EDIT

// see also https://github.com/geetarista/jquery-plugin-template/blob/master/jquery.plugin-template.js

// the semi-colon before function invocation is a safety net against concatenated

// scripts and/or other plugins which may not be closed properly.

;(function($, document, window, undefined) {

  // Optional, but considered best practice by some

  "use strict";

  // Name the plugin so it's only in one place

  var pluginName = 'utis_client';

  // Default options for the plugin as a simple object

  var defaults = {

    providers: {

      'bgbm-phycobank': 'PhycoBank',

      'diatombase' : 'DiatomBase',

      'worms': 'WoRMS'

      //'pesi': 'PESI'

    },

    webserviceUrl : 'https://cybertaxonomy.eu/eu-bon/utis/1.3',

    // webserviceUrl : 'http://test.e-taxonomy.eu/eubon-utis',

    //  webserviceUrl : 'http://localhost:8081/',

    pageSize: 20,

    spinnerIcon: null

  };

  // Plugin constructor

  // This is the boilerplate to set up the plugin to keep our actual logic in one place

  function Plugin(element, options) {

    this.element = element;

    this.formItemQueryText = null;

    this.formItemProviderCheckboxes = null;

    this.formItemProviderSeachMode = null;

    this.resultContainer = null;

    this.spinnerContainer = null;

    this.pageIndex = 0;

    this.autoLoadTolerance = 20; // start autoloading x pixels before the bottom of the result container

    this.externalLinkIconMarkup = '[open]';

    // firebug console stub (avoids errors if firebug is not active)

    if (typeof console === "undefined") {

      console = {

        log: function () {

        }

      };

    }

    // Merge the options given by the user with the defaults

    this.options = $.extend({}, defaults, options);

    // Attach data to the elment

    this.$el      = $(element);

    this.$el.data(name, this);

    this._defaults = defaults;

    var meta      = this.$el.data(name + '-opts');

    this.opts     = $.extend(this._defaults, options, meta);

    // Initialization code to get the ball rolling

    // If your plugin is simple, this may not be necessary and

    // you could place your implementation here

    this.init();

  }

  Plugin.prototype = {

    // Public functions accessible to users

    // Prototype methods are shared across all elements

    // You have access to this.options and this.element

    // If your plugin is complex, you can split functionality into more

    // methods like this one

    init: function () {

      // Plugin initializer - prepare your plugin

      var plugin = this;

      var form = $("<form/>",

        {

          style: 'vertical-align: top;'

        }

      );

      this.formItemQueryText = $("<input/>",

        {

          type: 'text',

          placeholder: 'scientific name query string',

          name: 'query',

          // value: "Navicula", // search term preset for testing

          style: 'width:100%'

        }

      ).keypress(function(event){

        if ( event.which == 13 ) { // 13 = ENTER

          event.preventDefault();

          form.submit();

        }

      });

      var checkBoxesDiv = $('<div/>',

        {

          'class': 'checkboxes',

           style: 'display: inline-block; width:30%; vertical-align: top;'

        });

      var checkboxesArray = [];

      $.each(Object.keys(plugin.options.providers), function (index, key) {

        var checkbox_id = 'checkbox_' + key;

        var disabled = key == '--unused--'; // the disable state has been used for worms

        var checkbox =   $("<input/>",

          {

            type: 'checkbox',

            name: 'provider',

            checked: index == 0 ? 'checked' : '',

            value: key,

            id:  checkbox_id,

            disabled: disabled

          }

        );

        var label = $('<label for="' + checkbox_id + '" style="display: inline-block; vertical-align: top; ' + (disabled ? 'color:#bbbbbb;': '') + '">&nbsp;' +  plugin.options.providers[key] + '</label><br/>');

        // label.append(checkbox);

        checkBoxesDiv.append(checkbox).append(label);

        if(disabled){

          checkBoxesDiv.append($('<div style="font-size:small; color:#bbbbbb;">' + plugin.options.providers[key] + ' disabled due to unresolved potential copyright issues.</div>'))

        }

        if(  key == 'worms'){

          checkBoxesDiv.append($('<div style="font-size:small; color:#bbbbbb;">WoRMS includes data from different databases. Please consider data sources, data citations, and licensing as given by WoRMS.</div>'));

        }

        checkboxesArray.push(checkbox);

      });

      this.formItemProviderCheckboxes = checkboxesArray;

      var submit = $("<input/>",

        {

          type: 'submit',

          value: 'Search',

          style: 'width:100%; margin-top: 1em;'

        }

      );

      this.resultContainer = $('<div/>',

        {

          'class': 'results',

          style: 'overflow-y: auto; height: 20em; border: inset 1px rgb(239, 240, 241); margin-top: 1em;'

        }

        ).hide().bind('scroll', function() {

          if($(this).scrollTop() + $(this).innerHeight() >= $(this)[0].scrollHeight - plugin.autoLoadTolerance) {

            plugin.pageIndex++;

            plugin.executeQuery(plugin);

