Some BII Explanatory code.

Snippet--output

MS/SPEC Raw Data > JIC107_GlucoseO2_0.20_External_2_1.txt (meas:metabolite profiling, tech: mass spectrometry)
MS/SPEC Derived Data > PRIDE_Exp_Complete_Ac_8763.xml (meas:protein expression profiling, tech: mass spectrometry)
MS/SPEC Raw Data > spectrum.mzdata (meas:protein expression profiling, tech: mass spectrometry)
MS/SPEC Derived Data > PRIDE_Exp_Complete_Ac_8762.xml (meas:protein expression profiling, tech: mass spectrometry)
MS/SPEC Derived Data > PRIDE_Exp_Complete_Ac_8761.xml (meas:protein expression profiling, tech: mass spectrometry)
MS/SPEC Derived Data > PRIDE_Exp_Complete_Ac_8763.xml (meas:protein expression profiling, tech: mass spectrometry)
MS/SPEC Derived Data > PRIDE_Exp_Complete_Ac_8763.xml (meas:protein expression profiling, tech: mass spectrometry)
MS/SPEC Derived Data > PRIDE_Exp_Complete_Ac_8761.xml (meas:protein expression profiling, tech: mass spectrometry)
MS/SPEC Derived Data > PRIDE_Exp_Complete_Ac_8763.xml (meas:protein expression profiling, tech: mass spectrometry)
MS/SPEC Derived Data > PRIDE_Exp_Complete_Ac_8761.xml (meas:protein expression profiling, tech: mass spectrometry)
MS/SPEC Derived Data > PRIDE_Exp_Complete_Ac_8761.xml (meas:protein expression profiling, tech: mass spectrometry)
MS/SPEC Derived Data > PRIDE_Exp_Complete_Ac_8762.xml (meas:protein expression profiling, tech: mass spectrometry)
MS/SPEC Derived Data > PRIDE_Exp_Complete_Ac_8761.xml (meas:protein expression profiling, tech: mass spectrometry)

.... and so on.

Snippet.java

//Given this piece of code

Investigation investigation = validator.getStore().valueOfType(Investigation.class);
        for(Study study : investigation.getStudies()) {

            for (Assay assay : study.getAssays()) {
                Collection<AssayResult> results = ProcessingUtils.findAllDataInAssay(assay);

                for(AssayResult assayResult : results) {
                    out.println(assayResult.getData().getType().getName() + " > " + assayResult.getData().getUrl() + " (meas:" + assay.getMeasurement().getName() + ", tech: " + assay.getTechnologyName() + ")");
                }
            }
        }

// utilising this method in ProcessingUtils

/**
     * An helper that finds all the AssayResults related to the assay parameter. It is based on the experimental pipeline
     * the assay's material belong in. 
     */
    public static Collection<AssayResult> findAllDataInAssay ( Assay assay )
    {
        if ( assay == null )
            throw new RuntimeException ( "findAllDataInAssay(): null assay passed to the method" );

        Material material = assay.getMaterial ();
        if ( material == null )
            throw new RuntimeException ( "findAllDataInAssay( " + assay + "): no material associated to the assay" );

        final Study study = assay.getStudy ();
        if ( study == null )
            throw new RuntimeException ( "findAllDataInAssay ( " + assay + " ): no study associated to the assay" );

        final Collection<AssayResult> result = new HashSet<AssayResult> ();
        ProcessingVisitAction visitor = new ProcessingVisitAction ()
        {
            public boolean visit ( GraphElement graphElement )
            {
                if ( ! ( graphElement instanceof DataNode ) ) return true;
                Data data = ( (DataNode) graphElement ).getData ();
                result.add(new AssayResult(data, study));
                return true;
            }
        };

        new ExperimentalPipelineVisitor ( visitor ).visitForward ( material.getMaterialNode () );
        return result;
    }

// We can get the snippet output attached.