@nfdi4plants/arctrl 1.0.0-alpha6

package/ISA/ISA.Spreadsheet/Metadata/Study.js

@@ -0,0 +1,260 @@
+import { Record } from "../../../fable_modules/fable-library.4.1.4/Types.js";
+import { record_type, list_type, string_type } from "../../../fable_modules/fable-library.4.1.4/Reflection.js";
+import { Comment$_$reflection } from "../../ISA/JsonTypes/Comment.js";
+import { ofSeq, append, toArray, reverse, cons, empty, map, ofArray } from "../../../fable_modules/fable-library.4.1.4/List.js";
+import { Comment_toString, Comment_fromString } from "./Comment.js";
+import { SparseRowModule_fromValues, SparseTable_ToRows_6A3D4534, SparseTable_FromRows_Z5579EC29, SparseTable, SparseTable_Create_Z2192E64B, SparseTable__TryGetValueDefault_5BAE6133 } from "./SparseTable.js";
+import { Study_fileNameFromIdentifier, createMissingIdentifier } from "../../ISA/Identifier.js";
+import { addToDict } from "../../../fable_modules/fable-library.4.1.4/MapUtil.js";
+import { defaultArg } from "../../../fable_modules/fable-library.4.1.4/Option.js";
+import { List_distinct } from "../../../fable_modules/fable-library.4.1.4/Seq2.js";
+import { stringHash } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+import { Option_fromValueWithDefault } from "./Conversions.js";
+import { ArcTable } from "../../ISA/ArcTypes/ArcTable.js";
+import { ArcStudy } from "../../ISA/ArcTypes/ArcTypes.js";
+import { toRows as toRows_1, fromRows as fromRows_1 } from "./DesignDescriptors.js";
+import { toRows as toRows_2, fromRows as fromRows_2 } from "./Publication.js";
+import { toRows as toRows_3, fromRows as fromRows_3 } from "./Factors.js";
+import { toRows as toRows_4, fromRows as fromRows_4 } from "./Assays.js";
+import { toRows as toRows_5, fromRows as fromRows_5 } from "./Protocols.js";
+import { toRows as toRows_6, fromRows as fromRows_6 } from "./Contacts.js";
+import { singleton, append as append_1, delay, collect } from "../../../fable_modules/fable-library.4.1.4/Seq.js";
+
+export class StudyInfo extends Record {
+    constructor(Identifier, Title, Description, SubmissionDate, PublicReleaseDate, FileName, Comments) {
+        super();
+        this.Identifier = Identifier;
+        this.Title = Title;
+        this.Description = Description;
+        this.SubmissionDate = SubmissionDate;
+        this.PublicReleaseDate = PublicReleaseDate;
+        this.FileName = FileName;
+        this.Comments = Comments;
+    }
+}
+
+export function StudyInfo_$reflection() {
+    return record_type("ARCtrl.ISA.Spreadsheet.Studies.StudyInfo", [], StudyInfo, () => [["Identifier", string_type], ["Title", string_type], ["Description", string_type], ["SubmissionDate", string_type], ["PublicReleaseDate", string_type], ["FileName", string_type], ["Comments", list_type(Comment$_$reflection())]]);
+}
+
+export function StudyInfo_create(identifier, title, description, submissionDate, publicReleaseDate, fileName, comments) {
+    return new StudyInfo(identifier, title, description, submissionDate, publicReleaseDate, fileName, comments);
+}
+
+export function StudyInfo_get_Labels() {
+    return ofArray(["Study Identifier", "Study Title", "Study Description", "Study Submission Date", "Study Public Release Date", "Study File Name"]);
+}
+
+export function StudyInfo_FromSparseTable_651559CC(matrix) {
+    const comments = map((k) => Comment_fromString(k, SparseTable__TryGetValueDefault_5BAE6133(matrix, "", [k, 0])), matrix.CommentKeys);
+    return StudyInfo_create(SparseTable__TryGetValueDefault_5BAE6133(matrix, createMissingIdentifier(), ["Study Identifier", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Study Title", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Study Description", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Study Submission Date", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Study Public Release Date", 0]), SparseTable__TryGetValueDefault_5BAE6133(matrix, "", ["Study File Name", 0]), comments);
+}
+
+export function StudyInfo_ToSparseTable_1B3D5E9B(study) {
