C5, ProcessInput_createImageFile_Z721C83C5, ProcessInput_createMaterial_2363974C, ProcessInput_createSample_Z6DF16D07, ProcessInput_createSource_7888CE42 } from "../JsonTypes/ProcessInput.js";
-import { toConsole, remove, printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { remove, printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
 import { ProcessOutput_getFactorValues_11830B70, ProcessOutput__isMaterial, ProcessOutput__isData, ProcessOutput_setFactorValues, ProcessOutput__get_Name, ProcessOutput__isSample, ProcessOutput, ProcessOutput_createDerivedData_Z721C83C5, ProcessOutput_createRawData_Z721C83C5, ProcessOutput_createImageFile_Z721C83C5, ProcessOutput_createMaterial_2363974C, ProcessOutput_createSample_Z6DF16D07 } from "../JsonTypes/ProcessOutput.js";
 import { IOType, CompositeHeader } from "./CompositeHeader.js";
 import { tryGetFactorColumnIndex, tryGetCharacteristicColumnIndex, tryGetComponentIndex, tryGetParameterColumnIndex, ARCtrl_ISA_OntologyAnnotation__OntologyAnnotation_SetColumnIndex_Z524259A4 } from "../JsonTypes/ColumnIndex.js";
@@ -940,7 +940,6 @@ export function ProcessParsing_groupProcesses(ps) {
  * Merges processes with the same name, protocol and param values
  */
 export function ProcessParsing_mergeIdenticalProcesses(processes) {
-    toConsole(printf("Merging identical processes aaaaaa"));
     const l = List_groupBy((x) => {
         if ((x.Name != null) && (Process_decomposeName_Z721C83C5(value_9(x.Name))[1] != null)) {
             return [Process_decomposeName_Z721C83C5(value_9(x.Name))[0], x.ExecutesProtocol, map_1(HashCodes_boxHashSeq, x.ParameterValues)];
@@ -955,7 +954,6 @@ export function ProcessParsing_mergeIdenticalProcesses(processes) {
         Equals: equalArrays,
         GetHashCode: arrayHash,
     });
-    toConsole(printf("Merging identical processes adwwdadawwda"));
     return mapIndexed((i, tupledArg) => {
         const _arg = tupledArg[0];
         const processes_1 = tupledArg[1];

