@nfdi4plants/arctrl 2.0.0-alpha.2 → 2.0.0-alpha.4

package/Core/Conversion.js

@@ -3,7 +3,7 @@ import { Comment$ } from "./Comment.js";
 import { zip as zip_1, fold, empty as empty_1, singleton as singleton_1, append, delay, map as map_1, filter, toList, indexed, tryPick, choose } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { unwrap, value as value_9, map, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
 import { Option_fromValueWithDefault, ResizeArray_filter } from "./Helper/Collections.js";
-import { Value as Value_1 } from "./Process/Value.js";
+import { Value as Value_2 } from "./Process/Value.js";
 import { Component_create_4208F9FC } from "./Process/Component.js";
 import { ProtocolParameter } from "./Process/ProtocolParameter.js";
 import { ProcessParameterValue } from "./Process/ProcessParameterValue.js";
@@ -12,13 +12,13 @@ import { Factor } from "./Process/Factor.js";
 import { toString } from "../fable_modules/fable-library-js.4.16.0/Types.js";
 import { MaterialAttributeValue_create_BE8DE56 } from "./Process/MaterialAttributeValue.js";
 import { MaterialAttribute_create_A220A8A } from "./Process/MaterialAttribute.js";
-import { ProcessInput_getCharacteristicValues_5B3D5BA9, ProcessInput__isMaterial, ProcessInput__isData, ProcessInput_setCharacteristicValues, ProcessInput__get_Name, ProcessInput__isSource, ProcessInput__isSample, ProcessInput, ProcessInput_createDerivedData_Z721C83C5, ProcessInput_createRawData_Z721C83C5, ProcessInput_createImageFile_Z721C83C5, ProcessInput_createMaterial_4452CB4C, ProcessInput_createSample_Z598187B7, ProcessInput_createSource_Z5E00540E } from "./Process/ProcessInput.js";
-import { ProcessOutput_getFactorValues_Z42C11600, ProcessOutput__isMaterial, ProcessOutput__isData, ProcessOutput_setFactorValues, ProcessOutput__get_Name, ProcessOutput__isSample, ProcessOutput, ProcessOutput_createDerivedData_Z721C83C5, ProcessOutput_createRawData_Z721C83C5, ProcessOutput_createImageFile_Z721C83C5, ProcessOutput_createMaterial_4452CB4C, ProcessOutput_createSample_Z598187B7 } from "./Process/ProcessOutput.js";
+import { ProcessInput_getCharacteristicValues_5B3D5BA9, ProcessInput__isMaterial, ProcessInput__isData, ProcessInput_setCharacteristicValues, ProcessInput__get_Name, ProcessInput__isSource, ProcessInput__isSample, ProcessInput, ProcessInput_createRawData_Z721C83C5, ProcessInput_createMaterial_4452CB4C, ProcessInput_createSample_Z598187B7, ProcessInput_createSource_Z5E00540E } from "./Process/ProcessInput.js";
+import { ProcessOutput_getFactorValues_Z42C11600, ProcessOutput__isMaterial, ProcessOutput__isData, ProcessOutput_setFactorValues, ProcessOutput__get_Name, ProcessOutput__isSample, ProcessOutput, ProcessOutput_createRawData_Z721C83C5, ProcessOutput_createMaterial_4452CB4C, ProcessOutput_createSample_Z598187B7 } from "./Process/ProcessOutput.js";
 import { CompositeCell } from "./Table/CompositeCell.js";
+import { OntologyAnnotation } from "./OntologyAnnotation.js";
 import { safeHash, equals, disposeSafe, getEnumerator, comparePrimitives, arrayHash, equalArrays, stringHash, int32ToString } from "../fable_modules/fable-library-js.4.16.0/Util.js";
 import { IOType, CompositeHeader } from "./Table/CompositeHeader.js";
 import { ActivePatterns_$007CRegex$007C_$007C } from "./Helper/Regex.js";
-import { OntologyAnnotation } from "./OntologyAnnotation.js";
 import { ARCtrl_Process_Component__Component_TryGetColumnIndex, ARCtrl_Process_ProtocolParameter__ProtocolParameter_TryGetColumnIndex, tryGetFactorColumnIndex, tryGetCharacteristicColumnIndex, tryGetComponentIndex, tryGetParameterColumnIndex, ARCtrl_OntologyAnnotation__OntologyAnnotation_setColumnIndex_Static, ARCtrl_OntologyAnnotation__OntologyAnnotation_SetColumnIndex_Z524259A4 } from "./Process/ColumnIndex.js";
 import { getItemFromDict } from "../fable_modules/fable-library-js.4.16.0/MapUtil.js";
 import { initialize, zip, append as append_1, sortBy, head, tryPick as tryPick_1, collect, mapIndexed, item, length, map as map_2, empty, ofArray, isEmpty, singleton, choose as choose_1 } from "../fable_modules/fable-library-js.4.16.0/List.js";
@@ -118,11 +118,23 @@ export function Person_setCommentFromORCID(person) {
 export function JsonTypes_valueOfCell(value) {
     switch (value.tag) {
         case 0:
-            return [new Value_1(0, [value.fields[0]]), void 0];
+            if (value.fields[0].isEmpty()) {
+                return [void 0, void 0];
+            }
+            else {
+                return [new Value_2(0, [value.fields[0]]), void 0];
+            }
         case 2:
-            return [Value_1.fromString(value.fields[0]), value.fields[1]];
+            return [(value.fields[0] === "") ? void 0 : Value_2.fromString(value.fields[0]), value.fields[1].isEmpty() ? void 0 : value.fields[1]];
+        case 3:
+            throw new Error("Data cell should not be parsed to isa value");
         default:
-            return [Value_1.fromString(value.fields[0]), void 0];
+            if (value.fields[0] === "") {
+                return [void 0, void 0];
+            }
+            else {
+                return [Value_2.fromString(value.fields[0]), void 0];
+            }
     }
 }
 
