On Mon, Nov 18, 2013 at 12:35 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Sun, Nov 17, 2013 at 8:30 AM, John Chilton wrote:
>> With these change, I was able to write working functional tests for
>> your tool using the template you outlined in the Trello card. ...
>> I discovered no problems with auto_primary versus basic composite
>> types here, just the things listed above.
>
> Not for me though, even if I rename the masking "file" param to
> avoid the ambiguous "file" parameters ...
>
> I find that changing the order of the <extra_files> tags in the test seems
> to alter the failure - which supports my hunch that something is
> scrambling the order of the extra files, so that it fails to compare the
> generated blastdb.phr with the provided four_human_proteins.fasta.phd

John's replies via Twitter:

https://twitter.com/jmchilton/status/402436500131807232
> @pjacock Hard to argue with @travisci but your makeblastdb
> test works unmodified on my box and I can reorder the extras.
> I'm still looking..

https://twitter.com/jmchilton/status/402446372231581696
> @pjacock Got it, you are overriding display_data in blast DB
> datatypes. This breaks much! Is how the test framework/API/etc
> access datasets.

There may be trouble ahead... the current display_data override
is to give some meaningful output to the user when they click
the "eye ball" icon for a BLAST database - rather than something
unhelpful and scary like a blank page.

A more slick option would be to override display_data to run
blastdbcmd live, but that means a run time dependency of the
datatype definition on (a specific version of) the BLAST+ binaries
- which could be problematic.

I had considered capturing the makeblastdb stdout to a file as
blastdb.log and having that as the (human viewable) primary
file of a composite datatype - but that would cause trouble if and
when I manage to support user uploaded BLAST databases.

Thanks,

Peter
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