@nfdi4plants/arctrl 2.5.1 → 3.0.0-alpha.2

package/FileSystem/FileSystemTree.js

@@ -1,275 +0,0 @@
-import { unwrap, defaultArg } from "../fable_modules/fable-library-js.4.24.0/Option.js";
-import { append as append_1, choose, equalsWith, tail, head, map, tryFind } from "../fable_modules/fable-library-js.4.24.0/Array.js";
-import { singleton, append, delay, toArray } from "../fable_modules/fable-library-js.4.24.0/Seq.js";
-import { Array_distinct, Array_groupBy } from "../fable_modules/fable-library-js.4.24.0/Seq2.js";
-import { curry2, arrayHash, stringHash } from "../fable_modules/fable-library-js.4.24.0/Util.js";
-import { combineMany, split } from "./Path.js";
-import { empty, reverse, toArray as toArray_1, cons } from "../fable_modules/fable-library-js.4.24.0/List.js";
-import { Union } from "../fable_modules/fable-library-js.4.24.0/Types.js";
-import { union_type, array_type, string_type } from "../fable_modules/fable-library-js.4.24.0/Reflection.js";
-
-export 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$.tag === 1) {
-            n = this$.fields[0];
-        }
-        else {
-            n = this$.fields[0];
-        }
-        return n;
-    }
-    get isFolder() {
-        const this$ = this;
-        return this$.tag === 1;
-    }
-    get isFile() {
-        const this$ = this;
-        return this$.tag === 0;
-    }
-    static get ROOT_NAME() {
-        return "root";
-    }
-    static createFile(name) {
-        return new FileSystemTree(0, [name]);
-    }
-    static createFolder(name, children) {
-        return new FileSystemTree(1, [name, defaultArg(children, [])]);
-    }
-    static createRootFolder(children) {
-        return new FileSystemTree(1, [FileSystemTree.ROOT_NAME, children]);
-    }
-    TryGetChildByName(name) {
-        const this$ = this;
-        return (this$.tag === 0) ? undefined : tryFind((c) => (c.Name === name), this$.fields[1]);
-    }
-    static tryGetChildByName(name) {
-        return (fst) => fst.TryGetChildByName(name);
-    }
-    ContainsChildWithName(name) {
-        const this$ = this;
-        return (this$.tag === 0) ? false : this$.fields[1].some((c) => (c.Name === name));
-    }
-    static containsChildWithName(name) {
-        return (fst) => fst.ContainsChildWithName(name);
-    }
-    AddFile(path) {
-        const this$ = this;
-        const existingPaths = this$.ToFilePaths();
-        const filePaths = toArray(delay(() => append(singleton(path), delay(() => existingPaths))));
-        return FileSystemTree.fromFilePaths(filePaths);
-    }
-    static addFile(path) {
-        return (tree) => tree.AddFile(path);
-    }
-    static fromFilePaths(paths) {
-        const loop = (paths_1, parent) => {
-            const files = map((arg) => {
-                const name = head(arg);
-                return FileSystemTree.createFile(name);
-            }, paths_1.filter((p) => (p.length === 1)));
-            const folders = map((tupledArg) => {
-                const parent_1 = FileSystemTree.createFolder(tupledArg[0], []);
-                return loop(map(tail, tupledArg[1]), parent_1);
-            }, Array_groupBy(head, paths_1.filter((p_1) => (p_1.length > 1)), {
-                Equals: (x_3, y_2) => (x_3 === y_2),
-                GetHashCode: stringHash,
-            }));
-            if (parent.tag === 1) {
-                return FileSystemTree.createFolder(parent.fields[0], toArray(delay(() => append(files, delay(() => folders)))));
-            }
-            else {
-                return parent;
-            }
-        };
-        return loop(Array_distinct(map(split, paths), {
-            Equals: (x, y) => equalsWith((x_1, y_1) => (x_1 === y_1), x, y),
-            GetHashCode: arrayHash,
-        }), FileSystemTree.createFolder(FileSystemTree.ROOT_NAME, []));
-    }
-    ToFilePaths(removeRoot) {
-        const this$ = this;
-        const res = [];
-        const loop = (output, parent) => {
-            if (parent.tag === 1) {
-                parent.fields[1].forEach((filest) => {
-                    loop(cons(parent.fields[0], output), filest);
-                });
-            }
-            else {
-                const item = combineMany(toArray_1(reverse(cons(parent.fields[0], output))));
-                void (res.push(item));
-            }
-        };
-        if (defaultArg(removeRoot, true)) {
-            if (this$.tag === 0) {
