@nfdi4plants/arctrl 1.2.0 → 2.0.0-alpha.2

package/{ISA/ISA/ArcTypes → Core}/ArcTypes.js

@@ -1,47 +1,37 @@
-import { map as map_1, defaultArg, unwrap } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { concat, collect, append as append_4, tryFind, removeAt, tryFindIndex, exists, choose, item, map as map_2, delay, toList, fold, length, forAll, contains, filter, toArray } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
-import { defaultOf, safeHash, equals, disposeSafe, getEnumerator, stringHash } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { addRangeInPlace, removeInPlace, equalsWith, append as append_3, contains as contains_1, map } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
-import { distinctBy, Array_distinct } from "../../../fable_modules/fable-library-js.4.13.0/Seq2.js";
-import { printf, toText } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
-import { ActivePatterns_$007CRegex$007C_$007C } from "../Regex.js";
-import { OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
-import { Value } from "../JsonTypes/Value.js";
-import { ArcTablesAux_applyIOMap, ArcTablesAux_getIOMap, ArcTables_$reflection, ArcTables } from "./ArcTables.js";
-import { AssayMaterials_get_empty, AssayMaterials_create_Z253F0553 } from "../JsonTypes/AssayMaterials.js";
-import { ResizeArray_choose, ResizeArray_filter, 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-js.4.13.0/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-js.4.13.0/Range.js";
-import { class_type } from "../../../fable_modules/fable-library-js.4.13.0/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-js.4.13.0/Types.js";
+import { value as value_4, defaultArg, unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { collect, append as append_3, tryFind, removeAt, tryFindIndex, exists, choose, item, map, 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 { addRangeInPlace, removeInPlace, contains as contains_1 } from "../fable_modules/fable-library-js.4.16.0/Array.js";
+import { printf, toText } from "../fable_modules/fable-library-js.4.16.0/String.js";
+import { rangeDouble } from "../fable_modules/fable-library-js.4.16.0/Range.js";
+import { boxHashSeq, boxHashOption, boxHashArray } from "./Helper/HashCodes.js";
+import { ArcTablesAux_applyIOMap, ArcTablesAux_getIOMap, ArcTables_$reflection, ArcTables } from "./Table/ArcTables.js";
+import { class_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
+import { Array_distinct } from "../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { FSharpRef } from "../fable_modules/fable-library-js.4.16.0/Types.js";
 
 export class ArcAssay extends ArcTables {
     constructor(identifier, measurementType, technologyType, technologyPlatform, tables, performers, comments) {
         super(defaultArg(tables, []));
         const performers_1 = defaultArg(performers, []);
         const comments_1 = defaultArg(comments, []);
-        this["identifier@96"] = identifier;
+        this["identifier@109"] = identifier;
         this.investigation = void 0;
-        this["measurementType@98"] = measurementType;
-        this["technologyType@99"] = technologyType;
-        this["technologyPlatform@100"] = technologyPlatform;
-        this["performers@101-1"] = performers_1;
-        this["comments@102-1"] = comments_1;
+        this["measurementType@111"] = measurementType;
+        this["technologyType@112"] = technologyType;
+        this["technologyPlatform@113"] = technologyPlatform;
+        this["performers@114-1"] = performers_1;
+        this["comments@115-1"] = comments_1;
         this.staticHash = 0;
     }
     get Identifier() {
         const this$ = this;
-        return this$["identifier@96"];
+        return this$["identifier@109"];
     }
     set Identifier(i) {
         const this$ = this;
-        this$["identifier@96"] = i;
+        this$["identifier@109"] = i;
     }
     get Investigation() {
         const this$ = this;
@@ -53,43 +43,43 @@ export class ArcAssay extends ArcTables {
     }
     get MeasurementType() {
         const this$ = this;
-        return unwrap(this$["measurementType@98"]);
+        return unwrap(this$["measurementType@111"]);
     }
     set MeasurementType(n) {
         const this$ = this;
-        this$["measurementType@98"] = n;
+        this$["measurementType@111"] = n;
     }
     get TechnologyType() {
         const this$ = this;
-        return unwrap(this$["technologyType@99"]);
+        return unwrap(this$["technologyType@112"]);
     }
     set TechnologyType(n) {
         const this$ = this;
-        this$["technologyType@99"] = n;
+        this$["technologyType@112"] = n;
     }
     get TechnologyPlatform() {
         const this$ = this;
-        return unwrap(this$["technologyPlatform@100"]);
+        return unwrap(this$["technologyPlatform@113"]);
     }
     set TechnologyPlatform(n) {
         const this$ = this;
-        this$["technologyPlatform@100"] = n;
+        this$["technologyPlatform@113"] = n;
     }
     get Performers() {
         const this$ = this;
-        return this$["performers@101-1"];
+        return this$["performers@114-1"];
     }
     set Performers(n) {
         const this$ = this;
-        this$["performers@101-1"] = n;
+        this$["performers@114-1"] = n;
     }
     get Comments() {
         const this$ = this;
-        return this$["comments@102-1"];
+        return this$["comments@115-1"];
     }
     set Comments(n) {
         const this$ = this;
-        this$["comments@102-1"] = n;
+        this$["comments@115-1"] = n;
     }
     get StaticHash() {
         const this$ = this;
@@ -363,8 +353,8 @@ export class ArcAssay extends ArcTables {
         finally {
             disposeSafe(enumerator);
         }
-        const nextComments = map((c) => c.Copy(), this$.Comments);
-        const nextPerformers = map((c_1) => c_1.Copy(), this$.Performers);
+        const nextComments = ResizeArray_map((c) => c.Copy(), this$.Comments);
+        const nextPerformers = ResizeArray_map((c_1) => c_1.Copy(), this$.Performers);
         const identifier = this$.Identifier;
         const measurementType = this$.MeasurementType;
         const technologyType = this$.TechnologyType;
@@ -390,25 +380,41 @@ export class ArcAssay extends ArcTables {
             const origin = this$.Tables;
             const next = assay.Tables;
             if (!appendSequences_1) {
-                s = next;
+                s = ResizeArray_map((x) => x, next);
             }
             else {
-                let enumerator = getEnumerator(next);
+                const combined = [];
+                let enumerator = getEnumerator(origin);
                 try {
                     while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
                         const e = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
-                        if (!contains_1(e, origin, {
+                        if (!contains_1(e, combined, {
                             Equals: equals,
                             GetHashCode: safeHash,
                         })) {
-                            void (origin.push(e));
+                            void (combined.push(e));
                         }
                     }
                 }
                 finally {
                     disposeSafe(enumerator);
                 }
-                s = origin;
+                let enumerator_1 = getEnumerator(next);
+                try {
+                    while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
+                        const e_1 = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                        if (!contains_1(e_1, combined, {
