Examples with RDFJenaConvertor ambit2.rest.RDFJenaConvertor used on opensource projects

Example 1 with RDFJenaConvertor

use of ambit2.rest.RDFJenaConvertor in project ambit-mirror by ideaconsult.

the class StructureQueryResource method createConvertor.

@Override
public RepresentationConvertor createConvertor(Variant variant) throws AmbitException, ResourceException {
    /* workaround for clients not being able to set accept headers */
    if ((queryObject == null) && !(variant.getMediaType().equals(MediaType.TEXT_HTML)))
        throw new NotFoundException();
    setTemplate(template);
    Form acceptform = getResourceRef(getRequest()).getQueryAsForm();
    String media = acceptform.getFirstValue("accept-header");
    if (media != null) {
        variant.setMediaType(new MediaType(media));
    }
    String filenamePrefix = getRequest().getResourceRef().getPath();
    if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_MDLSDF)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new SDFReporter<QueryStructureByID>(template, getGroupProperties(), changeLineSeparators), ChemicalMediaType.CHEMICAL_MDLSDF, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_MDLMOL)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new SDFReporter<QueryStructureByID>(new Template(), getGroupProperties(), true, changeLineSeparators), ChemicalMediaType.CHEMICAL_MDLMOL, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_CML)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new CMLReporter<QueryStructureByID>(), ChemicalMediaType.CHEMICAL_CML, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_SMILES)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new SmilesReporter<QueryStructureByID>(true, getTemplate()), ChemicalMediaType.CHEMICAL_SMILES, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_INCHI)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new SmilesReporter<QueryStructureByID>(false, Mode.InChI, getTemplate()), ChemicalMediaType.CHEMICAL_INCHI, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_PDF)) {
        return new PDFConvertor<IStructureRecord, QueryStructureByID, PDFReporter<QueryStructureByID>>(new PDFReporter<QueryStructureByID>(getTemplate(), getGroupProperties()), filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.TEXT_PLAIN)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(createTXTReporter(), MediaType.TEXT_PLAIN);
    } else if (variant.getMediaType().equals(MediaType.TEXT_URI_LIST)) {
        ConformerURIReporter<QueryStructureByID> reporter = new ConformerURIReporter<QueryStructureByID>(getCompoundInDatasetPrefix(), getRequest(), queryObject.isPrescreen());
        return new StringConvertor(reporter, MediaType.TEXT_URI_LIST, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.IMAGE_PNG)) {
        return new ImageConvertor<IStructureRecord, QueryStructureByID>(new ImageReporter<QueryStructureByID>(MediaType.IMAGE_PNG.getMainType(), MediaType.IMAGE_PNG.getSubType()), MediaType.IMAGE_PNG);
    } else if (variant.getMediaType().equals(MediaType.IMAGE_GIF)) {
