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Revision 7516

lookup the title for EML files when registering DOIs.
lookup the creator from DataONE CN (if available).
add EML-based test. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5513

View differences:

test/tao.14563.1.xml
1 1
<?xml version="1.0" encoding="UTF-8"?>
2
<eml:eml packageId="tao.14563.1" system="knb" xmlns:eml="eml://ecoinformatics.org/eml-2.1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="eml://ecoinformatics.org/eml-2.1.0 eml.xsd"> <access authSystem="knb" order="allowFirst"> <allow><principal>public</principal>
3
<permission>read</permission>
4
</allow>
5
</access>
6
 <dataset> <title>public-readable from morpho</title>
7
 <creator id="1320966812705"> <individualName><surName>adfasd</surName>
8

  
9
</individualName>
10
</creator>
11
 <abstract><para>adf</para>
12
</abstract>
13
<keywordSet><keyword>SAEON, South Africa</keyword>
14
</keywordSet>
15
<contact id="1320966816821"><individualName><surName>asdfdas</surName>
16
</individualName>
17
</contact>
18
</dataset>
19
 </eml:eml>
20

  
2
<eml:eml packageId="tao.14563.1" system="knb"
3
	xmlns:eml="eml://ecoinformatics.org/eml-2.1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
4
	xsi:schemaLocation="eml://ecoinformatics.org/eml-2.1.0 eml.xsd">
5
	<access authSystem="knb" order="allowFirst">
6
		<allow>
7
			<principal>public</principal>
8
			<permission>read</permission>
9
		</allow>
10
	</access>
11
	<dataset>
12
		<title>Test EML package - public-readable from morpho</title>
13
		<creator id="1320966812705">
14
			<individualName>
15
				<surName>adfasd</surName>
16
			</individualName>
17
		</creator>
18
		<abstract>
19
			<para>adf</para>
20
		</abstract>
21
		<keywordSet>
22
			<keyword>SAEON, South Africa</keyword>
23
		</keywordSet>
24
		<contact id="1320966816821">
25
			<individualName>
26
				<surName>asdfdas</surName>
27
			</individualName>
28
		</contact>
29
	</dataset>
30
</eml:eml>
test/edu/ucsb/nceas/metacat/dataone/RegisterDOITest.java
27 27

  
28 28

  
29 29
import java.io.ByteArrayInputStream;
30
import java.io.FileInputStream;
31
import java.io.FileNotFoundException;
30 32
import java.io.InputStream;
31 33
import java.util.HashMap;
32 34

  
33 35
import junit.framework.Test;
34 36
import junit.framework.TestSuite;
35 37

  
38
import org.dataone.client.ObjectFormatCache;
36 39
import org.dataone.configuration.Settings;
37 40
import org.dataone.service.types.v1.Identifier;
38 41
import org.dataone.service.types.v1.Session;
42
import org.dataone.service.types.v1.Subject;
39 43
import org.dataone.service.types.v1.SystemMetadata;
40 44
import org.junit.After;
41 45
import org.junit.Before;
......
53 57
 */
54 58
public class RegisterDOITest extends D1NodeServiceTest {
55 59

  
56
  /**
57
   * Set up the test fixtures
58
   * 
59
   * @throws Exception
60
   */
61
  @Before
62
  public void setUp() throws Exception {
63
    super.setUp();
64
    // set up the configuration for d1client
65
    Settings.getConfiguration().setProperty("D1Client.cnClassName", MockCNode.class.getName());
66
  }
60
	
61
	
62
	/**
63
	 * Set up the test fixtures
64
	 * 
65
	 * @throws Exception
66
	 */
67
	@Before
68
	public void setUp() throws Exception {
69
		super.setUp();
70
		// set up the configuration for d1client
71
		Settings.getConfiguration().setProperty("D1Client.cnClassName",
72
				MockCNode.class.getName());
73
	}
67 74

  
68
  /**
69
   * Remove the test fixtures
70
   */
71
  @After
72
  public void tearDown() {
73
  }
74
  
75
  /**
76
   * Build the test suite
77
   * @return
78
   */
79
  public static Test suite() {
80
    