+                            Equals: equals,
+                            GetHashCode: safeHash,
+                        })) {
+                            void (combined.push(e_1));
+                        }
+                    }
+                }
+                finally {
+                    disposeSafe(enumerator_1);
+                }
+                s = combined;
             }
             this$.Tables = s;
         }
@@ -416,20 +422,86 @@ export class ArcAssay extends ArcTables {
             let s_1;
             const origin_1 = this$.Performers;
             const next_1 = assay.Performers;
-            s_1 = (!appendSequences_1 ? next_1 : Array_distinct(append_3(origin_1, next_1), {
-                Equals: equals,
-                GetHashCode: safeHash,
-            }));
+            if (!appendSequences_1) {
+                s_1 = ResizeArray_map((x_3) => x_3, next_1);
+            }
+            else {
+                const combined_1 = [];
+                let enumerator_2 = getEnumerator(origin_1);
+                try {
+                    while (enumerator_2["System.Collections.IEnumerator.MoveNext"]()) {
+                        const e_2 = enumerator_2["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                        if (!contains_1(e_2, combined_1, {
+                            Equals: equals,
+                            GetHashCode: safeHash,
+                        })) {
+                            void (combined_1.push(e_2));
+                        }
+                    }
+                }
+                finally {
+                    disposeSafe(enumerator_2);
+                }
+                let enumerator_1_1 = getEnumerator(next_1);
+                try {
+                    while (enumerator_1_1["System.Collections.IEnumerator.MoveNext"]()) {
+                        const e_1_1 = enumerator_1_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                        if (!contains_1(e_1_1, combined_1, {
+                            Equals: equals,
+                            GetHashCode: safeHash,
+                        })) {
+                            void (combined_1.push(e_1_1));
+                        }
+                    }
+                }
+                finally {
+                    disposeSafe(enumerator_1_1);
+                }
+                s_1 = combined_1;
+            }
             this$.Performers = s_1;
         }
         if ((assay.Comments.length !== 0) ? true : updateAlways) {
             let s_2;
             const origin_2 = this$.Comments;
             const next_2 = assay.Comments;
-            s_2 = (!appendSequences_1 ? next_2 : Array_distinct(append_3(origin_2, next_2), {
-                Equals: equals,
-                GetHashCode: safeHash,
-            }));
+            if (!appendSequences_1) {
+                s_2 = ResizeArray_map((x_6) => x_6, next_2);
+            }
+            else {
+                const combined_2 = [];
+                let enumerator_3 = getEnumerator(origin_2);
+                try {
+                    while (enumerator_3["System.Collections.IEnumerator.MoveNext"]()) {
+                        const e_3 = enumerator_3["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                        if (!contains_1(e_3, combined_2, {
+                            Equals: equals,
+                            GetHashCode: safeHash,
+                        })) {
+                            void (combined_2.push(e_3));
+                        }
+                    }
+                }
+                finally {
+                    disposeSafe(enumerator_3);
+                }
+                let enumerator_1_2 = getEnumerator(next_2);
+                try {
+                    while (enumerator_1_2["System.Collections.IEnumerator.MoveNext"]()) {
+                        const e_1_2 = enumerator_1_2["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                        if (!contains_1(e_1_2, combined_2, {
+                            Equals: equals,
+                            GetHashCode: safeHash,
+                        })) {
+                            void (combined_2.push(e_1_2));
+                        }
+                    }
+                }
+                finally {
+                    disposeSafe(enumerator_1_2);
+                }
+                s_2 = combined_2;
+            }
             this$.Comments = s_2;
         }
     }
@@ -444,26 +516,6 @@ export class ArcAssay extends ArcTables {
         const arg_6 = this$.Comments;
         return toText(printf("ArcAssay({\r\n    Identifier = \"%s\",\r\n    MeasurementType = %A,\r\n    TechnologyType = %A,\r\n    TechnologyPlatform = %A,\r\n    Tables = %A,\r\n    Performers = %A,\r\n    Comments = %A\r\n})"))(arg)(arg_1)(arg_2)(arg_3)(arg_4)(arg_5)(arg_6);
     }
-    static composeTechnologyPlatform(tp) {
-        const matchValue = tp.TANInfo;
-        return (matchValue == null) ? (`${tp.NameText}`) : (`${tp.NameText} (${tp.TermAccessionShort})`);
-    }
-    static decomposeTechnologyPlatform(name) {
-        const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("(?<value>[^\\(]+) \\((?<ontology>[^(]*:[^)]*)\\)", name);
-        if (activePatternResult != null) {
-            const r = activePatternResult;
-            let oa;
-            const termAnnotation = (r.groups && r.groups.ontology) || "";
-            oa = OntologyAnnotation.fromTermAnnotation(termAnnotation);
-            let v;
-            const value = (r.groups && r.groups.value) || "";
-            v = Value.fromString(value);
-            return new OntologyAnnotation(oa.ID, v.Text, oa.TermSourceREF, oa.TermAccessionNumber, oa.Comments);
-        }
-        else {
-            return OntologyAnnotation.fromString(name);
-        }
-    }
     AddToInvestigation(investigation) {
         const this$ = this;
         this$.Investigation = investigation;
@@ -494,24 +546,6 @@ export class ArcAssay extends ArcTables {
             this$.Performers = assay.Performers;
         }
     }
-    ToAssay() {
-        const this$ = this;
-        const processSeq = (new ArcTables(this$.Tables)).GetProcesses();
-        let assayMaterials;
-        const v_2 = AssayMaterials_create_Z253F0553(unwrap(Option_fromValueWithDefault(empty(), getSamples(processSeq))), unwrap(Option_fromValueWithDefault(empty(), getMaterials(processSeq))));
-        assayMaterials = Option_fromValueWithDefault(AssayMaterials_get_empty(), v_2);
-        return Assay_create_3D372A24(void 0, unwrap(isMissingIdentifier(this$.Identifier) ? void 0 : Assay_fileNameFromIdentifier(this$.Identifier)), unwrap(this$.MeasurementType), unwrap(this$.TechnologyType), unwrap(map_1((tp) => ArcAssay.composeTechnologyPlatform(tp), this$.TechnologyPlatform)), unwrap(Option_fromValueWithDefault(empty(), getData(processSeq))), unwrap(assayMaterials), unwrap(Option_fromValueWithDefault(empty(), getCharacteristics(processSeq))), unwrap(Option_fromValueWithDefault(empty(), getUnits(processSeq))), unwrap(Option_fromValueWithDefault(empty(), processSeq)), unwrap(Option_fromValueWithDefault(empty(), ofArray(this$.Comments))));
-    }
-    static fromAssay(a) {
-        const tables = map_1((arg) => {
-            const t = ArcTables.fromProcesses(arg);
-            return t.Tables;
-        }, a.ProcessSequence);
-        let identifer;
-        const matchValue = a.FileName;
-        identifer = ((matchValue == null) ? createMissingIdentifier() : Assay_identifierFromFileName(matchValue));