package/ISA/ISA.Json/ArcTypes/ArcAssay.js

@@ -0,0 +1,197 @@
+import { OntologySourceReference_encoder, OntologyAnnotation_encoder, OntologySourceReference_decoder, OntologyAnnotation_decoder } from "../Ontology.js";
+import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor } from "../ConverterOptions.js";
+import { fromString, object as object_1, string, list as list_1 } from "../../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { uncurry2 } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { ArcTable_encoder, ArcTable_decoder } from "./ArcTable.js";
+import { encoder, decoder as decoder_1 } from "../Person.js";
+import { encoder as encoder_1, decoder as decoder_2 } from "../Comment.js";
+import { Factor_encoder, Factor_decoder } from "../Factor.js";
+import { encoder as encoder_2, decoder as decoder_3 } from "../Publication.js";
+import { value as value_3, map, defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { toArray } from "../../../fable_modules/fable-library.4.5.0/List.js";
+import { toString, object, seq } from "../../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
+import { empty, singleton, append, delay, toList, map as map_1 } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { ArcAssay } from "../../ISA/ArcTypes/ArcTypes.js";
+import { Assay_decoder, Assay_encoder } from "../Assay.js";
+import { fromJsonString } from "../Decode.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+
+export const JsonHelper_DecodeOa = OntologyAnnotation_decoder(ConverterOptions_$ctor());
+
+export const JsonHelper_DecodeTables = (path) => ((value) => list_1(uncurry2(ArcTable_decoder), path, value));
+
+export const JsonHelper_DecodePersons = (() => {
+    const decoder = decoder_1(ConverterOptions_$ctor());
+    return (path) => ((value) => list_1(uncurry2(decoder), path, value));
+})();
+
+export const JsonHelper_DecodeComments = (() => {
+    const decoder = decoder_2(ConverterOptions_$ctor());
+    return (path) => ((value) => list_1(uncurry2(decoder), path, value));
+})();
+
+export const JsonHelper_DecodeFactors = (() => {
+    const decoder = Factor_decoder(ConverterOptions_$ctor());
+    return (path) => ((value) => list_1(uncurry2(decoder), path, value));
+})();
+
+export const JsonHelper_DecodePublications = (() => {
+    const decoder = decoder_3(ConverterOptions_$ctor());
+    return (path) => ((value) => list_1(uncurry2(decoder), path, value));
+})();
+
+export const JsonHelper_DecodeOntologySourceReferences = (() => {
+    const decoder = OntologySourceReference_decoder(ConverterOptions_$ctor());
+    return (path) => ((value) => list_1(uncurry2(decoder), path, value));
+})();
+
+export function JsonHelper_tryGetTables(get$, fieldName) {
+    let objectArg;
+    return defaultArg(map((collection) => Array.from(collection), (objectArg = get$.Optional, objectArg.Field(fieldName, uncurry2(JsonHelper_DecodeTables)))), []);
+}
+
+export function JsonHelper_tryGetPersons(get$, fieldName) {
+    let objectArg;
+    return defaultArg(map(toArray, (objectArg = get$.Optional, objectArg.Field(fieldName, uncurry2(JsonHelper_DecodePersons)))), new Array(0));
+}
+
+export function JsonHelper_tryGetComments(get$, fieldName) {
+    let objectArg;
+    return defaultArg(map(toArray, (objectArg = get$.Optional, objectArg.Field(fieldName, uncurry2(JsonHelper_DecodeComments)))), new Array(0));
+}
+
+export function JsonHelper_tryGetPublications(get$, fieldName) {
+    let objectArg;
+    return defaultArg(map(toArray, (objectArg = get$.Optional, objectArg.Field(fieldName, uncurry2(JsonHelper_DecodePublications)))), new Array(0));
+}
+
+export function JsonHelper_tryGetOAs(get$, fieldName) {
+    let objectArg;
+    return defaultArg(map(toArray, (objectArg = get$.Optional, objectArg.Field(fieldName, (path, value) => list_1(uncurry2(JsonHelper_DecodeOa), path, value)))), new Array(0));
+}
+
+export function JsonHelper_tryGetFactors(get$, fieldName) {
+    let objectArg;
+    return defaultArg(map(toArray, (objectArg = get$.Optional, objectArg.Field(fieldName, uncurry2(JsonHelper_DecodeFactors)))), new Array(0));
+}
+
+export function JsonHelper_tryGetStringResizeArray(get$, fieldName) {
+    let objectArg;
+    return defaultArg(map((collection) => Array.from(collection), (objectArg = get$.Optional, objectArg.Field(fieldName, (path_1, value_1) => list_1(string, path_1, value_1)))), []);
+}
+
+export function JsonHelper_tryGetOntologySourceReferences(get$, fieldName) {
+    let objectArg;
+    return defaultArg(map(toArray, (objectArg = get$.Optional, objectArg.Field(fieldName, uncurry2(JsonHelper_DecodeOntologySourceReferences)))), new Array(0));
+}
+
+export function JsonHelper_EncoderOA(t) {
+    return OntologyAnnotation_encoder(ConverterOptions_$ctor(), t);
+}
+
+export function JsonHelper_EncoderOAs(t) {
+    return seq(map_1(JsonHelper_EncoderOA, t));
+}
+
+export function JsonHelper_EncoderTables(t) {
+    return seq(map_1(ArcTable_encoder, t));
+}
+
+export function JsonHelper_EncoderPerson(t) {
+    return encoder(ConverterOptions_$ctor(), t);
+}
+
+export function JsonHelper_EncoderPersons(t) {
+    return seq(map_1(JsonHelper_EncoderPerson, t));
+}
+
+export function JsonHelper_EncoderComment(t) {
+    return encoder_1(ConverterOptions_$ctor(), t);
+}
+
+export function JsonHelper_EncoderComments(t) {
+    return seq(map_1(JsonHelper_EncoderComment, t));
+}
+
+export function JsonHelper_EncoderPublication(t) {
+    return encoder_2(ConverterOptions_$ctor(), t);
+}
+
+export function JsonHelper_EncoderPublications(t) {
+    return seq(map_1(JsonHelper_EncoderPublication, t));
+}
+
+export function JsonHelper_EncoderFactor(t) {
+    return Factor_encoder(ConverterOptions_$ctor(), t);
+}
+
+export function JsonHelper_EncoderFactors(t) {
+    return seq(map_1(JsonHelper_EncoderFactor, t));
+}
+
+export function JsonHelper_EncoderOntologySourceReference(t) {
+    return OntologySourceReference_encoder(ConverterOptions_$ctor(), t);
+}
+
+export function JsonHelper_EncoderOntologySourceReferences(t) {
+    return seq(map_1(JsonHelper_EncoderOntologySourceReference, t));
+}
+
+export function ArcAssay_encoder(assay) {
+    return object(toList(delay(() => append(singleton(["Identifier", assay.Identifier]), delay(() => append((assay.MeasurementType != null) ? singleton(["MeasurementType", JsonHelper_EncoderOA(value_3(assay.MeasurementType))]) : empty(), delay(() => append((assay.TechnologyType != null) ? singleton(["TechnologyType", JsonHelper_EncoderOA(value_3(assay.TechnologyType))]) : empty(), delay(() => append((assay.TechnologyPlatform != null) ? singleton(["TechnologyPlatform", JsonHelper_EncoderOA(value_3(assay.TechnologyPlatform))]) : empty(), delay(() => append((assay.Tables.length !== 0) ? singleton(["Tables", JsonHelper_EncoderTables(assay.Tables)]) : empty(), delay(() => append((assay.Performers.length !== 0) ? singleton(["Performers", JsonHelper_EncoderPersons(assay.Performers)]) : empty(), delay(() => ((assay.Comments.length !== 0) ? singleton(["Comments", JsonHelper_EncoderComments(assay.Comments)]) : empty()))))))))))))))));
+}
+
+export const ArcAssay_decoder = (path_1) => ((v) => object_1((get$) => {
+    let identifier;
+    const objectArg = get$.Required;
+    identifier = objectArg.Field("Identifier", string);
+    let measurementType;
+    const objectArg_1 = get$.Optional;
+    measurementType = objectArg_1.Field("MeasurementType", uncurry2(JsonHelper_DecodeOa));
+    let technologyType;
+    const objectArg_2 = get$.Optional;
+    technologyType = objectArg_2.Field("TechnologyType", uncurry2(JsonHelper_DecodeOa));
+    let technologyPlatform;
+    const objectArg_3 = get$.Optional;
+    technologyPlatform = objectArg_3.Field("TechnologyPlatform", uncurry2(JsonHelper_DecodeOa));
+    const tables = JsonHelper_tryGetTables(get$, "Tables");
+    const performers = JsonHelper_tryGetPersons(get$, "Performers");
+    const comments = JsonHelper_tryGetComments(get$, "Comments");
+    return ArcAssay.make(identifier, measurementType, technologyType, technologyPlatform, tables, performers, comments);
+}, path_1, v));
+
+/**
+ * exports in json-ld format
+ */
+export function ArcAssay_toStringLD(a) {
+    let returnVal;
+    return toString(2, Assay_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), a.ToAssay()));
+}
+
+export function ArcAssay_fromJsonString(s) {
+    const a = fromJsonString(uncurry2(Assay_decoder(ConverterOptions_$ctor())), s);
+    return ArcAssay.fromAssay(a);
+}
+
+export function ArcAssay_toJsonString(a) {
+    return toString(2, Assay_encoder(ConverterOptions_$ctor(), a.ToAssay()));
+}
+
+export function ARCtrl_ISA_ArcAssay__ArcAssay_fromArcJsonString_Static_Z721C83C5(jsonString) {
+    const matchValue = fromString(uncurry2(ArcAssay_decoder), jsonString);
+    if (matchValue.tag === 1) {
+        return toFail(printf("Error. Unable to parse json string to ArcAssay: %s"))(matchValue.fields[0]);
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_ISA_ArcAssay__ArcAssay_ToArcJsonString_71136F3F(this$, spaces) {
+    return toString(defaultArg(spaces, 0), ArcAssay_encoder(this$));
+}
+
+export function ARCtrl_ISA_ArcAssay__ArcAssay_toArcJsonString_Static_1C75D08D(a) {
+    return ARCtrl_ISA_ArcAssay__ArcAssay_ToArcJsonString_71136F3F(a);
+}
+

