@nfdi4plants/arctrl 1.0.0-beta.4 → 1.0.0-beta.6

package/ISA/ISA/ArcTypes/ArcTableAux.js

@@ -1,23 +1,23 @@
-import { getItemFromDict, addToDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
-import { map as map_1, defaultArg, unwrap, value as value_9, some } from "../../../fable_modules/fable-library.4.4.1/Option.js";
-import { empty as empty_2, singleton as singleton_1, append, delay, map, tryPick, toList, indexed, initialize, filter, tryFindIndex, maxBy } from "../../../fable_modules/fable-library.4.4.1/Seq.js";
-import { arrayHash, equalArrays, stringHash, int32ToString, compareArrays, disposeSafe, getEnumerator, compare, equals, comparePrimitives } from "../../../fable_modules/fable-library.4.4.1/Util.js";
-import { pick, exists, zip, append as append_1, sortBy, tryPick as tryPick_1, collect, mapIndexed, item, length, map as map_2, ofArray, singleton, choose, ofSeq, empty as empty_1, head, tail as tail_1, isEmpty, cons } from "../../../fable_modules/fable-library.4.4.1/List.js";
+import { getItemFromDict, addToDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
+import { map as map_1, defaultArg, unwrap, value as value_9, some } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { empty as empty_2, singleton as singleton_1, append, delay, map, tryPick, toList, indexed, initialize, filter, tryFindIndex, maxBy } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { arrayHash, equalArrays, stringHash, int32ToString, compareArrays, disposeSafe, getEnumerator, compare, equals, comparePrimitives } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { pick, exists, zip, append as append_1, sortBy, tryPick as tryPick_1, collect, mapIndexed, item, length, map as map_2, ofArray, singleton, choose, ofSeq, empty as empty_1, head, tail as tail_1, isEmpty, cons } from "../../../fable_modules/fable-library.4.5.0/List.js";
 import { CompositeCell } from "./CompositeCell.js";
-import { max } from "../../../fable_modules/fable-library.4.4.1/Double.js";
-import { iterateIndexed } from "../../../fable_modules/fable-library.4.4.1/Array.js";
-import { FSharpSet__get_MinimumElement, FSharpSet__get_IsEmpty, difference, ofSeq as ofSeq_1 } from "../../../fable_modules/fable-library.4.4.1/Set.js";
+import { max } from "../../../fable_modules/fable-library.4.5.0/Double.js";
+import { iterateIndexed } from "../../../fable_modules/fable-library.4.5.0/Array.js";
+import { FSharpSet__get_MinimumElement, FSharpSet__get_IsEmpty, difference, ofSeq as ofSeq_1 } from "../../../fable_modules/fable-library.4.5.0/Set.js";
 import { Value_fromString_Z721C83C5, Value as Value_1 } from "../JsonTypes/Value.js";
 import { Component_fromOptions } from "../JsonTypes/Component.js";
 import { ProcessParameterValue_create_569825F3 } from "../JsonTypes/ProcessParameterValue.js";
 import { ProtocolParameter_create_Z6C54B221 } from "../JsonTypes/ProtocolParameter.js";
 import { FactorValue_create_18335379 } from "../JsonTypes/FactorValue.js";
 import { Factor } from "../JsonTypes/Factor.js";
-import { toString } from "../../../fable_modules/fable-library.4.4.1/Types.js";
+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 { remove, printf, toFail } from "../../../fable_modules/fable-library.4.4.1/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";
@@ -26,9 +26,9 @@ import { Sample_create_E50ED22 } from "../JsonTypes/Sample.js";
 import { Process_create_Z42860F3E, Process_decomposeName_Z721C83C5, Process_make, Process_composeName } from "../JsonTypes/Process.js";
 import { List_tryPickAndRemove, Option_fromValueWithDefault } from "../Helper.js";
 import { Protocol_make } from "../JsonTypes/Protocol.js";
-import { List_groupBy } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
+import { List_groupBy } from "../../../fable_modules/fable-library.4.5.0/Seq2.js";
 import { createMissingIdentifier } from "../Identifier.js";
-import { Dictionary } from "../../../fable_modules/fable-library.4.4.1/MutableMap.js";
+import { Dictionary } from "../../../fable_modules/fable-library.4.5.0/MutableMap.js";
 
 /**
  * Returns the dictionary with the binding added to the given dictionary.

