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Revision 7853

Added by ben leinfelder over 11 years ago

MN.getPackage() - test with ORE that includes 2 data files and a "metadata" file (still should be using EML for that test). https://projects.ecoinformatics.org/ecoinfo/issues/6026

View differences:

test/edu/ucsb/nceas/metacat/dataone/MNodeServiceTest.java
28 28 

  		




  29
  29
  
    
import gov.loc.repository.bagit.Bag;


  		




  30
  30
  
    
import gov.loc.repository.bagit.BagFactory;


  		




  
  31
  
    
import gov.loc.repository.bagit.BagFile;


  		




  
  32
  
    
import gov.loc.repository.bagit.Manifest;


  		




  31
  33
  
    

  		




  32
  34
  
    
import java.io.ByteArrayInputStream;


  		




  33
  35
  
    
import java.io.ByteArrayOutputStream;


  		




  ......




  40
  42
  
    
import java.util.ArrayList;


  		




  41
  43
  
    
import java.util.Calendar;


  		




  42
  44
  
    
import java.util.Date;


  		




  
  45
  
    
import java.util.HashMap;


  		




  
  46
  
    
import java.util.Iterator;


  		




  43
  47
  
    
import java.util.List;


  		




  
  48
  
    
import java.util.Map;


  		




  44
  49
  
    

  		




  45
  50
  
    
import junit.framework.Test;


  		




  46
  51
  
    
import junit.framework.TestSuite;


  		




  47
  52
  
    

  		




  48
  53
  
    
import org.apache.commons.io.IOUtils;


  		




  
  54
  
    
import org.dataone.client.ObjectFormatCache;


  		




  49
  55
  
    
import org.dataone.configuration.Settings;


  		




  
  56
  
    
import org.dataone.ore.ResourceMapFactory;


  		




  50
  57
  
    
import org.dataone.service.util.TypeMarshaller;


  		




  51
  58
  
    
import org.dataone.service.exceptions.IdentifierNotUnique;


  		




  52
  59
  
    
import org.dataone.service.exceptions.InsufficientResources;


  		




  ......




  77
  84
  
    
import org.dataone.service.types.v1.Subject;


  		




  78
  85
  
    
import org.dataone.service.types.v1.SubjectInfo;


  		




  79
  86
  
    
import org.dataone.service.types.v1.SystemMetadata;


  		




  
  87
  
    
import org.dspace.foresite.ResourceMap;


  		




  80
  88
  
    
import org.jibx.runtime.JiBXException;


  		




  81
  89
  
    
import org.junit.After;


  		




  82
  90
  
    
import org.junit.Before;


  		




  ......




  149
  157
  
    
    suite.addTest(new MNodeServiceTest("testReplicate"));


  		




  150
  158
  
    
    // MN packaging tests


  		




  151
  159
  
    
    suite.addTest(new MNodeServiceTest("testGetPackage"));


  		




  
  160
  
    
    suite.addTest(new MNodeServiceTest("testGetOREPackage"));


  		




  152
  161
  
    
    


  		




  153
  162
  
    
    


  		




  154
  163
  
    
    return suite;


  		




  ......




  1112
  1121
  
    
			SystemMetadata sysmeta = createSystemMetadata(guid, session.getSubject(), object);


  		




  1113
  1122
  
    
			Identifier pid = MNodeService.getInstance(request).create(session, guid, object, sysmeta);


  		




  1114
  1123
  
    
			InputStream bagStream = MNodeService.getInstance(request).getPackage(session, pid);


  		




  1115
  
  
    
			File bagFile = File.createTempFile("bagit", ".zip");


  		




  
  1124
  
    
			File bagFile = File.createTempFile("bagit.", ".zip");


  		




  1116
  1125
  
    
			IOUtils.copy(bagStream, new FileOutputStream(bagFile));


  		




  1117
  1126
  
    
			BagFactory bagFactory = new BagFactory();


  		




  1118
  1127
  
    
			Bag bag = bagFactory.createBag(bagFile);


  		




  ......




  1133
  1142
  
    
			fail("Unexpected error: " + e.getMessage());


  		




  1134
  1143
  
    
		}


  		




  1135
  1144
  
    
	}


  		




  
  1145
  
    
	


  		




  
  1146
  
    
	


  		




  
  1147
  
    
	/**


  		




  
  1148
  
    
	 * Test getting a known object


  		




  
  1149
  
    
	 */


  		




  
  1150
  
    
	public void testGetOREPackage() {


  		




  
  1151
  
    
		printTestHeader("testGetOREPackage");


  		




  
  1152
  
    

  		




  
  1153
  
    
		try {


  		




  
  1154
  
    
			


  		




  
  1155
  
    
			// construct the ORE package


  		




  
  1156
  
    
			Identifier resourceMapId = new Identifier();


  		




  
  1157
  
    
			//resourceMapId.setValue("doi://1234/AA/map.1.1");


  		




  
  1158
  
    
			resourceMapId.setValue("testGetOREPackage." + System.currentTimeMillis());


  		




  
  1159
  
    
			Identifier metadataId = new Identifier();


