@nfdi4plants/arctrl 2.0.0-alpha.8 → 2.0.0-beta.2

package/ARC.js

@@ -2,11 +2,11 @@ import { concat, fold, map, exactlyOne, tryPick, choose } from "./fable_modules/
 import { ARCtrl_ArcAssay__ArcAssay_ToUpdateContract, ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49, ARCtrl_ArcAssay__ArcAssay_ToDeleteContract, ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F } from "./Contract/ArcAssay.js";
 import { ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static } from "./Contract/Datamap.js";
 import { ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49, ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F } from "./Contract/ArcStudy.js";
-import { ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49, ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F } from "./Contract/ArcInvestigation.js";
+import { ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract, ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F } from "./Contract/ArcInvestigation.js";
 import { collect, empty, iterate, find, tryFind, map as map_1, singleton, append, delay, toList, contains, toArray } from "./fable_modules/fable-library-js.4.16.0/Seq.js";
 import { FileSystemTree } from "./FileSystem/FileSystemTree.js";
 import { FileSystem } from "./FileSystem/FileSystem.js";
-import { bind, map as map_2, value as value_2, defaultArg, unwrap } from "./fable_modules/fable-library-js.4.16.0/Option.js";
+import { bind, map as map_2, defaultArg, value as value_2, unwrap } from "./fable_modules/fable-library-js.4.16.0/Option.js";
 import { comparePrimitives, safeHash, stringHash } from "./fable_modules/fable-library-js.4.16.0/Util.js";
 import { getStudyFolderPath, getAssayFolderPath } from "./FileSystem/Path.js";
 import { printf, toText, replace } from "./fable_modules/fable-library-js.4.16.0/String.js";
@@ -15,14 +15,14 @@ import { ofArray } from "./fable_modules/fable-library-js.4.16.0/List.js";
 import { tryISAReadContractFromPath } from "./Contract/ARC.js";
 import { ArcTables } from "./Core/Table/ArcTables.js";
 import { addToDict } from "./fable_modules/fable-library-js.4.16.0/MapUtil.js";
-import { toFsWorkbook, toLightFsWorkbook } from "./Spreadsheet/ArcInvestigation.js";
+import { toFsWorkbook } from "./Spreadsheet/ArcInvestigation.js";
 import { ArcInvestigation } from "./Core/ArcTypes.js";
 import { Assay_datamapFileNameFromIdentifier, Assay_fileNameFromIdentifier, Study_datamapFileNameFromIdentifier, Study_fileNameFromIdentifier } from "./Core/Helper/Identifier.js";
 import { ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_353D0DB7 } from "./Spreadsheet/ArcStudy.js";
 import { DataMap__get_StaticHash, DataMap__set_StaticHash_Z524259A4 } from "./Core/Table/DataMap.js";
 import { toFsWorkbook as toFsWorkbook_1 } from "./Spreadsheet/DataMap.js";
 import { toFsWorkbook as toFsWorkbook_2 } from "./Spreadsheet/ArcAssay.js";
-import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.6.1.2/Cells/FsCellsCollection.fs.js";
+import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.6.2.0/Cells/FsCellsCollection.fs.js";
 import { Clone_createCloneContract_5000466F, Init_createAddRemoteContract_Z721C83C5, gitignoreContract, gitattributesContract, Init_createInitContract_6DFDD678 } from "./Contract/Git.js";
 import { FSharpSet__Contains, ofSeq, unionMany } from "./fable_modules/fable-library-js.4.16.0/Set.js";
 import { ofSeq as ofSeq_1 } from "./fable_modules/fable-library-js.4.16.0/Map.js";
@@ -142,7 +142,7 @@ export class ARC {
         const assayFolderPath = getAssayFolderPath(assayIdentifier);
         const filteredPaths = paths.filter((p) => !(p.indexOf(assayFolderPath) === 0));
         this$.SetFilePaths(filteredPaths);
-        const collection = toList(delay(() => append(singleton(ARCtrl_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() => append(singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49(isa)), delay(() => map_1(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, studies)))))));
+        const collection = toList(delay(() => append(singleton(ARCtrl_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() => append(singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(isa)), delay(() => map_1(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, studies)))))));
         return Array.from(collection);
     }
     RenameAssay(oldAssayIdentifier, newAssayIdentifier) {
@@ -187,7 +187,7 @@ export class ARC {
         const studyFolderPath = getStudyFolderPath(studyIdentifier);
         const filteredPaths = paths.filter((p) => !(p.indexOf(studyFolderPath) === 0));
         this$.SetFilePaths(filteredPaths);
-        const collection = ofArray([Contract.createDelete(studyFolderPath), ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49(isa)]);
+        const collection = ofArray([Contract.createDelete(studyFolderPath), ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(isa)]);
         return Array.from(collection);
     }
     RenameStudy(oldStudyIdentifier, newStudyIdentifier) {
@@ -292,17 +292,16 @@ export class ARC {
         newFS = ARCAux_updateFSByCWL(this$._cwl, fs);
         this$._fs = newFS;
     }
-    GetWriteContracts(isLight) {
+    GetWriteContracts() {
         const this$ = this;
-        const isLight_1 = defaultArg(isLight, true);
         const workbooks = new Map([]);
         const matchValue = this$.ISA;
         if (matchValue == null) {
-            addToDict(workbooks, "isa.investigation.xlsx", ["ISA_Investigation", toLightFsWorkbook(ArcInvestigation.create("MISSING_IDENTIFIER_"))]);
+            addToDict(workbooks, "isa.investigation.xlsx", ["ISA_Investigation", toFsWorkbook(ArcInvestigation.create("MISSING_IDENTIFIER_"))]);
         }
         else {
             const inv = matchValue;
-            addToDict(workbooks, "isa.investigation.xlsx", ["ISA_Investigation", (isLight_1 ? (toLightFsWorkbook) : (toFsWorkbook))(inv)]);
+            addToDict(workbooks, "isa.investigation.xlsx", ["ISA_Investigation", toFsWorkbook(inv)]);
             inv.StaticHash = (inv.GetLightHashCode() | 0);
             iterate((s) => {
                 s.StaticHash = (s.GetLightHashCode() | 0);
@@ -335,14 +334,13 @@ export class ARC {
             }
         }, this$._fs.Tree.ToFilePaths(true));
     }
-    GetUpdateContracts(isLight) {
+    GetUpdateContracts() {
         let inv, inv_1, inv_2;
         const this$ = this;
-        const isLight_1 = defaultArg(isLight, true);
         const matchValue = this$.ISA;
-        return (matchValue != null) ? (((inv = matchValue, inv.StaticHash === 0)) ? ((inv_1 = matchValue, this$.GetWriteContracts(isLight_1))) : ((inv_2 = matchValue, toArray(delay(() => {
+        return (matchValue != null) ? (((inv = matchValue, inv.StaticHash === 0)) ? ((inv_1 = matchValue, this$.GetWriteContracts())) : ((inv_2 = matchValue, toArray(delay(() => {
             const hash = inv_2.GetLightHashCode() | 0;
-            return append((inv_2.StaticHash !== hash) ? singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49(inv_2, isLight_1)) : empty(), delay(() => {
+            return append((inv_2.StaticHash !== hash) ? singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(inv_2)) : empty(), delay(() => {
                 inv_2.StaticHash = (hash | 0);
                 return append(collect((s) => {
                     const hash_1 = s.GetLightHashCode() | 0;
@@ -424,7 +422,7 @@ export class ARC {
                     }));
                 }, inv_2.Assays)));
             }));
-        }))))) : this$.GetWriteContracts(isLight_1);
+        }))))) : this$.GetWriteContracts();
     }
     GetGitInitContracts(branch, repositoryAddress, defaultGitignore) {
         const defaultGitignore_1 = defaultArg(defaultGitignore, false);

