@nfdi4plants/arctrl 1.2.0 → 2.0.0-alpha.2

package/{ISA/ISA/JsonTypes → Core/Process}/Sample.js

@@ -1,8 +1,8 @@
-import { Record, toString } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
-import { append, choose, empty, length } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
-import { defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { printf, toText } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
-import { record_type, list_type, option_type, string_type } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Record, toString } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
+import { append, choose, empty, length } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { printf, toText } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { record_type, list_type, option_type, string_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
 import { MaterialAttributeValue_$reflection } from "./MaterialAttributeValue.js";
 import { FactorValue_$reflection } from "./FactorValue.js";
 import { Source_$reflection } from "./Source.js";
@@ -30,35 +30,35 @@ export class Sample extends Record {
 }
 
 export function Sample_$reflection() {
-    return record_type("ARCtrl.ISA.Sample", [], Sample, () => [["ID", option_type(string_type)], ["Name", option_type(string_type)], ["Characteristics", option_type(list_type(MaterialAttributeValue_$reflection()))], ["FactorValues", option_type(list_type(FactorValue_$reflection()))], ["DerivesFrom", option_type(list_type(Source_$reflection()))]]);
+    return record_type("ARCtrl.Process.Sample", [], Sample, () => [["ID", option_type(string_type)], ["Name", option_type(string_type)], ["Characteristics", option_type(list_type(MaterialAttributeValue_$reflection()))], ["FactorValues", option_type(list_type(FactorValue_$reflection()))], ["DerivesFrom", option_type(list_type(Source_$reflection()))]]);
 }
 
 export function Sample_make(id, name, characteristics, factorValues, derivesFrom) {
     return new Sample(id, name, characteristics, factorValues, derivesFrom);
 }
 
-export function Sample_create_E50ED22(Id, Name, Characteristics, FactorValues, DerivesFrom) {
+export function Sample_create_62424AD2(Id, Name, Characteristics, FactorValues, DerivesFrom) {
     return Sample_make(Id, Name, Characteristics, FactorValues, DerivesFrom);
 }
 
 export function Sample_get_empty() {
-    return Sample_create_E50ED22();
+    return Sample_create_62424AD2();
 }
 
 export function Sample__get_NameAsString(this$) {
     return defaultArg(this$.Name, "");
 }
 
-export function Sample_getCharacteristicUnits_Z29207F1E(s) {
+export function Sample_getCharacteristicUnits_53716792(s) {
     return choose((c) => c.Unit, defaultArg(s.Characteristics, empty()));
 }
 
-export function Sample_getFactorUnits_Z29207F1E(s) {
+export function Sample_getFactorUnits_53716792(s) {
     return choose((c) => c.Unit, defaultArg(s.FactorValues, empty()));
 }
 
-export function Sample_getUnits_Z29207F1E(s) {
-    return append(Sample_getCharacteristicUnits_Z29207F1E(s), Sample_getFactorUnits_Z29207F1E(s));
+export function Sample_getUnits_53716792(s) {
+    return append(Sample_getCharacteristicUnits_53716792(s), Sample_getFactorUnits_53716792(s));
 }
 
 export function Sample_setCharacteristicValues(values, s) {

package/{ISA/ISA/JsonTypes → Core/Process}/Source.js

@@ -1,8 +1,8 @@
-import { Record, toString } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
-import { choose, empty, length } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
-import { defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { printf, toText } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
-import { record_type, list_type, option_type, string_type } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Record, toString } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
+import { choose, empty, length } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { printf, toText } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { record_type, list_type, option_type, string_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
 import { MaterialAttributeValue_$reflection } from "./MaterialAttributeValue.js";
 
 export class Source extends Record {
@@ -25,26 +25,26 @@ export class Source extends Record {
 }
 
 export function Source_$reflection() {
-    return record_type("ARCtrl.ISA.Source", [], Source, () => [["ID", option_type(string_type)], ["Name", option_type(string_type)], ["Characteristics", option_type(list_type(MaterialAttributeValue_$reflection()))]]);
+    return record_type("ARCtrl.Process.Source", [], Source, () => [["ID", option_type(string_type)], ["Name", option_type(string_type)], ["Characteristics", option_type(list_type(MaterialAttributeValue_$reflection()))]]);
 }
 
 export function Source_make(id, name, characteristics) {
     return new Source(id, name, characteristics);
 }
 
