[Biojava-dev] Scop page seems to be gone, build is broken.

[Andreas Prlic]

actually, to support the new berkeley-scop version 1.75C we needed a small
patch in ScopFactory... just got committed... did a quick and dirty check
and it looks like there was no change in the file formats, so all is
working as expected.

Andreas


On Mon, Oct 14, 2013 at 3:26 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:

> It looks like MRC SCOP is back up, so the tests should pass again.
>
> 1.75C should be accessible by passing a custom version to the
> BerkeleyScopInstallation class, but I haven't done any tests on it.
>
> BTW, I've been slowly working on a more complete set of tests for the scop
> package. There's still a bit of stubbed out functionality in
> RemoteScopInstallation that needs to get finished before they all pass and
> I can check them in.
>
> -Spencer
>
>
> On Mon, Oct 14, 2013 at 1:27 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
>> Hi Steve,
>>
>> I have not tried it yet, is anything broken for you? The last few times
>> they kept the files exactly the same, so it was easy to switch between
>> versions...
>>
>> Andreas
>>
>>
>> On Mon, Oct 14, 2013 at 1:18 PM, Steve Darnell <darnells at dnastar.com>
>> wrote:
>>
>> > Greetings,
>> >
>> > I read in the PDB mailing list that SCOP and ASTRAL were updated to
>> > version 1.75C last Thursday (10/10/2013). Did they make any changes to
>> > break to Scop services in Biojava?
>> >
>> > ~Steve
>> >
>> > -----Original Message-----
>> > From: biojava-dev-bounces at lists.open-bio.org [mailto:
>> > biojava-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic
>> > Sent: Sunday, October 13, 2013 11:28 PM
>> > To: John Chilton
>> > Cc: biojava-dev at lists.open-bio.org
>> > Subject: Re: [Biojava-dev] Scop page seems to be gone, build is broken.
>> >
>> > Hi John,
>> >
>> > yes, you are right, it looks as if SCOP is currently down. Uncommenting
>> > the junit test is prob a good temporary fix, until they are back online
>> > again.
>> >
>> > Andreas
>> >
>> >
>> > On Sun, Oct 13, 2013 at 9:05 PM, John Chilton <jchilton22 at gmail.com>
>> > wrote:
>> >
>> > > ATTN Andreas Prlic, you are listed as an author on ScopInstallation.
>> > >
>> > > I'm trying to do a "mvn install" to run tests and generate a working
>> > > jar but getting the following:
>> > >
>> > > Tests in error:
>> > >   ScopInstallationTest.testComments:41 ? NullPointer
>> > >
>> > > Debugging the test found that the Scop file download location seems to
>> > > be down (the ScopInstallation class tries to download "
>> > > http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.com.scop.txt_1.75").
>> > >
>> > > Indeed, even the link to the homepage from Google is down. I will keep
>> > > trying through the week, but in case the page is actually gone, how
>> > > would you like to proceed?
>> > >
>> > > I will comment out this test for now.
>> > >
>> > > John Chilton
>> > > _______________________________________________
>> > > biojava-dev mailing list
>> > > biojava-dev at lists.open-bio.org
>> > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>> > >
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