@nfdi4plants/arctrl 1.1.0 → 2.0.0-alpha.1

package/Json/context/rocrate/rocrate_context.js

@@ -0,0 +1,23 @@
+import { Record } from "../../../fable_modules/fable-library-js.4.16.0/Types.js";
+import { record_type, string_type } from "../../../fable_modules/fable-library-js.4.16.0/Reflection.js";
+import { Json } from "../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+
+export class IContext extends Record {
+    constructor(sdo, arc, CreativeWork, about, conformsTo) {
+        super();
+        this.sdo = sdo;
+        this.arc = arc;
+        this.CreativeWork = CreativeWork;
+        this.about = about;
+        this.conformsTo = conformsTo;
+    }
+}
+
+export function IContext_$reflection() {
+    return record_type("ARCtrl.Json.ROCrateContext.ROCrate.IContext", [], IContext, () => [["sdo", string_type], ["arc", string_type], ["CreativeWork", string_type], ["about", string_type], ["conformsTo", string_type]]);
+}
+
+export const conformsTo_jsonvalue = new Json(5, [[["@id", new Json(0, ["https://w3id.org/ro/crate/1.1"])]]]);
+
+export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["arc", new Json(0, ["http://purl.org/nfdi4plants/ontology/"])], ["CreativeWork", new Json(0, ["sdo:CreativeWork"])], ["about", new Json(0, ["sdo:about"])], ["conformsTo", new Json(0, ["sdo:conformsTo"])]]]);
+

