Ok so to amend my earlier question, thinking about it I took a look at the security settings which I hadn't really examined before, and found these settings enabled. I wasn't expecting this since I could query manually, but disabling that for testing did lead me to a new error:
org.openrdf.query.QueryEvaluationException: no result format specified or unsupported result format org.openrdf.repository.sparql.query.SPARQLTupleQuery.evaluate(SPARQLTupleQuery.java:59) org.openrdf.query.algebra.evaluation.federation.SPARQLFederatedService.evaluate(SPARQLFederatedService.java:150) org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:332) org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl.evaluate(EvaluationStrategyImpl.java:586) ... This error is being sent back from Marmotta since it's not happy with the lack of an output parameter.. or multiple accepts headers. I'm not sure yet how the source query is being generated, but it does look like the openrdf library is likely adding multiple accept headers much like: https://issues.apache.org/jira/browse/MARMOTTA-585 (In HttpClient.sendTupleQueryViaHttp as a reference) So it looks like this is likely the source, and I'll go down this path for the time being. Thanks! paul