Examples with NotFoundException net.idea.modbcum.i.exceptions.NotFoundException used on opensource projects

Example 1 with NotFoundException

use of net.idea.modbcum.i.exceptions.NotFoundException 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 NotFoundException

use of net.idea.modbcum.i.exceptions.NotFoundException in project ambit-mirror by ideaconsult.

the class CSLSResource method get.

@Override
protected Representation get(Variant variant) throws ResourceException {
    setFrameOptions("SAMEORIGIN");
    try {
        if (term != null) {
            if (variant.getMediaType().equals(ChemicalMediaType.CHEMICAL_MDLSDF))
                return new OutputRepresentation(variant.getMediaType()) {

                    @Override
                    public void write(OutputStream stream) throws IOException {
                        try {
                            CSLSRequest<InputStream> q = new CSLSRequest<InputStream>() {

                                /**
                                 */
                                private static final long serialVersionUID = 2638378178348461366L;

                                @Override
                                protected InputStream read(InputStream in) throws Exception {
                                    return in;
                                }
                            };
                            q.setRepresentation(representation);
                            DownloadTool.download(q.process(term), stream);
                            stream.flush();
                        } catch (ResourceException x) {
                            throw x;
                        } catch (AmbitException x) {
                            throw new ResourceException(Status.SERVER_ERROR_INTERNAL, x.getMessage(), x);
                        // throw new IOException(x.getMessage());
                        } finally {
                            try {
                                if (stream != null)
                                    stream.flush();
                            } catch (Exception x) {
                                getLogger().log(Level.WARNING, x.getMessage(), x);
                            }
                        }
                    }
                };
            else {
                CSLSStringRequest q = new CSLSStringRequest();
                q.setRepresentation(representation);
                return new StringRepresentation(q.process(term), MediaType.TEXT_PLAIN);
            }
        } else
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST);
    } catch (NotFoundException x) {
        getResponse().setStatus(Status.CLIENT_ERROR_NOT_FOUND, "No results for query " + term);
        return null;
    } catch (ResourceException x) {
        throw x;
    } catch (Exception x) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, x);
    }
}

Example 3 with NotFoundException

use of net.idea.modbcum.i.exceptions.NotFoundException in project ambit-mirror by ideaconsult.

the class QueryResource method getRepresentation.

