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Revision 58513

[maven-release-plugin] copy for tag dnet-openaireplus-mapping-utils-6.3.43

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modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/deploy.info
1
{"type_source": "SVN", "goal": "package -U source:jar", 
2
"url": "http://svn-public.driver.research-infrastructures.eu/driver/dnet45/modules/dnet-openaireplus-mapping-utils/trunk/", "deploy_repository": "dnet45-snapshots", "version": "4", "mail": "sandro.labruzzo@isti.cnr.it,michele.artini@isti.cnr.it, claudio.atzori@isti.cnr.it, alessia.bardi@isti.cnr.it", "deploy_repository_url": "http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-snapshots", "name": "dnet-openaireplus-mapping-utils"}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/openaire/exporter/model/ProjectTest.java
1
package eu.dnetlib.openaire.exporter.model;
2

  
3
import org.junit.Before;
4
import org.junit.Test;
5

  
6
import static org.junit.Assert.assertEquals;
7

  
8
public class ProjectTest {
9

  
10
	Project pMZOS;
11
	Project pFP7;
12

  
13
	@Before
14
	public void setUp() throws Exception {
15
		pMZOS = new Project()
16
				.setFunder("MZOS")
17
				.setJurisdiction("HR")
18
				.setFundingpathid("irb_hr______::MZOS")
19
				.setAcronym("")
20
				.setTitle("Project Title")
21
				.setCode("115-1152437-2500")
22
				.setStartdate("2007-01-01")
23
				.setEnddate("2009-01-01");
24

  
25
		pFP7 = new Project()
26
				.setFunder("EC")
27
				.setJurisdiction("EU")
28
				.setFundingpathid("ec__________::EC::FP7::SP1::NMP")
29
				.setAcronym("REFFIBRE")
30
				.setTitle("Project Title")
31
				.setCode("604187")
32
				.setStartdate("2013-11-01")
33
				.setEnddate("20015-01-01");
34
	}
35

  
36
	@Test
37
	public void testIdNamespaceMZOS(){
38
		String ns = pMZOS.getIdnamespace();
39
		assertEquals("info:eu-repo/grantAgreement/MZOS//115-1152437-2500/HR", ns);
40
	}
41

  
42
	@Test
43
	public void testIdNamespaceFP7(){
44
		String ns = pFP7.getIdnamespace();
45
		assertEquals("info:eu-repo/grantAgreement/EC/FP7/604187/EU", ns);
46
	}
47

  
48

  
49

  
50
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/openaire/exporter/model/ProjectDetailTest.java
1
package eu.dnetlib.openaire.exporter.model;
2

  
3
import java.io.IOException;
4
import java.io.StringReader;
5

  
6
import com.google.common.collect.Lists;
7
import org.apache.commons.io.IOUtils;
8
import org.springframework.core.io.ClassPathResource;
9
import org.springframework.core.io.Resource;
10

  
11
import static org.junit.Assert.assertEquals;
12

  
13
/**
14
 * Created by claudio on 22/09/16.
15
 */
16
public class ProjectDetailTest {
17

  
18
	private Resource projectsCsv = new ClassPathResource("/eu/dnetlib/openaire/exporter/model/projectDetails.csv");
19
	private Resource projectsJson = new ClassPathResource("/eu/dnetlib/openaire/exporter/model/projectDetails.json");
20

  
21
	//@Test
22
	public void testSerialisationCSV() throws IOException {
23
		final String csv = IOUtils.toString(projectsCsv.getInputStream());
24
		doTest(csv, "csv");
25
	}
26

  
27
	//@Test
28
	public void testSerialisationCSV2() throws IOException {
29
		final ProjectDetail p = new ProjectDetail()
30
				.setAcronym("acro")
31
				.setCode("01")
32
				.setOptional1("op1")
33
				.setOptional2("op2")
34
				.setProjectId("project_01")
35
				.setJsonextrainfo("extraInfo")
36
				.setFundingPath(Lists.newArrayList("fundingpath1", "fundingpath2"));
37

  
38
		doTest(p.asCSV(), "csv");
39
	}
40

  
41
	//@Test
42
	public void testSerialisationJSON() throws IOException {
43
		final String json = IOUtils.toString(projectsJson.getInputStream());
44
		doTest(json, "json");
45
	}
46

  
47
	private void doTest(final String data, final String format) throws IOException {
48
		final StringReader reader = new StringReader(data);
49
		for(String line : IOUtils.readLines(reader)) {
50
			System.out.println("line:          " + line);
51
			ProjectDetail p;
52
			String s = "";
53
			switch (format) {
54
			case "csv":
55
				p = ProjectDetail.fromCSV(line);
56
				s = p.asCSV();
57
				break;
58
			case "json":
59
				p = ProjectDetail.fromJson(line);
60
				s = p.asJson();
61
				break;
62
			default: throw new IllegalArgumentException("invalid format: " + format);
63
			}
64
			System.out.println("serialisation: " + s);
65
			assertEquals(s, line);
66
		}
67
	}
68

  
69
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/mapreduce/util/OafDecoderTest.java
1
package eu.dnetlib.data.mapreduce.util;
2

