@nfdi4plants/arctrl 2.4.0 → 2.5.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/ARC.js +103 -12
- package/CWL/CWLTypes.js +2 -2
- package/CWL/Decode.js +2 -2
- package/CWL/Inputs.js +2 -2
- package/CWL/Outputs.js +2 -2
- package/CWL/Requirements.js +2 -2
- package/CWL/ToolDescription.js +1 -1
- package/CWL/WorkflowDescription.js +1 -1
- package/CWL/WorkflowSteps.js +1 -1
- package/ColumnIndex.js +258 -0
- package/Conversion.js +1679 -0
- package/Core/Data.js +28 -3
- package/Core/DataFile.js +19 -3
- package/Core/Helper/Collections.js +107 -4
- package/Core/Helper/DateTime.js +17 -0
- package/Core/Helper/ORCID.js +39 -0
- package/Json/Decode.js +3 -3
- package/Json/Encode.js +9 -0
- package/Json/OntologySourceReference.js +4 -4
- package/Json/ROCrate/LDContext.js +121 -0
- package/Json/ROCrate/LDGraph.js +87 -0
- package/Json/{LDObject.js → ROCrate/LDNode.js} +55 -46
- package/Json/ROCrate/LDRef.js +25 -0
- package/Json/ROCrate/LDValue.js +66 -0
- package/JsonIO/LDObject.js +30 -5
- package/ROCrate/ArcROCrateMetadata.js +14 -13
- package/ROCrate/Generic/Comment.js +115 -0
- package/ROCrate/Generic/Dataset.js +669 -0
- package/ROCrate/Generic/DefinedTerm.js +115 -0
- package/ROCrate/Generic/File.js +200 -0
- package/ROCrate/Generic/LabProcess.js +238 -0
- package/ROCrate/Generic/LabProtocol.js +275 -0
- package/ROCrate/Generic/Organization.js +71 -0
- package/ROCrate/Generic/Person.js +411 -0
- package/ROCrate/Generic/PostalAddress.js +159 -0
- package/ROCrate/Generic/PropertyValue.js +548 -0
- package/ROCrate/Generic/Sample.js +139 -0
- package/ROCrate/Generic/ScholarlyArticle.js +187 -0
- package/ROCrate/Helper.js +6 -0
- package/ROCrate/ISAProfile/Assay.js +3 -3
- package/ROCrate/ISAProfile/Data.js +7 -7
- package/ROCrate/ISAProfile/Dataset.js +7 -6
- package/ROCrate/ISAProfile/Investigation.js +3 -3
- package/ROCrate/ISAProfile/LabProcess.js +7 -7
- package/ROCrate/ISAProfile/LabProtocol.js +7 -7
- package/ROCrate/ISAProfile/Person.js +7 -7
- package/ROCrate/ISAProfile/PropertyValue.js +7 -7
- package/ROCrate/ISAProfile/Sample.js +7 -7
- package/ROCrate/ISAProfile/ScholarlyArticle.js +7 -7
- package/ROCrate/ISAProfile/Study.js +3 -3
- package/ROCrate/LDContext.js +283 -0
- package/ROCrate/LDObject.js +902 -36
- package/ROCrate/ROCrateContext.js +44 -0
- package/ROCrateIO.js +62 -0
- package/Spreadsheet/DataMapTable/DataMapHeader.js +3 -2
- package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/DynObj.fs +31 -1
- package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/DynObj.fs.js +30 -1
- package/fable_modules/DynamicObj.7.0.1/DynamicObj.fs +1025 -0
- package/fable_modules/DynamicObj.7.0.1/DynamicObj.fs.js +433 -0
- package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/FableJS.fs +16 -0
- package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/FablePy.fs +14 -0
- package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/HashCodes.fs +15 -0
- package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/HashCodes.fs.js +4 -0
- package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/obj/Debug/netstandard2.0/DynamicObj.AssemblyInfo.fs +1 -1
- package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/obj/Release/netstandard2.0/DynamicObj.AssemblyInfo.fs +3 -3
- package/fable_modules/project_cracked.json +1 -1
- package/package.json +1 -1
- package/Json/ARC.js +0 -31
- package/JsonIO/ARC.js +0 -31
- package/fable_modules/DynamicObj.4.0.3/DynamicObj.fs +0 -310
- package/fable_modules/DynamicObj.4.0.3/DynamicObj.fs.js +0 -166
- /package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/DynamicObj.fableproj +0 -0
- /package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/FableJS.fs.js +0 -0
- /package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/PropertyHelper.fs +0 -0
- /package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/PropertyHelper.fs.js +0 -0
- /package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/ReflectionUtils.fs +0 -0
- /package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/ReflectionUtils.fs.js +0 -0
- /package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/obj/Debug/netstandard2.0/.NETStandard,Version=v2.0.AssemblyAttributes.fs +0 -0