package/Json.js

@@ -0,0 +1,193 @@
+import { ARCtrl_OntologyAnnotation__OntologyAnnotation_toROCrateJsonString_Static_71136F3F, ARCtrl_OntologyAnnotation__OntologyAnnotation_toISAJsonString_Static_71136F3F, ARCtrl_OntologyAnnotation__OntologyAnnotation_toJsonString_Static_71136F3F, ARCtrl_OntologyAnnotation__OntologyAnnotation_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_OntologyAnnotation__OntologyAnnotation_fromISAJsonString_Static_Z721C83C5, ARCtrl_OntologyAnnotation__OntologyAnnotation_fromJsonString_Static_Z721C83C5 } from "./Json/OntologyAnnotation.js";
+import { unwrap } from "./fable_modules/fable-library-js.4.16.0/Option.js";
+import { class_type } from "./fable_modules/fable-library-js.4.16.0/Reflection.js";
+import { ARCtrl_ArcAssay__ArcAssay_toROCrateJsonString_Static_5CABCA47, ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_71136F3F, ARCtrl_ArcAssay__ArcAssay_toCompressedJsonString_Static_71136F3F, ARCtrl_ArcAssay__ArcAssay_toJsonString_Static_71136F3F, ARCtrl_ArcAssay__ArcAssay_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ArcAssay__ArcAssay_fromISAJsonString_Static_Z721C83C5, ARCtrl_ArcAssay__ArcAssay_fromCompressedJsonString_Static_Z721C83C5, ARCtrl_ArcAssay__ArcAssay_fromJsonString_Static_Z721C83C5 } from "./Json/Assay.js";
+import { ARCtrl_ArcStudy__ArcStudy_toROCrateJsonString_Static_3BA23086, ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_3BA23086, ARCtrl_ArcStudy__ArcStudy_toCompressedJsonString_Static_71136F3F, ARCtrl_ArcStudy__ArcStudy_toJsonString_Static_71136F3F, ARCtrl_ArcStudy__ArcStudy_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromISAJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromCompressedJsonString_Static_Z721C83C5, ARCtrl_ArcStudy__ArcStudy_fromJsonString_Static_Z721C83C5 } from "./Json/Study.js";
+import { ARCtrl_ArcInvestigation__ArcInvestigation_toROCrateJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_toISAJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_toCompressedJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_toJsonString_Static_71136F3F, ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromISAJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromCompressedJsonString_Static_Z721C83C5, ARCtrl_ArcInvestigation__ArcInvestigation_fromJsonString_Static_Z721C83C5 } from "./Json/Investigation.js";
+import { ARC } from "./ARC.js";
+
+export class JsonHelper_OntologyAnnotationJson {
+    constructor() {
+    }
+    fromJsonString(s) {
+        return ARCtrl_OntologyAnnotation__OntologyAnnotation_fromJsonString_Static_Z721C83C5(s);
+    }
+    fromISAJsonString(s) {
+        return ARCtrl_OntologyAnnotation__OntologyAnnotation_fromISAJsonString_Static_Z721C83C5(s);
+    }
+    fromROCrateJsonString(s) {
+        return ARCtrl_OntologyAnnotation__OntologyAnnotation_fromROCrateJsonString_Static_Z721C83C5(s);
+    }
+    toJsonString(oa, spaces) {
+        return ARCtrl_OntologyAnnotation__OntologyAnnotation_toJsonString_Static_71136F3F(unwrap(spaces))(oa);
+    }
+    toISAJsonString(oa, spaces) {
+        return ARCtrl_OntologyAnnotation__OntologyAnnotation_toISAJsonString_Static_71136F3F(unwrap(spaces))(oa);
+    }
+    toROCrateJsonString(oa, spaces) {
+        return ARCtrl_OntologyAnnotation__OntologyAnnotation_toROCrateJsonString_Static_71136F3F(unwrap(spaces))(oa);
+    }
+}
+
+export function JsonHelper_OntologyAnnotationJson_$reflection() {
+    return class_type("ARCtrl.JsonHelper.OntologyAnnotationJson", void 0, JsonHelper_OntologyAnnotationJson);
+}
+
+export function JsonHelper_OntologyAnnotationJson_$ctor() {
+    return new JsonHelper_OntologyAnnotationJson();
+}
+
+export class JsonHelper_AssayJson {
+    constructor() {
+    }
+    fromJsonString(s) {
+        return ARCtrl_ArcAssay__ArcAssay_fromJsonString_Static_Z721C83C5(s);
+    }
+    fromCompressedJsonString(s) {
+        return ARCtrl_ArcAssay__ArcAssay_fromCompressedJsonString_Static_Z721C83C5(s);
+    }
+    fromISAJsonString(s) {
+        return ARCtrl_ArcAssay__ArcAssay_fromISAJsonString_Static_Z721C83C5(s);
+    }
+    fromROCrateJsonString(s) {
+        return ARCtrl_ArcAssay__ArcAssay_fromROCrateJsonString_Static_Z721C83C5(s);
+    }
+    toJsonString(assay, spaces) {
+        return ARCtrl_ArcAssay__ArcAssay_toJsonString_Static_71136F3F(unwrap(spaces))(assay);
+    }
+    toCompressedJsonString(assay, spaces) {
+        return ARCtrl_ArcAssay__ArcAssay_toCompressedJsonString_Static_71136F3F(unwrap(spaces))(assay);
+    }
+    toISAJsonString(assay, spaces) {
+        return ARCtrl_ArcAssay__ArcAssay_toISAJsonString_Static_71136F3F(unwrap(spaces))(assay);