+    const matrix = SparseTable_Create_Z2192E64B(void 0, StudyInfo_get_Labels(), void 0, 2);
+    let commentKeys = empty();
+    const patternInput = (study.Identifier.indexOf("MISSING_IDENTIFIER_") === 0) ? ["", ""] : [study.Identifier, Study_fileNameFromIdentifier(study.Identifier)];
+    addToDict(matrix.Matrix, ["Study Identifier", 1], patternInput[0]);
+    addToDict(matrix.Matrix, ["Study Title", 1], defaultArg(study.Title, ""));
+    addToDict(matrix.Matrix, ["Study Description", 1], defaultArg(study.Description, ""));
+    addToDict(matrix.Matrix, ["Study Submission Date", 1], defaultArg(study.SubmissionDate, ""));
+    addToDict(matrix.Matrix, ["Study Public Release Date", 1], defaultArg(study.PublicReleaseDate, ""));
+    addToDict(matrix.Matrix, ["Study File Name", 1], patternInput[1]);
+    if (!(study.Comments.length === 0)) {
+        const array = study.Comments;
+        array.forEach((comment) => {
+            const patternInput_1 = Comment_toString(comment);
+            const n = patternInput_1[0];
+            commentKeys = cons(n, commentKeys);
+            addToDict(matrix.Matrix, [n, 1], patternInput_1[1]);
+        });
+    }
+    return new SparseTable(matrix.Matrix, matrix.Keys, reverse(List_distinct(commentKeys, {
+        Equals: (x, y) => (x === y),
+        GetHashCode: stringHash,
+    })), matrix.ColumnCount);
+}
+
+export function StudyInfo_fromRows(lineNumber, rows) {
+    const tupledArg = SparseTable_FromRows_Z5579EC29(rows, StudyInfo_get_Labels(), lineNumber);
+    return [tupledArg[0], tupledArg[1], tupledArg[2], StudyInfo_FromSparseTable_651559CC(tupledArg[3])];
+}
+
+export function StudyInfo_toRows_1B3D5E9B(study) {
+    return SparseTable_ToRows_6A3D4534(StudyInfo_ToSparseTable_1B3D5E9B(study));
+}
+
+export function fromParts(studyInfo, designDescriptors, publications, factors, assays, protocols, contacts) {
+    const assayIdentifiers = map((assay) => assay.Identifier, assays);
+    let arcstudy;
+    const arg_1 = Option_fromValueWithDefault("", studyInfo.Title);
+    const arg_2 = Option_fromValueWithDefault("", studyInfo.Description);
+    const arg_3 = Option_fromValueWithDefault("", studyInfo.SubmissionDate);
+    const arg_4 = Option_fromValueWithDefault("", studyInfo.PublicReleaseDate);
+    const arg_5 = toArray(publications);
+    const arg_6 = toArray(contacts);
+    const arg_7 = toArray(designDescriptors);
+    let arg_8;
+    const arg_13 = map((arg_12) => ArcTable.fromProtocol(arg_12), protocols);
+    arg_8 = Array.from(arg_13);
+    const arg_9 = Array.from(assayIdentifiers);
+    const arg_10 = toArray(factors);
+    const arg_11 = toArray(studyInfo.Comments);
+    arcstudy = ArcStudy.make(studyInfo.Identifier, arg_1, arg_2, arg_3, arg_4, arg_5, arg_6, arg_7, arg_8, arg_9, arg_10, arg_11);
+    if (arcstudy.isEmpty && (arcstudy.Identifier === "")) {
+        return void 0;
+    }
+    else {
+        return [arcstudy, assays];
+    }
+}
+
+export function fromRows(lineNumber, en) {
+    const loop = (lastLine_mut, studyInfo_mut, designDescriptors_mut, publications_mut, factors_mut, assays_mut, protocols_mut, contacts_mut, remarks_mut, lineNumber_1_mut) => {
+        loop:
+        while (true) {
+            const lastLine = lastLine_mut, studyInfo = studyInfo_mut, designDescriptors = designDescriptors_mut, publications = publications_mut, factors = factors_mut, assays = assays_mut, protocols = protocols_mut, contacts = contacts_mut, remarks = remarks_mut, lineNumber_1 = lineNumber_1_mut;
+            let matchResult, k_6, k_7, k_8, k_9, k_10, k_11, k_12;
+            if (lastLine != null) {
+                switch (lastLine) {
+                    case "STUDY DESIGN DESCRIPTORS": {
+                        matchResult = 0;
+                        k_6 = lastLine;
+                        break;
+                    }
+                    case "STUDY PUBLICATIONS": {
+                        matchResult = 1;
+                        k_7 = lastLine;
+                        break;
+                    }
+                    case "STUDY FACTORS": {
