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

Allan Kamau kamauallan at gmail.com
Mon Oct 1 11:41:08 BST 2012


It worked I did the following while my working directory is
"malariamine/integrate".

mkdir src;mkdir resources;


Step 7.1 completes successfully.


On Mon, Oct 1, 2012 at 1:28 PM, Julie Sullivan <julie at flymine.org> wrote:
> Try this:
>
>         mkdir intermine/malariamine/integrate/src
>
> And then do step 7.1 again.
>
> When we added our code to Github, we didn't realise git didn't include empty
> directories. Our ant tasks are dumb and don't expect the directories to be
> missing so we get these errors. I thought I had all of them fixed but
> apparently not!
>
>
>
> On 01/10/12 11:22, Allan Kamau wrote:
>>
>> 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
>>>>>>
>>>>>>
>>>>
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>>>> dev mailing list
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>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>>
>>>
>>
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>



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