Scripting Interface Feedback

Feedback Feature Suggestions
1

Scripting Interface Feedback

linked from scripting page

2

well, I dream of

Lib.foldWithConstraint(sequence, constraint)

and

Lib.energyOfStruct(sequence, structure)

3

I’d *love* to see an RNAsubopt-like hook that gave back up to some number of alternative shapes within so many kcals of the MFE solution, sorted by energy.

Lib.RNAsubopt(sequence, maxDeltaKcal, maxShapes)

e.g.:

Lib.RNAsubopt(“AGCGAAAGCGAAAGCA”, 2.0, 10)

returns:

[[’.((…))…’, -1.40], [’…((…)).’, -1.20]]

but using the EteRNA energy model (of course).

4

Hi,

I just noticed that (some of) the scripting interface is actually active on the main server, so I started playing with it.

Ran into an issue with this submitted script http://eterna.cmu.edu/web/script/2426641/, I swear it works before submitting it, but once submitted, it’s “dead”, no reactions any more (and sorry for the clutter, please just delete the 2 other copies)

5

Hi again,

I just submitted a little utility http://eterna.cmu.edu/web/script/2443… and although I selected the ‘etc’ category, it seems the script was tested as if it had been declared a ‘puzzle solving’ one. Not sure this is a problem or not, but that doesn’t look very logical to me…

6

Currently

Lib.getStructure(puzzle id)

doesn’t work for me, error says that getSync() method doesn’t exist (which seems correct)

The pervasive clear() is not instantiated/initialized

ReferenceError: clear is not defined

 BuilderScriptPage.prototype.initialize\_pervasives = function() { 
 return eval("window.out=this.out;window.outln=this.outln;"); 
 };
7

Please provide a sample script on how to use the Test Tutorials button.

9

I’ve been trying to get something out of it, but no luck so far. Here’s what I found out :

  • the scripts are executed on the server-side for this part of the testing
  • they are run with a secondary structure (not a puzzle id) as first parameter
  • the javascript interpretor on the server-side is a lot more sensitive to coding-style, and won’t accept a number of “natural” constructs that you can see on client-side scripts.
  • the server isn’t ready yet to accept submissions, since I get “RNAElement is not defined” when I try to test a script of mine (after cleaning the syntax to make acceptable by the server interpretor). Which means, the server-side environment doesn’t know that class, and has not been fully prepared yet

Hope this helps.

10

Puzzle 553817 seems difficult to parse for the RNA/RNAElement classes. The loop at base 35 is not marked as multiloop, and much worse, the loop at 97 is missing…

I’m starting to wonder… Is this the right place for reporting bugs and/or issues ?

12

I ran your script just before now and it completely made randome names without error. please heck out script again!!

14

Yes, you’re right nando. I also think only puzzle solving script be tested.

Thank you for your report and the issue has been added github issue tracker

at

https://github.com/EteRNAgame/EteRNA-…

16

Thanks for your report.

This has been added to our issue tracker with ticker number #122

You can check the issue at

https://github.com/EteRNAgame/EteRNA-…

Thanks for your idea!

EteRNA team

18

Thanks jincol. Your opinion has been added to our issue tracker with

ticker number #123

https://github.com/EteRNAgame/EteRNA-…

Test tutorials button will be changed to “Test on player puzzles” button.

This button will send your script to remote evaluation server.

The evaluation server will randomly get the information of player puzzles base on

how many people solved that puzzle. From now on, the evaluation server

get one 0 people solved puzzle, one 1~5 people solved puzzle, one 6~10 and so on…

After that, the server will evaluate your script with puzzle information.

The server automatically put puzzle’s secondary structure as first parameter.

So if you want your script be evaluated correctly, you have to make your

script getting first parameter as secondary structure.

And finally the test result will be send back to the main server and the script

will be saved.

I’m sorry but the remote evaluation server isn’t perfect now but you can think

evaluation environment is perfectly same with main server. Thank you!!

20

I’m really sorry for my late response. I’ll fix bug in RNA/RNAElement classes as soon as possible.

Your opinion has been added to our issue tracker with ticker number #124

at

https://github.com/EteRNAgame/EteRNA-…

Thank you!!

22

This has been added to our issue tracker with ticker number #125

You can check the issue at

https://github.com/EteRNAgame/EteRNA-…

Thank your!!

23

Thanks for answering, kws4769

Another one: Lib.EternaScript() is not working for me at the moment…

25

Yes, the problem apparently corrected itself, a few hours or days after I reported the problem here.

27

I assume the return value is the sequence to solve the puzzle. Also, can you add the puzzle id to the input? I would prefer it as the first parameter, but passing it as the second parameter will do. Thanks

29

Thanks for your report!!

Your opinion has been added to our issue tracker with ticker number #129

at

https://github.com/EteRNAgame/EteRNA-…

31

This has been added to our issue tracker with ticker number #132

You can check the issue at

https://github.com/EteRNAgame/EteRNA-…

Thank your!!