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Is it possible to append to a YXDB instead of having to read in the whole thing, union the new records, and then re-create it?
The short answer is, No, because of what a YXDB file is. This article is based on the comments resulting from an Idea posted here.
The YXDB file format is designed for some very specific needs around high speed reading and writing as well as having random I/O (for browsing) and a spatial index (for mapping/spatial join, etc...) This makes it not suited to more database like operations like append or query. When looking for a desktop file format that has database like functionality, SQLITE is the way to go. It is well supported in Alteryx, allows you to append/query etc. And then if you want indexes and stuff, you can build them with a separate tool and Alteryx will be able to use them.
Simply choose SQLite(*.sqlite) from Files of Type...
From both the Input and Output tool configuartions, all of the expected options for reading and writing to traditional databases are there - such as specifying a table or query, Pre and Post SQL statements and the output options of Append, Drop, Create and Overwrite.
One thing you may notice with working with SQLite databases is that the files are larger than a YXDB. This is due to the fact the YXDB file is compressed (as explained above). That compression is part of what makes it so you can't append to one. The actual compression will vary based on what data you write to it. SQLite is appendable and queryable which inherently would be very difficult or impossible to support compression.