@nfdi4plants/arctrl 3.0.0-beta.2 → 3.0.0-beta.4

package/dist/ts/ts/FileSystem/DefaultGitattributes.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"DefaultGitattributes.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/FileSystem/DefaultGitattributes.ts"],"names":[],"mappings":"AACA,eAAO,MAAM,GAAG,sDAAsD,CAAC"}

package/dist/ts/ts/FileSystem/DefaultGitattributes.js

@@ -0,0 +1,3 @@
+const dga = "**/dataset/** filter=lfs diff=lfs merge=lfs -text";
+
+export { dga };

package/dist/ts/ts/FileSystem/DefaultGitignore.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"DefaultGitignore.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/FileSystem/DefaultGitignore.ts"],"names":[],"mappings":"AACA,eAAO,MAAM,GAAG,u9CAAu9C,CAAC"}

package/dist/ts/ts/FileSystem/DefaultGitignore.js

@@ -0,0 +1,3 @@
+const dgi = "# ----- macos rules -----\r\n# taken from https://github.com/github/gitignore/blob/main/Global/macOS.gitignore\r\n# General\r\n.DS_Store\r\n.AppleDouble\r\n.LSOverride\r\n# Icon must end with two \\r\r\nIcon\r\n# Thumbnails\r\n._*\r\n# Files that might appear in the root of a volume\r\n.DocumentRevisions-V100\r\n.fseventsd\r\n.Spotlight-V100\r\n.TemporaryItems\r\n.Trashes\r\n.VolumeIcon.icns\r\n.com.apple.timemachine.donotpresent\r\n# Directories potentially created on remote AFP share\r\n.AppleDB\r\n.AppleDesktop\r\nNetwork Trash Folder\r\nTemporary Items\r\n.apdisk\r\n# ----- windows rules -----\r\n# taken from https://github.com/github/gitignore/blob/main/Global/Windows.gitignore\r\n# Windows thumbnail cache files\r\nThumbs.db\r\nThumbs.db:encryptable\r\nehthumbs.db\r\nehthumbs_vista.db\r\n# Dump file\r\n*.stackdump\r\n# Folder config file\r\n[Dd]esktop.ini\r\n# Recycle Bin used on file shares\r\n$RECYCLE.BIN/\r\n# Windows Installer files\r\n*.cab\r\n*.msi\r\n*.msix\r\n*.msm\r\n*.msp\r\n# Windows shortcuts\r\n*.lnk\r\n# ----- linux rules -----\r\n# taken from https://github.com/github/gitignore/blob/main/Global/Linux.gitignore\r\n*~\r\n# temporary files which can be created if a process still has a handle open of a deleted file\r\n.fuse_hidden*\r\n# KDE directory preferences\r\n.directory\r\n# Linux trash folder which might appear on any partition or disk\r\n.Trash-*\r\n# .nfs files are created when an open file is removed but is still being accessed\r\n.nfs*\r\n";
+
+export { dgi };

package/dist/ts/ts/FileSystem/FileSystem.d.ts

@@ -0,0 +1,21 @@
+import { Commit } from './Commit.js';
+import { FileSystemTree_$union } from './FileSystemTree.js';
+import { Record } from '@fable-org/fable-library-js/Types.js';
+import { IComparable, IEquatable } from '@fable-org/fable-library-js/Util.js';
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+export declare class FileSystem extends Record implements IEquatable<FileSystem>, IComparable<FileSystem> {
+    readonly Tree: FileSystemTree_$union;
+    readonly History: Commit[];
+    constructor(Tree: FileSystemTree_$union, History: Commit[]);
+    static create({ tree, history }: {
+        tree: FileSystemTree_$union;
+        history?: Commit[];
+    }): FileSystem;
+    AddFile(path: string): FileSystem;
+    static addFile(path: string): ((arg0: FileSystem) => FileSystem);
+    static fromFilePaths(paths: string[]): FileSystem;
+    Union(other: FileSystem): FileSystem;
+    Copy(): FileSystem;
+}
+export declare function FileSystem_$reflection(): TypeInfo;
+//# sourceMappingURL=FileSystem.d.ts.map