+                        matchResult = 2;
+                        k_8 = lastLine;
+                        break;
+                    }
+                    case "STUDY ASSAYS": {
+                        matchResult = 3;
+                        k_9 = lastLine;
+                        break;
+                    }
+                    case "STUDY PROTOCOLS": {
+                        matchResult = 4;
+                        k_10 = lastLine;
+                        break;
+                    }
+                    case "STUDY CONTACTS": {
+                        matchResult = 5;
+                        k_11 = lastLine;
+                        break;
+                    }
+                    default: {
+                        matchResult = 6;
+                        k_12 = lastLine;
+                    }
+                }
+            }
+            else {
+                matchResult = 6;
+                k_12 = lastLine;
+            }
+            switch (matchResult) {
+                case 0: {
+                    const patternInput = fromRows_1("Study Design", lineNumber_1 + 1, en);
+                    lastLine_mut = patternInput[0];
+                    studyInfo_mut = studyInfo;
+                    designDescriptors_mut = patternInput[3];
+                    publications_mut = publications;
+                    factors_mut = factors;
+                    assays_mut = assays;
+                    protocols_mut = protocols;
+                    contacts_mut = contacts;
+                    remarks_mut = append(remarks, patternInput[2]);
+                    lineNumber_1_mut = patternInput[1];
+                    continue loop;
+                }
+                case 1: {
+                    const patternInput_1 = fromRows_2("Study Publication", lineNumber_1 + 1, en);
+                    lastLine_mut = patternInput_1[0];
+                    studyInfo_mut = studyInfo;
+                    designDescriptors_mut = designDescriptors;
+                    publications_mut = patternInput_1[3];
+                    factors_mut = factors;
+                    assays_mut = assays;
+                    protocols_mut = protocols;
+                    contacts_mut = contacts;
+                    remarks_mut = append(remarks, patternInput_1[2]);
+                    lineNumber_1_mut = patternInput_1[1];
+                    continue loop;
+                }
+                case 2: {
+                    const patternInput_2 = fromRows_3("Study Factor", lineNumber_1 + 1, en);
+                    lastLine_mut = patternInput_2[0];
+                    studyInfo_mut = studyInfo;
+                    designDescriptors_mut = designDescriptors;
+                    publications_mut = publications;
+                    factors_mut = patternInput_2[3];
+                    assays_mut = assays;
+                    protocols_mut = protocols;
+                    contacts_mut = contacts;
+                    remarks_mut = append(remarks, patternInput_2[2]);
+                    lineNumber_1_mut = patternInput_2[1];
+                    continue loop;
+                }
+                case 3: {
+                    const patternInput_3 = fromRows_4("Study Assay", lineNumber_1 + 1, en);
+                    lastLine_mut = patternInput_3[0];
+                    studyInfo_mut = studyInfo;
+                    designDescriptors_mut = designDescriptors;
+                    publications_mut = publications;
+                    factors_mut = factors;
+                    assays_mut = patternInput_3[3];
+                    protocols_mut = protocols;
+                    contacts_mut = contacts;
+                    remarks_mut = append(remarks, patternInput_3[2]);
+                    lineNumber_1_mut = patternInput_3[1];
+                    continue loop;
+                }
+                case 4: {
+                    const patternInput_4 = fromRows_5("Study Protocol", lineNumber_1 + 1, en);
+                    lastLine_mut = patternInput_4[0];
