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

Allan Kamau kamauallan at gmail.com
Mon Oct 1 13:38:02 BST 2012


I needed to create the following directories for the step "11.2 Run
the post-processing" to conclude successfully.
>From within "malariamine/postprocess" directory,
mkdir main/src/;mkdir main/resources;mkdir src;


I was able to run the entire example including section 13.4
successfully and I can access the new intermine installation on the
server via my web-browser.

A minor note with section "13.3 Deploying the webapp".
When installing intermine on Debian with tomcat installed via the
package manager. The tomcat installation may not have the tomcat
"manager" web application installed, "apt-get install tomcat6-admin"
does install it. This process is not required when using the
standalone self contained tomcat binary packaging downloaded from the
apache web site.

Thank you Julie, Fengyuan and others who guided me through my first
setup of Intermine.

Allan.

On Mon, Oct 1, 2012 at 1:41 PM, Allan Kamau <kamauallan at gmail.com> wrote:
> 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
>>>>>>>
>>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>
>>



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