Malformed structure strings

I’ve noticed that some of the structure strings in the database seem to be malformed. For example:

Xs
http://kws.eternadev.org/web/puzzle/1…
…((((((((…))))))))…(((…)))…((((…)))).x.x

Pseudoknot
http://kws.eternadev.org/web/puzzle/1…
((((…((((((…)))))).((((((((…))))))))…((((((…((((((…((((…(((…)))))))…)))))).(((((…((((…))))…)))))….[[[[…(((((((((…(((((((((…)))))))))…)))))))))…((((((((((…))))))))))…))))))…(((((((((((…)))))))))))…]]]]…))))

Space
http://kws.eternadev.org/web/puzzle/1…
.((((((.(((((…)))))…((((…))))…)) ))))

Space
http://kws.eternadev.org/web/puzzle/1…
((((((((…(((((((… …)))))))…))))))))…

Spaces
http://kws.eternadev.org/web/puzzle/1…
(((((((.(((((((((((((((((((((((((((…))))))))))) )))))))…(((((…(((((((((((…))))))))))). …))))).)))))))))…)))))))

Space
http://kws.eternadev.org/web/puzzle/1…
…(.(…((((((…))))))…).)…((((…(((.(((((( (((…)))))…)))))))))))…((((((((…))))))))…

And that’s just in the first 60 or so…

Need a script to hunt them down and list them for manual repair.

I tried to write one, but it takes O(1s) to fetch each secondary structure string from the server and the script kept hanging/timing out my browser even when I set the timeout to some large number. This should probably be done by devops on the server. In the meantime, I’m striping/ignoring spaces in my scripts. :stuck_out_tongue:

I wonder how EteRNA is handling these, do they display properly and does energy calc function on them properly? Seems likely they strip spaces too.

Thanks for your report jandersonlee. But carefully test you script on dev server( kws.eternadev.org ) because all of data in dev server can be different from production server. I mean since dev server is completely separated from main one (even databases), it is possible that data has been corrupted during testing and far different from production server. Fortunately(?), both puzzles in dev and main have malformed data so I’ll fix it. Also this issue has been added our github issue tracker.

Thanks!!