org.molgenis.dataexplorer.controller.AnnotationJob Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of molgenis-dataexplorer Show documentation
There is a newer version: 8.4.5
Show newest version
package org.molgenis.dataexplorer.controller;

import static java.util.Objects.requireNonNull;

import java.util.List;

import org.apache.commons.lang3.StringUtils;
import org.molgenis.data.Repository;
import org.molgenis.data.annotation.CrudRepositoryAnnotator;
import org.molgenis.data.annotation.RepositoryAnnotator;
import org.molgenis.data.jobs.Job;
import org.molgenis.data.jobs.Progress;
import org.springframework.security.core.Authentication;
import org.springframework.transaction.support.TransactionTemplate;

import com.google.common.collect.Lists;

public class AnnotationJob extends Job
{
	private final CrudRepositoryAnnotator crudRepositoryAnnotator;
	private final String username;
	private final List annotators;
	private final Repository repository;
	List successfulAnnotators = Lists.newArrayList();
	List failedAnnotators = Lists.newArrayList();
	Exception firstException = null;

	public AnnotationJob(CrudRepositoryAnnotator crudRepositoryAnnotator, String username,
			List annotators, Repository repository, Progress progress,
			Authentication userAuthentication, TransactionTemplate transactionTemplate)
	{
		super(progress, transactionTemplate, userAuthentication);

		this.crudRepositoryAnnotator = requireNonNull(crudRepositoryAnnotator);
		this.username = requireNonNull(username);
		this.annotators = requireNonNull(annotators);
		this.repository = requireNonNull(repository);
	}

	@Override
	public Void call(Progress progress) throws Exception
	{
		progress.setProgressMax(annotators.size());
		int i = 0;

		for (RepositoryAnnotator annotator : annotators)
		{
			progress.progress(i, getMessage(i, annotator));
			try
			{
				crudRepositoryAnnotator.annotate(annotator, repository);
				successfulAnnotators.add(annotator.getSimpleName());
			}
			catch (Exception ex)
			{
				if (firstException == null)
				{
					firstException = ex;
				}
				failedAnnotators.add(annotator.getSimpleName());
			}
			i++;
		}
		progress.progress(annotators.size(), getMessage());
		try
		{
			// TODO: Workaround to make sure that the progress bar gets loaded
			Thread.sleep(1000);
		}
		catch (InterruptedException e)
		{
		}
		if (firstException != null)
		{
			progress.status("Failed annotators: " + StringUtils.join(failedAnnotators, ",") + ". Successful annotators: "
					+ StringUtils.join(successfulAnnotators, ","));
			throw firstException;
		}
		return null;
	}

	private String getMessage()
	{
		return String.format("Annotated \"%s\" with %s (started by \"%s\")", repository.getEntityMetaData().getLabel(),
				StringUtils.join(successfulAnnotators, ","), username);
	}

	private String getMessage(int i, RepositoryAnnotator annotator)
	{
		return String.format("Annotating \"%s\" with %s (annotator %d of %d, started by \"%s\")",
				repository.getEntityMetaData().getLabel(), annotator.getSimpleName(), i + 1, annotators.size(),
				username);
	}
}