BagIt2N3BagJob.java

/**
 * Copyright 2008 The University of North Carolina at Chapel Hill
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package edu.unc.lib.deposit.normalize;

import static edu.unc.lib.deposit.work.DepositGraphUtils.dprop;
import static edu.unc.lib.deposit.work.DepositGraphUtils.fprop;
import static edu.unc.lib.dl.util.ContentModelHelper.DepositRelationship.md5sum;
import static edu.unc.lib.dl.util.ContentModelHelper.Model.SIMPLE;

import java.io.File;
import java.net.URI;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Collection;
import java.util.Map;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.Resource;

import edu.unc.lib.dl.util.ContentModelHelper.DepositRelationship;
import edu.unc.lib.dl.util.ContentModelHelper.FedoraProperty;
import edu.unc.lib.dl.util.RedisWorkerConstants.DepositField;
import edu.unc.lib.staging.StagingException;
import gov.loc.repository.bagit.Bag;
import gov.loc.repository.bagit.Bag.Format;
import gov.loc.repository.bagit.BagFactory;
import gov.loc.repository.bagit.BagFile;
import gov.loc.repository.bagit.BagHelper;
import gov.loc.repository.bagit.Manifest;
import gov.loc.repository.bagit.utilities.SimpleResult;

/**
 * Transforms bagit bags stored in a staging location into n3 for deposit
 * 
 * @author bbpennel
 * @author daines
 * @date Nov 9, 2015
 */
public class BagIt2N3BagJob extends AbstractFileServerToBagJob {
	private static final Logger log = LoggerFactory.getLogger(BagIt2N3BagJob.class);
	
	public BagIt2N3BagJob() {
		super();
	}

	public BagIt2N3BagJob(String uuid, String depositUUID) {
		super(uuid, depositUUID);
	}

	@Override
	public void runJob() {
		
		Model model = getWritableModel();
		com.hp.hpl.jena.rdf.model.Bag depositBag = model.createBag(getDepositPID().getURI().toString());
		
		Map<String, String> status = getDepositStatus();
		String sourcePath = status.get(DepositField.sourcePath.name());
		
		File sourceFile = new File(sourcePath);
		
		if (BagHelper.getVersion(sourceFile) == null) {
			failJob("Can't find BagIt bag", "A BagIt bag could not be found at the source path.");
		}
		
		BagFactory bagFactory = new BagFactory();
		Bag bag = bagFactory.createBag(sourceFile);
		
		if (bag.getFormat() != Format.FILESYSTEM) {
			failJob("Unsupported BagIt bag format", "Only filesystem bags are supported.");
		}
		
		// Verify that the bag has all the required parts
		SimpleResult completeResult = bag.verifyComplete();
		if (!bag.verifyComplete().isSuccess()) {
			// Bag did not validate, generate error report and throw exception
			StringBuilder msg = new StringBuilder();
			for (String error : completeResult.getErrorMessages()) {
				msg.append(error).append("\n");
			}
			
			failJob("Unable to normalize bag " + sourcePath + ", it was not complete according to bagit specifications",
					msg.toString());
		}
		
		Collection<BagFile> payload = bag.getPayload();
		
		Property labelProp = dprop(model, DepositRelationship.label);
		Property hasModelProp = fprop(model, FedoraProperty.hasModel);
		Property md5sumProp = dprop(model, md5sum);
		Property locationProp = dprop(model, DepositRelationship.stagingLocation);
		Resource simpleResource = model.createResource(SIMPLE.getURI().toString());
		
		// Turn the bag itself into the top level folder for this deposit
		com.hp.hpl.jena.rdf.model.Bag sourceBag = getSourceBag(depositBag, sourceFile);
		
		int i = 0;
		// Add all of the payload objects into the bag folder
		for (BagFile file : payload) {
			log.debug("Adding object {}: {}", i++, file.getFilepath());
			
			String filePath = file.getFilepath();
			
			Map<Manifest.Algorithm, String> checksums = bag.getChecksums(filePath);
			
			Resource fileResource = getFileResource(sourceBag, filePath);
			
			// add checksum, size, label
			String filename = filePath.substring(filePath.lastIndexOf("/") + 1);
			model.add(fileResource, labelProp, filename);
			model.add(fileResource, hasModelProp, simpleResource);
			if (checksums.containsKey(Manifest.Algorithm.MD5)) {
				model.add(fileResource, md5sumProp, checksums.get(Manifest.Algorithm.MD5));
			}
			
			// Find staged path for the file
			Path storedPath = Paths.get(sourceFile.getAbsolutePath(), filePath);
			try {
				URI stagedURI = stages.getStagedURI(storedPath.toUri());
				model.add(fileResource, locationProp, stagedURI.toString());
			} catch (StagingException e) {
				failJob(e, "Unable to get staged path for file {}", storedPath);
			}
			
		}
		
		String sourceAbsPath = sourceFile.getAbsolutePath();
		// Register tag file as deposit manifests, then register  them for cleanup later 
		for (BagFile tag : bag.getTags()) {
			Path path = Paths.get(sourceAbsPath, tag.getFilepath());
			try {
				URI stagedURI = stages.getStagedURI(path.toUri());
				if (stagedURI != null) {
					getDepositStatusFactory().addManifest(getDepositUUID(), stagedURI.toString());
					model.add(depositBag, dprop(model, DepositRelationship.cleanupLocation), stagedURI.toString());
				}
			} catch (StagingException e) {
				failJob(e, "Unable to get staged path for file {}", path);
			}
		}
		
		// Register the bag itself for cleanup
		Path storedPath = sourceFile.toPath();
		try {
			URI stagedURI = stages.getStagedURI(storedPath.toUri());
			
			if (stagedURI != null) {
				model.add(depositBag, dprop(model, DepositRelationship.cleanupLocation), stagedURI.toString());
			}
		} catch (StagingException e) {
			failJob(e, "Unable to get staged path for file {}", storedPath);
		}
		
	}
	
}