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Fix generated protocol templates

Samuel GAIST requested to merge fix_generated_protocol_templates into master

The original work done for the protocol template was working however it has been discovered that the helper script did not correctly generate the protocol templates.

The script has been fixed in !134 (merged) however the test data were not.

This merge request fixes that. As a byproduct of this cleanup, it has been found that the large database was in fact wrongly written and thus has been fixed as well.

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