Yes, the debugger is my tool of choice as well. Another important 
breakpoint is gt-app-schema 
DataAccessMappingFeatureIterator.computeNext, where you can see features 
being built and check their content:
https://github.com/geotools/geotools/blob/master/modules/extension/app-schema/app-schema/src/main/java/org/geotools/data/complex/DataAccessMappingFeatureIterator.java#L968

Other things to try before the debugger include targetAttributeNode if 
your types are too general, although app-schema is now quite good at 
searching substitution groups.

Kevin, what elements are missing and what is their type?

Kind regards,
Ben.

On 09/12/16 05:03, Nuno Oliveira wrote:
> Hello,
>
> I have the same issue and unfortunately I didn't find any nice way to
> troubleshot this kind of problems too.
> So if someone knows a better way to do this kind of trouble shooting I
> would love to hear it too.
>
> So far I rely on debugging to understand what I "did wrong" with my
> mappings.
> I typically put a debug point around this lines and check if the complex
> entity as all the expected info:
> https://github.com/geotools/geotools/blob/master/modules/extension/xsd/xsd-core/src/main/java/org/geotools/xml/Encoder.java#L759-L775
>
> In my case when I don't get the data encoded this typically means that
> the Encoder doesn't like my XML schema and refuses to encode the data.
> So try to paste the excerpt of your schema that is not encoded here with
> some context (the schema and the mappings) and maybe someone will give
> you some feedback (I will try).
>
> Regards,
>
> Nuno Oliveira
>
> On 12/08/2016 02:52 PM, kweis...@harris.com wrote:
>> Hello again everyone,
>> I'm working on creating some app-schema mapping files for some complex 
>> schemas and have been having a few issues.  Specifically, I've got some 
>> elements that for some reason refuse to populate.  I don't get any errors 
>> during boot up nor when a request is processed, the element is just omitted 
>> in the final output.  With verbose logging enabled it appears that the data 
>> is loaded.  A TRACE log message [org.geotools.data.complex.filter] displays 
>> when a request is made and does contain the element (and sub-elements) in 
>> question.
>>
>> I'm curious if there's any additional troubleshooting I can perform to 
>> figure out this issue.
>>
>> GeoServer: 2.10.0
>> Tomcat: 8.0.33
>>
>> Thanks,
>>
>> Kevin M. Weiss
>> Software Engineer
>> CRITICAL NETWORKS / HARRIS CORPORATION
>> harris.com  / kevin.we...@harris.com
>>
>>
>>
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-- 
Ben Caradoc-Davies <b...@transient.nz>
Director
Transient Software Limited <http://transient.nz/>
New Zealand

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