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I see the same issue, repeatedly on my galaxy instance. Running
unmodified from the galaxy-dist/default branch.

Since I'm running the uncompressed data.js, I get a bit more information
from my errors than Peter's

> [10:05:12.293] TypeError: j is undefined @
> http://xxx/galaxy/static/scripts/mvc/data.js:1
> [10:05:12.291] "TabularButtonTrackster : Chromosome column
> undefined."

Mine points to line 188 in data.js, specifically the "else if" in this
function.

    _renderCell: function(cell_contents, index, colspan) {
        var column_types = this.model.get_metadata('column_types');
        if (colspan !== undefined) {
            return $('<td>').attr('colspan',
colspan).addClass('stringalign').text(cell_contents);
        }
        else if (column_types[index] === 'str' || column_types === 'list') {
            /* Left align all str columns, right align the rest */
            return $('<td>').addClass('stringalign').text(cell_contents);
        }
        else {
            return $('<td>').text(cell_contents);
        }
    },

I get an error:

"Uncaught TypeError: Cannot read property '0' of undefined", indicating
that upon attempting to read index 0 of "column_types" it determines
that column_types is null.

I commented out the else-if block and found that everything else was
working, it just rendered as right aligned.

Hope this helps!

Eric Rasche

On 10/03/2013 10:44 AM, Peter Cock wrote:
> The good news is that running the default branch from galaxy-central
> seems to work, so at some point the fix/change/regression should
> reach the stable releases on galaxy-dist as well.
>
> Peter
>
>
> On Thu, Oct 3, 2013 at 3:12 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
>> On Thu, Oct 3, 2013 at 2:47 PM, sam guerler <aysam.guerler@gmail.com> wrote:
>>> Hi Peter,
>>>
>>> I cannot reproduce the type error you are observing, but that one might be
>>> critical. The second message is rather an information than an error message.
>>> Is it possible that data.js is modified in your local galaxy version? You
>>> could apply an hg diff on data.js or maybe send the first few code lines in
>>> order verify this?
>>>
>>> Thanks,
>>> Sam
>>
>> Thanks Sam,
>>
>> Unfortunately my data.js seems to match galaxy-dist perfectly:
>>
>> $ wget https://bitbucket.org/galaxy/galaxy-dist/raw/c42567f43aa762a45f7eb7fc0917260edcaa5636/static/scripts/mvc/data.js
>> ...
>> $ diff data.js /mnt/galaxy/galaxy-dist/static/scripts/mvc/data.js
>> (no difference)
>>
>> I wonder if part of the issue is which tool created the tabular file, and
>> if it uses some of the special column names like chromosome etc.
>> The tools I've noticed this with do not use column name metadata
>> (but do tend to have a #comment line with column names as the
>> first line).
>>
>> Peter

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