@nfdi4plants/arctrl 2.4.0 → 2.5.1

package/ARC.js

@@ -1,9 +1,9 @@
-import { append as append_1, contains as contains_1, concat, fold, map, exactlyOne, tryPick, choose } from "./fable_modules/fable-library-js.4.24.0/Array.js";
+import { append as append_1, contains as contains_2, concat, fold, map, exactlyOne, tryPick, choose } from "./fable_modules/fable-library-js.4.24.0/Array.js";
 import { ARCtrl_ArcAssay__ArcAssay_ToUpdateContract, ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49, ARCtrl_ArcAssay__ArcAssay_ToDeleteContract, ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F } from "./Contract/ArcAssay.js";
 import { ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static } from "./Contract/Datamap.js";
 import { ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49, ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F } from "./Contract/ArcStudy.js";
 import { ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract, ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F } from "./Contract/ArcInvestigation.js";
-import { toList, collect, empty, iterate, find, tryFind, map as map_1, singleton, append, delay, contains, toArray } from "./fable_modules/fable-library-js.4.24.0/Seq.js";
+import { toList, collect, empty, find, tryFind, iterate, map as map_1, singleton, append, delay, contains, toArray } from "./fable_modules/fable-library-js.4.24.0/Seq.js";
 import { FileSystemTree } from "./FileSystem/FileSystemTree.js";
 import { FileSystem } from "./FileSystem/FileSystem.js";
 import { bind, map as map_2, defaultArg, value as value_2, unwrap } from "./fable_modules/fable-library-js.4.24.0/Option.js";
@@ -12,10 +12,12 @@ import { PromiseBuilder__Delay_62FBFDE1, PromiseBuilder__Run_212F1D4B } from "./
 import { promise } from "./fable_modules/Fable.Promise.3.2.0/PromiseImpl.fs.js";
 import { getAllFilePathsAsync } from "./ContractIO/FileSystemHelper.js";
 import { FSharpResult$2 } from "./fable_modules/fable-library-js.4.24.0/Result.js";
-import { comparePrimitives, safeHash, stringHash } from "./fable_modules/fable-library-js.4.24.0/Util.js";
+import { safeHash, curry2, comparePrimitives, stringHash } from "./fable_modules/fable-library-js.4.24.0/Util.js";
 import { getStudyFolderPath, getAssayFolderPath } from "./FileSystem/Path.js";
 import { toText, printf, toFail, join, replace } from "./fable_modules/fable-library-js.4.24.0/String.js";
 import { Contract } from "./Contract/Contract.js";
+import { FSharpSet__Contains, unionMany, contains as contains_1, ofSeq } from "./fable_modules/fable-library-js.4.24.0/Set.js";
+import { DataMap__get_StaticHash, DataMap__set_StaticHash_Z524259A4, DataMap__get_DataContexts } from "./Core/DataMap.js";
 import { tryISAReadContractFromPath } from "./Contract/ARC.js";
 import { ArcTables } from "./Core/Table/ArcTables.js";
 import { addToDict } from "./fable_modules/fable-library-js.4.24.0/MapUtil.js";
@@ -23,15 +25,13 @@ import { ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF
 import { ArcInvestigation } from "./Core/ArcTypes.js";
 import { Assay_datamapFileNameFromIdentifier, Assay_fileNameFromIdentifier, Study_datamapFileNameFromIdentifier, Study_fileNameFromIdentifier } from "./Core/Helper/Identifier.js";
 import { ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522 } from "./Spreadsheet/ArcStudy.js";
-import { DataMap__get_StaticHash, DataMap__set_StaticHash_Z524259A4 } from "./Core/DataMap.js";
 import { toFsWorkbook } from "./Spreadsheet/DataMap.js";