package/ISA/ISA/ArcTypes/ArcTables.js

@@ -1,17 +1,17 @@
-import { append, toArray, reduce, choose, map as map_1, delay, toList, length, findIndex, tryFindIndex } from "../../../fable_modules/fable-library.4.4.1/Seq.js";
+import { append, toArray, reduce, choose, map as map_1, delay, toList, length, findIndex, tryFindIndex } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
 import { Dict_tryFind } from "../Helper.js";
-import { addToSet, addToDict } from "../../../fable_modules/fable-library.4.4.1/MapUtil.js";
-import { toIterator, equals, comparePrimitives, stringHash, compare, disposeSafe, getEnumerator } from "../../../fable_modules/fable-library.4.4.1/Util.js";
-import { bind, map as map_3, unwrap, defaultArg, value as value_2 } from "../../../fable_modules/fable-library.4.4.1/Option.js";
-import { collect as collect_1, map as map_4, insertRangeInPlace, fold } from "../../../fable_modules/fable-library.4.4.1/Array.js";
+import { addToSet, addToDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
+import { toIterator, equals, comparePrimitives, stringHash, compare, disposeSafe, getEnumerator } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { bind, map as map_3, unwrap, defaultArg, value as value_2 } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { collect as collect_1, map as map_4, insertRangeInPlace, fold } from "../../../fable_modules/fable-library.4.5.0/Array.js";
 import { CompositeHeader } from "./CompositeHeader.js";
-import { Array_groupBy, distinct } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
-import { FSharpSet__get_IsEmpty, ofSeq, intersect } from "../../../fable_modules/fable-library.4.4.1/Set.js";
+import { Array_groupBy, distinct } from "../../../fable_modules/fable-library.4.5.0/Seq2.js";
+import { FSharpSet__get_IsEmpty, ofSeq, intersect } from "../../../fable_modules/fable-library.4.5.0/Set.js";
 import { ArcTable } from "./ArcTable.js";
-import { map as map_2, collect } from "../../../fable_modules/fable-library.4.4.1/List.js";
+import { map as map_2, collect } from "../../../fable_modules/fable-library.4.5.0/List.js";
 import { Unchecked_fillMissingCells, ProcessParsing_groupProcesses, ProcessParsing_processToRows, ProcessParsing_alignByHeaders } from "./ArcTableAux.js";
-import { tryFind, ofSeq as ofSeq_1 } from "../../../fable_modules/fable-library.4.4.1/Map.js";
-import { class_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.js";
+import { tryFind, ofSeq as ofSeq_1 } from "../../../fable_modules/fable-library.4.5.0/Map.js";
+import { class_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
 
 /**
  * If a table with the given name exists in the TableList, returns it, else returns None.
@@ -60,7 +60,7 @@ export function ArcTablesAux_getIOMap(tables) {
             }
             else {
                 const ic = matchValue_1;
-                const ioType_1 = value_2(ic.Header.tryInput());
+                const ioType_1 = value_2(ic.Header.TryInput());
                 ic.Cells.forEach((c) => {
                     includeInMap(c.ToFreeTextCell().AsFreeText, ioType_1);
                 });
@@ -70,7 +70,7 @@ export function ArcTablesAux_getIOMap(tables) {
             }
             else {
                 const oc = matchValue_2;
-                const ioType_2 = value_2(oc.Header.tryOutput());
+                const ioType_2 = value_2(oc.Header.TryOutput());
                 oc.Cells.forEach((c_1) => {
                     includeInMap(c_1.ToFreeTextCell().AsFreeText, ioType_2);
                 });
@@ -103,7 +103,7 @@ export function ArcTablesAux_applyIOMap(map, tables) {
                         const newIO = matchValue_1;
                         return io.Merge(newIO);
                     }
-                }, value_2(ic.Header.tryInput()), ic.Cells);
+                }, value_2(ic.Header.TryInput()), ic.Cells);
                 table.UpdateHeader(index, new CompositeHeader(11, [newIOType]));
             }
             const matchValue_2 = table.TryGetOutputColumn();
@@ -121,7 +121,7 @@ export function ArcTablesAux_applyIOMap(map, tables) {
                         const newIO_1 = matchValue_3;
                         return io_1.Merge(newIO_1);
                     }
-                }, value_2(oc.Header.tryOutput()), oc.Cells);
+                }, value_2(oc.Header.TryOutput()), oc.Cells);
                 table.UpdateHeader(index_1, new CompositeHeader(12, [newIOType_1]));
             }
         }
@@ -210,6 +210,10 @@ export class ArcTables {
         const __ = this;
         __["Tables@"] = v;
     }
+    get_Item(index) {
+        const this$ = this;
+        return this$.Tables[index];
+    }
     get TableNames() {
         const this$ = this;
         return toList(delay(() => map_1((s) => s.Name, this$.Tables)));
@@ -412,6 +416,12 @@ export class ArcTables {
     static ofSeq(tables) {
         return new ArcTables(Array.from(tables));
     }
+    MoveTable(oldIndex, newIndex) {
+        const this$ = this;
+        const table = this$.GetTableAt(oldIndex);
+        this$.Tables.splice(oldIndex, 1);
+        this$.Tables.splice(newIndex, 0, table);
+    }
     static fromProcesses(ps) {
         let collection;
         return new ArcTables((collection = map_2((tupledArg) => {