package/dist/ts/ts/FileSystem/FileSystem.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"FileSystem.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/FileSystem/FileSystem.ts"],"names":[],"mappings":"AACA,OAAO,EAAsB,MAAM,EAAE,MAAM,aAAa,CAAC;AACzD,OAAO,EAA8C,qBAAqB,EAAE,MAAM,qBAAqB,CAAC;AAExG,OAAO,EAAE,MAAM,EAAE,MAAM,sCAAsC,CAAC;AAC9D,OAAO,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,qCAAqC,CAAC;AAC9E,OAAO,EAA2B,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAE9F,qBAAa,UAAW,SAAQ,MAAO,YAAW,UAAU,CAAC,UAAU,CAAC,EAAE,WAAW,CAAC,UAAU,CAAC;IAC7F,QAAQ,CAAC,IAAI,EAAE,qBAAqB,CAAC;IACrC,QAAQ,CAAC,OAAO,EAAE,MAAM,EAAE,CAAC;gBACf,IAAI,EAAE,qBAAqB,EAAE,OAAO,EAAE,MAAM,EAAE;IAK1D,MAAM,CAAC,MAAM,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,EAAE;QAAC,IAAI,EAAE,qBAAqB,CAAC;QAAC,OAAO,CAAC,EAAE,MAAM,EAAE,CAAA;KAAE,GAAG,UAAU;IAGhG,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,UAAU;IAIjC,MAAM,CAAC,OAAO,CAAC,IAAI,EAAE,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,UAAU,KAAK,UAAU,CAAC;IAGhE,MAAM,CAAC,aAAa,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,UAAU;IAMjD,KAAK,CAAC,KAAK,EAAE,UAAU,GAAG,UAAU;IASpC,IAAI,IAAI,UAAU;CASrB;AAED,wBAAgB,sBAAsB,IAAI,QAAQ,CAEjD"}

package/dist/ts/ts/FileSystem/FileSystem.js

@@ -0,0 +1,48 @@
+import { defaultArg } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { Record } from '../../node_modules/@fable-org/fable-library-js/Types.js';
+import { FileSystemTree } from './FileSystemTree.js';
+import { append, map } from '../../node_modules/@fable-org/fable-library-js/Array.js';
+
+class FileSystem extends Record {
+  constructor(Tree, History) {
+    super();
+    this.Tree = Tree;
+    this.History = History;
+  }
+  static create({ tree, history }) {
+    return new FileSystem(tree, defaultArg(history, []));
+  }
+  AddFile(path) {
+    const this$ = this;
+    return new FileSystem(this$.Tree.AddFile(path), this$.History);
+  }
+  static addFile(path) {
+    return (fs) => fs.AddFile(path);
+  }
+  static fromFilePaths(paths) {
+    const tree = FileSystemTree.fromFilePaths(paths);
+    return FileSystem.create({
+      tree
+    });
+  }
+  Union(other) {
+    const this$ = this;
+    const tree = this$.Tree.Union(other.Tree);
+    const history = append(this$.History, other.History);
+    return FileSystem.create({
+      tree,
+      history
+    });
+  }
+  Copy() {
+    const this$ = this;
+    const fstCopy = this$.Tree.Copy();
+    const historyCopy = map((x) => x, this$.History);
+    return FileSystem.create({
+      tree: fstCopy,
+      history: historyCopy
+    });
+  }
+}
+
+export { FileSystem };