+    }
+    toROCrateJsonString(assay, studyName, spaces) {
+        return ARCtrl_ArcAssay__ArcAssay_toROCrateJsonString_Static_5CABCA47(studyName, unwrap(spaces))(assay);
+    }
+}
+
+export function JsonHelper_AssayJson_$reflection() {
+    return class_type("ARCtrl.JsonHelper.AssayJson", void 0, JsonHelper_AssayJson);
+}
+
+export function JsonHelper_AssayJson_$ctor() {
+    return new JsonHelper_AssayJson();
+}
+
+export class JsonHelper_StudyJson {
+    constructor() {
+    }
+    fromJsonString(s) {
+        return ARCtrl_ArcStudy__ArcStudy_fromJsonString_Static_Z721C83C5(s);
+    }
+    fromCompressedJsonString(s) {
+        return ARCtrl_ArcStudy__ArcStudy_fromCompressedJsonString_Static_Z721C83C5(s);
+    }
+    fromISAJsonString(s) {
+        return ARCtrl_ArcStudy__ArcStudy_fromISAJsonString_Static_Z721C83C5(s);
+    }
+    fromROCrateJsonString(s) {
+        return ARCtrl_ArcStudy__ArcStudy_fromROCrateJsonString_Static_Z721C83C5(s);
+    }
+    toJsonString(study, spaces) {
+        return ARCtrl_ArcStudy__ArcStudy_toJsonString_Static_71136F3F(unwrap(spaces))(study);
+    }
+    toCompressedJsonString(study, spaces) {
+        return ARCtrl_ArcStudy__ArcStudy_toCompressedJsonString_Static_71136F3F(unwrap(spaces))(study);
+    }
+    toISAJsonString(study, assays, spaces) {
+        return ARCtrl_ArcStudy__ArcStudy_toISAJsonString_Static_3BA23086(unwrap(assays), unwrap(spaces))(study);
+    }
+    toROCrateJsonString(study, assays, spaces) {
+        return ARCtrl_ArcStudy__ArcStudy_toROCrateJsonString_Static_3BA23086(unwrap(assays), unwrap(spaces))(study);
+    }
+}
+
+export function JsonHelper_StudyJson_$reflection() {
+    return class_type("ARCtrl.JsonHelper.StudyJson", void 0, JsonHelper_StudyJson);
+}
+
+export function JsonHelper_StudyJson_$ctor() {
+    return new JsonHelper_StudyJson();
+}
+
+export class JsonHelper_InvestigationJson {
+    constructor() {
+    }
+    fromJsonString(s) {
+        return ARCtrl_ArcInvestigation__ArcInvestigation_fromJsonString_Static_Z721C83C5(s);
+    }
+    fromCompressedJsonString(s) {
+        return ARCtrl_ArcInvestigation__ArcInvestigation_fromCompressedJsonString_Static_Z721C83C5(s);
+    }
+    fromISAJsonString(s) {
+        return ARCtrl_ArcInvestigation__ArcInvestigation_fromISAJsonString_Static_Z721C83C5(s);
+    }
+    fromROCrateJsonString(s) {
+        return ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateJsonString_Static_Z721C83C5(s);
+    }
+    toJsonString(investigation, spaces) {
+        return ARCtrl_ArcInvestigation__ArcInvestigation_toJsonString_Static_71136F3F(unwrap(spaces))(investigation);
+    }
+    toCompressedJsonString(investigation, spaces) {
+        return ARCtrl_ArcInvestigation__ArcInvestigation_toCompressedJsonString_Static_71136F3F(unwrap(spaces))(investigation);
+    }
+    toISAJsonString(investigation, spaces) {
+        return ARCtrl_ArcInvestigation__ArcInvestigation_toISAJsonString_Static_71136F3F(unwrap(spaces))(investigation);
+    }
+    toROCrateJsonString(investigation, spaces) {
+        return ARCtrl_ArcInvestigation__ArcInvestigation_toROCrateJsonString_Static_71136F3F(unwrap(spaces))(investigation);
+    }
+}
+
+export function JsonHelper_InvestigationJson_$reflection() {
+    return class_type("ARCtrl.JsonHelper.InvestigationJson", void 0, JsonHelper_InvestigationJson);
+}
+
+export function JsonHelper_InvestigationJson_$ctor() {
+    return new JsonHelper_InvestigationJson();
+}
+
+export class JsonHelper_ARCJson {
+    constructor() {
+    }
+    fromROCrateJsonString(s) {
+        return ARC.fromROCrateJsonString(s);
+    }
+    toROCrateJsonString(spaces) {
+        return ARC.toROCrateJsonString(unwrap(spaces));
+    }
+}
+
+export function JsonHelper_ARCJson_$reflection() {
+    return class_type("ARCtrl.JsonHelper.ARCJson", void 0, JsonHelper_ARCJson);
+}
+
+export function JsonHelper_ARCJson_$ctor() {
+    return new JsonHelper_ARCJson();
+}
+
+export class JsonController {
+    constructor() {
+    }
+    static get OntologyAnnotation() {
+        return new JsonHelper_OntologyAnnotationJson();
+    }
+    static get Assay() {
+        return new JsonHelper_AssayJson();
+    }
+    static get Study() {
+        return new JsonHelper_StudyJson();
+    }
+    static get Investigation() {
+        return new JsonHelper_InvestigationJson();
+    }
+    static get ARC() {
+        return new JsonHelper_ARCJson();
+    }
+}
+
+export function JsonController_$reflection() {
+    return class_type("ARCtrl.JsonController", void 0, JsonController);
+}
+