@@ -131,7 +143,7 @@ export function JsonTypes_valueOfCell(value) {
  */
 export function JsonTypes_composeComponent(header, value) {
     const patternInput = JsonTypes_valueOfCell(value);
-    return Component_create_4208F9FC(patternInput[0], unwrap(patternInput[1]), header.ToTerm());
+    return Component_create_4208F9FC(unwrap(patternInput[0]), unwrap(patternInput[1]), header.ToTerm());
 }
 
 /**
@@ -140,7 +152,7 @@ export function JsonTypes_composeComponent(header, value) {
 export function JsonTypes_composeParameterValue(header, value) {
     const patternInput = JsonTypes_valueOfCell(value);
     const p = ProtocolParameter.create(void 0, header.ToTerm());
-    return ProcessParameterValue.create(p, patternInput[0], unwrap(patternInput[1]));
+    return ProcessParameterValue.create(p, unwrap(patternInput[0]), unwrap(patternInput[1]));
 }
 
 /**
@@ -148,7 +160,7 @@ export function JsonTypes_composeParameterValue(header, value) {
  */
 export function JsonTypes_composeFactorValue(header, value) {
     const patternInput = JsonTypes_valueOfCell(value);
-    return FactorValue_create_29259B2C(void 0, Factor.create(toString(header), header.ToTerm()), patternInput[0], unwrap(patternInput[1]));
+    return FactorValue_create_29259B2C(void 0, Factor.create(toString(header), header.ToTerm()), unwrap(patternInput[0]), unwrap(patternInput[1]));
 }
 
 /**
@@ -156,7 +168,7 @@ export function JsonTypes_composeFactorValue(header, value) {
  */
 export function JsonTypes_composeCharacteristicValue(header, value) {
     const patternInput = JsonTypes_valueOfCell(value);
-    return MaterialAttributeValue_create_BE8DE56(void 0, MaterialAttribute_create_A220A8A(void 0, header.ToTerm()), patternInput[0], unwrap(patternInput[1]));
+    return MaterialAttributeValue_create_BE8DE56(void 0, MaterialAttribute_create_A220A8A(void 0, header.ToTerm()), unwrap(patternInput[0]), unwrap(patternInput[1]));
 }
 