package/ISA/ISA/ArcTypes/ArcTypes.js

@@ -1,26 +1,26 @@
-import { map as map_1, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.4.1/Option.js";
-import { concat, collect, append as append_4, tryFind, removeAt, tryFindIndex, item as item_1, map as map_2, delay, toList, fold, length, forAll, contains, filter, toArray } from "../../../fable_modules/fable-library.4.4.1/Seq.js";
-import { defaultOf, safeHash, equals, disposeSafe, getEnumerator, stringHash } from "../../../fable_modules/fable-library.4.4.1/Util.js";
-import { addRangeInPlace, tryFind as tryFind_1, removeInPlace, equalsWith, append as append_3, contains as contains_1, map } from "../../../fable_modules/fable-library.4.4.1/Array.js";
-import { distinctBy, Array_distinct } from "../../../fable_modules/fable-library.4.4.1/Seq2.js";
-import { printf, toText } from "../../../fable_modules/fable-library.4.4.1/String.js";
-import { create, match } from "../../../fable_modules/fable-library.4.4.1/RegExp.js";
+import { map as map_1, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { concat, collect, append as append_4, tryFind, removeAt, tryFindIndex, choose, item, map as map_2, delay, toList, fold, length, forAll, contains, filter, toArray } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { defaultOf, safeHash, equals, disposeSafe, getEnumerator, stringHash } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { addRangeInPlace, tryFind as tryFind_1, removeInPlace, equalsWith, append as append_3, contains as contains_1, map } from "../../../fable_modules/fable-library.4.5.0/Array.js";
+import { distinctBy, Array_distinct } from "../../../fable_modules/fable-library.4.5.0/Seq2.js";
+import { printf, toText } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { create, match } from "../../../fable_modules/fable-library.4.5.0/RegExp.js";
 import { OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
 import { Value_fromString_Z721C83C5, Value__get_Text } from "../JsonTypes/Value.js";
 import { AnnotationValue } from "../JsonTypes/AnnotationValue.js";
 import { ArcTablesAux_applyIOMap, ArcTablesAux_getIOMap, ArcTables_$reflection, ArcTables } from "./ArcTables.js";
 import { AssayMaterials_get_empty, AssayMaterials_create_Z253F0553 } from "../JsonTypes/AssayMaterials.js";
-import { HashCodes_boxHashOption, HashCodes_boxHashArray, Option_fromValueWithDefault } from "../Helper.js";
-import { unzip, ofSeq, map as map_3, toArray as toArray_1, ofArray, empty } from "../../../fable_modules/fable-library.4.4.1/List.js";
+import { ResizeArray_map, HashCodes_boxHashOption, HashCodes_boxHashArray, Option_fromValueWithDefault } from "../Helper.js";
+import { unzip, ofSeq, map as map_3, toArray as toArray_1, ofArray, empty } from "../../../fable_modules/fable-library.4.5.0/List.js";
 import { getSources, getProtocols, getUnits, getCharacteristics, getData, getMaterials, getSamples } from "../JsonTypes/ProcessSequence.js";
 import { Assay_create_3D372A24 } from "../JsonTypes/Assay.js";
 import { Study_identifierFromFileName, Study_fileNameFromIdentifier, Assay_identifierFromFileName, createMissingIdentifier, Assay_fileNameFromIdentifier, isMissingIdentifier } from "../Identifier.js";
-import { rangeDouble } from "../../../fable_modules/fable-library.4.4.1/Range.js";
-import { class_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.js";
+import { rangeDouble } from "../../../fable_modules/fable-library.4.5.0/Range.js";
+import { class_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
 import { StudyMaterials_get_empty, StudyMaterials_create_1BE9FA55 } from "../JsonTypes/StudyMaterials.js";
 import { Study_create_Z2D28E954 } from "../JsonTypes/Study.js";
 import { Investigation_create_4AD66BBE } from "../JsonTypes/Investigation.js";
-import { FSharpRef } from "../../../fable_modules/fable-library.4.4.1/Types.js";
+import { FSharpRef } from "../../../fable_modules/fable-library.4.5.0/Types.js";
 