  
3
import static org.junit.Assert.assertFalse;
4
import static org.junit.Assert.assertNotNull;
5

  
6
import java.util.List;
7

  
8
import org.junit.Test;
9

  
10
import eu.dnetlib.data.proto.KindProtos.Kind;
11
import eu.dnetlib.miscutils.functional.xml.IndentXmlString;
12

  
13
public class OafDecoderTest {
14

  
15
	@Test
16
	public void testAsXml() {
17

  
18
		final OafDecoder decoder = OafTest.embed(OafTest.getResult("50|id_1"), Kind.entity);
19

  
20
		assertNotNull(decoder);
21

  
22
		assertNotNull(decoder.asXml());
23

  
24
		System.out.println(IndentXmlString.apply(decoder.asXml()));
25

  
26
	}
27

  
28
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/mapreduce/util/OafRowKeyDecoderTest.java
1
package eu.dnetlib.data.mapreduce.util;
2

  
3
import org.junit.Test;
4

  
5
public class OafRowKeyDecoderTest {
6

  
7
	@Test
8
	public void test() {
9

  
10
		String id1 = "50|acnbad______::0a454baf9c61e63d42fb83ab549f8062";
11

  
12
		OafRowKeyDecoder d = OafRowKeyDecoder.decode(id1);
13

  
14
		System.out.println(d.getId());
15
	}
16

  
17
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/mapreduce/util/OafRelDecoderTest.java
1
package eu.dnetlib.data.mapreduce.util;
2

  
3
import eu.dnetlib.data.proto.DedupProtos.Dedup.RelName;
4
import eu.dnetlib.data.proto.OafProtos.OafRel;
5
import eu.dnetlib.data.proto.RelTypeProtos.RelType;
6
import eu.dnetlib.data.proto.RelTypeProtos.SubRelType;
7
import org.junit.Before;
8
import org.junit.Test;
9

  
10
import static org.junit.Assert.assertEquals;
11
import static org.junit.Assert.assertNotNull;
12

  
13
public class OafRelDecoderTest {
14

  
15
	private OafRel oafRel;
16

  
17
	@Before
18
	public void setUp() {
19
		oafRel = OafTest.getDedupRel("ID_1", "ID_2", RelType.resultResult, "isMergedIn");
20
	}
21

  
22
	@Test
23
	public void testSetClass() {
24

  
25
		OafRelDecoder d1 = OafRelDecoder.decode(oafRel);
26

  
27
		assertNotNull(d1);
28
		assertEquals("isMergedIn", d1.getRelClass());
29

  
30
		OafRelDecoder d2 = OafRelDecoder.decode(d1.setClassId("isMergedIn").build());
31

  
32
		assertEquals("isMergedIn", d2.getRelClass());
33
		assertEquals("isMergedIn", d2.getRelMetadata().getSemantics().getClassid());
34
		assertEquals("isMergedIn", d2.getRelMetadata().getSemantics().getClassname());
35

  
36
	}
37

  
38
	@Test
39
	public void testGetCF() {
40
		assertEquals("resultResult_dedup_isMergedIn", OafRelDecoder.getCFQ(RelType.resultResult, SubRelType.dedup, RelName.isMergedIn));
41
		assertEquals("resultResult_dedup_isMergedIn", OafRelDecoder.getCFQ(RelType.resultResult, SubRelType.dedup, "isMergedIn"));
42
	}
43

  
44
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/bulktag/CommunityConfigurationFactoryTest.java
1
package eu.dnetlib.data.bulktag;
2

  
3
import com.google.gson.Gson;
4

  
5
import eu.dnetlib.data.bulktag.selectioncriteria.VerbResolver;
6
import eu.dnetlib.data.bulktag.selectioncriteria.VerbResolverFactory;
7
import junit.framework.Assert;
8
import org.apache.commons.io.IOUtils;
9
import org.apache.commons.lang3.StringUtils;
10
import org.dom4j.DocumentException;
11
import org.junit.Before;
12
import org.junit.Ignore;
13
import org.junit.Test;
14
import java.io.IOException;
15
import java.lang.reflect.InvocationTargetException;
16
import java.util.*;
17

  
18
import static org.junit.Assert.assertEquals;
19
import static org.junit.Assert.assertTrue;
20

  
21
/**
22
 * Created by miriam on 03/08/2018.
23
 */
24

  
25

  
26
public class CommunityConfigurationFactoryTest {
27

  
28
    private String xml;
29
    private String xml1;
30

  
31
    private final VerbResolver resolver = new VerbResolver();
32

  
33
    @Before
34
    public void setUp() throws IOException, DocumentException {
35
        xml = IOUtils.toString(getClass().getResourceAsStream("community_configuration.xml"));
36
        xml1 = IOUtils.toString(getClass().getResourceAsStream("community_configuration_selcrit.xml"));
37

  
38
    }
39

  
40
    @Test
41
    public void parseTest() throws DocumentException {
42

  
43
        final CommunityConfiguration cc = CommunityConfigurationFactory.newInstance(xml);
44
        assertEquals(5,cc.size());
45
        cc.getCommunityList().forEach(c -> assertTrue(StringUtils.isNoneBlank(c.getId())));
46

