@nfdi4plants/arctrl 1.0.0-beta.7 → 1.0.0-beta.8

package/ISA/ISA/ArcTypes/ArcTypes.js

@@ -1,5 +1,5 @@
 import { map as map_1, defaultArg, unwrap } from "../../../fable_modules/fable-library.4.5.0/Option.js";
-import { concat, collect, append as append_4, tryFind, removeAt, tryFindIndex, choose, item, map as map_2, delay, toList, fold, length, forAll, contains, filter, toArray } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { concat, collect, append as append_4, tryFind, removeAt, tryFindIndex, exists, choose, item, map as map_2, delay, toList, fold, length, forAll, contains, filter, toArray } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
 import { defaultOf, safeHash, equals, disposeSafe, getEnumerator, stringHash } from "../../../fable_modules/fable-library.4.5.0/Util.js";
 import { addRangeInPlace, tryFind as tryFind_1, removeInPlace, equalsWith, append as append_3, contains as contains_1, map } from "../../../fable_modules/fable-library.4.5.0/Array.js";
 import { distinctBy, Array_distinct } from "../../../fable_modules/fable-library.4.5.0/Seq2.js";
@@ -10,7 +10,7 @@ import { Value_fromString_Z721C83C5, Value__get_Text } from "../JsonTypes/Value.
 import { AnnotationValue } from "../JsonTypes/AnnotationValue.js";
 import { ArcTablesAux_applyIOMap, ArcTablesAux_getIOMap, ArcTables_$reflection, ArcTables } from "./ArcTables.js";
 import { AssayMaterials_get_empty, AssayMaterials_create_Z253F0553 } from "../JsonTypes/AssayMaterials.js";
-import { ResizeArray_map, HashCodes_boxHashOption, HashCodes_boxHashArray, Option_fromValueWithDefault } from "../Helper.js";
+import { ResizeArray_choose, ResizeArray_filter, ResizeArray_map, HashCodes_boxHashOption, HashCodes_boxHashArray, Option_fromValueWithDefault } from "../Helper.js";
 import { unzip, ofSeq, map as map_3, toArray as toArray_1, ofArray, empty } from "../../../fable_modules/fable-library.4.5.0/List.js";
 import { getSources, getProtocols, getUnits, getCharacteristics, getData, getMaterials, getSamples } from "../JsonTypes/ProcessSequence.js";
 import { Assay_create_3D372A24 } from "../JsonTypes/Assay.js";
@@ -683,10 +683,14 @@ export class ArcStudy extends ArcTables {
     static get FileName() {
         return "isa.study.xlsx";
     }
-    get RegisteredAssayCount() {
+    get RegisteredAssayIdentifierCount() {
         const this$ = this;
         return this$.RegisteredAssayIdentifiers.length | 0;
     }
+    get RegisteredAssayCount() {
+        const this$ = this;
+        return this$.RegisteredAssays.length | 0;
+    }
     get RegisteredAssays() {
         const this$ = this;
         let inv;
@@ -700,6 +704,19 @@ export class ArcStudy extends ArcTables {
         const collection = choose((assayIdentifier) => inv.TryGetAssay(assayIdentifier), this$.RegisteredAssayIdentifiers);
         return Array.from(collection);
     }
+    get VacantAssayIdentifiers() {
+        const this$ = this;
+        let inv;
+        const investigation = this$.Investigation;
+        if (investigation != null) {
+            inv = investigation;
+        }
+        else {
+            throw new Error("Cannot execute this function. Object is not part of ArcInvestigation.");
+        }
+        const collection = filter((arg) => !inv.ContainsAssay(arg), this$.RegisteredAssayIdentifiers);
+        return Array.from(collection);
+    }
     AddRegisteredAssay(assay) {
         const this$ = this;
         let inv;
@@ -1249,7 +1266,7 @@ export class ArcInvestigation {
         const registeredStudyIdentifiers_1 = defaultArg(registeredStudyIdentifiers, []);
         const comments_1 = defaultArg(comments, []);
         const remarks_1 = defaultArg(remarks, []);