          }

        });

      form.append($('<div />', {style: 'width: 30%; display: inline-block; vertical-align: top; padding-right: 1em;'}).append(this.formItemQueryText).append(submit));

      form.append(checkBoxesDiv);

      // form.append(submit);

      form.submit(function(event){

        event.stopPropagation();

        event.preventDefault();

        // reset the page index when the form was submitted

        plugin.pageIndex = 0;

        plugin.executeQuery(plugin);

        return false;

      });

      this.$el.append(form);

      this.$el.append(this.resultContainer);

      this.spinnerContainer = $('<div class="spinner" style="position: relative; bottom: 50px; width: 100%; height: 50px; margin: auto; text-align: center;"></div>');

      this.spinnerContainer.hide();

      this.resultContainer.append(this.spinnerContainer);

      if(this.options.spinnerIcon !== undefined){

        var icon = $(this.options.spinnerIcon);

        this.spinnerContainer.append(icon);

      }

      if(this.options.externalLinkIcon !== undefined){

        this.externalLinkIconMarkup = this.options.externalLinkIcon;

      }

    },

  /**

   *

   * @returns {string}

   */

  providerSelection: function(){

    var checkboxes = this.formItemProviderCheckboxes;

    return function(){

    var providerSelection = [];

      $.each(checkboxes, function (index, checkbox) {

        if(checkbox.is(':checked')){

          providerSelection.push(checkbox.attr('value'));

        }

      });

      return providerSelection.join(',');

    }

  },

  /**

   *

   * @returns {string}

   */

  queryString: function(){

    var textField = this.formItemQueryText;

    return function(){

     return textField.val();

    }

  },

  /**

   *

   * @param plugin

   */

  executeQuery: function (plugin) {

    plugin.resultContainer.show();

    plugin.spinnerContainer.show();

    $.getJSON(plugin.options.webserviceUrl + '/search',

      {

        providers: plugin.providerSelection(), // Closure!

        searchMode: 'scientificNameLike',

        query: plugin.queryString(), // Closure!

        pageSize: plugin.options.pageSize,

        pageIndex: plugin.pageIndex

      },

      function (tnrMsg, textStatus, jqXHR) {

        if(plugin.pageIndex === 0){

          plugin.resultContainer.empty();

          plugin.resultContainer.append(plugin.spinnerContainer);

        }

        // in UTIS there is always only one query

        var response = tnrMsg.query[0].response;

        var count = 0;

        $.each(response, function (index, record) {

          if(record.matchingNameString !== null){

            // ignore deleted names (WoRMS, DiatomBase)

            plugin.spinnerContainer.before(plugin.makeResultEntry(record));

            count++;

          }

        });

        if(count === 0 && plugin.pageIndex === 0){

          plugin.spinnerContainer.before($('<div/>', {'class': 'no-results', style: 'height: 100%; text-align: center; v-align: middle;'}).text("No results."))

        }

        plugin.spinnerContainer.hide();

      });

  },

  makeResultEntry: function (record) {

    var resultEntry = $('<div/>', {'class': 'result-entry'});

    var taxonContainer = $('<div/>');

    taxonContainer.append($('<span/>', {'class': 'matching-name', style: 'font-weight: bold; padding-right: 0.3em;'}).text(record.matchingNameString));

    if(record.taxon.url){

      taxonContainer.append($('<a/>', {href: record.taxon.url, target: 'provider'}).append($(this.externalLinkIconMarkup)));

    }

    resultEntry.append(taxonContainer);

    var relation = record.matchingNameType;

    var taxonName = record.taxon.taxonName.scientificName;

    if(relation !== undefined){

      relation = relation.toLowerCase();

      if(relation !== 'taxon') {

        resultEntry

          .append($('<span/>', {'class': 'relation', style: 'opacity: 0.5;'}).text(relation + ' for '))

          .append($('<span/>', {'class': 'taxon'}).text(taxonName));

      }

      resultEntry.append($('<div/>', {'class': 'checklist', style: 'opacity: 0.5; '}).text('Checklist: ') // text-align: right?

          .append($('<a/>', { href: record.checklistUrl, target: 'provider'}).text(record.checklist)

          )

      );

    }

    return resultEntry;

  }

  }; // END of  Plugin.prototype

  $.fn[pluginName] = function(options) {

    // Iterate through each DOM element and return it

    return this.each(function() {

      // prevent multiple instantiations

      if (!$.data(this, 'plugin_' + pluginName)) {

        $.data(this, 'plugin_' + pluginName, new Plugin(this, options));

      }

    });

  };

  // ---------------------

    /*

    function getFootnoteClassName(object){

      return '.'+$(object).attr('href').substr(1);

    }

    function getFootnoteKeyClassName(object){

      return '.'+$(object).attr('href').substr(1).replace(/-/gi, '-key-') + ' a';

    }

    */

})(jQuery, document, window);