@nfdi4plants/arctrl 2.0.0-beta.2 → 2.0.0

package/Json/{Process/PropertyValue.js → PropertyValue.js}

@@ -1,13 +1,13 @@
-import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { unwrap, map } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
-import { ofArray, choose } from "../../fable_modules/fable-library-js.4.16.0/List.js";
-import { equals } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
-import { tryInclude } from "../Encode.js";
-import { context_jsonvalue } from "../context/rocrate/property_value_context.js";
-import { string, object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
-import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
-import { AnnotationValue_decoder } from "../OntologyAnnotation.js";
-import { Value } from "../../Core/Process/Value.js";
+import { Json } from "../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+import { unwrap, map } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { ofArray, choose } from "../fable_modules/fable-library-js.4.16.0/List.js";
+import { equals } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { tryInclude } from "./Encode.js";
+import { context_jsonvalue } from "./context/rocrate/property_value_context.js";
+import { string, object } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
+import { OntologyAnnotation } from "../Core/OntologyAnnotation.js";
+import { AnnotationValue_decoder } from "./OntologyAnnotation.js";
+import { Value } from "../Core/Value.js";
 
 export function genID(p) {
     const matchValue = p.GetCategory();
@@ -97,19 +97,28 @@ export function encoder(pv) {
         else {
             return [tupledArg[0], v_1];
         }
-    }, ofArray([["@id", new Json(0, [genID(pv)])], ["@type", new Json(0, ["PropertyValue"])], ["additionalType", new Json(0, [pv.GetAdditionalType()])], tryInclude("category", (value_11) => (new Json(0, [value_11])), patternInput[0]), tryInclude("categoryCode", (value_13) => (new Json(0, [value_13])), patternInput[1]), tryInclude("value", (x) => x, patternInput_1[0]), tryInclude("valueCode", (x_1) => x_1, patternInput_1[1]), tryInclude("unit", (value_15) => (new Json(0, [value_15])), patternInput_2[0]), tryInclude("unitCode", (value_17) => (new Json(0, [value_17])), patternInput_2[1]), ["@context", context_jsonvalue]]))]);
+    }, ofArray([["@id", new Json(0, [genID(pv)])], ["@type", new Json(0, ["PropertyValue"])], ["additionalType", new Json(0, [pv.GetAdditionalType()])], tryInclude("alternateName", (value_11) => (new Json(0, [value_11])), pv.AlternateName()), tryInclude("measurementMethod", (value_13) => (new Json(0, [value_13])), pv.MeasurementMethod()), tryInclude("description", (value_15) => (new Json(0, [value_15])), pv.Description()), tryInclude("category", (value_17) => (new Json(0, [value_17])), patternInput[0]), tryInclude("categoryCode", (value_19) => (new Json(0, [value_19])), patternInput[1]), tryInclude("value", (x) => x, patternInput_1[0]), tryInclude("valueCode", (x_1) => x_1, patternInput_1[1]), tryInclude("unit", (value_21) => (new Json(0, [value_21])), patternInput_2[0]), tryInclude("unitCode", (value_23) => (new Json(0, [value_23])), patternInput_2[1]), ["@context", context_jsonvalue]]))]);
 }
 
 export function decoder(create) {
     return object((get$) => {
-        let value, objectArg_4, code_4, objectArg_5;
+        let value, objectArg_7, code_4, objectArg_8;
+        let alternateName;
+        const objectArg = get$.Optional;
+        alternateName = objectArg.Field("alternateName", string);
+        let measurementMethod;
+        const objectArg_1 = get$.Optional;
+        measurementMethod = objectArg_1.Field("measurementMethod", string);
+        let description;
+        const objectArg_2 = get$.Optional;
+        description = objectArg_2.Field("description", string);
         let category;
         let name;
-        const objectArg = get$.Optional;
-        name = objectArg.Field("category", string);
+        const objectArg_3 = get$.Optional;
+        name = objectArg_3.Field("category", string);
         let code;
-        const objectArg_1 = get$.Optional;
-        code = objectArg_1.Field("categoryCode", string);
+        const objectArg_4 = get$.Optional;
+        code = objectArg_4.Field("categoryCode", string);
         let matchResult, code_1;
         if (name == null) {
             if (code != null) {
@@ -161,11 +170,11 @@ export function decoder(create) {
         }
         let unit;
         let name_1;
-        const objectArg_2 = get$.Optional;
-        name_1 = objectArg_2.Field("unit", string);
+        const objectArg_5 = get$.Optional;
+        name_1 = objectArg_5.Field("unit", string);
         let code_2;
-        const objectArg_3 = get$.Optional;
-        code_2 = objectArg_3.Field("unitCode", string);
+        const objectArg_6 = get$.Optional;
+        code_2 = objectArg_6.Field("unitCode", string);
         let matchResult_1, code_3;
         if (name_1 == null) {
             if (code_2 != null) {
@@ -215,7 +224,7 @@ export function decoder(create) {
                     throw new Error(`Error while decoding unit (name:${name_1}, code:${code_3}): ${err_3}`);
                 }
         }
-        return create(category, (value = ((objectArg_4 = get$.Optional, objectArg_4.Field("value", AnnotationValue_decoder))), (code_4 = ((objectArg_5 = get$.Optional, objectArg_5.Field("valueCode", string))), ((value == null) && (code_4 == null)) ? void 0 : (() => {
+        return create(alternateName, measurementMethod, description, category, (value = ((objectArg_7 = get$.Optional, objectArg_7.Field("value", AnnotationValue_decoder))), (code_4 = ((objectArg_8 = get$.Optional, objectArg_8.Field("valueCode", string))), ((value == null) && (code_4 == null)) ? void 0 : (() => {
             try {
                 return Value.fromOptions(value, void 0, code_4);
             }