-export function Source_create_7A281ED9(Id, Name, Characteristics) {
+export function Source_create_Z5CA08497(Id, Name, Characteristics) {
     return Source_make(Id, Name, Characteristics);
 }
 
 export function Source_get_empty() {
-    return Source_create_7A281ED9();
+    return Source_create_Z5CA08497();
 }
 
 export function Source__get_NameAsString(this$) {
     return defaultArg(this$.Name, "");
 }
 
-export function Source_getUnits_Z28BE5327(m) {
+export function Source_getUnits_53E41069(m) {
     return choose((c) => c.Unit, defaultArg(m.Characteristics, empty()));
 }
 

package/{ISA/ISA/JsonTypes → Core/Process}/Value.js

@@ -1,11 +1,11 @@
-import { tryParse } from "../../../fable_modules/fable-library-js.4.13.0/Int32.js";
-import { Union, toString, FSharpRef } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
-import { tryParse as tryParse_1 } from "../../../fable_modules/fable-library-js.4.13.0/Double.js";
-import { OntologyAnnotation_$reflection, OntologyAnnotation } from "./OntologyAnnotation.js";
-import { defaultArg } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { int32ToString } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { printf, toText } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
-import { union_type, string_type, float64_type, int32_type } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { tryParse } from "../../fable_modules/fable-library-js.4.16.0/Int32.js";
+import { Union, toString, FSharpRef } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
+import { tryParse as tryParse_1 } from "../../fable_modules/fable-library-js.4.16.0/Double.js";
+import { OntologyAnnotation_$reflection, OntologyAnnotation } from "../OntologyAnnotation.js";
+import { defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { int32ToString } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
+import { printf, toText } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { union_type, string_type, float64_type, int32_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
 
 export class Value extends Union {
     constructor(tag, fields) {
@@ -28,15 +28,15 @@ export class Value extends Union {
         else {
             let matchValue_1;
             let outArg_1 = 0;
-            matchValue_1 = [tryParse_1(value, new FSharpRef(() => outArg_1, (v_1) => {
-                outArg_1 = v_1;
+            matchValue_1 = [tryParse_1(value, new FSharpRef(() => outArg_1, (v_2) => {
+                outArg_1 = v_2;
             })), outArg_1];
-            return matchValue_1[0] ? (new Value(2, [matchValue_1[1]])) : (new Value(3, [value]));
+            return matchValue_1[0] ? (new Value(2, [matchValue_1[1]])) : (new Value(0, [OntologyAnnotation.create(value)]));
         }
     }
     static fromOptions(value, termSource, termAccesssion) {
         let value_1;
-        return (value == null) ? ((termSource == null) ? ((termAccesssion == null) ? void 0 : (new Value(0, [OntologyAnnotation.fromString(defaultArg(value, ""), termSource, termAccesssion)]))) : (new Value(0, [OntologyAnnotation.fromString(defaultArg(value, ""), termSource, termAccesssion)]))) : ((termSource == null) ? ((termAccesssion == null) ? ((value_1 = value, Value.fromString(value_1))) : (new Value(0, [OntologyAnnotation.fromString(defaultArg(value, ""), termSource, termAccesssion)]))) : (new Value(0, [OntologyAnnotation.fromString(defaultArg(value, ""), termSource, termAccesssion)])));
+        return (value == null) ? ((termSource == null) ? ((termAccesssion == null) ? void 0 : (new Value(0, [OntologyAnnotation.create(defaultArg(value, ""), termSource, termAccesssion)]))) : (new Value(0, [OntologyAnnotation.create(defaultArg(value, ""), termSource, termAccesssion)]))) : ((termSource == null) ? ((termAccesssion == null) ? ((value_1 = value, Value.fromString(value_1))) : (new Value(0, [OntologyAnnotation.create(defaultArg(value, ""), termSource, termAccesssion)]))) : (new Value(0, [OntologyAnnotation.create(defaultArg(value, ""), termSource, termAccesssion)])));
     }
     static toOptions(value) {
         switch (value.tag) {
@@ -132,6 +132,6 @@ export class Value extends Union {
 }
 
