Java tutorial
/* * MIT License * * Copyright (c) 2016 EPAM Systems * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in all * copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE * SOFTWARE. */ package com.epam.ngb.cli.manager.command.handler.http; import static com.epam.ngb.cli.constants.MessageConstants.MINIMUM_COMMAND_ARGUMENTS; import java.net.URISyntaxException; import java.util.ArrayList; import java.util.List; import org.apache.http.client.methods.HttpPost; import org.apache.http.client.utils.URIBuilder; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.epam.ngb.cli.app.ApplicationOptions; import com.epam.ngb.cli.constants.MessageConstants; import com.epam.ngb.cli.entity.BiologicalDataItem; import com.epam.ngb.cli.entity.ProjectItem; import com.epam.ngb.cli.entity.RegistrationRequest; import com.epam.ngb.cli.exception.ApplicationException; import com.epam.ngb.cli.manager.command.handler.Command; /** * {@code {@link DatasetRegistrationHandler}} represents a tool for handling 'register_dataset' command and * creating new datasets (ex-projects) on NGB server. This command requires at least two arguments: * reference ID or name and dataset name. The command also supports creating a dataset with files, that can * be either already registered in the server (addressed by name or ID) or new files (path to files * must be provided in this case). New files at first will be registered with help of * {@code {@link FileRegistrationHandler}} and then added to a dataset. * Command supports hierarchical datasets, parent dataset is specified by 'parent' option. */ @Command(type = Command.Type.REQUEST, command = { "register_dataset" }) public class DatasetRegistrationHandler extends AbstractHTTPCommandHandler { /** * Name of a created dataset, name must be unique */ private String name; /** * Pretty name of a created dataset */ private String prettyName; /** * ID of a parent dataset in case of hierarchical datasets */ private Long parentId; /** * List of files in a dataset, at least one - reference - file is required for * dataset registration */ private List<ProjectItem> items; /** * If true command will output result of dataset registration in a json format */ private boolean printJson; /** * If true command will output result of dataset registration in a table format */ private boolean printTable; private static final Logger LOGGER = LoggerFactory.getLogger(DatasetRegistrationHandler.class); /** * Verifies that input arguments contain the required parameters: * first argument must be reference ID or name, second dataset name and optional following * arguments may specify files to be added to the dataset (registered on the server files are * addressed by name or ID, for new files path should be provided). * If new files are registered by this command, all rules and restrictions that are * applied to file registration are used. * If a dataset is a part of hierarchical project, it's parent dataset may ne specified * by 'parentID' option (name or ID of parent dataset). * @param arguments command line arguments for 'register_dataset' command * @param options to specify a parentID of the dataset and output options */ @Override public void parseAndVerifyArguments(List<String> arguments, ApplicationOptions options) { if (arguments.size() < 2) { throw new IllegalArgumentException( MessageConstants.getMessage(MINIMUM_COMMAND_ARGUMENTS, getCommand(), 2, arguments.size())); } name = arguments.get(1); prettyName = options.getPrettyName(); if (options.getParent() != null) { parentId = parseProjectId(options.getParent()); } items = new ArrayList<>(); Long referenceId = parseFileId(arguments.get(0)); printJson = options.isPrintJson(); printTable = options.isPrintTable(); items.add(new ProjectItem(referenceId, false)); Long referenceUniqueId = null; for (int i = 2; i < arguments.size(); i++) { String file = arguments.get(i); try { Long id = parseFileId(file); items.add(new ProjectItem(id, false)); continue; } catch (ApplicationException e) { LOGGER.debug(e.getMessage(), e); } ApplicationOptions registerOptions = new ApplicationOptions(); registerOptions.setDoIndex(options.isDoIndex()); referenceUniqueId = referenceUniqueId == null ? loadReferenceId(arguments.get(0)) : referenceUniqueId; FileRegistrationHandler handler = new FileRegistrationHandler(file, referenceUniqueId, this, registerOptions); handler.setRequestUrl(handler.getServerParameters().getRegistrationUrl()); handler.setRequestType("POST"); List<BiologicalDataItem> registeredFiles = handler.registerItems(); if (!registeredFiles.isEmpty()) { registeredFiles.forEach(f -> items.add(new ProjectItem(f.getBioDataItemId(), false))); } } } /** * Performs a dataset registration request to NGB server and prints registration result to * StdOut if it is specified by the command line options * @return 0 if request completed successfully */ @Override public int runCommand() { try { URIBuilder builder = new URIBuilder(serverParameters.getServerUrl() + getRequestUrl()); if (parentId != null) { builder.addParameter("parentId", String.valueOf(parentId)); } HttpPost post = new HttpPost(builder.build()); setDefaultHeader(post); if (isSecure()) { addAuthorizationToRequest(post); } RegistrationRequest registration = new RegistrationRequest(); registration.setName(name); registration.setItems(items); registration.setPrettyName(prettyName); String result = getPostResult(registration, post); checkAndPrintDatasetResult(result, printJson, printTable); } catch (URISyntaxException e) { throw new ApplicationException(e.getMessage(), e); } return 0; } }