 export class ArcAssay extends ArcTables {
     constructor(identifier, measurementType, technologyType, technologyPlatform, tables, performers, comments) {
@@ -510,21 +510,21 @@ export class ArcAssay extends ArcTables {
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_1) => equals(item_1(i_1, a), item_1(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Performers, (b_1 = other.Performers, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
+        }, true, toList(delay(() => map_2((i_1) => equals(item(i_1, a), item(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Performers, (b_1 = other.Performers, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
             if (acc_1) {
                 return e_1;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_2) => equals(item_1(i_2, a_1), item_1(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.Comments, (b_2 = other.Comments, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
+        }, true, toList(delay(() => map_2((i_2) => equals(item(i_2, a_1), item(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.Comments, (b_2 = other.Comments, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
             if (acc_2) {
                 return e_2;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_3) => equals(item_1(i_3, a_2), item_1(i_3, b_2)), rangeDouble(0, 1, length(a_2) - 1)))))))]);
+        }, true, toList(delay(() => map_2((i_3) => equals(item(i_3, a_2), item(i_3, b_2)), rangeDouble(0, 1, length(a_2) - 1)))))))]);
     }
     ReferenceEquals(other) {
         const this$ = this;
@@ -697,23 +697,8 @@ export class ArcStudy extends ArcTables {
         else {
             throw new Error("Cannot execute this function. Object is not part of ArcInvestigation.");
         }
-        const assays = [];
-        let enumerator = getEnumerator(inv.Assays);
-        try {
-            while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
-                const assay = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
-                if (contains(assay.Identifier, this$.RegisteredAssayIdentifiers, {
-                    Equals: (x, y) => (x === y),
-                    GetHashCode: stringHash,
-                })) {
-                    void (assays.push(assay));
-                }
-            }
-        }
-        finally {
-            disposeSafe(enumerator);
-        }
-        return assays;
+        const collection = choose((assayIdentifier) => inv.TryGetAssay(assayIdentifier), this$.RegisteredAssayIdentifiers);
+        return Array.from(collection);
     }
     AddRegisteredAssay(assay) {
         const this$ = this;
@@ -812,12 +797,19 @@ export class ArcStudy extends ArcTables {
         const this$ = this;
         const matchValue = this$.Investigation;
         if (matchValue == null) {
-            const collection = map_2((identifier) => ArcAssay.init(identifier), this$.RegisteredAssayIdentifiers);
-            return Array.from(collection);
+            return ResizeArray_map((identifier_1) => ArcAssay.init(identifier_1), this$.RegisteredAssayIdentifiers);
         }
         else {
             const i = matchValue;
-            return this$.RegisteredAssays;
+            return ResizeArray_map((identifier) => {
+                const matchValue_1 = i.TryGetAssay(identifier);
+                if (matchValue_1 == null) {
+                    return ArcAssay.init(identifier);
+                }
+                else {
+                    return matchValue_1;
+                }
+            }, this$.RegisteredAssayIdentifiers);
         }
     }
     static getRegisteredAssaysOrIdentifier() {
@@ -1154,49 +1146,49 @@ export class ArcStudy extends ArcTables {
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_1) => equals(item_1(i_1, a), item_1(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Contacts, (b_1 = other.Contacts, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
+        }, true, toList(delay(() => map_2((i_1) => equals(item(i_1, a), item(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Contacts, (b_1 = other.Contacts, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
             if (acc_1) {
                 return e_1;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_2) => equals(item_1(i_2, a_1), item_1(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.StudyDesignDescriptors, (b_2 = other.StudyDesignDescriptors, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