 import { ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F } from "./Spreadsheet/ArcAssay.js";
 import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.6.3.1/Cells/FsCellsCollection.fs.js";
 import { Clone_createCloneContract_5000466F, Init_createAddRemoteContract_Z721C83C5, gitignoreContract, gitattributesContract, Init_createInitContract_6DFDD678 } from "./Contract/Git.js";
-import { FSharpSet__Contains, ofSeq, unionMany } from "./fable_modules/fable-library-js.4.24.0/Set.js";
 import { ofSeq as ofSeq_1 } from "./fable_modules/fable-library-js.4.24.0/Map.js";
 import { fromString } from "./fable_modules/Thoth.Json.JavaScript.0.3.0/Decode.fs.js";
-import { encoder, decoder as decoder_1 } from "./JsonIO/ARC.js";
+import { ROCrate_encoder_8A8D439, ROCrate_get_decoder, ROCrate_get_decoderDeprecated } from "./ROCrateIO.js";
 import { toString } from "./fable_modules/Thoth.Json.JavaScript.0.3.0/Encode.fs.js";
 import { defaultSpaces } from "./Json/Encode.js";
 import { ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_tryFromReadContract_Static_7570923F, ValidationPackagesConfigHelper_ReadContract, ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toDeleteContract_Static_724DAE55, ARCtrl_ValidationPackages_ValidationPackagesConfig__ValidationPackagesConfig_toCreateContract_Static_724DAE55, ValidationPackagesConfigHelper_ConfigFilePath } from "./Contract/ValidationPackagesConfig.js";
@@ -355,6 +355,77 @@ export class ARC {
             }
         }))));
     }
+    MakeDataFilesAbsolute() {
+        const this$ = this;
+        const filesPaths = ofSeq(this$.FileSystem.Tree.ToFilePaths(), {
+            Compare: comparePrimitives,
+        });
+        const checkExistenceFromRoot = (p) => contains_1(p, filesPaths);
+        const updateColumnOption = (dataNameFunction, col) => {
+            let col_1;
+            let matchResult, col_2;
+            if (col != null) {
+                if ((col_1 = col, col_1.Header.IsDataColumn)) {
+                    matchResult = 0;
+                    col_2 = col;
+                }
+                else {
+                    matchResult = 1;
+                }
+            }
+            else {
+                matchResult = 1;
+            }
+            switch (matchResult) {
+                case 0: {
+                    col_2.Cells.forEach((c) => {
+                        if (c.AsData.FilePath != null) {
+                            const newFilePath = dataNameFunction(c.AsData);
+                            c.AsData.FilePath = newFilePath;
+                        }
+                    });
+                    break;
+                }
+                case 1: {
+                    break;
+                }
+            }
+        };
+        const updateTable = (dataNameFunction_1, t) => {
+            updateColumnOption(dataNameFunction_1, t.TryGetInputColumn());
+            updateColumnOption(dataNameFunction_1, t.TryGetOutputColumn());
+        };
+        const updateDataMap = (dataNameFunction_2, dm) => {
+            iterate((c_1) => {
+                if (c_1.FilePath != null) {
+                    const newFilePath_1 = dataNameFunction_2(c_1);
+                    c_1.FilePath = newFilePath_1;
+                }
+            }, DataMap__get_DataContexts(dm));
+        };
+        const matchValue = this$.ISA;
+        if (matchValue == null) {
+        }
+        else {
+            const inv = matchValue;
+            iterate((s) => {