+                    studyInfo_mut = studyInfo;
+                    designDescriptors_mut = designDescriptors;
+                    publications_mut = publications;
+                    factors_mut = factors;
+                    assays_mut = assays;
+                    protocols_mut = patternInput_4[3];
+                    contacts_mut = contacts;
+                    remarks_mut = append(remarks, patternInput_4[2]);
+                    lineNumber_1_mut = patternInput_4[1];
+                    continue loop;
+                }
+                case 5: {
+                    const patternInput_5 = fromRows_6("Study Person", lineNumber_1 + 1, en);
+                    lastLine_mut = patternInput_5[0];
+                    studyInfo_mut = studyInfo;
+                    designDescriptors_mut = designDescriptors;
+                    publications_mut = publications;
+                    factors_mut = factors;
+                    assays_mut = assays;
+                    protocols_mut = protocols;
+                    contacts_mut = patternInput_5[3];
+                    remarks_mut = append(remarks, patternInput_5[2]);
+                    lineNumber_1_mut = patternInput_5[1];
+                    continue loop;
+                }
+                default:
+                    return [k_12, lineNumber_1, remarks, fromParts(studyInfo, designDescriptors, publications, factors, assays, protocols, contacts)];
+            }
+            break;
+        }
+    };
+    const patternInput_6 = StudyInfo_fromRows(lineNumber, en);
+    return loop(patternInput_6[0], patternInput_6[3], empty(), empty(), empty(), empty(), empty(), empty(), patternInput_6[2], patternInput_6[1]);
+}
+
+export function toRows(study, assays) {
+    const protocols = ofSeq(collect((p) => p.GetProtocols(), study.Tables));
+    const assays_1 = defaultArg(assays, ofSeq(study.GetRegisteredAssaysOrIdentifier()));
+    return delay(() => append_1(StudyInfo_toRows_1B3D5E9B(study), delay(() => append_1(singleton(SparseRowModule_fromValues(["STUDY DESIGN DESCRIPTORS"])), delay(() => append_1(toRows_1("Study Design", ofArray(study.StudyDesignDescriptors)), delay(() => append_1(singleton(SparseRowModule_fromValues(["STUDY PUBLICATIONS"])), delay(() => append_1(toRows_2("Study Publication", ofArray(study.Publications)), delay(() => append_1(singleton(SparseRowModule_fromValues(["STUDY FACTORS"])), delay(() => append_1(toRows_3("Study Factor", ofArray(study.Factors)), delay(() => append_1(singleton(SparseRowModule_fromValues(["STUDY ASSAYS"])), delay(() => append_1(toRows_4("Study Assay", assays_1), delay(() => append_1(singleton(SparseRowModule_fromValues(["STUDY PROTOCOLS"])), delay(() => append_1(toRows_5("Study Protocol", protocols), delay(() => append_1(singleton(SparseRowModule_fromValues(["STUDY CONTACTS"])), delay(() => toRows_6("Study Person", ofArray(study.Contacts)))))))))))))))))))))))))));
+}
+

package/README.md

@@ -0,0 +1,277 @@
+# ARCtrl
+Top level ARC DataModel and API function descriptions.
+
+- [ARCtrl](#arctrl)
+  - [Jargon/Nomenclature](#jargonnomenclature)
+  - [API Design](#api-design)
+  - [Top level overview](#top-level-overview)
+  - [Stack](#stack)
+- [Libraries](#libraries)
+  - [Design choices](#design-choices)
+    - [Fable compatibility as top priority](#fable-compatibility-as-top-priority)
+
+## Sub-Libraries
+
+[ISA README.md](src/ISA/README.md) :books:
+
+[Contracts README.md](src/Contract/README.md) :books:
+
+# Jargon/Nomenclature
+
+In general, a distinction is made between `DataModel`s,  `API`s, and `Tools`:
+- `DataModel`s are the data structures which represent the ARC or it's respective parts in memory. They are serializable and can be used as data exchange format between tool implementations:
+  - `FileSystem`: Represents the file system structure of an ARC. All files and their path relative to the arc root folder are contained here.
+  - `ISA`: Represents the experimental metadata of the ARC that is stored in the ISA-XLSX format (investigation, studies and assays).