 /**
@@ -174,28 +186,20 @@ export function JsonTypes_composeProcessInput(header, value) {
                 matchResult = 1;
                 break;
             }
-            case 5: {
+            case 3: {
                 matchResult = 2;
                 break;
             }
-            case 4: {
-                matchResult = 3;
-                break;
-            }
             case 2: {
-                matchResult = 4;
-                break;
-            }
-            case 3: {
-                matchResult = 5;
+                matchResult = 3;
                 break;
             }
             default:
-                matchResult = 6;
+                matchResult = 4;
         }
     }
     else {
-        matchResult = 6;
+        matchResult = 4;
     }
     switch (matchResult) {
         case 0:
@@ -205,11 +209,7 @@ export function JsonTypes_composeProcessInput(header, value) {
         case 2:
             return ProcessInput_createMaterial_4452CB4C(toString(value));
         case 3:
-            return ProcessInput_createImageFile_Z721C83C5(toString(value));
-        case 4:
             return ProcessInput_createRawData_Z721C83C5(toString(value));
-        case 5:
-            return ProcessInput_createDerivedData_Z721C83C5(toString(value));
         default:
             return toFail(printf("Could not parse input header %O"))(header);
     }
@@ -226,28 +226,20 @@ export function JsonTypes_composeProcessOutput(header, value) {
                 matchResult = 0;
                 break;
             }
-            case 5: {
+            case 3: {
                 matchResult = 1;
                 break;
             }
-            case 4: {
-                matchResult = 2;
-                break;
-            }
             case 2: {
-                matchResult = 3;
-                break;
-            }
-            case 3: {
-                matchResult = 4;
+                matchResult = 2;
                 break;
             }
             default:
-                matchResult = 5;
+                matchResult = 3;
         }
     }
     else {
-        matchResult = 5;
+        matchResult = 3;
     }
     switch (matchResult) {
         case 0:
@@ -255,11 +247,7 @@ export function JsonTypes_composeProcessOutput(header, value) {
         case 1:
             return ProcessOutput_createMaterial_4452CB4C(toString(value));
         case 2:
-            return ProcessOutput_createImageFile_Z721C83C5(toString(value));
-        case 3:
             return ProcessOutput_createRawData_Z721C83C5(toString(value));
-        case 4:
-            return ProcessOutput_createDerivedData_Z721C83C5(toString(value));
         default:
             return toFail(printf("Could not parse output header %O"))(header);
     }
@@ -269,40 +257,84 @@ export function JsonTypes_composeProcessOutput(header, value) {
  * Convert an ISA Value and Unit tuple to a CompositeCell
  */
 export function JsonTypes_cellOfValue(value, unit) {
-    const value_2 = defaultArg(value, new Value_1(3, [""]));
+    const value_2 = defaultArg(value, new Value_2(3, [""]));
+    let matchResult, oa, text, name, u, f, u_1, f_1, i, u_2, i_1;
     switch (value_2.tag) {
-        case 3:
-            if (unit != null) {
-                const u = unit;
-                return new CompositeCell(2, [value_2.fields[0], u]);
+        case 3: {
+            if (value_2.fields[0] === "") {
+                if (unit != null) {
+                    matchResult = 3;
+                    name = value_2.fields[0];
+                    u = unit;
+                }
+                else {
+                    matchResult = 1;
+                }
+            }
+            else if (unit != null) {
+                matchResult = 3;
+                name = value_2.fields[0];
+                u = unit;
             }
             else {
-                return new CompositeCell(1, [value_2.fields[0]]);
+                matchResult = 2;
+                text = value_2.fields[0];
             }
-        case 2:
+            break;
+        }
+        case 2: {
             if (unit == null) {
-                return new CompositeCell(1, [value_2.fields[0].toString()]);
+                matchResult = 5;
+                f_1 = value_2.fields[0];
             }
             else {
-                const u_1 = unit;
-                return new CompositeCell(2, [value_2.fields[0].toString(), u_1]);
+                matchResult = 4;
+                f = value_2.fields[0];
+                u_1 = unit;
             }
-        case 1:
+            break;
+        }
+        case 1: {
             if (unit == null) {
-                return new CompositeCell(1, [int32ToString(value_2.fields[0])]);
+                matchResult = 7;
+                i_1 = value_2.fields[0];
             }
             else {
-                const u_2 = unit;
-                return new CompositeCell(2, [int32ToString(value_2.fields[0]), u_2]);
+                matchResult = 6;
+                i = value_2.fields[0];
+                u_2 = unit;
             }
+            break;
+        }
         default:
             if (unit == null) {
-                return new CompositeCell(0, [value_2.fields[0]]);
+                matchResult = 0;
+                oa = value_2.fields[0];
             }
             else {
-                return toFail(printf("Could not parse value %O with unit %O"))(value_2)(unit);
+                matchResult = 8;
             }
     }
+    switch (matchResult) {
+        case 0:
+            return new CompositeCell(0, [oa]);
+        case 1:
+            return new CompositeCell(0, [new OntologyAnnotation()]);
+        case 2:
+            return new CompositeCell(0, [new OntologyAnnotation(text)]);
+        case 3:
+            return new CompositeCell(2, [name, u]);
+        case 4:
+            return new CompositeCell(2, [f.toString(), u_1]);
+        case 5:
+            return new CompositeCell(2, [f_1.toString(), new OntologyAnnotation()]);
+        case 6:
+            return new CompositeCell(2, [int32ToString(i), u_2]);
+        case 7:
+            return new CompositeCell(2, [int32ToString(i_1), new OntologyAnnotation()]);
+        default:
+            return toFail(printf("Could not parse value %O with unit %O"))(value_2)(unit);
+    }
 }
 