+                const f = (d) => d.GetAbsolutePathForStudy(s.Identifier, checkExistenceFromRoot);
+                const source_1 = s.Tables;
+                iterate(curry2(updateTable)(f), source_1);
+                if (s.DataMap != null) {
+                    updateDataMap(f, value_2(s.DataMap));
+                }
+            }, inv.Studies);
+            iterate((a) => {
+                const f_1 = (d_1) => d_1.GetAbsolutePathForAssay(a.Identifier, checkExistenceFromRoot);
+                const source_3 = a.Tables;
+                iterate(curry2(updateTable)(f_1), source_3);
+                if (a.DataMap != null) {
+                    updateDataMap(f_1, value_2(a.DataMap));
+                }
+            }, inv.Assays);
+        }
+    }
     static fromFilePaths(filePaths) {
         return new ARC(undefined, undefined, FileSystem.fromFilePaths(filePaths));
     }
@@ -648,15 +719,35 @@ export class ARC {
             Compare: comparePrimitives,
         });
     }
+    static fromDeprecatedROCrateJsonString(s) {
+        let matchValue;
+        try {
+            const s_1 = replace(s, "bio:additionalProperty", "sdo:additionalProperty");
+            return new ARC((matchValue = fromString(ROCrate_get_decoderDeprecated(), s_1), (matchValue.tag === 1) ? (() => {
+                throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+            })() : matchValue.fields[0]));
+        }
+        catch (ex) {
+            const arg_1 = ex.message;
+            return toFail(printf("Could not parse deprecated ARC-RO-Crate metadata: \n%s"))(arg_1);
+        }
+    }
     static fromROCrateJsonString(s) {
         let matchValue;
-        return new ARC(unwrap((matchValue = fromString(decoder_1, s), (matchValue.tag === 1) ? (() => {
-            throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
-        })() : matchValue.fields[0])));
+        try {
+            return new ARC((matchValue = fromString(ROCrate_get_decoder(), s), (matchValue.tag === 1) ? (() => {
+                throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
+            })() : matchValue.fields[0]));
+        }
+        catch (ex) {
+            const arg_1 = ex.message;
+            return toFail(printf("Could not parse ARC-RO-Crate metadata: \n%s"))(arg_1);
+        }
     }
     ToROCrateJsonString(spaces) {
         const this$ = this;
-        const value = encoder(value_2(this$._isa));
+        this$.MakeDataFilesAbsolute();
+        const value = ROCrate_encoder_8A8D439(value_2(this$._isa));
         return toString(defaultSpaces(spaces), value);
     }
     static toROCrateJsonString(spaces) {
@@ -665,7 +756,7 @@ export class ARC {
     GetValidationPackagesConfigWriteContract(vpc) {
         const this$ = this;
         const paths = this$.FileSystem.Tree.ToFilePaths();
-        if (!contains_1(ValidationPackagesConfigHelper_ConfigFilePath, paths, {
+        if (!contains_2(ValidationPackagesConfigHelper_ConfigFilePath, paths, {
             Equals: (x, y) => (x === y),
             GetHashCode: stringHash,
         })) {
@@ -677,7 +768,7 @@ export class ARC {
     GetValidationPackagesConfigDeleteContract(vpc) {
         const this$ = this;
         const paths = this$.FileSystem.Tree.ToFilePaths();
-        if (contains_1(ValidationPackagesConfigHelper_ConfigFilePath, paths, {
+        if (contains_2(ValidationPackagesConfigHelper_ConfigFilePath, paths, {
             Equals: (x, y) => (x === y),
             GetHashCode: stringHash,
         })) {