+  - `CWL`: Represents the workflow definitions of the ARC in the CWL format.
+- `API`s are static methods on the `DataModel` types that perfrom operations on the `DataModel`s. Often, these are CRUD-like operations, and are aimed to be be composable. 
+  
+  **Example**: A `ARC.addAssay` function has to do several things:
+  - Add a new assay to the `ISA`
+  - Add a new assay to the `FileSystem`
+  it should therefore combine the respective functions of `ISA API` and `FileSystem API` to achieve this.
+
+- `Tools` or `Clients` are user-facing software such as Swate, ARCitect, or the ARCCommander. They should ideally compose their functionality from the `API`s and work with an in-memory representation of the ARC via `DataModel`s. There are operations such as IO for reading/writing actual files to the file system, which are not part of the `API`s, but rather part of the `Tools`.
+
+## Local Setup
+
+1. `dotnet tool restore`
+2. `npm install` in *root* (this will also run `npm install` in `src/ISA`).
+
+## API Design
+
+Command syntax should be inspired by ArcCommander commands, as they are already well established and known to the power user base.
+See syntax : https://nfdi4plants.github.io/arcCommander-docs/docs/01GeneralCLIStructure.html
+See selection: https://nfdi4plants.github.io/arcCommander-docs/docs/02SubcommandVerbs.html
+
+## Top level overview
+
+In the following, the dependency graph of the proposed arcAPI toolstack can be seen:
+
+```mermaid
+flowchart TD
+
+%% ----- Nodes ------
+
+
+subgraph ARCtrl
+    arc[ARC]
+    
+    subgraph ISA
+        isaj[ISA.Json]
+        isax[ISA.Spreadsheet]      
+        isaa[ISA]
+    end
+    subgraph FileSystem
+        fs[FileSystem]
+    end
+    subgraph CWL
+        cwl[CWL]
+    end
+end
+
+subgraph DataTransferObject
+    fsspread[FsSpreadsheet]
+    thoth["Thoth.Json (string)"]
+end
+
+subgraph IO
+    node[node.fs]   
+    fsspreadx[FsSpreadsheet.ExcelIO]   
+    excelJS[exceljs]
+    systemio[System.IO]
+end
+
+
+%% ----- Edges ------
+
+
+%% Arc
+arc --> ISA
+arc --> FileSystem
+arc --> CWL
+
+%% ISA
+isaj --> isaa
+isax --> isaa
+isaj --> thoth
+
+isax --> fsspread
+
+%% ------ Tools ---------
+
+subgraph Tools
+    arcdotnet[/arcIO.NET\]
+    arcitect[[ARCitect]]
+    arccom[[arcCommander]]
+    swate[[Swate]]
+end 
+
+%% ----- Edges ------
+
+Tools --> ARCtrl
+
+arcdotnet --> fsspreadx
+arcdotnet --> systemio
+arcitect --> excelJS
+arcitect --> node
+arccom --> arcdotnet
+
+
+fsspreadx -.-> fsspread
+systemio -.-> thoth
+excelJS -.-> fsspread
+node -.-> thoth
+
+%% ----- Styling ------
+
+%% dotnet
+style Tools stroke:#3A0EC6,stroke-width:2px
+style fsspreadx fill:#8C71E3,stroke:#3A0EC6,stroke-width:2px,color: black
+style arcdotnet fill:#8C71E3,stroke:#3A0EC6,stroke-width:2px,color: black
+style arccom fill:#8C71E3,stroke:#3A0EC6,stroke-width:2px,color: black
+style systemio fill:#8C71E3,stroke:#3A0EC6,stroke-width:2px,color: black
+
+%% javascript
+style excelJS fill:#C1AD09,stroke:#EFD81D,stroke-width:2px,color: black
+style arcitect fill:#C1AD09,stroke:#EFD81D,stroke-width:2px,color: black
+style swate fill:#C1AD09,stroke:#EFD81D,stroke-width:2px,color: black
+style node fill:#C1AD09,stroke:#EFD81D,stroke-width:2px,color: black
+
+
+%% fable
+style ARCtrl stroke:#007B00,stroke-width:2px
+style ISA stroke:#007B00,stroke-width:2px
+style FileSystem stroke:#007B00,stroke-width:2px
+style CWL stroke:#007B00,stroke-width:2px
+style DataTransferObject stroke:#007B00,stroke-width:2px
+