package/dist/ts/ts/FileSystem/FileSystemTree.d.ts

@@ -0,0 +1,55 @@
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { Union } from '@fable-org/fable-library-js/Types.js';
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+export type FileSystemTree_$union = FileSystemTree<0> | FileSystemTree<1>;
+export type FileSystemTree_$cases = {
+    0: ["File", [string]];
+    1: ["Folder", [string, FileSystemTree_$union[]]];
+};
+export declare function FileSystemTree_File(name: string): FileSystemTree<0>;
+export declare function FileSystemTree_Folder(name: string, children: FileSystemTree_$union[]): FileSystemTree<1>;
+export declare class FileSystemTree<Tag extends keyof FileSystemTree_$cases> extends Union<Tag, FileSystemTree_$cases[Tag][0]> {
+    readonly tag: Tag;
+    readonly fields: FileSystemTree_$cases[Tag][1];
+    constructor(tag: Tag, fields: FileSystemTree_$cases[Tag][1]);
+    cases(): string[];
+    get Name(): string;
+    get isFolder(): boolean;
+    get isFile(): boolean;
+    static get ROOT_NAME(): string;
+    static createFile(name: string): FileSystemTree_$union;
+    static createFolder(name: string, children?: FileSystemTree_$union[]): FileSystemTree_$union;
+    static createRootFolder(children: FileSystemTree_$union[]): FileSystemTree_$union;
+    TryGetChildByName(name: string): Option<FileSystemTree_$union>;
+    static tryGetChildByName(name: string): ((arg0: FileSystemTree_$union) => Option<FileSystemTree_$union>);
+    ContainsChildWithName(name: string): boolean;
+    static containsChildWithName(name: string): ((arg0: FileSystemTree_$union) => boolean);
+    TryGetPath(path: string): Option<FileSystemTree_$union>;
+    AddFile(path: string): FileSystemTree_$union;
+    static addFile(path: string): ((arg0: FileSystemTree_$union) => FileSystemTree_$union);
+    static fromFilePaths(paths: string[]): FileSystemTree_$union;
+    ToFilePaths(removeRoot?: boolean): string[];
+    static toFilePaths(removeRoot?: boolean): ((arg0: FileSystemTree_$union) => string[]);
+    FilterFiles(predicate: ((arg0: string) => boolean)): Option<FileSystemTree_$union>;
+    static filterFiles(predicate: ((arg0: string) => boolean)): ((arg0: FileSystemTree_$union) => Option<FileSystemTree_$union>);
+    FilterFolders(predicate: ((arg0: string) => boolean)): Option<FileSystemTree_$union>;
+    static filterFolders(predicate: ((arg0: string) => boolean)): ((arg0: FileSystemTree_$union) => Option<FileSystemTree_$union>);
+    Filter(predicate: ((arg0: string) => boolean)): Option<FileSystemTree_$union>;
+    static filter(predicate: ((arg0: string) => boolean)): ((arg0: FileSystemTree_$union) => Option<FileSystemTree_$union>);
+    Union(otherFST: FileSystemTree_$union): FileSystemTree_$union;
+    Copy(): FileSystemTree_$union;
+    static createGitKeepFile(): FileSystemTree_$union;
+    static createReadmeFile(): FileSystemTree_$union;
+    static createEmptyFolder(name: string): FileSystemTree_$union;
+    static createAssayFolder(assayName: string, hasDataMap?: boolean): FileSystemTree_$union;
+    static createStudyFolder(studyName: string, hasDataMap?: boolean): FileSystemTree_$union;
+    static createWorkflowFolder(workflowName: string, hasDataMap?: boolean): FileSystemTree_$union;
+    static createRunFolder(runName: string, hasDataMap?: boolean): FileSystemTree_$union;
+    static createInvestigationFile(): FileSystemTree_$union;
+    static createAssaysFolder(assays: FileSystemTree_$union[]): FileSystemTree_$union;
+    static createStudiesFolder(studies: FileSystemTree_$union[]): FileSystemTree_$union;
+    static createWorkflowsFolder(workflows: FileSystemTree_$union[]): FileSystemTree_$union;
+    static createRunsFolder(runs: FileSystemTree_$union[]): FileSystemTree_$union;
+}
+export declare function FileSystemTree_$reflection(): TypeInfo;
+//# sourceMappingURL=FileSystemTree.d.ts.map

package/dist/ts/ts/FileSystem/FileSystemTree.d.ts.map

@@ -0,0 +1 @@
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package/dist/ts/ts/FileSystem/FileSystemTree.js