package/CWL/CWLTypes.js

@@ -1,8 +1,8 @@
-import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.4.0.3/DynamicObj.fs.js";
+import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.7.0.1/DynamicObj.fs.js";
 import { array_type, union_type, record_type, bool_type, option_type, string_type, class_type } from "../fable_modules/fable-library-js.4.24.0/Reflection.js";
 import { FSharpRef, Union, Record } from "../fable_modules/fable-library-js.4.24.0/Types.js";
 import { defaultOf } from "../fable_modules/fable-library-js.4.24.0/Util.js";
-import { setProperty } from "../fable_modules/DynamicObj.4.0.3/DynObj.fs.js";
+import { setProperty } from "../fable_modules/DynamicObj.7.0.1/DynObj.fs.js";
 
 export class FileInstance extends DynamicObj {
     constructor() {

package/CWL/Decode.js

@@ -1,6 +1,6 @@
 import { disposeSafe, getEnumerator } from "../fable_modules/fable-library-js.4.24.0/Util.js";
-import { setOptionalProperty, setProperty } from "../fable_modules/DynamicObj.4.0.3/DynObj.fs.js";
-import { DynamicObj } from "../fable_modules/DynamicObj.4.0.3/DynamicObj.fs.js";
+import { setOptionalProperty, setProperty } from "../fable_modules/DynamicObj.7.0.1/DynObj.fs.js";
+import { DynamicObj } from "../fable_modules/DynamicObj.7.0.1/DynamicObj.fs.js";
 import { ofArray, tail, head, isEmpty, empty, map, iterate } from "../fable_modules/fable-library-js.4.24.0/List.js";
 import { read, int, float, resizearray, map as map_1, bool, string, object } from "../fable_modules/YAMLicious.0.0.3/Decode.fs.js";
 import { replace, toFail, printf, toText } from "../fable_modules/fable-library-js.4.24.0/String.js";

package/CWL/Inputs.js

@@ -3,8 +3,8 @@ import { class_type, record_type, bool_type, int32_type, option_type, string_typ
 import { value, unwrap } from "../fable_modules/fable-library-js.4.24.0/Option.js";
 import { CWLType } from "./CWLTypes.js";
 import { defaultOf } from "../fable_modules/fable-library-js.4.24.0/Util.js";
-import { setOptionalProperty } from "../fable_modules/DynamicObj.4.0.3/DynObj.fs.js";
-import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.4.0.3/DynamicObj.fs.js";
+import { setOptionalProperty } from "../fable_modules/DynamicObj.7.0.1/DynObj.fs.js";
+import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.7.0.1/DynamicObj.fs.js";
 
 export class InputBinding extends Record {
     constructor(Prefix, Position, ItemSeparator, Separate) {

package/CWL/Outputs.js

@@ -3,8 +3,8 @@ import { class_type, record_type, option_type, string_type } from "../fable_modu
 import { value, unwrap } from "../fable_modules/fable-library-js.4.24.0/Option.js";
 import { CWLType } from "./CWLTypes.js";
 import { defaultOf } from "../fable_modules/fable-library-js.4.24.0/Util.js";
-import { setOptionalProperty } from "../fable_modules/DynamicObj.4.0.3/DynObj.fs.js";
-import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.4.0.3/DynamicObj.fs.js";
+import { setOptionalProperty } from "../fable_modules/DynamicObj.7.0.1/DynObj.fs.js";
+import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.7.0.1/DynamicObj.fs.js";
 
 export class OutputBinding extends Record {
     constructor(Glob) {

package/CWL/Requirements.js

@@ -1,8 +1,8 @@
 import { Union, FSharpRef, Record } from "../fable_modules/fable-library-js.4.24.0/Types.js";
 import { union_type, float64_type, array_type, record_type, class_type, option_type, string_type } from "../fable_modules/fable-library-js.4.24.0/Reflection.js";
 import { defaultOf } from "../fable_modules/fable-library-js.4.24.0/Util.js";
-import { setOptionalProperty } from "../fable_modules/DynamicObj.4.0.3/DynObj.fs.js";
-import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.4.0.3/DynamicObj.fs.js";
+import { setOptionalProperty } from "../fable_modules/DynamicObj.7.0.1/DynObj.fs.js";
+import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.7.0.1/DynamicObj.fs.js";
 import { CWLType_$reflection, SoftwarePackage_$reflection, SchemaDefRequirementType_$reflection } from "./CWLTypes.js";
 
 export class DockerRequirement extends Record {

package/CWL/ToolDescription.js

@@ -1,5 +1,5 @@
 import { defaultArg, unwrap } from "../fable_modules/fable-library-js.4.24.0/Option.js";
-import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.4.0.3/DynamicObj.fs.js";
+import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.7.0.1/DynamicObj.fs.js";
 import { class_type } from "../fable_modules/fable-library-js.4.24.0/Reflection.js";
 
 export class CWLToolDescription extends DynamicObj {

package/CWL/WorkflowDescription.js

@@ -1,5 +1,5 @@
 import { defaultArg, unwrap } from "../fable_modules/fable-library-js.4.24.0/Option.js";
-import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.4.0.3/DynamicObj.fs.js";
+import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.7.0.1/DynamicObj.fs.js";
 import { class_type } from "../fable_modules/fable-library-js.4.24.0/Reflection.js";
 