package/Json/Study.js

@@ -9,6 +9,7 @@ import { Publication_ISAJson_decoder, Publication_ISAJson_encoder, Publication_R
 import { Person_ISAJson_decoder, Person_ISAJson_encoder, Person_ROCrate_decoder, Person_ROCrate_encoder, Person_decoder, Person_encoder } from "./Person.js";
 import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder, OntologyAnnotation_ROCrate_decoderDefinedTerm, OntologyAnnotation_ROCrate_encoderDefinedTerm, OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./OntologyAnnotation.js";
 import { ArcTable_decoderCompressed, ArcTable_encoderCompressed, ArcTable_decoder, ArcTable_encoder } from "./Table/ArcTable.js";
+import { decoderCompressed, encoderCompressed, decoder as decoder_1, encoder as encoder_4 } from "./DataMap/DataMap.js";
 import { Comment_ISAJson_decoder, Comment_ISAJson_encoder, Comment_ROCrate_decoder, Comment_ROCrate_encoder, Comment_decoder, Comment_encoder } from "./Comment.js";
 import { list as list_2, string, object } from "../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
 import { Decode_objectNoAdditionalProperties, Decode_resizeArray } from "./Decode.js";
@@ -22,7 +23,7 @@ import { context_jsonvalue } from "./context/rocrate/isa_study_context.js";
 import { getProtocols, getCharacteristics, getFactors, getUnits } from "../Core/Process/ProcessSequence.js";
 import { Factor_ISAJson_encoder } from "./Process/Factor.js";
 import { MaterialAttribute_ISAJson_encoder } from "./Process/MaterialAttribute.js";
-import { encoder as encoder_4 } from "./Process/StudyMaterials.js";
+import { encoder as encoder_5 } from "./Process/StudyMaterials.js";
 import { Protocol_ISAJson_encoder } from "./Process/Protocol.js";
 import { encode } from "./IDTable.js";
 import { isEmpty } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
@@ -51,12 +52,12 @@ export function Study_encoder(study) {
         else {
             return [tupledArg[0], v];
         }
-    }, ofArray([["Identifier", new Json(0, [study.Identifier])], tryInclude("Title", (value_1) => (new Json(0, [value_1])), study.Title), tryInclude("Description", (value_3) => (new Json(0, [value_3])), study.Description), tryInclude("SubmissionDate", (value_5) => (new Json(0, [value_5])), study.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => (new Json(0, [value_7])), study.PublicReleaseDate), tryIncludeSeq("Publications", Publication_encoder, study.Publications), tryIncludeSeq("Contacts", Person_encoder, study.Contacts), tryIncludeSeq("StudyDesignDescriptors", OntologyAnnotation_encoder, study.StudyDesignDescriptors), tryIncludeSeq("Tables", ArcTable_encoder, study.Tables), tryIncludeSeq("RegisteredAssayIdentifiers", (value_9) => (new Json(0, [value_9])), study.RegisteredAssayIdentifiers), tryIncludeSeq("Comments", Comment_encoder, study.Comments)]))]);
+    }, ofArray([["Identifier", new Json(0, [study.Identifier])], tryInclude("Title", (value_1) => (new Json(0, [value_1])), study.Title), tryInclude("Description", (value_3) => (new Json(0, [value_3])), study.Description), tryInclude("SubmissionDate", (value_5) => (new Json(0, [value_5])), study.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => (new Json(0, [value_7])), study.PublicReleaseDate), tryIncludeSeq("Publications", Publication_encoder, study.Publications), tryIncludeSeq("Contacts", Person_encoder, study.Contacts), tryIncludeSeq("StudyDesignDescriptors", OntologyAnnotation_encoder, study.StudyDesignDescriptors), tryIncludeSeq("Tables", ArcTable_encoder, study.Tables), tryInclude("DataMap", encoder_4, study.DataMap), tryIncludeSeq("RegisteredAssayIdentifiers", (value_9) => (new Json(0, [value_9])), study.RegisteredAssayIdentifiers), tryIncludeSeq("Comments", Comment_encoder, study.Comments)]))]);
 }
 