package/Contract/ArcAssay.js

@@ -42,7 +42,7 @@ export function ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49(this$, WithF
     const c = Contract.createCreate(path, "ISA_Assay", toFsWorkbook(this$));
     return toArray(delay(() => {
         let folderFS;
-        return append(withFolder ? ((folderFS = FileSystemTree.createAssayFolder(this$.Identifier), collect((p) => ((p !== path) ? singleton(Contract.createCreate(p, "PlainText")) : empty()), folderFS.ToFilePaths(false)))) : empty(), delay(() => singleton(c)));
+        return append(withFolder ? ((folderFS = FileSystemTree.createAssaysFolder([FileSystemTree.createAssayFolder(this$.Identifier)]), collect((p) => (((p !== path) && (p !== "assays/.gitkeep")) ? singleton(Contract.createCreate(p, "PlainText")) : empty()), folderFS.ToFilePaths(false)))) : empty(), delay(() => singleton(c)));
     }));
 }
 

package/Contract/ArcInvestigation.js

@@ -1,9 +1,8 @@
 import { combineMany } from "../FileSystem/Path.js";
 import { item, equalsWith } from "../fable_modules/fable-library-js.4.16.0/Array.js";
 import { defaultOf } from "../fable_modules/fable-library-js.4.16.0/Util.js";
-import { unwrap, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
-import { fromFsWorkbook, toFsWorkbook, toLightFsWorkbook } from "../Spreadsheet/ArcInvestigation.js";
 import { Contract } from "./Contract.js";
+import { fromFsWorkbook, toFsWorkbook } from "../Spreadsheet/ArcInvestigation.js";
 
 export function $007CInvestigationPath$007C_$007C(input) {
     let matchResult;
@@ -26,22 +25,20 @@ export function $007CInvestigationPath$007C_$007C(input) {
     }
 }
 