  		




  
  1160
  
    
			metadataId.setValue("doi://1234/AA/meta.1." + + System.currentTimeMillis());


  		




  
  1161
  
    
			List<Identifier> dataIds = new ArrayList<Identifier>();


  		




  
  1162
  
    
			Identifier dataId = new Identifier();


  		




  
  1163
  
    
			dataId.setValue("doi://1234/AA/data.1." + System.currentTimeMillis());


  		




  
  1164
  
    
			Identifier dataId2 = new Identifier();


  		




  
  1165
  
    
			dataId2.setValue("doi://1234/AA/data.2." + System.currentTimeMillis());


  		




  
  1166
  
    
			dataIds.add(dataId);


  		




  
  1167
  
    
			dataIds.add(dataId2);


  		




  
  1168
  
    
			Map<Identifier, List<Identifier>> idMap = new HashMap<Identifier, List<Identifier>>();


  		




  
  1169
  
    
			idMap.put(metadataId, dataIds);


  		




  
  1170
  
    
			ResourceMapFactory rmf = ResourceMapFactory.getInstance();


  		




  
  1171
  
    
			ResourceMap resourceMap = rmf.createResourceMap(resourceMapId, idMap);


  		




  
  1172
  
    
			assertNotNull(resourceMap);


  		




  
  1173
  
    
			String rdfXml = ResourceMapFactory.getInstance().serializeResourceMap(resourceMap);


  		




  
  1174
  
    
			assertNotNull(rdfXml);


  		




  
  1175
  
    
			


  		




  
  1176
  
    
			Session session = getTestSession();


  		




  
  1177
  
    
			InputStream object = null;


  		




  
  1178
  
    
			SystemMetadata sysmeta = null;


  		




  
  1179
  
    
			


  		




  
  1180
  
    
			// save the data objects (data just contains their ID)


  		




  
  1181
  
    
			InputStream dataObject1 = new ByteArrayInputStream(dataId.getValue().getBytes("UTF-8"));


  		




  
  1182
  
    
			sysmeta = createSystemMetadata(dataId, session.getSubject(), dataObject1);


  		




  
  1183
  
    
			MNodeService.getInstance(request).create(session, dataId, dataObject1, sysmeta);


  		




  
  1184
  
    
			// second data file


  		




  
  1185
  
    
			InputStream dataObject2 = new ByteArrayInputStream(dataId2.getValue().getBytes("UTF-8"));


  		




  
  1186
  
    
			sysmeta = createSystemMetadata(dataId2, session.getSubject(), dataObject2);


  		




  
  1187
  
    
			MNodeService.getInstance(request).create(session, dataId2, dataObject2, sysmeta);


  		




  
  1188
  
    
			// metadata file


  		




  
  1189
  
    
			InputStream metadataObject = new ByteArrayInputStream(metadataId.getValue().getBytes("UTF-8"));


  		




  
  1190
  
    
			sysmeta = createSystemMetadata(metadataId, session.getSubject(), metadataObject);


  		




  
  1191
  
    
			MNodeService.getInstance(request).create(session, metadataId, metadataObject, sysmeta);


  		




  
  1192
  
    
						


  		




  
  1193
  
    
			// save the ORE object


  		




  
  1194
  
    
			object = new ByteArrayInputStream(rdfXml.getBytes("UTF-8"));


  		




  
  1195
  
    
			sysmeta = createSystemMetadata(resourceMapId, session.getSubject(), object);


  		




  
  1196
  
    
			sysmeta.setFormatId(ObjectFormatCache.getInstance().getFormat("http://www.openarchives.org/ore/terms").getFormatId());


  		




  
  1197
  
    
			Identifier pid = MNodeService.getInstance(request).create(session, resourceMapId, object, sysmeta);


  		




  
  1198
  
    
			


  		




  
  1199
  
    
			// get the package we uploaded


  		




  
  1200
  
    
			InputStream bagStream = MNodeService.getInstance(request).getPackage(session, pid);


  		




  
  1201
  
    
			File bagFile = File.createTempFile("bagit.", ".zip");


  		




  
  1202
  
    
			IOUtils.copy(bagStream, new FileOutputStream(bagFile));


  		




  
  1203
  
    
			BagFactory bagFactory = new BagFactory();


  		




  
  1204
  
    
			Bag bag = bagFactory.createBag(bagFile);


  		




  
  1205
  
    
			Iterator<Manifest> manifestIter = bag.getTagManifests().iterator();


  		




  
  1206
  
    
			while (manifestIter.hasNext()) {


  		




  
  1207
  
    
				String filepath = manifestIter.next().getFilepath();


  		




  
  1208
  
    
				BagFile entryFile = bag.getBagFile(filepath);


  		




  
  1209
  
    
				InputStream result = entryFile.newInputStream();


  		




  
  1210
  
    
				// check ORE


  		




  
  1211
  
    
				if (filepath.contains(resourceMapId.getValue())) {


  		




  
  1212
  
    
					object.reset();


  		




  
  1213
  
    
					assertTrue(object.available() > 0);