-        this["identifier@1148"] = identifier;
+        this["identifier@1162"] = identifier;
         this["Title@"] = title;
         this["Description@"] = description;
         this["SubmissionDate@"] = submissionDate;
@@ -1262,15 +1279,15 @@ export class ArcInvestigation {
         this["RegisteredStudyIdentifiers@"] = registeredStudyIdentifiers_1;
         this["Comments@"] = comments_1;
         this["Remarks@"] = remarks_1;
-        this["init@1129"] = 1;
+        this["init@1143"] = 1;
     }
     get Identifier() {
         const this$ = this;
-        return this$["identifier@1148"];
+        return this$["identifier@1162"];
     }
     set Identifier(i) {
         const this$ = this;
-        this$["identifier@1148"] = i;
+        this$["identifier@1162"] = i;
     }
     get Title() {
         const __ = this;
@@ -1388,6 +1405,10 @@ export class ArcInvestigation {
         const this$ = this;
         return Array.from(map_2((x) => x.Identifier, this$.Assays));
     }
+    get UnregisteredAssays() {
+        const this$ = this;
+        return ResizeArray_filter((a) => !exists((s) => exists((i) => (i === a.Identifier), s.RegisteredAssayIdentifiers), this$.RegisteredStudies), this$.Assays);
+    }
     AddAssay(assay) {
         const this$ = this;
         const assayIdent = assay.Identifier;
@@ -1550,10 +1571,28 @@ export class ArcInvestigation {
             return newInvestigation.TryGetAssay(assayIdentifier);
         };
     }
+    ContainsAssay(assayIdentifier) {
+        const this$ = this;
+        return exists((a) => (a.Identifier === assayIdentifier), this$.Assays);
+    }
+    static containsAssay(assayIdentifier) {
+        return (inv) => inv.ContainsAssay(assayIdentifier);
+    }
+    get RegisteredStudyIdentifierCount() {
+        const this$ = this;
+        return this$.RegisteredStudyIdentifiers.length | 0;
+    }
     get RegisteredStudies() {
         const this$ = this;
-        const collection = choose((identifier) => this$.TryGetStudy(identifier), this$.RegisteredStudyIdentifiers);
-        return Array.from(collection);
+        return ResizeArray_choose((identifier) => this$.TryGetStudy(identifier), this$.RegisteredStudyIdentifiers);
+    }
+    get RegisteredStudyCount() {
+        const this$ = this;
+        return this$.RegisteredStudies.length | 0;
+    }
+    get VacantStudyIdentifiers() {
+        const this$ = this;
+        return ResizeArray_filter((arg) => !this$.ContainsStudy(arg), this$.RegisteredStudyIdentifiers);
     }
     get StudyCount() {
         const this$ = this;
@@ -1563,6 +1602,13 @@ export class ArcInvestigation {
         const this$ = this;
         return toArray(map_2((x) => x.Identifier, this$.Studies));
     }
+    get UnregisteredStudies() {
+        const this$ = this;
+        return ResizeArray_filter((s) => {
+            let source, x;
+            return !((source = this$.RegisteredStudyIdentifiers, exists((x = s.Identifier, (y) => (x === y)), source)));
+        }, this$.Studies);
+    }
     AddStudy(study) {
         const this$ = this;
         const study_1 = study;
@@ -1752,6 +1798,13 @@ export class ArcInvestigation {
             return newInv.TryGetStudy(studyIdentifier);
         };
     }
+    ContainsStudy(studyIdentifier) {
+        const this$ = this;
+        return exists((s) => (s.Identifier === studyIdentifier), this$.Studies);
+    }
+    static containsStudy(studyIdentifier) {
+        return (inv) => inv.ContainsStudy(studyIdentifier);
+    }
     RegisterAssayAt(studyIndex, assayIdentifier) {
         const this$ = this;
         const study = this$.GetStudyAt(studyIndex);