@@ -0,0 +1,339 @@
+import { defaultArg, unwrap } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { tryFind, map, append, item, tryPick, head, tail, choose, equalsWith } from '../../node_modules/@fable-org/fable-library-js/Array.js';
+import { split, combineMany } from './Path.js';
+import { toArray, delay, append as append$1, singleton } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { Array_distinct, Array_groupBy } from '../../node_modules/@fable-org/fable-library-js/Seq2.js';
+import { curry2, arrayHash, stringHash } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { empty, cons, toArray as toArray$1, reverse } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { Union } from '../../node_modules/@fable-org/fable-library-js/Types.js';
+
+function FileSystemTree_File(name) {
+  return new FileSystemTree(0, [name]);
+}
+function FileSystemTree_Folder(name, children) {
+  return new FileSystemTree(1, [name, children]);
+}
+class FileSystemTree extends Union {
+  constructor(tag, fields) {
+    super();
+    this.tag = tag;
+    this.fields = fields;
+  }
+  cases() {
+    return ["File", "Folder"];
+  }
+  get Name() {
+    const this$ = this;
+    let n;
+    if (this$.tag === /* Folder */
+    1) {
+      n = this$.fields[0];
+    } else {
+      n = this$.fields[0];
+    }
+    return n;
+  }
+  get isFolder() {
+    const this$ = this;
+    return this$.tag === /* Folder */
+    1;
+  }
+  get isFile() {
+    const this$ = this;
+    return this$.tag === /* File */
+    0;
+  }
+  static get ROOT_NAME() {
+    return "root";
+  }
+  static createFile(name) {
+    return FileSystemTree_File(name);
+  }
+  static createFolder(name, children) {
+    return FileSystemTree_Folder(name, defaultArg(children, []));
+  }
+  static createRootFolder(children) {
+    return FileSystemTree_Folder(FileSystemTree.ROOT_NAME, children);
+  }
+  TryGetChildByName(name) {
+    const this$ = this;
+    return this$.tag === /* File */
+    0 ? void 0 : tryFind((c) => c.Name === name, this$.fields[1]);
+  }
+  static tryGetChildByName(name) {
+    return (fst) => fst.TryGetChildByName(name);
+  }
+  ContainsChildWithName(name) {
+    const this$ = this;
+    if (this$.tag === /* File */
+    0) {
+      return false;
+    } else {
+      const array = this$.fields[1];
+      return array.some((c) => c.Name === name);
+    }
+  }
+  static containsChildWithName(name) {
+    return (fst) => fst.ContainsChildWithName(name);
+  }
+  TryGetPath(path) {
+    const this$ = this;
+    const loop = (parent, pathParts) => {
+      if (parent.tag === /* File */
+      0) {
+        const name_1 = parent.fields[0];
+        if (pathParts.length === 1 && item(0, pathParts) === name_1) {
+          return parent;
+        } else {
+          return void 0;
+        }
+      } else if (parent.fields[0] === "root") {
+        const children = parent.fields[1];
+        return tryPick((child) => loop(child, pathParts), children);
+      } else {
+        const children_1 = parent.fields[1];
+        const name = parent.fields[0];
+        if (name === head(pathParts)) {
+          if (pathParts.length === 1) {
+            return parent;
+          } else {
+            const remainingParts = tail(pathParts);
+            return tryPick((child_1) => loop(child_1, remainingParts), children_1);
+          }
+        } else {
+          return void 0;
+        }
+      }
+    };
+    return loop(this$, split(path));
+  }
+  AddFile(path) {
+    const this$ = this;
+    const existingPaths = this$.ToFilePaths();
+    const filePaths = toArray(delay(() => append$1(singleton(path), delay(() => existingPaths))));
+    return FileSystemTree.fromFilePaths(filePaths);
+  }
+  static addFile(path) {
+    return (tree) => tree.AddFile(path);
+  }
+  static fromFilePaths(paths) {
+    const loop = (paths_1, parent) => {
+      const files = map((arg) => {
+        const name = head(arg);
+        return FileSystemTree.createFile(name);