-                void (res.push(this$.fields[0]));
-            }
-            else {
-                const action_1 = curry2(loop)(empty());
-                this$.fields[1].forEach(action_1);
-            }
-        }
-        else {
-            loop(empty(), this$);
-        }
-        return Array.from(res);
-    }
-    static toFilePaths(removeRoot) {
-        return (root) => root.ToFilePaths(unwrap(removeRoot));
-    }
-    FilterFiles(predicate) {
-        const this$ = this;
-        const loop = (parent) => {
-            if (parent.tag === 1) {
-                return new FileSystemTree(1, [parent.fields[0], choose(loop, parent.fields[1])]);
-            }
-            else {
-                const n = parent.fields[0];
-                if (predicate(n)) {
-                    return new FileSystemTree(0, [n]);
-                }
-                else {
-                    return undefined;
-                }
-            }
-        };
-        return loop(this$);
-    }
-    static filterFiles(predicate) {
-        return (tree) => tree.FilterFiles(predicate);
-    }
-    FilterFolders(predicate) {
-        const this$ = this;
-        const loop = (parent) => {
-            if (parent.tag === 1) {
-                const n_1 = parent.fields[0];
-                if (predicate(n_1)) {
-                    return new FileSystemTree(1, [n_1, choose(loop, parent.fields[1])]);
-                }
-                else {
-                    return undefined;
-                }
-            }
-            else {
-                return new FileSystemTree(0, [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 === 1) {
-                const n_1 = parent.fields[0];
-                if (predicate(n_1)) {
-                    const filteredChildren = choose(loop, parent.fields[1]);
-                    if (filteredChildren.length === 0) {
-                        return undefined;
-                    }
-                    else {
-                        return new FileSystemTree(1, [n_1, filteredChildren]);
-                    }
-                }
-                else {
-                    return undefined;
-                }
-            }
-            else {
-                const n = parent.fields[0];
-                if (predicate(n)) {
-                    return new FileSystemTree(0, [n]);
-                }
-                else {
-                    return undefined;
-                }
-            }
-        };
-        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$.ToFilePaths(), append_1(otherFST.ToFilePaths(), array_1)), {
-            Equals: (x, y) => (x === y),
-            GetHashCode: stringHash,
-        });
-        return FileSystemTree.fromFilePaths(paths);
-    }
-    Copy() {
-        const this$ = this;
-        return (this$.tag === 0) ? (new FileSystemTree(0, [this$.fields[0]])) : (new FileSystemTree(1, [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 createInvestigationFile() {
-        return FileSystemTree.createFile("isa.investigation.xlsx");
-    }
-    static createAssaysFolder(assays) {
-        return FileSystemTree.createFolder("assays", append_1([FileSystemTree.createGitKeepFile()], assays));
-    }
-    static createStudiesFolder(studies) {
-        return FileSystemTree.createFolder("studies", append_1([FileSystemTree.createGitKeepFile()], studies));
-    }
-    static createWorkflowsFolder(workflows) {
-        return FileSystemTree.createFolder("workflows", append_1([FileSystemTree.createGitKeepFile()], workflows));
-    }
-    static createRunsFolder(runs) {
-        return FileSystemTree.createFolder("runs", append_1([FileSystemTree.createGitKeepFile()], runs));
-    }
-}
-
-export function FileSystemTree_$reflection() {
-    return union_type("ARCtrl.FileSystem.FileSystemTree", [], FileSystemTree, () => [[["name", string_type]], [["name", string_type], ["children", array_type(FileSystemTree_$reflection())]]]);
-}
-

package/FileSystem/Path.js

@@ -1,54 +0,0 @@
-import { trim, join, trimStart, trimEnd, split as split_1 } from "../fable_modules/fable-library-js.4.24.0/String.js";
-import { last, mapIndexed } from "../fable_modules/fable-library-js.4.24.0/Array.js";
-
-export const seperators = ["/", "\\"];
-
-export function split(path) {
-    const array = split_1(path, seperators, undefined, 3);
-    return array.filter((p) => {
-        if (p !== "") {
-            return p !== ".";
