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I'm using this module External Link module which adds "ext" as a class to any anchor tag matching the regex defined via the admin UI provided by the module. I then bind a click event to trigger colorbox for anchor tags with the "ext" tag. Now my issue is, any anchor tags added to the colorbox container are also being added a class "ext".

I understand that this has to do with Drupal.behaviors attach method implemented in the contrib module, but how do I "detach" this behaviors from my custom js file? Specifically for the links within the modal container.

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we faced the same issue here we are using lightbox module what we did is we dint used any extra module in common we wrote a Behaviour to add a external class and added condition to when colorbox is added remove external class

Define your base URL in any module in it

"Drupal.settings.baseUrl"

/* external links*/
 Drupal.behaviors.external_link = {
    attach: function (context, settings) {
      $("body .view-content a").once(function() {
                    var anchorlink = '';
                    anchorlink = jQuery(this).attr('href');
                    if(anchorlink != "#" && !$(this).hasClass('lightbox-processed'))
                    {
                        if(!(anchorlink.lastIndexOf('http') == -1) && anchorlink.lastIndexOf(Drupal.settings.baseUrl) == -1 && !jQuery(this).hasClass("external"))
                        {
                            if($(this).parent().hasClass('lightbox-processed')){
                                    jQuery(this).removeClass("external");
                            }else{
                                    jQuery(this).addClass("external");
                                    var targ = "_blank";
                                    jQuery(this).attr("target", targ);

                            }
                        Drupal.attachBehaviors();
                        }
                    }
      });
   }
  };

instead of lightbox-processed replace your class hope this will help you :)

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