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MutationStepListener.java
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MutationStepListener.java
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package org.cbio.gdcpipeline.listener;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.cbio.gdcpipeline.util.CommonDataUtil;
import org.springframework.batch.core.ExitStatus;
import org.springframework.batch.core.StepExecution;
import org.springframework.batch.core.StepExecutionListener;
import org.springframework.beans.factory.annotation.Value;
import java.io.File;
import java.nio.file.*;
import java.util.ArrayList;
import java.util.List;
import org.cbio.gdcpipeline.model.ManifestFileData;
/**
* @author Dixit Patel
**/
public class MutationStepListener implements StepExecutionListener {
private static Log LOG = LogFactory.getLog(MutationStepListener.class);
@Value("${mutation.data.file.prefix}")
private String MUTATION_DATA_FILE_PREFIX;
@Value("${mutation.default.merged.maf.file}")
private String MUTATION_DEFAULT_MERGED_MAF_FILE;
@Value("#{jobParameters[sourceDirectory]}")
private String sourceDir;
@Value("#{jobParameters[outputDirectory]}")
private String outputDir;
@Value("#{jobExecutionContext[gdcManifestData]}")
private List<ManifestFileData> gdcManifestData;
@Value("#{jobParameters[separate_mafs]}")
private String separate_mafs;
@Override
public void beforeStep(StepExecution stepExecution) {
List<File> maf_files ;
if (stepExecution.getJobExecution().getExecutionContext().containsKey("maf_files")) {
maf_files = (List<File>)stepExecution.getJobExecution().getExecutionContext().get("maf_files");
}
else {
maf_files = getMutationFileList();
}
if (!maf_files.isEmpty()) {
if (!separate_mafs.isEmpty()) {
if (separate_mafs.equalsIgnoreCase("true")) {
//used by metadata step
List<String> maf_filenames = new ArrayList<>();
for(File file : maf_files){
maf_filenames.add(MUTATION_DATA_FILE_PREFIX+file.getName());
}
stepExecution.getJobExecution().getExecutionContext().put("mutation_data_filenames", maf_filenames);
//read individually
List<File> mafToProcess = new ArrayList<>();
mafToProcess.add(maf_files.remove(0));
stepExecution.getJobExecution().getExecutionContext().put("maf_files", maf_files);
stepExecution.getExecutionContext().put("mafToProcess", mafToProcess);
} else {
//Read all MAF's together
List<String> mutation_data_filenames = new ArrayList<>();
mutation_data_filenames.add(MUTATION_DEFAULT_MERGED_MAF_FILE);
stepExecution.getJobExecution().getExecutionContext().put("mutation_data_filenames",mutation_data_filenames );
stepExecution.getExecutionContext().put("mafToProcess", maf_files);
}
}
}
}
@Override
public ExitStatus afterStep(StepExecution stepExecution) {
if (!separate_mafs.isEmpty()) {
if (separate_mafs.equalsIgnoreCase("true")) {
List<String> mafList = (List<String>) stepExecution.getJobExecution().getExecutionContext().get("maf_files");
if (!mafList.isEmpty()) {
return new ExitStatus("CONTINUE");
}
}
//delete temp directory
CommonDataUtil.deleteTempDir();
}
return ExitStatus.COMPLETED;
}
public List<File> getMutationFileList() {
List<File> mutationFileList = new ArrayList<>();
for (ManifestFileData dataFile : gdcManifestData) {
if (CommonDataUtil.GDC_TYPE.MUTATION.toString().equals(dataFile.getNormalizedDatatype())) {
Path path = Paths.get(sourceDir, dataFile.getId(), dataFile.getFilename());
File file = path.toFile();
mutationFileList.add(file);
}
}
try {
if (!mutationFileList.isEmpty()) {
mutationFileList = CommonDataUtil.extractCompressedFiles(mutationFileList);
}
else {
LOG.error("Mutation file list empty");
}
}
catch (Exception e) {
LOG.error("Could not extract maf files!");
}
return mutationFileList;
}
}