[InterMine Dev] Tweaking the webapp

JD Wong jdmswong at gmail.com
Thu Sep 29 22:50:53 BST 2011


If anyone encounters my problem: It turned out the webapp used the GOTerm
class which is only included in the data model if the GO source is included.
 I copied the go source model additions into the core model and everything
worked fine.  Please include this in the next bug fix!

The most recent version of 0_97 didn't solve my issues: black on black text,
error dialog in gene report.  Is there a more recent version (with bugfixes)
I can download?

Thanks!
-JD

On Thu, Sep 29, 2011 at 12:57 PM, JD Wong <jdmswong at gmail.com> wrote:

> Hi Julie,
>
> I downloaded the most recent version (0.97), and replaced my old 0_97
> folder with it, building the data warehouse until ant -v
> build-db-userprofile throws me this:
>
> [dependencies]
> /home/jdmswong/intermine_0_97/bio/webapp/src/org/intermine/bio/web/displayer/GeneOntologyDisplayer.java:30:
> cannot find symbol
> [dependencies] symbol  : class GOTerm
> [dependencies] location: package org.intermine.model.bio
> [dependencies] import org.intermine.model.bio.GOTerm;
> [dependencies]                               ^
> ...........
> BUILD FAILED
> /home/jdmswong/intermine_0_97/imbuild/library.xml:78: The following error
> occurred while executing this line:
> /home/jdmswong/intermine_0_97/imbuild/library.xml:118: The following error
> occurred while executing this line:
> /home/jdmswong/intermine_0_97/imbuild/library.xml:258: Compile failed; see
> the compiler error output for details.
>  at org.apache.tools.ant.taskdefs.Javac.compile(Javac.java:1150)
> at org.apache.tools.ant.taskdefs.Javac.execute(Javac.java:912)
>  at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> at sun.reflect.GeneratedMethodAccessor49.invoke(Unknown Source)
>  at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
>  at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
>  at org.apache.tools.ant.taskdefs.Sequential.execute(Sequential.java:68)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>  at sun.reflect.GeneratedMethodAccessor49.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>  at java.lang.reflect.Method.invoke(Method.java:597)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>  at org.apache.tools.ant.Task.perform(Task.java:348)
> at
> org.apache.tools.ant.taskdefs.MacroInstance.execute(MacroInstance.java:398)
>  at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> at sun.reflect.GeneratedMethodAccessor49.invoke(Unknown Source)
>  at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
>  at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
>  at org.apache.tools.ant.Target.execute(Target.java:390)
> at org.apache.tools.ant.Target.performTasks(Target.java:411)
>  at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
> at
> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>  at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
> at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
>  at org.intermine.task.Dependencies.execute(Dependencies.java:304)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>  at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>  at java.lang.reflect.Method.invoke(Method.java:597)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>  at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:390)
>  at org.apache.tools.ant.Target.performTasks(Target.java:411)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
>  at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
> at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>  at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
> at org.apache.tools.ant.Main.runBuild(Main.java:809)
>  at org.apache.tools.ant.Main.startAnt(Main.java:217)
> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>  at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>
> I could copy/paste the GOTerm.class from flymine/dbmodel/build, but is
> there a more proper way of resolving this error?
>
> Thanks!
> -JD
>
>
> On Thu, Sep 29, 2011 at 3:58 AM, Julie Sullivan <julie at flymine.org> wrote:
>
>> Hi JD
>>
>> 1. the black on black is a bug that's fixed in InterMine 0.98.  I think it
>> was fixed in 0.97 actually.  Can you do an svn update and re-release your
>> webapp?
>> 2. I'll forward you the docs on how to update the theme for your webapp.
>> 3. the intermine links bug is fixed in InterMine 0.98.  The report page is
>> report.jsp.  If you want to remove that displayer manually, remove the tile
>> labeled "friendlyMinesLinks".
>>
>> Remember that custom changes you make in intermine/webapp have to be
>> merged back in every time you do an upgrade.  This can be tedious, difficult
>> or impossible if the core code has been modified.
>>
>>
>> On 28/09/11 23:20, JD Wong wrote:
>>
>>> Hi dev,
>>>
>>> I am trying to change a few aspects of the webapp away from the default
>>> such
>>> as: changing the text color on the table report page away from black on
>>> black, changing the mosquito logo to a fly one, and removing the 'link to
>>> other intermines' section that throws error dialogs.  Are these easy ways
>>> of
>>> doing these things (and others), besides checking out all the jsps
>>> in /intermine/webapp/main/**resources/webapp/ :)
>>>
>>> Thanks!
>>> -JD
>>>
>>>
>>>
>>>
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>>> dev mailing list
>>> dev at intermine.org
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>>>
>>
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>>
>
>
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