        return new ImageConvertor<IStructureRecord, QueryStructureByID>(new ImageReporter<QueryStructureByID>(MediaType.IMAGE_GIF.getMainType(), MediaType.IMAGE_GIF.getSubType()), MediaType.IMAGE_GIF);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_JSON)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new CompoundJSONReporter(getTemplate(), getGroupProperties(), folders, bundles, getRequest(), getRequest().getRootRef().toString() + getCompoundInDatasetPrefix(), includeMol, null), MediaType.APPLICATION_JSON, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_JAVASCRIPT)) {
        String jsonpcallback = getParams().getFirstValue("jsonp");
        if (jsonpcallback == null)
            jsonpcallback = getParams().getFirstValue("callback");
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new CompoundJSONReporter(getTemplate(), getGroupProperties(), folders, bundles, getRequest(), getRequest().getRootRef().toString() + getCompoundInDatasetPrefix(), includeMol, jsonpcallback), MediaType.APPLICATION_JAVASCRIPT, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.WEKA_ARFF)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new ARFFResourceReporter(getTemplate(), getGroupProperties(), getRequest(), String.format("%s%s", getRequest().getRootRef(), getCompoundInDatasetPrefix())), ChemicalMediaType.WEKA_ARFF, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.THREECOL_ARFF)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new ARFF3ColResourceReporter(getTemplate(), getGroupProperties(), getRequest(), String.format("%s%s", getRequest().getRootRef(), getCompoundInDatasetPrefix())), ChemicalMediaType.THREECOL_ARFF, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.TEXT_CSV)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(createCSVReporter(), MediaType.TEXT_CSV, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_RDF_XML)) {
        switch(rdfwriter) {
            case stax:
                {
                    return new RDFStaXConvertor<IStructureRecord, IQueryRetrieval<IStructureRecord>>(new DatasetRDFStaxReporter(getCompoundInDatasetPrefix(), getRequest(), getTemplate(), getGroupProperties()), filenamePrefix);
                }
            default:
                {
                    // jena
                    return new RDFJenaConvertor<IStructureRecord, IQueryRetrieval<IStructureRecord>>(new DatasetRDFReporter(getCompoundInDatasetPrefix(), getRequest(), variant.getMediaType(), getTemplate(), getGroupProperties()), variant.getMediaType(), filenamePrefix);
                }
        }
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_RDF_TURTLE) || variant.getMediaType().equals(MediaType.TEXT_RDF_N3) || variant.getMediaType().equals(MediaType.TEXT_RDF_NTRIPLES) || variant.getMediaType().equals(MediaType.APPLICATION_RDF_TRIG) || variant.getMediaType().equals(MediaType.APPLICATION_RDF_TRIX) || variant.getMediaType().equals(ChemicalMediaType.APPLICATION_JSONLD)) {
        return new RDFJenaConvertor<IStructureRecord, IQueryRetrieval<IStructureRecord>>(new DatasetRDFReporter(getCompoundInDatasetPrefix(), getRequest(), variant.getMediaType(), getTemplate(), getGroupProperties()), variant.getMediaType(), filenamePrefix);
    } else
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new SDFReporter<QueryStructureByID>(template, getGroupProperties(), changeLineSeparators), ChemicalMediaType.CHEMICAL_MDLSDF, filenamePrefix);
}

