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After reviewing base_metadata_template.py and sample_template.py, it appears that there is code to check that the proper required columns are present in a sample-template when it is loaded/updated/extended. There also needs to be a check to ensure that a loaded/updated/extended sample-template does not contain columns with names matching those found in our prep-info and similar files.
Duplicates will cause an error when a prep-info file is loaded into Qiita during an SPP run, because the underlying database table can't have two columns with identical names e.g.: 'well_id_384'.
The list of columns found in a prep-info file can be found in metapool by including it as a dependency or perhaps as simply a list of known reserved words to be modified manually.