 export const Study_decoder = object((get$) => {
-    let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10;
-    return new ArcStudy((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("Title", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("Description", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("SubmissionDate", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("PublicReleaseDate", string))), unwrap((arg_11 = Decode_resizeArray(Publication_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("Publications", arg_11)))), unwrap((arg_13 = Decode_resizeArray(Person_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("Contacts", arg_13)))), unwrap((arg_15 = Decode_resizeArray(OntologyAnnotation_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("StudyDesignDescriptors", arg_15)))), unwrap((arg_17 = Decode_resizeArray(ArcTable_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("Tables", arg_17)))), void 0, unwrap((arg_19 = Decode_resizeArray(string), (objectArg_9 = get$.Optional, objectArg_9.Field("RegisteredAssayIdentifiers", arg_19)))), unwrap((arg_21 = Decode_resizeArray(Comment_decoder), (objectArg_10 = get$.Optional, objectArg_10.Field("Comments", arg_21)))));
+    let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, objectArg_9, arg_21, objectArg_10, arg_23, objectArg_11;
+    return new ArcStudy((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("Title", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("Description", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("SubmissionDate", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("PublicReleaseDate", string))), unwrap((arg_11 = Decode_resizeArray(Publication_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("Publications", arg_11)))), unwrap((arg_13 = Decode_resizeArray(Person_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("Contacts", arg_13)))), unwrap((arg_15 = Decode_resizeArray(OntologyAnnotation_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("StudyDesignDescriptors", arg_15)))), unwrap((arg_17 = Decode_resizeArray(ArcTable_decoder), (objectArg_8 = get$.Optional, objectArg_8.Field("Tables", arg_17)))), unwrap((objectArg_9 = get$.Optional, objectArg_9.Field("DataMap", decoder_1))), unwrap((arg_21 = Decode_resizeArray(string), (objectArg_10 = get$.Optional, objectArg_10.Field("RegisteredAssayIdentifiers", arg_21)))), unwrap((arg_23 = Decode_resizeArray(Comment_decoder), (objectArg_11 = get$.Optional, objectArg_11.Field("Comments", arg_23)))));
 });
 
 export function Study_encoderCompressed(stringTable, oaTable, cellTable, study) {
@@ -68,13 +69,13 @@ export function Study_encoderCompressed(stringTable, oaTable, cellTable, study)
         else {
             return [tupledArg[0], v];
         }
-    }, ofArray([["Identifier", new Json(0, [study.Identifier])], tryInclude("Title", (value_1) => (new Json(0, [value_1])), study.Title), tryInclude("Description", (value_3) => (new Json(0, [value_3])), study.Description), tryInclude("SubmissionDate", (value_5) => (new Json(0, [value_5])), study.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => (new Json(0, [value_7])), study.PublicReleaseDate), tryIncludeSeq("Publications", Publication_encoder, study.Publications), tryIncludeSeq("Contacts", Person_encoder, study.Contacts), tryIncludeSeq("StudyDesignDescriptors", OntologyAnnotation_encoder, study.StudyDesignDescriptors), tryIncludeSeq("Tables", (table) => ArcTable_encoderCompressed(stringTable, oaTable, cellTable, table), study.Tables), tryIncludeSeq("RegisteredAssayIdentifiers", (value_9) => (new Json(0, [value_9])), study.RegisteredAssayIdentifiers), tryIncludeSeq("Comments", Comment_encoder, study.Comments)]))]);
+    }, ofArray([["Identifier", new Json(0, [study.Identifier])], tryInclude("Title", (value_1) => (new Json(0, [value_1])), study.Title), tryInclude("Description", (value_3) => (new Json(0, [value_3])), study.Description), tryInclude("SubmissionDate", (value_5) => (new Json(0, [value_5])), study.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => (new Json(0, [value_7])), study.PublicReleaseDate), tryIncludeSeq("Publications", Publication_encoder, study.Publications), tryIncludeSeq("Contacts", Person_encoder, study.Contacts), tryIncludeSeq("StudyDesignDescriptors", OntologyAnnotation_encoder, study.StudyDesignDescriptors), tryIncludeSeq("Tables", (table) => ArcTable_encoderCompressed(stringTable, oaTable, cellTable, table), study.Tables), tryInclude("DataMap", (dm) => encoderCompressed(stringTable, oaTable, cellTable, dm), study.DataMap), tryIncludeSeq("RegisteredAssayIdentifiers", (value_9) => (new Json(0, [value_9])), study.RegisteredAssayIdentifiers), tryIncludeSeq("Comments", Comment_encoder, study.Comments)]))]);
 }
 