+        }, true, toList(delay(() => map_2((i_2) => equals(item(i_2, a_1), item(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.StudyDesignDescriptors, (b_2 = other.StudyDesignDescriptors, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
             if (acc_2) {
                 return e_2;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_3) => equals(item_1(i_3, a_2), item_1(i_3, b_2)), rangeDouble(0, 1, length(a_2) - 1))))))), (a_3 = this$.Tables, (b_3 = other.Tables, (length(a_3) === length(b_3)) && fold((acc_3, e_3) => {
+        }, true, toList(delay(() => map_2((i_3) => equals(item(i_3, a_2), item(i_3, b_2)), rangeDouble(0, 1, length(a_2) - 1))))))), (a_3 = this$.Tables, (b_3 = other.Tables, (length(a_3) === length(b_3)) && fold((acc_3, e_3) => {
             if (acc_3) {
                 return e_3;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_4) => equals(item_1(i_4, a_3), item_1(i_4, b_3)), rangeDouble(0, 1, length(a_3) - 1))))))), (a_4 = this$.RegisteredAssayIdentifiers, (b_4 = other.RegisteredAssayIdentifiers, (length(a_4) === length(b_4)) && fold((acc_4, e_4) => {
+        }, true, toList(delay(() => map_2((i_4) => equals(item(i_4, a_3), item(i_4, b_3)), rangeDouble(0, 1, length(a_3) - 1))))))), (a_4 = this$.RegisteredAssayIdentifiers, (b_4 = other.RegisteredAssayIdentifiers, (length(a_4) === length(b_4)) && fold((acc_4, e_4) => {
             if (acc_4) {
                 return e_4;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_5) => (item_1(i_5, a_4) === item_1(i_5, b_4)), rangeDouble(0, 1, length(a_4) - 1))))))), (a_5 = this$.Factors, (b_5 = other.Factors, (length(a_5) === length(b_5)) && fold((acc_5, e_5) => {
+        }, true, toList(delay(() => map_2((i_5) => (item(i_5, a_4) === item(i_5, b_4)), rangeDouble(0, 1, length(a_4) - 1))))))), (a_5 = this$.Factors, (b_5 = other.Factors, (length(a_5) === length(b_5)) && fold((acc_5, e_5) => {
             if (acc_5) {
                 return e_5;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_6) => equals(item_1(i_6, a_5), item_1(i_6, b_5)), rangeDouble(0, 1, length(a_5) - 1))))))), (a_6 = this$.Comments, (b_6 = other.Comments, (length(a_6) === length(b_6)) && fold((acc_6, e_6) => {
+        }, true, toList(delay(() => map_2((i_6) => equals(item(i_6, a_5), item(i_6, b_5)), rangeDouble(0, 1, length(a_5) - 1))))))), (a_6 = this$.Comments, (b_6 = other.Comments, (length(a_6) === length(b_6)) && fold((acc_6, e_6) => {
             if (acc_6) {
                 return e_6;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_7) => equals(item_1(i_7, a_6), item_1(i_7, b_6)), rangeDouble(0, 1, length(a_6) - 1)))))))]);
+        }, true, toList(delay(() => map_2((i_7) => equals(item(i_7, a_6), item(i_7, b_6)), rangeDouble(0, 1, length(a_6) - 1)))))))]);
     }
     ReferenceEquals(other) {
         const this$ = this;
@@ -1257,7 +1249,7 @@ export class ArcInvestigation {
         const registeredStudyIdentifiers_1 = defaultArg(registeredStudyIdentifiers, []);
         const comments_1 = defaultArg(comments, []);
         const remarks_1 = defaultArg(remarks, []);
-        this["identifier@1144"] = identifier;
+        this["identifier@1148"] = identifier;
         this["Title@"] = title;
         this["Description@"] = description;
         this["SubmissionDate@"] = submissionDate;
@@ -1270,15 +1262,15 @@ export class ArcInvestigation {
         this["RegisteredStudyIdentifiers@"] = registeredStudyIdentifiers_1;
         this["Comments@"] = comments_1;
         this["Remarks@"] = remarks_1;
-        this["init@1125"] = 1;
+        this["init@1129"] = 1;
     }
     get Identifier() {
         const this$ = this;
-        return this$["identifier@1144"];
+        return this$["identifier@1148"];
     }
     set Identifier(i) {
         const this$ = this;
-        this$["identifier@1144"] = i;
+        this$["identifier@1148"] = i;
     }
     get Title() {
         const __ = this;
@@ -1427,10 +1419,43 @@ export class ArcInvestigation {
             return newInvestigation.InitAssay(assayIdentifier);
         };
     }
+    DeleteAssayAt(index) {
+        const this$ = this;
+        this$.Assays.splice(index, 1);
+    }
+    static deleteAssayAt(index) {
+        return (inv) => {
+            const newInvestigation = inv.Copy();
+            newInvestigation.DeleteAssayAt(index);
+            return newInvestigation;
+        };
+    }
+    DeleteAssay(assayIdentifier) {
+        const this$ = this;
+        const index = this$.GetAssayIndex(assayIdentifier) | 0;