  
47

  
48
    }
49

  
50
    @Test
51
    public void applyVerb() throws InvocationTargetException, IllegalAccessException, NoSuchMethodException, InstantiationException {
52
        Constraint sc = new Constraint();
53
        String verb = "not_contains";
54
        sc.setVerb("not_contains");
55
        sc.setField("contributor");
56
        sc.setValue("DARIAH");
57
        sc.setSelection(resolver.getSelectionCriteria(sc.getVerb(),sc.getValue()));
58
        String metadata = "This work has been partially supported by DARIAH-EU infrastructure";
59

  
60
        Assert.assertFalse(sc.verifyCriteria(metadata));
61
    }
62

  
63

  
64
    @Test
65
    public void loadSelCriteriaTest() throws DocumentException {
66
        final CommunityConfiguration cc = CommunityConfigurationFactory.newInstance(xml1);
67
        Map<String,List<String>> param = new HashMap<>();
68
        param.put("author",new ArrayList<>(Collections.singletonList("Pippo Pippi")));
69
        param.put("description",new ArrayList<>(Collections.singletonList("This work has been partially supported by DARIAH-EU infrastructure")));
70
        param.put("contributor",new ArrayList<>(Collections.singletonList("Pallino ha aiutato a scrivere il paper. Pallino lavora per DARIAH")));
71
        List<String> comm = cc.getCommunityForDatasource("openaire____::1cfdb2e14977f31a98e0118283401f32",param);
72
        Assert.assertEquals(1,comm.size());
73
        Assert.assertEquals("dariah",comm.get(0));
74

  
75
    }
76

  
77
    @Test
78
    public void test4() throws DocumentException, IOException {
79
        final CommunityConfiguration cc = CommunityConfigurationFactory.fromJson(IOUtils.toString(getClass().getResourceAsStream("community_configuration_selcrit.json")));
80
        cc.toString();
81

  
82

  
83
    }
84

  
85
    @Test
86
    public void test5() throws IOException, DocumentException {
87

  
88
        //final CommunityConfiguration cc = CommunityConfigurationFactory.newInstance(IOUtils.toString(getClass().getResourceAsStream("test.xml")));
89
        final CommunityConfiguration cc = CommunityConfigurationFactory.fromJson(IOUtils.toString(getClass().getResourceAsStream("community_configuration.json")));
90
        
91
        System.out.println(cc.toJson());
92
    }
93

  
94

  
95
    @Test
96
    public void test6() {
97
        String json = "{\"criteria\":[{\"constraint\":[{\"verb\":\"contains\",\"field\":\"contributor\",\"value\":\"DARIAH\"}]}]}";
98

  
99
//        String step1 = "{\"verb\":\"contains\",\"field\":\"contributor\",\"value\":\"DARIAH\"}";
100
//
101
//        Constraint c = new Gson().fromJson(step1, Constraint.class);
102
//
103
//        String step2 = "{\"constraint\":[{\"verb\":\"contains\",\"field\":\"contributor\",\"value\":\"DARIAH\"}]}";
104
//
105
//        ConstraintEncapsulator ce = new Gson().fromJson(step2,ConstraintEncapsulator.class);
106
//
107
//
108
//        String step3 = "{\"ce\":{\"constraint\":[{\"verb\":\"contains\",\"field\":\"contributor\",\"value\":\"DARIAH\"}]}}";
109
//
110
//        Constraints cons = new Gson().fromJson(step3,Constraints.class);
111
//
112
//        String step4 = "{\"criteria\":[{\"ce\":{\"constraint\":[{\"verb\":\"contains\",\"field\":\"contributor\",\"value\":\"DARIAH\"}]}}]}";
113
//
114
//        ConstraintsList cl = new Gson().fromJson(step4,ConstraintsList.class);
115
//
116
//        String step5 = "{\"cl\":{\"criteria\":[{\"ce\":{\"constraint\":[{\"verb\":\"contains\",\"field\":\"contributor\",\"value\":\"DARIAH\"}]}}]}}";
117
        SelectionConstraints sl = new Gson().fromJson(json,SelectionConstraints.class);
118

  
119

  
120
    }
121

  
122

  
123

  
124

  
125
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/transform/ParserToProtoIT.java
1
package eu.dnetlib.data.transform;
2

  
3
import java.io.IOException;
4
import java.io.InputStream;
5
import java.io.StringReader;
6
import java.util.List;
7
import java.util.Objects;
8
import java.util.Properties;
9
import java.util.concurrent.atomic.AtomicInteger;
10
import java.util.function.Function;
11
import java.util.stream.Collectors;
12
import java.util.stream.StreamSupport;
13