- /package/fable_modules/{DynamicObj.4.0.3 → DynamicObj.7.0.1}/obj/Release/netstandard2.0/.NETStandard,Version=v2.0.AssemblyAttributes.fs +0 -0
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import { dateTime } from "
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import { resizeArrayOrSingleton, dateTime } from "../Encode.js";
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import { LDNode, LDRef, LDValue } from "../../ROCrate/LDObject.js";
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import { decoder as decoder_2, encoder as encoder_1 } from "./LDValue.js";
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import { decoder as decoder_3, encoder as encoder_2 } from "./LDRef.js";
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import { int32ToString, disposeSafe, getEnumerator, isIterable, defaultOf, equals } from "../../fable_modules/fable-library-js.4.24.0/Util.js";
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import { list } from "../../fable_modules/Thoth.Json.Core.0.4.0/Encode.fs.js";
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import { collect, empty, singleton, append, enumerateFromFunctions, map, delay, toList } from "../../fable_modules/fable-library-js.4.24.0/Seq.js";
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import { decoder as decoder_1, encoder as encoder_3 } from "./LDContext.js";
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import { decimal, int, oneOf, map as map_1, Getters$2__get_Errors, string, Getters$2_$ctor_Z4BE6C149 } from "../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js";
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import { Helpers_prependPath, Decode_resizeArrayOrSingleton } from "../Decode.js";
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import { value as value_12, unwrap } from "../../fable_modules/fable-library-js.4.24.0/Option.js";
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import { ofArray, head, length, isEmpty } from "../../fable_modules/fable-library-js.4.24.0/List.js";
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import { ErrorReason$1 } from "../../fable_modules/Thoth.Json.Core.0.4.0/Types.fs.js";
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import { FSharpResult$2 } from "../../fable_modules/fable-library-js.4.24.0/Result.js";
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import { fold } from "../../fable_modules/fable-library-js.4.24.0/Array.js";
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export function genericEncoder(obj) {
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else if (obj instanceof LDValue) {
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return encoder_1(obj);
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}
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else if (obj instanceof LDRef) {
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}
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if (((l !== "id") && (l !== "schematype")) && (l !== "additionaltype")) {
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return [kv[0], genericEncoder(kv[1])];
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values = append(toList(delay(() => {
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})]), delay(() => append(singleton(["@type", resizeArrayOrSingleton((value_1) => ({
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return helpers_1.encodeString(value_1);
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}), obj.SchemaType)]), delay(() => append((obj.AdditionalType.length !== 0) ? singleton(["additionalType", resizeArrayOrSingleton((value_3) => ({
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}), obj.AdditionalType)]) : empty(), delay(() => {
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return ((((((l !== "id") && (l !== "schematype")) && (l !== "additionaltype")) && (l !== "@context")) && !l.startsWith("init@")) && !l.startsWith("init_")) ? singleton([kv[0], genericEncoder(kv[1])]) : empty();