81
    TestSuite suite = new TestSuite();
82
    suite.addTest(new RegisterDOITest("initialize"));
83
    
84
    // DOI registration test
85
    suite.addTest(new RegisterDOITest("testCreateDOI"));
86
    suite.addTest(new RegisterDOITest("testMintAndCreateDOI"));
75
	/**
76
	 * Remove the test fixtures
77
	 */
78
	@After
79
	public void tearDown() {
80
	}
87 81

  
88
    return suite;
89
    
90
  }
91
  
92
  /**
93
   * Constructor for the tests
94
   * 
95
   * @param name - the name of the test
96
   */
97
  public RegisterDOITest(String name) {
98
    super(name);
99
    
100
  }
82
	/**
83
	 * Build the test suite
84
	 * 
85
	 * @return
86
	 */
87
	public static Test suite() {
101 88

  
102
  /**
103
   * Initial blank test
104
   */
105
  public void initialize() {
106
    assertTrue(1 == 1);
107
    
108
  }
89
		TestSuite suite = new TestSuite();
90
		suite.addTest(new RegisterDOITest("initialize"));
91

  
92
		// DOI registration test
93
		suite.addTest(new RegisterDOITest("testCreateDOI"));
94
		suite.addTest(new RegisterDOITest("testMintAndCreateDOI"));
95
		suite.addTest(new RegisterDOITest("testMintAndCreateForEML"));
96

  
97
		return suite;
98

  
99
	}
100

  
101
	/**
102
	 * Constructor for the tests
103
	 * 
104
	 * @param name
105
	 *            - the name of the test
106
	 */
107
	public RegisterDOITest(String name) {
108
		super(name);
109

  
110
	}
111

  
112
	/**
113
	 * Initial blank test
114
	 */
115
	public void initialize() {
116
		assertTrue(1 == 1);
117

  
118
	}
119
	
120
	/**
121
	 * constructs a "fake" session with a test subject
122
	 * @return
123
	 */
124
	@Override
125
	public Session getTestSession() throws Exception {
126
		Session session = new Session();
127
        Subject subject = new Subject();
128
        subject.setValue("CN=Benjamin Leinfelder A515,O=University of Chicago,C=US,DC=cilogon,DC=org");
129
        session.setSubject(subject);
130
        return session;
131
	}
109 132
  
110
  	/**
133
	public void testMintAndCreateDOI() {
134
		printTestHeader("testMintAndCreateDOI");
135
		testMintAndCreateDOI(null);
136
	}
137
  	
138
	public void testMintAndCreateForEML() {
139
		printTestHeader("testMintAndCreateForEML");
140
		String emlFile = "test/tao.14563.1.xml";
141
		InputStream content = null;
142
		try {
143
			content = new FileInputStream(emlFile);
144
		} catch (FileNotFoundException e) {
145
			e.printStackTrace();
146
			fail(e.getMessage());
147
		}
148
		testMintAndCreateDOI(content);
149
	}
150
	
151
	/**
111 152
	 * Test object creation
112 153
	 */
113
	public void testMintAndCreateDOI() {
114
		printTestHeader("testMintAndCreateDOI");
154
	private void testMintAndCreateDOI(InputStream inputStream) {
155
		printTestHeader("testMintAndCreateDOI - common");
115 156

  
116 157
		try {
117 158
			// get ezid config properties
......
131 172
			assertNotNull(metadata);
132 173

  
133 174
			// add the actual object for the newly-minted DOI
134
			InputStream object = new ByteArrayInputStream( "test".getBytes("UTF-8"));
135
			SystemMetadata sysmeta = createSystemMetadata(guid, session.getSubject(), object);
175
			SystemMetadata sysmeta = null;
176
			InputStream object = null;
177
			if (inputStream != null) {
178
				sysmeta = createSystemMetadata(guid, session.getSubject(), null);
179
				object = inputStream;
180
		        sysmeta.setFormatId(ObjectFormatCache.getInstance().getFormat("eml://ecoinformatics.org/eml-2.1.0").getFormatId());
181
			} else {
182
				object = new ByteArrayInputStream("test".getBytes("UTF-8"));
183
				sysmeta = createSystemMetadata(guid, session.getSubject(), object);
184
			}
185

  
136 186
			Identifier pid = MNodeService.getInstance(request).create(session, guid, object, sysmeta);
137 187
			assertEquals(guid.getValue(), pid.getValue());
138 188

  
......
141 191
			assertNotNull(metadata);
142 192
			assertTrue(metadata.containsKey(DataCiteProfile.TITLE.toString()));
143 193
			