-        return ArcAssay.create(identifer, unwrap(map_1((x) => x.Copy(), a.MeasurementType)), unwrap(map_1((x_1) => x_1.Copy(), a.TechnologyType)), unwrap(map_1((name) => ArcAssay.decomposeTechnologyPlatform(name), a.TechnologyPlatform)), unwrap(tables), void 0, unwrap(map_1(toArray_1, a.Comments)));
-    }
     StructurallyEquals(other) {
         let a, b, a_1, b_1, a_2, b_2;
         const this$ = this;
@@ -522,21 +556,21 @@ export class ArcAssay extends ArcTables {
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_1) => equals(item(i_1, a), item(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Performers, (b_1 = other.Performers, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
+        }, true, toList(delay(() => map((i_1) => equals(item(i_1, a), item(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Performers, (b_1 = other.Performers, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
             if (acc_1) {
                 return e_1;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_2) => equals(item(i_2, a_1), item(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.Comments, (b_2 = other.Comments, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
+        }, true, toList(delay(() => map((i_2) => equals(item(i_2, a_1), item(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.Comments, (b_2 = other.Comments, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
             if (acc_2) {
                 return e_2;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_3) => equals(item(i_3, a_2), item(i_3, b_2)), rangeDouble(0, 1, length(a_2) - 1)))))))]);
+        }, true, toList(delay(() => map((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;
@@ -549,48 +583,46 @@ export class ArcAssay extends ArcTables {
     }
     GetHashCode() {
         const this$ = this;
-        return HashCodes_boxHashArray([this$.Identifier, HashCodes_boxHashOption(this$.MeasurementType), HashCodes_boxHashOption(this$.TechnologyType), HashCodes_boxHashOption(this$.TechnologyPlatform), HashCodes_boxHashArray(Array.from(this$.Tables)), HashCodes_boxHashArray(this$.Performers), HashCodes_boxHashArray(this$.Comments)]) | 0;
+        return boxHashArray([this$.Identifier, boxHashOption(this$.MeasurementType), boxHashOption(this$.TechnologyType), boxHashOption(this$.TechnologyPlatform), boxHashSeq(this$.Tables), boxHashSeq(this$.Performers), boxHashSeq(this$.Comments)]) | 0;
     }
 }
 
 export function ArcAssay_$reflection() {
-    return class_type("ARCtrl.ISA.ArcAssay", void 0, ArcAssay, ArcTables_$reflection());
+    return class_type("ARCtrl.ArcAssay", void 0, ArcAssay, ArcTables_$reflection());
 }
 
-export function ArcAssay_$ctor_Z1126B596(identifier, measurementType, technologyType, technologyPlatform, tables, performers, comments) {
+export function ArcAssay_$ctor_1CE2732A(identifier, measurementType, technologyType, technologyPlatform, tables, performers, comments) {
     return new ArcAssay(identifier, measurementType, technologyType, technologyPlatform, tables, performers, comments);
 }
 
 export class ArcStudy extends ArcTables {
-    constructor(identifier, title, description, submissionDate, publicReleaseDate, publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, factors, comments) {
+    constructor(identifier, title, description, submissionDate, publicReleaseDate, publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, comments) {
         super(defaultArg(tables, []));
         const publications_1 = defaultArg(publications, []);
         const contacts_1 = defaultArg(contacts, []);
         const studyDesignDescriptors_1 = defaultArg(studyDesignDescriptors, []);
         const registeredAssayIdentifiers_1 = defaultArg(registeredAssayIdentifiers, []);
-        const factors_1 = defaultArg(factors, []);
         const comments_1 = defaultArg(comments, []);
-        this["identifier@572"] = identifier;
+        this["identifier@511"] = identifier;
         this.investigation = void 0;
-        this["title@574"] = title;
-        this["description@575"] = description;
-        this["submissionDate@576"] = submissionDate;
-        this["publicReleaseDate@577"] = publicReleaseDate;
-        this["publications@578-1"] = publications_1;
-        this["contacts@579-1"] = contacts_1;
-        this["studyDesignDescriptors@580-1"] = studyDesignDescriptors_1;
-        this["registeredAssayIdentifiers@581-1"] = registeredAssayIdentifiers_1;
-        this["factors@582-1"] = factors_1;
-        this["comments@583-1"] = comments_1;
+        this["title@513"] = title;
+        this["description@514"] = description;
+        this["submissionDate@515"] = submissionDate;
+        this["publicReleaseDate@516"] = publicReleaseDate;
+        this["publications@517-1"] = publications_1;
+        this["contacts@518-1"] = contacts_1;
+        this["studyDesignDescriptors@519-1"] = studyDesignDescriptors_1;
+        this["registeredAssayIdentifiers@520-1"] = registeredAssayIdentifiers_1;
+        this["comments@521-1"] = comments_1;
         this.staticHash = 0;
     }
     get Identifier() {
         const this$ = this;
-        return this$["identifier@572"];
+        return this$["identifier@511"];
     }
     set Identifier(i) {
         const this$ = this;
-        this$["identifier@572"] = i;
+        this$["identifier@511"] = i;
     }
     get Investigation() {
         const this$ = this;
@@ -602,83 +634,75 @@ export class ArcStudy extends ArcTables {
     }
     get Title() {
         const this$ = this;
-        return unwrap(this$["title@574"]);
+        return unwrap(this$["title@513"]);
     }
     set Title(n) {
         const this$ = this;
-        this$["title@574"] = n;
+        this$["title@513"] = n;
     }
     get Description() {
         const this$ = this;
-        return unwrap(this$["description@575"]);
+        return unwrap(this$["description@514"]);
     }
     set Description(n) {
         const this$ = this;
-        this$["description@575"] = n;
+        this$["description@514"] = n;
     }
     get SubmissionDate() {
         const this$ = this;
-        return unwrap(this$["submissionDate@576"]);
+        return unwrap(this$["submissionDate@515"]);
     }
     set SubmissionDate(n) {
         const this$ = this;
-        this$["submissionDate@576"] = n;
+        this$["submissionDate@515"] = n;
     }
     get PublicReleaseDate() {
         const this$ = this;
-        return unwrap(this$["publicReleaseDate@577"]);
+        return unwrap(this$["publicReleaseDate@516"]);
     }
     set PublicReleaseDate(n) {
         const this$ = this;
-        this$["publicReleaseDate@577"] = n;
+        this$["publicReleaseDate@516"] = n;
     }
     get Publications() {
         const this$ = this;
-        return this$["publications@578-1"];
+        return this$["publications@517-1"];
     }
     set Publications(n) {
         const this$ = this;
-        this$["publications@578-1"] = n;
+        this$["publications@517-1"] = n;
     }
     get Contacts() {
         const this$ = this;
-        return this$["contacts@579-1"];
+        return this$["contacts@518-1"];
     }
     set Contacts(n) {
         const this$ = this;
-        this$["contacts@579-1"] = n;
+        this$["contacts@518-1"] = n;
     }
     get StudyDesignDescriptors() {
         const this$ = this;
-        return this$["studyDesignDescriptors@580-1"];
+        return this$["studyDesignDescriptors@519-1"];
     }
     set StudyDesignDescriptors(n) {
         const this$ = this;
-        this$["studyDesignDescriptors@580-1"] = n;
+        this$["studyDesignDescriptors@519-1"] = n;
