MestReNova script to batch-reexport NMR spectra from .mnova files

reexport.qs

/**
 * Batch Export Script for LOGS Data Bundle (.zip)
 * 
 * This script processes all `.mnova` files in the specified directory, 
 * extracts 1D NMR spectra, and exports each file as a LOGS Data Bundle (.zip).
 *
 * It's partially based on the `LOGSDataBundle.qs` script by MestReNova.
 * 
 * - Uses `saveAsLOGSDataBundle()` to perform the export.
 * - Opens each `.mnova` file using `serialization.open()`.
 * - Generates a `.zip` file for each dataset in the output directory.
 * - Ensures proper error handling and document cleanup. 
 * 
 * Notes:
 * - The script closes each file after processing to free memory.
 * - Skips any `.mnova` files that fail to open.
 * - Logs success and failure messages to the console.
 */ 
 

// Define input/output directories
var inputDir = "/home/ra/Datasets/2023-VanBramer-Bastin/c_reexport";
var outputDir = "/home/ra/Datasets/2023-VanBramer-Bastin/c_reexport";


/**
 * saveAsLOGSDataBundle - Exports the active Mnova document as a LOGS Data Bundle (.zip).
 * 
 * This function extracts 1D NMR spectrum data from the active document,
 * saves each spectrum as a JSON file, and optionally includes the full .mnova file.
 * The exported files are compressed into a timestamped ZIP archive.
 *
 * Usage:
 * - `saveAsLOGSDataBundle("/path/to/output.zip");`  // Default, Mnova file NOT saved
 * - `saveAsLOGSDataBundle("/path/to/output.zip", true);`  // Mnova file INCLUDED
 *
 * @param {string} outputPath - Full path where the LOGS Data Bundle (.zip) will be saved.
 * @param {boolean} saveMnovaFile - Whether to include the full .mnova file in the ZIP.
 * 
 * @returns {boolean} - Returns `true` if export was successful, `false` otherwise.
 *
 * Notes:
 * - If no active document is found, the function exits with a warning.
 * - The ZIP file contains JSON representations of valid 1D NMR spectra.
 * - A timestamped directory is created for temporary storage and cleaned up after export.
 */ 
function saveAsLOGSDataBundle(outputPath, saveMnovaFile) {
    "use strict";

    // Ensure an active document is loaded
    var doc = mainWindow.activeDocument;
    if (!doc) {
        print("⚠️ No active document found.");
        return false;
    }

    // Extract filename and path components
    function extractPathAndName(filePath) {
        filePath = filePath.replace(/[\\\/]+$/, '');  // Remove trailing slashes
        var parts = filePath.split(/[\\\/]/);
        var lastElement = parts[parts.length - 1];

        var isFile = /\.\w+$/.test(lastElement);
        var name = isFile ? lastElement.replace(/\.[^/.]+$/, '') : lastElement;
        var path = isFile ? parts.slice(0, -1).join(parts[0].indexOf("\\") !== -1 ? "\\" : "/") : filePath;

        return { path: path, name: name };
    }

    var result = extractPathAndName(outputPath);
    var path = result.path;
    var name = result.name;

    // Create timestamped output directory
    var startDate = date2ISOString(new Date()).replace(/\:/g, ".") + "_LOGS";
    var resultDir = new Dir(path);
    resultDir.mkdir(startDate);
    resultDir.cd(startDate);
    var tempResultName = path + "/" + startDate;

    // Collect NMR spectrum data
    var nmrItems = doc.itemsByName('NMR Spectrum');
    var jsonArray = [];
    var pageArray = [];

    for (var i = 0; i < nmrItems.length; i++) {
        var spec = new NMRSpectrum(nmrItems[i]);
        if (spec.isValid() && spec.dimCount === 1) {
            var jsonFile = tempResultName + "/" + spec.uuid + ".json";
            jsonArray.push(jsonFile);
            pageArray.push(nmrItems[i].page);
        }
    }

    // Initialize ZIP file for export
    var zip = new Zip(outputPath);
    var flag = zip.open() === 0;

    if (flag) {
        for (var i = 0; i < jsonArray.length; i++) {
            doc.setCurPage(pageArray[i]);
            serialization.save(jsonArray[i], "JSON NMR (*.json)");

            if (!File.exists(jsonArray[i])) {
                print("❌ Failed to save JSON: " + jsonArray[i]);
                flag = false;
            } else {
                zip.addFile(jsonArray[i], "", Zip.SkipPaths);
            }
        }

        // Save Mnova file (only if enabled)
        if (saveMnovaFile) {
            var mnovaFile = tempResultName + "/" + name + ".mnova";
            serialization.save(mnovaFile, "mnova");

            if (!File.exists(mnovaFile)) {
                print("❌ Failed to save Mnova file: " + mnovaFile);
                flag = false;
            } else {
                zip.addFile(mnovaFile, "", Zip.SkipPaths);
            }
        }
    } else {
        print("❌ Failed to open ZIP file for writing.");
        flag = false;
    }

    zip.close();

    // Clean up temporary directory
    var tempResultDir = new Dir(tempResultName);
    tempResultDir.removeRecursively();

    if (flag) {
        print("✅ Successfully exported: " + outputPath);
    } else {
        print("⚠️ Export process completed with errors.");
    }

    return flag;
}



// Ensure output directory exists
if (!File.exists(outputDir)) {
    new Dir(outputDir).mkdir();
}

// Get list of .mnova files in the input folder
var dir = new Dir(inputDir);
var files = dir.entryList("*.mnova", Dir.Files);

if (files.length === 0) {
    print("No .mnova files found in " + inputDir);
    return;
}

print("Starting batch export of " + files.length + " files...");

for (var i = 0; i < files.length; i++) {
    var filePath = inputDir + "/" + files[i];

    print("Opening: " + filePath);

    // Open file using serialization.open()
    var success = serialization.open(filePath);
    if (!success) {
        print("❌ Failed to open: " + filePath);
        continue;  // Skip to the next file
    }

    // Construct output path for the LOGS Data Bundle
    var fileName = filePath.substring(filePath.lastIndexOf("/") + 1, filePath.lastIndexOf("."));
    var exportPath = outputDir + "/" + fileName + ".zip";

    // Call the function to export
    var saveMnovaFile = false;
    var exportSuccess = saveAsLOGSDataBundle(exportPath, saveMnovaFile);

    if (!exportSuccess) {
        print("❌ Export failed: " + filePath);
    }

    // Close document to free memory
    mainWindow.activeDocument.close();
}

print("Batch export completed.");