-        }
-        else {
-            return false;
-        }
-    });
-}
-
-export function combine(path1, path2) {
-    return (trimEnd(path1, ...seperators) + "/") + trimStart(path2, ...seperators);
-}
-
-export 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));
-}
-
-export function getFileName(path) {
-    return last(split(path));
-}
-
-/**
- * Checks if `path` points to a file with the name `fileName`
- */
-export function isFile(fileName, path) {
-    return getFileName(path) === fileName;
-}
-
-export function getAssayFolderPath(assayIdentifier) {
-    return combine("assays", assayIdentifier);
-}
-
-export function getStudyFolderPath(studyIdentifier) {
-    return combine("studies", studyIdentifier);
-}
-

package/FileSystem.js

@@ -1,102 +0,0 @@
-// const fs = require('fs/promises');
-// const pathModule = require('path');
-
-import fs from 'fs/promises'
-import * as pathModule from 'path'
-
-// Check if a directory exists
-export async function directoryExists(path) {
-    try {
-        const stats = await fs.stat(path);
-        return stats.isDirectory();
-    } catch (err) {
-        if (err.code === 'ENOENT') return false;
-        throw err;
-    }
-}
-
-// Create a directory
-export async function createDirectory(path) {
-    await fs.mkdir(path, { recursive: true });
-}
-
-// Ensure a directory exists
-export async function ensureDirectory(path) {
-    if (!(await directoryExists(path))) {
-        await createDirectory(path);
-    }
-}
-
-// Ensure the directory for a file exists
-export async function ensureDirectoryOfFile(filePath) {
-    const dir = pathModule.dirname(filePath);
-    await ensureDirectory(dir);
-}
-
-// Check if a file exists
-export async function fileExists(path) {
-    try {
-        const stats = await fs.stat(path);
-        return stats.isFile();
-    } catch (err) {
-        if (err.code === 'ENOENT') return false;
-        throw err;
-    }
-}
-
-// Get subdirectories in a directory combined with the input path
-export async function getSubDirectories(path) {
-    const entries = await fs.readdir(path, { withFileTypes: true });
-    return entries.filter(entry => entry.isDirectory()).map(entry => pathModule.join(path, entry.name));
-}
-
-// write a function which returns the path of all files in a directory combined with the input path
-export async function getSubFiles(path) {
-    const entries = await fs.readdir(path, { withFileTypes: true });
-    return entries.filter(entry => entry.isFile()).map(entry => pathModule.join(path, entry.name));
-    }
-
-// Move a file
-export async function moveFile(oldPath, newPath) {
-    await fs.rename(oldPath, newPath);
-}
-
-// Move a directory
-export async function moveDirectory(oldPath, newPath) {
-    await fs.rename(oldPath, newPath);
-}
-
-// Delete a file
-export async function deleteFile(path) {
-    try {
-        await fs.unlink(path);
-    }
-    catch (err) {
-        if (err.code !== 'ENOENT') throw err;
-    }
-}
-
-// Delete a directory (and its contents)
-export async function deleteDirectory(path) {
-    await fs.rm(path, { recursive: true, force: true });
-}
-
-// Read file as text
-export async function readFileText(path) {
-    return await fs.readFile(path, 'utf-8');
-}
-
-// Read file as binary
-export async function readFileBinary(path) {
-    return await fs.readFile(path);
-}
-
-// Write text to a file
-export async function writeFileText(path, text) {
-    await fs.writeFile(path, text, 'utf-8');
-}
-
-// Write binary data to a file
-export async function writeFileBinary(path, bytes) {
-    await fs.writeFile(path, bytes);
-}

package/Json/Assay.js

@@ -1,171 +0,0 @@
-import { empty, singleton, ofArray, choose } from "../fable_modules/fable-library-js.4.24.0/List.js";
-import { bind, defaultArg, unwrap, map } from "../fable_modules/fable-library-js.4.24.0/Option.js";
-import { tryIncludeList, tryIncludeSeq, tryInclude } from "./Encode.js";
-import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder, OntologyAnnotation_ROCrate_decoderDefinedTerm, OntologyAnnotation_ROCrate_decoderPropertyValue, OntologyAnnotation_ROCrate_encoderDefinedTerm, OntologyAnnotation_ROCrate_encoderPropertyValue, OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./OntologyAnnotation.js";
-import { decoderCompressed as decoderCompressed_2, encoderCompressed as encoderCompressed_2, decoder as decoder_2, encoder as encoder_4 } from "./DataMap/DataMap.js";