package/ISA/ISA.Json/ArcTypes/ArcInvestigation.js

@@ -0,0 +1,79 @@
+import { toString, seq, object } from "../../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
+import { map, empty, singleton, append, delay, toList } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { map as map_1, defaultArg, value as value_9 } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { JsonHelper_tryGetComments, JsonHelper_tryGetStringResizeArray, ArcAssay_decoder, JsonHelper_tryGetPersons, JsonHelper_tryGetPublications, JsonHelper_tryGetOntologySourceReferences, JsonHelper_EncoderComments, ArcAssay_encoder, JsonHelper_EncoderPersons, JsonHelper_EncoderPublications, JsonHelper_EncoderOntologySourceReferences } from "./ArcAssay.js";
+import { ArcStudy_decoder, ArcStudy_encoder } from "./ArcStudy.js";
+import { fromString, list, string, object as object_1 } from "../../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { uncurry2 } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { ArcInvestigation } from "../../ISA/ArcTypes/ArcTypes.js";
+import { decoder as decoder_2, encoder } from "../Investigation.js";
+import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor } from "../ConverterOptions.js";
+import { fromJsonString } from "../Decode.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+
+export function ArcInvestigation_encoder(inv) {
+    return object(toList(delay(() => append(singleton(["Identifier", inv.Identifier]), delay(() => append((inv.Title != null) ? singleton(["Title", value_9(inv.Title)]) : empty(), delay(() => append((inv.Description != null) ? singleton(["Description", value_9(inv.Description)]) : empty(), delay(() => append((inv.SubmissionDate != null) ? singleton(["SubmissionDate", value_9(inv.SubmissionDate)]) : empty(), delay(() => append((inv.PublicReleaseDate != null) ? singleton(["PublicReleaseDate", value_9(inv.PublicReleaseDate)]) : empty(), delay(() => append((inv.OntologySourceReferences.length !== 0) ? singleton(["OntologySourceReferences", JsonHelper_EncoderOntologySourceReferences(inv.OntologySourceReferences)]) : empty(), delay(() => append((inv.Publications.length !== 0) ? singleton(["Publications", JsonHelper_EncoderPublications(inv.Publications)]) : empty(), delay(() => append((inv.Contacts.length !== 0) ? singleton(["Contacts", JsonHelper_EncoderPersons(inv.Contacts)]) : empty(), delay(() => append((inv.Assays.length !== 0) ? singleton(["Assays", seq(map(ArcAssay_encoder, inv.Assays))]) : empty(), delay(() => append((inv.Studies.length !== 0) ? singleton(["Studies", seq(map(ArcStudy_encoder, inv.Studies))]) : empty(), delay(() => append((inv.RegisteredStudyIdentifiers.length !== 0) ? singleton(["RegisteredStudyIdentifiers", seq(map((value_5) => value_5, inv.RegisteredStudyIdentifiers))]) : empty(), delay(() => ((inv.Comments.length !== 0) ? singleton(["Comments", JsonHelper_EncoderComments(inv.Comments)]) : empty()))))))))))))))))))))))))));
+}
+
+export const ArcInvestigation_decoder = (path_7) => ((v) => object_1((get$_2) => {
+    let objectArg, objectArg_1;
+    let identifier;
+    const objectArg_2 = get$_2.Required;
+    identifier = objectArg_2.Field("Identifier", string);
+    let title;
+    const objectArg_3 = get$_2.Optional;
+    title = objectArg_3.Field("Title", string);
+    let description;
+    const objectArg_4 = get$_2.Optional;
+    description = objectArg_4.Field("Description", string);
+    let submissionDate;
+    const objectArg_5 = get$_2.Optional;
+    submissionDate = objectArg_5.Field("SubmissionDate", string);
+    let publicReleaseDate;
+    const objectArg_6 = get$_2.Optional;
+    publicReleaseDate = objectArg_6.Field("PublicReleaseDate", string);
+    const ontologySourceReferences = JsonHelper_tryGetOntologySourceReferences(get$_2, "OntologySourceReferences");
+    const publications = JsonHelper_tryGetPublications(get$_2, "Publications");
+    const contacts = JsonHelper_tryGetPersons(get$_2, "Contacts");
+    const assays = defaultArg(map_1((collection) => Array.from(collection), (objectArg = get$_2.Optional, objectArg.Field("Assays", (path, value) => list(uncurry2(ArcAssay_decoder), path, value)))), []);
+    const studies = defaultArg(map_1((collection_1) => Array.from(collection_1), (objectArg_1 = get$_2.Optional, objectArg_1.Field("Studies", (path_1, value_1) => list(uncurry2(ArcStudy_decoder), path_1, value_1)))), []);
+    const registeredStudyIdentifiers = JsonHelper_tryGetStringResizeArray(get$_2, "RegisteredStudyIdentifiers");
+    const comments = JsonHelper_tryGetComments(get$_2, "Comments");
+    return ArcInvestigation.make(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, registeredStudyIdentifiers, comments, []);
+}, path_7, v));
+
+/**
+ * exports in json-ld format
+ */
+export function ArcInvestigation_toStringLD(a) {
+    let returnVal;
+    return toString(2, encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), a.ToInvestigation()));
+}
+
+export function ArcInvestigation_fromJsonString(s) {
+    const i = fromJsonString(uncurry2(decoder_2(ConverterOptions_$ctor())), s);
+    return ArcInvestigation.fromInvestigation(i);
+}
+
+export function ArcInvestigation_toJsonString(a) {
+    return toString(2, encoder(ConverterOptions_$ctor(), a.ToInvestigation()));
+}
+
+export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_fromArcJsonString_Static_Z721C83C5(jsonString) {
+    const matchValue = fromString(uncurry2(ArcInvestigation_decoder), jsonString);
+    if (matchValue.tag === 1) {
+        return toFail(printf("Error. Unable to parse json string to ArcInvestigation: %s"))(matchValue.fields[0]);
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToArcJsonString_71136F3F(this$, spaces) {
+    return toString(defaultArg(spaces, 0), ArcInvestigation_encoder(this$));
+}
+
+export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_toArcJsonString_Static_Z4D87C88C(a) {
+    return ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToArcJsonString_71136F3F(a);
+}
+

package/ISA/ISA.Json/ArcTypes/ArcStudy.js

@@ -0,0 +1,77 @@
+import { toString, seq, object } from "../../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
+import { map, empty, singleton, append, delay, toList } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { defaultArg, value as value_7 } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { JsonHelper_tryGetComments, JsonHelper_tryGetFactors, JsonHelper_tryGetStringResizeArray, JsonHelper_tryGetTables, JsonHelper_tryGetOAs, JsonHelper_tryGetPersons, JsonHelper_tryGetPublications, JsonHelper_EncoderComments, JsonHelper_EncoderFactors, JsonHelper_EncoderTables, JsonHelper_EncoderOAs, JsonHelper_EncoderPersons, JsonHelper_EncoderPublications } from "./ArcAssay.js";
+import { fromString, string, object as object_1 } from "../../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { ArcStudy } from "../../ISA/ArcTypes/ArcTypes.js";
+import { Study_decoder, Study_encoder } from "../Study.js";
+import { ConverterOptions__set_IncludeType_Z1FBCCD16, ConverterOptions__set_SetID_Z1FBCCD16, ConverterOptions_$ctor } from "../ConverterOptions.js";
+import { fromJsonString } from "../Decode.js";
+import { uncurry2 } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+
+export function ArcStudy_encoder(study) {
+    return object(toList(delay(() => append(singleton(["Identifier", study.Identifier]), delay(() => append((study.Title != null) ? singleton(["Title", value_7(study.Title)]) : empty(), delay(() => append((study.Description != null) ? singleton(["Description", value_7(study.Description)]) : empty(), delay(() => append((study.SubmissionDate != null) ? singleton(["SubmissionDate", value_7(study.SubmissionDate)]) : empty(), delay(() => append((study.PublicReleaseDate != null) ? singleton(["PublicReleaseDate", value_7(study.PublicReleaseDate)]) : empty(), delay(() => append((study.Publications.length !== 0) ? singleton(["Publications", JsonHelper_EncoderPublications(study.Publications)]) : empty(), delay(() => append((study.Contacts.length !== 0) ? singleton(["Contacts", JsonHelper_EncoderPersons(study.Contacts)]) : empty(), delay(() => append((study.StudyDesignDescriptors.length !== 0) ? singleton(["StudyDesignDescriptors", JsonHelper_EncoderOAs(study.StudyDesignDescriptors)]) : empty(), delay(() => append((study.TableCount !== 0) ? singleton(["Tables", JsonHelper_EncoderTables(study.Tables)]) : empty(), delay(() => append((study.RegisteredAssayIdentifiers.length !== 0) ? singleton(["RegisteredAssayIdentifiers", seq(map((value_5) => value_5, study.RegisteredAssayIdentifiers))]) : empty(), delay(() => append((study.Factors.length !== 0) ? singleton(["Factors", JsonHelper_EncoderFactors(study.Factors)]) : empty(), delay(() => ((study.Comments.length !== 0) ? singleton(["Comments", JsonHelper_EncoderComments(study.Comments)]) : empty()))))))))))))))))))))))))));
+}
+
+export const ArcStudy_decoder = (path_5) => ((v) => object_1((get$) => {
+    let identifier;
+    const objectArg = get$.Required;
+    identifier = objectArg.Field("Identifier", string);
+    let title;
+    const objectArg_1 = get$.Optional;
+    title = objectArg_1.Field("Title", string);
+    let description;
+    const objectArg_2 = get$.Optional;
+    description = objectArg_2.Field("Description", string);
+    let submissionDate;
+    const objectArg_3 = get$.Optional;
+    submissionDate = objectArg_3.Field("SubmissionDate", string);
+    let publicReleaseDate;
+    const objectArg_4 = get$.Optional;
+    publicReleaseDate = objectArg_4.Field("PublicReleaseDate", string);
+    const publications = JsonHelper_tryGetPublications(get$, "Publications");
+    const contacts = JsonHelper_tryGetPersons(get$, "Contacts");
+    const studyDesignDescriptors = JsonHelper_tryGetOAs(get$, "StudyDesignDescriptors");
+    const tables = JsonHelper_tryGetTables(get$, "Tables");
+    const registeredAssayIdentifiers = JsonHelper_tryGetStringResizeArray(get$, "RegisteredAssayIdentifiers");
+    const factors = JsonHelper_tryGetFactors(get$, "Factors");
+    const comments = JsonHelper_tryGetComments(get$, "Comments");
+    return ArcStudy.make(identifier, title, description, submissionDate, publicReleaseDate, publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, factors, comments);
+}, path_5, v));
+
+/**
+ * exports in json-ld format
+ */
+export function ArcStudy_toStringLD(a, assays) {
+    let returnVal;
+    return toString(2, Study_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), a.ToStudy(assays)));
+}
+
+export function ArcStudy_fromJsonString(s) {
+    const s_1 = fromJsonString(uncurry2(Study_decoder(ConverterOptions_$ctor())), s);
+    return ArcStudy.fromStudy(s_1);
+}
+
+export function ArcStudy_toJsonString(a, assays) {
+    return toString(2, Study_encoder(ConverterOptions_$ctor(), a.ToStudy(assays)));
+}
+
+export function ARCtrl_ISA_ArcStudy__ArcStudy_fromArcJsonString_Static_Z721C83C5(jsonString) {
+    const matchValue = fromString(uncurry2(ArcStudy_decoder), jsonString);
+    if (matchValue.tag === 1) {
+        return toFail(printf("Error. Unable to parse json string to ArcStudy: %s"))(matchValue.fields[0]);
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_ISA_ArcStudy__ArcStudy_ToArcJsonString_71136F3F(this$, spaces) {
+    return toString(defaultArg(spaces, 0), ArcStudy_encoder(this$));
+}
+
+export function ARCtrl_ISA_ArcStudy__ArcStudy_toArcJsonString_Static_1B3D5E9B(a) {
+    return ARCtrl_ISA_ArcStudy__ArcStudy_ToArcJsonString_71136F3F(a);
+}
+