  
14
import com.google.protobuf.InvalidProtocolBufferException;
15
import com.mongodb.client.MongoCollection;
16
import com.mongodb.client.MongoDatabase;
17
import eu.dnetlib.data.proto.OafProtos.Oaf;
18
import eu.dnetlib.data.proto.OafProtos.OafEntity;
19
import eu.dnetlib.data.transform.xml2.DatasetToProto;
20
import eu.dnetlib.miscutils.collections.Pair;
21
import eu.dnetlib.miscutils.datetime.HumanTime;
22
import org.apache.commons.io.IOUtils;
23
import org.apache.commons.lang3.time.StopWatch;
24
import org.apache.commons.logging.Log;
25
import org.apache.commons.logging.LogFactory;
26
import org.apache.commons.math.stat.descriptive.DescriptiveStatistics;
27
import org.bson.Document;
28
import org.dom4j.DocumentException;
29
import org.dom4j.io.SAXReader;
30
import org.junit.Before;
31
import org.junit.Ignore;
32
import org.junit.Test;
33
import org.junit.runner.RunWith;
34
import org.springframework.beans.factory.annotation.Autowired;
35
import org.springframework.test.context.ContextConfiguration;
36
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
37

  
38
import static org.junit.Assert.assertFalse;
39
import static org.junit.Assert.assertNotNull;
40
import static org.junit.Assert.assertTrue;
41

  
42
@RunWith(SpringJUnit4ClassRunner.class)
43
@ContextConfiguration(classes = { ConfigurationTestConfig.class })
44
public class ParserToProtoIT {
45

  
46
	private static final Log log = LogFactory.getLog(ParserToProtoIT.class);
47

  
48
	private static final String DATACITE = "datacite";
49
	private static final String NARCIS = "narcis";
50

  
51
	private static final int BATCH_SIZE = 10000;
52
	private static final int LOG_FREQ = 5000;
53
	private static final int LIMIT = 10000;
54
	public static final String BODY = "body";
55

  
56
	private static String basePathProfiles = "/eu/dnetlib/test/profiles/TransformationRuleDSResources/TransformationRuleDSResourceType/";
57

  
58
	private int batchSize = BATCH_SIZE;
59
	private int logFreq = LOG_FREQ;
60
	private int limit = LIMIT;
61

  
62
	@Autowired
63
	private MongoDatabase db;
64

  
65
	@Autowired()
66
	private Properties testProperties;
67

  
68
	@Before
69
	public void setUp() {
70
		logFreq = Integer.valueOf(testProperties.getProperty("test.logFreq", String.valueOf(LOG_FREQ)));
71
		batchSize = Integer.valueOf(testProperties.getProperty("test.batchSize", String.valueOf(BATCH_SIZE)));
72
		limit = Integer.valueOf(testProperties.getProperty("test.limit", String.valueOf(limit)));
73
	}
74

  
75
	@Test
76
	@Ignore
77
	public void testParseDataciteWithVTD() throws IOException {
78
		doTest(s -> new Pair<>(s, new DatasetToProto().apply(s)), DATACITE);
79
	}
80

  
81
	@Test
82
	@Ignore
83
	public void testParseDataciteWithXSLT() throws IOException {
84
		final String xslt = IOUtils.toString(loadFromTransformationProfile("odf2hbase.xml"));
85
		final XsltRowTransformer transformer = XsltRowTransformerFactory.newInstance(xslt);
86

  
87
		doTest(rowToOaf(transformer), DATACITE);
88
	}
89

  
90
	@Test
91
	@Ignore
92
	public void testParseNarcisWithXSLT() throws IOException {
93
		final String xslt = IOUtils.toString(loadFromTransformationProfile("oaf2hbase.xml"));
94
		final XsltRowTransformer transformer = XsltRowTransformerFactory.newInstance(xslt);
95

  
96
		doTest(rowToOaf(transformer), NARCIS);
97
	}
98

  
99
	//// HELPERS
100

  
101
	private void doTest(final Function<String, Pair<String, Oaf>> mapper, final String collectionName) {
102
		final MongoCollection<Document> collection = db.getCollection(collectionName);
103

  
104
		final long collectionSize = collection.count();
105
		log.info(String.format("found %s records in collection '%s'", collectionSize, collectionName));
106

  
107
		final AtomicInteger read = new AtomicInteger(0);
108
		final DescriptiveStatistics stats = new DescriptiveStatistics();
109

  
110
		final StopWatch recordTimer = new StopWatch();
111
		final StopWatch totalTimer = StopWatch.createStarted();
112

  
113
		StreamSupport.stream(collection.find().batchSize(batchSize).spliterator(), false)
114
				.limit(limit)
115
				.peek(d -> {
116
					if (read.addAndGet(1) % logFreq == 0) {
117
						log.info(String.format("records read so far %s", read.get()));
118
						//log.info(String.format("stats so far %s", stats.toString()));
119
					}
120
				})
121
				.map(d -> (String) d.get("body"))
122
				.filter(Objects::nonNull)
123
				.collect(Collectors.toList())   // load them in memory first
124
				.stream()
125
				.peek(s -> recordTimer.start())
126
				.map(mapper)
127
				.forEach(pair -> {
128
					recordTimer.stop();
129
					stats.addValue(recordTimer.getTime());
130
					recordTimer.reset();
131

  
132
					assertNotNull(pair);
133
					assertTrue(pair.getValue().hasEntity());
134

  
135
					try {
136
						final org.dom4j.Document doc = new SAXReader().read(new StringReader(pair.getKey()));
137
						final OafEntity entity = pair.getValue().getEntity();
138

  
139
						//TODO add more asserts
140
						assertTrue(entity.getId().contains(doc.valueOf("/*[local-name() = 'record']/*[local-name() = 'header']/*[local-name() = 'objIdentifier']/text()")));
141