-import { decoderCompressed as decoderCompressed_1, encoderCompressed as encoderCompressed_1, decoder as decoder_1, encoder as encoder_5 } from "./Table/ArcTable.js";
-import { ROCrate_decoder as ROCrate_decoder_2, ROCrate_encoder as ROCrate_encoder_1, decoder as decoder_3, encoder as encoder_6 } from "./Person.js";
-import { ISAJson_decoder as ISAJson_decoder_2, ISAJson_encoder as ISAJson_encoder_3, ROCrate_decoder as ROCrate_decoder_3, ROCrate_encoder as ROCrate_encoder_4, decoder as decoder_4, encoder as encoder_7 } from "./Comment.js";
-import { map as map_1 } from "../fable_modules/fable-library-js.4.24.0/Seq.js";
-import { map as map_2, list as list_2, resizeArray, string, object } from "../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js";
-import { ArcAssay } from "../Core/ArcTypes.js";
-import { replace } from "../fable_modules/fable-library-js.4.24.0/String.js";
-import { Assay_tryIdentifierFromFileName, createMissingIdentifier, Assay_fileNameFromIdentifier } from "../Core/Helper/Identifier.js";
-import { JsonTypes_decomposeTechnologyPlatform, JsonTypes_composeTechnologyPlatform, ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D, ARCtrl_ArcTables__ArcTables_GetProcesses } from "../Core/Conversion.js";
-import { getCharacteristics, getUnits, getData } from "../Core/Process/ProcessSequence.js";
-import { list as list_1 } from "../fable_modules/Thoth.Json.Core.0.4.0/Encode.fs.js";
-import { ISAJson_encoder as ISAJson_encoder_1, ROCrate_encoder as ROCrate_encoder_2 } from "./Data.js";
-import { ISAJson_decoder as ISAJson_decoder_1, ISAJson_encoder as ISAJson_encoder_2, ROCrate_decoder as ROCrate_decoder_1, ROCrate_encoder as ROCrate_encoder_3 } from "./Process/Process.js";
-import { context_jsonvalue } from "./context/rocrate/isa_assay_context.js";
-import { encoder as encoder_8 } from "./Process/MaterialAttribute.js";
-import { encoder as encoder_9 } from "./Process/AssayMaterials.js";
-import { Option_fromValueWithDefault } from "../Core/Helper/Collections.js";
-import { encode } from "./IDTable.js";
-import { Decode_objectNoAdditionalProperties } from "./Decode.js";
-
-export function encoder(assay) {
-    let value;
-    const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["Identifier", (value = assay.Identifier, {
-        Encode(helpers) {
-            return helpers.encodeString(value);
-        },
-    })], tryInclude("MeasurementType", OntologyAnnotation_encoder, assay.MeasurementType), tryInclude("TechnologyType", OntologyAnnotation_encoder, assay.TechnologyType), tryInclude("TechnologyPlatform", OntologyAnnotation_encoder, assay.TechnologyPlatform), tryInclude("DataMap", encoder_4, assay.DataMap), tryIncludeSeq("Tables", encoder_5, assay.Tables), tryIncludeSeq("Performers", encoder_6, assay.Performers), tryIncludeSeq("Comments", encoder_7, assay.Comments)]));
-    return {
-        Encode(helpers_1) {
-            const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_1)], values);
-            return helpers_1.encodeObject(arg);
-        },
-    };
-}
-
-export const decoder = object((get$) => {
-    let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7;
-    return ArcAssay.create((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("MeasurementType", OntologyAnnotation_decoder))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("TechnologyType", OntologyAnnotation_decoder))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("TechnologyPlatform", OntologyAnnotation_decoder))), unwrap((arg_9 = resizeArray(decoder_1), (objectArg_4 = get$.Optional, objectArg_4.Field("Tables", arg_9)))), unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("DataMap", decoder_2))), unwrap((arg_13 = resizeArray(decoder_3), (objectArg_6 = get$.Optional, objectArg_6.Field("Performers", arg_13)))), unwrap((arg_15 = resizeArray(decoder_4), (objectArg_7 = get$.Optional, objectArg_7.Field("Comments", arg_15)))));
-});
-
-export function encoderCompressed(stringTable, oaTable, cellTable, assay) {
-    let value;
-    const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["Identifier", (value = assay.Identifier, {
-        Encode(helpers) {
-            return helpers.encodeString(value);
-        },