+style fsspread fill:#39B539,stroke:#007B00,stroke-width:2px,color: black
+style isax fill:#39B539,stroke:#007B00,stroke-width:2px,color: black
+style isaa fill:#39B539,stroke:#007B00,stroke-width:2px,color: black
+style isaj fill:#39B539,stroke:#007B00,stroke-width:2px,color: black
+style arc fill:#39B539,stroke:#007B00,stroke-width:2px,color: black
+style fs fill:#39B539,stroke:#007B00,stroke-width:2px,color: black
+style cwl fill:#39B539,stroke:#007B00,stroke-width:2px,color: black
+style thoth fill:#39B539,stroke:#007B00,stroke-width:2px,color: black
+```
+
+## Stack
+
+```mermaid
+classDiagram 
+
+class arc["ARCtrl"] {
+    ISA
+    CWL
+    FileSystem
+}
+class isa["ISA"] {
+    Investigation
+    Studies
+    Assays
+    ArcTable
+    CompositeColumn
+    CompositeHeader
+    CompositeCell
+}
+class file ["FileSystem"] {
+    - FileSystemTree
+    - History
+}
+class cwl["CWL"] {
+    CommandlineTool?
+    Workflows
+}
+class io["IO"] {
+    FsSpreadsheet.ExcelIO
+    System.IO
+    exceljs
+    node fs
+}
+io <|--|> arc : Contracts
+arc <|--|> isa
+arc <|--|> cwl
+arc <|--|> file
+
+```
+
+# Libraries
+
+Mockups for each library are in the `ARC` folder. They contain API/Domain stubs to draft and test the new library designs.
+
+## Design choices
+
+### Fable compatibility as top priority
+
+All libraries should be Fable compatible, and produce javascript/typescript code that is ergonomic to use in a js/ts environment, therefore:
+- we use classes with static members over nested modules
+- we use the `[<AttachMembers>]` fable attribute for each class
+  - Using overloads with the `[<AttachMembers>]` attribute will make js functions shadow itself. Never use this!
+- we use the `[<NamedParams(n)>]` fable attribute for all optional parameters in static methods that use tupled, named params.
+- we use `Array<'T>` for all collections in F#, since they get transpiled to native js arrays.
+- we use the `[<Erase>]` fable attribute for union cases that contain data 
+    ```fsharp
+     [<Erase>] type X = | Y of string | Z of int
+    ```
+- we use the `[<StringEnum>]` for unions that contain no data (e.g.)
+    ```fsharp
+     [<StringEnum>] type YesOrNo = | Yes | No
+    ```
+    
+**Example:**
+
+```fsharp
+[<AttachMembers>]
+type Study = 
+    {
+        Identifier : string option
+        Assays : Assay array option
+    }
+
+    [<NamedParams>]
+    static member create (?Identifier, ?Assays : Assay array) = 
+        {
+            Identifier = Identifier
+            Assays = Assays
+        }
+```
+
+will become the following javascript code:
+
+```javascript
+export class Study extends Record {
+    constructor(Identifier, Assays) {
+        super();
+        this.Identifier = Identifier;
+        this.Assays = Assays;
+    }
+    static create({ Identifier, Assays }) {
+        return new Study(Identifier, Assays);
+    }
+```
+
+and the following typescript code:
+
+```typescript
+export class Study extends Record implements IEquatable<Study>, IComparable<Study> {
+    readonly Identifier: Option<string>;
+    readonly Assays: Option<Assay[]>;
+    constructor(Identifier: Option<string>, Assays: Option<Assay[]>) {
+        super();
+        this.Identifier = Identifier;
+        this.Assays = Assays;
+    }
+    static create({ Identifier, Assays }: {Identifier?: string, Assays?: Assay[] }): Study {
+        return new Study(Identifier, Assays);
+    }
+```
+
+## Development
+
+### Setup
+
+1. `dotnet tool restore`
+2. `dotnet paket install`
+3. `npm install`
+
+Verify correct setup with `./build.cmd runtests` ✨