194
			System.out.println("tested with DOI: " + pid.getValue());
195
			
144 196
		} catch (Exception e) {
145 197
			e.printStackTrace();
146 198
			fail("Unexpected error: " + e.getMessage());
src/edu/ucsb/nceas/metacat/dataone/DOIService.java
22 22
 */
23 23
package edu.ucsb.nceas.metacat.dataone;
24 24

  
25
import java.io.InputStream;
25 26
import java.text.SimpleDateFormat;
27
import java.util.Arrays;
28
import java.util.Collections;
26 29
import java.util.HashMap;
27 30

  
28 31
import org.apache.log4j.Logger;
32
import org.apache.wicket.protocol.http.MockHttpServletRequest;
33
import org.dataone.client.D1Client;
34
import org.dataone.service.exceptions.InsufficientResources;
29 35
import org.dataone.service.exceptions.InvalidRequest;
36
import org.dataone.service.exceptions.InvalidToken;
37
import org.dataone.service.exceptions.NotAuthorized;
38
import org.dataone.service.exceptions.NotFound;
30 39
import org.dataone.service.exceptions.NotImplemented;
31 40
import org.dataone.service.exceptions.ServiceFailure;
32 41
import org.dataone.service.types.v1.Identifier;
33 42
import org.dataone.service.types.v1.Node;
43
import org.dataone.service.types.v1.Permission;
44
import org.dataone.service.types.v1.Person;
45
import org.dataone.service.types.v1.Session;
46
import org.dataone.service.types.v1.Subject;
47
import org.dataone.service.types.v1.SubjectInfo;
34 48
import org.dataone.service.types.v1.SystemMetadata;
49
import org.dataone.service.types.v1.util.AuthUtils;
50
import org.dataone.service.util.Constants;
51
import org.ecoinformatics.datamanager.parser.DataPackage;
52
import org.ecoinformatics.datamanager.parser.generic.DataPackageParserInterface;
53
import org.ecoinformatics.datamanager.parser.generic.Eml200DataPackageParser;
35 54

  
36 55
import edu.ucsb.nceas.ezid.EZIDException;
37 56
import edu.ucsb.nceas.ezid.EZIDService;
......
131 150
				// confuses the API if we send the original metadata that it gave us, so start from scratch
132 151
				metadata = new HashMap<String, String>();
133 152
				
134
				// TODO: set title and creator to better values
153
				// title 
154
				String title = ErcMissingValueCode.UNKNOWN.toString();
155
				try {
156
					title = lookupTitle(sysMeta);
157
				} catch (Exception e) {
158
					e.printStackTrace();
159
					// ignore
160
				}
161
				
162
				// creator
163
				String creator = sysMeta.getRightsHolder().getValue();
164
				try {
165
					creator = lookupCreator(sysMeta.getRightsHolder());
166
				} catch (Exception e) {
167
					// ignore and use default
168
				}
169
				
170
				// publisher
171
				String publisher = ErcMissingValueCode.UNKNOWN.toString();
135 172
				Node node = MNodeService.getInstance(null).getCapabilities();
173
				publisher = node.getName();
174
				
175
				// publication year
136 176
				SimpleDateFormat sdf = new SimpleDateFormat("yyyy");
137 177
				String year = sdf .format(sysMeta.getDateUploaded());
138
				metadata.put(DataCiteProfile.TITLE.toString(), ErcMissingValueCode.UNKNOWN.toString());
139
				metadata.put(DataCiteProfile.CREATOR.toString(), sysMeta.getRightsHolder().getValue());
140
				metadata.put(DataCiteProfile.PUBLISHER.toString(), node.getName());
178
				
179
				// type
180
				String resourceType = DataCiteProfileResourceTypeValues.DATASET.toString() + "/" + sysMeta.getFormatId().getValue();
181
				
182
				// target (URL)
183
				String target = node.getBaseURL() + "/v1/object/" + identifier;
184
				
185
				// status and export fields for public/protected data
186
				String status = InternalProfileValues.UNAVAILABLE.toString();
187
				String export = InternalProfileValues.NO.toString();
188
				Subject publicSubject = new Subject();
189
				publicSubject.setValue(Constants.SUBJECT_PUBLIC);
190
				if (AuthUtils.isAuthorized(Arrays.asList(new Subject[] {publicSubject}), Permission.READ, sysMeta)) {
191
					status = InternalProfileValues.PUBLIC.toString();
192
					export = InternalProfileValues.YES.toString();
193
				}
194
				