 export function Study_decoderCompressed(stringTable, oaTable, cellTable) {
     return object((get$) => {
-        let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10;
-        return new ArcStudy((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("Title", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("Description", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("SubmissionDate", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("PublicReleaseDate", string))), unwrap((arg_11 = Decode_resizeArray(Publication_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("Publications", arg_11)))), unwrap((arg_13 = Decode_resizeArray(Person_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("Contacts", arg_13)))), unwrap((arg_15 = Decode_resizeArray(OntologyAnnotation_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("StudyDesignDescriptors", arg_15)))), unwrap((arg_17 = Decode_resizeArray(ArcTable_decoderCompressed(stringTable, oaTable, cellTable)), (objectArg_8 = get$.Optional, objectArg_8.Field("Tables", arg_17)))), void 0, unwrap((arg_19 = Decode_resizeArray(string), (objectArg_9 = get$.Optional, objectArg_9.Field("RegisteredAssayIdentifiers", arg_19)))), unwrap((arg_21 = Decode_resizeArray(Comment_decoder), (objectArg_10 = get$.Optional, objectArg_10.Field("Comments", arg_21)))));
+        let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10, arg_23, objectArg_11;
+        return new ArcStudy((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("Title", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("Description", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("SubmissionDate", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("PublicReleaseDate", string))), unwrap((arg_11 = Decode_resizeArray(Publication_decoder), (objectArg_5 = get$.Optional, objectArg_5.Field("Publications", arg_11)))), unwrap((arg_13 = Decode_resizeArray(Person_decoder), (objectArg_6 = get$.Optional, objectArg_6.Field("Contacts", arg_13)))), unwrap((arg_15 = Decode_resizeArray(OntologyAnnotation_decoder), (objectArg_7 = get$.Optional, objectArg_7.Field("StudyDesignDescriptors", arg_15)))), unwrap((arg_17 = Decode_resizeArray(ArcTable_decoderCompressed(stringTable, oaTable, cellTable)), (objectArg_8 = get$.Optional, objectArg_8.Field("Tables", arg_17)))), unwrap((arg_19 = decoderCompressed(stringTable, oaTable, cellTable), (objectArg_9 = get$.Optional, objectArg_9.Field("DataMap", arg_19)))), unwrap((arg_21 = Decode_resizeArray(string), (objectArg_10 = get$.Optional, objectArg_10.Field("RegisteredAssayIdentifiers", arg_21)))), unwrap((arg_23 = Decode_resizeArray(Comment_decoder), (objectArg_11 = get$.Optional, objectArg_11.Field("Comments", arg_23)))));
     });
 }
 
@@ -156,7 +157,7 @@ export function Study_ISAJson_encoder(idMap, assays, s) {
         const encodedUnits = tryIncludeList("unitCategories", (oa) => OntologyAnnotation_ISAJson_encoder(idMap, oa), getUnits(processes));
         const encodedFactors = tryIncludeList("factors", (value_1) => Factor_ISAJson_encoder(idMap, value_1), getFactors(processes));
         const encodedCharacteristics = tryIncludeList("characteristicCategories", (value_3) => MaterialAttribute_ISAJson_encoder(idMap, value_3), getCharacteristics(processes));
-        const encodedMaterials = tryInclude("materials", (ps) => encoder_4(idMap, ps), Option_fromValueWithDefault(empty(), processes));
+        const encodedMaterials = tryInclude("materials", (ps) => encoder_5(idMap, ps), Option_fromValueWithDefault(empty(), processes));
         let encodedProtocols;
         const value_5 = getProtocols(processes);
         encodedProtocols = tryIncludeList("protocols", (studyName = s_1.Identifier, (oa_1) => Protocol_ISAJson_encoder(studyName, void 0, void 0, idMap, oa_1)), value_5);