package/SemVer.js

@@ -0,0 +1,60 @@
+import { match, create } from "./fable_modules/fable-library.4.1.4/RegExp.js";
+import { toString, Record } from "./fable_modules/fable-library.4.1.4/Types.js";
+import { record_type, option_type, string_type, int32_type } from "./fable_modules/fable-library.4.1.4/Reflection.js";
+import { parse } from "./fable_modules/fable-library.4.1.4/Int32.js";
+import { value as value_3, unwrap } from "./fable_modules/fable-library.4.1.4/Option.js";
+import { StringBuilder__Append_Z721C83C5, StringBuilder_$ctor } from "./fable_modules/fable-library.4.1.4/System.Text.js";
+import { printf, toText } from "./fable_modules/fable-library.4.1.4/String.js";
+
+const SemVerAux_Pattern = "^(?<major>\\d+)(\\.(?<minor>\\d+))?(\\.(?<patch>\\d+))?(-(?<pre>[0-9A-Za-z-\\.]+))?(\\+(?<build>[0-9A-Za-z-\\.]+))?$";
+
+export const SemVerAux_SemVerRegex = create(SemVerAux_Pattern);
+
+export class SemVer extends Record {
+    constructor(Major, Minor, Patch, PreRelease, Metadata) {
+        super();
+        this.Major = (Major | 0);
+        this.Minor = (Minor | 0);
+        this.Patch = (Patch | 0);
+        this.PreRelease = PreRelease;
+        this.Metadata = Metadata;
+    }
+}
+
+export function SemVer_$reflection() {
+    return record_type("ARCtrl.SemVer.SemVer", [], SemVer, () => [["Major", int32_type], ["Minor", int32_type], ["Patch", int32_type], ["PreRelease", option_type(string_type)], ["Metadata", option_type(string_type)]]);
+}
+
+export function SemVer_make(major, minor, patch, pre, meta) {
+    return new SemVer(major, minor, patch, pre, meta);
+}
+
+export function SemVer_create_Z55658624(major, minor, patch, pre, meta) {
+    return new SemVer(major, minor, patch, pre, meta);
+}
+
+export function SemVer_tryOfString_Z721C83C5(str) {
+    const m = match(SemVerAux_SemVerRegex, str);
+    const matchValue = m != null;
+    if (matchValue) {
+        const g = m;
+        return SemVer_create_Z55658624(parse((g.groups && g.groups.major) || "", 511, false, 32), parse((g.groups && g.groups.minor) || "", 511, false, 32), parse((g.groups && g.groups.patch) || "", 511, false, 32), unwrap(((g.groups && g.groups.pre) != null) ? ((g.groups && g.groups.pre) || "") : void 0), unwrap(((g.groups && g.groups.build) != null) ? ((g.groups && g.groups.build) || "") : void 0));
+    }
+    else {
+        return void 0;
+    }
+}
+
+export function SemVer__AsString(this$) {
+    let arg_3, arg_4;
+    const sb = StringBuilder_$ctor();
+    StringBuilder__Append_Z721C83C5(sb, toText(printf("%i.%i.%i"))(this$.Major)(this$.Minor)(this$.Patch));
+    if (this$.PreRelease != null) {
+        StringBuilder__Append_Z721C83C5(sb, (arg_3 = value_3(this$.PreRelease), toText(printf("-%s"))(arg_3)));
+    }
+    if (this$.Metadata != null) {
+        StringBuilder__Append_Z721C83C5(sb, (arg_4 = value_3(this$.Metadata), toText(printf("+%s"))(arg_4)));
+    }
+    return toString(sb);
+}
+

package/Templates/Templates.Json.js

@@ -0,0 +1,40 @@
+import { toString } from "../fable_modules/fable-library.4.1.4/Types.js";
+import { datetimeUtc, array, map as map_2, list as list_2, guid as guid_1, object as object_1, string, succeed, andThen } from "../fable_modules/Thoth.Json.10.1.0/Decode.fs.js";
+import { uncurry2, uncurry3 } from "../fable_modules/fable-library.4.1.4/Util.js";
+import { Template, Organisation } from "./Templates.js";
+import { ConverterOptions_$ctor } from "../ISA/ISA.Json/ConverterOptions.js";
+import { decoder as decoder_2, encoder } from "../ISA/ISA.Json/Person.js";
