List of usage examples for org.apache.commons.configuration BaseConfiguration getList
public List getList(String key)
From source file:uk.ac.sanger.cgp.wwdocker.workflow.SangerWorkflow.java
@Override public List filesToPush(File iniFile) { List files = new ArrayList(); files.add(iniFile);/*from w w w . j a v a 2 s. c o m*/ logger.trace(iniFile); BaseConfiguration wkflConf = Config.loadConfig(iniFile.getAbsolutePath(), new Character(':'), false); if (wkflConf.getBoolean("testMode")) { logger.info(iniFile.getAbsolutePath() + " is set as testMode=true, no BAMs to transfer"); } else { // Add construct the paths to the local files List analysisIds = wkflConf.getList("tumourAnalysisIds"); analysisIds.add(wkflConf.getList("controlAnalysisId")); List bamFiles = wkflConf.getList("tumourBams"); bamFiles.add(wkflConf.getList("controlBam")); if (analysisIds.size() != bamFiles.size()) { throw new RuntimeException( "Number of *AnalysisId[s] is not equal to the number of *Bam[s] in workfile: " + iniFile.getAbsolutePath()); } for (int i = 0; i < analysisIds.size(); i++) { String analysisId = (String) analysisIds.get(i); String bamFile = (String) bamFiles.get(i); File bamPath = new File( config.getString("data_root").concat("/").concat(analysisId).concat("/").concat(bamFile)); if (!bamPath.exists()) { throw new RuntimeException("Unable to find BAM file (" + bamPath.getAbsolutePath() + ") expected from worfile: " + iniFile.getAbsolutePath()); } files.add(bamPath); } } return files; }