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See request at https://commons.wikimedia.org/wiki/Commons_talk:GLAM_dashboard#More_than_100_categories The query finds categories which are used by a page in the bucket category AND where the categories are not children of the bucket category. The default GLAMdashboard report is limited to the top 100 matches.
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SQL
USE commonswiki_p; SELECT c.cl_to AS category, COUNT(DISTINCT page_id) AS total FROM page INNER JOIN categorylinks AS c ON page_id=c.cl_from AND c.cl_to NOT IN ("Scans_by_the_Internet_Archive_selected_by_BEIC") INNER JOIN categorylinks AS cc ON page_id=cc.cl_from AND cc.cl_to IN ("Scans_by_the_Internet_Archive_selected_by_BEIC") WHERE c.cl_to NOT REGEXP "Files_from|CC-BY|Files_with|test_|Uploaded_with|Self-pub|Items_with_OTRS|GFDL|FAL|PD-|PD_Old|uploaded_by_|Flickr_images_reviewed|Flickr_images_uploaded" GROUP BY c.cl_to HAVING total>1 ORDER BY COUNT(page_id) DESC LIMIT 1000;
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