-export function ARCtrl_ArcInvestigation__ArcInvestigation_ToCreateContract_6FCE9E49(this$, isLight) {
-    const converter = defaultArg(isLight, true) ? (toLightFsWorkbook) : (toFsWorkbook);
-    return Contract.createCreate("isa.investigation.xlsx", "ISA_Investigation", converter(this$));
+export function ARCtrl_ArcInvestigation__ArcInvestigation_ToCreateContract(this$) {
+    return Contract.createCreate("isa.investigation.xlsx", "ISA_Investigation", toFsWorkbook(this$));
 }
 
-export function ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49(this$, isLight) {
-    const converter = defaultArg(isLight, true) ? (toLightFsWorkbook) : (toFsWorkbook);
-    return Contract.createUpdate("isa.investigation.xlsx", "ISA_Investigation", converter(this$));
+export function ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(this$) {
+    return Contract.createUpdate("isa.investigation.xlsx", "ISA_Investigation", toFsWorkbook(this$));
 }
 
-export function ARCtrl_ArcInvestigation__ArcInvestigation_toCreateContract_Static_23B73268(inv, isLight) {
-    return ARCtrl_ArcInvestigation__ArcInvestigation_ToCreateContract_6FCE9E49(inv, unwrap(isLight));
+export function ARCtrl_ArcInvestigation__ArcInvestigation_toCreateContract_Static_Z720BD3FF(inv) {
+    return ARCtrl_ArcInvestigation__ArcInvestigation_ToCreateContract(inv);
 }
 
-export function ARCtrl_ArcInvestigation__ArcInvestigation_toUpdateContract_Static_23B73268(inv, isLight) {
-    return ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49(inv, unwrap(isLight));
+export function ARCtrl_ArcInvestigation__ArcInvestigation_toUpdateContract_Static_Z720BD3FF(inv) {
+    return ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(inv);
 }
 
 export function ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F(c) {

package/Contract/ArcStudy.js

@@ -42,7 +42,7 @@ export function ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49(this$, WithF
     const c = Contract.createCreate(path, "ISA_Study", ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_353D0DB7(this$));
     return toArray(delay(() => {
         let folderFS;
-        return append(withFolder ? ((folderFS = FileSystemTree.createStudiesFolder([FileSystemTree.createStudyFolder(this$.Identifier)]), collect((p) => ((p !== path) ? singleton(Contract.createCreate(p, "PlainText")) : empty()), folderFS.ToFilePaths(false)))) : empty(), delay(() => singleton(c)));
+        return append(withFolder ? ((folderFS = FileSystemTree.createStudiesFolder([FileSystemTree.createStudyFolder(this$.Identifier)]), collect((p) => (((p !== path) && (p !== "studies/.gitkeep")) ? singleton(Contract.createCreate(p, "PlainText")) : empty()), folderFS.ToFilePaths(false)))) : empty(), delay(() => singleton(c)));
     }));
 }
 

package/Core/ArcTypes.js

@@ -1,5 +1,5 @@
 import { value as value_4, defaultArg, map, unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
-import { collect, append as append_3, tryFind, removeAt, iterateIndexed, iterate, tryFindIndex, exists, choose, item, map as map_1, delay, toList, fold, length, forAll, contains, filter, toArray } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { collect, append as append_3, tryFind, removeAt, iterate, tryFindIndex, exists, choose, item, map as map_1, delay, toList, fold, length, forAll, contains, filter, toArray } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { defaultOf, safeHash, equals, disposeSafe, getEnumerator, stringHash } from "../fable_modules/fable-library-js.4.16.0/Util.js";
 import { ResizeArray_choose, ResizeArray_filter, ResizeArray_map } from "./Helper/Collections.js";
 import { DataMap__Copy } from "./Table/DataMap.js";
@@ -1276,7 +1276,7 @@ export class ArcStudy extends ArcTables {
     }
     GetLightHashCode() {
         const this$ = this;
-        return boxHashArray([this$.Identifier, boxHashOption(this$.Title), boxHashOption(this$.Description), boxHashOption(this$.SubmissionDate), boxHashOption(this$.PublicReleaseDate), boxHashSeq(this$.Publications), boxHashSeq(this$.Contacts), boxHashSeq(this$.StudyDesignDescriptors), boxHashSeq(this$.Tables), boxHashSeq(this$.Comments)]) | 0;
+        return boxHashArray([this$.Identifier, boxHashOption(this$.Title), boxHashOption(this$.Description), boxHashOption(this$.SubmissionDate), boxHashOption(this$.PublicReleaseDate), boxHashSeq(this$.Publications), boxHashSeq(this$.Contacts), boxHashSeq(this$.StudyDesignDescriptors), boxHashSeq(this$.Tables), boxHashSeq(this$.RegisteredAssayIdentifiers), boxHashSeq(this$.Comments)]) | 0;
     }
 }
 