package/ISA/ISA/ArcTypes/CompositeCell.js

@@ -176,6 +176,15 @@ export class CompositeCell extends Union {
         const this$ = this;
         return (this$.tag === 1) ? this$.fields[0] : ((this$.tag === 2) ? (`${this$.fields[0]} ${this$.fields[1].NameText}`) : (`${this$.fields[0].NameText}`));
     }
+    static term(oa) {
+        return new CompositeCell(0, [oa]);
+    }
+    static freeText(s) {
+        return new CompositeCell(1, [s]);
+    }
+    static unitized(v, oa) {
+        return new CompositeCell(2, [v, oa]);
+    }
 }
 
 export function CompositeCell_$reflection() {

package/ISA/ISA/ArcTypes/CompositeHeader.js

@@ -215,6 +215,27 @@ export class IOType extends Union {
                 throw new Error(`Unable to parse combination to existing IOType: \`${iotype}\``);
         }
     }
+    static source() {
+        return new IOType(0, []);
+    }
+    static sample() {
+        return new IOType(1, []);
+    }
+    static rawDataFile() {
+        return new IOType(2, []);
+    }
+    static derivedDataFile() {
+        return new IOType(3, []);
+    }
+    static imageFile() {
+        return new IOType(4, []);
+    }
+    static material() {
+        return new IOType(5, []);
+    }
+    static freeText(s) {
+        return new IOType(6, [s]);
+    }
 }
 
 export function IOType_$reflection() {
@@ -684,6 +705,48 @@ export class CompositeHeader extends Union {
                 throw new Error(`Unable to parse combination to existing CompositeHeader: \`${header}\``);
         }
     }
+    static component(oa) {
+        return new CompositeHeader(0, [oa]);
+    }
+    static characteristic(oa) {
+        return new CompositeHeader(1, [oa]);
+    }
+    static factor(oa) {
+        return new CompositeHeader(2, [oa]);
+    }
+    static parameter(oa) {
+        return new CompositeHeader(3, [oa]);
+    }
+    static protocolType() {
+        return new CompositeHeader(4, []);
+    }
+    static protocolDescription() {
+        return new CompositeHeader(5, []);
+    }
+    static protocolUri() {
+        return new CompositeHeader(6, []);
+    }
+    static protocolVersion() {
+        return new CompositeHeader(7, []);
+    }
+    static protocolREF() {
+        return new CompositeHeader(8, []);
+    }
+    static performer() {
+        return new CompositeHeader(9, []);
+    }
+    static date() {
+        return new CompositeHeader(10, []);
+    }
+    static input(io) {
+        return new CompositeHeader(11, [io]);
+    }
+    static output(io) {
+        return new CompositeHeader(12, [io]);
+    }
+    static freeText(s) {
+        return new CompositeHeader(13, [s]);
+    }
 }
 
 export function CompositeHeader_$reflection() {

package/README.md

@@ -5,8 +5,9 @@ and __JavaScript__! ❤️
 
 | Version | Downloads |
 | :--------|-----------:|
-|![Nuget (with prereleases)](https://img.shields.io/nuget/vpre/ARCtrl?logo=nuget&color=%234fb3d9)|![Nuget](https://img.shields.io/nuget/dt/ARCtrl?color=%234FB3D9)|
-|![npm (scoped with tag)](https://img.shields.io/npm/v/%40nfdi4plants/arctrl/next?logo=npm&color=%234fb3d9)|![npm](https://img.shields.io/npm/dt/%40nfdi4plants%2Farctrl?color=%234fb3d9)|
+|<a href="https://www.nuget.org/packages/ARCtrl/"><img alt="Nuget" src="https://img.shields.io/nuget/vpre/ARCtrl?logo=nuget&color=%234fb3d9"></a>|<a href="https://www.nuget.org/packages/ARCtrl/"><img alt="Nuget" src="https://img.shields.io/nuget/dt/ARCtrl?color=%234FB3D9"></a>|
+|<a href="https://www.npmjs.com/package/@nfdi4plants/arctrl"><img alt="NPM" src="https://img.shields.io/npm/v/%40nfdi4plants/arctrl/next?logo=npm&color=%234fb3d9"></a>|<a href="https://www.npmjs.com/package/@nfdi4plants/arctrl"><img alt="NPM" src="https://img.shields.io/npm/dt/%40nfdi4plants%2Farctrl?color=%234fb3d9"></a>|
+
 
 ## Install
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@nfdi4plants/arctrl",
-  "version": "1.0.0-beta.7+1c6c4fa",
+  "version": "1.0.0-beta.8+1c6c4fa",
   "description": "Top level ARC DataModel and API function descriptions.",
   "type": "module",
   "main": "Index.js",