+      }, paths_1.filter((p) => p.length === 1));
+      const folders = map((tupledArg) => {
+        const parent_1 = FileSystemTree.createFolder(tupledArg[0], []);
+        return loop(map(tail, tupledArg[1]), parent_1);
+      }, Array_groupBy(head, paths_1.filter((p_1) => p_1.length > 1), {
+        Equals: (x_3, y_2) => x_3 === y_2,
+        GetHashCode: stringHash
+      }));
+      if (parent.tag === /* Folder */
+      1) {
+        const name_1 = parent.fields[0];
+        return FileSystemTree.createFolder(name_1, toArray(delay(() => append$1(files, delay(() => folders)))));
+      } else {
+        return parent;
+      }
+    };
+    return loop(Array_distinct(map(split, paths), {
+      Equals: (x, y) => equalsWith((x_1, y_1) => x_1 === y_1, x, y),
+      GetHashCode: arrayHash
+    }), FileSystemTree.createFolder(FileSystemTree.ROOT_NAME, []));
+  }
+  ToFilePaths(removeRoot) {
+    const this$ = this;
+    const res = [];
+    const loop = (output, parent) => {
+      if (parent.tag === /* Folder */
+      1) {
+        const n_1 = parent.fields[0];
+        const array = parent.fields[1];
+        array.forEach((filest) => {
+          loop(cons(n_1, output), filest);
+        });
+      } else {
+        const item = combineMany(toArray$1(reverse(cons(parent.fields[0], output))));
+        void res.push(item);
+      }
+    };
+    if (defaultArg(removeRoot, true)) {
+      if (this$.tag === /* File */
+      0) {
+        const n_2 = this$.fields[0];
+        void res.push(n_2);
+      } else {
+        const children_1 = this$.fields[1];
+        const action_1 = curry2(loop)(empty());
+        children_1.forEach(action_1);
+      }
+    } else {
+      loop(empty(), this$);
+    }
+    return Array.from(res);
+  }
+  static toFilePaths(removeRoot) {
+    return (root) => root.ToFilePaths(unwrap(removeRoot));
+  }
+  FilterFiles(predicate) {
+    const this$ = this;
+    const loop = (parent) => {
+      if (parent.tag === /* Folder */
+      1) {
+        return FileSystemTree_Folder(parent.fields[0], choose(loop, parent.fields[1]));
+      } else {
+        const n = parent.fields[0];
+        if (predicate(n)) {
+          return FileSystemTree_File(n);
+        } else {
+          return void 0;
+        }
+      }
+    };
+    return loop(this$);
+  }
+  static filterFiles(predicate) {
+    return (tree) => tree.FilterFiles(predicate);
+  }
+  FilterFolders(predicate) {
+    const this$ = this;
+    const loop = (parent) => {
+      if (parent.tag === /* Folder */
+      1) {
+        const n_1 = parent.fields[0];
+        const children = parent.fields[1];
+        if (predicate(n_1)) {
+          return FileSystemTree_Folder(n_1, choose(loop, children));
+        } else {
+          return void 0;
+        }
+      } else {
+        return FileSystemTree_File(parent.fields[0]);
+      }
+    };
+    return loop(this$);
+  }
+  static filterFolders(predicate) {
+    return (tree) => tree.FilterFolders(predicate);
+  }
+  Filter(predicate) {
+    const this$ = this;
+    const loop = (parent) => {
+      if (parent.tag === /* Folder */
+      1) {
+        const n_1 = parent.fields[0];
+        const children = parent.fields[1];
+        if (predicate(n_1)) {
+          const filteredChildren = choose(loop, children);
+          if (filteredChildren.length === 0) {
+            return void 0;
+          } else {
+            return FileSystemTree_Folder(n_1, filteredChildren);
+          }
+        } else {
+          return void 0;
+        }
+      } else {
+        const n = parent.fields[0];
+        if (predicate(n)) {
+          return FileSystemTree_File(n);
+        } else {
+          return void 0;
+        }
+      }
+    };
+    return loop(this$);
+  }
+  static filter(predicate) {
+    return (tree) => tree.Filter(predicate);
+  }
+  Union(otherFST) {
+    let array_1;
+    const this$ = this;