  
142
					} catch (DocumentException e) {
143
						throw new IllegalArgumentException("unable to parse record " + pair.getKey(), e);
144
					}
145
				});
146

  
147
		totalTimer.stop();
148
		log.info(String.format("processed %s/%s records in %s", read.get(), collectionSize, HumanTime.exactly(totalTimer.getTime())));
149
		log.info(stats.toString());
150
	}
151

  
152
	private Function<String, Pair<String, Oaf>> rowToOaf(final XsltRowTransformer transformer) {
153
		return xml -> {
154
			final List<Row> rows = transformer.apply(xml);
155
			if (rows.isEmpty()) {
156
				return null;
157
			}
158

  
159
			return rows.stream()
160
					.filter(row -> row.getColumn(BODY) != null)
161
					.map(row -> row.getColumn(BODY))
162
					.map(c -> c.getValue())
163
					.map(b -> {
164
						try {
165
							return Oaf.parseFrom(b);
166
						} catch (InvalidProtocolBufferException e) {
167
							throw new IllegalStateException(e);
168
						}
169
					})
170
					.filter(Objects::nonNull)
171
					.map(oaf -> new Pair<>(xml, oaf))
172
					.findFirst()
173
					.get();
174
		};
175
	}
176

  
177
	private InputStream loadFromTransformationProfile(final String profilePath) {
178
		log.info("Loading xslt from: " + basePathProfiles + profilePath);
179
		InputStream profile = getClass().getResourceAsStream(basePathProfiles + profilePath);
180
		SAXReader saxReader = new SAXReader();
181
		org.dom4j.Document doc = null;
182
		try {
183
			doc = saxReader.read(profile);
184
		} catch (DocumentException e) {
185
			e.printStackTrace();
186
			throw new RuntimeException(e);
187
		}
188
		String xslt = doc.selectSingleNode("//SCRIPT/CODE/*[local-name()='stylesheet']").asXML();
189
		//log.info(xslt);
190
		return IOUtils.toInputStream(xslt);
191
	}
192

  
193

  
194
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/transform/xml/OpenTrialsXsltFunctionsTest.java
1
package eu.dnetlib.data.transform.xml;
2

  
3
import java.util.List;
4

  
5
import eu.dnetlib.data.transform.xml.OpenTrialsXsltFunctions.JsonProv;
6
import org.junit.After;
7
import org.junit.Before;
8
import org.junit.Test;
9

  
10
import static org.junit.Assert.assertEquals;
11

  
12

  
13
/**
14
 * OpenTrialsXsltFunctions Tester.
15
 *
16
 */
17
public class OpenTrialsXsltFunctionsTest {
18

  
19
	private String jsonProv = "[{\"url\" : \"http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT00378508\", \"sourceID\" : \"77eb42c5-0ec7-4e31-963a-5736b66f2d26\", \"sourceName\" : \"ictrp\"},{\"url\" : \"https://www.clinicaltrials.gov/ct2/show/NCT00378508?lup_e=02%2F04%2F2016&lup_s=01%2F01%2F2001&rank=175075&resultsxml=true\", \"sourceID\" : \"b389497c-0833-432b-a09b-930526b7b4d4\", \"sourceName\" : \"nct\"}]";
20
	private String jsonProvWithNull = "[{\"url\" : \"\", \"sourceID\" : \"77eb42c5-0ec7-4e31-963a-5736b66f2d26\", \"sourceName\" : \"ictrp\"},{\"url\" : \"https://www.clinicaltrials.gov/ct2/show/NCT00378508?lup_e=02%2F04%2F2016&lup_s=01%2F01%2F2001&rank=175075&resultsxml=true\", \"sourceID\" : \"b389497c-0833-432b-a09b-930526b7b4d4\", \"sourceName\" : \"nct\"}]";
21
	private String jidentifiers = "{112683,NCT00920439}";
22

  
23

  
24
	private String jsonRecord = "[{\"source_id\" : \"nct\", \"source_url\" : \"https://clinicaltrials.gov/ct2/show/NCT02321059\", \"is_primary\" : true},{\"source_id\" : \"ictrp\", \"source_url\" : \"http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT02321059\", \"is_primary\" : false}]";
25
	private String jsonRecordNull = "[{\"source_id\" : \"nct\", \"source_url\" : \"https://clinicaltrials.gov/ct2/show/NCT02321059\"},{\"source_id\" : \"ictrp\", \"source_url\" : \"http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT02321059\", \"is_primary\" : false}]";
26
	private String jsonRecordVoid = "[{\"source_id\" : \"\", \"source_url\" : \"\", \"is_primary\" : \"\"}]";
27
	private String jsonRecondPrimary = "[{\"source_id\" : \"nct\", \"source_url\" : \"https://clinicaltrials.gov/ct2/show/NCT02321059\", \"is_primary\" : false},{\"source_id\" : \"ictrp\", \"source_url\" : \"http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT02321059\", \"is_primary\" : false}]";
28

