[InterMine Dev] Tweaking the webapp

Julie Sullivan julie at flymine.org
Fri Sep 30 08:49:38 BST 2011


Sorry JD!  These issues are resolved in 0.98 which will (probably) be released 
on Monday.

On 29/09/11 22:50, JD Wong wrote:
> 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
>>>>
>>>>
>>>>
>>>>
>>>> ______________________________**_________________
>>>> dev mailing list
>>>> dev at intermine.org
>>>> http://mail.intermine.org/cgi-**bin/mailman/listinfo/dev<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<http://mail.intermine.org/cgi-bin/mailman/listinfo/dev>
>>>
>>
>>
>



More information about the dev mailing list