 export function Value_$reflection() {
-    return union_type("ARCtrl.ISA.Value", [], Value, () => [[["Item", OntologyAnnotation_$reflection()]], [["Item", int32_type]], [["Item", float64_type]], [["Item", string_type]]]);
+    return union_type("ARCtrl.Process.Value", [], Value, () => [[["Item", OntologyAnnotation_$reflection()]], [["Item", int32_type]], [["Item", float64_type]], [["Item", string_type]]]);
 }
 

package/Core/Publication.js

@@ -0,0 +1,116 @@
+import { map as map_1, defaultArg, unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { ResizeArray_map } from "./Helper/Collections.js";
+import { boxHashSeq, boxHashOption, boxHashArray } from "./Helper/HashCodes.js";
+import { safeHash } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { StringBuilder__Append_Z721C83C5, StringBuilder_$ctor } from "../fable_modules/fable-library-js.4.16.0/System.Text.js";
+import { printf, toText, join } from "../fable_modules/fable-library-js.4.16.0/String.js";
+import { ofArray, choose, map } from "../fable_modules/fable-library-js.4.16.0/List.js";
+import { length } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { toString } from "../fable_modules/fable-library-js.4.16.0/Types.js";
+import { class_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
+
+export class Publication {
+    constructor(pubMedID, doi, authors, title, status, comments) {
+        this._pubMedID = pubMedID;
+        this._doi = doi;
+        this._authors = authors;
+        this._title = title;
+        this._status = status;
+        this._comments = defaultArg(comments, []);
+    }
+    get PubMedID() {
+        const this$ = this;
+        return unwrap(this$._pubMedID);
+    }
+    set PubMedID(pubMedID) {
+        const this$ = this;
+        this$._pubMedID = pubMedID;
+    }
+    get DOI() {
+        const this$ = this;
+        return unwrap(this$._doi);
+    }
+    set DOI(doi) {
+        const this$ = this;
+        this$._doi = doi;
+    }
+    get Authors() {
+        const this$ = this;
+        return unwrap(this$._authors);
+    }
+    set Authors(authors) {
+        const this$ = this;
+        this$._authors = authors;
+    }
+    get Title() {
+        const this$ = this;
+        return unwrap(this$._title);
+    }
+    set Title(title) {
+        const this$ = this;
+        this$._title = title;
+    }
+    get Status() {
+        const this$ = this;
+        return unwrap(this$._status);
+    }
+    set Status(status) {
+        const this$ = this;
+        this$._status = status;
+    }
+    get Comments() {
+        const this$ = this;