  
29
	private String jsonPeopleVoid ="[{\"person_name\" : null, \"person_id\" : null, \"person_role\" : null}]";
30
	private String jsonPeopleOne = "[{\"person_name\" : \"Henk Verheul, M.D., PhD\", \"person_id\" : \"116438e9-f8b1-46e5-a1f8-20f851cab73c\", \"person_role\" : \"principal_investigator\"}]";
31
	private String jsonPeopleMore = "[{\"person_name\" : \"Henk Verheul, M.D., PhD\", \"person_id\" : \"116438e9-f8b1-46e5-a1f8-20f851cab73c\", \"person_role\" : \"principal_investigator\"},{\"person_name\" : \"Miriam Pippolippo Baglioni, PhD\", \"person_id\" : \"fake\", \"person_role\" : \"principal_investigator\"}]";
32

  
33
	private String jsonOrganizationVoid = "[{\"organization_name\" : null, \"organization_id\" : null, \"organization_role\" : null}]";
34
	private String jsonOrganizationOne = "[{\"organization_name\" : \"Södertälje sjukhus AB\", \"organization_id\" : \"15f0d004-b82b-408c-8605-38a57352468d\", \"organization_role\" : \"sponsor\"}]";
35
	private String jsonOrganizationMore = "[{\"organization_name\" : \"Södertälje sjukhus AB\", \"organization_id\" : \"15f0d004-b82b-408c-8605-38a57352468d\", \"organization_role\" : \"sponsor\"},{\"organization_name\" : \"Miriam Baglioni AB\", \"organization_id\" : \"fake\", \"organization_role\" : \"primary_sponsor\"}]";
36

  
37
	private String jsonLocationVoid = "[{\"location_name\" : null}]";
38
	private String jsonLocationOne = "[{\"location_name\" : \"China\"}]";
39
	private String jsonLocationMore = "[{\"location_name\" : \"China\"},{\"location_name\" : \"North Korea\"}]";
40

  
41
	@Before
42
	public void before() throws Exception {
43
	}
44

  
45
	@After
46
	public void after() throws Exception {
47
	}
48

  
49
	/**
50
	 * Method: getProvs(String jsonProvList)
51
	 */
52
	@Test
53
	public void testGetProvs() throws Exception {
54
		List<JsonProv> list = OpenTrialsXsltFunctions.getProvs(jsonProv);
55
		assertEquals(2, list.size());
56
	}
57

  
58
	/**
59
	 * Method: getMainIdentifierURL(String jsonProvList)
60
	 */
61
	@Test
62
	public void testGetMainIdentifierURL() throws Exception {
63
		String url = OpenTrialsXsltFunctions.getMainIdentifierURL(jsonProv);
64
		assertEquals( "http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT00378508", url );
65
		url = OpenTrialsXsltFunctions.getMainIdentifierURL(jsonProvWithNull);
66
		assertEquals("https://www.clinicaltrials.gov/ct2/show/NCT00378508?lup_e=02%2F04%2F2016&lup_s=01%2F01%2F2001&rank=175075&resultsxml=true", url);
67
	}
68

  
69
	@Test
70
	public void testGetPrimaryRecordUrl(){
71
		String url = OpenTrialsXsltFunctions.getPrimaryRecordUrl(jsonRecord);
72
		assertEquals("https://clinicaltrials.gov/ct2/show/NCT02321059", url);
73
	}
74

  
75
	@Test
76
	public void testGetPrimaryRecordID(){
77
		String id = OpenTrialsXsltFunctions.getPrimaryRecordIdentifier(jsonRecord);
78
		assertEquals("nct", id);
79
	}
80

  
81
	@Test
82
	public void testGetPrimaryRecordUrlNull(){
83
		String url = OpenTrialsXsltFunctions.getPrimaryRecordUrl(jsonRecordNull);
84
		assertEquals("https://clinicaltrials.gov/ct2/show/NCT02321059", url);
85
	}
86

  
87
	@Test
88
	public void testGetPrimaryRecordUrlVoid(){
89
		String url = OpenTrialsXsltFunctions.getPrimaryRecordUrl(jsonRecordVoid);
90
		assertEquals("", url);
91
	}
92

  
93
	@Test
94
	public void testGetPrimaryRecordUrlNoPrimary(){
95
		String url = OpenTrialsXsltFunctions.getPrimaryRecordUrl(jsonRecondPrimary);
96
		assertEquals("https://clinicaltrials.gov/ct2/show/NCT02321059", url);
97
	}
98
	@Test
99
	public void testGetPrimaryRecordIDNoPrimary(){
100
		String id = OpenTrialsXsltFunctions.getPrimaryRecordIdentifier(jsonRecondPrimary);
101
		assertEquals("nct", id);
102
	}
103
	@Test
104
	public void testGetPrincipalInvestigatorsVoid(){
105
		String url = OpenTrialsXsltFunctions.getPrincipalInvestigators(jsonPeopleVoid);
106
		assertEquals("",url);
107
	}
108

  
109

  
110
	@Test
111
	public void testGetPrincipalInvestigatorsOne(){
112
		String url = OpenTrialsXsltFunctions.getPrincipalInvestigators(jsonPeopleOne);
113
		assertEquals("Verheul, Henk", url);
114
	}
115