     }
     get RegisteredAssayIdentifiers() {
         const this$ = this;
-        return this$["registeredAssayIdentifiers@581-1"];
+        return this$["registeredAssayIdentifiers@520-1"];
     }
     set RegisteredAssayIdentifiers(n) {
         const this$ = this;
-        this$["registeredAssayIdentifiers@581-1"] = n;
-    }
-    get Factors() {
-        const this$ = this;
-        return this$["factors@582-1"];
-    }
-    set Factors(n) {
-        const this$ = this;
-        this$["factors@582-1"] = n;
+        this$["registeredAssayIdentifiers@520-1"] = n;
     }
     get Comments() {
         const this$ = this;
-        return this$["comments@583-1"];
+        return this$["comments@521-1"];
     }
     set Comments(n) {
         const this$ = this;
-        this$["comments@583-1"] = n;
+        this$["comments@521-1"] = n;
     }
     get StaticHash() {
         const this$ = this;
@@ -691,15 +715,15 @@ export class ArcStudy extends ArcTables {
     static init(identifier) {
         return new ArcStudy(identifier);
     }
-    static create(identifier, title, description, submissionDate, publicReleaseDate, publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, factors, comments) {
-        return new ArcStudy(identifier, unwrap(title), unwrap(description), unwrap(submissionDate), unwrap(publicReleaseDate), unwrap(publications), unwrap(contacts), unwrap(studyDesignDescriptors), unwrap(tables), unwrap(registeredAssayIdentifiers), unwrap(factors), unwrap(comments));
+    static create(identifier, title, description, submissionDate, publicReleaseDate, publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, comments) {
+        return new ArcStudy(identifier, unwrap(title), unwrap(description), unwrap(submissionDate), unwrap(publicReleaseDate), unwrap(publications), unwrap(contacts), unwrap(studyDesignDescriptors), unwrap(tables), unwrap(registeredAssayIdentifiers), unwrap(comments));
     }
-    static make(identifier, title, description, submissionDate, publicReleaseDate, publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, factors, comments) {
-        return new ArcStudy(identifier, unwrap(title), unwrap(description), unwrap(submissionDate), unwrap(publicReleaseDate), publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, factors, comments);
+    static make(identifier, title, description, submissionDate, publicReleaseDate, publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, comments) {
+        return new ArcStudy(identifier, unwrap(title), unwrap(description), unwrap(submissionDate), unwrap(publicReleaseDate), publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, comments);
     }
     get isEmpty() {
         const this$ = this;
-        return (((((((((equals(this$.Title, void 0) && equals(this$.Description, void 0)) && equals(this$.SubmissionDate, void 0)) && equals(this$.PublicReleaseDate, void 0)) && equalsWith(equals, this$.Publications, [])) && equalsWith(equals, this$.Contacts, [])) && equalsWith(equals, this$.StudyDesignDescriptors, [])) && (this$.Tables.length === 0)) && (this$.RegisteredAssayIdentifiers.length === 0)) && equalsWith(equals, this$.Factors, [])) && equalsWith(equals, this$.Comments, []);
+        return ((((((((equals(this$.Title, void 0) && equals(this$.Description, void 0)) && equals(this$.SubmissionDate, void 0)) && equals(this$.PublicReleaseDate, void 0)) && (this$.Publications.length === 0)) && (this$.Contacts.length === 0)) && (this$.StudyDesignDescriptors.length === 0)) && (this$.Tables.length === 0)) && (this$.RegisteredAssayIdentifiers.length === 0)) && (this$.Comments.length === 0);
     }
     static get FileName() {
         return "isa.study.xlsx";
@@ -1081,8 +1105,9 @@ export class ArcStudy extends ArcTables {
         const this$ = this;
         this$.Investigation = void 0;
     }
-    Copy() {
+    Copy(copyInvestigationRef) {
         const this$ = this;
+        const copyInvestigationRef_1 = defaultArg(copyInvestigationRef, false);
         const nextTables = [];
         const nextAssayIdentifiers = Array.from(this$.RegisteredAssayIdentifiers);
         let enumerator = getEnumerator(this$.Tables);
@@ -1096,17 +1121,21 @@ export class ArcStudy extends ArcTables {
         finally {
             disposeSafe(enumerator);
         }
-        const nextComments = map((c) => c.Copy(), this$.Comments);
-        const nextFactors = map((c_1) => c_1.Copy(), this$.Factors);
-        const nextContacts = map((c_2) => c_2.Copy(), this$.Contacts);
-        const nextPublications = map((c_3) => c_3.Copy(), this$.Publications);
-        const nextStudyDesignDescriptors = map((c_4) => c_4.Copy(), this$.StudyDesignDescriptors);
+        const nextComments = ResizeArray_map((c) => c.Copy(), this$.Comments);
+        const nextContacts = ResizeArray_map((c_1) => c_1.Copy(), this$.Contacts);
+        const nextPublications = ResizeArray_map((c_2) => c_2.Copy(), this$.Publications);
+        const nextStudyDesignDescriptors = ResizeArray_map((c_3) => c_3.Copy(), this$.StudyDesignDescriptors);
+        let study;
         const identifier = this$.Identifier;
         const title = this$.Title;
         const description = this$.Description;
         const submissionDate = this$.SubmissionDate;
         const publicReleaseDate = this$.PublicReleaseDate;
-        return ArcStudy.make(identifier, title, description, submissionDate, publicReleaseDate, nextPublications, nextContacts, nextStudyDesignDescriptors, nextTables, nextAssayIdentifiers, nextFactors, nextComments);
+        study = ArcStudy.make(identifier, title, description, submissionDate, publicReleaseDate, nextPublications, nextContacts, nextStudyDesignDescriptors, nextTables, nextAssayIdentifiers, nextComments);
+        if (copyInvestigationRef_1) {
+            study.Investigation = this$.Investigation;
+        }
+        return study;
     }
     UpdateReferenceByStudyFile(study, onlyReplaceExisting, keepUnusedRefTables) {
         const this$ = this;
@@ -1139,43 +1168,12 @@ export class ArcStudy extends ArcTables {
         if ((study.RegisteredAssayIdentifiers.length !== 0) ? true : updateAlways) {
             this$.RegisteredAssayIdentifiers = study.RegisteredAssayIdentifiers;
         }
-        if ((study.Factors.length !== 0) ? true : updateAlways) {
-            this$.Factors = study.Factors;
-        }
         if ((study.Comments.length !== 0) ? true : updateAlways) {
             this$.Comments = study.Comments;
         }
     }
-    ToStudy(arcAssays) {
-        const this$ = this;
-        const processSeq = (new ArcTables(this$.Tables)).GetProcesses();
-        const protocols = Option_fromValueWithDefault(empty(), getProtocols(processSeq));
-        let studyMaterials;
-        const v_4 = StudyMaterials_create_1BE9FA55(unwrap(Option_fromValueWithDefault(empty(), getSources(processSeq))), unwrap(Option_fromValueWithDefault(empty(), getSamples(processSeq))), unwrap(Option_fromValueWithDefault(empty(), getMaterials(processSeq))));
-        studyMaterials = Option_fromValueWithDefault(StudyMaterials_get_empty(), v_4);
-        const patternInput = isMissingIdentifier(this$.Identifier) ? [void 0, void 0] : [this$.Identifier, Study_fileNameFromIdentifier(this$.Identifier)];
-        const assays = map_3((a) => a.ToAssay(), ofSeq(defaultArg(arcAssays, this$.GetRegisteredAssaysOrIdentifier())));