 /**
@@ -341,7 +373,7 @@ export function JsonTypes_decomposeProcessInput(pi) {
         case 1:
             return [new CompositeHeader(11, [new IOType(1, [])]), new CompositeCell(1, [defaultArg(pi.fields[0].Name, "")])];
         case 3:
-            return [new CompositeHeader(11, [new IOType(5, [])]), new CompositeCell(1, [defaultArg(pi.fields[0].Name, "")])];
+            return [new CompositeHeader(11, [new IOType(3, [])]), new CompositeCell(1, [defaultArg(pi.fields[0].Name, "")])];
         case 2: {
             const d = pi.fields[0];
             const dataType = value_9(d.DataType);
@@ -349,9 +381,9 @@ export function JsonTypes_decomposeProcessInput(pi) {
                 case 0:
                     return [new CompositeHeader(11, [new IOType(2, [])]), new CompositeCell(1, [defaultArg(d.Name, "")])];
                 case 1:
-                    return [new CompositeHeader(11, [new IOType(3, [])]), new CompositeCell(1, [defaultArg(d.Name, "")])];
+                    return [new CompositeHeader(11, [new IOType(2, [])]), new CompositeCell(1, [defaultArg(d.Name, "")])];
                 default:
-                    return [new CompositeHeader(11, [new IOType(4, [])]), new CompositeCell(1, [defaultArg(d.Name, "")])];
+                    return [new CompositeHeader(11, [new IOType(2, [])]), new CompositeCell(1, [defaultArg(d.Name, "")])];
             }
         }
         default:
@@ -365,7 +397,7 @@ export function JsonTypes_decomposeProcessInput(pi) {
 export function JsonTypes_decomposeProcessOutput(po) {
     switch (po.tag) {
         case 2:
-            return [new CompositeHeader(12, [new IOType(5, [])]), new CompositeCell(1, [defaultArg(po.fields[0].Name, "")])];
+            return [new CompositeHeader(12, [new IOType(3, [])]), new CompositeCell(1, [defaultArg(po.fields[0].Name, "")])];
         case 1: {
             const d = po.fields[0];
             const dataType = value_9(d.DataType);
@@ -373,9 +405,9 @@ export function JsonTypes_decomposeProcessOutput(po) {
                 case 0:
                     return [new CompositeHeader(12, [new IOType(2, [])]), new CompositeCell(1, [defaultArg(d.Name, "")])];
                 case 1:
-                    return [new CompositeHeader(12, [new IOType(3, [])]), new CompositeCell(1, [defaultArg(d.Name, "")])];
+                    return [new CompositeHeader(12, [new IOType(2, [])]), new CompositeCell(1, [defaultArg(d.Name, "")])];
                 default:
-                    return [new CompositeHeader(12, [new IOType(4, [])]), new CompositeCell(1, [defaultArg(d.Name, "")])];
+                    return [new CompositeHeader(12, [new IOType(2, [])]), new CompositeCell(1, [defaultArg(d.Name, "")])];
             }
         }
         default:
@@ -907,9 +939,9 @@ export function CompositeRow_toProtocol(tableName, row) {
             case 5:
                 return Protocol_addParameter(ProtocolParameter.create(void 0, oa_1), p);
             case 6:
-                return Protocol_addComponent(Component_create_4208F9FC(Value_1.fromString(v_4), unit, oa_2), p);
+                return Protocol_addComponent(Component_create_4208F9FC(Value_2.fromString(v_4), unit, oa_2), p);
             case 7:
-                return Protocol_addComponent(Component_create_4208F9FC(new Value_1(0, [t]), void 0, oa_3), p);
+                return Protocol_addComponent(Component_create_4208F9FC(new Value_2(0, [t]), void 0, oa_3), p);
             default:
                 return p;
         }