@@ -1324,125 +1324,125 @@ export class ArcInvestigation {
         const registeredStudyIdentifiers_1 = defaultArg(registeredStudyIdentifiers, []);
         const comments_1 = defaultArg(comments, []);
         const remarks_1 = defaultArg(remarks, []);
-        this["identifier@1118"] = identifier;
-        this["title@1119"] = title;
-        this["description@1120"] = description;
-        this["submissionDate@1121"] = submissionDate;
-        this["publicReleaseDate@1122"] = publicReleaseDate;
-        this["ontologySourceReferences@1123-1"] = ontologySourceReferences_1;
-        this["publications@1124-1"] = publications_1;
-        this["contacts@1125-1"] = contacts_1;
-        this["assays@1126-1"] = assays_1;
-        this["studies@1127-1"] = studies_1;
-        this["registeredStudyIdentifiers@1128-1"] = registeredStudyIdentifiers_1;
-        this["comments@1129-1"] = comments_1;
-        this["remarks@1130-1"] = remarks_1;
+        this["identifier@1119"] = identifier;
+        this["title@1120"] = title;
+        this["description@1121"] = description;
+        this["submissionDate@1122"] = submissionDate;
+        this["publicReleaseDate@1123"] = publicReleaseDate;
+        this["ontologySourceReferences@1124-1"] = ontologySourceReferences_1;
+        this["publications@1125-1"] = publications_1;
+        this["contacts@1126-1"] = contacts_1;
+        this["assays@1127-1"] = assays_1;
+        this["studies@1128-1"] = studies_1;
+        this["registeredStudyIdentifiers@1129-1"] = registeredStudyIdentifiers_1;
+        this["comments@1130-1"] = comments_1;
+        this["remarks@1131-1"] = remarks_1;
         this.staticHash = 0;
-        this["init@1099"] = 1;
+        this["init@1100"] = 1;
     }
     get Identifier() {
         const this$ = this;
-        return this$["identifier@1118"];
+        return this$["identifier@1119"];
     }
     set Identifier(i) {
         const this$ = this;
-        this$["identifier@1118"] = i;
+        this$["identifier@1119"] = i;
     }
     get Title() {
         const this$ = this;
-        return unwrap(this$["title@1119"]);
+        return unwrap(this$["title@1120"]);
     }
     set Title(n) {
         const this$ = this;
-        this$["title@1119"] = n;
+        this$["title@1120"] = n;
     }
     get Description() {
         const this$ = this;
-        return unwrap(this$["description@1120"]);
+        return unwrap(this$["description@1121"]);
     }
     set Description(n) {
         const this$ = this;
-        this$["description@1120"] = n;
+        this$["description@1121"] = n;
     }
     get SubmissionDate() {
         const this$ = this;
-        return unwrap(this$["submissionDate@1121"]);
+        return unwrap(this$["submissionDate@1122"]);
     }
     set SubmissionDate(n) {
         const this$ = this;
-        this$["submissionDate@1121"] = n;
+        this$["submissionDate@1122"] = n;
     }
     get PublicReleaseDate() {
         const this$ = this;
-        return unwrap(this$["publicReleaseDate@1122"]);
+        return unwrap(this$["publicReleaseDate@1123"]);
     }
     set PublicReleaseDate(n) {
         const this$ = this;
-        this$["publicReleaseDate@1122"] = n;
+        this$["publicReleaseDate@1123"] = n;
     }
     get OntologySourceReferences() {
         const this$ = this;
-        return this$["ontologySourceReferences@1123-1"];
+        return this$["ontologySourceReferences@1124-1"];
     }
     set OntologySourceReferences(n) {
         const this$ = this;
-        this$["ontologySourceReferences@1123-1"] = n;
+        this$["ontologySourceReferences@1124-1"] = n;
     }
     get Publications() {
         const this$ = this;
-        return this$["publications@1124-1"];
+        return this$["publications@1125-1"];
     }
     set Publications(n) {
         const this$ = this;
-        this$["publications@1124-1"] = n;
+        this$["publications@1125-1"] = n;
     }
     get Contacts() {
         const this$ = this;
-        return this$["contacts@1125-1"];