  
116
	@Test
117
	public void testGetPrincipalInvestigatorsMore(){
118
		String url = OpenTrialsXsltFunctions.getPrincipalInvestigators(jsonPeopleMore);
119
		assertEquals("Verheul, Henk@@Baglioni, Miriam Pippolippo", url);
120
	}
121

  
122

  
123

  
124
	@Test
125
	public void testgGetTrialOrganizationsVoid(){
126
		String url = OpenTrialsXsltFunctions.getTrialOrganizations(jsonOrganizationVoid);
127
		assertEquals("",url);
128
	}
129

  
130

  
131
	@Test
132
	public void testgGetTrialOrganizationsOne(){
133
		String url = OpenTrialsXsltFunctions.getTrialOrganizations(jsonOrganizationOne);
134
		assertEquals("Södertälje sjukhus AB@sponsor", url);
135
	}
136

  
137
	@Test
138
	public void testgGetTrialOrganizationsMore(){
139
		String url = OpenTrialsXsltFunctions.getTrialOrganizations(jsonOrganizationMore);
140
		assertEquals("Södertälje sjukhus AB@sponsor@@Miriam Baglioni AB@sponsor", url);
141
	}
142

  
143
	@Test
144
	public void testgGetTrialLocationsVoid(){
145
		String url = OpenTrialsXsltFunctions.getTrialLocations(jsonLocationVoid);
146
		assertEquals("",url);
147
	}
148

  
149

  
150
	@Test
151
	public void testgGetTrialLocationsOne(){
152
		String url = OpenTrialsXsltFunctions.getTrialLocations(jsonLocationOne);
153
		assertEquals("China", url);
154
	}
155

  
156
	@Test
157
	public void testgGetTrialLocationsMore(){
158
		String url = OpenTrialsXsltFunctions.getTrialLocations(jsonLocationMore);
159
		assertEquals("China@@North Korea", url);
160
	}
161

  
162
	@Test
163
	public void testGetNotPrimaryRecordUrlPrimary(){
164
		String url = OpenTrialsXsltFunctions.getNotPrimaryRecordUrl(jsonRecondPrimary);
165
		assertEquals("http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT02321059", url);
166
	}
167

  
168
	@Test
169
	public void testGetNotPrimaryRecordUrlVoid(){
170
		String url = OpenTrialsXsltFunctions.getNotPrimaryRecordUrl(jsonRecordVoid);
171
		assertEquals("", url);
172
	}
173

  
174
	@Test
175
	public void testGetNotPrimaryRecordUrl(){
176
		String url = OpenTrialsXsltFunctions.getNotPrimaryRecordUrl(jsonRecord);
177
		assertEquals("http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT02321059", url);
178
	}
179

  
180

  
181
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/transform/xml/FWFXsltFunctionsTest.java
1
package eu.dnetlib.data.transform.xml;
2

  
3
import org.junit.After;
4
import org.junit.Before;
5
import org.junit.Test;
6

  
7
import static org.junit.Assert.assertEquals;
8
import static org.junit.Assert.assertNotNull;
9

  
10
/**
11
 *
12
 * Created by miriam on 04/05/2017.
13
 */
14
public class FWFXsltFunctionsTest {
15
	private String namesurname ="Gerhard SOMMER";
16
	private String noSurname = "Gerhard";
17
	private String noName = "SOMMER";
18
	private String twoNames = "Gerhard Pippo SOMMER";
19
	private String twoSurname = "Gerhard PIPPO SOMMER";
20
	private String nonamesurname = "";
21
	private String organization ="Universität Linz - Institut für Computational Perception; Universität für Musik und darstellende Kunst Graz - Institut 1: Komposition, Musiktheorie, Musikgeschichte und Dirigieren; Universität Mozarteum Salzburg - Institut für Musikalische Rezeptions- und Interpretationsgeschichte; Anton Bruckner Privatuniversität - Institut für Theorie und Geschichte der Musik; Eliette und Herbert von Karajan Institut - Eliette und Herbert von Karajan Institut";
22

  
23
	@Before
24
	public void before() throws Exception {
25
	}
26

  
27
	@After
28
	public void after() throws Exception {
29
	}
30

  
31
	@Test
32
	public void testGetNamesNameNoNameSurname() throws Exception {
33
		String ret = FWFXsltFunctions.getName(nonamesurname,true);
34
		assertEquals("",ret );
35
	}
36

  
37
	@Test
38
	public void testGetNamesSurnameNoNameSurname() throws Exception {
39
		String ret = FWFXsltFunctions.getName(nonamesurname,false);
40
		assertEquals("",ret );
41
	}
42

  
43
	@Test
44
	public void testGetNamesNameTwoSurname() throws Exception {
45
		String ret = FWFXsltFunctions.getName(twoSurname,true);
46
		assertEquals("Gerhard",ret );
47
	}
48

  
49
	@Test
50
	public void testGetNamesSurnameTwoSurname() throws Exception {
51
		String ret = FWFXsltFunctions.getName(twoSurname,false);
52
		assertEquals("PIPPO SOMMER",ret );
53
	}
54

