Overwrite only some partitions in a partitioned spark Dataset

Since Spark 2.3.0 this is an option when overwriting a table. To overwrite it, you need to set the new spark.sql.sources.partitionOverwriteMode setting to dynamic, the dataset needs to be partitioned, and the write mode overwrite.
Example in scala:

spark.conf.set(
  "spark.sql.sources.partitionOverwriteMode", "dynamic"
)
data.write.mode("overwrite").insertInto("partitioned_table")

I recommend doing a repartition based on your partition column before writing, so you won’t end up with 400 files per folder.

Before Spark 2.3.0, the best solution would be to launch SQL statements to delete those partitions and then write them with mode append.

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