Example 2 with RDFJenaConvertor

use of ambit2.rest.RDFJenaConvertor in project ambit-mirror by ideaconsult.

the class BundlePropertyResource method createConvertor.

@Override
public IProcessor<Q, Representation> createConvertor(Variant variant) throws AmbitException, ResourceException {
    /* workaround for clients not being able to set accept headers */
    Form acceptform = getResourceRef(getRequest()).getQueryAsForm();
    Dimension d = new Dimension(250, 250);
    try {
        d.width = Integer.parseInt(acceptform.getFirstValue("w").toString());
    } catch (Exception x) {
    }
    try {
        d.height = Integer.parseInt(acceptform.getFirstValue("h").toString());
    } catch (Exception x) {
    }
    String media = acceptform.getFirstValue("accept-header");
    if (media != null)
        variant.setMediaType(new MediaType(media));
    String filenamePrefix = getRequest().getResourceRef().getPath();
    if (variant.getMediaType().equals(MediaType.TEXT_URI_LIST)) {
        QueryURIReporter r = (QueryURIReporter) getURIReporter(getRequest());
        return new StringConvertor(r, MediaType.TEXT_URI_LIST, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.IMAGE_PNG)) {
        return new ImageConvertor(new ImageReporter(variant.getMediaType().getMainType(), variant.getMediaType().getSubType(), d), variant.getMediaType());
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_JAVASCRIPT)) {
        String jsonpcallback = getParams().getFirstValue("jsonp");
        if (jsonpcallback == null)
            jsonpcallback = getParams().getFirstValue("callback");
        return new OutputWriterConvertor(new PropertyJSONReporter(getRequest(), jsonpcallback), MediaType.APPLICATION_JAVASCRIPT);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_RDF_XML) || variant.getMediaType().equals(MediaType.APPLICATION_RDF_TURTLE) || variant.getMediaType().equals(MediaType.TEXT_RDF_N3) || variant.getMediaType().equals(MediaType.TEXT_RDF_NTRIPLES) || variant.getMediaType().equals(ChemicalMediaType.APPLICATION_JSONLD)) {
        RDFJenaConvertor convertor = new RDFJenaConvertor<Property, IQueryRetrieval<Property>>(new PropertyRDFReporter<IQueryRetrieval<Property>>(getRequest(), variant.getMediaType()), variant.getMediaType(), filenamePrefix);
        return convertor;
    } else {
        // (variant.getMediaType().equals(MediaType.APPLICATION_JSON)) {
        return new OutputWriterConvertor(new PropertyJSONReporter(getRequest()), MediaType.APPLICATION_JSON);
    }
}

