missing hibernate libraries in April 2014 version of Web Apollo?

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missing hibernate libraries in April 2014 version of Web Apollo?

Monica Poelchau
Hi everyone,

We were having trouble getting the chado adapter to work for the April 2014 version of Web Apollo. It looks like the problem was missing hibernate libraries in WEB-INF/lib/ - once we installed them, the chado export worked fine. 

Has anyone else experienced the same problem? Would it be possible to double-check to make sure that the correct hibernate libraries are in the current distribution of Web Apollo?

Thanks!

Monica
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Re: missing hibernate libraries in April 2014 version of Web Apollo?

Colin
Hi Monica,

I think you are correct. I get errors like "java.lang.ClassNotFoundException: org.hibernate.HibernateException" in a stack trace when doing Chado export. I also see that there are many missing libs in WEB-INF/lib in the 2014-04-03 version. From my notes, this version is lacking pretty much all GBOL libs, so I added the GBOL libs back into our build environment so we can get this fixed in the future.

As you mentioned though, to patch the problem, you can also copy the jar files from WEB-INF/libs from an older release into the latest one to fix it as well.

Thanks for the report!

-Colin




On Wed, Jun 25, 2014 at 1:24 PM, Monica Poelchau <[hidden email]> wrote:
Hi everyone,

We were having trouble getting the chado adapter to work for the April 2014 version of Web Apollo. It looks like the problem was missing hibernate libraries in WEB-INF/lib/ - once we installed them, the chado export worked fine. 

Has anyone else experienced the same problem? Would it be possible to double-check to make sure that the correct hibernate libraries are in the current distribution of Web Apollo?

Thanks!

Monica

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Re: missing hibernate libraries in April 2014 version of Web Apollo?

Suzanna Lewis-3
Hi Monica and all,

My sincere apologies for the extra work you've had to do because of this. This really shouldn't have slipped out the door without these libraries. We're starting to work right away to get a complete release out as soon as we can.

Hi Colin,

To that end, we must get a release out as soon as possible that includes the missing libraries. It doesn't need to have all of the latest features you and the hackathon crew have been working on. Just what's in the staging area plus any necessary patches that overlay this. Would you look at this and send Chris and I an estimate of when it might be done. (naturally you should discuss with Chris there). But we need to let the community know.

Thanks once more Monica!

-S





On Wed, Jun 25, 2014 at 1:19 PM, Colin <[hidden email]> wrote:
Hi Monica,

I think you are correct. I get errors like "java.lang.ClassNotFoundException: org.hibernate.HibernateException" in a stack trace when doing Chado export. I also see that there are many missing libs in WEB-INF/lib in the 2014-04-03 version. From my notes, this version is lacking pretty much all GBOL libs, so I added the GBOL libs back into our build environment so we can get this fixed in the future.

As you mentioned though, to patch the problem, you can also copy the jar files from WEB-INF/libs from an older release into the latest one to fix it as well.

Thanks for the report!

-Colin




On Wed, Jun 25, 2014 at 1:24 PM, Monica Poelchau <[hidden email]> wrote:
Hi everyone,

We were having trouble getting the chado adapter to work for the April 2014 version of Web Apollo. It looks like the problem was missing hibernate libraries in WEB-INF/lib/ - once we installed them, the chado export worked fine. 

Has anyone else experienced the same problem? Would it be possible to double-check to make sure that the correct hibernate libraries are in the current distribution of Web Apollo?

Thanks!

Monica


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Re: missing hibernate libraries in April 2014 version of Web Apollo?

Divakaran Karunakaran
Can someone please tell me how to un enroll from this group ?

On Wednesday, June 25, 2014, Suzanna Lewis <[hidden email]> wrote:
Hi Monica and all,

My sincere apologies for the extra work you've had to do because of this. This really shouldn't have slipped out the door without these libraries. We're starting to work right away to get a complete release out as soon as we can.

Hi Colin,

To that end, we must get a release out as soon as possible that includes the missing libraries. It doesn't need to have all of the latest features you and the hackathon crew have been working on. Just what's in the staging area plus any necessary patches that overlay this. Would you look at this and send Chris and I an estimate of when it might be done. (naturally you should discuss with Chris there). But we need to let the community know.

Thanks once more Monica!

-S





On Wed, Jun 25, 2014 at 1:19 PM, Colin <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;colin.diesh@gmail.com&#39;);" target="_blank">colin.diesh@...> wrote:
Hi Monica,

I think you are correct. I get errors like "java.lang.ClassNotFoundException: org.hibernate.HibernateException" in a stack trace when doing Chado export. I also see that there are many missing libs in WEB-INF/lib in the 2014-04-03 version. From my notes, this version is lacking pretty much all GBOL libs, so I added the GBOL libs back into our build environment so we can get this fixed in the future.

As you mentioned though, to patch the problem, you can also copy the jar files from WEB-INF/libs from an older release into the latest one to fix it as well.

Thanks for the report!

-Colin




On Wed, Jun 25, 2014 at 1:24 PM, Monica Poelchau <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;mpoelchau@gmail.com&#39;);" target="_blank">mpoelchau@...> wrote:
Hi everyone,

We were having trouble getting the chado adapter to work for the April 2014 version of Web Apollo. It looks like the problem was missing hibernate libraries in WEB-INF/lib/ - once we installed them, the chado export worked fine. 

Has anyone else experienced the same problem? Would it be possible to double-check to make sure that the correct hibernate libraries are in the current distribution of Web Apollo?

Thanks!

Monica


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Re: missing hibernate libraries in April 2014 version of Web Apollo?

Monica Poelchau
In reply to this post by Suzanna Lewis-3
Hi Suzi,

The thanks go to our intrepid grad student Han for figuring this out, and to you guys for developing such a great tool and being so prompt with your user support!

Best,

Monica


On Wed, Jun 25, 2014 at 5:00 PM, Suzanna Lewis <[hidden email]> wrote:
Hi Monica and all,

My sincere apologies for the extra work you've had to do because of this. This really shouldn't have slipped out the door without these libraries. We're starting to work right away to get a complete release out as soon as we can.

Hi Colin,

To that end, we must get a release out as soon as possible that includes the missing libraries. It doesn't need to have all of the latest features you and the hackathon crew have been working on. Just what's in the staging area plus any necessary patches that overlay this. Would you look at this and send Chris and I an estimate of when it might be done. (naturally you should discuss with Chris there). But we need to let the community know.

Thanks once more Monica!

-S





On Wed, Jun 25, 2014 at 1:19 PM, Colin <[hidden email]> wrote:
Hi Monica,

I think you are correct. I get errors like "java.lang.ClassNotFoundException: org.hibernate.HibernateException" in a stack trace when doing Chado export. I also see that there are many missing libs in WEB-INF/lib in the 2014-04-03 version. From my notes, this version is lacking pretty much all GBOL libs, so I added the GBOL libs back into our build environment so we can get this fixed in the future.

As you mentioned though, to patch the problem, you can also copy the jar files from WEB-INF/libs from an older release into the latest one to fix it as well.

Thanks for the report!

-Colin




On Wed, Jun 25, 2014 at 1:24 PM, Monica Poelchau <[hidden email]> wrote:
Hi everyone,

We were having trouble getting the chado adapter to work for the April 2014 version of Web Apollo. It looks like the problem was missing hibernate libraries in WEB-INF/lib/ - once we installed them, the chado export worked fine. 

Has anyone else experienced the same problem? Would it be possible to double-check to make sure that the correct hibernate libraries are in the current distribution of Web Apollo?

Thanks!

Monica