package/ISA/ISA.Json/ArcTypes/ArcTable.js

@@ -0,0 +1,57 @@
+import { toString, tuple2, map as map_1, list, object } from "../../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
+import { collect, empty, map, singleton, append, delay, toList } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { CompositeHeader_decoder, CompositeHeader_encoder } from "./CompositeHeader.js";
+import { CompositeCell_decoder, CompositeCell_encoder } from "./CompositeCell.js";
+import { empty as empty_2, ofSeq } from "../../../fable_modules/fable-library.4.5.0/Map.js";
+import { arrayHash, equalArrays, uncurry2, compareArrays } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { fromString, string, int, tuple2 as tuple2_1, map$0027, list as list_1, object as object_1 } from "../../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { empty as empty_1 } from "../../../fable_modules/fable-library.4.5.0/List.js";
+import { Dictionary } from "../../../fable_modules/fable-library.4.5.0/MutableMap.js";
+import { ArcTable } from "../../ISA/ArcTypes/ArcTable.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+
+export function ArcTable_encoder(table) {
+    return object(toList(delay(() => append(singleton(["name", table.Name]), delay(() => append((table.Headers.length !== 0) ? singleton(["header", list(toList(delay(() => map(CompositeHeader_encoder, table.Headers))))]) : empty(), delay(() => ((table.Values.size !== 0) ? singleton(["values", map_1((tupledArg) => tuple2((value) => value, (value_2) => value_2, tupledArg[0], tupledArg[1]), CompositeCell_encoder, ofSeq(toList(delay(() => collect((matchValue) => {
+        const activePatternResult = matchValue;
+        return singleton([activePatternResult[0], activePatternResult[1]]);
+    }, table.Values))), {
+        Compare: compareArrays,
+    }))]) : empty()))))))));
+}
+
+export const ArcTable_decoder = (path_2) => ((v) => object_1((get$) => {
+    let objectArg, arg_5, objectArg_1, objectArg_2;
+    let decodedHeader;
+    const collection = defaultArg((objectArg = get$.Optional, objectArg.Field("header", (path, value) => list_1(uncurry2(CompositeHeader_decoder), path, value))), empty_1());
+    decodedHeader = Array.from(collection);
+    const decodedValues = new Dictionary(defaultArg((arg_5 = map$0027(uncurry2(tuple2_1(uncurry2(int), uncurry2(int))), uncurry2((arg_2) => {
+        const clo = CompositeCell_decoder(arg_2);
+        return clo;
+    })), (objectArg_1 = get$.Optional, objectArg_1.Field("values", uncurry2(arg_5)))), empty_2({
+        Compare: compareArrays,
+    })), {
+        Equals: equalArrays,
+        GetHashCode: arrayHash,
+    });
+    return ArcTable.create((objectArg_2 = get$.Required, objectArg_2.Field("name", string)), decodedHeader, decodedValues);
+}, path_2, v));
+
+export function ARCtrl_ISA_ArcTable__ArcTable_fromJsonString_Static_Z721C83C5(jsonString) {
+    const matchValue = fromString(uncurry2(ArcTable_decoder), jsonString);
+    if (matchValue.tag === 1) {
+        return toFail(printf("Error. Unable to parse json string to ArcTable: %s"))(matchValue.fields[0]);
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_ISA_ArcTable__ArcTable_ToJsonString_71136F3F(this$, spaces) {
+    return toString(defaultArg(spaces, 0), ArcTable_encoder(this$));
+}
+
+export function ARCtrl_ISA_ArcTable__ArcTable_toJsonString_Static_1B2566EA(a) {
+    return ARCtrl_ISA_ArcTable__ArcTable_ToJsonString_71136F3F(a);
+}
+