Example 3 with RDFJenaConvertor

use of ambit2.rest.RDFJenaConvertor in project ambit-mirror by ideaconsult.

the class CompoundResource method createConvertor.

@Override
public RepresentationConvertor createConvertor(Variant variant) throws AmbitException, ResourceException {
    /* workaround for clients not being able to set accept headers */
    if (!variant.getMediaType().equals(MediaType.IMAGE_PNG)) {
        setTemplate(createTemplate(getContext(), getRequest(), getResponse()));
        setGroupProperties(getContext(), getRequest(), getResponse());
    }
    Form acceptform = getResourceRef(getRequest()).getQueryAsForm();
    String media = acceptform.getFirstValue("accept-header");
    if (media != null) {
        variant.setMediaType(new MediaType(media));
    }
    String filenamePrefix = getRequest().getResourceRef().getPath();
    if ((queryObject == null) && !(variant.getMediaType().equals(MediaType.TEXT_HTML)))
        throw new NotFoundException();
    if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_CML))
        // StructureReporter((getRequest()==null)?null:getRequest().getRootRef()));
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new CMLReporter<QueryStructureByID>(), ChemicalMediaType.CHEMICAL_CML, filenamePrefix);
    else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_MDLSDF)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new SDFReporter<QueryStructureByID>(getTemplate(), getGroupProperties(), changeLineSeparators), ChemicalMediaType.CHEMICAL_MDLSDF, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_MDLMOL)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new SDFReporter<QueryStructureByID>(new Template(), getGroupProperties(), true, changeLineSeparators), ChemicalMediaType.CHEMICAL_MDLMOL, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_SMILES)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new SmilesReporter<QueryStructureByID>(), ChemicalMediaType.CHEMICAL_SMILES, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_INCHI)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new SmilesReporter<QueryStructureByID>(false, Mode.InChI, getTemplate()), ChemicalMediaType.CHEMICAL_INCHI, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.TEXT_PLAIN)) {
        return new StringConvertor(new SmilesReporter<QueryStructureByID>(true, getTemplate()), MediaType.TEXT_PLAIN);
    } else if (variant.getMediaType().equals(MediaType.IMAGE_PNG) || variant.getMediaType().equals(MediaType.IMAGE_BMP) || variant.getMediaType().equals(MediaType.IMAGE_JPEG) || variant.getMediaType().equals(MediaType.IMAGE_TIFF) || variant.getMediaType().equals(MediaType.IMAGE_GIF)) {
        return createImageConvertor(variant);
    } else if (variant.getMediaType().equals(ChemicalMediaType.IMAGE_JSON)) {
        return createImageStringConvertor(variant);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_PDF)) {
        return new PDFConvertor<IStructureRecord, QueryStructureByID, PDFReporter<QueryStructureByID>>(new PDFReporter<QueryStructureByID>(getTemplate(), getGroupProperties()));
    } else if (variant.getMediaType().equals(MediaType.TEXT_URI_LIST)) {
        QueryURIReporter r = (QueryURIReporter) getURIReporter();
        return new StringConvertor(r, MediaType.TEXT_URI_LIST, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.WEKA_ARFF)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new ARFFResourceReporter(getTemplate(), getGroupProperties(), getRequest(), getRequest().getRootRef().toString() + getCompoundInDatasetPrefix()), ChemicalMediaType.WEKA_ARFF, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.THREECOL_ARFF)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new ARFF3ColResourceReporter(getTemplate(), getGroupProperties(), getRequest(), getRequest().getRootRef().toString() + getCompoundInDatasetPrefix()), ChemicalMediaType.THREECOL_ARFF, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_JSON)) {
        CompoundJSONReporter cmpreporter = new CompoundJSONReporter(getTemplate(), getGroupProperties(), folders, bundles, getRequest(), getRequest().getRootRef().toString() + getCompoundInDatasetPrefix(), includeMol, null);
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(cmpreporter, MediaType.APPLICATION_JSON, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_JAVASCRIPT)) {
        String jsonpcallback = getParams().getFirstValue("jsonp");
        if (jsonpcallback == null)
            jsonpcallback = getParams().getFirstValue("callback");
        CompoundJSONReporter cmpreporter = new CompoundJSONReporter(getTemplate(), getGroupProperties(), folders, bundles, getRequest(), getRequest().getRootRef().toString() + getCompoundInDatasetPrefix(), includeMol, jsonpcallback);
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(cmpreporter, MediaType.APPLICATION_JAVASCRIPT, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.TEXT_CSV)) {
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new CSVReporter(getRequest().getRootRef().toString(), getTemplate(), getGroupProperties(), getRequest().getRootRef().toString() + getCompoundInDatasetPrefix()), MediaType.TEXT_CSV, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.NANO_CML)) {
        // StructureReporter((getRequest()==null)?null:getRequest().getRootRef()));
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(new CMLReporter<QueryStructureByID>(), ChemicalMediaType.NANO_CML, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_RDF_XML) || variant.getMediaType().equals(MediaType.APPLICATION_RDF_TURTLE) || variant.getMediaType().equals(MediaType.TEXT_RDF_N3) || variant.getMediaType().equals(MediaType.TEXT_RDF_NTRIPLES) || variant.getMediaType().equals(MediaType.APPLICATION_RDF_TRIG) || variant.getMediaType().equals(MediaType.APPLICATION_RDF_TRIX)) {
        return new RDFJenaConvertor<IStructureRecord, IQueryRetrieval<IStructureRecord>>(new DatasetRDFReporter(getCompoundInDatasetPrefix(), getRequest(), variant.getMediaType(), getTemplate(), getGroupProperties()), variant.getMediaType(), filenamePrefix);
    } else {
        CompoundJSONReporter cmpreporter = new CompoundJSONReporter(getTemplate(), getGroupProperties(), folders, bundles, getRequest(), getRequest().getRootRef().toString() + getCompoundInDatasetPrefix(), includeMol, null);
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(cmpreporter, MediaType.APPLICATION_JSON, filenamePrefix);
    }
}