-        return Study_create_Z2D28E954(void 0, unwrap(patternInput[1]), unwrap(patternInput[0]), unwrap(this$.Title), unwrap(this$.Description), unwrap(this$.SubmissionDate), unwrap(this$.PublicReleaseDate), unwrap(Option_fromValueWithDefault(empty(), ofArray(this$.Publications))), unwrap(Option_fromValueWithDefault(empty(), ofArray(this$.Contacts))), unwrap(Option_fromValueWithDefault(empty(), ofArray(this$.StudyDesignDescriptors))), unwrap(protocols), unwrap(studyMaterials), unwrap(Option_fromValueWithDefault(empty(), processSeq)), unwrap(Option_fromValueWithDefault(empty(), assays)), unwrap(Option_fromValueWithDefault(empty(), ofArray(this$.Factors))), unwrap(Option_fromValueWithDefault(empty(), getCharacteristics(processSeq))), unwrap(Option_fromValueWithDefault(empty(), getUnits(processSeq))), unwrap(Option_fromValueWithDefault(empty(), ofArray(this$.Comments))));
-    }
-    static fromStudy(s) {
-        const tables = map_1((arg) => {
-            const t = ArcTables.fromProcesses(arg);
-            return t.Tables;
-        }, s.ProcessSequence);
-        let identifer;
-        const matchValue = s.FileName;
-        identifer = ((matchValue == null) ? createMissingIdentifier() : Study_identifierFromFileName(matchValue));
-        const assays = defaultArg(map_1((arg_1) => {
-            const collection = map_3((a) => ArcAssay.fromAssay(a), arg_1);
-            return Array.from(collection);
-        }, s.Assays), []);
-        let assaysIdentifiers;
-        const collection_1 = map_2((a_1) => a_1.Identifier, assays);
-        assaysIdentifiers = Array.from(collection_1);
-        return [ArcStudy.create(identifer, unwrap(s.Title), unwrap(s.Description), unwrap(s.SubmissionDate), unwrap(s.PublicReleaseDate), unwrap(map_1(toArray_1, s.Publications)), unwrap(map_1(toArray_1, s.Contacts)), unwrap(map_1(toArray_1, s.StudyDesignDescriptors)), unwrap(tables), assaysIdentifiers, unwrap(map_1(toArray_1, s.Factors)), unwrap(map_1(toArray_1, s.Comments))), assays];
-    }
     StructurallyEquals(other) {
-        let a, b, a_1, b_1, a_2, b_2, a_3, b_3, a_4, b_4, a_5, b_5, a_6, b_6;
+        let a, b, a_1, b_1, a_2, b_2, a_3, b_3, a_4, b_4, a_5, b_5;
         const this$ = this;
         return forAll((x) => (x === true), [this$.Identifier === other.Identifier, equals(this$.Title, other.Title), equals(this$.Description, other.Description), equals(this$.SubmissionDate, other.SubmissionDate), equals(this$.PublicReleaseDate, other.PublicReleaseDate), (a = this$.Publications, (b = other.Publications, (length(a) === length(b)) && fold((acc, e) => {
             if (acc) {
@@ -1184,54 +1182,62 @@ export class ArcStudy extends ArcTables {
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_1) => equals(item(i_1, a), item(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Contacts, (b_1 = other.Contacts, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
+        }, true, toList(delay(() => map((i_1) => equals(item(i_1, a), item(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Contacts, (b_1 = other.Contacts, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
             if (acc_1) {
                 return e_1;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_2) => equals(item(i_2, a_1), item(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.StudyDesignDescriptors, (b_2 = other.StudyDesignDescriptors, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
+        }, true, toList(delay(() => map((i_2) => equals(item(i_2, a_1), item(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.StudyDesignDescriptors, (b_2 = other.StudyDesignDescriptors, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
             if (acc_2) {
                 return e_2;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_3) => equals(item(i_3, a_2), item(i_3, b_2)), rangeDouble(0, 1, length(a_2) - 1))))))), (a_3 = this$.Tables, (b_3 = other.Tables, (length(a_3) === length(b_3)) && fold((acc_3, e_3) => {
+        }, true, toList(delay(() => map((i_3) => equals(item(i_3, a_2), item(i_3, b_2)), rangeDouble(0, 1, length(a_2) - 1))))))), (a_3 = this$.Tables, (b_3 = other.Tables, (length(a_3) === length(b_3)) && fold((acc_3, e_3) => {
             if (acc_3) {
                 return e_3;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_4) => equals(item(i_4, a_3), item(i_4, b_3)), rangeDouble(0, 1, length(a_3) - 1))))))), (a_4 = this$.RegisteredAssayIdentifiers, (b_4 = other.RegisteredAssayIdentifiers, (length(a_4) === length(b_4)) && fold((acc_4, e_4) => {
+        }, true, toList(delay(() => map((i_4) => equals(item(i_4, a_3), item(i_4, b_3)), rangeDouble(0, 1, length(a_3) - 1))))))), (a_4 = this$.RegisteredAssayIdentifiers, (b_4 = other.RegisteredAssayIdentifiers, (length(a_4) === length(b_4)) && fold((acc_4, e_4) => {
             if (acc_4) {
                 return e_4;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_5) => (item(i_5, a_4) === item(i_5, b_4)), rangeDouble(0, 1, length(a_4) - 1))))))), (a_5 = this$.Factors, (b_5 = other.Factors, (length(a_5) === length(b_5)) && fold((acc_5, e_5) => {
+        }, true, toList(delay(() => map((i_5) => (item(i_5, a_4) === item(i_5, b_4)), rangeDouble(0, 1, length(a_4) - 1))))))), (a_5 = this$.Comments, (b_5 = other.Comments, (length(a_5) === length(b_5)) && fold((acc_5, e_5) => {
             if (acc_5) {
                 return e_5;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_6) => equals(item(i_6, a_5), item(i_6, b_5)), rangeDouble(0, 1, length(a_5) - 1))))))), (a_6 = this$.Comments, (b_6 = other.Comments, (length(a_6) === length(b_6)) && fold((acc_6, e_6) => {
-            if (acc_6) {
-                return e_6;
-            }
-            else {
-                return false;
-            }
-        }, true, toList(delay(() => map_2((i_7) => equals(item(i_7, a_6), item(i_7, b_6)), rangeDouble(0, 1, length(a_6) - 1)))))))]);
+        }, true, toList(delay(() => map((i_6) => equals(item(i_6, a_5), item(i_6, b_5)), rangeDouble(0, 1, length(a_5) - 1)))))))]);
     }
     ReferenceEquals(other) {
         const this$ = this;
         return this$ === other;
     }
+    toString() {
+        const this$ = this;
+        const arg = this$.Identifier;
+        const arg_1 = this$.Title;
+        const arg_2 = this$.Description;
+        const arg_3 = this$.SubmissionDate;
+        const arg_4 = this$.PublicReleaseDate;
+        const arg_5 = this$.Publications;
+        const arg_6 = this$.Contacts;
+        const arg_7 = this$.StudyDesignDescriptors;
+        const arg_8 = this$.Tables;
+        const arg_9 = this$.RegisteredAssayIdentifiers;
+        const arg_10 = this$.Comments;
+        return toText(printf("ArcStudy {\r\n    Identifier = %A,\r\n    Title = %A,\r\n    Description = %A,\r\n    SubmissionDate = %A,\r\n    PublicReleaseDate = %A,\r\n    Publications = %A,\r\n    Contacts = %A,\r\n    StudyDesignDescriptors = %A,\r\n    Tables = %A,\r\n    RegisteredAssayIdentifiers = %A,\r\n    Comments = %A,\r\n}"))(arg)(arg_1)(arg_2)(arg_3)(arg_4)(arg_5)(arg_6)(arg_7)(arg_8)(arg_9)(arg_10);
+    }
     Equals(other) {
         let s;
         const this$ = this;
@@ -1239,20 +1245,20 @@ export class ArcStudy extends ArcTables {
     }
     GetHashCode() {
         const this$ = this;
-        return HashCodes_boxHashArray([this$.Identifier, HashCodes_boxHashOption(this$.Title), HashCodes_boxHashOption(this$.Description), HashCodes_boxHashOption(this$.SubmissionDate), HashCodes_boxHashOption(this$.PublicReleaseDate), HashCodes_boxHashArray(this$.Publications), HashCodes_boxHashArray(this$.Contacts), HashCodes_boxHashArray(this$.StudyDesignDescriptors), HashCodes_boxHashArray(Array.from(this$.Tables)), HashCodes_boxHashArray(Array.from(this$.RegisteredAssayIdentifiers)), HashCodes_boxHashArray(this$.Factors), HashCodes_boxHashArray(this$.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$.Comments)]) | 0;