package/ISA/ISA.Json/ArcTypes/CompositeCell.js

@@ -0,0 +1,51 @@
+import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "../Ontology.js";
+import { ConverterOptions_$ctor } from "../ConverterOptions.js";
+import { ofArray, singleton } from "../../../fable_modules/fable-library.4.5.0/List.js";
+import { toString, list, object } from "../../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
+import { fromString, index, string, object as object_1 } from "../../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { CompositeCell } from "../../ISA/ArcTypes/CompositeCell.js";
+import { uncurry2 } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+
+export function CompositeCell_encoder(cc) {
+    const oaToJsonString = (oa) => OntologyAnnotation_encoder(ConverterOptions_$ctor(), oa);
+    const patternInput = (cc.tag === 0) ? ["Term", singleton(oaToJsonString(cc.fields[0]))] : ((cc.tag === 2) ? ["Unitized", ofArray([cc.fields[0], oaToJsonString(cc.fields[1])])] : ["FreeText", singleton(cc.fields[0])]);
+    return object([["celltype", patternInput[0]], ["values", list(patternInput[1])]]);
+}
+
+export const CompositeCell_decoder = (path_7) => ((v_1) => object_1((get$) => {
+    let objectArg_1, arg_5, decoder_1, objectArg_2, objectArg_3, arg_9, decoder_3, objectArg_4;
+    let matchValue;
+    const objectArg = get$.Required;
+    matchValue = objectArg.Field("celltype", string);
+    switch (matchValue) {
+        case "FreeText":
+            return new CompositeCell(1, [(objectArg_1 = get$.Required, objectArg_1.Field("values", (path_2, value_2) => index(0, string, path_2, value_2)))]);
+        case "Term":
+            return new CompositeCell(0, [(arg_5 = ((decoder_1 = OntologyAnnotation_decoder(ConverterOptions_$ctor()), (path_3) => ((value_3) => index(0, uncurry2(decoder_1), path_3, value_3)))), (objectArg_2 = get$.Required, objectArg_2.Field("values", uncurry2(arg_5))))]);
+        case "Unitized":
+            return new CompositeCell(2, [(objectArg_3 = get$.Required, objectArg_3.Field("values", (path_4, value_4) => index(0, string, path_4, value_4))), (arg_9 = ((decoder_3 = OntologyAnnotation_decoder(ConverterOptions_$ctor()), (path_6) => ((value_6) => index(1, uncurry2(decoder_3), path_6, value_6)))), (objectArg_4 = get$.Required, objectArg_4.Field("values", uncurry2(arg_9))))]);
+        default:
+            return toFail(printf("Error reading CompositeCell from json string: %A"))(matchValue);
+    }
+}, path_7, v_1));
+
+export function ARCtrl_ISA_CompositeCell__CompositeCell_fromJsonString_Static_Z721C83C5(jsonString) {
+    const matchValue = fromString(uncurry2(CompositeCell_decoder), jsonString);
+    if (matchValue.tag === 1) {
+        return toFail(printf("Error. Unable to parse json string to CompositeCell: %s"))(matchValue.fields[0]);
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_ISA_CompositeCell__CompositeCell_ToJsonString_71136F3F(this$, spaces) {
+    return toString(defaultArg(spaces, 0), CompositeCell_encoder(this$));
+}
+
+export function ARCtrl_ISA_CompositeCell__CompositeCell_toJsonString_Static_1B703D57(a) {
+    return ARCtrl_ISA_CompositeCell__CompositeCell_ToJsonString_71136F3F(a);
+}
+

package/ISA/ISA.Json/ArcTypes/CompositeHeader.js

@@ -0,0 +1,82 @@
+import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "../Ontology.js";
+import { ConverterOptions_$ctor } from "../ConverterOptions.js";
+import { empty, singleton } from "../../../fable_modules/fable-library.4.5.0/List.js";
+import { IOType_decoder, IOType_encoder } from "./IOType.js";
+import { toString, list, object } from "../../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
+import { fromString, index, string, object as object_1 } from "../../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { uncurry2 } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { CompositeHeader } from "../../ISA/ArcTypes/CompositeHeader.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+
+export function CompositeHeader_encoder(ch) {
+    const oaToJsonString = (oa) => OntologyAnnotation_encoder(ConverterOptions_$ctor(), oa);
+    const patternInput = (ch.tag === 3) ? ["Parameter", singleton(oaToJsonString(ch.fields[0]))] : ((ch.tag === 2) ? ["Factor", singleton(oaToJsonString(ch.fields[0]))] : ((ch.tag === 1) ? ["Characteristic", singleton(oaToJsonString(ch.fields[0]))] : ((ch.tag === 0) ? ["Component", singleton(oaToJsonString(ch.fields[0]))] : ((ch.tag === 4) ? ["ProtocolType", empty()] : ((ch.tag === 8) ? ["ProtocolREF", empty()] : ((ch.tag === 5) ? ["ProtocolDescription", empty()] : ((ch.tag === 6) ? ["ProtocolUri", empty()] : ((ch.tag === 7) ? ["ProtocolVersion", empty()] : ((ch.tag === 9) ? ["Performer", empty()] : ((ch.tag === 10) ? ["Date", empty()] : ((ch.tag === 11) ? ["Input", singleton(IOType_encoder(ch.fields[0]))] : ((ch.tag === 12) ? ["Output", singleton(IOType_encoder(ch.fields[0]))] : [ch.fields[0], empty()]))))))))))));
+    return object([["headertype", patternInput[0]], ["values", list(patternInput[1])]]);
+}
+
+export const CompositeHeader_decoder = (path_3) => ((v) => object_1((get$) => {
+    let headerType;
+    const objectArg = get$.Required;
+    headerType = objectArg.Field("headertype", string);
+    const oa = () => {
+        let arg_3;
+        const decoder = OntologyAnnotation_decoder(ConverterOptions_$ctor());
+        arg_3 = ((path_1) => ((value_1) => index(0, uncurry2(decoder), path_1, value_1)));
+        const objectArg_1 = get$.Required;
+        return objectArg_1.Field("values", uncurry2(arg_3));
+    };
+    const io = () => {
+        const objectArg_2 = get$.Required;
+        return objectArg_2.Field("values", (path_2, value_2) => index(0, uncurry2(IOType_decoder), path_2, value_2));
+    };
+    switch (headerType) {
+        case "Characteristic":
+            return new CompositeHeader(1, [oa()]);
+        case "Parameter":
+            return new CompositeHeader(3, [oa()]);
+        case "Component":
+            return new CompositeHeader(0, [oa()]);
+        case "Factor":
+            return new CompositeHeader(2, [oa()]);
+        case "Input":
+            return new CompositeHeader(11, [io()]);
+        case "Output":
+            return new CompositeHeader(12, [io()]);
+        case "ProtocolType":
+            return new CompositeHeader(4, []);
+        case "ProtocolREF":
+            return new CompositeHeader(8, []);
+        case "ProtocolDescription":
+            return new CompositeHeader(5, []);
+        case "ProtocolUri":
+            return new CompositeHeader(6, []);
+        case "ProtocolVersion":
+            return new CompositeHeader(7, []);
+        case "Performer":
+            return new CompositeHeader(9, []);
+        case "Date":
+            return new CompositeHeader(10, []);
+        default:
+            return new CompositeHeader(13, [headerType]);
+    }
+}, path_3, v));
+
+export function ARCtrl_ISA_CompositeHeader__CompositeHeader_fromJsonString_Static_Z721C83C5(jsonString) {
+    const matchValue = fromString(uncurry2(CompositeHeader_decoder), jsonString);
+    if (matchValue.tag === 1) {
+        return toFail(printf("Error. Unable to parse json string to CompositeHeader: %s"))(matchValue.fields[0]);
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_ISA_CompositeHeader__CompositeHeader_ToJsonString_71136F3F(this$, spaces) {
+    return toString(defaultArg(spaces, 0), CompositeHeader_encoder(this$));
+}
+
+export function ARCtrl_ISA_CompositeHeader__CompositeHeader_toJsonString_Static_Z331CE692(a) {
+    return ARCtrl_ISA_CompositeHeader__CompositeHeader_ToJsonString_71136F3F(a);
+}
+

