Examples with ImportSubstanceException ambit2.rest.exception.ImportSubstanceException used on opensource projects

Example 1 with ImportSubstanceException

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

the class TaskJSONReporter method processItem.

@Override
public void processItem(UUID item, Writer output) {
    try {
        if (comma != null)
            output.write(comma);
        ITask<ITaskResult, USERID> task = storage.findTask(item);
        String uri = task.getUri() == null ? null : task.getUri().toString();
        StringWriter errorTrace = null;
        if (task.getError() != null) {
            try {
                ResourceException exception = task.getError();
                errorTrace = new StringWriter();
                if (exception instanceof ImportSubstanceException) {
                    errorTrace.write(((ImportSubstanceException) exception).getDetails());
                } else if (exception.getCause() == null)
                    exception.printStackTrace(new PrintWriter(errorTrace));
                else
                    exception.getCause().printStackTrace(new PrintWriter(errorTrace));
            } catch (Exception x) {
            }
        }
        output.write(String.format(format, uri, item.toString(), task.getName() == null ? "" : JSONUtils.jsonEscape(task.getName()), task.getError() == null ? "" : JSONUtils.jsonEscape(task.getError().toString()), task.getPolicyError() == null ? "" : JSONUtils.jsonEscape(task.getPolicyError().toString()), task.getStatus() == null ? "" : task.getStatus(), task.getStarted(), task.getTimeCompleted(), task.getUri() == null ? "" : task.getUri(), errorTrace == null ? null : JSONUtils.jsonQuote(JSONUtils.jsonEscape(errorTrace.toString()))));
        comma = ",";
    } catch (IOException x) {
        Context.getCurrentLogger().severe(x.getMessage());
    }
}

Example 2 with ImportSubstanceException

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

the class CallableSubstanceI5Query method doCall.