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return oneOf(ofArray([map_1((value_5) => value_5, decoder_2), map_1((value_6) => value_6, decodeObject), map_1((value_7) => value_7, decoder_3), map_1((value_8) => value_8, resizeArray), map_1((value_9) => value_9, string), map_1((value_10) => value_10, int), map_1((value_11) => value_11, decimal)]));
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let objectArg, objectArg_1;
|
|
49
|
+
return new LDValue((objectArg = decoders.Required, objectArg.Field("@value", genericDecoder)), unwrap((objectArg_1 = decoders.Optional, objectArg_1.Field("@type", string))));
|
|
50
|
+
});
|
|
51
|
+
|
|
52
|
+
export function encoder(v) {
|
|
53
|
+
let value;
|
|
54
|
+
const values = ofArray([["@value", genericEncoder(v.Value)], ["@type", (value = v.ValueType, {
|
|
55
|
+
Encode(helpers) {
|
|
56
|
+
return helpers.encodeString(value);
|
|
57
|
+
},
|
|
58
|
+
})]]);
|
|
59
|
+
return {
|
|
60
|
+
Encode(helpers_1) {
|
|
61
|
+
const arg = map_1((tupledArg) => [tupledArg[0], tupledArg[1].Encode(helpers_1)], values);
|
|
62
|
+
return helpers_1.encodeObject(arg);
|
|
63
|
+
},
|
|
64
|
+
};
|
|
65
|
+
}
|
|
66
|
+
|
package/JsonIO/LDObject.js
CHANGED
|
@@ -1,11 +1,12 @@
|
|
|
1
1
|
import { fromString } from "../fable_modules/Thoth.Json.JavaScript.0.3.0/Decode.fs.js";
|
|
2
|
-
import { encoder, decoder as decoder_1 } from "../Json/
|
|
2
|
+
import { encoder, decoder as decoder_1 } from "../Json/ROCrate/LDNode.js";
|
|
3
3
|
import { printf, toText } from "../fable_modules/fable-library-js.4.24.0/String.js";
|
|
4
4
|
import { toString } from "../fable_modules/Thoth.Json.JavaScript.0.3.0/Encode.fs.js";
|
|
5
5
|
import { defaultSpaces } from "../Json/Encode.js";
|
|
6
6
|
import { unwrap } from "../fable_modules/fable-library-js.4.24.0/Option.js";
|
|
7
|
+
import { encoder as encoder_1, decoder as decoder_2 } from "../Json/ROCrate/LDGraph.js";
|
|
7
8
|
|
|
8
|
-
export function
|
|
9
|
+
export function ARCtrl_ROCrate_LDNode__LDNode_fromROCrateJsonString_Static_Z721C83C5(s) {
|
|
9
10
|
const matchValue = fromString(decoder_1, s);
|
|
10
11
|
if (matchValue.tag === 1) {
|
|
11
12
|
throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
|
|
@@ -18,14 +19,38 @@ export function ARCtrl_ROCrate_LDObject__LDObject_fromROCrateJsonString_Static_Z
|
|
|
18
19
|
/**
|
|
19
20
|
* exports in json-ld format
|
|
20
21
|
*/
|
|
21
|
-
export function
|
|
22
|
+
export function ARCtrl_ROCrate_LDNode__LDNode_toROCrateJsonString_Static_71136F3F(spaces) {
|
|
22
23
|
return (obj) => {
|
|
23
24
|
const value = encoder(obj);
|
|
24
25
|
return toString(defaultSpaces(spaces), value);
|
|
25
26
|
};
|
|
26
27
|
}
|
|
27
28
|
|
|
28
|
-
export function
|
|
29
|
-
return
|
|
29
|
+
export function ARCtrl_ROCrate_LDNode__LDNode_ToROCrateJsonString_71136F3F(this$, spaces) {
|
|
30
|
+
return ARCtrl_ROCrate_LDNode__LDNode_toROCrateJsonString_Static_71136F3F(unwrap(spaces))(this$);
|
|
31
|
+
}
|
|
32
|
+
|
|
33
|
+
export function ARCtrl_ROCrate_LDGraph__LDGraph_fromROCrateJsonString_Static_Z721C83C5(s) {
|
|
34
|
+
const matchValue = fromString(decoder_2, s);
|
|
35
|
+
if (matchValue.tag === 1) {
|
|
36
|
+
throw new Error(toText(printf("Error decoding string: %O"))(matchValue.fields[0]));
|
|
37
|
+
}
|
|
38
|
+
else {
|
|
39
|
+
return matchValue.fields[0];
|
|
40
|
+
}
|
|
41
|
+
}
|
|
42
|
+
|
|
43
|
+
/**
|
|
44
|
+
* exports in json-ld format
|
|
45
|
+
*/
|
|
46
|
+
export function ARCtrl_ROCrate_LDGraph__LDGraph_toROCrateJsonString_Static_71136F3F(spaces) {
|
|
47
|
+
return (obj) => {
|
|
48
|
+
const value = encoder_1(obj);
|
|
49
|
+
return toString(defaultSpaces(spaces), value);
|
|
50
|
+
};
|
|
51
|
+
}
|
|
52
|
+
|
|
53
|
+
export function ARCtrl_ROCrate_LDGraph__LDGraph_ToROCrateJsonString_71136F3F(this$, spaces) {
|
|
54
|
+
return ARCtrl_ROCrate_LDGraph__LDGraph_toROCrateJsonString_Static_71136F3F(unwrap(spaces))(this$);
|
|
30
55
|
}
|
|
31
56
|
|
|
@@ -1,13 +1,14 @@
|
|
|
1
1
|
import { defaultOf } from "../fable_modules/fable-library-js.4.24.0/Util.js";
|
|
2
2
|
import { FSharpRef } from "../fable_modules/fable-library-js.4.24.0/Types.js";
|
|
3
|
-
import { setOptionalProperty } from "../fable_modules/DynamicObj.
|
|
4
|
-
import { DynamicObj } from "../fable_modules/DynamicObj.