+        return this$["contacts@1126-1"];
     }
     set Contacts(n) {
         const this$ = this;
-        this$["contacts@1125-1"] = n;
+        this$["contacts@1126-1"] = n;
     }
     get Assays() {
         const this$ = this;
-        return this$["assays@1126-1"];
+        return this$["assays@1127-1"];
     }
     set Assays(n) {
         const this$ = this;
-        this$["assays@1126-1"] = n;
+        this$["assays@1127-1"] = n;
     }
     get Studies() {
         const this$ = this;
-        return this$["studies@1127-1"];
+        return this$["studies@1128-1"];
     }
     set Studies(n) {
         const this$ = this;
-        this$["studies@1127-1"] = n;
+        this$["studies@1128-1"] = n;
     }
     get RegisteredStudyIdentifiers() {
         const this$ = this;
-        return this$["registeredStudyIdentifiers@1128-1"];
+        return this$["registeredStudyIdentifiers@1129-1"];
     }
     set RegisteredStudyIdentifiers(n) {
         const this$ = this;
-        this$["registeredStudyIdentifiers@1128-1"] = n;
+        this$["registeredStudyIdentifiers@1129-1"] = n;
     }
     get Comments() {
         const this$ = this;
-        return this$["comments@1129-1"];
+        return this$["comments@1130-1"];
     }
     set Comments(n) {
         const this$ = this;
-        this$["comments@1129-1"] = n;
+        this$["comments@1130-1"] = n;
     }
     get Remarks() {
         const this$ = this;
-        return this$["remarks@1130-1"];
+        return this$["remarks@1131-1"];
     }
     set Remarks(n) {
         const this$ = this;
-        this$["remarks@1130-1"] = n;
+        this$["remarks@1131-1"] = n;
     }
     get StaticHash() {
         const this$ = this;
@@ -1584,11 +1584,11 @@ export class ArcInvestigation {
             }
         }, this$.Assays);
         iterate((s) => {
-            iterateIndexed((i, ai) => {
-                if (ai === oldIdentifier) {
-                    s.RegisteredAssayIdentifiers[i] = newIdentifier;
-                }
-            }, s.RegisteredAssayIdentifiers);
+            const index = tryFindIndex((ai) => (ai === oldIdentifier), s.RegisteredAssayIdentifiers);
+            if (index != null) {
+                const index_1 = index | 0;
+                s.RegisteredAssayIdentifiers[index_1] = newIdentifier;
+            }
         }, this$.Studies);
     }
     static renameAssay(oldIdentifier, newIdentifier) {
@@ -1839,11 +1839,11 @@ export class ArcInvestigation {
                 s.Identifier = newIdentifier;
             }
         }, this$.Studies);
-        iterateIndexed((i, si) => {
-            if (si === oldIdentifier) {
-                this$.RegisteredStudyIdentifiers[i] = newIdentifier;
-            }
-        }, this$.RegisteredStudyIdentifiers);
+        const index = tryFindIndex((si) => (si === oldIdentifier), this$.RegisteredStudyIdentifiers);
+        if (index != null) {
+            const index_1 = index | 0;
+            this$.RegisteredStudyIdentifiers[index_1] = newIdentifier;
+        }
     }
     static renameStudy(oldIdentifier, newIdentifier) {
         return (inv) => {
@@ -2249,7 +2249,7 @@ export class ArcInvestigation {
     }
     GetLightHashCode() {
         const this$ = this;
-        return boxHashArray([this$.Identifier, boxHashOption(this$.Title), boxHashOption(this$.Description), boxHashOption(this$.SubmissionDate), boxHashOption(this$.PublicReleaseDate), boxHashSeq(this$.Publications), boxHashSeq(this$.Contacts), boxHashSeq(this$.OntologySourceReferences), boxHashSeq(this$.Comments), boxHashSeq(this$.Remarks)]) | 0;
+        return boxHashArray([this$.Identifier, boxHashOption(this$.Title), boxHashOption(this$.Description), boxHashOption(this$.SubmissionDate), boxHashOption(this$.PublicReleaseDate), boxHashSeq(this$.Publications), boxHashSeq(this$.Contacts), boxHashSeq(this$.OntologySourceReferences), boxHashSeq(this$.RegisteredStudyIdentifiers), boxHashSeq(this$.Comments), boxHashSeq(this$.Remarks)]) | 0;
     }
 }
 