protected Representation getRepresentation(Variant variant) throws ResourceException {
    try {
        if (MediaType.APPLICATION_JAVA_OBJECT.equals(variant.getMediaType())) {
            if ((queryObject != null) && (queryObject instanceof Serializable))
                return new ObjectRepresentation((Serializable) returnQueryObject(), MediaType.APPLICATION_JAVA_OBJECT);
            else
                throw new ResourceException(Status.CLIENT_ERROR_NOT_ACCEPTABLE);
        }
        if (MediaType.APPLICATION_JAVASCRIPT.equals(variant.getMediaType())) {
            if (!isJSONPEnabled())
                throw new ResourceException(Status.CLIENT_ERROR_UNSUPPORTED_MEDIA_TYPE);
        }
        if (queryObject != null) {
            IProcessor<Q, Representation> convertor = null;
            Connection connection = null;
            int retry = 0;
            while (retry < maxRetry) {
                try {
                    DBConnection dbc = new DBConnection(getContext());
                    configureRDFWriterOption(((AmbitApplication) getApplication()).getProperties().getRDFwriter());
                    configureSDFLineSeparators(((AmbitApplication) getApplication()).getProperties().getConfigChangeLineSeparator());
                    configureDatasetMembersPrefixOption(((AmbitApplication) getApplication()).getProperties().isDatasetMembersPrefix());
                    convertor = createConvertor(variant);
                    if (convertor instanceof RepresentationConvertor)
                        ((RepresentationConvertor) convertor).setLicenseURI(getLicenseURI());
                    connection = dbc.getConnection();
                    Reporter reporter = ((RepresentationConvertor) convertor).getReporter();
                    if (reporter instanceof IDBProcessor)
                        ((IDBProcessor) reporter).setConnection(connection);
                    Representation r = convertor.process(queryObject);
                    r.setCharacterSet(CharacterSet.UTF_8);
                    return r;
                } catch (ResourceException x) {
                    throw x;
                } catch (NotFoundException x) {
                    Representation r = processNotFound(x, retry);
                    retry++;
                    if (r != null)
                        return r;
                } catch (BatchProcessingException x) {
                    if (x.getCause() instanceof NotFoundException) {
                        Representation r = processNotFound((NotFoundException) x.getCause(), retry);
                        retry++;
                        if (r != null)
                            return r;
                    } else {
                        Context.getCurrentLogger().severe(x.getMessage());
                        throw new RResourceException(Status.SERVER_ERROR_INTERNAL, x, variant);
                    }
                } catch (SQLException x) {
                    Representation r = processSQLError(x, retry, variant);
                    retry++;
                    if (r == null)
                        continue;
                    else
                        return r;
                } catch (Exception x) {
                    Context.getCurrentLogger().severe(x.getMessage());
                    throw new RResourceException(Status.SERVER_ERROR_INTERNAL, x, variant);
                } finally {
                // try { if (connection !=null) connection.close(); }
                // catch (Exception x) {};
                // try { if ((convertor !=null) &&
                // (convertor.getReporter() !=null))
                // convertor.getReporter().close(); } catch (Exception
                // x) {}
                }
            }
            return null;
        } else {
            if (variant.getMediaType().equals(MediaType.TEXT_HTML))
                try {
                    IProcessor<Q, Representation> convertor = createConvertor(variant);
                    Representation r = convertor.process(null);
                    return r;
                } catch (Exception x) {
                    throw new RResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x, variant);
                }
            else {
                throw new RResourceException(Status.CLIENT_ERROR_BAD_REQUEST, error, variant);
            }
        }
    } catch (RResourceException x) {
        throw x;
    } catch (ResourceException x) {
        throw new RResourceException(x.getStatus(), x, variant);
    } catch (Exception x) {
        throw new RResourceException(Status.SERVER_ERROR_INTERNAL, x, variant);
    }
}

Example 4 with NotFoundException

use of net.idea.modbcum.i.exceptions.NotFoundException in project ambit-mirror by ideaconsult.

the class CompoundImageJSONResource method createConvertor.

@Override
public RepresentationConvertor createConvertor(Variant variant) throws AmbitException, ResourceException {
    Form acceptform = getResourceRef(getRequest()).getQueryAsForm();
    String media = acceptform.getFirstValue("accept-header");
    if (media != null) {
        variant.setMediaType(new MediaType(media));
    }
    if ((queryObject == null) && !(variant.getMediaType().equals(MediaType.TEXT_HTML)))
        throw new NotFoundException();
    return createImageStringConvertor(variant);
}

Example 5 with NotFoundException

use of net.idea.modbcum.i.exceptions.NotFoundException in project ambit-mirror by ideaconsult.

the class AbstractPairwiseResource 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(MediaType.TEXT_HTML)) {
        Dimension d = new Dimension(150, 150);
        Form form = getResourceRef(getRequest()).getQueryAsForm();
        try {
            d.width = Integer.parseInt(form.getFirstValue("w").toString());
        } catch (Exception x) {
        }
        try {
            d.height = Integer.parseInt(form.getFirstValue("h").toString());
        } catch (Exception x) {
        }
        return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(createHTMLReporter(d), MediaType.TEXT_HTML);
    } 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>(createJSONReporter(jsonpcallback), MediaType.APPLICATION_JSON, filenamePrefix);
    }
    return new OutputWriterConvertor<IStructureRecord, QueryStructureByID>(createJSONReporter(), MediaType.APPLICATION_JSON, filenamePrefix);
}