package cmd;

import java.io.BufferedReader;

import java.io.File;

import java.nio.file.Paths;

import java.util.Arrays;

import java.util.List;

import java.util.concurrent.Callable;

import java.util.concurrent.ExecutorService;

import java.util.concurrent.Executors;

import java.util.stream.Collectors;

import gui.STDataAssembly;

import io.SpatialDataIO;

import io.TextFileAccess;

import io.TextFileIO;

import net.imglib2.img.Img;

import net.imglib2.img.array.ArrayImgs;

import net.imglib2.type.numeric.integer.IntType;

import picocli.CommandLine;

import picocli.CommandLine.Command;

import picocli.CommandLine.Option;

import org.apache.logging.log4j.Logger;

import util.LoggerUtil;

@Command(name = "st-add-annotations", mixinStandardHelpOptions = true, version = "0.3.2-SNAPSHOT", description = "Spatial Transcriptomics as IMages project - add annotations to slice-dataset")

public class AddAnnotations implements Callable<Void> {

private static final Logger logger = LoggerUtil.getLogger();

@Option(names = {"-i", "--input"}, required = true, description = "input dataset, e.g. -i /home/ssq.n5/Puck_180528_20")

private String inputPath = null;

@Option(names = {"-a", "--annotation"}, required = true, description = "comma separated list of one or more annotation info, e.g. -m '/home/celltypes_180528_20.csv,/home/clustering_180528_22.csv'")

private String annotations = null;

@Option(names = {"-l", "--label"}, required = false, description = "comma separated list of one or more labels for annotation, e.g. -l celltypes,clustering; default: filenames of annotation files")

private String labels = null;

@Override

public Void call() throws Exception {

if (inputPath == null) {

logger.error("No input path defined. Stopping.");

return null;

}

final List<String> annotationList = Arrays.stream(annotations.split(",")).map(String::trim).collect(Collectors.toList());

final List<String> labelList;

if (labels == null) {

logger.error("No labels given; using filenames as labels.");

labelList = annotationList.stream()

.map(s -> Paths.get(new File(s).getAbsolutePath()).getFileName().toString().split("\\.")[0])

.collect(Collectors.toList());

}

else

labelList = Arrays.stream(labels.split(",")).map(String::trim).collect(Collectors.toList());

if (annotationList.isEmpty()) {

logger.error( "no annotation files specified. stopping.");

return null;

}

if (annotationList.size() != labelList.size()) {

logger.error("number of annotation files ({}) does not match number of labels ({}). stopping.", annotationList.size(), labelList.size());

return null;

}

logger.info("adding annotations to {}", inputPath);

final ExecutorService service = Executors.newFixedThreadPool(8);

final SpatialDataIO sdio = SpatialDataIO.open(inputPath, service);

final STDataAssembly stData = sdio.readData();

for (int i = 0; i < annotationList.size(); ++i) {

final String annotationName = annotationList.get(i);

final String label = labelList.get(i);

logger.debug("\n>>> Processing {}", annotationName);

final File in = new File(annotationName);

final BufferedReader readsIn;

if ( !in.exists() ||

in.getAbsolutePath().toLowerCase().endsWith( ".zip" ) ||

in.getAbsolutePath().toLowerCase().endsWith( ".gz" ) ||

in.getAbsolutePath().toLowerCase().endsWith( ".tar" ) )

readsIn = Resave.openCompressedFile( in ); // try opening as compressed file

else

readsIn = TextFileAccess.openFileRead( in );

if (readsIn == null) {

logger.error("Could not open file '{}'. Stopping.", in.getAbsolutePath());

return null;

}

else {

logger.debug("Loading file '{}' as label '{}'", in.getAbsolutePath(), label);

}

final int[] ids;

final boolean barcodesUnavailable = stData.data().getBarcodes().get(0).isEmpty();

if (barcodesUnavailable)

ids = TextFileIO.readAnnotations(readsIn, (int) stData.data().numLocations());

else

ids = TextFileIO.readAnnotations(readsIn, stData.data().getBarcodes());

readsIn.close();

final Img<IntType> img = ArrayImgs.ints(ids, (int) stData.data().numLocations());

stData.data().getAnnotations().put(label, img);

}

sdio.updateStoredAnnotations(stData.data().getAnnotations());

logger.debug( "Done." );

service.shutdown();

return null;

}

public static void main(final String... args) {

final CommandLine cmd = new CommandLine(new AddAnnotations());

cmd.execute(args);

}

}