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

[Steve Darnell]

Hi Andreas,

I'm sorry, but I didn't read John's email carefully. He was referring to a file for SCOP at Cambridge (BTW, the link is functional again). The update that I referred to was for SCOP at Berkeley. I don't use the SCOP functionality in BioJava, so I can't comment on whether the updated changed anything. The SCOP version number (e.g. 1.75C) is in the Berkeley filename. I imagine BioJava is referring directly to 1.75B, so I wouldn't expect any problems since the old versions are still hosted.

~Steve

From: andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] On Behalf Of Andreas Prlic
Sent: Monday, October 14, 2013 3:28 PM
To: Steve Darnell
Cc: John Chilton; biojava-dev at lists.open-bio.org
Subject: Re: [Biojava-dev] Scop page seems to be gone, build is broken.

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<mailto: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> [mailto: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<mailto: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<mailto: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
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> biojava-dev mailing list
> biojava-dev at lists.open-bio.org<mailto:biojava-dev at lists.open-bio.org>
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>
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