-    })], tryInclude("MeasurementType", OntologyAnnotation_encoder, assay.MeasurementType), tryInclude("TechnologyType", OntologyAnnotation_encoder, assay.TechnologyType), tryInclude("TechnologyPlatform", OntologyAnnotation_encoder, assay.TechnologyPlatform), tryIncludeSeq("Tables", (table) => encoderCompressed_1(stringTable, oaTable, cellTable, table), assay.Tables), tryInclude("DataMap", (dm) => encoderCompressed_2(stringTable, oaTable, cellTable, dm), assay.DataMap), tryIncludeSeq("Performers", encoder_6, assay.Performers), tryIncludeSeq("Comments", encoder_7, assay.Comments)]));
-    return {
-        Encode(helpers_1) {
-            const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_1)], values);
-            return helpers_1.encodeObject(arg);
-        },
-    };
-}
-
-export function decoderCompressed(stringTable, oaTable, cellTable) {
-    return object((get$) => {
-        let objectArg, objectArg_1, objectArg_2, objectArg_3, arg_9, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7;
-        return ArcAssay.create((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("MeasurementType", OntologyAnnotation_decoder))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("TechnologyType", OntologyAnnotation_decoder))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("TechnologyPlatform", OntologyAnnotation_decoder))), unwrap((arg_9 = resizeArray(decoderCompressed_1(stringTable, oaTable, cellTable)), (objectArg_4 = get$.Optional, objectArg_4.Field("Tables", arg_9)))), unwrap((arg_11 = decoderCompressed_2(stringTable, oaTable, cellTable), (objectArg_5 = get$.Optional, objectArg_5.Field("DataMap", arg_11)))), unwrap((arg_13 = resizeArray(decoder_3), (objectArg_6 = get$.Optional, objectArg_6.Field("Performers", arg_13)))), unwrap((arg_15 = resizeArray(decoder_4), (objectArg_7 = get$.Optional, objectArg_7.Field("Comments", arg_15)))));
-    });
-}
-
-export function ROCrate_genID(a) {
-    const matchValue = a.Identifier;
-    if (matchValue === "") {
-        return "#EmptyAssay";
-    }
-    else {
-        return `assays/${replace(matchValue, " ", "_")}/`;
-    }
-}
-
-export function ROCrate_encoder(studyName, a) {
-    let value, value_3, assayName;
-    const fileName = Assay_fileNameFromIdentifier(a.Identifier);
-    const processes = ARCtrl_ArcTables__ArcTables_GetProcesses(a);
-    const dataFiles = getData(processes);
-    const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["@id", (value = ROCrate_genID(a), {
-        Encode(helpers) {
-            return helpers.encodeString(value);
-        },
-    })], ["@type", list_1(singleton({
-        Encode(helpers_1) {
-            return helpers_1.encodeString("Assay");
-        },
-    }))], ["additionalType", {
-        Encode(helpers_2) {
-            return helpers_2.encodeString("Assay");
-        },
-    }], ["identifier", (value_3 = a.Identifier, {
-        Encode(helpers_3) {
-            return helpers_3.encodeString(value_3);
-        },
-    })], ["filename", {
-        Encode(helpers_4) {
-            return helpers_4.encodeString(fileName);
-        },
-    }], tryInclude("measurementType", OntologyAnnotation_ROCrate_encoderPropertyValue, a.MeasurementType), tryInclude("technologyType", OntologyAnnotation_ROCrate_encoderDefinedTerm, a.TechnologyType), tryInclude("technologyPlatform", OntologyAnnotation_ROCrate_encoderDefinedTerm, a.TechnologyPlatform), tryIncludeSeq("performers", ROCrate_encoder_1, a.Performers), tryIncludeList("dataFiles", ROCrate_encoder_2, dataFiles), tryIncludeList("processSequence", (assayName = a.Identifier, (oa_5) => ROCrate_encoder_3(studyName, assayName, oa_5)), processes), tryIncludeSeq("comments", ROCrate_encoder_4, a.Comments), ["@context", context_jsonvalue]]));
-    return {
-        Encode(helpers_5) {
-            const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_5)], values);
-            return helpers_5.encodeObject(arg);
-        },
-    };
-}
-
-export const ROCrate_decoder = object((get$) => {
-    let objectArg, arg_3, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_12, objectArg_5, arg_14, objectArg_6;
-    const identifier = defaultArg((objectArg = get$.Optional, objectArg.Field("identifier", string)), createMissingIdentifier());
-    const tables = map((arg_4) => {
-        const a = ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(arg_4);
-        return a.Tables;
-    }, (arg_3 = list_2(ROCrate_decoder_1), (objectArg_1 = get$.Optional, objectArg_1.Field("processSequence", arg_3))));