package/Json/Table/CompositeCell.js

@@ -1,7 +1,7 @@
 import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "../OntologyAnnotation.js";
 import { ofArray, singleton } from "../../fable_modules/fable-library-js.4.16.0/List.js";
 import { Json } from "../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
-import { Data_compressedDecoder, Data_compressedEncoder, Data_decoder, Data_encoder } from "../Process/Data.js";
+import { Data_compressedDecoder, Data_compressedEncoder, Data_decoder, Data_encoder } from "../Data.js";
 import { list } from "../../fable_modules/Thoth.Json.Core.0.2.1/Encode.fs.js";
 import { index, string, object } from "../../fable_modules/Thoth.Json.Core.0.2.1/Decode.fs.js";
 import { CompositeCell } from "../../Core/Table/CompositeCell.js";

package/Json/context/rocrate/isa_data_context.js

@@ -19,7 +19,7 @@ export function IContext_$reflection() {
     return record_type("ARCtrl.Json.ROCrateContext.Data.IContext", [], IContext, () => [["sdo", string_type], ["arc", string_type], ["Data", string_type], ["ArcData", string_type], ["type", string_type], ["name", string_type], ["comments", string_type]]);
 }
 
-export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["Data", new Json(0, ["sdo:MediaObject"])], ["type", new Json(0, ["sdo:disambiguatingDescription"])], ["name", new Json(0, ["sdo:name"])], ["comments", new Json(0, ["sdo:comment"])]]]);
+export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["Data", new Json(0, ["sdo:MediaObject"])], ["type", new Json(0, ["sdo:disambiguatingDescription"])], ["encodingFormat", new Json(0, ["sdo:encodingFormat"])], ["usageInfo", new Json(0, ["sdo:usageInfo"])], ["name", new Json(0, ["sdo:name"])], ["comments", new Json(0, ["sdo:comment"])]]]);
 
 export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"Data\": \"sdo:MediaObject\",\r\n    \"ArcData\": \"arc:ARC#ARC_00000076\",\r\n\r\n    \"type\": \"arc:ARC#ARC_00000107\",\r\n\r\n    \"name\": \"sdo:name\",\r\n    \"comments\": \"sdo:disambiguatingDescription\"\r\n  }\r\n}\r\n    ";
 

package/Json/context/rocrate/isa_investigation_context.js

@@ -29,5 +29,5 @@ export function IContext_$reflection() {
 
 export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["Investigation", new Json(0, ["sdo:Dataset"])], ["identifier", new Json(0, ["sdo:identifier"])], ["title", new Json(0, ["sdo:headline"])], ["additionalType", new Json(0, ["sdo:additionalType"])], ["description", new Json(0, ["sdo:description"])], ["submissionDate", new Json(0, ["sdo:dateCreated"])], ["publicReleaseDate", new Json(0, ["sdo:datePublished"])], ["publications", new Json(0, ["sdo:citation"])], ["people", new Json(0, ["sdo:creator"])], ["studies", new Json(0, ["sdo:hasPart"])], ["ontologySourceReferences", new Json(0, ["sdo:mentions"])], ["comments", new Json(0, ["sdo:comment"])], ["filename", new Json(0, ["sdo:alternateName"])]]]);
 
-export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"Investigation\": \"sdo:Dataset\",\r\n\r\n    \"identifier\" : \"sdo:identifier\",\r\n    \"title\": \"sdo:headline\",\r\n    \"description\": \"sdo:description\",\r\n    \"submissionDate\": \"sdo:dateCreated\",\r\n    \"publicReleaseDate\": \"sdo:datePublished\",\r\n    \"publications\": \"sdo:citation\",\r\n    \"people\": \"sdo:creator\",\r\n    \"studies\": \"sdo:hasPart\",\r\n    \"ontologySourceReferences\": \"sdo:mentions\",\r\n    \"comments\": \"sdo:disambiguatingDescription\",\r\n\r\n    \"publications?\": \"sdo:subjectOf?\",\r\n    \"filename\": \"sdo:alternateName\"\r\n  }\r\n}\r\n    ";
+export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"Investigation\": \"sdo:Dataset\",\r\n\r\n    \"identifier\" : \"sdo:identifier\",\r\n    \"title\": \"sdo:headline\",\r\n    \"description\": \"sdo:description\",\r\n    \"submissionDate\": \"sdo:dateCreated\",\r\n    \"publicReleaseDate\": \"sdo:datePublished\",\r\n    \"publications\": \"sdo:citation\",\r\n    \"people\": \"sdo:creator\",\r\n    \"studies\": \"sdo:hasPart\",\r\n    \"ontologySourceReferences\": \"sdo:mentions\",\r\n    \"comments\": \"sdo:disambiguatingDescription\",\r\n\r\n    \"publications?\": \"sdo:SubjectOf?\",\r\n    \"filename\": \"sdo:alternateName\"\r\n  }\r\n}\r\n    ";
 

package/Json/context/rocrate/property_value_context.js

@@ -1,4 +1,4 @@
 import { Json } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
 