+import { OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "../ISA/ISA.Json/Ontology.js";
+import { datetime, list as list_1, guid, object } from "../fable_modules/Thoth.Json.10.1.0/Encode.fs.js";
+import { map } from "../fable_modules/fable-library.4.1.4/List.js";
+import { Process_decoder, Process_encoder } from "../ISA/ISA.Json/Process.js";
+import { map as map_1, delay, toList } from "../fable_modules/fable-library.4.1.4/Seq.js";
+import { ArcTables_fromProcesses_134EBDED, ArcTables__get_Item_Z524259A4 } from "../ISA/ISA/ArcTypes/ArcTables.js";
+
+export const Organisation_encode = toString;
+
+export const Organisation_decode = (path_1) => ((value_1) => andThen(uncurry3((textValue) => {
+    const output = Organisation.ofString(textValue);
+    return (arg10$0040) => ((arg20$0040) => succeed(output, arg10$0040, arg20$0040));
+}), string, path_1, value_1));
+
+export function Template_encode(template) {
+    let list, options_2;
+    let personEncoder;
+    const options = ConverterOptions_$ctor();
+    personEncoder = ((oa) => encoder(options, oa));
+    let oaEncoder;
+    const options_1 = ConverterOptions_$ctor();
+    oaEncoder = ((oa_1) => OntologyAnnotation_encoder(options_1, oa_1));
+    return object([["id", guid(template.Id)], ["table", list_1((list = template.Table.GetProcesses(), map((options_2 = ConverterOptions_$ctor(), (oa_2) => Process_encoder(options_2, oa_2)), list)))], ["name", template.Name], ["description", template.Description], ["organisation", Organisation_encode(template.Organisation)], ["version", template.Version], ["authors", list_1(toList(delay(() => map_1(personEncoder, template.Authors))))], ["endpoint_repositories", list_1(toList(delay(() => map_1(oaEncoder, template.EndpointRepositories))))], ["tags", list_1(toList(delay(() => map_1(oaEncoder, template.Tags))))], ["last_updated", datetime(template.LastUpdated)]]);
+}
+
+export const Template_decode = (() => {
+    const personDecoder = decoder_2(ConverterOptions_$ctor());
+    const oaDecoder = OntologyAnnotation_decoder(ConverterOptions_$ctor());
+    return (path_10) => ((v) => object_1((get$) => {
+        let objectArg, arg_3, d, decoder, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, objectArg_7, objectArg_8, objectArg_9;
+        return Template.create((objectArg = get$.Required, objectArg.Field("id", guid_1)), (arg_3 = ((d = ((decoder = Process_decoder(ConverterOptions_$ctor()), (path_1) => ((value_1) => list_2(uncurry2(decoder), path_1, value_1)))), (path_2) => ((value_2) => map_2((ps) => ArcTables__get_Item_Z524259A4(ArcTables_fromProcesses_134EBDED(ps), 0), uncurry2(d), path_2, value_2)))), (objectArg_1 = get$.Required, objectArg_1.Field("table", uncurry2(arg_3)))), (objectArg_2 = get$.Required, objectArg_2.Field("name", string)), (objectArg_3 = get$.Required, objectArg_3.Field("description", string)), (objectArg_4 = get$.Required, objectArg_4.Field("organisation", uncurry2(Organisation_decode))), (objectArg_5 = get$.Required, objectArg_5.Field("version", string)), (objectArg_6 = get$.Required, objectArg_6.Field("authors", (path_6, value_6) => array(uncurry2(personDecoder), path_6, value_6))), (objectArg_7 = get$.Required, objectArg_7.Field("endpoint_repositories", (path_7, value_7) => array(uncurry2(oaDecoder), path_7, value_7))), (objectArg_8 = get$.Required, objectArg_8.Field("tags", (path_8, value_8) => array(uncurry2(oaDecoder), path_8, value_8))), (objectArg_9 = get$.Required, objectArg_9.Field("last_updated", datetimeUtc)));
+    }, path_10, v));
+})();
+