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Does the input data tool use a Gallery alias? If so, please rename file %APPDATA%\Alteryx\Engine\GalleryAlias.xml to GalleryAlias.xml (example: C:\Users\my_name\AppData\Roaming\Alteryx\Engine\GalleryAlias.xml.old) and restart Alteryx Designer.
One additional point: This can also happen on Gallery if you remove the last gallery alias. The gallery file may be left in an invalid XML format, causing the workers referencing that file to fail with this error.
I'm getting the same error for a dynamic input tool in my macro. My input files are of type xml. I created a blank file with type xml and dynamically replace the file with the actual xml file name. This worked perfectly the first few times I ran the workflow but suddenly stopped working and produced the errror:Invalid document structure at LIne:2 and Column:1. How do I get rid of this error?
bir1bv the issue you are experiencing is a little different than what is covered in this post, but I will try to help.
Since you are using these files as input, this error tells me one of the xml files you are passing through has an invalid document structure. Can you isolate the file(s) that cause the input tool to error? If so, I would then take those files and use an xml validator (such as https://www.w3schools.com/xml/xml_validator.asp) to identify the cause of the invalid state.
Also, do the files have the same general document structure? If you send your workflow and some examples I may be able to help more thoroughly.