[InterMine Dev] Error when running "ant build-db-userprofile".

Allan Kamau kamauallan at gmail.com
Mon Oct 1 11:22:16 BST 2012


Hi Julie,
Interesting I seem to been working with the development branch as you
had pointed out. A call to "git branch" returns "*dev".
But I have no clue as to how I ended up having the "dev" branch as
opposed to the "master" branch.

Now I have restarted the "Intermine" installation as follows.
In an empty directory I executed the following commands.
1)git clone git at github.com:git_username/intermine.git
followed by
2)git checkout master

I have edited the file "~/.intermine/malariamine.properties" according.
I have gone through to step 7.1 where "ant -Dsource=uniprot-malaria
-v" fails claiming at malariamine/integrate/src directory does not
exist. (yes directory "src" it does not exist in my
malariamine/integrate directory). Does the master branch have
"malariamine/integrate/src" directory?

BUILD FAILED
/apps/src/intermine.201210011222hrs/intermine/imbuild/library.xml:117:
The following error occurred while executing this line:
/apps/src/intermine.201210011222hrs/intermine/imbuild/library.xml:257:
srcdir "/apps/src/intermine.201210011222hrs/intermine/malariamine/integrate/src"
does not exist!


Allan.

On Mon, Oct 1, 2012 at 12:05 PM, Julie Sullivan <julie at flymine.org> wrote:
> Hi Allan
>
> We are going to be introducing the idea of "sharing" lists in InterMine 1.1.
> This feature is not on the 1.0 branch yet (master) it's only on dev. So
> whichever code generated the first error you sent was not on the master
> branch.
>
> From your last email I assume that you are now using the correct branch.
> Check this by running this command:
>
>         git branch
>
> And you should see something like:
>
>    dev
> *  master
>
> However you have built your databases using the wrong branch, and I think
> that may be causing errors. Can you drop and recreate your userprofile
> database?
>
>         dropdb userprofile (or whatever you named it)
>         createdb userprofile
>
> Then try the build-db-userprofile again?
>
> If that doesn't fix your problem, send us the log file and hopefully that
> will tell us what's going on!
>
> Thanks
> Julie
>
>
> On 30/09/12 15:23, Allan Kamau wrote:
>>
>> I had obtained the master branch using "git checkout master". I did a
>> full clone to a different directory today and when though all the
>> steps but got stuck once again at "ant -v build-db-userprofile".
>> Looking at the databases, I see database objects have been created
>> meaning that the access to the database server may not be the problem.
>>
>> Should I send the log file (about 165584 bytes in size) as an attachement?
>>
>> Allan.
>>
>> On Sun, Sep 30, 2012 at 10:37 AM,<julie at flymine.org>  wrote:
>>>
>>> Hi Allan
>>>
>>>  From your error message it looks like you are working off of the "dev"
>>> branch when you actually want to be using the "master" branch. The "dev"
>>> branch is what the InterMine developers are using and may not be tested
>>> thoroughly, the "master" branch is the latest stable InterMine release.
>>>
>>> Here's how to switch branches:
>>>
>>> http://git-scm.com/book/en/Git-Branching-Basic-Branching-and-Merging
>>>
>>> Here are our docs on getting the InterMine code:
>>>
>>> http://intermine.org/wiki/Git
>>>
>>> Julie
>>>
>>>> I am getting the error below when I run "ant build-db-userprofile"
>>>> from malariamine/webapp directory.
>>>>
>>>> What could be the cause of this error?
>>>>
>>>>
>>>> -do-build-db-userprofile:
>>>>   [build-db] Our new url ->
>>>> jdbc:postgresql://localhost/userprofile-malariamine
>>>>   [build-db] Our new url ->
>>>> jdbc:postgresql://localhost/userprofile-malariamine
>>>>
>>>> -load-default-templates:
>>>> [load-default-templates] Loading default templates and tags into
>>>> profile test_user at mail_account
>>>> [load-default-templates] java.lang.RuntimeException: Error retrieving
>>>> the bag with bagId : null
>>>> [load-default-templates]      at
>>>>
>>>> org.intermine.api.bag.SharedBagManager.getSharedBags(SharedBagManager.java:161)
>>>> [load-default-templates]      at
>>>> org.intermine.api.profile.Profile.getSharedBags(Profile.java:735)
>>>>
>>>> _______________________________________________
>>>> dev mailing list
>>>> dev at intermine.org
>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>>
>>>>
>>
>> _______________________________________________
>> dev mailing list
>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>



More information about the dev mailing list