/* * Copyright 2015-2016 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package org.opencb.opencga.storage.app; import com.beust.jcommander.ParameterException; import org.opencb.opencga.core.common.GitRepositoryState; import org.opencb.opencga.storage.app.cli.CommandExecutor; import org.opencb.opencga.storage.app.cli.client.executors.AlignmentCommandExecutor; import org.opencb.opencga.storage.app.cli.client.CliOptionsParser; import org.opencb.opencga.storage.app.cli.client.executors.VariantCommandExecutor; import java.io.IOException; /** * Created by imedina on 02/03/15. */ public class StorageMain { public static void main(String[] args) { System.exit(privateMain(args)); } public static int privateMain(String[] args) { CliOptionsParser cliOptionsParser = new CliOptionsParser(); try { cliOptionsParser.parse(args); } catch (ParameterException e) { System.err.println(e.getMessage()); cliOptionsParser.printUsage(); return 1; } String parsedCommand = cliOptionsParser.getCommand(); if (parsedCommand == null || parsedCommand.isEmpty()) { if (cliOptionsParser.getGeneralOptions().version) { System.out.println("Version " + GitRepositoryState.get().getBuildVersion()); System.out.println("Git version: " + GitRepositoryState.get().getBranch() + " " + GitRepositoryState.get().getCommitId()); // System.out.println(GitRepositoryState.get()); return 0; } else if (cliOptionsParser.getGeneralOptions().help) { cliOptionsParser.printUsage(); return 0; } else { cliOptionsParser.printUsage(); return 1; } } else { CommandExecutor commandExecutor = null; // Check if any command -h option is present if (cliOptionsParser.isHelp()) { cliOptionsParser.printUsage(); return 0; } else { String parsedSubCommand = cliOptionsParser.getSubCommand(); if (parsedSubCommand == null || parsedSubCommand.isEmpty()) { cliOptionsParser.printUsage(); } else { switch (parsedCommand) { // case "feature": // commandExecutor = new IndexAlignmentsCommandExecutor(cliOptionsParser.getIndexAlignmentsCommandOptions()); // break; case "alignment": commandExecutor = new AlignmentCommandExecutor(cliOptionsParser.getAlignmentCommandOptions()); break; case "variant": commandExecutor = new VariantCommandExecutor(cliOptionsParser.getVariantCommandOptions()); break; default: System.out.printf("ERROR: not valid command passed: '" + parsedCommand + "'"); break; } if (commandExecutor != null) { try { commandExecutor.loadStorageConfiguration(); } catch (IOException ex) { if (commandExecutor.getLogger() == null) { ex.printStackTrace(); } else { commandExecutor.getLogger().error("Error reading OpenCGA Storage configuration: " + ex.getMessage()); } } try { commandExecutor.execute(); } catch (IOException ex) { ex.printStackTrace(); return 1; } catch (Exception e) { e.printStackTrace(); return 1; } } else { cliOptionsParser.printUsage(); return 1; } } } } return 0; } }