package/ISA/ISA.Json/ArcTypes/IOType.js

@@ -0,0 +1,35 @@
+import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
+import { fromString, string, succeed, andThen } from "../../../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { uncurry2, uncurry3 } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { IOType } from "../../ISA/ArcTypes/CompositeHeader.js";
+import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { toString as toString_1 } from "../../../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
+import { defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+
+export function IOType_encoder(io) {
+    return toString(io);
+}
+
+export const IOType_decoder = (path_1) => ((value_1) => andThen(uncurry3((s) => {
+    const output = IOType.ofString(s);
+    return (arg10$0040) => ((arg20$0040) => succeed(output, arg10$0040, arg20$0040));
+}), string, path_1, value_1));
+
+export function ARCtrl_ISA_IOType__IOType_fromJsonString_Static_Z721C83C5(jsonString) {
+    const matchValue = fromString(uncurry2(IOType_decoder), jsonString);
+    if (matchValue.tag === 1) {
+        return toFail(printf("Error. Unable to parse json string to IOType: %s"))(matchValue.fields[0]);
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+
+export function ARCtrl_ISA_IOType__IOType_ToJsonString_71136F3F(this$, spaces) {
+    return toString_1(defaultArg(spaces, 0), IOType_encoder(this$));
+}
+
+export function ARCtrl_ISA_IOType__IOType_toJsonString_Static_Z359DBB26(a) {
+    return ARCtrl_ISA_IOType__IOType_ToJsonString_71136F3F(a);
+}
+

package/ISA/ISA.Json/Assay.js

@@ -14,7 +14,6 @@ import { Process_decoder, Process_encoder } from "./Process.js";
 import { decoder as decoder_5, encoder } from "./Comment.js";
 import { fromJsonString, uri } from "./Decode.js";
 import { Assay } from "../ISA/JsonTypes/Assay.js";
-import { ArcAssay } from "../ISA/ArcTypes/ArcTypes.js";
 
 export function AssayMaterials_encoder(options, oa) {
     return object_22(choose((tupledArg) => {
@@ -104,20 +103,3 @@ 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_fromJsonString(s) {
-    const a = fromJsonString(uncurry2(Assay_decoder(ConverterOptions_$ctor())), s);
-    return ArcAssay.fromAssay(a);
-}
-
-export function ArcAssay_toJsonString(a) {
-    return toString(2, Assay_encoder(ConverterOptions_$ctor(), a.ToAssay()));
-}
-
-/**
- * exports in json-ld format
- */
-export function ArcAssay_toStringLD(a) {
-    let returnVal;
-    return toString(2, Assay_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), a.ToAssay()));
-}
-

package/ISA/ISA.Json/Investigation.js

@@ -7,16 +7,15 @@ 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 { OntologySourceReference_decoder, OntologySourceReference_encoder } from "./Ontology.js";
-import { decoder as decoder_5, encoder } from "./Publication.js";
-import { decoder as decoder_6, encoder as encoder_1 } from "./Person.js";
+import { decoder as decoder_6, encoder as encoder_1 } from "./Publication.js";
+import { decoder as decoder_7, encoder as encoder_2 } from "./Person.js";
 import { Study_decoder, Study_encoder } from "./Study.js";
-import { decoder as decoder_7, encoder as encoder_2 } from "./Comment.js";
+import { decoder as decoder_8, encoder as encoder_3 } 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 { fromJsonString } from "./Decode.js";
-import { ArcInvestigation } from "../ISA/ArcTypes/ArcTypes.js";
+import { fromJsonString as fromJsonString_1 } from "./Decode.js";
 
-export function Investigation_genID(i) {
+export function genID(i) {
     const matchValue = i.ID;
     if (matchValue == null) {
         const matchValue_1 = i.FileName;
@@ -44,7 +43,7 @@ export function Investigation_genID(i) {
     }
 }
 
-export function Investigation_encoder(options, oa) {
+export function encoder(options, oa) {
     return object_24(choose((tupledArg) => {
         const v = tupledArg[1];
         if (equals(v, nil)) {
@@ -55,7 +54,7 @@ export function Investigation_encoder(options, oa) {
         }
     }, toList(delay(() => {
         let value, s;
-        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = Investigation_genID(oa), (typeof value === "string") ? ((s = value, s)) : nil)]) : singleton(tryInclude("@id", (value_2) => {
+        return append(ConverterOptions__get_SetID(options) ? singleton(["@id", (value = genID(oa), (typeof value === "string") ? ((s = value, s)) : nil)]) : singleton(tryInclude("@id", (value_2) => {
             let s_1;
             const value_3 = value_2;
             return (typeof value_3 === "string") ? ((s_1 = value_3, s_1)) : nil;
@@ -85,48 +84,31 @@ export function Investigation_encoder(options, oa) {
                 let s_8;
                 const value_23 = value_22;
                 return (typeof value_23 === "string") ? ((s_8 = value_23, s_8)) : nil;
-            }, oa["PublicReleaseDate"])), delay(() => append(singleton(tryInclude("ontologySourceReferences", (osr) => OntologySourceReference_encoder(options, osr), oa["OntologySourceReferences"])), 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("studies", (oa_3) => Study_encoder(options, oa_3), oa["Studies"])), delay(() => singleton(tryInclude("comments", (comment) => encoder_2(options, comment), oa["Comments"]))))))))))))))))))))))));
+            }, oa["PublicReleaseDate"])), delay(() => append(singleton(tryInclude("ontologySourceReferences", (osr) => OntologySourceReference_encoder(options, osr), oa["OntologySourceReferences"])), delay(() => append(singleton(tryInclude("publications", (oa_1) => encoder_1(options, oa_1), oa["Publications"])), delay(() => append(singleton(tryInclude("people", (oa_2) => encoder_2(options, oa_2), oa["Contacts"])), delay(() => append(singleton(tryInclude("studies", (oa_3) => Study_encoder(options, oa_3), oa["Studies"])), delay(() => singleton(tryInclude("comments", (comment) => encoder_3(options, comment), oa["Comments"]))))))))))))))))))))))));
         }));
     }))));
 }
 
