Via the External API we are able to add journal entries. We provide the tax ids in the lines, but Odoo doesn't automatically calculates the tax. In the journal entry in Odoo it shows the correct tax for each line. 
We tried by providing also the lines for tax, but that doesn't work either. 

Is there some sort of flag we need to send across in our code to do this?

The journal is created via this line:
je_id = models.execute_kw(account["odoo"]["dbname"], uid, account["odoo"]["password"], 'account.move', 'create', [journal])