package/README.md

@@ -1,34 +1,37 @@
 # ARCtrl
 
-> **ARCtrl** the easy way to read, manipulate and write ARCs in __.NET__ 
-and __JavaScript__! ❤️
+> **ARCtrl** the easy way to read, manipulate and write ARCs in __.NET__, __JavaScript__ and __Python__! ❤️
 
 | Version | Downloads |
 | :--------|-----------:|
 |<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?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>|
-
+|<a href="https://pypi.org/project/ARCtrl/"><img alt="PyPI" src="https://img.shields.io/pypi/v/arctrl?logo=pypi&color=%234fb3d9"></a>|<a href="https://pypi.org/project/ARCtrl/"><img alt="PyPI" src="https://img.shields.io/pepy/dt/arctrl?color=%234fb3d9"></a>|
 
 ## Install
 
-(currently only prereleases available, check the [nuget page](https://www.nuget.org/packages/ARCtrl) or [npm page](https://www.npmjs.com/package/@nfdi4plants/arctrl) respectively)
-
-### .NET
+#### .NET
 
 ```fsharp
 #r "nuget: ARCtrl"
 ``` 
 
 ```bash
-<PackageReference Include="ARCtrl" Version="1.0.0-beta.1" />
+<PackageReference Include="ARCtrl" Version="1.1.0" />
 ```
 
-### JavaScript
+#### JavaScript
 
 ```bash
 npm i @nfdi4plants/arctrl
 ```
 
+#### Python
+
+```bash
+pip install arctrl
+```
+
 ## Docs
 
 Currently we provide some documentation in form of markdown files in the `/docs` folder of this repository!
@@ -37,17 +40,52 @@ Currently we provide some documentation in form of markdown files in the `/docs`
 
 ## Development
 
-### Requirements
+#### Requirements
 
 - [nodejs and npm](https://nodejs.org/en/download)
     - verify with `node --version` (Tested with v18.16.1)
     - verify with `npm --version` (Tested with v9.2.0)
 - [.NET SDK](https://dotnet.microsoft.com/en-us/download)
     - verify with `dotnet --version` (Tested with 7.0.306)
+- [Python](https://www.python.org/downloads/)
+    - verify with `py --version` (Tested with 3.12.2, known to work only for >=3.11)
+
+#### Local Setup
+
+On windows you can use the `setup.cmd` to run the following steps automatically!
 
-### Local Setup
+1. Setup dotnet tools
 
-1. `dotnet tool restore`
-3. `npm install`
+   `dotnet tool restore`
+
+
+2. Install NPM dependencies
+   
+    `npm install`
+
+3. Setup python environment
+    
+    `py -m venv .venv`
+
+4. Install [Poetry](https://python-poetry.org/) and dependencies
+
+   1. `.\.venv\Scripts\python.exe -m pip install -U pip setuptools`
+   2. `.\.venv\Scripts\python.exe -m pip install poetry`
+   3. `.\.venv\Scripts\python.exe -m poetry install --no-root`
 
 Verify correct setup with `./build.cmd runtests` ✨
+
+## Performance
+
+Measured on 13th Gen Intel(R) Core(TM) i7-13800H
+
+| Name | Description | FSharp Time (ms) | JavaScript Time (ms) | Python Time (ms) |
+| --- | --- | --- | --- | --- |
+| Table_GetHashCode | From a table with 1 column and 10000 rows, retrieve the Hash Code |  5 | 21 | 226 |
+| Table_AddRows | Add 10000 rows to a table with 4 columns. |  15 | 22 | 289 |
+| Table_fillMissingCells | For a table 6 columns and 20000 rows, where each row has one missing value, fill those values with default values. | 49 | 108 | 4813 |
+| Table_ToJson | Serialize a table with 5 columns and 10000 rows to json. |  1099 | 481 | 6833 |
+| Table_ToCompressedJson | Serialize a table with 5 columns and 10000 rows to compressed json. |  261 |  2266 | 717334 |
+| Assay_toJson | Parse an assay with one table with 10000 rows and 6 columns to json |  915 | 2459 | 28799 |
+| Study_FromWorkbook | Parse a workbook with one study with 10000 rows and 6 columns to an ArcStudy |  97 | 87 | 1249 |
+| Investigation_ToWorkbook_ManyStudies | Parse an investigation with 1500 studies to a workbook |  621 | 379 | 9974 |