-export function Investigation_decoder(options) {
+export function decoder(options) {
     return (path_12) => ((v) => object_25((get$) => {
-        let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, arg_15, decoder, objectArg_7, arg_17, decoder_1, objectArg_8, arg_19, decoder_2, objectArg_9, arg_21, decoder_3, objectArg_10, arg_23, decoder_4, objectArg_11;
-        return new Investigation((objectArg = get$.Optional, objectArg.Field("@id", string)), (objectArg_1 = get$.Optional, objectArg_1.Field("filename", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("identifier", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("title", string)), (objectArg_4 = get$.Optional, objectArg_4.Field("description", string)), (objectArg_5 = get$.Optional, objectArg_5.Field("submissionDate", string)), (objectArg_6 = get$.Optional, objectArg_6.Field("publicReleaseDate", string)), (arg_15 = ((decoder = OntologySourceReference_decoder(options), (path_7) => ((value_7) => list_1(uncurry2(decoder), path_7, value_7)))), (objectArg_7 = get$.Optional, objectArg_7.Field("ontologySourceReferences", uncurry2(arg_15)))), (arg_17 = ((decoder_1 = decoder_5(options), (path_8) => ((value_8) => list_1(uncurry2(decoder_1), path_8, value_8)))), (objectArg_8 = get$.Optional, objectArg_8.Field("publications", uncurry2(arg_17)))), (arg_19 = ((decoder_2 = decoder_6(options), (path_9) => ((value_9) => list_1(uncurry2(decoder_2), path_9, value_9)))), (objectArg_9 = get$.Optional, objectArg_9.Field("people", uncurry2(arg_19)))), (arg_21 = ((decoder_3 = Study_decoder(options), (path_10) => ((value_10) => list_1(uncurry2(decoder_3), path_10, value_10)))), (objectArg_10 = get$.Optional, objectArg_10.Field("studies", uncurry2(arg_21)))), (arg_23 = ((decoder_4 = decoder_7(options), (path_11) => ((value_11) => list_1(uncurry2(decoder_4), path_11, value_11)))), (objectArg_11 = get$.Optional, objectArg_11.Field("comments", uncurry2(arg_23)))), empty_1());
+        let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, arg_15, decoder_1, objectArg_7, arg_17, decoder_2, objectArg_8, arg_19, decoder_3, objectArg_9, arg_21, decoder_4, objectArg_10, arg_23, decoder_5, objectArg_11;
+        return new Investigation((objectArg = get$.Optional, objectArg.Field("@id", string)), (objectArg_1 = get$.Optional, objectArg_1.Field("filename", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("identifier", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("title", string)), (objectArg_4 = get$.Optional, objectArg_4.Field("description", string)), (objectArg_5 = get$.Optional, objectArg_5.Field("submissionDate", string)), (objectArg_6 = get$.Optional, objectArg_6.Field("publicReleaseDate", string)), (arg_15 = ((decoder_1 = OntologySourceReference_decoder(options), (path_7) => ((value_7) => list_1(uncurry2(decoder_1), path_7, value_7)))), (objectArg_7 = get$.Optional, objectArg_7.Field("ontologySourceReferences", uncurry2(arg_15)))), (arg_17 = ((decoder_2 = decoder_6(options), (path_8) => ((value_8) => list_1(uncurry2(decoder_2), path_8, value_8)))), (objectArg_8 = get$.Optional, objectArg_8.Field("publications", uncurry2(arg_17)))), (arg_19 = ((decoder_3 = decoder_7(options), (path_9) => ((value_9) => list_1(uncurry2(decoder_3), path_9, value_9)))), (objectArg_9 = get$.Optional, objectArg_9.Field("people", uncurry2(arg_19)))), (arg_21 = ((decoder_4 = Study_decoder(options), (path_10) => ((value_10) => list_1(uncurry2(decoder_4), path_10, value_10)))), (objectArg_10 = get$.Optional, objectArg_10.Field("studies", uncurry2(arg_21)))), (arg_23 = ((decoder_5 = decoder_8(options), (path_11) => ((value_11) => list_1(uncurry2(decoder_5), path_11, value_11)))), (objectArg_11 = get$.Optional, objectArg_11.Field("comments", uncurry2(arg_23)))), empty_1());
     }, path_12, v));
 }
 
-export function Investigation_fromJsonString(s) {
-    return fromJsonString(uncurry2(Investigation_decoder(ConverterOptions_$ctor())), s);
+export function fromJsonString(s) {
+    return fromJsonString_1(uncurry2(decoder(ConverterOptions_$ctor())), s);
 }
 
-export function Investigation_toJsonString(p) {
-    return toString(2, Investigation_encoder(ConverterOptions_$ctor(), p));
+export function toJsonString(p) {
+    return toString(2, encoder(ConverterOptions_$ctor(), p));
 }
 
 /**
  * exports in json-ld format
  */
-export function Investigation_toStringLD(i) {
+export function toStringLD(i) {
     let returnVal;
-    return toString(2, Investigation_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), i));
-}
-
-export function ArcInvestigation_fromJsonString(s) {
-    const i = fromJsonString(uncurry2(Investigation_decoder(ConverterOptions_$ctor())), s);
-    return ArcInvestigation.fromInvestigation(i);
-}
-
-export function ArcInvestigation_toJsonString(a) {
-    return toString(2, Investigation_encoder(ConverterOptions_$ctor(), a.ToInvestigation()));
-}
-
-/**
- * exports in json-ld format
- */
-export function ArcInvestigation_toStringLD(a) {
-    let returnVal;
-    return toString(2, Investigation_encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), a.ToInvestigation()));
+    return toString(2, encoder((returnVal = ConverterOptions_$ctor(), ((ConverterOptions__set_SetID_Z1FBCCD16(returnVal, true), ConverterOptions__set_IncludeType_Z1FBCCD16(returnVal, true)), returnVal)), i));
 }
 

package/ISA/ISA.Json/Study.js

@@ -20,7 +20,6 @@ import { Factor_decoder, Factor_encoder } from "./Factor.js";
 import { decoder as decoder_12, encoder as encoder_2 } from "./Comment.js";
 import { fromJsonString, 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) => {
@@ -211,20 +210,3 @@ export function Study_toStringLD(s) {
     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_fromJsonString(s) {
-    const s_1 = fromJsonString(uncurry2(Study_decoder(ConverterOptions_$ctor())), s);
-    return ArcStudy.fromStudy(s_1);
-}
-
-export function ArcStudy_toJsonString(a, assays) {
-    return toString(2, Study_encoder(ConverterOptions_$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.Spreadsheet/ArcAssay.js

@@ -127,9 +127,9 @@ export function fromFsWorkbook(doc) {
     else {
         assayMetaData = fromMetadataSheet(matchValue);
     }
-    const tables = choose(tryFromFsWorksheet, doc.GetWorksheets());
-    if (!isEmpty_1(tables)) {
-        assayMetaData.Tables = Array.from(tables);
+    const annotationTables = choose(tryFromFsWorksheet, doc.GetWorksheets());
+    if (!isEmpty_1(annotationTables)) {
+        assayMetaData.Tables = Array.from(annotationTables);
     }
     return assayMetaData;
 }

package/ISA/ISA.Spreadsheet/ArcStudy.js

@@ -9,7 +9,6 @@ import { createMissingIdentifier } from "../ISA/Identifier.js";
 import { empty } from "../../fable_modules/fable-library.4.5.0/List.js";
 import { printf, toConsole } from "../../fable_modules/fable-library.4.5.0/String.js";
 import { toFsWorksheet, tryFromFsWorksheet } from "./AnnotationTable/ArcTable.js";
-import { ArcTables } from "../ISA/ArcTypes/ArcTables.js";
 import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.0.1/FsWorkbook.fs.js";
 
 export function ArcStudy_toMetadataSheet(study, assays) {
@@ -46,10 +45,9 @@ export function ARCtrl_ISA_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D(doc
         patternInput = ArcStudy_fromMetadataSheet(matchValue);
     }
     const studyMetadata = patternInput[0];
-    const sheets = choose(tryFromFsWorksheet, doc.GetWorksheets());
-    if (!isEmpty(sheets)) {
-        const updatedTables = ArcTables.updateReferenceTablesBySheets(new ArcTables(studyMetadata.Tables), new ArcTables(Array.from(sheets)), true);
-        studyMetadata.Tables = updatedTables.Tables;
+    const annotationTables = choose(tryFromFsWorksheet, doc.GetWorksheets());
+    if (!isEmpty(annotationTables)) {
+        studyMetadata.Tables = Array.from(annotationTables);
     }
     return [studyMetadata, patternInput[1]];
 }

