I have HTML and JavaScript that run just fine in a SharePoint 2013 content-editor web-part, from which I can access the Ewa.EwaControl object (https://msdn.microsoft.com/en-us/library/office/ee589018.aspx) to get to the various Excel Web Parts hosted on the page.

The Ewa has some limitations that I'd like to overcome by using the office.js (https://msdn.microsoft.com/en-us/library/office/fp142185.aspx).

Also, both Ewa and office.js seem to do a similar thing, but I can't find anything on the internet that indicates which is deprecated in favor of which. With SharePoint 2016 requiring Office Online Server, and Excel Web Parts now being subsumed by Office Online Server, what does that mean with regard to the future of either office.js or Ewa? They seem to have overlapping features and it's unclear which we should invest in.

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They are not the same - most of office.js won't work in the manner you want to use it.

The EWA library is specifically for Excel services running inside SharePoint.

Office.js is for the Office clients (thick, web, and supported mobile versions). Office.js is generally positioned for "Office add-ins" where EWA would be leveraged in SharePoint Add-Ins, or like you are using thru script parts.

I've have not yet had hands on time with 2016 - and it's only preview so I'm not sure if Excel Web services will be available for migrated legacy services.

Depending on what you are doing and your audience you are going to have a mix of these libraries. The on-prem products are still in preview, so no definitive answer can yet be placed there. O365 has not added anything to the Road Map in regards to retiring Excel services or API's.

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