package/{ISA/ISA.Spreadsheet → Spreadsheet}/AnnotationTable/ArcTable.js

@@ -1,16 +1,16 @@
-import { iterateIndexed, length, ofArray, sortBy, collect, toArray, empty, tail, head, isEmpty, cons, singleton, fold, map, reverse } from "../../../fable_modules/fable-library.4.5.0/List.js";
-import { tryParseReferenceColumnHeader } from "../../ISA/Regex.js";
-import { map as map_1, toList, tryFind } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { iterateIndexed, length, ofArray, sortBy, collect, toArray, empty, tail, head, isEmpty, cons, singleton, fold, map, reverse } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { tryParseReferenceColumnHeader } from "../../Core/Helper/Regex.js";
+import { map as map_1, toList, tryFind } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { toFsColumns, fixDeprecatedIOHeader, fromFsColumns } from "./CompositeColumn.js";
-import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
-import { ArcTable } from "../../ISA/ArcTypes/ArcTable.js";
-import { FsWorksheet } from "../../../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.js";
-import { comparePrimitives } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { FsRangeAddress_$ctor_7E77A4A0 } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeAddress.fs.js";
-import { FsAddress_$ctor_Z37302880 } from "../../../fable_modules/FsSpreadsheet.5.1.3/FsAddress.fs.js";
-import { Dictionary_tryGet } from "../../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCellsCollection.fs.js";
-import { addToDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
-import { FsRangeBase__Cell_Z3407A44B } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeBase.fs.js";
+import { printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { ArcTable } from "../../Core/Table/ArcTable.js";
+import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.js";
+import { comparePrimitives } from "../../fable_modules/fable-library-js.4.16.0/Util.js";
+import { FsRangeAddress_$ctor_7E77A4A0 } from "../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeAddress.fs.js";
+import { FsAddress_$ctor_Z37302880 } from "../../fable_modules/FsSpreadsheet.5.1.3/FsAddress.fs.js";
+import { Dictionary_tryGet } from "../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCellsCollection.fs.js";
+import { addToDict } from "../../fable_modules/fable-library-js.4.16.0/MapUtil.js";
+import { FsRangeBase__Cell_Z3407A44B } from "../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeBase.fs.js";
 
 /**
  * Iterates over elements of the input list and groups adjacent elements.

package/{ISA/ISA.Spreadsheet → Spreadsheet}/AnnotationTable/CompositeCell.js

@@ -1,7 +1,8 @@
-import { singleton, ofArray, head, tail, isEmpty, map } from "../../../fable_modules/fable-library.4.5.0/List.js";
-import { CompositeCell } from "../../ISA/ArcTypes/CompositeCell.js";
-import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
-import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCell.fs.js";
+import { singleton, ofArray, head, tail, isEmpty, map } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { CompositeCell } from "../../Core/Table/CompositeCell.js";
+import { printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { FsCell } from "../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCell.fs.js";
+import { defaultArg } from "../../fable_modules/fable-library-js.4.16.0/Option.js";
 
