Examples with DatasetRDFReporter ambit2.rest.dataset.DatasetRDFReporter used on opensource projects

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Example 1 with DatasetRDFReporter

use of ambit2.rest.dataset.DatasetRDFReporter 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);
}
Also used : Form(org.restlet.data.Form) OutputWriterConvertor(net.idea.restnet.db.convertors.OutputWriterConvertor) PDFReporter(ambit2.db.reporters.PDFReporter) NotFoundException(net.idea.modbcum.i.exceptions.NotFoundException) QueryStructureByID(ambit2.db.search.structure.QueryStructureByID) Template(ambit2.base.data.Template) IStructureRecord(ambit2.base.interfaces.IStructureRecord) ARFF3ColResourceReporter(ambit2.rest.dataset.ARFF3ColResourceReporter) SDFReporter(ambit2.db.reporters.SDFReporter) ChemicalMediaType(net.idea.restnet.c.ChemicalMediaType) MediaType(org.restlet.data.MediaType) RDFJenaConvertor(ambit2.rest.RDFJenaConvertor) CompoundJSONReporter(ambit2.rest.structure.CompoundJSONReporter) SmilesReporter(ambit2.db.reporters.SmilesReporter) DatasetRDFStaxReporter(ambit2.rest.dataset.DatasetRDFStaxReporter) StringConvertor(net.idea.restnet.c.StringConvertor) ImageReporter(ambit2.db.reporters.ImageReporter) RDFStaXConvertor(ambit2.rest.RDFStaXConvertor) ARFFResourceReporter(ambit2.rest.dataset.ARFFResourceReporter) ConformerURIReporter(ambit2.rest.structure.ConformerURIReporter) ImageConvertor(ambit2.rest.ImageConvertor) DatasetRDFReporter(ambit2.rest.dataset.DatasetRDFReporter)

Example 2 with DatasetRDFReporter

use of ambit2.rest.dataset.DatasetRDFReporter 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);
    }
}
Also used : SmilesReporter(ambit2.db.reporters.SmilesReporter) Form(org.restlet.data.Form) OutputWriterConvertor(net.idea.restnet.db.convertors.OutputWriterConvertor) StringConvertor(net.idea.restnet.c.StringConvertor) NotFoundException(net.idea.modbcum.i.exceptions.NotFoundException) CSVReporter(ambit2.db.reporters.CSVReporter) CMLReporter(ambit2.db.reporters.CMLReporter) QueryStructureByID(ambit2.db.search.structure.QueryStructureByID) Template(ambit2.base.data.Template) IStructureRecord(ambit2.base.interfaces.IStructureRecord) ARFFResourceReporter(ambit2.rest.dataset.ARFFResourceReporter) ARFF3ColResourceReporter(ambit2.rest.dataset.ARFF3ColResourceReporter) SDFReporter(ambit2.db.reporters.SDFReporter) PDFConvertor(ambit2.rest.PDFConvertor) DatasetRDFReporter(ambit2.rest.dataset.DatasetRDFReporter) ChemicalMediaType(net.idea.restnet.c.ChemicalMediaType) MediaType(org.restlet.data.MediaType) RDFJenaConvertor(ambit2.rest.RDFJenaConvertor) QueryURIReporter(net.idea.restnet.db.QueryURIReporter)

Example 3 with DatasetRDFReporter

use of ambit2.rest.dataset.DatasetRDFReporter 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);
}
Also used : SubstanceName(ambit2.base.data.substance.SubstanceName) SubstanceOwner(ambit2.base.data.substance.SubstanceOwner) SubstanceUUID(ambit2.base.data.substance.SubstanceUUID) DatasetRDFReporter(ambit2.rest.dataset.DatasetRDFReporter) RDFJenaConvertor(ambit2.rest.RDFJenaConvertor) Property(ambit2.base.data.Property) ProtocolEffectRecord2SubstanceProperty(ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty) SubstanceProperty(ambit2.base.data.substance.SubstanceProperty) SubstancePublicName(ambit2.base.data.substance.SubstancePublicName)