Example 4 with RDFJenaConvertor

use of ambit2.rest.RDFJenaConvertor in project ambit-mirror by ideaconsult.

the class SubstanceResource method createConvertor.

@Override
public IProcessor<Q, Representation> createConvertor(Variant variant) throws AmbitException, ResourceException {
    /* workaround for clients not being able to set accept headers */
    Form acceptform = getResourceRef(getRequest()).getQueryAsForm();
    String configResource = String.format("config-%s.js", ((IFreeMarkerApplication) getApplication()).getProfile());
    try {
        retrieveStudySummary = Boolean.parseBoolean(acceptform.getFirstValue("studysummary"));
    } catch (Exception x) {
        retrieveStudySummary = false;
    }
    String media = acceptform.getFirstValue("accept-header");
    if (media != null)
        variant.setMediaType(new MediaType(media));
    String filenamePrefix = getRequest().getResourceRef().getPath();
    if (variant.getMediaType().equals(MediaType.TEXT_URI_LIST)) {
        QueryURIReporter r = (QueryURIReporter) getURIReporter(getRequest());
        return new StringConvertor(r, MediaType.TEXT_URI_LIST, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.IMAGE_PNG)) {
        Dimension d = new Dimension(250, 250);
        try {
            d.width = Integer.parseInt(acceptform.getFirstValue("w").toString());
        } catch (Exception x) {
        }
        try {
            d.height = Integer.parseInt(acceptform.getFirstValue("h").toString());
        } catch (Exception x) {
        }
        return new ImageConvertor(new ImageReporter(variant.getMediaType().getMainType(), variant.getMediaType().getSubType(), d), variant.getMediaType());
    } else if (variant.getMediaType().equals(MediaType.TEXT_CSV)) {
        SubstanceCSVReporter csvreporter = new SubstanceCSVReporter(getRequest(), bundles);
        return new OutputWriterConvertor<SubstanceRecord, Q>(csvreporter, MediaType.TEXT_CSV, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_MSOFFICE_XLSX)) {
        SubstanceRecordXLSXReporter xlsxreporter = new SubstanceRecordXLSXReporter(getRequest().getRootRef().toString(), false, bundles, configResource);
        return new OutputStreamConvertor<SubstanceRecord, Q>(xlsxreporter, MediaType.APPLICATION_MSOFFICE_XLSX, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_EXCEL)) {
        SubstanceRecordXLSXReporter xlsxreporter = new SubstanceRecordXLSXReporter(getRequest().getRootRef().toString(), true, bundles, configResource);
        return new OutputStreamConvertor<SubstanceRecord, Q>(xlsxreporter, MediaType.APPLICATION_EXCEL, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_RDF_XML) || // filenamePrefix);
    variant.getMediaType().equals(MediaType.APPLICATION_RDF_TURTLE) || variant.getMediaType().equals(MediaType.TEXT_RDF_NTRIPLES) || variant.getMediaType().equals(MediaType.TEXT_RDF_N3) || variant.getMediaType().equals(ChemicalMediaType.APPLICATION_JSONLD)) {
        SubstanceRecordAnnotationProcessor annotator = null;
        try {
            annotator = new SubstanceRecordAnnotationProcessor(new File(((AmbitFreeMarkerApplication) getApplication()).getProperties().getMapFolder()), false);
        } catch (Exception x) {
            Logger.getGlobal().log(Level.WARNING, x.getMessage());
            annotator = null;
        }
        return new RDFJenaConvertor(new SubstanceRDFReporter(getRequest(), variant.getMediaType(), annotator), variant.getMediaType(), filenamePrefix) {

            @Override
            protected OntModel createOutput(IQueryRetrieval query) throws AmbitException {
                try {
                    OntModel jenaModel = OT.createModel();
                    jenaModel.setNsPrefix("sio", "http://semanticscience.org/resource/");
                    jenaModel.setNsPrefix("obo", "http://purl.obolibrary.org/obo/");
                    jenaModel.setNsPrefix("bao", "http://www.bioassayontology.org/bao#");
                    jenaModel.setNsPrefix("npo", "http://purl.bioontology.org/ontology/npo/");
                    jenaModel.setNsPrefix("enm", "http://purl.enanomapper.org/onto/");
                    return jenaModel;
                } catch (Exception x) {
                    throw new AmbitException(x);
                }
            }
        };
    } else if (variant.getMediaType().equals(ISAJSON)) {
        return new OutputStreamConvertor<SubstanceRecord, Q>(createISAReporter(getRequest()), MediaType.APPLICATION_JAVASCRIPT, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_JAVASCRIPT)) {
        return createJSONReporter(filenamePrefix);
    } else
        // json by default
        return createJSONReporter(filenamePrefix);
}

Example 5 with RDFJenaConvertor

use of ambit2.rest.RDFJenaConvertor in project ambit-mirror by ideaconsult.

the class SubstanceDatasetResource method createRDFReporter.

protected IProcessor<Q, Representation> createRDFReporter(MediaType media, String filenamePrefix) {
    groupProperties.add(new SubstancePublicName());
    groupProperties.add(new SubstanceName());
    groupProperties.add(new SubstanceUUID());
    groupProperties.add(new SubstanceOwner());
    DatasetRDFReporter reporter = new DatasetRDFReporter(getRequest(), media, getTemplate(), getGroupProperties()) {

        @Override
        protected boolean acceptProperty(Property p) {
            return true;
        }

        @Override
        protected void configurePropertyProcessors() {
            getProcessors().add(getPropertyProcessors(false, false));
        }
    };
    return new RDFJenaConvertor(reporter, media, filenamePrefix);
}