     }
     GetLightHashCode() {
         const this$ = this;
-        return HashCodes_boxHashArray([this$.Identifier, HashCodes_boxHashOption(this$.Title), HashCodes_boxHashOption(this$.Description), HashCodes_boxHashOption(this$.SubmissionDate), HashCodes_boxHashOption(this$.PublicReleaseDate), HashCodes_boxHashArray(this$.Publications), HashCodes_boxHashArray(this$.Contacts), HashCodes_boxHashArray(this$.StudyDesignDescriptors), HashCodes_boxHashArray(Array.from(this$.Tables)), HashCodes_boxHashArray(this$.Factors), HashCodes_boxHashArray(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$.Comments)]) | 0;
     }
 }
 
 export function ArcStudy_$reflection() {
-    return class_type("ARCtrl.ISA.ArcStudy", void 0, ArcStudy, ArcTables_$reflection());
+    return class_type("ARCtrl.ArcStudy", void 0, ArcStudy, ArcTables_$reflection());
 }
 
-export function ArcStudy_$ctor_Z4F2D842F(identifier, title, description, submissionDate, publicReleaseDate, publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, factors, comments) {
-    return new ArcStudy(identifier, title, description, submissionDate, publicReleaseDate, publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, factors, comments);
+export function ArcStudy_$ctor_Z187CCF3B(identifier, title, description, submissionDate, publicReleaseDate, publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, comments) {
+    return new ArcStudy(identifier, title, description, submissionDate, publicReleaseDate, publications, contacts, studyDesignDescriptors, tables, registeredAssayIdentifiers, comments);
 }
 
 export class ArcInvestigation {
@@ -1291,125 +1297,125 @@ export class ArcInvestigation {
         const registeredStudyIdentifiers_1 = defaultArg(registeredStudyIdentifiers, []);
         const comments_1 = defaultArg(comments, []);
         const remarks_1 = defaultArg(remarks, []);
-        this["identifier@1195"] = identifier;
-        this["title@1196"] = title;
-        this["description@1197"] = description;
-        this["submissionDate@1198"] = submissionDate;
-        this["publicReleaseDate@1199"] = publicReleaseDate;
-        this["ontologySourceReferences@1200-1"] = ontologySourceReferences_1;
-        this["publications@1201-1"] = publications_1;
-        this["contacts@1202-1"] = contacts_1;
-        this["assays@1203-1"] = assays_1;
-        this["studies@1204-1"] = studies_1;
-        this["registeredStudyIdentifiers@1205-1"] = registeredStudyIdentifiers_1;
-        this["comments@1206-1"] = comments_1;
-        this["remarks@1207-1"] = remarks_1;
+        this["identifier@1089"] = identifier;
+        this["title@1090"] = title;
+        this["description@1091"] = description;
+        this["submissionDate@1092"] = submissionDate;
+        this["publicReleaseDate@1093"] = publicReleaseDate;
+        this["ontologySourceReferences@1094-1"] = ontologySourceReferences_1;
+        this["publications@1095-1"] = publications_1;
+        this["contacts@1096-1"] = contacts_1;
+        this["assays@1097-1"] = assays_1;
+        this["studies@1098-1"] = studies_1;
+        this["registeredStudyIdentifiers@1099-1"] = registeredStudyIdentifiers_1;
+        this["comments@1100-1"] = comments_1;
+        this["remarks@1101-1"] = remarks_1;
         this.staticHash = 0;
-        this["init@1176"] = 1;
+        this["init@1070"] = 1;
     }
     get Identifier() {
         const this$ = this;
-        return this$["identifier@1195"];
+        return this$["identifier@1089"];
     }
     set Identifier(i) {
         const this$ = this;
-        this$["identifier@1195"] = i;
+        this$["identifier@1089"] = i;
     }
     get Title() {
         const this$ = this;
-        return unwrap(this$["title@1196"]);
+        return unwrap(this$["title@1090"]);
     }
     set Title(n) {
         const this$ = this;
-        this$["title@1196"] = n;
+        this$["title@1090"] = n;
     }
     get Description() {
         const this$ = this;
-        return unwrap(this$["description@1197"]);
+        return unwrap(this$["description@1091"]);
     }
     set Description(n) {
         const this$ = this;
-        this$["description@1197"] = n;
+        this$["description@1091"] = n;
     }
     get SubmissionDate() {
         const this$ = this;
-        return unwrap(this$["submissionDate@1198"]);
+        return unwrap(this$["submissionDate@1092"]);
     }
     set SubmissionDate(n) {
         const this$ = this;
-        this$["submissionDate@1198"] = n;
+        this$["submissionDate@1092"] = n;
     }
     get PublicReleaseDate() {
         const this$ = this;
-        return unwrap(this$["publicReleaseDate@1199"]);
+        return unwrap(this$["publicReleaseDate@1093"]);
     }
     set PublicReleaseDate(n) {
         const this$ = this;
-        this$["publicReleaseDate@1199"] = n;
+        this$["publicReleaseDate@1093"] = n;
     }
     get OntologySourceReferences() {
         const this$ = this;
-        return this$["ontologySourceReferences@1200-1"];
+        return this$["ontologySourceReferences@1094-1"];
     }
     set OntologySourceReferences(n) {
         const this$ = this;
-        this$["ontologySourceReferences@1200-1"] = n;
+        this$["ontologySourceReferences@1094-1"] = n;
     }
     get Publications() {
         const this$ = this;
-        return this$["publications@1201-1"];
+        return this$["publications@1095-1"];
     }
     set Publications(n) {
         const this$ = this;
-        this$["publications@1201-1"] = n;
+        this$["publications@1095-1"] = n;
     }
     get Contacts() {
         const this$ = this;
-        return this$["contacts@1202-1"];
+        return this$["contacts@1096-1"];
     }
     set Contacts(n) {
         const this$ = this;
-        this$["contacts@1202-1"] = n;
+        this$["contacts@1096-1"] = n;
     }
     get Assays() {
         const this$ = this;
-        return this$["assays@1203-1"];
+        return this$["assays@1097-1"];
     }
     set Assays(n) {
         const this$ = this;
-        this$["assays@1203-1"] = n;
+        this$["assays@1097-1"] = n;
     }
     get Studies() {
         const this$ = this;
-        return this$["studies@1204-1"];
+        return this$["studies@1098-1"];
     }
     set Studies(n) {
         const this$ = this;
-        this$["studies@1204-1"] = n;
+        this$["studies@1098-1"] = n;
     }
     get RegisteredStudyIdentifiers() {
         const this$ = this;
-        return this$["registeredStudyIdentifiers@1205-1"];
+        return this$["registeredStudyIdentifiers@1099-1"];
     }
     set RegisteredStudyIdentifiers(n) {
         const this$ = this;
-        this$["registeredStudyIdentifiers@1205-1"] = n;
+        this$["registeredStudyIdentifiers@1099-1"] = n;
     }
     get Comments() {
         const this$ = this;
-        return this$["comments@1206-1"];
+        return this$["comments@1100-1"];
     }
     set Comments(n) {
         const this$ = this;
-        this$["comments@1206-1"] = n;
+        this$["comments@1100-1"] = n;
     }
     get Remarks() {
         const this$ = this;
-        return this$["remarks@1207-1"];
+        return this$["remarks@1101-1"];
     }
     set Remarks(n) {
         const this$ = this;
-        this$["remarks@1207-1"] = n;
+        this$["remarks@1101-1"] = n;
     }
     get StaticHash() {
         const this$ = this;
@@ -1437,16 +1443,16 @@ export class ArcInvestigation {
     }
     get AssayIdentifiers() {
         const this$ = this;
-        return Array.from(map_2((x) => x.Identifier, this$.Assays));
