package cmd;

import io.SpatialDataContainer;

import picocli.CommandLine;

import picocli.CommandLine.Option;

import picocli.CommandLine.Command;

import java.io.File;

import java.util.concurrent.Callable;

import java.util.concurrent.ExecutorService;

import java.util.concurrent.Executors;

import org.apache.logging.log4j.Logger;

import util.LoggerUtil;

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

public class AddSlice 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")

private String inputDatasetPath = null;

@Option(names = {"-c", "--container"}, required = true, description = "container to add dataset to; if it doesn't exist, it will be created")

private String containerPath = null;

@Option(names = {"-m", "--move"}, required = false, description = "flag to indicate if dataset should be moved to container; if not, it is linked")

private boolean shouldBeMoved = false;

@Option(names = {"-l", "--locations"}, required = false, description = "path to locations within the dataset; if not given, the standard path is assumed")

private String locationPath = null;

@Option(names = {"-e", "--expression-values"}, required = false, description = "path to expression values within the dataset; if not given, the standard path is assumed")

private String exprValPath = null;

@Option(names = {"-a", "--annotations"}, required = false, description = "path to annotations within the dataset; if not given, the standard path is assumed")

private String annotationPath = null;

@Override

public Void call() throws Exception {

if (containerPath == null) {

logger.error("No container defined. Stopping.");

return null;

}

if (inputDatasetPath == null) {

logger.error("No dataset defined. Stopping.");

return null;

}

final File containerFile = new File(containerPath);

final boolean containerExists = (containerFile.exists());

logger.info("Container '{}' {}", containerFile.getAbsolutePath(), containerExists ? "exists" : "is new ...");

ExecutorService service = Executors.newFixedThreadPool(1);

SpatialDataContainer container = containerExists

? SpatialDataContainer.openExisting(containerPath, service)

: SpatialDataContainer.createNew(containerPath, service);

if (shouldBeMoved)

container.addExistingDataset(inputDatasetPath, locationPath, exprValPath, annotationPath, null);

else

container.linkExistingDataset(inputDatasetPath, locationPath, exprValPath, annotationPath, null);

final String operation = shouldBeMoved ? "Moved" : "Linked";

logger.info("{} dataset '{}' to container '{}'.", operation, inputDatasetPath, containerPath);

service.shutdown();

return null;

}

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

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

cmd.execute(args);

}

}