Protractor: Unable select input element inside a shadow DOM (Polymer) using by.deepCss('input')

Just create a new locator :

/**
 * Usage:
 *   O  element(by.css_sr('#parentElement #innerElement'))          <=> $('#parentElement #innerElement')
 *   O  element(by.css_sr('#parentElement::sr #innerElement'))      <=> $('#parentElement').shadowRoot.$('#innerElement')
 *   O  element.all(by.css_sr('#parentElement .inner-element'))     <=> $$('#parentElement .inner-element')
 *   O  element.all(by.css_sr('#parentElement::sr .inner-element')) <=> $$('#parentElement').shadowRoot.$$('.inner-element')
 *   O  parentElement.element(by.css_sr('#innerElement'))           <=> parentElement.$('#innerElement')
 *   O  parentElement.element(by.css_sr('::sr #innerElement'))      <=> parentElement.shadowRoot.$('#innerElement')
 *   O  parentElement.all(by.css_sr('.inner-element'))              <=> parentElement.$$('.inner-element')
 *   O  parentElement.all(by.css_sr('::sr .inner-element'))         <=> parentElement.shadowRoot.$$('.inner-element')
 */
by.addLocator('css_sr', (cssSelector: string, opt_parentElement, opt_rootSelector) => {
    let selectors = cssSelector.split('::sr');
    if (selectors.length === 0) {
        return [];
    }

    let shadowDomInUse = (document.head.createShadowRoot || document.head.attachShadow);
    let getShadowRoot  = (el) => ((el && shadowDomInUse) ? el.shadowRoot : el);
    let findAllMatches = (selector: string, targets: any[], firstTry: boolean) => {
        let using, i, matches = [];
        for (i = 0; i < targets.length; ++i) {
            using = (firstTry) ? targets[i] : getShadowRoot(targets[i]);
            if (using) {
                if (selector === '') {
                    matches.push(using);
                } else {
                    Array.prototype.push.apply(matches, using.querySelectorAll(selector));
                }
            }
        }
        return matches;
    };

    let matches = findAllMatches(selectors.shift().trim(), [opt_parentElement || document], true);
    while (selectors.length > 0 && matches.length > 0) {
        matches = findAllMatches(selectors.shift().trim(), matches, false);
    }
    return matches;
});

See here for help.

You can call it like this :

inputs = element(by.css_sr('.polyFName::sr input'))
// OR
inputs = polymerFirstName.element(by.css_sr('::sr input')
inputs.clear();