 export function fromFsCells(cells) {
     const cellValues = map((c) => c.ValueAsString(), cells);
@@ -56,13 +57,13 @@ export function toFsCells(isTerm, hasUnit, cell) {
     switch (cell.tag) {
         case 0:
             if (hasUnit) {
-                return ofArray([new FsCell(cell.fields[0].NameText), new FsCell(""), new FsCell(cell.fields[0].TermSourceREFString), new FsCell(cell.fields[0].TermAccessionOntobeeUrl)]);
+                return ofArray([new FsCell(cell.fields[0].NameText), new FsCell(""), new FsCell(defaultArg(cell.fields[0].TermSourceREF, "")), new FsCell(cell.fields[0].TermAccessionOntobeeUrl)]);
             }
             else {
-                return ofArray([new FsCell(cell.fields[0].NameText), new FsCell(cell.fields[0].TermSourceREFString), new FsCell(cell.fields[0].TermAccessionOntobeeUrl)]);
+                return ofArray([new FsCell(cell.fields[0].NameText), new FsCell(defaultArg(cell.fields[0].TermSourceREF, "")), new FsCell(cell.fields[0].TermAccessionOntobeeUrl)]);
             }
         case 2:
-            return ofArray([new FsCell(cell.fields[0]), new FsCell(cell.fields[1].NameText), new FsCell(cell.fields[1].TermSourceREFString), new FsCell(cell.fields[1].TermAccessionOntobeeUrl)]);
+            return ofArray([new FsCell(cell.fields[0]), new FsCell(cell.fields[1].NameText), new FsCell(defaultArg(cell.fields[1].TermSourceREF, "")), new FsCell(cell.fields[1].TermAccessionOntobeeUrl)]);
         default:
             if (hasUnit) {
                 return ofArray([new FsCell(cell.fields[0]), new FsCell(""), new FsCell(""), new FsCell("")]);

package/Spreadsheet/AnnotationTable/CompositeColumn.js

@@ -0,0 +1,59 @@
+import { CompositeHeader, IOType } from "../../Core/Table/CompositeHeader.js";
+import { toString } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
+import { toFsCells, fromFsCells } from "./CompositeHeader.js";
+import { singleton as singleton_1, ofArray, item, map } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { FsAddress__get_RowNumber } from "../../fable_modules/FsSpreadsheet.5.1.3/FsAddress.fs.js";
+import { FsRangeAddress__get_LastAddress } from "../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeAddress.fs.js";
+import { FsRangeBase__get_RangeAddress } from "../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeBase.fs.js";
+import { singleton, append, toList, exists, map as map_1, delay, toArray } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { toFsCells as toFsCells_1, fromFsCells as fromFsCells_1 } from "./CompositeCell.js";
+import { rangeDouble } from "../../fable_modules/fable-library-js.4.16.0/Range.js";
+import { CompositeColumn } from "../../Core/Table/CompositeColumn.js";
+import { item as item_1, map as map_2 } from "../../fable_modules/fable-library-js.4.16.0/Array.js";
+
+/**
+ * Checks if the column header is a deprecated IO Header. If so, fixes it.
+ * 
+ * The old format of IO Headers was only the type of IO so, e.g. "Source Name" or "Raw Data File".
+ * 
+ * A "Source Name" column will now be mapped to the propper "Input [Source Name]", and all other IO types will be mapped to "Output [<IO Type>]".
+ */
+export function fixDeprecatedIOHeader(col) {
+    const matchValue = IOType.ofString(col.Item(1).ValueAsString());
+    switch (matchValue.tag) {
+        case 6:
+            return col;
+        case 0: {
+            col.Item(1).SetValueAs(toString(new CompositeHeader(11, [new IOType(0, [])])));
+            return col;
+        }
+        default: {
+            col.Item(1).SetValueAs(toString(new CompositeHeader(12, [matchValue])));
+            return col;
+        }
+    }
+}
+
+export function fromFsColumns(columns) {
+    const header = fromFsCells(map((c) => c.Item(1), columns));
+    const l = FsAddress__get_RowNumber(FsRangeAddress__get_LastAddress(FsRangeBase__get_RangeAddress(item(0, columns)))) | 0;
+    const cells_2 = toArray(delay(() => map_1((i) => fromFsCells_1(map((c_1) => c_1.Item(i), columns)), rangeDouble(2, 1, l))));
+    return CompositeColumn.create(header, cells_2);
+}
+
+export function toFsColumns(column) {
+    const hasUnit = exists((c) => c.isUnitized, column.Cells);
+    const isTerm = column.Header.IsTermColumn;
+    const header = toFsCells(hasUnit, column.Header);
+    const cells = map_2((cell) => toFsCells_1(isTerm, hasUnit, cell), column.Cells);
+    if (hasUnit) {
+        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i) => item(0, item_1(i, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_1) => item(1, item_1(i_1, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_2) => item(2, item_1(i_2, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(3, header)), delay(() => map_1((i_3) => item(3, item_1(i_3, cells)), rangeDouble(0, 1, column.Cells.length - 1))))))]);
+    }
+    else if (isTerm) {
+        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_4) => item(0, item_1(i_4, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_5) => item(1, item_1(i_5, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_6) => item(2, item_1(i_6, cells)), rangeDouble(0, 1, column.Cells.length - 1))))))]);
+    }
+    else {
+        return singleton_1(toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_7) => item(0, item_1(i_7, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))));
+    }
+}
+

