Re: [galaxy-dev] Tabular data not displaying in main panel

Hi Sam,

any chance to commit that fix to Galaxy-stable?

Thanks! Bjoern

Thanks Eric. I updated the data.js file in an attempt to catch this error.

On Thu, Oct 3, 2013 at 12:14 PM, Eric Rasche rasche.eric@yandex.ru wrote: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1

    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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