package/Templates/Template.Json.js

@@ -1,16 +1,15 @@
 import { toString } from "../fable_modules/fable-library.4.5.0/Types.js";
-import { dict, fromString, datetimeUtc, array as array_1, map as map_2, list as list_2, guid as guid_1, object as object_1, string, succeed, andThen } from "../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { dict, fromString, datetimeUtc, array as array_1, guid as guid_1, object as object_1, string, succeed, andThen } from "../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
 import { uncurry2, uncurry3 } from "../fable_modules/fable-library.4.5.0/Util.js";
 import { Template, Organisation } from "./Template.js";
 import { ConverterOptions_$ctor } from "../ISA/ISA.Json/ConverterOptions.js";
-import { decoder as decoder_2, encoder } from "../ISA/ISA.Json/Person.js";
+import { decoder as decoder_1, encoder } from "../ISA/ISA.Json/Person.js";
 import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "../ISA/ISA.Json/Ontology.js";
 import { toString as toString_1, datetime, list as list_1, guid, object } from "../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
-import { ofArray, map } from "../fable_modules/fable-library.4.5.0/List.js";
-import { Process_decoder, Process_encoder } from "../ISA/ISA.Json/Process.js";
-import { map as map_1, delay, toList } from "../fable_modules/fable-library.4.5.0/Seq.js";
-import { ArcTables } from "../ISA/ISA/ArcTypes/ArcTables.js";
+import { ArcTable_decoder, ArcTable_encoder } from "../ISA/ISA.Json/ArcTypes/ArcTable.js";
+import { map, delay, toList } from "../fable_modules/fable-library.4.5.0/Seq.js";
 import { printf, toFail } from "../fable_modules/fable-library.4.5.0/String.js";
+import { ofArray, map as map_1 } from "../fable_modules/fable-library.4.5.0/List.js";
 import { FSharpMap__get_Values } from "../fable_modules/fable-library.4.5.0/Map.js";
 import { defaultArg } from "../fable_modules/fable-library.4.5.0/Option.js";
 
@@ -22,26 +21,22 @@ export const Organisation_decode = (path_1) => ((value_1) => andThen(uncurry3((t
 }), string, path_1, value_1));
 
 export function Template_encode(template) {
-    let list, options_2;
     let personEncoder;
     const options = ConverterOptions_$ctor();
     personEncoder = ((oa) => encoder(options, oa));
     let oaEncoder;
     const options_1 = ConverterOptions_$ctor();
     oaEncoder = ((oa_1) => OntologyAnnotation_encoder(options_1, oa_1));
-    return object([["id", guid(template.Id)], ["table", list_1((list = template.Table.GetProcesses(), map((options_2 = ConverterOptions_$ctor(), (oa_2) => Process_encoder(options_2, oa_2)), list)))], ["name", template.Name], ["description", template.Description], ["organisation", Organisation_encode(template.Organisation)], ["version", template.Version], ["authors", list_1(toList(delay(() => map_1(personEncoder, template.Authors))))], ["endpoint_repositories", list_1(toList(delay(() => map_1(oaEncoder, template.EndpointRepositories))))], ["tags", list_1(toList(delay(() => map_1(oaEncoder, template.Tags))))], ["last_updated", datetime(template.LastUpdated)]]);
+    return object([["id", guid(template.Id)], ["table", ArcTable_encoder(template.Table)], ["name", template.Name], ["description", template.Description], ["organisation", Organisation_encode(template.Organisation)], ["version", template.Version], ["authors", list_1(toList(delay(() => map(personEncoder, template.Authors))))], ["endpoint_repositories", list_1(toList(delay(() => map(oaEncoder, template.EndpointRepositories))))], ["tags", list_1(toList(delay(() => map(oaEncoder, template.Tags))))], ["last_updated", datetime(template.LastUpdated)]]);
 }
 
 export const Template_decode = (() => {
-    const personDecoder = decoder_2(ConverterOptions_$ctor());
+    const personDecoder = decoder_1(ConverterOptions_$ctor());
     const oaDecoder = OntologyAnnotation_decoder(ConverterOptions_$ctor());
-    return (path_10) => ((v) => object_1((get$) => {
-        let objectArg, arg_3, d, decoder, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, objectArg_7, objectArg_8, objectArg_9;
-        return Template.create((objectArg = get$.Required, objectArg.Field("id", guid_1)), (arg_3 = ((d = ((decoder = Process_decoder(ConverterOptions_$ctor()), (path_1) => ((value_1) => list_2(uncurry2(decoder), path_1, value_1)))), (path_2) => ((value_2) => map_2((ps) => {
-            const arctbls = ArcTables.fromProcesses(ps);
-            return arctbls.Tables[0];
-        }, uncurry2(d), path_2, value_2)))), (objectArg_1 = get$.Required, objectArg_1.Field("table", uncurry2(arg_3)))), (objectArg_2 = get$.Required, objectArg_2.Field("name", string)), (objectArg_3 = get$.Required, objectArg_3.Field("description", string)), (objectArg_4 = get$.Required, objectArg_4.Field("organisation", uncurry2(Organisation_decode))), (objectArg_5 = get$.Required, objectArg_5.Field("version", string)), (objectArg_6 = get$.Required, objectArg_6.Field("authors", (path_6, value_6) => array_1(uncurry2(personDecoder), path_6, value_6))), (objectArg_7 = get$.Required, objectArg_7.Field("endpoint_repositories", (path_7, value_7) => array_1(uncurry2(oaDecoder), path_7, value_7))), (objectArg_8 = get$.Required, objectArg_8.Field("tags", (path_8, value_8) => array_1(uncurry2(oaDecoder), path_8, value_8))), (objectArg_9 = get$.Required, objectArg_9.Field("last_updated", datetimeUtc)));
-    }, path_10, v));
+    return (path_8) => ((v) => object_1((get$) => {
+        let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, objectArg_7, objectArg_8, objectArg_9;
+        return Template.create((objectArg = get$.Required, objectArg.Field("id", guid_1)), (objectArg_1 = get$.Required, objectArg_1.Field("table", uncurry2(ArcTable_decoder))), (objectArg_2 = get$.Required, objectArg_2.Field("name", string)), (objectArg_3 = get$.Required, objectArg_3.Field("description", string)), (objectArg_4 = get$.Required, objectArg_4.Field("organisation", uncurry2(Organisation_decode))), (objectArg_5 = get$.Required, objectArg_5.Field("version", string)), (objectArg_6 = get$.Required, objectArg_6.Field("authors", (path_4, value_4) => array_1(uncurry2(personDecoder), path_4, value_4))), (objectArg_7 = get$.Required, objectArg_7.Field("endpoint_repositories", (path_5, value_5) => array_1(uncurry2(oaDecoder), path_5, value_5))), (objectArg_8 = get$.Required, objectArg_8.Field("tags", (path_6, value_6) => array_1(uncurry2(oaDecoder), path_6, value_6))), (objectArg_9 = get$.Required, objectArg_9.Field("last_updated", datetimeUtc)));
+    }, path_8, v));
 })();
 
 export function Template_fromJsonString(jsonString) {
@@ -59,7 +54,7 @@ export function Template_toJsonString(spaces, template) {
 }
 
 export function Templates_encode(templateList) {
-    return object(map((tupledArg) => [tupledArg[0], Template_encode(tupledArg[1])], ofArray(templateList)));
+    return object(map_1((tupledArg) => [tupledArg[0], Template_encode(tupledArg[1])], ofArray(templateList)));
 }
 
 export const Templates_decode = (() => {

package/fable_modules/project_cracked.json

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@nfdi4plants/arctrl",
-  "version": "1.0.0-beta.9+1c6c4fa",
+  "version": "1.0.0+b42bd6f",
   "description": "Top level ARC DataModel and API function descriptions.",
   "type": "module",
   "main": "index.js",