package/{ISA/ISA.Spreadsheet → Spreadsheet}/AnnotationTable/CompositeHeader.js

@@ -1,11 +1,11 @@
-import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
-import { singleton, tail, head, isEmpty, map } from "../../../fable_modules/fable-library.4.5.0/List.js";
-import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
-import { ActivePatterns_$007COutputColumnHeader$007C_$007C, ActivePatterns_$007CInputColumnHeader$007C_$007C, tryParseComponentColumnHeader, tryParseCharacteristicColumnHeader, tryParseFactorColumnHeader, tryParseParameterColumnHeader, ActivePatterns_$007CUnitColumnHeader$007C_$007C, ActivePatterns_$007CTANColumnHeader$007C_$007C, ActivePatterns_$007CTSRColumnHeader$007C_$007C } from "../../ISA/Regex.js";
-import { IOType, CompositeHeader } from "../../ISA/ArcTypes/CompositeHeader.js";
-import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCell.fs.js";
-import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
-import { empty, singleton as singleton_1, append, delay, toList } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { printf, toFail } from "../../fable_modules/fable-library-js.4.16.0/String.js";
+import { singleton, tail, head, isEmpty, map } from "../../fable_modules/fable-library-js.4.16.0/List.js";
+import { OntologyAnnotation } from "../../Core/OntologyAnnotation.js";
+import { ActivePatterns_$007COutputColumnHeader$007C_$007C, ActivePatterns_$007CInputColumnHeader$007C_$007C, tryParseComponentColumnHeader, tryParseCharacteristicColumnHeader, tryParseFactorColumnHeader, tryParseParameterColumnHeader, ActivePatterns_$007CUnitColumnHeader$007C_$007C, ActivePatterns_$007CTANColumnHeader$007C_$007C, ActivePatterns_$007CTSRColumnHeader$007C_$007C } from "../../Core/Helper/Regex.js";
+import { IOType, CompositeHeader } from "../../Core/Table/CompositeHeader.js";
+import { FsCell } from "../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCell.fs.js";
+import { toString } from "../../fable_modules/fable-library-js.4.16.0/Types.js";
+import { empty, singleton as singleton_1, append, delay, toList } from "../../fable_modules/fable-library-js.4.16.0/Seq.js";
 
 export function ActivePattern_mergeIDInfo(idSpace1, localID1, idSpace2, localID2) {
     if (idSpace1 !== idSpace2) {
@@ -44,7 +44,7 @@ export function ActivePattern_$007CTerm$007C_$007C(categoryParser, f, cells) {
     }
     switch (matchResult) {
         case 0:
-            return f(OntologyAnnotation.fromString(name));
+            return f(OntologyAnnotation.create(name));
         default: {
             let matchResult_1, name_1, term1, term2;
             if (!isEmpty(cellValues)) {
@@ -180,7 +180,7 @@ export function ActivePattern_$007CTerm$007C_$007C(categoryParser, f, cells) {
             switch (matchResult_1) {
                 case 0: {
                     const term = ActivePattern_mergeIDInfo(term1.IDSpace, term1.LocalID, term2.IDSpace, term2.LocalID);
-                    return f(OntologyAnnotation.fromString(name_1, term.TermSourceRef, term.TermAccessionNumber));
+                    return f(OntologyAnnotation.create(name_1, term.TermSourceRef, term.TermAccessionNumber));
                 }
                 default:
                     return void 0;