package/Core/Data.js

@@ -0,0 +1,119 @@
+import { defaultArg, unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { ResizeArray_map } from "./Helper/Collections.js";
+import { hash, boxHashSeq, boxHashOption, boxHashArray } from "./Helper/HashCodes.js";
+import { toString } from "../fable_modules/fable-library-js.4.16.0/Types.js";
+import { printf, toText } from "../fable_modules/fable-library-js.4.16.0/String.js";
+import { DataFile__get_AsString } from "./DataFile.js";
+import { class_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
+
+export class Data {
+    constructor(id, name, dataType, format, selectorFormat, comments) {
+        this._id = id;
+        this._name = name;
+        this._dataType = dataType;
+        this._format = format;
+        this._selectorFormat = selectorFormat;
+        this._comments = defaultArg(comments, []);
+    }
+    get ID() {
+        const this$ = this;
+        return unwrap(this$._id);
+    }
+    set ID(id) {
+        const this$ = this;
+        this$._id = id;
+    }
+    get Name() {
+        const this$ = this;
+        return unwrap(this$._name);
+    }
+    set Name(name) {
+        const this$ = this;
+        this$._name = name;
+    }
+    get DataType() {
+        const this$ = this;
+        return unwrap(this$._dataType);
+    }
+    set DataType(dataType) {
+        const this$ = this;
+        this$._dataType = dataType;
+    }
+    get Format() {
+        const this$ = this;
+        return unwrap(this$._format);
+    }
+    set Format(format) {
+        const this$ = this;
+        this$._format = format;
+    }
+    get SelectorFormat() {
+        const this$ = this;
+        return unwrap(this$._selectorFormat);
+    }
+    set SelectorFormat(selectorFormat) {
+        const this$ = this;
+        this$._selectorFormat = selectorFormat;
+    }
+    get Comments() {
+        const this$ = this;
+        return this$._comments;
+    }
+    set Comments(comments) {
+        const this$ = this;
+        this$._comments = comments;
+    }
+    static make(id, name, dataType, format, selectorFormat, comments) {
+        return new Data(unwrap(id), unwrap(name), unwrap(dataType), unwrap(format), unwrap(selectorFormat), unwrap(comments));
+    }
+    static create(Id, Name, DataType, Format, SelectorFormat, Comments) {
+        return Data.make(Id, Name, DataType, Format, SelectorFormat, Comments);
+    }
+    static get empty() {
+        return Data.create();
+    }
+    get NameText() {
+        const this$ = this;
+        return defaultArg(this$.Name, "");
+    }
+    Copy() {
+        const this$ = this;
+        const nextComments = ResizeArray_map((c) => c.Copy(), this$.Comments);
+        return new Data(unwrap(this$.ID), unwrap(this$.Name), unwrap(this$.DataType), unwrap(this$.Format), unwrap(this$.SelectorFormat), nextComments);
+    }
+    GetHashCode() {
+        const this$ = this;
+        return boxHashArray([boxHashOption(this$.ID), boxHashOption(this$.Name), boxHashOption(this$.DataType), boxHashOption(this$.Format), boxHashOption(this$.SelectorFormat), boxHashSeq(this$.Comments)]) | 0;
+    }
+    Equals(obj) {
+        const this$ = this;
+        return hash(this$) === hash(obj);
+    }
+    Print() {
+        const this$ = this;
+        return toString(this$);
+    }
+    PrintCompact() {
+        const this$ = this;
+        const matchValue = this$.DataType;
+        if (matchValue == null) {
+            const arg_2 = this$.NameText;
+            return toText(printf("%s"))(arg_2);
+        }
+        else {
+            const t = matchValue;
+            const arg = this$.NameText;
+            const arg_1 = DataFile__get_AsString(t);
+            return toText(printf("%s [%s]"))(arg)(arg_1);
+        }
+    }
+}
+
+export function Data_$reflection() {
+    return class_type("ARCtrl.Data", void 0, Data);
+}
+
+export function Data_$ctor_5909441C(id, name, dataType, format, selectorFormat, comments) {
+    return new Data(id, name, dataType, format, selectorFormat, comments);
+}
+