+        return this$._comments;
+    }
+    set Comments(comments) {
+        const this$ = this;
+        this$._comments = comments;
+    }
+    static make(pubMedID, doi, authors, title, status, comments) {
+        return new Publication(unwrap(pubMedID), unwrap(doi), unwrap(authors), unwrap(title), unwrap(status), comments);
+    }
+    static create(pubMedID, doi, authors, title, status, comments) {
+        const comments_1 = defaultArg(comments, []);
+        return Publication.make(pubMedID, doi, authors, title, status, comments_1);
+    }
+    static empty() {
+        return Publication.create();
+    }
+    Copy() {
+        const this$ = this;
+        const nextComments = ResizeArray_map((c) => c.Copy(), this$.Comments);
+        const pubMedID = this$.PubMedID;
+        const doi = this$.DOI;
+        const authors = this$.Authors;
+        const title = this$.Title;
+        const status = this$.Status;
+        return Publication.make(pubMedID, doi, authors, title, status, nextComments);
+    }
+    GetHashCode() {
+        const this$ = this;
+        return boxHashArray([boxHashOption(this$.DOI), boxHashOption(this$.Title), boxHashOption(this$.Authors), boxHashOption(this$.PubMedID), boxHashOption(this$.Status), boxHashSeq(this$.Comments)]) | 0;
+    }
+    Equals(obj) {
+        let p;
+        const this$ = this;
+        return (obj instanceof Publication) && ((p = obj, safeHash(this$) === safeHash(p)));
+    }
+    toString() {
+        let option, clo, arg_1;
+        const this$ = this;
+        const sb = StringBuilder_$ctor();
+        StringBuilder__Append_Z721C83C5(sb, "Publication {\n\t");
+        StringBuilder__Append_Z721C83C5(sb, join(",\n\t", map((tupledArg_1) => toText(printf("%s = %A"))(tupledArg_1[0])(tupledArg_1[1]), choose((tupledArg) => map_1((o) => [tupledArg[0], o], tupledArg[1]), ofArray([["PubMedID", this$.PubMedID], ["DOI", this$.DOI], ["Authors", this$.Authors], ["Title", this$.Title], ["Status", (option = this$.Status, map_1((clo = toText(printf("%A")), clo), option))], ["Comments", (length(this$.Comments) > 0) ? ((arg_1 = this$.Comments, toText(printf("%A"))(arg_1))) : void 0]])))));
+        StringBuilder__Append_Z721C83C5(sb, "\n}");
+        return toString(sb);
+    }
+}
+
+export function Publication_$reflection() {
+    return class_type("ARCtrl.Publication", void 0, Publication);
+}
+
+export function Publication_$ctor_Z645CED36(pubMedID, doi, authors, title, status, comments) {
+    return new Publication(pubMedID, doi, authors, title, status, comments);
+}
+