+    const paths = Array_distinct((array_1 = this$.ToFilePaths(), append(otherFST.ToFilePaths(), array_1)), {
+      Equals: (x, y) => x === y,
+      GetHashCode: stringHash
+    });
+    return FileSystemTree.fromFilePaths(paths);
+  }
+  Copy() {
+    const this$ = this;
+    return this$.tag === /* File */
+    0 ? FileSystemTree_File(this$.fields[0]) : FileSystemTree_Folder(this$.fields[0], map((c) => c.Copy(), this$.fields[1]));
+  }
+  static createGitKeepFile() {
+    return FileSystemTree.createFile(".gitkeep");
+  }
+  static createReadmeFile() {
+    return FileSystemTree.createFile("README.md");
+  }
+  static createEmptyFolder(name) {
+    return FileSystemTree.createFolder(name, [FileSystemTree.createGitKeepFile()]);
+  }
+  static createAssayFolder(assayName, hasDataMap) {
+    const hasDataMap_1 = defaultArg(hasDataMap, false);
+    const dataset = FileSystemTree.createEmptyFolder("dataset");
+    const protocols = FileSystemTree.createEmptyFolder("protocols");
+    const readme = FileSystemTree.createReadmeFile();
+    const assayFile = FileSystemTree.createFile("isa.assay.xlsx");
+    if (hasDataMap_1) {
+      const dataMapFile = FileSystemTree.createFile("isa.datamap.xlsx");
+      return FileSystemTree.createFolder(assayName, [dataset, protocols, assayFile, readme, dataMapFile]);
+    } else {
+      return FileSystemTree.createFolder(assayName, [dataset, protocols, assayFile, readme]);
+    }
+  }
+  static createStudyFolder(studyName, hasDataMap) {
+    const hasDataMap_1 = defaultArg(hasDataMap, false);
+    const resources = FileSystemTree.createEmptyFolder("resources");
+    const protocols = FileSystemTree.createEmptyFolder("protocols");
+    const readme = FileSystemTree.createReadmeFile();
+    const studyFile = FileSystemTree.createFile("isa.study.xlsx");
+    if (hasDataMap_1) {
+      const dataMapFile = FileSystemTree.createFile("isa.datamap.xlsx");
+      return FileSystemTree.createFolder(studyName, [resources, protocols, studyFile, readme, dataMapFile]);
+    } else {
+      return FileSystemTree.createFolder(studyName, [resources, protocols, studyFile, readme]);
+    }
+  }
+  static createWorkflowFolder(workflowName, hasDataMap) {
+    const hasDataMap_1 = defaultArg(hasDataMap, false);
+    const readme = FileSystemTree.createReadmeFile();
+    const workflowFile = FileSystemTree.createFile("isa.workflow.xlsx");
+    if (hasDataMap_1) {
+      const dataMapFile = FileSystemTree.createFile("isa.datamap.xlsx");
+      return FileSystemTree.createFolder(workflowName, [workflowFile, readme, dataMapFile]);
+    } else {
+      return FileSystemTree.createFolder(workflowName, [workflowFile, readme]);
+    }
+  }
+  static createRunFolder(runName, hasDataMap) {
+    const hasDataMap_1 = defaultArg(hasDataMap, false);
+    const readme = FileSystemTree.createReadmeFile();
+    const runFile = FileSystemTree.createFile("isa.run.xlsx");
+    if (hasDataMap_1) {
+      const dataMapFile = FileSystemTree.createFile("isa.datamap.xlsx");
+      return FileSystemTree.createFolder(runName, [runFile, readme, dataMapFile]);
+    } else {
+      return FileSystemTree.createFolder(runName, [runFile, readme]);
+    }
+  }
+  static createInvestigationFile() {
+    return FileSystemTree.createFile("isa.investigation.xlsx");
+  }
+  static createAssaysFolder(assays) {
+    return FileSystemTree.createFolder("assays", append([FileSystemTree.createGitKeepFile()], assays));
+  }
+  static createStudiesFolder(studies) {
+    return FileSystemTree.createFolder("studies", append([FileSystemTree.createGitKeepFile()], studies));
+  }
+  static createWorkflowsFolder(workflows) {
+    return FileSystemTree.createFolder("workflows", append([FileSystemTree.createGitKeepFile()], workflows));
+  }
+  static createRunsFolder(runs) {
+    return FileSystemTree.createFolder("runs", append([FileSystemTree.createGitKeepFile()], runs));
+  }
+}
+
+export { FileSystemTree, FileSystemTree_File, FileSystemTree_Folder };

