As it turns out, the automated testing framework was not correctly
handling the situation where dataset metadata is set externally. I've
committed a fix for that in 10295:59243394031a, and this should result
in seq_rename now being correctly tested.
When it comes to the sniffer situation, I've created a trello card for
that issue, where you can track the status:
On 8/2/13 05:14:54.000, Peter Cock wrote:
On Thu, Aug 1, 2013 at 8:43 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
As of 10290:d34d6d1da813, nsltradamus and effectivet3 should start returning
valid test results.
Great - so this was a sniffer bug for the twobit format going wrong,
As for seq_rename, it looks like the columns in
four_human_proteins.rename.tabular are not being detected correctly, even
though they are tab separated. I'll continue to investigate, and let you
know what I discover.
I was assuming (wrongly perhaps) that if the tool XML for the test
defined an ftype this would be used as the datatype - overriding
any sniffer guess (or even skipping the sniffer tests).
(You can think of this a like testing the process where a user has
uploaded a given file and manually overridden the datatype.)
i.e. It is good that this issue has apparently uncovered some
sniffer bugs, but that doesn't seem to be the root issue.
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