 export class CWLWorkflowDescription extends DynamicObj {

package/CWL/WorkflowSteps.js

@@ -1,7 +1,7 @@
 import { Record } from "../fable_modules/fable-library-js.4.24.0/Types.js";
 import { class_type, array_type, record_type, option_type, string_type } from "../fable_modules/fable-library-js.4.24.0/Reflection.js";
 import { unwrap } from "../fable_modules/fable-library-js.4.24.0/Option.js";
-import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.4.0.3/DynamicObj.fs.js";
+import { DynamicObj_$reflection, DynamicObj } from "../fable_modules/DynamicObj.7.0.1/DynamicObj.fs.js";
 
 export class StepInput extends Record {
     constructor(Id, Source, DefaultValue, ValueFrom) {

package/ColumnIndex.js

@@ -0,0 +1,258 @@
+import { tryParse } from "./fable_modules/fable-library-js.4.24.0/Int32.js";
+import { FSharpRef } from "./fable_modules/fable-library-js.4.24.0/Types.js";
+import { Comment$ } from "./Core/Comment.js";
+import { equals, int32ToString } from "./fable_modules/fable-library-js.4.24.0/Util.js";
+import { tryItem } from "./Core/CommentList.js";
+import { findIndex } from "./fable_modules/fable-library-js.4.24.0/Seq.js";
+import { value, bind } from "./fable_modules/fable-library-js.4.24.0/Option.js";
+import { Factor } from "./Core/Process/Factor.js";
+import { MaterialAttribute_fromString_5980DC03 } from "./Core/Process/MaterialAttribute.js";
+import { ProtocolParameter } from "./Core/Process/ProtocolParameter.js";
+import { Component_fromISAString_7C9A7CF8 } from "./Core/Process/Component.js";
+
+function tryInt(str) {
+    let matchValue;
+    let outArg = 0;
+    matchValue = [tryParse(str, 511, false, 32, new FSharpRef(() => outArg, (v) => {
+        outArg = (v | 0);
+    })), outArg];
+    if (matchValue[0]) {
+        return matchValue[1];
+    }
+    else {
+        return undefined;
+    }
+}
+
+export const orderName = "ColumnIndex";
+
+export function createOrderComment(index) {
+    return Comment$.create(orderName, int32ToString(index));
+}
+
+export function tryGetIndex(comments) {
+    const matchValue = tryItem(orderName, comments);
+    if (matchValue != null) {
+        const ci = matchValue;
+        const i = findIndex((c) => equals(c.Name, orderName), comments) | 0;
+        comments.splice(i, 1);
+        return tryInt(ci);
+    }
+    else {
+        return undefined;
+    }
+}
+
+export function setOntologyAnnotationIndexInplace(i, oa) {
+    void (oa.Comments.push(createOrderComment(i)));
+}
+
+export function setOntologyAnnotationIndex(i, oa) {
+    const oac = oa.Copy();
+    setOntologyAnnotationIndexInplace(i, oac);
+    return oac;
+}
+
+export function tryGetOntologyAnnotationIndex(oa) {
+    return tryGetIndex(oa.Comments);
+}
+
+export function tryGetParameterIndex(param) {
+    return bind((oa) => tryGetIndex(oa.Comments), param.ParameterName);
+}
+
+export function tryGetParameterColumnIndex(paramValue) {
+    return bind(tryGetParameterIndex, paramValue.Category);
+}
+
+export function tryGetFactorIndex(factor) {
+    return bind((oa) => tryGetIndex(oa.Comments), factor.FactorType);
+}
+
+export function tryGetFactorColumnIndex(factorValue) {
+    return bind(tryGetFactorIndex, factorValue.Category);
+}
+
+export function tryGetCharacteristicIndex(characteristic) {
+    return bind((oa) => tryGetIndex(oa.Comments), characteristic.CharacteristicType);
+}
+