package/Core/{Process/DataFile.js → DataFile.js}

@@ -1,5 +1,5 @@
-import { Union } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
-import { union_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
+import { Union } from "../fable_modules/fable-library-js.4.16.0/Types.js";
+import { union_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
 
 export class DataFile extends Union {
     constructor(tag, fields) {
@@ -13,7 +13,7 @@ export class DataFile extends Union {
 }
 
 export function DataFile_$reflection() {
-    return union_type("ARCtrl.Process.DataFile", [], DataFile, () => [[], [], []]);
+    return union_type("ARCtrl.DataFile", [], DataFile, () => [[], [], []]);
 }
 
 export function DataFile_get_RawDataFileJson() {

package/Core/Helper/Identifier.js

@@ -89,6 +89,26 @@ export function Assay_tryFileNameFromIdentifier(identifier) {
     }
 }
 
+/**
+ * On writing a xlsx file we unify our output to a relative path to ARC root. So: `assays/assayIdentifier/isa.datamap.xlsx`.
+ */
+export function Assay_datamapFileNameFromIdentifier(identifier) {
+    checkValidCharacters(identifier);
+    return combineMany(["assays", identifier, "isa.datamap.xlsx"]);
+}
+
+/**
+ * On writing a xlsx file we unify our output to a relative path to ARC root. So: `assays/assayIdentifier/isa.datamap.xlsx`.
+ */
+export function Assay_tryDatamapFileNameFromIdentifier(identifier) {
+    if (tryCheckValidCharacters(identifier)) {
+        return combineMany(["assays", identifier, "isa.datamap.xlsx"]);
+    }
+    else {
+        return void 0;
+    }
+}
+
 /**
  * On read-in the FileName can be any combination of "studies" (study folder name), studyIdentifier and "isa.study.xlsx" (the actual file name).
  * 
@@ -141,3 +161,23 @@ export function Study_tryFileNameFromIdentifier(identifier) {
     }
 }
 