+        return Array.from(map((x) => x.Identifier, this$.Assays));
     }
     get UnregisteredAssays() {
         const this$ = this;
         return ResizeArray_filter((a) => !exists((s) => exists((i) => (i === a.Identifier), s.RegisteredAssayIdentifiers), this$.RegisteredStudies), this$.Assays);
     }
-    AddAssay(assay) {
+    AddAssay(assay, registerIn) {
         const this$ = this;
         const assayIdent = assay.Identifier;
-        const matchValue = tryFindIndex((x_1) => (x_1 === assayIdent), map_2((x) => x.Identifier, this$.Assays));
+        const matchValue = tryFindIndex((x_1) => (x_1 === assayIdent), map((x) => x.Identifier, this$.Assays));
         if (matchValue == null) {
         }
         else {
@@ -1454,24 +1460,36 @@ export class ArcInvestigation {
         }
         assay.Investigation = this$;
         void (this$.Assays.push(assay));
+        if (registerIn != null) {
+            let enumerator = getEnumerator(value_4(registerIn));
+            try {
+                while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+                    const study = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                    study.RegisterAssay(assay.Identifier);
+                }
+            }
+            finally {
+                disposeSafe(enumerator);
+            }
+        }
     }
-    static addAssay(assay) {
+    static addAssay(assay, registerIn) {
         return (inv) => {
             const newInvestigation = inv.Copy();
-            newInvestigation.AddAssay(assay);
+            newInvestigation.AddAssay(assay, unwrap(registerIn));
             return newInvestigation;
         };
     }
-    InitAssay(assayIdentifier) {
+    InitAssay(assayIdentifier, registerIn) {
         const this$ = this;
         const assay = new ArcAssay(assayIdentifier);
-        this$.AddAssay(assay);
+        this$.AddAssay(assay, unwrap(registerIn));
         return assay;
     }
-    static initAssay(assayIdentifier) {
+    static initAssay(assayIdentifier, registerIn) {
         return (inv) => {
             const newInvestigation = inv.Copy();
-            return newInvestigation.InitAssay(assayIdentifier);
+            return newInvestigation.InitAssay(assayIdentifier, unwrap(registerIn));
         };
     }
     DeleteAssayAt(index) {
@@ -1534,7 +1552,7 @@ export class ArcInvestigation {
     SetAssayAt(index, assay) {
         const this$ = this;
         const assayIdent = assay.Identifier;
-        const matchValue = tryFindIndex((x) => (x === assayIdent), map_2((a) => a.Identifier, removeAt(index, this$.Assays)));
+        const matchValue = tryFindIndex((x) => (x === assayIdent), map((a) => a.Identifier, removeAt(index, this$.Assays)));
         if (matchValue == null) {
         }
         else {
@@ -1639,7 +1657,7 @@ export class ArcInvestigation {
     }
     get StudyIdentifiers() {
         const this$ = this;
-        return toArray(map_2((x) => x.Identifier, this$.Studies));
+        return toArray(map((x) => x.Identifier, this$.Studies));
     }
     get UnregisteredStudies() {
         const this$ = this;
@@ -1853,7 +1871,7 @@ export class ArcInvestigation {
     RegisterAssayAt(studyIndex, assayIdentifier) {
         const this$ = this;
         const study = this$.GetStudyAt(studyIndex);
-        const matchValue = tryFind((x) => (x === assayIdentifier), map_2((a) => a.Identifier, this$.Assays));
+        const matchValue = tryFind((x) => (x === assayIdentifier), map((a) => a.Identifier, this$.Assays));
         if (matchValue != null) {
         }
         else {
@@ -2013,7 +2031,7 @@ export class ArcInvestigation {
     UpdateIOTypeByEntityID() {
         let collection;
         const this$ = this;
-        const ioMap = ArcTablesAux_getIOMap((collection = toList(delay(() => append_4(collect((study) => study.Tables, this$.Studies), delay(() => collect((assay) => assay.Tables, this$.Assays))))), Array.from(collection)));
+        const ioMap = ArcTablesAux_getIOMap((collection = toList(delay(() => append_3(collect((study) => study.Tables, this$.Studies), delay(() => collect((assay) => assay.Tables, this$.Assays))))), Array.from(collection)));
         let enumerator = getEnumerator(this$.Studies);
         try {
             while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
@@ -2061,37 +2079,14 @@ export class ArcInvestigation {
         finally {
             disposeSafe(enumerator_1);
         }
-        const nextComments = map((c) => c.Copy(), this$.Comments);
-        const nextRemarks = map((c_1) => c_1.Copy(), this$.Remarks);
-        const nextContacts = map((c_2) => c_2.Copy(), this$.Contacts);
-        const nextPublications = map((c_3) => c_3.Copy(), this$.Publications);
-        const nextOntologySourceReferences = map((c_4) => c_4.Copy(), this$.OntologySourceReferences);
+        const nextComments = ResizeArray_map((c) => c.Copy(), this$.Comments);
+        const nextRemarks = ResizeArray_map((c_1) => c_1.Copy(), this$.Remarks);
+        const nextContacts = ResizeArray_map((c_2) => c_2.Copy(), this$.Contacts);
+        const nextPublications = ResizeArray_map((c_3) => c_3.Copy(), this$.Publications);
+        const nextOntologySourceReferences = ResizeArray_map((c_4) => c_4.Copy(), this$.OntologySourceReferences);
         const nextStudyIdentifiers = Array.from(this$.RegisteredStudyIdentifiers);
         return new ArcInvestigation(this$.Identifier, unwrap(this$.Title), unwrap(this$.Description), unwrap(this$.SubmissionDate), unwrap(this$.PublicReleaseDate), nextOntologySourceReferences, nextPublications, nextContacts, nextAssays, nextStudies, nextStudyIdentifiers, nextComments, nextRemarks);
     }
-    ToInvestigation() {
-        const this$ = this;
-        const studies = Option_fromValueWithDefault(empty(), map_3((a) => a.ToStudy(), toList(this$.RegisteredStudies)));
-        return Investigation_create_4AD66BBE(void 0, "isa.investigation.xlsx", isMissingIdentifier(this$.Identifier) ? void 0 : this$.Identifier, this$.Title, this$.Description, this$.SubmissionDate, this$.PublicReleaseDate, void 0, Option_fromValueWithDefault(empty(), ofArray(this$.Publications)), Option_fromValueWithDefault(empty(), ofArray(this$.Contacts)), studies, Option_fromValueWithDefault(empty(), ofArray(this$.Comments)));
-    }
-    static fromInvestigation(i) {
-        let identifer;
-        const matchValue = i.Identifier;
-        identifer = ((matchValue == null) ? createMissingIdentifier() : matchValue);
-        const patternInput = unzip(map_3((s) => ArcStudy.fromStudy(s), defaultArg(i.Studies, empty())));
-        const studiesRaw = patternInput[0];
-        const studies = Array.from(studiesRaw);
-        let studyIdentifiers;
-        const collection = map_2((a) => a.Identifier, studiesRaw);
-        studyIdentifiers = Array.from(collection);
-        let assays;
-        const collection_1 = distinctBy((a_1) => a_1.Identifier, concat(patternInput[1]), {
-            Equals: (x, y) => (x === y),
-            GetHashCode: stringHash,
-        });
-        assays = Array.from(collection_1);
-        return ArcInvestigation.create(identifer, i.Title, i.Description, i.SubmissionDate, i.PublicReleaseDate, void 0, map_1(toArray_1, i.Publications), map_1(toArray_1, i.Contacts), assays, studies, studyIdentifiers, map_1(toArray_1, i.Comments));
-    }
     StructurallyEquals(other) {
         let a, b, a_1, b_1, a_2, b_2, a_3, b_3, a_4, b_4, a_5, b_5, a_6, b_6, a_7, b_7;
         const this$ = this;
@@ -2102,61 +2097,78 @@ export class ArcInvestigation {