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

@@ -1,59 +1,54 @@
-import { Dictionary } from "../../../fable_modules/fable-library-js.4.13.0/MutableMap.js";
-import { compareArrays, safeHash, disposeSafe, getEnumerator, comparePrimitives, equals, arrayHash, equalArrays } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
-import { value as value_9, map as map_2, defaultArg, unwrap } from "../../../fable_modules/fable-library-js.4.13.0/Option.js";
-import { boxHashValues, Unchecked_extendToRowCount, ProcessParsing_processToRows, ProcessParsing_alignByHeaders, ProcessParsing_mergeIdenticalProcesses, ProcessParsing_getProcessGetter, Unchecked_removeRowCells_withIndexChange, Unchecked_addRows, Unchecked_addRow, Unchecked_getEmptyCellForHeader, Unchecked_removeColumnCells_withIndexChange, tryFindDuplicateUniqueInArray, Unchecked_removeColumnCells, Unchecked_removeHeader, Unchecked_fillMissingCells, Unchecked_addColumn, tryFindDuplicateUnique, Unchecked_setCellAt, SanityChecks_validateColumn, SanityChecks_validateRowIndex, SanityChecks_validateColumnIndex, Unchecked_tryGetCellAt, getRowCount, getColumnCount } from "./ArcTableAux.js";
-import { item as item_1, append as append_1, indexed as indexed_1, choose, toList, zip, fold, filter, length, tryFindIndex, empty, singleton, collect, removeAt, map, delay, toArray } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
-import { rangeDouble } from "../../../fable_modules/fable-library-js.4.13.0/Range.js";
+import { boxHashValues, Unchecked_alignByHeaders, Unchecked_extendToRowCount, Unchecked_removeRowCells_withIndexChange, Unchecked_addRows, Unchecked_addRow, Unchecked_getEmptyCellForHeader, Unchecked_removeColumnCells_withIndexChange, tryFindDuplicateUniqueInArray, Unchecked_removeColumnCells, Unchecked_removeHeader, Unchecked_fillMissingCells, Unchecked_addColumn, tryFindDuplicateUnique, Unchecked_setCellAt, SanityChecks_validateColumn, SanityChecks_validateRowIndex, SanityChecks_validateColumnIndex, Unchecked_tryGetCellAt, getRowCount, getColumnCount, SanityChecks_validate } from "./ArcTableAux.js";
+import { Dictionary } from "../../fable_modules/fable-library-js.4.16.0/MutableMap.js";
+import { compareArrays, safeHash, comparePrimitives, equals, arrayHash, equalArrays } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
+import { value as value_3, map as map_2, unwrap, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { item as item_1, fold, append as append_1, toList, indexed as indexed_1, choose, filter, length, tryFindIndex, empty, singleton, collect, removeAt, map, delay, toArray } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { rangeDouble } from "../../fable_modules/fable-library-js.4.16.0/Range.js";
 import { CompositeColumn } from "./CompositeColumn.js";
-import { sortBy, indexed, mapIndexed, singleton as singleton_1, initialize, item, sortDescending, iterateIndexed, map as map_1 } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
-import { append, collect as collect_1, initialize as initialize_1, singleton as singleton_2, empty as empty_1, iterate, isEmpty } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
-import { StringBuilder__AppendLine_Z721C83C5, StringBuilder_$ctor } from "../../../fable_modules/fable-library-js.4.13.0/System.Text.js";
-import { toString } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
-import { join, printf, toFail } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
+import { sortBy, indexed, mapIndexed, initialize, item, sortDescending, iterateIndexed, map as map_1 } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
+import { append, iterate, isEmpty } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { StringBuilder__AppendLine_Z721C83C5, StringBuilder_$ctor } from "../../fable_modules/fable-library-js.4.16.0/System.Text.js";
+import { toString } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
+import { join, printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
 import { CompositeCell } from "./CompositeCell.js";
 import { CompositeHeader } from "./CompositeHeader.js";
-import { createMissingIdentifier } from "../Identifier.js";
-import { ARCtrl_ISA_Component__Component_TryGetColumnIndex, ARCtrl_ISA_ProtocolParameter__ProtocolParameter_TryGetColumnIndex } from "../JsonTypes/ColumnIndex.js";
-import { Protocol_create_Z7DFD6E67, Protocol_addComponent, Protocol_addParameter, Protocol_setName, Protocol_setDescription, Protocol_setUri, Protocol_setVersion, Protocol_setProtocolType } from "../JsonTypes/Protocol.js";
-import { OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
-import { ProtocolParameter } from "../JsonTypes/ProtocolParameter.js";
-import { Component_create_61502994 } from "../JsonTypes/Component.js";
-import { Array_groupBy, List_distinct } from "../../../fable_modules/fable-library-js.4.13.0/Seq2.js";
-import { toProtocol } from "./CompositeRow.js";
-import { Process_create_Z42860F3E } from "../JsonTypes/Process.js";
-import { getItemFromDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
-import { HashCodes_boxHashSeq, HashCodes_boxHashArray } from "../Helper.js";
-import { class_type } from "../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Array_groupBy } from "../../fable_modules/fable-library-js.4.16.0/Seq2.js";
+import { getItemFromDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+import { boxHashSeq, boxHashArray } from "../Helper/HashCodes.js";
+import { class_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
 
