@saper, this is the correct way to configure it:

$wgGraphAllowedDomains = [ 'wikiraw' => [ 'tools.wikimedia.pl' ], 'http' => [ 'tools.wikimedia.pl' ] ];

What do you mean by "my wiki lives in a subdirectory"?
I see you have http://tools.wikimedia.pl/~saper/b/api.php as the endpoint. Sadly, at this point the Graph extension is hardcoded to use /w/api.php. The quick hack is to change graph2.compiled.js file line 432 to use your api endpoint. Eventually, I should make it possible to configure non-default api endpoint in the settings.

@Yurik thank you very much, I forgot to add my workaround here: https://github.com/saper/mediawiki-extensions-Graph/commit/7985fd39623b345f9a446a8a59ecef240a748f97

One thing which wondered me when trying "wikiraw:" protocol is that internal MediaWiki functions are not used in case of "this" wiki. This way any strange MediaWiki configuration could be easily supported. What about T145977 to change this?

Also it was pretty confusing to need to add "http" in the configuration next to the "wikiraw" protocol. Technically this makes sense, since we go via http API, but maybe after T145977 we would need to.

One more thing, the documentation at the extension page listed some probably obsolete variables, which I have removed. Is this okay?

@saper see my explanation why the protocols were designed this way in T145977#2647013. Of course suggestions on how to make it better are welcome :) The documentation definitely need some love, and I will be very grateful for your help :)

could you please share how we can adjusted data source paths to wikiraw:///file-csv
I am getting same error too However, I keep getting "Error: URL hostname is not whitelisted: wikiraw:///file-csv" on the console.
I am having my file-csv page title of mediawiki