+        this$.DeleteAssayAt(index);
+    }
+    static deleteAssay(assayIdentifier) {
+        return (inv) => {
+            const newInv = inv.Copy();
+            newInv.DeleteAssay(assayIdentifier);
+            return newInv;
+        };
+    }
     RemoveAssayAt(index) {
         const this$ = this;
+        const ident = this$.GetAssayAt(index).Identifier;
         this$.Assays.splice(index, 1);
-        this$.DeregisterMissingAssays();
+        let enumerator = getEnumerator(this$.Studies);
+        try {
+            while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+                const study = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                study.DeregisterAssay(ident);
+            }
+        }
+        finally {
+            disposeSafe(enumerator);
+        }
     }
     static removeAssayAt(index) {
         return (inv) => {
@@ -1515,9 +1540,19 @@ export class ArcInvestigation {
             return newInvestigation.GetAssay(assayIdentifier);
         };
     }
+    TryGetAssay(assayIdentifier) {
+        const this$ = this;
+        return tryFind((a) => (a.Identifier === assayIdentifier), this$.Assays);
+    }
+    static tryGetAssay(assayIdentifier) {
+        return (inv) => {
+            const newInvestigation = inv.Copy();
+            return newInvestigation.TryGetAssay(assayIdentifier);
+        };
+    }
     get RegisteredStudies() {
         const this$ = this;
-        const collection = map_2((identifier) => this$.GetStudy(identifier), this$.RegisteredStudyIdentifiers);
+        const collection = choose((identifier) => this$.TryGetStudy(identifier), this$.RegisteredStudyIdentifiers);
         return Array.from(collection);
     }
     get StudyCount() {
@@ -1526,7 +1561,7 @@ export class ArcInvestigation {
     }
     get StudyIdentifiers() {
         const this$ = this;
-        return map_2((x) => x.Identifier, this$.Studies);
+        return toArray(map_2((x) => x.Identifier, this$.Studies));
     }
     AddStudy(study) {
         const this$ = this;
@@ -1597,9 +1632,34 @@ export class ArcInvestigation {
             return copy;
         };
     }
+    DeleteStudyAt(index) {
+        const this$ = this;
+        this$.Studies.splice(index, 1);
+    }
+    static deleteStudyAt(index) {
+        return (i) => {
+            const copy = i.Copy();
+            copy.DeleteStudyAt(index);
+            return copy;
+        };
+    }
+    DeleteStudy(studyIdentifier) {
+        const this$ = this;
+        const index = this$.Studies.findIndex((s) => (s.Identifier === studyIdentifier)) | 0;
+        this$.DeleteStudyAt(index);
+    }
+    static deleteStudy(studyIdentifier) {
+        return (i) => {
+            const copy = i.Copy();
+            copy.DeleteStudy(studyIdentifier);
+            return copy;
+        };
+    }
     RemoveStudyAt(index) {
         const this$ = this;
+        const ident = this$.GetStudyAt(index).Identifier;
         this$.Studies.splice(index, 1);
+        this$.DeregisterStudy(ident);
     }
     static removeStudyAt(index) {
         return (inv) => {
@@ -1610,10 +1670,8 @@ export class ArcInvestigation {
     }
     RemoveStudy(studyIdentifier) {
         const this$ = this;
-        removeInPlace(this$.GetStudy(studyIdentifier), this$.Studies, {
-            Equals: equals,
-            GetHashCode: safeHash,
-        });
+        const index = this$.GetStudyIndex(studyIdentifier) | 0;
+        this$.RemoveStudyAt(index);
     }
     static removeStudy(studyIdentifier) {
         return (inv) => {
@@ -1684,6 +1742,16 @@ export class ArcInvestigation {
             return newInv.GetStudy(studyIdentifier);
         };
     }
+    TryGetStudy(studyIdentifier) {
+        const this$ = this;
+        return tryFind((s) => (s.Identifier === studyIdentifier), this$.Studies);
+    }
+    static tryGetStudy(studyIdentifier) {
+        return (inv) => {
+            const newInv = inv.Copy();
+            return newInv.TryGetStudy(studyIdentifier);
+        };
+    }
     RegisterAssayAt(studyIndex, assayIdentifier) {
         const this$ = this;
         const study = this$.GetStudyAt(studyIndex);
@@ -1745,6 +1813,20 @@ export class ArcInvestigation {
             return copy;
         };
     }
+    DeregisterStudy(studyIdentifier) {
+        const this$ = this;
+        removeInPlace(studyIdentifier, this$.RegisteredStudyIdentifiers, {
+            Equals: (x, y) => (x === y),
+            GetHashCode: stringHash,
+        });
+    }