package/{ISA/ISA.Spreadsheet → Spreadsheet}/ArcAssay.js

@@ -1,23 +1,23 @@
-import { FsWorksheet } from "../../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.js";
-import { iterate, isEmpty as isEmpty_1, choose, tryHead, head, exists, map, singleton, append, delay, iterateIndexed } from "../../fable_modules/fable-library.4.5.0/Seq.js";
+import { FsWorksheet } from "../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.js";
+import { iterate, isEmpty as isEmpty_1, choose, tryHead, head, exists, map, singleton, append, delay, iterateIndexed } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { SparseRowModule_tryGetValueAt, SparseRowModule_fromFsRow, SparseRowModule_fromValues, SparseRowModule_writeToSheet } from "./Metadata/SparseTable.js";
 import { fromRows as fromRows_1, toRows as toRows_1 } from "./Metadata/Assays.js";
-import { empty, isEmpty, toArray, ofArray, singleton as singleton_1 } from "../../fable_modules/fable-library.4.5.0/List.js";
+import { empty, isEmpty, ofSeq, singleton as singleton_1 } from "../fable_modules/fable-library-js.4.16.0/List.js";
 import { fromRows as fromRows_2, toRows as toRows_2 } from "./Metadata/Contacts.js";
-import { toConsole, printf, toFail } from "../../fable_modules/fable-library.4.5.0/String.js";
-import { getEnumerator } from "../../fable_modules/fable-library.4.5.0/Util.js";
-import { ArcAssay } from "../ISA/ArcTypes/ArcTypes.js";
-import { createMissingIdentifier } from "../ISA/Identifier.js";
-import { defaultArg } from "../../fable_modules/fable-library.4.5.0/Option.js";
+import { toConsole, printf, toFail } from "../fable_modules/fable-library-js.4.16.0/String.js";
+import { getEnumerator } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { ArcAssay } from "../Core/ArcTypes.js";
+import { createMissingIdentifier } from "../Core/Helper/Identifier.js";
+import { defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
 import { toFsWorksheet, tryFromFsWorksheet } from "./AnnotationTable/ArcTable.js";
-import { FsWorkbook } from "../../fable_modules/FsSpreadsheet.5.1.3/FsWorkbook.fs.js";
+import { FsWorkbook } from "../fable_modules/FsSpreadsheet.5.1.3/FsWorkbook.fs.js";
 
 export function toMetadataSheet(assay) {
     let assay_1;
     const sheet = new FsWorksheet("isa_assay");
     iterateIndexed((rowI, r) => {
         SparseRowModule_writeToSheet(rowI + 1, r, sheet);
-    }, (assay_1 = assay, delay(() => append(singleton(SparseRowModule_fromValues(["ASSAY"])), delay(() => append(toRows_1("Assay", singleton_1(assay_1)), delay(() => append(singleton(SparseRowModule_fromValues(["ASSAY PERFORMERS"])), delay(() => toRows_2("Assay Person", ofArray(assay_1.Performers)))))))))));
+    }, (assay_1 = assay, delay(() => append(singleton(SparseRowModule_fromValues(["ASSAY"])), delay(() => append(toRows_1("Assay", singleton_1(assay_1)), delay(() => append(singleton(SparseRowModule_fromValues(["ASSAY PERFORMERS"])), delay(() => toRows_2("Assay Person", ofSeq(assay_1.Performers)))))))))));
     return sheet;
 }
 
@@ -91,7 +91,7 @@ export function fromMetadataSheet(sheet) {
                             case 0:
                                 return ArcAssay.create(createMissingIdentifier());
                             default: {
-                                const performers = toArray(contacts_2);
+                                const performers = Array.from(contacts_2);
                                 const assay = defaultArg(tryHead(assays_2), ArcAssay.create(createMissingIdentifier()));
                                 return ArcAssay.setPerformers(performers, assay);
                             }