@Override
public TaskResult doCall() throws Exception {
    Connection connection = null;
    DBConnection dbc = null;
    IUCLIDLightClient i5 = null;
    DBSubstanceWriter writer = null;
    FileHandler logHandler = null;
    StreamHandler streamHandler = null;
    OutputStream out = new ByteArrayOutputStream();
    try {
        logger.log(Level.INFO, String.format("Logging to %s", logFile));
        logHandler = new FileHandler(logFile);
        localLogger.addHandler(logHandler);
        SimpleFormatter formatter = new SimpleFormatter();
        streamHandler = new StreamHandler(out, formatter);
        localLogger.addHandler(streamHandler);
        logHandler.setFormatter(formatter);
        localLogger.setUseParentHandlers(false);
        localLogger.fine("Start()");
        if (useUUID) {
            if (substanceUUID == null || "".equals(substanceUUID))
                throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Empty UUID");
            dbc = new DBConnection(context);
            if (server == null)
                server = dbc.getProperty(iuclidversion.getProperty(".server"));
            if (user == null)
                user = dbc.getProperty(iuclidversion.getProperty(".user"));
            if (pass == null)
                pass = dbc.getProperty(iuclidversion.getProperty(".pass"));
            try {
                i5 = iuclidversion.createClient(server);
                if (i5.login(user, pass)) {
                    IContainerClient ccli = i5.getContainerClient();
                    substanceUUID = iuclidversion.formatQueryUUID(substanceUUID);
                    localLogger.log(Level.FINE, String.format("Retieving %s from %s", substanceUUID, server));
                    List<IIdentifiableResource<IIdentifier>> container = null;
                    try {
                        container = ccli.get(new Identifier(substanceUUID));
                    } catch (Exception x) {
                        localLogger.log(Level.SEVERE, String.format("Failed to retrieve %s from %s. Error %s", substanceUUID, server, x.getMessage()));
                        streamHandler.flush();
                        String msg = out.toString();
                        throw new ImportSubstanceException(new Status(Status.SERVER_ERROR_BAD_GATEWAY, String.format("Failed to retrieve %s", substanceUUID)), msg);
                    }
                    connection = dbc.getConnection();
                    localLogger.log(Level.INFO, String.format("Importing %s", substanceUUID, server));
                    writer = new DBSubstanceWriter(DBSubstanceWriter.datasetMeta(), new SubstanceRecord(), clearMeasurements, clearComposition);
                    writer.setI5mode(true);
                    writer.setCloseConnection(false);
                    writer.setConnection(connection);
                    writer.open();
                    IIdentifiableResource<IIdentifier> result = processContainer(container, writer, server);
                } else
                    throw new ImportSubstanceException(new Status(Status.SERVER_ERROR_BAD_GATEWAY, "IUCLID5 server login failed"), "IUCLID5 server login failed [" + server + "].");
            } catch (ResourceException x) {
                throw x;
            } catch (Exception x) {
                streamHandler.flush();
                String msg = out.toString();
                throw new ImportSubstanceException(new Status(Status.SERVER_ERROR_BAD_GATEWAY, x.getMessage()), msg);
            }
        } else {
            // query
            if (extIDType == null || extIDValue == null)
                throw new ImportSubstanceException(new Status(Status.CLIENT_ERROR_BAD_REQUEST, "Invalid query"), "Invalid query");
            dbc = new DBConnection(context);
            if (server == null)
                server = dbc.getProperty(iuclidversion.getProperty(".server"));
            if (user == null)
                user = dbc.getProperty(iuclidversion.getProperty(".user"));
            if (pass == null)
                pass = dbc.getProperty(iuclidversion.getProperty(".pass"));
            try {
                i5 = iuclidversion.createClient(server);
                if (i5.login(user, pass)) {
                    IQueryToolClient cli = i5.getQueryToolClient();
                    List<IIdentifiableResource<IIdentifier>> queryResults = cli.executeQuery(iuclidversion.createQuery(extIDValue), extIDType, extIDValue);
                    if (queryResults != null && queryResults.size() > 0) {
                        connection = dbc.getConnection();
                        writer = new DBSubstanceWriter(DBSubstanceWriter.datasetMeta(), new SubstanceRecord(), clearMeasurements, clearComposition);
                        writer.setI5mode(true);
                        writer.setCloseConnection(false);
                        writer.setConnection(connection);
                        writer.open();
                        IContainerClient ccli = i5.getContainerClient();
                        int imported = 0;
                        int importError = 0;
                        for (IIdentifiableResource<IIdentifier> item : queryResults) try {
                            localLogger.log(Level.FINE, item.getResourceIdentifier().toString());
                            List<IIdentifiableResource<IIdentifier>> container = ccli.get(new Identifier(iuclidversion.formatQueryUUID(item.getResourceIdentifier().toString())));
                            processContainer(container, writer, server);
                            imported++;
                        } catch (Exception x) {
                            localLogger.log(Level.SEVERE, x.getMessage());
                            importError++;
                        }
                        String foundMsg = String.format("Found %d substance(s), imported %d substance(s) %d error(s).", queryResults.size(), imported, importError);
                        localLogger.log(Level.INFO, foundMsg);
                        streamHandler.flush();
                        String msg = out.toString();
                        if (importError != 0) {
                            if (imported > 0) {
                                TaskResult result = createReference(connection);
                                msg = msg + String.format("The imported substances are available at %s", result.getUri());
                            }
                            throw new ImportSubstanceException(new Status(Status.SERVER_ERROR_BAD_GATEWAY, foundMsg), msg);
                        } else if (imported == 0) {
                            throw new ImportSubstanceException(new Status(Status.CLIENT_ERROR_NOT_FOUND, foundMsg), msg);
                        }
                    } else {
                        streamHandler.flush();
                        String msg = out.toString();
                        throw new ImportSubstanceException(new Status(Status.CLIENT_ERROR_NOT_FOUND, "No substances found."), msg);
                    }
                } else
                    throw new ImportSubstanceException(new Status(Status.SERVER_ERROR_BAD_GATEWAY, "IUCLID server login failed"), "IUCLID server login failed [" + server + "].");
            } catch (ResourceException x) {
                throw x;
            } catch (Exception x) {
                localLogger.log(Level.SEVERE, x.getMessage());
                streamHandler.flush();
                String msg = out.toString();
                throw new ImportSubstanceException(new Status(Status.SERVER_ERROR_BAD_GATEWAY, "Error when retrieving substances"), msg);
            }
        }
        return createReference(connection);
    } catch (ResourceException x) {
        localLogger.log(Level.SEVERE, x.getMessage(), x);
        throw x;
    } catch (Exception x) {
        localLogger.log(Level.SEVERE, x.getMessage(), x);
        throw x;
    } finally {
        localLogger.fine("Done");
        try {
            if (i5 != null)
                i5.logout();
        } catch (Exception x) {
            localLogger.warning(x.getMessage());
        }
        try {
            if (i5 != null)
                i5.close();
        } catch (Exception x) {
            localLogger.warning(x.getMessage());
        }
        try {
            writer.setConnection(null);
        } catch (Exception x) {
        }
        try {
            writer.close();
        } catch (Exception x) {
        }
        try {
            if (connection != null)
                connection.close();
        } catch (Exception x) {
            localLogger.warning(x.getMessage());
        }
        try {
            if (logHandler != null) {
                localLogger.setUseParentHandlers(true);
                localLogger.removeHandler(logHandler);
                localLogger.removeHandler(streamHandler);
                logHandler.close();
            }
        } catch (Exception x) {
        }
    }
}