package/Core/Conversion.js

@@ -12,7 +12,7 @@ import { Factor } from "./Process/Factor.js";
 import { toString } from "../fable_modules/fable-library-js.4.16.0/Types.js";
 import { MaterialAttributeValue_create_BE8DE56 } from "./Process/MaterialAttributeValue.js";
 import { MaterialAttribute_create_A220A8A } from "./Process/MaterialAttribute.js";
-import { ProcessInput_getCharacteristicValues_5B3D5BA9, ProcessInput__isMaterial, ProcessInput__isData, ProcessInput_setCharacteristicValues, ProcessInput__get_Name, ProcessInput__isSource, ProcessInput__isSample, ProcessInput, ProcessInput_createRawData_Z721C83C5, ProcessInput_createMaterial_4452CB4C, ProcessInput_createSample_Z598187B7, ProcessInput_createSource_Z5E00540E } from "./Process/ProcessInput.js";
+import { ProcessInput_getCharacteristicValues_5B3D5BA9, ProcessInput__isMaterial, ProcessInput__isData, ProcessInput_setCharacteristicValues, ProcessInput__get_Name, ProcessInput__isSource, ProcessInput__isSample, ProcessInput, ProcessInput_createSource_Z5E00540E, ProcessInput_createRawData_Z721C83C5, ProcessInput_createMaterial_4452CB4C, ProcessInput_createSample_Z598187B7 } from "./Process/ProcessInput.js";
 import { ProcessOutput_getFactorValues_Z42C11600, ProcessOutput__isMaterial, ProcessOutput__isData, ProcessOutput_setFactorValues, ProcessOutput__get_Name, ProcessOutput__isSample, ProcessOutput, ProcessOutput_createRawData_Z721C83C5, ProcessOutput_createMaterial_4452CB4C, ProcessOutput_createSample_Z598187B7 } from "./Process/ProcessOutput.js";
 import { CompositeCell } from "./Table/CompositeCell.js";
 import { OntologyAnnotation } from "./OntologyAnnotation.js";
@@ -21,7 +21,7 @@ import { IOType, CompositeHeader } from "./Table/CompositeHeader.js";
 import { ActivePatterns_$007CRegex$007C_$007C } from "./Helper/Regex.js";
 import { ARCtrl_Process_Component__Component_TryGetColumnIndex, ARCtrl_Process_ProtocolParameter__ProtocolParameter_TryGetColumnIndex, tryGetFactorColumnIndex, tryGetCharacteristicColumnIndex, tryGetComponentIndex, tryGetParameterColumnIndex, ARCtrl_OntologyAnnotation__OntologyAnnotation_setColumnIndex_Static, ARCtrl_OntologyAnnotation__OntologyAnnotation_SetColumnIndex_Z524259A4 } from "./Process/ColumnIndex.js";
 import { getItemFromDict } from "../fable_modules/fable-library-js.4.16.0/MapUtil.js";
-import { initialize, zip, append as append_1, sortBy, head, tryPick as tryPick_1, collect, mapIndexed, item, length, map as map_2, empty, ofArray, isEmpty, singleton, choose as choose_1 } from "../fable_modules/fable-library-js.4.16.0/List.js";
+import { initialize, zip, append as append_1, sortBy, head, tryPick as tryPick_1, collect, mapIndexed, item, map as map_2, empty, length, ofArray, isEmpty, singleton, choose as choose_1 } from "../fable_modules/fable-library-js.4.16.0/List.js";
 import { Source_create_Z5CA08497 } from "./Process/Source.js";
 import { Sample_create_62424AD2 } from "./Process/Sample.js";
 import { Process_create_Z7C1F7FA9, Process_decomposeName_Z721C83C5, Process_make, Process_composeName } from "./Process/Process.js";
@@ -171,47 +171,30 @@ export function JsonTypes_composeCharacteristicValue(header, value) {
     return MaterialAttributeValue_create_BE8DE56(void 0, MaterialAttribute_create_A220A8A(void 0, header.ToTerm()), unwrap(patternInput[0]), unwrap(patternInput[1]));
 }
 
+export function JsonTypes_composeFreetextMaterialName(headerFT, name) {
+    return `${headerFT}=${name}`;
+}
+
 /**
  * Convert a CompositeHeader and Cell tuple to a ISA ProcessInput
  */
 export function JsonTypes_composeProcessInput(header, value) {
-    let matchResult;
     if (header.tag === 11) {
         switch (header.fields[0].tag) {
-            case 0: {
-                matchResult = 0;
-                break;
-            }
-            case 1: {
-                matchResult = 1;
-                break;
-            }
-            case 3: {
-                matchResult = 2;
-                break;
-            }
-            case 2: {
-                matchResult = 3;
-                break;
-            }
+            case 1:
+                return ProcessInput_createSample_Z598187B7(toString(value));
+            case 3:
+                return ProcessInput_createMaterial_4452CB4C(toString(value));
+            case 2:
+                return ProcessInput_createRawData_Z721C83C5(toString(value));
+            case 4:
+                return ProcessInput_createMaterial_4452CB4C(JsonTypes_composeFreetextMaterialName(header.fields[0].fields[0], toString(value)));
             default:
-                matchResult = 4;
+                return ProcessInput_createSource_Z5E00540E(toString(value));
         }
     }
     else {
-        matchResult = 4;
-    }
-    switch (matchResult) {
-        case 0:
-            return ProcessInput_createSource_Z5E00540E(toString(value));
-        case 1:
-            return ProcessInput_createSample_Z598187B7(toString(value));
-        case 2:
-            return ProcessInput_createMaterial_4452CB4C(toString(value));
-        case 3:
-            return ProcessInput_createRawData_Z721C83C5(toString(value));
-        default:
-            return toFail(printf("Could not parse input header %O"))(header);
+        return toFail(printf("Could not parse input header %O"))(header);
     }
 }
 