+    static deregisterStudy(studyIdentifier) {
+        return (i) => {
+            const copy = i.Copy();
+            copy.DeregisterStudy(studyIdentifier);
+            return copy;
+        };
+    }
     GetAllPersons() {
         const this$ = this;
         const persons = [];
@@ -1921,56 +2003,56 @@ export class ArcInvestigation {
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_1) => equals(item_1(i_1, a), item_1(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Contacts, (b_1 = other.Contacts, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
+        }, true, toList(delay(() => map_2((i_1) => equals(item(i_1, a), item(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Contacts, (b_1 = other.Contacts, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
             if (acc_1) {
                 return e_1;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_2) => equals(item_1(i_2, a_1), item_1(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.OntologySourceReferences, (b_2 = other.OntologySourceReferences, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
+        }, true, toList(delay(() => map_2((i_2) => equals(item(i_2, a_1), item(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.OntologySourceReferences, (b_2 = other.OntologySourceReferences, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
             if (acc_2) {
                 return e_2;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_3) => equals(item_1(i_3, a_2), item_1(i_3, b_2)), rangeDouble(0, 1, length(a_2) - 1))))))), (a_3 = this$.Assays, (b_3 = other.Assays, (length(a_3) === length(b_3)) && fold((acc_3, e_3) => {
+        }, true, toList(delay(() => map_2((i_3) => equals(item(i_3, a_2), item(i_3, b_2)), rangeDouble(0, 1, length(a_2) - 1))))))), (a_3 = this$.Assays, (b_3 = other.Assays, (length(a_3) === length(b_3)) && fold((acc_3, e_3) => {
             if (acc_3) {
                 return e_3;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_4) => equals(item_1(i_4, a_3), item_1(i_4, b_3)), rangeDouble(0, 1, length(a_3) - 1))))))), (a_4 = this$.Studies, (b_4 = other.Studies, (length(a_4) === length(b_4)) && fold((acc_4, e_4) => {
+        }, true, toList(delay(() => map_2((i_4) => equals(item(i_4, a_3), item(i_4, b_3)), rangeDouble(0, 1, length(a_3) - 1))))))), (a_4 = this$.Studies, (b_4 = other.Studies, (length(a_4) === length(b_4)) && fold((acc_4, e_4) => {
             if (acc_4) {
                 return e_4;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_5) => equals(item_1(i_5, a_4), item_1(i_5, b_4)), rangeDouble(0, 1, length(a_4) - 1))))))), (a_5 = this$.RegisteredStudyIdentifiers, (b_5 = other.RegisteredStudyIdentifiers, (length(a_5) === length(b_5)) && fold((acc_5, e_5) => {
+        }, true, toList(delay(() => map_2((i_5) => equals(item(i_5, a_4), item(i_5, b_4)), rangeDouble(0, 1, length(a_4) - 1))))))), (a_5 = this$.RegisteredStudyIdentifiers, (b_5 = other.RegisteredStudyIdentifiers, (length(a_5) === length(b_5)) && fold((acc_5, e_5) => {
             if (acc_5) {
                 return e_5;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_6) => (item_1(i_6, a_5) === item_1(i_6, b_5)), rangeDouble(0, 1, length(a_5) - 1))))))), (a_6 = this$.Comments, (b_6 = other.Comments, (length(a_6) === length(b_6)) && fold((acc_6, e_6) => {
+        }, true, toList(delay(() => map_2((i_6) => (item(i_6, a_5) === item(i_6, b_5)), rangeDouble(0, 1, length(a_5) - 1))))))), (a_6 = this$.Comments, (b_6 = other.Comments, (length(a_6) === length(b_6)) && fold((acc_6, e_6) => {
             if (acc_6) {
                 return e_6;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_7) => equals(item_1(i_7, a_6), item_1(i_7, b_6)), rangeDouble(0, 1, length(a_6) - 1))))))), (a_7 = this$.Remarks, (b_7 = other.Remarks, (length(a_7) === length(b_7)) && fold((acc_7, e_7) => {
+        }, true, toList(delay(() => map_2((i_7) => equals(item(i_7, a_6), item(i_7, b_6)), rangeDouble(0, 1, length(a_6) - 1))))))), (a_7 = this$.Remarks, (b_7 = other.Remarks, (length(a_7) === length(b_7)) && fold((acc_7, e_7) => {
             if (acc_7) {
                 return e_7;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_8) => equals(item_1(i_8, a_7), item_1(i_8, b_7)), rangeDouble(0, 1, length(a_7) - 1)))))))]);
+        }, true, toList(delay(() => map_2((i_8) => equals(item(i_8, a_7), item(i_8, b_7)), rangeDouble(0, 1, length(a_7) - 1)))))))]);
     }
     ReferenceEquals(other) {
         const this$ = this;