-export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["additionalType", new Json(0, ["sdo:additionalType"])], ["category", new Json(0, ["sdo:name"])], ["categoryCode", new Json(0, ["sdo:propertyID"])], ["value", new Json(0, ["sdo:value"])], ["valueCode", new Json(0, ["sdo:valueReference"])], ["unit", new Json(0, ["sdo:unitText"])], ["unitCode", new Json(0, ["sdo:unitCode"])], ["comments", new Json(0, ["sdo:disambiguatingDescription"])]]]);
+export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["additionalType", new Json(0, ["sdo:additionalType"])], ["alternateName", new Json(0, ["sdo:alternateName"])], ["measurementMethod", new Json(0, ["sdo:measurementMethod"])], ["description", new Json(0, ["sdo:description"])], ["category", new Json(0, ["sdo:name"])], ["categoryCode", new Json(0, ["sdo:propertyID"])], ["value", new Json(0, ["sdo:value"])], ["valueCode", new Json(0, ["sdo:valueReference"])], ["unit", new Json(0, ["sdo:unitText"])], ["unitCode", new Json(0, ["sdo:unitCode"])], ["comments", new Json(0, ["sdo:disambiguatingDescription"])]]]);
 

package/Spreadsheet/AnnotationTable/ArcTable.js

@@ -118,7 +118,7 @@ export function tryFromFsWorksheet(sheet) {
     }
 }
 
-export function toFsWorksheet(table) {
+export function toFsWorksheet(index, table) {
     const stringCount = new Map([]);
     const ws = new FsWorksheet(table.Name);
     if (table.Columns.length === 0) {
@@ -130,7 +130,8 @@ export function toFsWorksheet(table) {
         }));
         const maxRow = length(head(columns)) | 0;
         const maxCol = length(columns) | 0;
-        const fsTable = ws.Table("annotationTable", FsRangeAddress_$ctor_7E77A4A0(FsAddress_$ctor_Z37302880(1, 1), FsAddress_$ctor_Z37302880(maxRow, maxCol)));
+        const name = (index == null) ? "annotationTable" : (`${"annotationTable"}${index}`);
+        const fsTable = ws.Table(name, FsRangeAddress_$ctor_7E77A4A0(FsAddress_$ctor_Z37302880(1, 1), FsAddress_$ctor_Z37302880(maxRow, maxCol)));
         iterateIndexed((colI, col) => {
             iterateIndexed((rowI, stringCell) => {
                 let value;

package/Spreadsheet/AnnotationTable/CompositeColumn.js

@@ -1,4 +1,4 @@
-import { map, setItem, item, skip } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
+import { tryItem, map, setItem, item, skip } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
 import { CompositeHeader, IOType } from "../../Core/Table/CompositeHeader.js";
 import { toString } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
 import { toStringCells, fromStringCells } from "./CompositeHeader.js";
@@ -6,6 +6,7 @@ import { empty, singleton, append, toList, exists, map as map_1, delay, toArray
 import { rangeDouble } from "../../fable_modules/fable-library-js.4.16.0/Range.js";
 import { CompositeColumn } from "../../Core/Table/CompositeColumn.js";
 import { toStringCells as toStringCells_1 } from "./CompositeCell.js";
+import { defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 import { map as map_2, singleton as singleton_1, ofArray } from "../../fable_modules/fable-library-js.4.16.0/List.js";
 import { FsCell } from "../../fable_modules/FsSpreadsheet.6.2.0/Cells/FsCell.fs.js";
 
