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At first sight this looks like a bug in canari when regenerating the new MTZ using the entities.mtz file and loosing the inheritance.
Somewhere in > /usr/local/lib/python3.6/dist-packages/canari/pkgutils/maltego.py(807)add_entity()
Once this PR is integrated in canari the problem will be resolved. In the meantime please edit the 3 entities manually and add the inheritance, to the BaseEntity of misp.MISPGalaxy as can be seen in the screenshot.
Some entities such as ThreatActor, Software do not have the proper inheritance configured.
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