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_1) => equals(item(i_1, a), item(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Contacts, (b_1 = other.Contacts, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
+        }, true, toList(delay(() => map((i_1) => equals(item(i_1, a), item(i_1, b)), rangeDouble(0, 1, length(a) - 1))))))), (a_1 = this$.Contacts, (b_1 = other.Contacts, (length(a_1) === length(b_1)) && fold((acc_1, e_1) => {
             if (acc_1) {
                 return e_1;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_2) => equals(item(i_2, a_1), item(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.OntologySourceReferences, (b_2 = other.OntologySourceReferences, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
+        }, true, toList(delay(() => map((i_2) => equals(item(i_2, a_1), item(i_2, b_1)), rangeDouble(0, 1, length(a_1) - 1))))))), (a_2 = this$.OntologySourceReferences, (b_2 = other.OntologySourceReferences, (length(a_2) === length(b_2)) && fold((acc_2, e_2) => {
             if (acc_2) {
                 return e_2;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_3) => equals(item(i_3, a_2), item(i_3, b_2)), rangeDouble(0, 1, length(a_2) - 1))))))), (a_3 = this$.Assays, (b_3 = other.Assays, (length(a_3) === length(b_3)) && fold((acc_3, e_3) => {
+        }, true, toList(delay(() => map((i_3) => equals(item(i_3, a_2), item(i_3, b_2)), rangeDouble(0, 1, length(a_2) - 1))))))), (a_3 = this$.Assays, (b_3 = other.Assays, (length(a_3) === length(b_3)) && fold((acc_3, e_3) => {
             if (acc_3) {
                 return e_3;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_4) => equals(item(i_4, a_3), item(i_4, b_3)), rangeDouble(0, 1, length(a_3) - 1))))))), (a_4 = this$.Studies, (b_4 = other.Studies, (length(a_4) === length(b_4)) && fold((acc_4, e_4) => {
+        }, true, toList(delay(() => map((i_4) => equals(item(i_4, a_3), item(i_4, b_3)), rangeDouble(0, 1, length(a_3) - 1))))))), (a_4 = this$.Studies, (b_4 = other.Studies, (length(a_4) === length(b_4)) && fold((acc_4, e_4) => {
             if (acc_4) {
                 return e_4;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_5) => equals(item(i_5, a_4), item(i_5, b_4)), rangeDouble(0, 1, length(a_4) - 1))))))), (a_5 = this$.RegisteredStudyIdentifiers, (b_5 = other.RegisteredStudyIdentifiers, (length(a_5) === length(b_5)) && fold((acc_5, e_5) => {
+        }, true, toList(delay(() => map((i_5) => equals(item(i_5, a_4), item(i_5, b_4)), rangeDouble(0, 1, length(a_4) - 1))))))), (a_5 = this$.RegisteredStudyIdentifiers, (b_5 = other.RegisteredStudyIdentifiers, (length(a_5) === length(b_5)) && fold((acc_5, e_5) => {
             if (acc_5) {
                 return e_5;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_6) => (item(i_6, a_5) === item(i_6, b_5)), rangeDouble(0, 1, length(a_5) - 1))))))), (a_6 = this$.Comments, (b_6 = other.Comments, (length(a_6) === length(b_6)) && fold((acc_6, e_6) => {
+        }, true, toList(delay(() => map((i_6) => (item(i_6, a_5) === item(i_6, b_5)), rangeDouble(0, 1, length(a_5) - 1))))))), (a_6 = this$.Comments, (b_6 = other.Comments, (length(a_6) === length(b_6)) && fold((acc_6, e_6) => {
             if (acc_6) {
                 return e_6;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_7) => equals(item(i_7, a_6), item(i_7, b_6)), rangeDouble(0, 1, length(a_6) - 1))))))), (a_7 = this$.Remarks, (b_7 = other.Remarks, (length(a_7) === length(b_7)) && fold((acc_7, e_7) => {
+        }, true, toList(delay(() => map((i_7) => equals(item(i_7, a_6), item(i_7, b_6)), rangeDouble(0, 1, length(a_6) - 1))))))), (a_7 = this$.Remarks, (b_7 = other.Remarks, (length(a_7) === length(b_7)) && fold((acc_7, e_7) => {
             if (acc_7) {
                 return e_7;
             }
             else {
                 return false;
             }
-        }, true, toList(delay(() => map_2((i_8) => equals(item(i_8, a_7), item(i_8, b_7)), rangeDouble(0, 1, length(a_7) - 1)))))))]);
+        }, true, toList(delay(() => map((i_8) => equals(item(i_8, a_7), item(i_8, b_7)), rangeDouble(0, 1, length(a_7) - 1)))))))]);
     }
     ReferenceEquals(other) {
         const this$ = this;
         return this$ === other;
     }
+    toString() {
+        const this$ = this;
+        const arg = this$.Identifier;
+        const arg_1 = this$.Title;
+        const arg_2 = this$.Description;
+        const arg_3 = this$.SubmissionDate;
+        const arg_4 = this$.PublicReleaseDate;
+        const arg_5 = this$.OntologySourceReferences;
+        const arg_6 = this$.Publications;
+        const arg_7 = this$.Contacts;
+        const arg_8 = this$.Assays;
+        const arg_9 = this$.Studies;
+        const arg_10 = this$.RegisteredStudyIdentifiers;
+        const arg_11 = this$.Comments;
+        const arg_12 = this$.Remarks;
+        return toText(printf("ArcStudy {\r\n    Identifier = %A,\r\n    Title = %A,\r\n    Description = %A,\r\n    SubmissionDate = %A,\r\n    PublicReleaseDate = %A,\r\n    OntologySourceReferences = %A,\r\n    Publications = %A,\r\n    Contacts = %A,\r\n    Assays = %A,\r\n    Studies = %A,\r\n    RegisteredStudyIdentifiers = %A,\r\n    Comments = %A,\r\n    Remarks = %A,\r\n}"))(arg)(arg_1)(arg_2)(arg_3)(arg_4)(arg_5)(arg_6)(arg_7)(arg_8)(arg_9)(arg_10)(arg_11)(arg_12);
+    }
     Equals(other) {
         let i;
         const this$ = this;
@@ -2164,19 +2176,19 @@ export class ArcInvestigation {
     }
     GetHashCode() {
         const this$ = this;
-        return HashCodes_boxHashArray([this$.Identifier, HashCodes_boxHashOption(this$.Title), HashCodes_boxHashOption(this$.Description), HashCodes_boxHashOption(this$.SubmissionDate), HashCodes_boxHashOption(this$.PublicReleaseDate), HashCodes_boxHashArray(this$.Publications), HashCodes_boxHashArray(this$.Contacts), HashCodes_boxHashArray(this$.OntologySourceReferences), HashCodes_boxHashArray(Array.from(this$.Assays)), HashCodes_boxHashArray(Array.from(this$.Studies)), HashCodes_boxHashArray(Array.from(this$.RegisteredStudyIdentifiers)), HashCodes_boxHashArray(this$.Comments), HashCodes_boxHashArray(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$.OntologySourceReferences), boxHashSeq(this$.Assays), boxHashSeq(this$.Studies), boxHashSeq(this$.RegisteredStudyIdentifiers), boxHashSeq(this$.Comments), boxHashSeq(this$.Remarks)]) | 0;
     }
     GetLightHashCode() {
         const this$ = this;
-        return HashCodes_boxHashArray([this$.Identifier, HashCodes_boxHashOption(this$.Title), HashCodes_boxHashOption(this$.Description), HashCodes_boxHashOption(this$.SubmissionDate), HashCodes_boxHashOption(this$.PublicReleaseDate), HashCodes_boxHashArray(this$.Publications), HashCodes_boxHashArray(this$.Contacts), HashCodes_boxHashArray(this$.OntologySourceReferences), HashCodes_boxHashArray(this$.Comments), HashCodes_boxHashArray(this$.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$.Comments), boxHashSeq(this$.Remarks)]) | 0;
     }
 }
 
 export function ArcInvestigation_$reflection() {
-    return class_type("ARCtrl.ISA.ArcInvestigation", void 0, ArcInvestigation);
+    return class_type("ARCtrl.ArcInvestigation", void 0, ArcInvestigation);
 }
 
-export function ArcInvestigation_$ctor_21AB11E9(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, registeredStudyIdentifiers, comments, remarks) {
+export function ArcInvestigation_$ctor_Z2ED5C612(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, registeredStudyIdentifiers, comments, remarks) {
     return new ArcInvestigation(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, registeredStudyIdentifiers, comments, remarks);
 }