  		




  
  1214
  
    
					assertTrue(result.available() > 0);


  		




  
  1215
  
    
					assertTrue(IOUtils.contentEquals(result, object));


  		




  
  1216
  
    
				}


  		




  
  1217
  
    
				// check metadata


  		




  
  1218
  
    
				if (filepath.contains(metadataId.getValue())) {


  		




  
  1219
  
    
					metadataObject.reset();


  		




  
  1220
  
    
					assertTrue(metadataObject.available() > 0);


  		




  
  1221
  
    
					assertTrue(result.available() > 0);


  		




  
  1222
  
    
					assertTrue(IOUtils.contentEquals(result, metadataObject));


  		




  
  1223
  
    
				}


  		




  
  1224
  
    
				if (filepath.contains(dataId.getValue())) {


  		




  
  1225
  
    
					dataObject1.reset();


  		




  
  1226
  
    
					assertTrue(dataObject1.available() > 0);


  		




  
  1227
  
    
					assertTrue(result.available() > 0);


  		




  
  1228
  
    
					assertTrue(IOUtils.contentEquals(result, dataObject1));


  		




  
  1229
  
    
				}


  		




  
  1230
  
    
				if (filepath.contains(dataId2.getValue())) {


  		




  
  1231
  
    
					dataObject2.reset();


  		




  
  1232
  
    
					assertTrue(dataObject2.available() > 0);


  		




  
  1233
  
    
					assertTrue(result.available() > 0);


  		




  
  1234
  
    
					assertTrue(IOUtils.contentEquals(result, dataObject2));


  		




  
  1235
  
    
				}


  		




  
  1236
  
    
				


  		




  
  1237
  
    
				


  		




  
  1238
  
    
			}


  		




  
  1239
  
    
			


  		




  
  1240
  
    
			// clean up


  		




  
  1241
  
    
			bagFile.delete();


  		




  
  1242
  
    

  		




  
  1243
  
    
		} catch (Exception e) {


  		




  
  1244
  
    
			e.printStackTrace();


  		




  
  1245
  
    
			fail("Unexpected error: " + e.getMessage());


  		




  
  1246
  
    
		}


  		




  
  1247
  
    
	}


  		




  
  1248
  
    
	


  		




  1136
  1249
  
    
  


  		




  1137
  
  
    
  


  		




  1138
  
  
    
  


  		




  1139
  1250
  
    
}


  		












  

    
      src/edu/ucsb/nceas/metacat/dataone/MNodeService.java
    
  





  1673
  1673
  
    
			packagePids.add(pid);


  		




  1674
  1674
  
    
		}


  		




  1675
  1675
  
    

  		




  
  1676
  
    
		// track the pid-to-file mapping


  		




  
  1677
  
    
		StringBuffer pidMapping = new StringBuffer();


  		




  1676
  1678
  
    
		// loop through the package contents


  		




  1677
  1679
  
    
		for (Identifier entryPid: packagePids) {


  		




  1678
  1680
  
    
			SystemMetadata entrySysMeta = this.getSystemMetadata(session, entryPid);


  		




  1679
  1681
  
    
			String extension = ObjectFormatInfo.instance().getExtension(entrySysMeta.getFormatId().getValue());


  		




  1680
  1682
  
    
	        String prefix = entryPid.getValue();


  		




  1681
  
  
    
			File tempFile = File.createTempFile(prefix + "_bagit", extension);


  		




  
  1683
  
    
	        prefix = "entry";


  		




  
  1684
  
    
			File tempFile = File.createTempFile(prefix + ".", extension);


  		




  1682
  1685
  
    
			tempFiles.add(tempFile);


  		




  1683
  1686
  
    
			InputStream entryInputStream = this.get(session, entryPid);


  		




  1684
  1687
  
    
			IOUtils.copy(entryInputStream, new FileOutputStream(tempFile));


  		




  1685
  1688
  
    
			bag.addFileToPayload(tempFile);


  		




  
  1689
  
    
			pidMapping.append(entryPid.getValue() + "\t" + "data/" + tempFile.getName() + "\n");


  		




  1686
  1690
  
    
		}


  		




  1687
  1691
  
    
		


  		




  
  1692
  
    
		//add the the pid to data file map


  		




  
  1693
  
    
		File pidMappingFile = File.createTempFile("pid-mapping.", ".txt");


  		




  
  1694
  
    
		IOUtils.write(pidMapping.toString(), new FileOutputStream(pidMappingFile));


  		




  
  1695
  
    
		bag.addFileAsTag(pidMappingFile);


  		




  
  1696
  
    

  		




  1688
  1697
  
    
		bag = bag.makeComplete();


  		




  1689
  
  
    
		File bagFile = File.createTempFile("bagit", ".zip");


  		




  
  1698
  
    
		File bagFile = File.createTempFile("bag.", ".zip");


  		




  1690
  1699
  
    
		// TODO: delete more confidently


  		




  1691
  1700
  
    
		bagFile.deleteOnExit();


  		




  1692
  1701
  
    
		bag.setFile(bagFile);


  		












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