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A: The issue was found when the client updated the API Token of the gateway. The trigger executes on that update and it runs a query search to the payment transaction object. It checks if the updated gateway has open transactions linked to it. If true, PP will not allow the changes otherwise proceed. Though technically, ProntoPayments only queries 1 record (see code below) salesforce performs table scans internally.
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Their The client’s org has more than 2M records so when salesforce runs the table scan it reaches the limit of the final threshold - 600k. GuideDogs has more than 600k+ thus making the query unselective.
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To make the query passable and successfully update the Gateway API key, you need to contact Salesforce and request to Index the possible fields inside the query (e.g. Payment Status).