[Share] Convert Covidence Exclusion Labels to Zotero Tags

[grolimur]

Description

Researchers who use Covidence for paper screening and may need to import references back to Zotero. This can be achieved by exporting from Covidence and import them into Zotero. This will create a Note under each item in a certain format.
Running this Action against it will create a tag for each exclusion note indicating the exclusion decision.
The names of the reviewers who commented are included.

Event

None

Operation

Script

Data

/**
 * Takes a Note, imported from Covidence, and add the corresponding Tag to the Item.
 * @source adapted from @rummens's script "Convert Rayyan Include/Exclude and Labels to Zotero Tags": https://github.com/windingwind/zotero-actions-tags/discussions/354
 * @author Zotero Community
 * @usage Extract Covidence exclusion decisions as Zotero tags
 * @link https://github.com/windingwind/zotero-actions-tags/discussions/611
 */

const Zotero = require("Zotero");
const window = require("window");

(async function () {
    const startTime = new Date();
    const keywordTagMap = {
        'Excluded': 'Excluded',
        'Included': 'Included'
      };
     
    const exclusionPrefix = 'Exclusion reason: ';

    // Prevent duplicate execution
    if (window.batchTagRunning) return;
    window.batchTagRunning = true;

    // Get items to edit based on user selection
    async function getItemsToEdit(triggerType, item, items) {
        const zoteroPane = Zotero.getActiveZoteroPane();
        if (triggerType === 'menu') {
            if (items && items.length > 0) {
                return items;
            } else if (item) {
                return [item];
            } else {
                window.alert("No items selected.");
                return null;
            }
        } else {
            let selectedItems = zoteroPane.getSelectedItems();
            if (!selectedItems.length) {
                window.alert("No items selected.");
                return null;
            }
            return selectedItems;
        }
    }

    // Log the elapsed time for a given operation
    function logTime(label, time) {
        try {
            Zotero.logError(`${label}: ${(time / 1000).toFixed(2)} seconds`);
        } catch (error) {
            Zotero.logError(`Failed to log time for ${label}: ${error.message}`);
        }
    }
    
    try {
        // Ensure items and item are provided
        if (!items && !item) {
            window.alert("Bulk Edit", "No item or items array provided.");
            window.batchTagRunning = false;
            return;
        }

        // Get items to edit based on user selection
        let itemsToEdit = await getItemsToEdit(triggerType, item, items);
        if (!itemsToEdit) {
            window.batchTagRunning = false;
            return;
        }

        Zotero.logError(`Total items to edit: ${itemsToEdit.length}`);

        for (let item of itemsToEdit) {
            // Skip if the item is of type 'note'
            if (item.isNote()) {
              continue;
            }
        
            // Get the notes for the item
            const noteIDs = item.getNotes();
            const notes = await Zotero.Items.get(noteIDs);
        
            for (let note of notes) {
              const noteContent = note.getNote();
        
              // Check for exclusion reasons
              const exclusionIndex = noteContent.indexOf(exclusionPrefix);
              if (exclusionIndex !== -1) {
				let allExcklusions = noteContent.substring(exclusionIndex + exclusionPrefix.length).split('#/#');
                for (let exclusionReason of allExcklusions) {
					exclusionReason = exclusionReason.replace(/<\/?[^>]+(>|$)/g, ""); // Remove HTML tags
					const exclusionTag = `Covidence Exclusion - ${exclusionReason}`;
					item.addTag(exclusionTag, 1);
					Zotero.logError(`Added tag: ${exclusionTag} to item: ${item.id}`);
				}
              }
            }
          }

        
    } catch (error) {
        Zotero.logError(`Error in batch tag script: ${error.message}`);
        window.alert(`An error occurred: ${error.message}`);
    } finally {
        window.batchTagRunning = false;
        const endTime = new Date();
        logTime("Total time", endTime - startTime);
    }
})();

Anything else

No response