+export function tryGetCharacteristicColumnIndex(characteristicValue) {
+    return bind(tryGetCharacteristicIndex, characteristicValue.Category);
+}
+
+export function tryGetComponentIndex(comp) {
+    return bind((oa) => tryGetIndex(oa.Comments), comp.ComponentType);
+}
+
+/**
+ * Create a ISAJson Factor from ISATab string entries
+ */
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_fromStringWithColumnIndex_Static(name, term, source, accession, valueIndex) {
+    return Factor.fromString(name, term, source, accession, [createOrderComment(valueIndex)]);
+}
+
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_getColumnIndex_Static_ZDED3A0F(f) {
+    return value(tryGetOntologyAnnotationIndex(f));
+}
+
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_GetColumnIndex(this$) {
+    return value(tryGetOntologyAnnotationIndex(this$));
+}
+
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_tryGetColumnIndex_Static_ZDED3A0F(f) {
+    return tryGetOntologyAnnotationIndex(f);
+}
+
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_TryGetColumnIndex(this$) {
+    return tryGetOntologyAnnotationIndex(this$);
+}
+
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_setColumnIndex_Static(i, oa) {
+    return setOntologyAnnotationIndex(i, oa);
+}
+
+export function ARCtrl_OntologyAnnotation__OntologyAnnotation_SetColumnIndex_Z524259A4(this$, i) {
+    setOntologyAnnotationIndexInplace(i, this$);
+}
+
+/**
+ * Create a ISAJson Factor from ISATab string entries
+ */
+export function ARCtrl_Process_Factor__Factor_fromStringWithColumnIndex_Static(name, term, source, accession, valueIndex) {
+    return Factor.fromString(name, term, source, accession, [createOrderComment(valueIndex)]);
+}
+
+export function ARCtrl_Process_Factor__Factor_getColumnIndex_Static_7206F0D9(f) {
+    return value(tryGetFactorIndex(f));
+}
+
+export function ARCtrl_Process_Factor__Factor_GetColumnIndex(this$) {
+    return value(tryGetFactorIndex(this$));
+}
+
+export function ARCtrl_Process_Factor__Factor_tryGetColumnIndex_Static_7206F0D9(f) {
+    return tryGetFactorIndex(f);
+}
+
+export function ARCtrl_Process_Factor__Factor_TryGetColumnIndex(this$) {
+    return tryGetFactorIndex(this$);
+}
+
+export function ARCtrl_Process_FactorValue__FactorValue_getColumnIndex_Static_7105C732(f) {
+    return value(tryGetFactorColumnIndex(f));
+}
+
+export function ARCtrl_Process_FactorValue__FactorValue_GetColumnIndex(this$) {
+    return value(tryGetFactorColumnIndex(this$));
+}
+
+export function ARCtrl_Process_FactorValue__FactorValue_tryGetColumnIndex_Static_7105C732(f) {
+    return tryGetFactorColumnIndex(f);
+}
+
+export function ARCtrl_Process_FactorValue__FactorValue_TryGetColumnIndex(this$) {
+    return tryGetFactorColumnIndex(this$);
+}
+
+/**
+ * Create a ISAJson characteristic from ISATab string entries
+ */
+export function ARCtrl_Process_MaterialAttribute__MaterialAttribute_fromStringWithColumnIndex_Static(term, source, accession, valueIndex) {
+    return MaterialAttribute_fromString_5980DC03(term, source, accession, [createOrderComment(valueIndex)]);
+}
+
+export function ARCtrl_Process_MaterialAttribute__MaterialAttribute_getColumnIndex_Static_Z1E3B85DD(m) {
+    return value(tryGetCharacteristicIndex(m));
+}
+
+export function ARCtrl_Process_MaterialAttribute__MaterialAttribute_GetColumnIndex(this$) {
+    return value(tryGetCharacteristicIndex(this$));