@@ -53,19 +54,20 @@ export function fromFsColumns(columns) {
 export function toStringCellColumns(column) {
     const hasUnit = exists((c) => c.isUnitized, column.Cells);
     const isTerm = column.Header.IsTermColumn;
-    const isData = column.Header.IsDataColumn;
+    const isData = column.Header.IsDataColumn && exists((c_1) => c_1.isData, column.Cells);
     const header = toStringCells(hasUnit, column.Header);
     const cells = map((cell) => toStringCells_1(isTerm, hasUnit, cell), column.Cells);
+    const getCellOrDefault = (ri, ci, cells_1) => defaultArg(tryItem(ci, item(ri, cells_1)), "");
     if (hasUnit) {
-        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i) => item(0, item(i, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_1) => item(1, item(i_1, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_2) => item(2, item(i_2, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(3, header)), delay(() => map_1((i_3) => item(3, item(i_3, cells)), rangeDouble(0, 1, column.Cells.length - 1))))))]);
+        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i) => getCellOrDefault(i, 0, cells), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_1) => getCellOrDefault(i_1, 1, cells), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_2) => getCellOrDefault(i_2, 2, cells), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(3, header)), delay(() => map_1((i_3) => getCellOrDefault(i_3, 3, cells), rangeDouble(0, 1, column.Cells.length - 1))))))]);
     }
     else if (isTerm) {
-        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_4) => item(0, item(i_4, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_5) => item(1, item(i_5, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_6) => item(2, item(i_6, cells)), rangeDouble(0, 1, column.Cells.length - 1))))))]);
+        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_4) => getCellOrDefault(i_4, 0, cells), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_5) => getCellOrDefault(i_5, 1, cells), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_6) => getCellOrDefault(i_6, 2, cells), rangeDouble(0, 1, column.Cells.length - 1))))))]);
     }
     else if (isData) {
-        const hasFormat = exists((c_1) => (c_1.AsData.Format != null), column.Cells);
-        const hasSelectorFormat = exists((c_2) => (c_2.AsData.SelectorFormat != null), column.Cells);
-        return toList(delay(() => append(singleton(toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_7) => item(0, item(i_7, cells)), rangeDouble(0, 1, column.Cells.length - 1))))))), delay(() => append(hasFormat ? singleton(toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_8) => item(1, item(i_8, cells)), rangeDouble(0, 1, column.Cells.length - 1))))))) : empty(), delay(() => (hasSelectorFormat ? singleton(toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_9) => item(2, item(i_9, cells)), rangeDouble(0, 1, column.Cells.length - 1))))))) : empty())))))));
+        const hasFormat = exists((c_2) => (c_2.ToDataCell().AsData.Format != null), column.Cells);
+        const hasSelectorFormat = exists((c_3) => (c_3.ToDataCell().AsData.SelectorFormat != null), column.Cells);
+        return toList(delay(() => append(singleton(toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_7) => getCellOrDefault(i_7, 0, cells), rangeDouble(0, 1, column.Cells.length - 1))))))), delay(() => append(hasFormat ? singleton(toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_8) => getCellOrDefault(i_8, 1, cells), rangeDouble(0, 1, column.Cells.length - 1))))))) : empty(), delay(() => (hasSelectorFormat ? singleton(toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_9) => getCellOrDefault(i_9, 2, cells), rangeDouble(0, 1, column.Cells.length - 1))))))) : empty())))))));
     }
     else {
         return singleton_1(toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_10) => item(0, item(i_10, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))));

package/Spreadsheet/ArcAssay.js

@@ -1,5 +1,5 @@
 import { FsWorksheet } from "../fable_modules/FsSpreadsheet.6.2.0/FsWorksheet.fs.js";
-import { iterate, isEmpty as isEmpty_1, choose, tryHead, head, exists, map, singleton, append, delay, iterateIndexed } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { iterate, isEmpty as isEmpty_1, tryPick, choose, tryFind, tryHead, head, exists, map, singleton, append, delay, iterateIndexed } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { SparseRowModule_tryGetValueAt, SparseRowModule_fromFsRow, SparseRowModule_fromValues, SparseRowModule_writeToSheet } from "./Metadata/SparseTable.js";
 import { fromRows as fromRows_1, toRows as toRows_1 } from "./Metadata/Assays.js";
 import { empty, isEmpty, ofSeq, singleton as singleton_1 } from "../fable_modules/fable-library-js.4.16.0/List.js";
@@ -8,11 +8,12 @@ import { toConsole, printf, toFail } from "../fable_modules/fable-library-js.4.1
 import { getEnumerator } from "../fable_modules/fable-library-js.4.16.0/Util.js";
 import { ArcAssay } from "../Core/ArcTypes.js";
 import { createMissingIdentifier } from "../Core/Helper/Identifier.js";
-import { defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
-import { toFsWorksheet, tryFromFsWorksheet } from "./AnnotationTable/ArcTable.js";
+import { unwrap, toArray, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { toFsWorksheet as toFsWorksheet_1, tryFromFsWorksheet } from "./AnnotationTable/ArcTable.js";
+import { toFsWorksheet, tryFromFsWorksheet as tryFromFsWorksheet_1 } from "./DataMapTable/DataMapTable.js";
 import { FsWorkbook } from "../fable_modules/FsSpreadsheet.6.2.0/FsWorkbook.fs.js";
 
-export function toMetadataSheet(assay) {
+export function ArcAssay_toMetadataSheet(assay) {
     let assay_1;
     const sheet = new FsWorksheet("isa_assay");
     iterateIndexed((rowI, r) => {
@@ -21,7 +22,7 @@ export function toMetadataSheet(assay) {
     return sheet;
 }
 