195
				// set the metadata fields
196
				metadata.put(DataCiteProfile.TITLE.toString(), title);
197
				metadata.put(DataCiteProfile.CREATOR.toString(), creator);
198
				metadata.put(DataCiteProfile.PUBLISHER.toString(), publisher);
141 199
				metadata.put(DataCiteProfile.PUBLICATION_YEAR.toString(), year);
142
				metadata.put(DataCiteProfile.RESOURCE_TYPE.toString(), DataCiteProfileResourceTypeValues.DATASET.toString() + "/" + sysMeta.getFormatId().getValue());
143
				metadata.put(InternalProfile.TARGET.toString(), node.getBaseURL() + "/v1/object/" + identifier);
144
				metadata.put(InternalProfile.STATUS.toString(), InternalProfileValues.PUBLIC.toString());
145
				metadata.put(InternalProfile.EXPORT.toString(), InternalProfileValues.YES.toString());
200
				metadata.put(DataCiteProfile.RESOURCE_TYPE.toString(), resourceType);
201
				metadata.put(InternalProfile.TARGET.toString(), target);
202
				metadata.put(InternalProfile.STATUS.toString(), status);
203
				metadata.put(InternalProfile.EXPORT.toString(), export);
146 204
	
147 205
				// set using the API
148 206
				if (create) {
......
212 270
		
213 271
		return identifier;
214 272
	}
273
	
274
	/**
275
	 * Locates an appropriate title for the object identified by the given SystemMetadata.
276
	 * Different types of objects will be handled differently for titles:
277
	 * 1. EML formats - parsed by the Datamanager library to find dataset title 
278
	 * 2. Data objects - TODO: use title from EML file that describes that data
279
	 * 3. ORE objects - TODO: use title from EML file contained in that package
280
	 * @param sysMeta
281
	 * @return appropriate title if known, or the missing value code
282
	 * @throws Exception
283
	 */
284
	private String lookupTitle(SystemMetadata sysMeta) throws Exception {
285
		String title = ErcMissingValueCode.UNKNOWN.toString();
286
		if (sysMeta.getFormatId().getValue().startsWith("eml://")) {
287
			DataPackageParserInterface parser = new Eml200DataPackageParser();
288
			// for using the MN API as the MN itself
289
			MockHttpServletRequest request = new MockHttpServletRequest(null, null, null);
290
			Session session = new Session();
291
	        Subject subject = MNodeService.getInstance(request).getCapabilities().getSubject(0);
292
	        session.setSubject(subject);
293
			InputStream emlStream = MNodeService.getInstance(request).get(session, sysMeta.getIdentifier());
294
			parser.parse(emlStream);
295
			DataPackage dataPackage = parser.getDataPackage();
296
			title = dataPackage.getTitle();
297
		}
298
		return title;
299
	}
215 300

  
301
	/**
302
	 * Lookup the citable name for the given Subject
303
	 * Calls the configured CN to determine this information.
304
	 * If the person is not registered with the CN identity service, 
305
	 * a NotFound exception will be raised as expected from the service.
306
	 * @param subject
307
	 * @return fullName if found
308
	 * @throws ServiceFailure
309
	 * @throws NotAuthorized
310
	 * @throws NotImplemented
311
	 * @throws NotFound
312
	 * @throws InvalidToken
313
	 */
314
	private String lookupCreator(Subject subject) throws ServiceFailure, NotAuthorized, NotImplemented, NotFound, InvalidToken {
315
		// default to given DN
316
		String fullName = subject.getValue();
317
		
318
		SubjectInfo subjectInfo = D1Client.getCN().getSubjectInfo(subject);
319
		if (subjectInfo != null && subjectInfo.getPersonList() != null) {
320
			for (Person p: subjectInfo.getPersonList()) {
321
				if (p.getSubject().equals(subject)) {
322
					fullName = p.getFamilyName();
323
					if (p.getGivenNameList() != null && p.getGivenNameList().size() > 0) {
324
						fullName = fullName + ", " + p.getGivenName(0);
325
					}
326
					break;
327
				}
328
			}
329
		}
330
		
331
		return fullName;
332
		
333
	}
216 334
	
217 335
}

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