+}
+
+export function ARCtrl_Process_MaterialAttribute__MaterialAttribute_tryGetColumnIndex_Static_Z1E3B85DD(m) {
+    return tryGetCharacteristicIndex(m);
+}
+
+export function ARCtrl_Process_MaterialAttribute__MaterialAttribute_TryGetColumnIndex(this$) {
+    return tryGetCharacteristicIndex(this$);
+}
+
+export function ARCtrl_Process_MaterialAttributeValue__MaterialAttributeValue_getColumnIndex_Static_Z772273B8(m) {
+    return value(tryGetCharacteristicColumnIndex(m));
+}
+
+export function ARCtrl_Process_MaterialAttributeValue__MaterialAttributeValue_GetColumnIndex(this$) {
+    return value(tryGetCharacteristicColumnIndex(this$));
+}
+
+export function ARCtrl_Process_MaterialAttributeValue__MaterialAttributeValue_tryGetColumnIndex_Static_Z772273B8(m) {
+    return tryGetCharacteristicColumnIndex(m);
+}
+
+export function ARCtrl_Process_MaterialAttributeValue__MaterialAttributeValue_TryGetColumnIndex(this$) {
+    return tryGetCharacteristicColumnIndex(this$);
+}
+
+/**
+ * Create a ISAJson parameter from ISATab string entries
+ */
+export function ARCtrl_Process_ProtocolParameter__ProtocolParameter_fromStringWithColumnIndex_Static(term, source, accession, valueIndex) {
+    return ProtocolParameter.fromString(term, source, accession, [createOrderComment(valueIndex)]);
+}
+
+export function ARCtrl_Process_ProtocolParameter__ProtocolParameter_getColumnIndex_Static_Z11F87B15(p) {
+    return value(tryGetParameterIndex(p));
+}
+
+export function ARCtrl_Process_ProtocolParameter__ProtocolParameter_GetColumnIndex(this$) {
+    return value(tryGetParameterIndex(this$));
+}
+
+export function ARCtrl_Process_ProtocolParameter__ProtocolParameter_tryGetColumnIndex_Static_Z11F87B15(p) {
+    return tryGetParameterIndex(p);
+}
+
+export function ARCtrl_Process_ProtocolParameter__ProtocolParameter_TryGetColumnIndex(this$) {
+    return tryGetParameterIndex(this$);
+}
+
+export function ARCtrl_Process_ProcessParameterValue__ProcessParameterValue_getColumnIndex_Static_Z1576263(p) {
+    return value(tryGetParameterColumnIndex(p));
+}
+
+export function ARCtrl_Process_ProcessParameterValue__ProcessParameterValue_GetColumnIndex(this$) {
+    return value(tryGetParameterColumnIndex(this$));
+}
+
+export function ARCtrl_Process_ProcessParameterValue__ProcessParameterValue_tryGetColumnIndex_Static_Z1576263(p) {
+    return tryGetParameterColumnIndex(p);
+}
+
+export function ARCtrl_Process_ProcessParameterValue__ProcessParameterValue_TryGetColumnIndex(this$) {
+    return tryGetParameterColumnIndex(this$);
+}
+
+/**
+ * Create a ISAJson Factor from ISATab string entries
+ */
+export function ARCtrl_Process_Component__Component_fromStringWithColumnIndex_Static(name, term, source, accession, valueIndex) {
+    return Component_fromISAString_7C9A7CF8(name, term, source, accession, [createOrderComment(valueIndex)]);
+}
+
+export function ARCtrl_Process_Component__Component_getColumnIndex_Static_Z685B8F25(f) {
+    return value(tryGetComponentIndex(f));
+}
+
+export function ARCtrl_Process_Component__Component_GetColumnIndex(this$) {
+    return value(tryGetComponentIndex(this$));
+}
+
+export function ARCtrl_Process_Component__Component_tryGetColumnIndex_Static_Z685B8F25(f) {
+    return tryGetComponentIndex(f);
+}
+
+export function ARCtrl_Process_Component__Component_TryGetColumnIndex(this$) {
+    return tryGetComponentIndex(this$);
+}
+