|
|
5
|
-
import {
|
|
3
|
+
import { setOptionalProperty } from "../fable_modules/DynamicObj.7.0.1/DynObj.fs.js";
|
|
4
|
+
import { DynamicObj } from "../fable_modules/DynamicObj.7.0.1/DynamicObj.fs.js";
|
|
5
|
+
import { LDContext } from "./LDContext.js";
|
|
6
|
+
import { LDNode_$reflection, LDNode } from "./LDObject.js";
|
|
6
7
|
import { class_type } from "../fable_modules/fable-library-js.4.24.0/Reflection.js";
|
|
7
8
|
|
|
8
|
-
export class ArcROCrateMetadata extends
|
|
9
|
+
export class ArcROCrateMetadata extends LDNode {
|
|
9
10
|
constructor(about) {
|
|
10
|
-
super("ro-crate-metadata", "CreativeWork");
|
|
11
|
+
super("ro-crate-metadata", ["CreativeWork"]);
|
|
11
12
|
const this$ = new FSharpRef(defaultOf());
|
|
12
13
|
this$.contents = this;
|
|
13
14
|
this["init@5"] = 1;
|
|
@@ -15,21 +16,21 @@ export class ArcROCrateMetadata extends LDObject {
|
|
|
15
16
|
const conformsTo = new DynamicObj();
|
|
16
17
|
conformsTo.SetProperty("@id", "https://w3id.org/ro/crate/1.1");
|
|
17
18
|
this$.contents.SetProperty("conformsTo", conformsTo);
|
|
18
|
-
const context =
|
|
19
|
-
context.
|
|
20
|
-
context.
|
|
21
|
-
context.
|
|
22
|
-
context.
|
|
23
|
-
context.
|
|
19
|
+
const context = new LDContext();
|
|
20
|
+
context.AddMapping("sdo", "http://schema.org/");
|
|
21
|
+
context.AddMapping("arc", "http://purl.org/nfdi4plants/ontology/");
|
|
22
|
+
context.AddMapping("CreativeWork", "sdo:CreativeWork");
|
|
23
|
+
context.AddMapping("about", "sdo:about");
|
|
24
|
+
context.AddMapping("conformsTo", "sdo:conformsTo");
|
|
24
25
|
this$.contents.SetProperty("@context", context);
|
|
25
26
|
}
|
|
26
27
|
}
|
|
27
28
|
|
|
28
29
|
export function ArcROCrateMetadata_$reflection() {
|
|
29
|
-
return class_type("ARCtrl.ROCrate.ArcROCrateMetadata", undefined, ArcROCrateMetadata,
|
|
30
|
+
return class_type("ARCtrl.ROCrate.ArcROCrateMetadata", undefined, ArcROCrateMetadata, LDNode_$reflection());
|
|
30
31
|
}
|
|
31
32
|
|
|
32
|
-
export function ArcROCrateMetadata_$
|
|
33
|
+
export function ArcROCrateMetadata_$ctor_Z7020538(about) {
|
|
33
34
|
return new ArcROCrateMetadata(about);
|
|
34
35
|
}
|
|
35
36
|
|
|
@@ -0,0 +1,115 @@
|
|
|
1
|
+
import { value, unwrap } from "../../fable_modules/fable-library-js.4.24.0/Option.js";
|
|
2
|
+
import { clean } from "../Helper.js";
|
|
3
|
+
import { LDNode } from "../LDObject.js";
|
|
4
|
+
import { class_type } from "../../fable_modules/fable-library-js.4.24.0/Reflection.js";
|
|
5
|
+
|
|
6
|
+
export class LDComment {
|
|
7
|
+
constructor() {
|
|
8
|
+
}
|
|
9
|
+
static get schemaType() {
|
|
10
|
+
return "http://schema.org/Comment";
|
|
11
|
+
}
|
|
12
|
+
static get text() {
|
|
13
|
+
return "http://schema.org/text";
|
|
14
|
+
}
|
|
15
|
+
static get name() {
|
|
16
|
+
return "http://schema.org/name";
|
|
17
|
+
}
|
|
18
|
+
static tryGetTextAsString(dt, context) {
|
|
19
|
+
const matchValue = dt.TryGetPropertyAsSingleton(LDComment.text, unwrap(context));
|
|
20
|
+
let matchResult, tc;
|
|
21
|
+
if (matchValue != null) {
|
|
22
|
+
if (typeof value(matchValue) === "string") {
|
|
23
|
+
matchResult = 0;
|
|
24
|
+
tc = value(matchValue);
|
|
25
|
+
}
|
|
26
|
+
else {
|
|
27
|
+
matchResult = 1;