 export class ArcTable {
     constructor(name, headers, values) {
-        this["name@20"] = name;
-        this["headers@21"] = headers;
-        this["values@22"] = values;
+        const valid = SanityChecks_validate(headers, values, true);
+        this["name@21"] = name;
+        this["headers@22"] = headers;
+        this["values@23"] = values;
     }
     get Headers() {
         const this$ = this;
-        return this$["headers@21"];
+        return this$["headers@22"];
     }
     set Headers(newHeaders) {
         const this$ = this;
-        this$["headers@21"] = newHeaders;
+        SanityChecks_validate(newHeaders, this$["values@23"], true);
+        this$["headers@22"] = newHeaders;
     }
     get Values() {
         const this$ = this;
-        return this$["values@22"];
+        return this$["values@23"];
     }
     set Values(newValues) {
         const this$ = this;
-        this$["values@22"] = newValues;
+        SanityChecks_validate(this$["headers@22"], newValues, true);
+        this$["values@23"] = newValues;
     }
     get Name() {
         const this$ = this;
-        return this$["name@20"];
+        return this$["name@21"];
     }
     set Name(newName) {
         const this$ = this;
-        this$["name@20"] = newName;
+        this$["name@21"] = newName;
     }
     static create(name, headers, values) {
         return new ArcTable(name, headers, values);
@@ -77,12 +72,8 @@ export class ArcTable {
     }
     Validate(raiseException) {
         const this$ = this;
-        let isValid = true;
-        for (let columnIndex = 0; columnIndex <= (this$.ColumnCount - 1); columnIndex++) {
-            const column = this$.GetColumn(columnIndex);
-            isValid = column.Validate(unwrap(raiseException));
-        }
-        return isValid;
+        const raiseException_1 = defaultArg(raiseException, true);
+        return SanityChecks_validate(this$.Headers, this$.Values, raiseException_1);
     }
     static validate(raiseException) {
         return (table) => table.Validate(unwrap(raiseException));
@@ -189,7 +180,7 @@ export class ArcTable {
             return newTable;
         };
     }
-    AddColumn(header, cells, index, forceReplace, SkipFillMissing) {
+    AddColumn(header, cells, index, forceReplace, skipFillMissing) {
         const this$ = this;
         const index_1 = defaultArg(index, this$.ColumnCount) | 0;
         const cells_1 = defaultArg(cells, []);
@@ -197,7 +188,7 @@ export class ArcTable {
         SanityChecks_validateColumnIndex(index_1, this$.ColumnCount, true);
         SanityChecks_validateColumn(CompositeColumn.create(header, cells_1));
         Unchecked_addColumn(header, cells_1, index_1, forceReplace_1, false, this$.Headers, this$.Values);
-        if (!equals(SkipFillMissing, true)) {
+        if (!equals(skipFillMissing, true)) {
             Unchecked_fillMissingCells(this$.Headers, this$.Values);
         }
     }
@@ -208,7 +199,7 @@ export class ArcTable {
             return newTable;
         };
     }
-    UpdateColumn(columnIndex, header, cells, SkipFillMissing) {
+    UpdateColumn(columnIndex, header, cells, skipFillMissing) {
         const this$ = this;
         SanityChecks_validateColumnIndex(columnIndex, this$.ColumnCount, false);
         const column = CompositeColumn.create(header, unwrap(cells));
@@ -224,7 +215,7 @@ export class ArcTable {
         iterateIndexed((rowIndex, v) => {
             Unchecked_setCellAt(columnIndex, rowIndex, v, this$.Values);
         }, column.Cells);
-        if (!equals(SkipFillMissing, true)) {
+        if (!equals(skipFillMissing, true)) {
             Unchecked_fillMissingCells(this$.Headers, this$.Values);
         }
     }
@@ -257,7 +248,7 @@ export class ArcTable {
             return newTable;
         };
     }
-    AddColumns(columns, index, forceReplace, SkipFillMissing) {
+    AddColumns(columns, index, forceReplace, skipFillMissing) {
         const this$ = this;
         let index_1 = defaultArg(index, this$.ColumnCount);
         const forceReplace_1 = defaultArg(forceReplace, false);
