Examples with StringConvertor net.idea.restnet.c.StringConvertor used on opensource projects

Example 1 with StringConvertor

use of net.idea.restnet.c.StringConvertor 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 StringConvertor

use of net.idea.restnet.c.StringConvertor in project ambit-mirror by ideaconsult.

the class AbstractDepict method process.

public Representation process(Variant variant) {
    try {
        Form form = getParams();
        w = 400;
        h = 200;
        recordType = "2d";
        try {
            w = Integer.parseInt(form.getFirstValue("w"));
        } catch (Exception x) {
            w = 400;
        }
        try {
            h = Integer.parseInt(form.getFirstValue("h"));
        } catch (Exception x) {
            h = 200;
        }
        try {
            recordType = form.getFirstValue("record_type");
        } catch (Exception x) {
        }
        try {
            qType = QueryType.valueOf(form.getFirstValue("type"));
        } catch (Exception x) {
            qType = QueryType.smiles;
        }
        switch(qType) {
            case mol:
                {
                    // base64 encoded mol files
                    smiles = form.getValuesArray(QueryResource.b64search_param);
                    if (smiles != null)
                        for (int i = 0; i < smiles.length; i++) smiles[i] = new String(Base64.decode(smiles[i]));
                    break;
                }
            default:
                {
                    smiles = form.getValuesArray(QueryResource.search_param);
                    if ((smiles == null) || (smiles.length < 1))
                        smiles = new String[] { null };
                    else
                        smiles[0] = smiles[0] == null ? "" : smiles[0].trim();
                }
        }
        setSmarts(form.getFirstValue("smarts"));
        setSmirks(null);
        String[] smirks_patterns = form.getValuesArray("smirks");
        for (String sm : smirks_patterns) if (sm != null) {
            setSmirks(sm);
            break;
        }
        if (variant.getMediaType().equals(MediaType.TEXT_HTML) || (smiles == null)) {
            StringConvertor convertor = new StringConvertor(new AbstractReporter<String, Writer>() {

                /**
                 */
                private static final long serialVersionUID = -6791292888357737097L;

                public void close() throws Exception {
                }

                public Writer process(String target) throws AmbitException {
                    try {
                        if (headless)
                            output.write(target);
                        else {
                            AmbitResource.writeTopHeader(output, smiles[0] == null ? "2D structural diagram" : smiles[0], getRequest(), getResourceRef(getRequest()), header_gplus);
                            writeSearchForm(output, smiles[0] == null ? "N/A" : smiles[0], getRequest(), "", Method.GET, params);
                            output.write(target);
                            AmbitResource.writeHTMLFooter(output, smiles[0] == null ? "" : smiles[0], getRequest());
                        }
                    } catch (Exception x) {
                    }
                    return output;
                }
            }, MediaType.TEXT_HTML);
            return convertor.process(getTitle(getResourceRef(getRequest()), smiles));
        }
        final BufferedImage image;
        if (smiles[0] != null) {
            image = getImage(smiles[0], w, h, recordType, qType);
            if (image == null) {
                getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST, String.format("Invalid smiles %s", smiles));
                return null;
            }
        } else
            image = createDefaultImage(w, h);
        return new OutputRepresentation(MediaType.IMAGE_PNG) {

            @Override
            public void write(OutputStream out) throws IOException {
                try {
                    ImageIO.write(image, "PNG", out);
                } catch (IOException x) {
                    throw x;
                } catch (Exception x) {
                } finally {
                    try {
                        out.flush();
                    } catch (Exception x) {
                    }
                    try {
                        out.close();
                    } catch (Exception x) {
                    }
                }
            }
        };
    } catch (ResourceException x) {
        getResponse().setStatus(x.getStatus(), x, x.getMessage());
        return null;
    } catch (Exception x) {
        getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST, x, x.getMessage());
        return null;
    }
}

Example 3 with StringConvertor

use of net.idea.restnet.c.StringConvertor in project ambit-mirror by ideaconsult.

the class CDKDepict method get.

@Override
public Representation get(Variant variant) {
    try {
        Form form = getParams();
        smiles = form.getValuesArray(QueryResource.search_param);
        if ((smiles == null) || (smiles.length < 1))
            smiles = new String[] { null };
        setSmarts(form.getFirstValue("smarts"));
        if (MediaType.TEXT_HTML.equals(variant.getMediaType())) {
            StringConvertor convertor = new StringConvertor(new AbstractReporter<String, Writer>() {

                /**
                 */
                private static final long serialVersionUID = -1232605257681949242L;

                public void close() throws Exception {
                }

                public Writer process(String target) throws AmbitException {
                    try {
                        AmbitResource.writeTopHeader(output, smiles[0] == null ? "2D structure diagram" : smiles[0], getRequest(), getResourceRef(getRequest()), "");
                        writeSearchForm(output, smiles[0], getRequest(), "", Method.GET, params);
                        output.write(target);
                        AmbitResource.writeHTMLFooter(output, smiles[0], getRequest());
                    } catch (Exception x) {
                    }
                    return output;
                }
            }, MediaType.TEXT_HTML);
            return convertor.process(getTitle(getResourceRef(getRequest()), smiles));
        } else {
            return process(variant);
        }
    } catch (Exception x) {
    }
    return null;
}

Example 4 with StringConvertor

use of net.idea.restnet.c.StringConvertor 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 5 with StringConvertor

use of net.idea.restnet.c.StringConvertor 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);
    }
}