[InterMine Dev] Error on web app deployment

Julie Sullivan julie at flymine.org
Mon Aug 3 09:07:16 BST 2015


Hi Paulo

You seem to be having trouble finding the AttributeDescriptor object.

Here I see your file contains no dependencies for the objectstore project:

https://github.com/WormBase/intermine/blob/dev/intermine/objectstore/main/project.properties

Compared with the InterMine file which has a dependency on the Model 
project, where the "AttributeDescriptor" class lives.

https://github.com/intermine/intermine/blob/beta/intermine/objectstore/main/project.properties

It would make sense that you are having issues if your dependencies are 
wrong. Do you know how this might have happened? Why your file is different?

This change was done in April 2014 so it was part of InterMine 1.4.

I assume you are using InterMine 1.4? Maybe you had a merging problem? 
Or need to do a clean? Can you look at the project properties file for 
the objectstore project (the project that is generating the error 
below), and confirm it does depend on the model project?

Let me know what you find!
Julie


On 03/08/15 07:56, Paulo Nuin wrote:
> Hi
>
> In our attempt to have an updated version of WormMine, we are having
> trouble deploying the Tomcat web app. The error happens on some javac
> compilation steps:
>
> [dependencies] warning: [options] bootstrap class path not set in
> conjunction with -source 1.6
> [dependencies]
> /mnt/data/intermine/intermine/objectstore/main/src/org/intermine/codegen/JavaModelOutput.java:512:
> error: cannot find symbol
> [dependencies] if (attr.isPrimitive() || attr.isNumeric()) {
> [dependencies]                              ^
> [dependencies]   symbol:   method isNumeric()
> [dependencies]   location: variable attr of type AttributeDescriptor
> [dependencies]
> /mnt/data/intermine/intermine/objectstore/main/src/org/intermine/modelproduction/ModelMerger.java:95:
> error: cannot find symbol
> [dependencies]                     original.getVersion(), new
> HashSet<ClassDescriptor>(newClasses.values()));
> [dependencies]                             ^
> [dependencies]   symbol:   method getVersion()
> [dependencies]   location: variable original of type Model
> [dependencies] Note:
> /mnt/data/intermine/intermine/objectstore/main/src/org/intermine/objectstore/query/QueryField.java
> uses or overrides a deprecated API.
> [dependencies] Note: Recompile with -Xlint:deprecation for details.
> [dependencies] Note: Some input files use unchecked or unsafe operations.
> [dependencies] Note: Recompile with -Xlint:unchecked for details.
> [dependencies] 2 errors
> [dependencies] 1 warning
>       [null] Exiting
> /mnt/data/intermine/intermine/objectstore/main/build.xml.
>
>
> The problems seem to be in attire.isNumeric and original.getVersion().
>
> Any help is appreciated.
>
> Thanks
>
> Paulo
>



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