package/dist/ts/ts/FileSystem/Path.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"Path.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/FileSystem/Path.ts"],"names":[],"mappings":"AAIA,eAAO,MAAM,UAAU,EAAE,MAAM,EAAgB,CAAC;AAEhD,wBAAgB,KAAK,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE,CAU5C;AAED,wBAAgB,OAAO,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,CAE5D;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,MAAM,CAYnD;AAED,wBAAgB,WAAW,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAEhD;AAED;;GAEG;AACH,wBAAgB,MAAM,CAAC,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,OAAO,CAE9D;AAED,wBAAgB,kBAAkB,CAAC,eAAe,EAAE,MAAM,GAAG,MAAM,CAElE;AAED,wBAAgB,kBAAkB,CAAC,eAAe,EAAE,MAAM,GAAG,MAAM,CAElE;AAED,wBAAgB,qBAAqB,CAAC,kBAAkB,EAAE,MAAM,GAAG,MAAM,CAExE;AAED,wBAAgB,gBAAgB,CAAC,aAAa,EAAE,MAAM,GAAG,MAAM,CAE9D"}

package/dist/ts/ts/FileSystem/Path.js

@@ -0,0 +1,36 @@
+import { join, split as split$1, trimEnd, trimStart, trim } from '../../node_modules/@fable-org/fable-library-js/String.js';
+import { mapIndexed } from '../../node_modules/@fable-org/fable-library-js/Array.js';
+
+const seperators = ["/", "\\"];
+function split(path) {
+  const array = split$1(path, seperators, void 0, 3);
+  return array.filter((p) => {
+    if (p !== "") {
+      return p !== ".";
+    } else {
+      return false;
+    }
+  });
+}
+function combine(path1, path2) {
+  return trimEnd(path1, ...seperators) + "/" + trimStart(path2, ...seperators);
+}
+function combineMany(paths) {
+  return join("/", mapIndexed((i, p) => {
+    if (i === 0) {
+      return trimEnd(p, ...seperators);
+    } else if (i === paths.length - 1) {
+      return trimStart(p, ...seperators);
+    } else {
+      return trim(p, ...seperators);
+    }
+  }, paths));
+}
+function getAssayFolderPath(assayIdentifier) {
+  return combine("assays", assayIdentifier);
+}
+function getStudyFolderPath(studyIdentifier) {
+  return combine("studies", studyIdentifier);
+}
+
+export { combine, combineMany, getAssayFolderPath, getStudyFolderPath, seperators, split };