@@ -219,13 +202,9 @@ export function JsonTypes_composeProcessInput(header, value) {
  * Convert a CompositeHeader and Cell tuple to a ISA ProcessOutput
  */
 export function JsonTypes_composeProcessOutput(header, value) {
-    let matchResult;
+    let matchResult, ft;
     if (header.tag === 12) {
         switch (header.fields[0].tag) {
-            case 1: {
-                matchResult = 0;
-                break;
-            }
             case 3: {
                 matchResult = 1;
                 break;
@@ -234,12 +213,17 @@ export function JsonTypes_composeProcessOutput(header, value) {
                 matchResult = 2;
                 break;
             }
-            default:
+            case 4: {
                 matchResult = 3;
+                ft = header.fields[0].fields[0];
+                break;
+            }
+            default:
+                matchResult = 0;
         }
     }
     else {
-        matchResult = 3;
+        matchResult = 4;
     }
     switch (matchResult) {
         case 0:
@@ -248,6 +232,8 @@ export function JsonTypes_composeProcessOutput(header, value) {
             return ProcessOutput_createMaterial_4452CB4C(toString(value));
         case 2:
             return ProcessOutput_createRawData_Z721C83C5(toString(value));
+        case 3:
+            return ProcessOutput_createMaterial_4452CB4C(JsonTypes_composeFreetextMaterialName(ft, toString(value)));
         default:
             return toFail(printf("Could not parse output header %O"))(header);
     }
@@ -641,7 +627,7 @@ export function ProcessParsing_getProcessGetter(processNameRoot, headers) {
         inputGetter_1 = ((matrix) => ((i) => {
             const chars = toList(map_1((f) => f(matrix)(i), charGetters));
             const input = inputGetter(matrix)(i);
-            return (!(ProcessInput__isSample(input) ? true : ProcessInput__isSource(input)) && !isEmpty(chars)) ? ofArray([input, ProcessInput_createSample_Z598187B7(ProcessInput__get_Name(input), chars)]) : singleton(ProcessInput_setCharacteristicValues(chars, input));
+            return (!(ProcessInput__isSample(input) ? true : ProcessInput__isSource(input)) && !isEmpty(chars)) ? ofArray([input, ProcessInput_createSample_Z598187B7(ProcessInput__get_Name(input), chars)]) : singleton((length(chars) > 0) ? ProcessInput_setCharacteristicValues(chars, input) : input);
         }));
     }
     let outputGetter_1;
@@ -654,7 +640,7 @@ export function ProcessParsing_getProcessGetter(processNameRoot, headers) {
         outputGetter_1 = ((matrix_2) => ((i_2) => {
             const factors = toList(map_1((f_2) => f_2(matrix_2)(i_2), factorValueGetters));
             const output = outputGetter(matrix_2)(i_2);
-            return (!ProcessOutput__isSample(output) && !isEmpty(factors)) ? ofArray([output, ProcessOutput_createSample_Z598187B7(ProcessOutput__get_Name(output), void 0, factors)]) : singleton(ProcessOutput_setFactorValues(factors, output));
+            return (!ProcessOutput__isSample(output) && !isEmpty(factors)) ? ofArray([output, ProcessOutput_createSample_Z598187B7(ProcessOutput__get_Name(output), void 0, factors)]) : singleton((length(factors) > 0) ? ProcessOutput_setFactorValues(factors, output) : output);
         }));
     }
     return (matrix_4) => ((i_4) => {

package/Spreadsheet/AnnotationTable/ArcTable.js

@@ -1,15 +1,17 @@
-import { iterateIndexed, length, sortBy, collect, toArray, exists, ofArray, empty, tail, head, isEmpty, cons, singleton, fold, map, reverse } from "../../fable_modules/fable-library-js.4.16.0/List.js";
-import { map as map_1, toList, tryFind } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
-import { toFsColumns, fixDeprecatedIOHeader, fromFsColumns } from "./CompositeColumn.js";
+import { iterateIndexed, length, sortBy, collect as collect_1, exists, toArray, ofArray, empty, tail, head, isEmpty, cons, singleton, fold, map, reverse } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { item, map as map_1 } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
+import { singleton as singleton_1, collect, map as map_2, delay, toArray as toArray_1, tryFind } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { toStringCellColumns, fixDeprecatedIOHeader, fromStringCellColumns } from "./CompositeColumn.js";
 import { printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { Dictionary_tryGet, FsCellsCollection__TryGetCell_Z37302880 } from "../../fable_modules/FsSpreadsheet.6.2.0/Cells/FsCellsCollection.fs.js";
+import { rangeDouble } from "../../fable_modules/fable-library-js.4.16.0/Range.js";
+import { FsAddress_$ctor_Z37302880, FsAddress__get_ColumnNumber, FsAddress__get_RowNumber } from "../../fable_modules/FsSpreadsheet.6.2.0/FsAddress.fs.js";
+import { FsRangeAddress_$ctor_7E77A4A0, FsRangeAddress__get_LastAddress } from "../../fable_modules/FsSpreadsheet.6.2.0/Ranges/FsRangeAddress.fs.js";
+import { FsRangeBase__Cell_Z3407A44B, FsRangeBase__get_RangeAddress } from "../../fable_modules/FsSpreadsheet.6.2.0/Ranges/FsRangeBase.fs.js";
 import { ArcTable } from "../../Core/Table/ArcTable.js";
-import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.6.1.2/FsWorksheet.fs.js";
+import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.6.2.0/FsWorksheet.fs.js";
 import { comparePrimitives } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
-import { FsRangeAddress_$ctor_7E77A4A0 } from "../../fable_modules/FsSpreadsheet.6.1.2/Ranges/FsRangeAddress.fs.js";
-import { FsAddress_$ctor_Z37302880 } from "../../fable_modules/FsSpreadsheet.6.1.2/FsAddress.fs.js";
-import { Dictionary_tryGet } from "../../fable_modules/FsSpreadsheet.6.1.2/Cells/FsCellsCollection.fs.js";
 import { addToDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
-import { FsRangeBase__Cell_Z3407A44B } from "../../fable_modules/FsSpreadsheet.6.1.2/Ranges/FsRangeBase.fs.js";
 