-export function fromMetadataSheet(sheet) {
+export function ArcAssay_fromMetadataSheet(sheet) {
     try {
         const rows_1 = map(SparseRowModule_fromFsRow, sheet.Rows);
         const patternInput = exists((row) => {
@@ -114,31 +115,45 @@ export function fromMetadataSheet(sheet) {
     }
 }
 
+export function ArcAssay_isMetadataSheetName(name) {
+    if (name === "isa_assay") {
+        return true;
+    }
+    else {
+        return name === "Assay";
+    }
+}
+
+export function ArcAssay_isMetadataSheet(sheet) {
+    return ArcAssay_isMetadataSheetName(sheet.Name);
+}
+
+export function ArcAssay_tryGetMetadataSheet(doc) {
+    return tryFind(ArcAssay_isMetadataSheet, doc.GetWorksheets());
+}
+
 /**
  * Reads an assay from a spreadsheet
  */
-export function fromFsWorkbook(doc) {
+export function ARCtrl_ArcAssay__ArcAssay_fromFsWorkbook_Static_32154C9D(doc) {
     try {
-        let assayMetaData;
-        const matchValue = doc.TryGetWorksheetByName("isa_assay");
+        let assayMetadata;
+        const matchValue = ArcAssay_tryGetMetadataSheet(doc);
         if (matchValue == null) {
-            const matchValue_1 = doc.TryGetWorksheetByName("Assay");
-            if (matchValue_1 == null) {
-                toConsole(printf("Cannot retrieve metadata: Assay file does not contain \"%s\" or \"%s\" sheet."))("isa_assay")("Assay");
-                assayMetaData = ArcAssay.create(createMissingIdentifier());
-            }
-            else {
-                assayMetaData = fromMetadataSheet(matchValue_1);
-            }
+            toConsole(printf("Cannot retrieve metadata: Assay file does not contain \"%s\" or \"%s\" sheet."))("isa_assay")("Assay");
+            assayMetadata = ArcAssay.create(createMissingIdentifier());
         }
         else {
-            assayMetaData = fromMetadataSheet(matchValue);
+            assayMetadata = ArcAssay_fromMetadataSheet(matchValue);
         }
-        const annotationTables = choose(tryFromFsWorksheet, doc.GetWorksheets());
+        const sheets = doc.GetWorksheets();
+        const annotationTables = choose(tryFromFsWorksheet, sheets);
+        const datamapSheet = tryPick(tryFromFsWorksheet_1, sheets);
         if (!isEmpty_1(annotationTables)) {
-            assayMetaData.Tables = Array.from(annotationTables);
+            assayMetadata.Tables = Array.from(annotationTables);
         }
-        return assayMetaData;
+        assayMetadata.DataMap = datamapSheet;
+        return assayMetadata;
     }
     catch (err) {
         const arg_2 = err.message;
@@ -146,14 +161,35 @@ export function fromFsWorkbook(doc) {
     }
 }
 
-export function toFsWorkbook(assay) {
+/**
+ * Write an assay to a spreadsheet
+ * 
+ * If datamapSheet is true, the datamap will be written to a worksheet inside assay workbook.
+ */
+export function ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(assay, datamapSheet) {
+    const datamapSheet_1 = defaultArg(datamapSheet, true);
     const doc = new FsWorkbook();
-    const metaDataSheet = toMetadataSheet(assay);
-    doc.AddWorksheet(metaDataSheet);
-    iterate((arg) => {
-        const sheet = toFsWorksheet(arg);
-        doc.AddWorksheet(sheet);
+    const metadataSheet = ArcAssay_toMetadataSheet(assay);
+    doc.AddWorksheet(metadataSheet);
+    if (datamapSheet_1) {
+        iterate((arg) => {
+            const sheet = toFsWorksheet(arg);
+            doc.AddWorksheet(sheet);
+        }, toArray(assay.DataMap));
+    }
+    iterateIndexed((i, arg_1) => {
+        const sheet_1 = toFsWorksheet_1(i, arg_1);
+        doc.AddWorksheet(sheet_1);
     }, assay.Tables);
     return doc;
 }
 
+/**
+ * Write an assay to a spreadsheet
+ * 
+ * If datamapSheet is true, the datamap will be written to a worksheet inside assay workbook.
+ */
+export function ARCtrl_ArcAssay__ArcAssay_ToFsWorkbook_6FCE9E49(this$, datamapSheet) {
+    return ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(this$, unwrap(datamapSheet));
+}
+