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<div>It *might* be possible to set this up on Travis-CI independently on Bio::FeatureIO, which would be beneficial from a testing viewpoint (as we need to track what works w/ refactored FeatureIO vs what doesn’t). </div>
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<div>I suppose what we need to check with a refactor (master branch) is:</div>
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<div>1) Maintaining a sane amount of compat. with Chado. ‘Sane' meaning Bio::SF::Annotated will need to be chucked or completely reimplemented from scratch, as it is much less than sane now</div>
<div>2) If needed having a concurrently developed version of Chado to make it work.</div>
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<div>It may not require much on #2 if Chado isn’t reliant on some of the less API-friendly parts of Bio::SF::Annotated (namely the heavy annotation associated with it). </div>
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<div>chris</div>
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<div>
<div>On Sep 16, 2014, at 4:53 PM, George Hartzell <<a href="mailto:hartzell.george@gene.com">hartzell.george@gene.com</a>> wrote:</div>
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<p style="margin:1.2em 0px!important"><strong>@scott</strong>, do you have test setup for the GMOD stuff?</p>
<p style="margin:1.2em 0px!important">g.</p>
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<div class="gmail_quote">On Tue, Sep 16, 2014 at 1:41 PM, Fields, Christopher J <span dir="ltr">
<<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Cool! I guess I could probably announce this as being released at some point now :)
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<div>chris<br>
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<div>PS - I may have a decent test environment set up for longer-term evaluation, but it would be nice to see if we can get something working with travis-ci or a smoker setup, just so I can check whether the main branch refactoring is clobbering chado (as I
suspect it is). </div>
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<div>On Sep 16, 2014, at 1:50 PM, George Hartzell <<a href="mailto:hartzell.george@gene.com" target="_blank">hartzell.george@gene.com</a>> wrote:</div>
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<p style="margin:1.2em 0px!important">Hi All,</p>
<p style="margin:1.2em 0px!important">It took a while, but I was finally able to run my little litmus test and the good news is that it appears to pass.</p>
<p style="margin:1.2em 0px!important">I modified my ansible playbook that implements the steps described in
<a href="https://svn.code.sf.net/p/gmod/svn/schema/trunk/chado/INSTALL.Chado" target="_blank">
INSTALL.Chado</a> so that it uses the version of Bio::FeatureIO that is now on CPAN instead of pulling the github master.</p>
<p style="margin:1.2em 0px!important">The resulting installation ran to completion and then was able to load the yeast gff3 file:</p>
<pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;margin:1.2em 0px"><code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline;background-color:rgb(248,248,248);white-space:pre-wrap;overflow:auto;border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block!important">cp /vagrant/saccharomyces_cerevisiae.gff .
<a href="http://gmod_gff3_preprocessor.pl/" target="_blank">gmod_gff3_preprocessor.pl</a> --gfffile saccharomyces_cerevisiae.gff --outfile saccharomyces_cerevisiae.sorted.gff
<a href="http://gmod_bulk_load_gff3.pl/" target="_blank">gmod_bulk_load_gff3.pl</a> --organism yeast --gfffile saccharomyces_cerevisiae.gff.sorted
</code></pre>
<p style="margin:1.2em 0px!important">and the resulting database seems to be stitched together reasonably (though I’m not a particularly informed judge of its character).</p>
<p style="margin:1.2em 0px!important"><strong>@chris</strong> thanks for the help on this!!!!</p>
<p style="margin:1.2em 0px!important">g.</p>
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<div class="gmail_quote">On Sat, Aug 30, 2014 at 9:24 PM, George Hartzell <span dir="ltr">
<<a href="mailto:hartzell@alerce.com" target="_blank">hartzell@alerce.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<span>Fields, Christopher J writes:<br>
> Just a quick update on this: I released a separate Bio::FeatureIO<br>
> release to CPAN that represents the code split out from the core<br>
> modules:<br>
><br>
> <a href="https://metacpan.org/pod/Bio::FeatureIO" target="_blank">https://metacpan.org/pod/Bio::FeatureIO</a><br>
><br>
> I had to do some cleanup to get code to work and tests passing with<br>
> some sanity. A *lot* of things were not passing tests when we<br>
> moved this over.<br>
><br>
> This should represent what was last working with Chado though.<br>
> However, I haven’t officially announced anything yet b/c I would<br>
> like to shake bugs out of it. Can either of you try this out on a<br>
> Chado run to make sure everything is up to snuff (or at least point<br>
> out issues)? Time depending, I would like to get something running<br>
> on (for instance) Travis-CI, maybe including some optional<br>
> Chado-related stuff. This would also help so that we can work on<br>
> merging what has been done on master so that these pass the same<br>
> tests.<br>
<br>
</span>I can't do anything until Tuesday, but will be happy to run it through<br>
the standard Chado build process when I get back to work.<br>
<br>
Thanks for digging into it.<br>
<span><font color="#888888"><br>
g.<br>
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