Re: [Treebase-devel] Wrong SQL for NEXUS file download?

[William P. <wil...@ya...>]

I noticed this error too. For what it's worth, uploading nexus files that only contain tree blocks works fine -- so headless Mesquite is good with trees. 

This SQL error only applies to storing matrices. Anyone know what the GAP field is? I'm guessing that if a row x column element in a matrix has a gap (e.g. "-") then the boolean is set to true, but if the row x column element is a "missing" value (e.g. "?") or any other character, then it gets a DISCRETECHARSTATE_ID that matches to a set of records that lists all character states assigned to that element.  But that's just a guess.

bp


On Jan 26, 2010, at 5:23 PM, Vladimir Gapeyev wrote:

> 
> When I try to upload a NEXUS file at http://treebase-dev.nescent.org:6666/treebase-web/user/uploadFile.html, I get a stack dump. 
> The dump mentions SQL insert 
> 
> INSERT INTO MATRIXELEMENT
> (TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES
> ('D', default, 1, 0, 16000002157, 0, 4, 0)
> 
> When I try to run it by hand I get 
> 
> ERROR:  column "gap" is of type boolean but expression is of type integer
> LINE 3: ('D', default, 1, 0, 16000002157, 0, 4, 0)
>                           ^
> HINT:  You will need to rewrite or cast the expression.
> 
> --Vladimir 
>