Zotero

Bookmarking customization.

For Ubuntu 22+ installation (updated 2023-11-07):

Download the binaries and extract to /opt/zotero. Note the permissions so that it can self-update.
Run ./set_launcher_icon to link installation directory.
Link the zotero.desktop file to ~/.local/share/applications/
May need to manually link MIME type, if not restarting:

# Update database
user:$ update-mime-database ~/.local/share/mime
user:$ update-desktop-database ~/.local/share/applications
user:$ gio mime x-scheme-handler/zotero
Default application for “x-scheme-handler/zotero”: zotero.desktop
Registered applications:
	zotero.desktop
Recommended applications:
	zotero.desktop
 
# Test link opening
user:$ xdg-open "zotero://select/library/items/PWJZFU2X"

See this for Zotero scheme link debugging.

Plugins

A collection of useful plugins:

Zutilo
PDF Preview (make sure to install v0.3.7 for Zotero 6)

Compatible with Zotero 7:

Scripts

import re
import tqdm
from pyzotero import zotero
 
# Get credentials from https://www.zotero.org/settings/keys
library_id = "CHANGEME"
api_key = "CHANGEME"
library_type = "user"  # personal library
 
zot = zotero.Zotero(library_id, library_type, api_key)
 
# My user-defined tags will either only be pure emoji, or include :
pattern = re.compile("^[A-Za-z0-9][^:]*$")
tags = zot.everything(zot.tags())
 
to_remove = [tag for tag in tags if pattern.search(tag) is not None]
batch_size = 50
for i in tqdm.tqdm(range(len(to_remove)//batch_size + 1)):
    to_remove_now = to_remove[i*batch_size : (i+1)*batch_size]
    zot.delete_tags(*to_remove_now)

Action script for Zotero link (Copy link, Ctrl+Shift+C shortcut):

// @author windingwind, garth74
// @link https://github.com/windingwind/zotero-actions-tags/discussions/115
// @usage Select an item in the library and press the assigned shortcut keys
// @update Mon, 22 Jan 2024 00:10:18 GMT (by new Date().toGMTString())
 
// EDIT THESE SETTINGS
 
/** @type {string} Name of the field to use as the link text. To use the citation key, set this to "citationKey". */
let linkTextField = "title";
 
/** @type {'html' | 'md' | 'plain'} What type of link to create. */
let linkType = "html";
 
/** @type {boolean} If true, make the link specific to the currently selected collection. */
let useColl = false;
 
/** @type {boolean} If true, use Better Notes zotero://note link when the selected item is a note. */
let useNoteLink = false;
 
/** @type {'select' | 'open-pdf' | 'auto'} Action of link*/
let linkAction = "auto"; // auto = open-pdf for PDFs and annotations, select for everything else
 
// END OF EDITABLE SETTINGS
 
// For efficiency, only execute once for all selected items
if (item) return;
item = items[0];
if (!item && !collection) return "[Copy Zotero Link] item is empty";
 
if (collection) {
  linkAction = "select";
  useColl = true;
}
 
if (linkAction === "auto") {
  if (item.isPDFAttachment() || item.isAnnotation()) {
    linkAction = "open-pdf";
  } else {
    linkAction = "select";
  }
}
 
const uriParts = [];
let uriParams = "";
 
let targetItem = item;
if (linkAction === "open-pdf") {
  uriParts.push("zotero://open-pdf");
  if (item.isRegularItem()) {
    targetItem = (await item.getBestAttachments()).find((att) =>
      att.isPDFAttachment()
    );
  } else if (item.isAnnotation()) {
    targetItem = item.parentItem;
    // If the item is an annotation, we want to open the PDF at the page of the annotation
    let pageIndex = 1;
    try {
      pageIndex = JSON.parse(item.annotationPosition).pageIndex + 1;
    } catch (e) {
      Zotero.warn(e);
    }
    uriParams = `?page=${pageIndex}&annotation=${item.key}`;
  }
} else {
  uriParts.push("zotero://select");
  if (item?.isAnnotation()) {
    targetItem = item.parentItem;
  }
}
 
if (!targetItem && !collection) return "[Copy Zotero Link] item is invalid";
 
// Get the link text using the `link_text_field` argument
let linkText;
if (collection) {
  // When `collection` is truthy, this script was triggered in the collection menu.
  // Use collection name if this is a collection link
  linkText = collection.name;
} else if (item.isAttachment()) {
  // Try to use top-level item for link text
  linkText = Zotero.Items.getTopLevel([item])[0].getField(linkTextField);
} else if (item.isAnnotation()) {
  // Add the annotation text to the link text
  linkText = `${targetItem.getField(linkTextField)}(${
    item.annotationComment || item.annotationText || "annotation"
  })`;
} else {
  // Use the item's field
  linkText = item.getField(linkTextField);
}
 
// Add the library or group URI part (collection must go first)
let libraryType = (collection || item).library.libraryType;
if (libraryType === "user") {
  uriParts.push("library");
} else {
  uriParts.push(
    `groups/${Zotero.Libraries.get((collection || item).libraryID).groupID}`
  );
}
 
// If useColl, make the link collection specific
if (useColl) {
  // see https://forums.zotero.org/discussion/73893/zotero-select-for-collections
  let coll = collection || Zotero.getActiveZoteroPane().getSelectedCollection();
 
  // It's possible that a collection isn't selected. When that's the case,
  // this will fall back to the typical library behavior.
 
  // If a collection is selected, add the collections URI part
  if (!!coll) uriParts.push(`collections/${coll.key}`);
}
 
if (!collection) {
  // Add the item URI part
  uriParts.push(`items/${targetItem.key}`);
}
 
// Join the parts together
let uri = uriParts.join("/");
 
// Add the URI parameters
if (uriParams) {
  uri += uriParams;
}
 
if (useNoteLink && item?.isNote() && Zotero.BetterNotes) {
  uri = Zotero.BetterNotes.api.convert.note2link(item);
}
 
// Format the link and copy it to the clipboard
const clipboard = new Zotero.ActionsTags.api.utils.ClipboardHelper();
if (linkType == "html") {
  clipboard.addText(`<a href="${uri}">${linkText}</a>`, "text/unicode");
} else if (linkType == "md") {
  clipboard.addText(`[${linkText}](${uri})`, "text/unicode");
} else {
  clipboard.addText(uri, "text/unicode");
}
 
clipboard.addText(`<a href="${uri}">${linkText}</a>`, "text/html");
 
clipboard.copy();
 
return `[Copy Zotero Link] link ${uri} copied.`;