package/ISA/ISA/ArcTypes/CompositeCell.js

@@ -1,9 +1,9 @@
-import { int32ToString } from "../../../fable_modules/fable-library.4.4.1/Util.js";
-import { defaultArg } from "../../../fable_modules/fable-library.4.4.1/Option.js";
+import { int32ToString } from "../../../fable_modules/fable-library.4.5.0/Util.js";
+import { defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
 import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
 import { AnnotationValue } from "../JsonTypes/AnnotationValue.js";
-import { Union } from "../../../fable_modules/fable-library.4.4.1/Types.js";
-import { union_type, string_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.js";
+import { Union } from "../../../fable_modules/fable-library.4.5.0/Types.js";
+import { union_type, string_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
 
 export class CompositeCell extends Union {
     constructor(tag, fields) {
@@ -89,6 +89,10 @@ export class CompositeCell extends Union {
         const this$ = this;
         return this$.tag === 1;
     }
+    GetEmptyCell() {
+        const this$ = this;
+        return (this$.tag === 2) ? CompositeCell.emptyUnitized : ((this$.tag === 1) ? CompositeCell.emptyFreeText : CompositeCell.emptyTerm);
+    }
     GetContent() {
         const this$ = this;
         switch (this$.tag) {

package/ISA/ISA/ArcTypes/CompositeColumn.js

@@ -1,9 +1,9 @@
-import { defaultArg } from "../../../fable_modules/fable-library.4.4.1/Option.js";
-import { empty, singleton, collect, delay, toArray } from "../../../fable_modules/fable-library.4.4.1/Seq.js";
-import { Record } from "../../../fable_modules/fable-library.4.4.1/Types.js";
+import { defaultArg } from "../../../fable_modules/fable-library.4.5.0/Option.js";
+import { fold, empty, singleton, collect, delay, toArray } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { CompositeCell_$reflection, CompositeCell } from "./CompositeCell.js";
+import { Record } from "../../../fable_modules/fable-library.4.5.0/Types.js";
 import { CompositeHeader_$reflection } from "./CompositeHeader.js";
-import { CompositeCell_$reflection } from "./CompositeCell.js";
-import { record_type, array_type } from "../../../fable_modules/fable-library.4.4.1/Reflection.js";
+import { record_type, array_type } from "../../../fable_modules/fable-library.4.5.0/Reflection.js";
 
 export class CompositeColumn extends Record {
     constructor(Header, Cells) {
@@ -40,6 +40,27 @@ export class CompositeColumn extends Record {
         const arr = toArray(delay(() => collect((cell) => (cell.isUnitized ? singleton(cell.AsUnitized[1]) : empty()), this$.Cells)));
         return (arr.length === 0) ? void 0 : arr;
     }
+    GetDefaultEmptyCell() {
+        const this$ = this;
+        if (!this$.Header.IsTermColumn) {
+            return CompositeCell.emptyFreeText;
+        }
+        else {
+            let patternInput;
+            const arg = [0, 0];
+            patternInput = fold((tupledArg, cell) => {
+                const units = tupledArg[0] | 0;
+                const terms = tupledArg[1] | 0;
+                if (cell.isUnitized) {
+                    return [units + 1, terms];
+                }
+                else {
+                    return [units, terms + 1];
+                }
+            }, [arg[0], arg[1]], this$.Cells);
+            return (patternInput[1] >= patternInput[0]) ? CompositeCell.emptyTerm : CompositeCell.emptyUnitized;
+        }
+    }
 }
 
 export function CompositeColumn_$reflection() {