+/**
+ * On writing a xlsx file we unify our output to a relative path to ARC root. So: `studies/studyIdentifier/isa.investigation.xlsx`.
+ */
+export function Study_datamapFileNameFromIdentifier(identifier) {
+    checkValidCharacters(identifier);
+    return combineMany(["studies", identifier, "isa.datamap.xlsx"]);
+}
+
+/**
+ * On writing a xlsx file we unify our output to a relative path to ARC root. So: `studies/studyIdentifier/isa.investigation.xlsx`.
+ */
+export function Study_tryDatamapFileNameFromIdentifier(identifier) {
+    if (tryCheckValidCharacters(identifier)) {
+        return combineMany(["studies", identifier, "isa.datamap.xlsx"]);
+    }
+    else {
+        return void 0;
+    }
+}
+

package/Core/OntologyAnnotation.js

@@ -66,10 +66,16 @@ export class OntologyAnnotation {
     static createUriAnnotation(termSourceRef, localTAN) {
         return `${"http://purl.obolibrary.org/obo/"}${termSourceRef}_${localTAN}`;
     }
-    static fromTermAnnotation(tan) {
-        const r = value_4(tryParseTermAnnotation(tan));
-        const accession = (r.IDSpace + ":") + r.LocalID;
-        return OntologyAnnotation.create("", r.IDSpace, accession);
+    static fromTermAnnotation(tan, name) {
+        const matchValue = tryParseTermAnnotation(tan);
+        if (matchValue == null) {
+            return OntologyAnnotation.create(name, void 0, tan);
+        }
+        else {
+            const r = matchValue;
+            const accession = (r.IDSpace + ":") + r.LocalID;
+            return OntologyAnnotation.create(name, r.IDSpace, accession);
+        }
     }
     get TermAccessionShort() {
         const this$ = this;
@@ -135,6 +141,10 @@ export class OntologyAnnotation {
         StringBuilder__Append_Z721C83C5(sb, "}");
         return toString(sb);
     }
+    isEmpty() {
+        const this$ = this;
+        return (((this$.Name == null) && (this$.TermSourceREF == null)) && (this$.TermAccessionNumber == null)) && (this$.Comments.length === 0);
+    }
     GetHashCode() {
         const this$ = this;
         return boxHashArray(toArray(delay(() => append(singleton(boxHashOption(this$.Name)), delay(() => {

package/Core/Process/ColumnIndex.js

@@ -1,9 +1,10 @@
 import { tryParse } from "../../fable_modules/fable-library-js.4.16.0/Int32.js";
 import { FSharpRef } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
 import { Comment$ } from "../Comment.js";
-import { int32ToString } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
-import { value, bind } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
+import { equals, int32ToString } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
 import { tryItem } from "../CommentList.js";
+import { findIndex } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { value, bind } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 import { Factor } from "./Factor.js";
 import { MaterialAttribute_fromString_5980DC03 } from "./MaterialAttribute.js";
 import { ProtocolParameter } from "./ProtocolParameter.js";
@@ -30,7 +31,16 @@ export function createOrderComment(index) {
 }
 
 export function tryGetIndex(comments) {
-    return bind(tryInt, tryItem(orderName, 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 void 0;
+    }
 }
 
 export function setOntologyAnnotationIndexInplace(i, oa) {

package/Core/Process/ProcessInput.js

@@ -2,12 +2,12 @@ import { Union, toString } from "../../fable_modules/fable-library-js.4.16.0/Typ
 import { printf, toText } from "../../fable_modules/fable-library-js.4.16.0/String.js";
 import { Source_create_Z5CA08497, Source_getUnits_53E41069, Source_setCharacteristicValues, Source_get_empty, Source_$reflection } from "./Source.js";
 import { Sample_create_62424AD2, Sample_getUnits_53716792, Sample_setCharacteristicValues, Sample_$reflection } from "./Sample.js";
-import { Data_create_Z2AF98BBE, Data_$reflection } from "./Data.js";
+import { Data, Data_$reflection } from "../Data.js";
 import { Material_create_Z66909A6D, Material_getUnits_ZBCDEB61, Material_setCharacteristicValues, Material_$reflection } from "./Material.js";
 import { union_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
 import { unwrap, map, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 import { empty, choose } from "../../fable_modules/fable-library-js.4.16.0/List.js";
-import { DataFile } from "./DataFile.js";
+import { DataFile } from "../DataFile.js";
 
