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

Example 1 with AmbitException

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

the class BookmarkJSONReporter method processItem.

@Override
public Object processItem(Bookmark item) throws AmbitException {
    try {
        Writer writer = getOutput();
        if (comma != null)
            writer.write(comma);
        writer.write(item.toJSON());
        comma = ",";
    } catch (Exception x) {
        logger.log(java.util.logging.Level.SEVERE, x.getMessage(), x);
    }
    return item;
}

Example 2 with AmbitException

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

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

the class ModelTextReporter method processItem.

@Override
public Object processItem(ModelQueryResults model) throws AmbitException {
    try {
        ModelPredictor predictor = ModelResource.getPredictor(model, request);
        getOutput().write(predictor.toString());
        return null;
    } catch (AmbitException x) {
        throw x;
    } catch (Exception x) {
        throw new AmbitException(x);
    }
}

Example 4 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException 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 5 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException 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;
}