package/dist/ts/ts/Json/Assay.d.ts

@@ -0,0 +1,19 @@
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { Decoder$1, IEncodable } from '../fable_modules/Thoth.Json.Core.0.7.0/Types.fs.js';
+import { OntologyAnnotation } from '../Core/OntologyAnnotation.js';
+import { ArcAssay } from '../Core/ArcTypes.js';
+import { IMap } from '@fable-org/fable-library-js/Util.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { CompositeCell_$union } from '../Core/Table/CompositeCell.js';
+export declare function encoder(assay: ArcAssay): IEncodable;
+export declare const decoder: Decoder$1<ArcAssay>;
+export declare function encoderCompressed(stringTable: IMap<string, int32>, oaTable: IMap<OntologyAnnotation, int32>, cellTable: IMap<CompositeCell_$union, int32>, assay: ArcAssay): IEncodable;
+export declare function decoderCompressed(stringTable: string[], oaTable: OntologyAnnotation[], cellTable: CompositeCell_$union[]): Decoder$1<ArcAssay>;
+export declare function ROCrate_genID(a: ArcAssay): string;
+export declare function ROCrate_encoder(studyName: Option<string>, a: ArcAssay): IEncodable;
+export declare const ROCrate_decoder: Decoder$1<ArcAssay>;
+export declare function ISAJson_encoder(studyName: Option<string>, idMap: Option<IMap<string, IEncodable>>, a: ArcAssay): IEncodable;
+export declare const ISAJson_allowedFields: FSharpList<string>;
+export declare const ISAJson_decoder: Decoder$1<ArcAssay>;
+//# sourceMappingURL=Assay.d.ts.map

package/dist/ts/ts/Json/Assay.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"Assay.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Json/Assay.ts"],"names":[],"mappings":"AAAA,OAAO,EAAoB,UAAU,EAAmB,MAAM,qCAAqC,CAAC;AACpG,OAAO,EAA8C,MAAM,EAAO,MAAM,uCAAuC,CAAC;AAChH,OAAO,EAAE,SAAS,EAAqB,UAAU,EAAE,MAAM,oDAAoD,CAAC;AAG9G,OAAO,EAAE,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AAUnE,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAE/C,OAAO,EAAE,IAAI,EAAE,MAAM,qCAAqC,CAAC;AAC3D,OAAO,EAAE,KAAK,EAAE,MAAM,sCAAsC,CAAC;AAC7D,OAAO,EAAE,oBAAoB,EAAE,MAAM,gCAAgC,CAAC;AAmBtE,wBAAgB,OAAO,CAAC,KAAK,EAAE,QAAQ,GAAG,UAAU,CAqBnD;AAED,eAAO,MAAM,OAAO,EAAE,SAAS,CAAC,QAAQ,CAGtC,CAAC;AAEH,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,IAAI,CAAC,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,IAAI,CAAC,kBAAkB,EAAE,KAAK,CAAC,EAAE,SAAS,EAAE,IAAI,CAAC,oBAAoB,EAAE,KAAK,CAAC,EAAE,KAAK,EAAE,QAAQ,GAAG,UAAU,CAqBvL;AAED,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,MAAM,EAAE,EAAE,OAAO,EAAE,kBAAkB,EAAE,EAAE,SAAS,EAAE,oBAAoB,EAAE,GAAG,SAAS,CAAC,QAAQ,CAAC,CAK9I;AAED,wBAAgB,aAAa,CAAC,CAAC,EAAE,QAAQ,GAAG,MAAM,CAQjD;AAED,wBAAgB,eAAe,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE,QAAQ,GAAG,UAAU,CAwClF;AAED,eAAO,MAAM,eAAe,EAAE,SAAS,CAAC,QAAQ,CAQ9C,CAAC;AAEH,wBAAgB,eAAe,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,GAAG,UAAU,CAqC3H;AAED,eAAO,MAAM,qBAAqB,EAAE,UAAU,CAAC,MAAM,CAAuN,CAAC;AAE7Q,eAAO,MAAM,eAAe,EAAE,SAAS,CAAC,QAAQ,CA+C9C,CAAC"}