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This might be due to data compatibility issue. By default, when a crawler defines tables for data stored in Amazon S3, it considers both data compatibility and schema similarity. Since you already selected option “Create a single schema for each S3 path”, schema similarity will be ignored in this case but it will still check for data compatibility. Please check here for more information: https://docs.aws.amazon.com/glue/latest/dg/crawler-configuration.html#crawler-grouping-policy
If the crawler identifies that data is not compatible even in a single file it will create a table for each file. Please open a support case with Glue team and provide crawler name, region and sample data (if possible) for us to troubleshoot further.
You are essentially creating the same schema twice, as you've already selected single schema. Crawlers take into consideration both the data compatibility and schema similarity, since your data compatibility is met it won't create another table. If however, the data wasn't compatible it will then create a table for each file.
I have tried check and uncheck that option (Create a single schema for each S3 path), the result is the same.
I may want to have a workflow with a pythonshell job that rebuilds your file structure to have bucket/basefolder/logfolder. Then have a crawler in the same workflow crawl the bucket structure. The confusion is coming from the crawler not knowing how to jump between the tags (directories) like that. You can maintain subfolders with partitions but probably not required. You might need to set a table level for the crawler as shown at bottom of this doc page. https://docs.aws.amazon.com/glue/latest/dg/crawler-configuration.html
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I have tried check and uncheck that option (Create a single schema for each S3 path), the result is the same.