Java tutorial
/* * EBI MetaboLights - http://www.ebi.ac.uk/metabolights * Cheminformatics and Metabolism group * * European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom * * Last modified: 4/24/14 11:10 AM * Modified by: conesa * * * , EMBL, European Bioinformatics Institute, 2014. * * 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 uk.ac.ebi.metabolights.utils.isatab; import org.apache.commons.io.filefilter.RegexFileFilter; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import javax.naming.ConfigurationException; import java.io.*; public class IsaTabUtils { private static final String DEFAULT_INVESTIGATION_PATTERN = "i_.*\\.txt"; private static final String FIELD_NAME_WITH_CONFIGURATION = "[created with configuration]"; private static final String DEFAULT_CONFIGURATION_FOLDER = "default"; private static final Logger logger = LoggerFactory.getLogger(IsaTabUtils.class); public static String getInvestigationFileName(String folder) throws FileNotFoundException { return getInvestigationFileName(folder, DEFAULT_INVESTIGATION_PATTERN); } public static String getInvestigationFileName(String folder, String investigationPattern) throws FileNotFoundException { File isaTabFolder = new File(folder); return getInvestigationFileName(isaTabFolder, investigationPattern); } public static String getInvestigationFileName(File folder) throws FileNotFoundException { return getInvestigationFileName(folder, DEFAULT_INVESTIGATION_PATTERN); } public static String getInvestigationFileName(File isaTabFolder, String investigationPattern) throws FileNotFoundException { File inv = getInvestigationFile(isaTabFolder, investigationPattern); return inv.getAbsolutePath(); } public static File getInvestigationFile(File folder) throws FileNotFoundException { return getInvestigationFile(folder, DEFAULT_INVESTIGATION_PATTERN); } public static File getInvestigationFile(String folder, String investigationPattern) throws FileNotFoundException { File isaTabFolder = new File(folder); File inv = getInvestigationFile(isaTabFolder, investigationPattern); return inv; } public static File getInvestigationFile(File isaTabFolder, String investigationPattern) throws FileNotFoundException { logger.debug("Getting Investigation file from " + isaTabFolder.getAbsolutePath() + ". Pattern: " + investigationPattern); //Search for the investigation file File[] fileList; FileFilter filter = new RegexFileFilter(investigationPattern); //Get the file list filtered fileList = isaTabFolder.listFiles(filter); //If there is not an investigation file... if (fileList.length == 0 || fileList == null) { throw new FileNotFoundException("File with Ids (" + investigationPattern + ") not found"); } logger.debug("Investigation file found: " + fileList[0].getAbsolutePath()); //There must be only one, so take the first return fileList[0]; } public static File getConfigurationFolderFromStudy(String isaTabFolder, String rootConfigFolder) throws IOException, ConfigurationException { return getConfigurationFolderFromStudy(isaTabFolder, rootConfigFolder, DEFAULT_CONFIGURATION_FOLDER); } public static File getConfigurationFolderFromStudy(String isaTabFolder, String rootConfigFolder, String defaultConfigurationFolder) throws IOException, ConfigurationException { return getConfigurationFolderFromStudy(new File(isaTabFolder), new File(rootConfigFolder), defaultConfigurationFolder); } /** * Gets the config files from the current study archive folder * @return Name from the line "[Last Opened With Configuration]" in the i_Investigation.txt file, but only if we have the same config, otherwise return the string "default" * @throws IOException */ public static File getConfigurationFolderFromStudy(File isaTabFolder, File rootConfigFolder, String defaultConfig) throws IOException, ConfigurationException { logger.debug("Getting configuration folder for " + isaTabFolder.getAbsolutePath()); logger.debug("Root configuration folder " + rootConfigFolder.getAbsolutePath() + ". Default configuration is " + defaultConfig); logger.debug("Looking for lowercase line with text: " + FIELD_NAME_WITH_CONFIGURATION); File investigationFile = getInvestigationFile(isaTabFolder); BufferedReader br = new BufferedReader(new FileReader(investigationFile)); String configFileFolder = DEFAULT_CONFIGURATION_FOLDER; //Just in case we Could not find the config files used in the investigation file try { String line = br.readLine(); String lastPart = null; while (line != null) { if (line.toLowerCase().contains(FIELD_NAME_WITH_CONFIGURATION)) { String[] lineParts = line.split("\""); //The config file name is always separated with " if (lineParts.length > 1) configFileFolder = lineParts[1]; //Should be the name of the *submitters* config file directory //Only use the last part of the path, split on both / and \ if (configFileFolder.contains("/")) { lastPart = configFileFolder.substring(configFileFolder.lastIndexOf("/")); lastPart = lastPart.replace("/", ""); } if (configFileFolder.contains("\\")) { lastPart = configFileFolder.substring(configFileFolder.lastIndexOf("\\")); lastPart = lastPart.replace("\\", ""); } if (lastPart != null) configFileFolder = lastPart; if (configFileFolder.equals("")) configFileFolder = DEFAULT_CONFIGURATION_FOLDER; logger.debug("Configuration line found: " + line); break; //Nothing more to do in this loop } line = br.readLine(); } } finally { br.close(); } //Have to try to fix Windows path problems, example: C:softwareISAcreatorMetaboLightsConfigurationsMetaboLightsConfig20120129 if (configFileFolder.contains(":")) { //Cannot just check for C:, what about D: ?? //So some Windows paths have been used String[] winPath = configFileFolder.split("Configurations"); //Not elegant, but normally configs would be under the ISAcreator folder "/Configurations/" configFileFolder = winPath[1]; } // Build the final config folder File configFolder = new File(rootConfigFolder.getAbsoluteFile() + File.separator + configFileFolder); if (configFolder.exists()) { logger.debug("Configuration found: " + configFolder.getAbsolutePath()); return configFolder; } else { logger.debug("Configuration not found: " + configFolder.getAbsolutePath() + ", using default"); // Build the final config folder with default config configFolder = new File(rootConfigFolder.getAbsoluteFile() + File.separator + defaultConfig); if (configFolder.exists()) { return configFolder; } else { throw new ConfigurationException("Isatab configuration folder does not exists for the study (" + isaTabFolder.getName() + ").\nConfiguration: " + configFileFolder); } } } }