@@ -281,14 +272,14 @@ export class ArcTable {
                 index_1 = ((index_1 + 1) | 0);
             }
         });
-        if (!equals(SkipFillMissing, true)) {
+        if (!equals(skipFillMissing, true)) {
             Unchecked_fillMissingCells(this$.Headers, this$.Values);
         }
     }
-    static addColumns(columns, index, SkipFillMissing) {
+    static addColumns(columns, index, skipFillMissing) {
         return (table) => {
             const newTable = table.Copy();
-            newTable.AddColumns(columns, unwrap(index), void 0, unwrap(SkipFillMissing));
+            newTable.AddColumns(columns, unwrap(index), void 0, unwrap(skipFillMissing));
             return newTable;
         };
     }
@@ -410,7 +401,7 @@ export class ArcTable {
     AddRow(cells, index) {
         const this$ = this;
         const index_1 = defaultArg(index, this$.RowCount) | 0;
-        const cells_1 = (cells == null) ? toArray(delay(() => collect((columnIndex) => singleton(Unchecked_getEmptyCellForHeader(this$.Headers[columnIndex], Unchecked_tryGetCellAt(columnIndex, 0, this$.Values))), rangeDouble(0, 1, this$.ColumnCount - 1)))) : value_9(cells);
+        const cells_1 = (cells == null) ? toArray(delay(() => collect((columnIndex) => singleton(Unchecked_getEmptyCellForHeader(this$.Headers[columnIndex], Unchecked_tryGetCellAt(columnIndex, 0, this$.Values))), rangeDouble(0, 1, this$.ColumnCount - 1)))) : value_3(cells);
         SanityChecks_validateRowIndex(index_1, this$.RowCount, true);
         const columnCount = this$.ColumnCount | 0;
         const newCellsCount = length(cells_1) | 0;
@@ -560,7 +551,7 @@ export class ArcTable {
         if (!equals(SkipValidation, true)) {
             SanityChecks_validateRowIndex(rowIndex, this$.RowCount, false);
         }
-        return toArray(delay(() => map((columnIndex) => value_9(this$.TryGetCellAt(columnIndex, rowIndex)), rangeDouble(0, 1, this$.ColumnCount - 1))));
+        return toArray(delay(() => map((columnIndex) => value_3(this$.TryGetCellAt(columnIndex, rowIndex)), rangeDouble(0, 1, this$.ColumnCount - 1))));
     }
     static getRow(index) {
         return (table) => table.GetRow(index);
@@ -615,12 +606,6 @@ export class ArcTable {
             return copy;
         };
     }
-    static insertParameterValue(t, p) {
-        throw new Error();
-    }
-    static getParameterValues(t) {
-        throw new Error();
-    }
     AddProtocolTypeColumn(types, index) {
         const this$ = this;
         const cells = map_2((array) => map_1((Item) => (new CompositeCell(0, [Item])), array), types);
@@ -674,97 +659,6 @@ export class ArcTable {
         const this$ = this;
         return map_1((h_1) => this$.GetColumnByHeader(h_1), toArray(filter((h) => h.isComponent, this$.Headers)));
     }
-    static fromProtocol(p) {
-        const t = ArcTable.init(defaultArg(p.Name, createMissingIdentifier()));
-        const enumerator = getEnumerator(defaultArg(p.Parameters, empty_1()));
-        try {
-            while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
-                const pp = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
-                t.AddColumn(new CompositeHeader(3, [value_9(pp.ParameterName)]), void 0, ARCtrl_ISA_ProtocolParameter__ProtocolParameter_TryGetColumnIndex(pp));
-            }
-        }
-        finally {
-            disposeSafe(enumerator);
-        }
-        const enumerator_1 = getEnumerator(defaultArg(p.Components, empty_1()));
-        try {
-            while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
-                const c = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
-                const v_1 = map_2((arg) => singleton_1(CompositeCell.fromValue(arg, unwrap(c.ComponentUnit))), c.ComponentValue);
-                t.AddColumn(new CompositeHeader(3, [value_9(c.ComponentType)]), v_1, ARCtrl_ISA_Component__Component_TryGetColumnIndex(c));
-            }
-        }
-        finally {
-            disposeSafe(enumerator_1);
-        }
-        map_2((d) => {
-            t.AddProtocolDescriptionColumn([d]);