 /**
  * Iterates over elements of the input list and groups adjacent elements.
@@ -64,11 +66,11 @@ export function classifyColumnOrder(column) {
 
 export const helperColumnStrings = ofArray(["Term Source REF", "Term Accession Number", "Unit", "Data Format", "Data Selector Format"]);
 
-export function groupColumnsByHeader(columns) {
-    return Aux_List_groupWhen((c) => {
-        const v = c.Item(1).ValueAsString();
+export function groupColumnsByHeader(stringCellColumns) {
+    return map_1(toArray, toArray(Aux_List_groupWhen((c) => {
+        const v = item(0, c);
         return !exists((s) => (v.indexOf(s) === 0), helperColumnStrings);
-    }, columns);
+    }, ofArray(stringCellColumns))));
 }
 
 /**
@@ -81,8 +83,8 @@ export function tryAnnotationTable(sheet) {
 /**
  * Groups and parses a collection of single columns into the according ISA composite columns
  */
-export function composeColumns(columns) {
-    return toArray(map(fromFsColumns, groupColumnsByHeader(toList(columns))));
+export function composeColumns(stringCellColumns) {
+    return map_1(fromStringCellColumns, groupColumnsByHeader(stringCellColumns));
 }
 
 /**
@@ -96,7 +98,16 @@ export function tryFromFsWorksheet(sheet) {
         }
         else {
             const t = matchValue;
-            const compositeColumns = composeColumns(map_1(fixDeprecatedIOHeader, t.GetColumns(sheet.CellCollection)));
+            const compositeColumns = composeColumns(map_1(fixDeprecatedIOHeader, toArray_1(delay(() => map_2((c) => toArray_1(delay(() => collect((r) => {
+                const matchValue_1 = FsCellsCollection__TryGetCell_Z37302880(sheet.CellCollection, r, c);
+                if (matchValue_1 == null) {
+                    return singleton_1("");
+                }
+                else {
+                    const cell = matchValue_1;
+                    return singleton_1(cell.ValueAsString());
+                }
+            }, rangeDouble(1, 1, FsAddress__get_RowNumber(FsRangeAddress__get_LastAddress(FsRangeBase__get_RangeAddress(t))))))), rangeDouble(1, 1, FsAddress__get_ColumnNumber(FsRangeAddress__get_LastAddress(FsRangeBase__get_RangeAddress(t)))))))));
             return ArcTable.addColumns(compositeColumns, void 0, true)(ArcTable.init(sheet.Name));
         }
     }
@@ -114,30 +125,29 @@ export function toFsWorksheet(table) {
         return ws;
     }
     else {
-        const columns = collect(toFsColumns, sortBy(classifyColumnOrder, ofArray(table.Columns), {
+        const columns = collect_1(toStringCellColumns, sortBy(classifyColumnOrder, ofArray(table.Columns), {
             Compare: comparePrimitives,
         }));
         const maxRow = length(head(columns)) | 0;
         const maxCol = length(columns) | 0;
         const fsTable = ws.Table("annotationTable", FsRangeAddress_$ctor_7E77A4A0(FsAddress_$ctor_Z37302880(1, 1), FsAddress_$ctor_Z37302880(maxRow, maxCol)));
         iterateIndexed((colI, col) => {
-            iterateIndexed((rowI, cell) => {
+            iterateIndexed((rowI, stringCell) => {
                 let value;
-                const v = cell.ValueAsString();
                 if (rowI === 0) {
-                    const matchValue = Dictionary_tryGet(v, stringCount);
+                    const matchValue = Dictionary_tryGet(stringCell, stringCount);
                     if (matchValue == null) {
-                        addToDict(stringCount, cell.ValueAsString(), "");
-                        value = v;
+                        addToDict(stringCount, stringCell, "");
+                        value = stringCell;
                     }
                     else {
                         const spaces = matchValue;
-                        stringCount.set(v, spaces + " ");
-                        value = ((v + " ") + spaces);
+                        stringCount.set(stringCell, spaces + " ");
+                        value = ((stringCell + " ") + spaces);
                     }
                 }
                 else {
-                    value = v;
+                    value = stringCell;
                 }
                 const address = FsAddress_$ctor_Z37302880(rowI + 1, colI + 1);
                 FsRangeBase__Cell_Z3407A44B(fsTable, address, ws.CellCollection).SetValueAs(value);