-    return new ArcAssay(identifier, unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("measurementType", OntologyAnnotation_ROCrate_decoderPropertyValue))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("technologyType", OntologyAnnotation_ROCrate_decoderDefinedTerm))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("technologyPlatform", OntologyAnnotation_ROCrate_decoderDefinedTerm))), unwrap(tables), undefined, unwrap((arg_12 = resizeArray(ROCrate_decoder_2), (objectArg_5 = get$.Optional, objectArg_5.Field("performers", arg_12)))), unwrap((arg_14 = resizeArray(ROCrate_decoder_3), (objectArg_6 = get$.Optional, objectArg_6.Field("comments", arg_14)))));
-});
-
-export function ISAJson_encoder(studyName, idMap, a) {
-    const f = (a_1) => {
-        let assayName;
-        const fileName = Assay_fileNameFromIdentifier(a_1.Identifier);
-        const processes = ARCtrl_ArcTables__ArcTables_GetProcesses(a_1);
-        const encodedUnits = tryIncludeList("unitCategories", (oa) => OntologyAnnotation_ISAJson_encoder(idMap, oa), getUnits(processes));
-        const encodedCharacteristics = tryIncludeList("characteristicCategories", (value_1) => encoder_8(idMap, value_1), getCharacteristics(processes));
-        const encodedMaterials = tryInclude("materials", (ps) => encoder_9(idMap, ps), Option_fromValueWithDefault(empty(), processes));
-        const encocedDataFiles = tryIncludeList("dataFiles", (oa_1) => ISAJson_encoder_1(idMap, oa_1), getData(processes));
-        const units = getUnits(processes);
-        const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["filename", {
-            Encode(helpers) {
-                return helpers.encodeString(fileName);
-            },
-        }], tryInclude("@id", (value_5) => ({
-            Encode(helpers_1) {
-                return helpers_1.encodeString(value_5);
-            },
-        }), ROCrate_genID(a_1)), tryInclude("measurementType", (oa_2) => OntologyAnnotation_ISAJson_encoder(idMap, oa_2), a_1.MeasurementType), tryInclude("technologyType", (oa_3) => OntologyAnnotation_ISAJson_encoder(idMap, oa_3), a_1.TechnologyType), tryInclude("technologyPlatform", (value_7) => ({
-            Encode(helpers_2) {
-                return helpers_2.encodeString(value_7);
-            },
-        }), map(JsonTypes_composeTechnologyPlatform, a_1.TechnologyPlatform)), encocedDataFiles, encodedMaterials, encodedCharacteristics, encodedUnits, tryIncludeList("processSequence", (assayName = a_1.Identifier, (oa_4) => ISAJson_encoder_2(studyName, assayName, idMap, oa_4)), processes), tryIncludeSeq("comments", (comment) => ISAJson_encoder_3(idMap, comment), a_1.Comments)]));
-        return {
-            Encode(helpers_3) {
-                const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_3)], values);
-                return helpers_3.encodeObject(arg);
-            },
-        };
-    };
-    if (idMap != null) {
-        return encode(ROCrate_genID, f, a, idMap);
-    }
-    else {
-        return f(a);
-    }
-}
-
-export const ISAJson_allowedFields = ofArray(["@id", "filename", "measurementType", "technologyType", "technologyPlatform", "dataFiles", "materials", "characteristicCategories", "unitCategories", "processSequence", "comments", "@type", "@context"]);
-
-export const ISAJson_decoder = Decode_objectNoAdditionalProperties(ISAJson_allowedFields, (get$) => {
-    let objectArg, arg_3, objectArg_1, objectArg_2, objectArg_3, arg_10, objectArg_4, arg_12, objectArg_5;
-    const identifier = defaultArg(bind(Assay_tryIdentifierFromFileName, (objectArg = get$.Optional, objectArg.Field("filename", string))), createMissingIdentifier());
-    const tables = map((arg_4) => {
-        const a = ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(arg_4);
-        return a.Tables;
-    }, (arg_3 = list_2(ISAJson_decoder_1), (objectArg_1 = get$.Optional, objectArg_1.Field("processSequence", arg_3))));
-    return new ArcAssay(identifier, unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("measurementType", OntologyAnnotation_ISAJson_decoder))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("technologyType", OntologyAnnotation_ISAJson_decoder))), unwrap((arg_10 = map_2(JsonTypes_decomposeTechnologyPlatform, string), (objectArg_4 = get$.Optional, objectArg_4.Field("technologyPlatform", arg_10)))), unwrap(tables), undefined, undefined, unwrap((arg_12 = resizeArray(ISAJson_decoder_2), (objectArg_5 = get$.Optional, objectArg_5.Field("comments", arg_12)))));
-});
-