-        }, p.Description);
-        map_2((d_1) => {
-            t.AddProtocolVersionColumn([d_1]);
-        }, p.Version);
-        map_2((d_2) => {
-            t.AddProtocolTypeColumn([d_2]);
-        }, p.ProtocolType);
-        map_2((d_3) => {
-            t.AddProtocolUriColumn([d_3]);
-        }, p.Uri);
-        map_2((d_4) => {
-            t.AddProtocolNameColumn([d_4]);
-        }, p.Name);
-        return t;
-    }
-    GetProtocols() {
-        let source;
-        const this$ = this;
-        return (this$.RowCount === 0) ? singleton_2((source = this$.Headers, fold((p, h) => {
-            switch (h.tag) {
-                case 4:
-                    return Protocol_setProtocolType(p, OntologyAnnotation.empty);
-                case 7:
-                    return Protocol_setVersion(p, "");
-                case 6:
-                    return Protocol_setUri(p, "");
-                case 5:
-                    return Protocol_setDescription(p, "");
-                case 8:
-                    return Protocol_setName(p, "");
-                case 3:
-                    return Protocol_addParameter(ProtocolParameter.create(void 0, h.fields[0]), p);
-                case 0:
-                    return Protocol_addComponent(Component_create_61502994(void 0, void 0, void 0, h.fields[0]), p);
-                default:
-                    return p;
-            }
-        }, Protocol_create_Z7DFD6E67(void 0, this$.Name), source))) : List_distinct(initialize_1(this$.RowCount, (i) => {
-            let row;
-            const source_2 = this$.GetRow(i, true);
-            row = zip(this$.Headers, source_2);
-            return toProtocol(this$.Name, row);
-        }), {
-            Equals: equals,
-            GetHashCode: safeHash,
-        });
-    }
-    GetProcesses() {
-        const this$ = this;
-        if (this$.RowCount === 0) {
-            return singleton_2(Process_create_Z42860F3E(void 0, this$.Name));
-        }
-        else {
-            let getter;
-            const clo = ProcessParsing_getProcessGetter(this$.Name, this$.Headers);
-            getter = ((arg) => {
-                const clo_1 = clo(arg);
-                return clo_1;
-            });
-            return ProcessParsing_mergeIdenticalProcesses(toList(delay(() => map((i) => getter(this$.Values)(i), rangeDouble(0, 1, this$.RowCount - 1)))));
-        }
-    }
-    static fromProcesses(name, ps) {
-        const tupledArg = ProcessParsing_alignByHeaders(true, collect_1(ProcessParsing_processToRows, ps));
-        return ArcTable.create(name, tupledArg[0], tupledArg[1]);
-    }
     static SplitByColumnValues(columnIndex) {
         return (table) => mapIndexed((i, indexGroup) => {
             let headers;
@@ -814,7 +708,7 @@ export class ArcTable {
     }
     static append(table1, table2) {
         const getList = (t) => toList(delay(() => map((row) => toList(delay(() => map((col) => [t.Headers[col], getItemFromDict(t.Values, [col, row])], rangeDouble(0, 1, t.ColumnCount - 1)))), rangeDouble(0, 1, t.RowCount - 1))));
-        const patternInput = ProcessParsing_alignByHeaders(false, append(getList(table1), getList(table2)));
+        const patternInput = Unchecked_alignByHeaders(false, append(getList(table1), getList(table2)));
         return ArcTable.create(table1.Name, patternInput[0], patternInput[1]);
     }
     toString() {
@@ -862,15 +756,15 @@ export class ArcTable {
     GetHashCode() {
         const this$ = this;
         const vHash = boxHashValues(this$.ColumnCount, this$.Values);
-        return HashCodes_boxHashArray([this$.Name, HashCodes_boxHashSeq(this$.Headers), vHash]) | 0;
+        return boxHashArray([this$.Name, boxHashSeq(this$.Headers), vHash]) | 0;
     }
 }
 
 export function ArcTable_$reflection() {
-    return class_type("ARCtrl.ISA.ArcTable", void 0, ArcTable);
+    return class_type("ARCtrl.ArcTable", void 0, ArcTable);
 }
 
-export function ArcTable_$ctor_474CDC4E(name, headers, values) {
+export function ArcTable_$ctor_76CAD84E(name, headers, values) {
     return new ArcTable(name, headers, values);
 }