|
|
28
|
+
}
|
|
29
|
+
}
|
|
30
|
+
else {
|
|
31
|
+
matchResult = 1;
|
|
32
|
+
}
|
|
33
|
+
switch (matchResult) {
|
|
34
|
+
case 0:
|
|
35
|
+
return tc;
|
|
36
|
+
default:
|
|
37
|
+
return undefined;
|
|
38
|
+
}
|
|
39
|
+
}
|
|
40
|
+
static getTextAsString(dt, context) {
|
|
41
|
+
const matchValue = dt.TryGetPropertyAsSingleton(LDComment.text, unwrap(context));
|
|
42
|
+
if (matchValue != null) {
|
|
43
|
+
if (typeof value(matchValue) === "string") {
|
|
44
|
+
const tc = value(matchValue);
|
|
45
|
+
return tc;
|
|
46
|
+
}
|
|
47
|
+
else {
|
|
48
|
+
throw new Error(`Property of \`text\` of object with @id \`${dt.Id}\` was not a string`);
|
|
49
|
+
}
|
|
50
|
+
}
|
|
51
|
+
else {
|
|
52
|
+
throw new Error(`Could not access property \`text\` of object with @id \`${dt.Id}\``);
|
|
53
|
+
}
|
|
54
|
+
}
|
|
55
|
+
static setTextAsString(dt, text, context) {
|
|
56
|
+
return dt.SetProperty(LDComment.text, text, unwrap(context));
|
|
57
|
+
}
|
|
58
|
+
static tryGetNameAsString(dt, context) {
|
|
59
|
+
const matchValue = dt.TryGetPropertyAsSingleton(LDComment.name, unwrap(context));
|
|
60
|
+
let matchResult, n;
|
|
61
|
+
if (matchValue != null) {
|
|
62
|
+
if (typeof value(matchValue) === "string") {
|
|
63
|
+
matchResult = 0;
|
|
64
|
+
n = value(matchValue);
|
|
65
|
+
}
|
|
66
|
+
else {
|
|
67
|
+
matchResult = 1;
|
|
68
|
+
}
|
|
69
|
+
}
|
|
70
|
+
else {
|
|
71
|
+
matchResult = 1;
|
|
72
|
+
}
|
|
73
|
+
switch (matchResult) {
|
|
74
|
+
case 0:
|
|
75
|
+
return n;
|
|
76
|
+
default:
|
|
77
|
+
return undefined;
|
|
78
|
+
}
|
|
79
|
+
}
|
|
80
|
+
static getNameAsString(dt, context) {
|
|
81
|
+
const matchValue = dt.TryGetPropertyAsSingleton(LDComment.name, unwrap(context));
|
|
82
|
+
if (matchValue != null) {
|
|
83
|
+
if (typeof value(matchValue) === "string") {
|
|
84
|
+
const n = value(matchValue);
|
|
85
|
+
return n;
|
|
86
|
+
}
|
|
87
|
+
else {
|
|
88
|
+
throw new Error(`Property of \`name\` of object with @id \`${dt.Id}\` was not a string`);
|
|
89
|
+
}
|
|
90
|
+
}
|
|
91
|
+
else {
|
|
92
|
+
throw new Error(`Could not access property \`name\` of object with @id \`${dt.Id}\``);
|
|
93
|
+
}
|
|
94
|
+
}
|
|
95
|
+
static setNameAsString(dt, name, context) {
|
|
96
|
+
return dt.SetProperty(LDComment.name, name, unwrap(context));
|
|
97
|
+
}
|
|
98
|
+
static genID(name, text) {
|
|
99
|
+
return clean((text == null) ? (`#LDComment_${name}`) : (`#LDComment_${name}_${text}`));
|
|
100
|
+
}
|
|
101
|
+
static validate(dt, context) {
|
|
102
|
+
return dt.HasType(LDComment.schemaType, unwrap(context)) && dt.HasProperty(LDComment.name, unwrap(context));
|
|
103
|
+
}
|
|
104
|
+
static create(name, id, text, context) {
|
|
105
|
+
const dt = new LDNode((id == null) ? LDComment.genID(name, unwrap(text)) : id, [LDComment.schemaType], undefined, unwrap(context));
|
|
106
|
+
dt.SetProperty(LDComment.name, name, unwrap(context));
|
|
107
|
+
dt.SetOptionalProperty(LDComment.text, text, unwrap(context));
|
|
108
|
+
return dt;
|
|
109
|
+
}
|
|
110
|
+
}
|
|
111
|
+
|
|
112
|
+
export function LDComment_$reflection() {
|
|
113
|
+
return class_type("ARCtrl.ROCrate.LDComment", undefined, LDComment);
|
|
114
|
+
}
|
|
115
|
+
|