 export class ProcessInput extends Union {
     constructor(tag, fields) {
@@ -284,14 +284,14 @@ export function ProcessInput_createMaterial_4452CB4C(name, characteristics, deri
 }
 
 export function ProcessInput_createImageFile_Z721C83C5(name) {
-    return new ProcessInput(2, [Data_create_Z2AF98BBE(void 0, name, new DataFile(2, []))]);
+    return new ProcessInput(2, [Data.create(void 0, name, new DataFile(2, []))]);
 }
 
 export function ProcessInput_createRawData_Z721C83C5(name) {
-    return new ProcessInput(2, [Data_create_Z2AF98BBE(void 0, name, new DataFile(0, []))]);
+    return new ProcessInput(2, [Data.create(void 0, name, new DataFile(0, []))]);
 }
 
 export function ProcessInput_createDerivedData_Z721C83C5(name) {
-    return new ProcessInput(2, [Data_create_Z2AF98BBE(void 0, name, new DataFile(1, []))]);
+    return new ProcessInput(2, [Data.create(void 0, name, new DataFile(1, []))]);
 }
 

package/Core/Process/ProcessOutput.js

@@ -1,12 +1,12 @@
 import { Union, toString } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
 import { printf, toText } from "../../fable_modules/fable-library-js.4.16.0/String.js";
 import { Sample_create_62424AD2, Sample_getUnits_53716792, Sample_setFactorValues, Sample_get_empty, Sample_$reflection } from "./Sample.js";
-import { Data_create_Z2AF98BBE, Data_$reflection } from "./Data.js";
+import { Data, Data_$reflection } from "../Data.js";
 import { Material_create_Z66909A6D, Material_getUnits_ZBCDEB61, Material_$reflection } from "./Material.js";
 import { union_type } from "../../fable_modules/fable-library-js.4.16.0/Reflection.js";
 import { unwrap, map, defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 import { empty, choose } from "../../fable_modules/fable-library-js.4.16.0/List.js";
-import { DataFile } from "./DataFile.js";
+import { DataFile } from "../DataFile.js";
 
 export class ProcessOutput extends Union {
     constructor(tag, fields) {
@@ -250,14 +250,14 @@ export function ProcessOutput_createMaterial_4452CB4C(name, characteristics, der
 }
 
 export function ProcessOutput_createImageFile_Z721C83C5(name) {
-    return new ProcessOutput(1, [Data_create_Z2AF98BBE(void 0, name, new DataFile(2, []))]);
+    return new ProcessOutput(1, [Data.create(void 0, name, new DataFile(2, []))]);
 }
 
 export function ProcessOutput_createRawData_Z721C83C5(name) {
-    return new ProcessOutput(1, [Data_create_Z2AF98BBE(void 0, name, new DataFile(0, []))]);
+    return new ProcessOutput(1, [Data.create(void 0, name, new DataFile(0, []))]);
 }
 
 export function ProcessOutput_createDerivedData_Z721C83C5(name) {
-    return new ProcessOutput(1, [Data_create_Z2AF98BBE(void 0, name, new DataFile(1, []))]);
+    return new ProcessOutput(1, [Data.create(void 0, name, new DataFile(1, []))]);
 }
 

package/Core/Process/Value.js

@@ -31,7 +31,7 @@ export class Value extends Union {
             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(0, [OntologyAnnotation.create(value)]));
+            return matchValue_1[0] ? (new Value(2, [matchValue_1[1]])) : (new Value(3, [value]));
         }
     }
     static fromOptions(value, termSource, termAccesssion) {