Example 4 with DatasetRDFReporter

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

the class BundleChemicalsResource 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_JSON)) {
        return new OutputWriterConvertor(new CompoundJSONReporter(getTemplate(), getGroupProperties(), folders, new SubstanceEndpointsBundle[] { bundle }, getRequest(), getRequest().getRootRef().toString(), 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(new CompoundJSONReporter(getTemplate(), getGroupProperties(), folders, new SubstanceEndpointsBundle[] { bundle }, getRequest(), getRequest().getRootRef().toString(), includeMol, jsonpcallback), MediaType.APPLICATION_JAVASCRIPT, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_MDLSDF)) {
        return new OutputWriterConvertor<IStructureRecord, Q>(new SDFReporter<Q>(template, getGroupProperties(), changeLineSeparators), ChemicalMediaType.CHEMICAL_MDLSDF, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_MDLMOL)) {
        return new OutputWriterConvertor<IStructureRecord, Q>(new SDFReporter<Q>(new Template(), getGroupProperties(), true, changeLineSeparators), ChemicalMediaType.CHEMICAL_MDLMOL, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_CML)) {
        return new OutputWriterConvertor<IStructureRecord, Q>(new CMLReporter<Q>(), ChemicalMediaType.CHEMICAL_CML, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_SMILES)) {
        return new OutputWriterConvertor<IStructureRecord, Q>(new SmilesReporter<Q>(true, getTemplate()), ChemicalMediaType.CHEMICAL_SMILES, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_INCHI)) {
        return new OutputWriterConvertor<IStructureRecord, Q>(new SmilesReporter<Q>(false, Mode.InChI, getTemplate()), ChemicalMediaType.CHEMICAL_INCHI, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.WEKA_ARFF)) {
        return new OutputWriterConvertor<IStructureRecord, Q>(new ARFFResourceReporter(getTemplate(), getGroupProperties(), getRequest(), String.format("%s%s", getRequest().getRootRef(), "")), ChemicalMediaType.WEKA_ARFF, filenamePrefix);
    } else if (variant.getMediaType().equals(ChemicalMediaType.THREECOL_ARFF)) {
        return new OutputWriterConvertor<IStructureRecord, Q>(new ARFF3ColResourceReporter(getTemplate(), getGroupProperties(), getRequest(), String.format("%s%s", getRequest().getRootRef(), "")), ChemicalMediaType.THREECOL_ARFF, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.TEXT_CSV)) {
        return new OutputWriterConvertor<IStructureRecord, Q>(new CSVReporter(getRequest().getRootRef().toString(), getTemplate(), groupProperties, String.format("%s%s", getRequest().getRootRef(), "")), MediaType.TEXT_CSV, filenamePrefix);
    } else if (variant.getMediaType().equals(MediaType.APPLICATION_RDF_XML)) {
        switch(rdfwriter) {
            case stax:
                {
                    return new RDFStaXConvertor<IStructureRecord, Q>(new DatasetRDFStaxReporter("", getRequest(), getTemplate(), getGroupProperties()), filenamePrefix);
                }
            default:
                {
                    // jena
                    return new RDFJenaConvertor<IStructureRecord, Q>(new DatasetRDFReporter("", 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, Q>(new DatasetRDFReporter("", getRequest(), variant.getMediaType(), getTemplate(), getGroupProperties()), variant.getMediaType(), filenamePrefix);
    } else {
        // JSON
        return new OutputWriterConvertor(new CompoundJSONReporter(getTemplate(), getGroupProperties(), folders, new SubstanceEndpointsBundle[] { bundle }, getRequest(), getRequest().getRootRef().toString(), includeMol, null), MediaType.APPLICATION_JSON, filenamePrefix);
    }
}
Also used : Form(org.restlet.data.Form) OutputWriterConvertor(net.idea.restnet.db.convertors.OutputWriterConvertor) Template(ambit2.base.data.Template) IStructureRecord(ambit2.base.interfaces.IStructureRecord) ARFF3ColResourceReporter(ambit2.rest.dataset.ARFF3ColResourceReporter) SDFReporter(ambit2.db.reporters.SDFReporter) SubstanceEndpointsBundle(ambit2.base.data.substance.SubstanceEndpointsBundle) ChemicalMediaType(net.idea.restnet.c.ChemicalMediaType) MediaType(org.restlet.data.MediaType) CompoundJSONReporter(ambit2.rest.structure.CompoundJSONReporter) SmilesReporter(ambit2.db.reporters.SmilesReporter) DatasetRDFStaxReporter(ambit2.rest.dataset.DatasetRDFStaxReporter) StringConvertor(net.idea.restnet.c.StringConvertor) ImageReporter(ambit2.db.reporters.ImageReporter) CSVReporter(ambit2.db.reporters.CSVReporter) Dimension(java.awt.Dimension) AmbitException(net.idea.modbcum.i.exceptions.AmbitException) ResourceException(org.restlet.resource.ResourceException) ARFFResourceReporter(ambit2.rest.dataset.ARFFResourceReporter) ImageConvertor(ambit2.rest.ImageConvertor) DatasetRDFReporter(ambit2.rest.dataset.DatasetRDFReporter) QueryURIReporter(net.idea.restnet.db.QueryURIReporter)

Aggregations

DatasetRDFReporter (ambit2.rest.dataset.DatasetRDFReporter)4 Template (ambit2.base.data.Template)3 IStructureRecord (ambit2.base.interfaces.IStructureRecord)3 SDFReporter (ambit2.db.reporters.SDFReporter)3 SmilesReporter (ambit2.db.reporters.SmilesReporter)3 RDFJenaConvertor (ambit2.rest.RDFJenaConvertor)3 ARFF3ColResourceReporter (ambit2.rest.dataset.ARFF3ColResourceReporter)3 ARFFResourceReporter (ambit2.rest.dataset.ARFFResourceReporter)3 ChemicalMediaType (net.idea.restnet.c.ChemicalMediaType)3 StringConvertor (net.idea.restnet.c.StringConvertor)3 OutputWriterConvertor (net.idea.restnet.db.convertors.OutputWriterConvertor)3 Form (org.restlet.data.Form)3 MediaType (org.restlet.data.MediaType)3 CSVReporter (ambit2.db.reporters.CSVReporter)2 ImageReporter (ambit2.db.reporters.ImageReporter)2 QueryStructureByID (ambit2.db.search.structure.QueryStructureByID)2 ImageConvertor (ambit2.rest.ImageConvertor)2 DatasetRDFStaxReporter (ambit2.rest.dataset.DatasetRDFStaxReporter)2 CompoundJSONReporter (ambit2.rest.structure.CompoundJSONReporter)2 NotFoundException (net.idea.modbcum.i.exceptions.NotFoundException)2
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