  
55
	@Test
56
	public void testGetNamesNameTwoNames() throws Exception {
57
		String ret = FWFXsltFunctions.getName(twoNames,true);
58
		assertEquals("Gerhard Pippo",ret );
59
	}
60

  
61
	@Test
62
	public void testGetNamesSurnameTwoNames() throws Exception {
63
		String ret = FWFXsltFunctions.getName(twoNames,false);
64
		assertEquals("SOMMER",ret );
65
	}
66

  
67
	/**
68
	 * Method: getProvs(String jsonProvList)
69
	 */
70
	@Test
71
	public void testGetNamesName() throws Exception {
72
		String ret = FWFXsltFunctions.getName(namesurname,true);
73
		assertEquals("Gerhard",ret );
74
	}
75

  
76
	@Test
77
	public void testGetNamesSurname() throws Exception {
78
		String ret = FWFXsltFunctions.getName(namesurname,false);
79
		assertEquals("SOMMER",ret );
80
	}
81

  
82
	@Test
83
	public void testGetNamesNameNoSurname() throws Exception {
84
		String ret = FWFXsltFunctions.getName(noSurname,true);
85
		assertEquals("Gerhard",ret );
86
	}
87

  
88
	@Test
89
	public void testGetNamesSurnameNoSurname() throws Exception {
90
		String ret = FWFXsltFunctions.getName(noSurname,false);
91
		assertEquals("",ret );
92
	}
93

  
94
	@Test
95
	public void testGetNamesNameNoName() throws Exception {
96
		String ret = FWFXsltFunctions.getName(noName,true);
97
		assertEquals("",ret );
98
	}
99

  
100
	@Test
101
	public void testGetNamesSurnameNoName() throws Exception {
102
		String ret = FWFXsltFunctions.getName(noName,false);
103
		assertEquals("SOMMER",ret );
104
	}
105

  
106
	@Test
107
	public void TestGetMd5()throws Exception{
108
		String md5 = FWFXsltFunctions.getMd5(organization);
109
		System.out.println(md5);
110
		assertNotNull(md5);
111
	}
112

  
113
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/transform/xml/vtd/VtdParserToProtoTest.java
1
package eu.dnetlib.data.transform.xml.vtd;
2

  
3
import java.io.IOException;
4
import java.util.function.Function;
5

  
6
import eu.dnetlib.data.proto.OafProtos.Oaf;
7
import eu.dnetlib.data.transform.xml2.DatasetToProto;
8
import eu.dnetlib.data.transform.xml2.PublicationToProto;
9
import org.apache.commons.io.IOUtils;
10
import org.apache.commons.logging.Log;
11
import org.apache.commons.logging.LogFactory;
12
import org.junit.Test;
13

  
14
import static org.junit.Assert.assertNotNull;
15

  
16
public class VtdParserToProtoTest {
17

  
18
	private static final Log log = LogFactory.getLog(VtdParserToProtoTest.class);
19

  
20
	@Test
21
	public void testParsePublication() throws IOException {
22
		doTest("/eu/dnetlib/data/transform/publication.xml", new PublicationToProto());
23
	}
24

  
25
	@Test
26
	public void testParseDataset() throws IOException {
27
		doTest("/eu/dnetlib/data/transform/dataset.xml", new DatasetToProto());
28
	}
29

  
30
	@Test
31
	public void testParseDataset2() throws IOException {
32
		doTest("/eu/dnetlib/data/transform/dataset2.xml", new DatasetToProto());
33
	}
34

  
35
	private void doTest(final String filePath, Function<String, Oaf> f) throws IOException {
36
		final String xml = IOUtils.toString(getClass().getResourceAsStream(filePath));
37

  
38
		assertNotNull(xml);
39

  
40
		final Oaf oaf = f.apply(xml);
41

  
42
		assertNotNull(oaf);
43

  
44
		log.info(oaf.toString());
45
	}
46

  
47
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/transform/xml/vtd/ConfigurationTestConfig.java
1
package eu.dnetlib.data.transform.xml.vtd;
2

  
3
import java.io.IOException;
4
import java.io.InputStream;
5
import java.util.Properties;
6

  
7
import com.mongodb.MongoClient;
8
import com.mongodb.client.MongoDatabase;
9
import org.springframework.context.annotation.Bean;
10
import org.springframework.context.annotation.Configuration;
11
import org.springframework.core.io.ClassPathResource;
12

  
13
@Configuration
14
public class ConfigurationTestConfig {
15

  
16
	@Bean
17
	public MongoDatabase db() throws IOException {
18

  
19
		final Properties p = new Properties();
20
		final ClassPathResource cp = new ClassPathResource("test.properties");
21
		try (final InputStream stream = cp.getInputStream()) {
22
			p.load(stream);
23
		}
24

  
25
		final MongoClient mongo = new MongoClient(
26
				p.getProperty("mongodb.host"),
27
				Integer.valueOf(p.getProperty("mongodb.port")));
28
		return mongo.getDatabase(p.getProperty("mongodb.dbname"));
29
	}
30

  
31
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/transform/xml/vtd/VtdParserToProtoIT.java
1
package eu.dnetlib.data.transform.xml.vtd;
2

  
3
import com.mongodb.client.MongoCollection;
4
import com.mongodb.client.MongoDatabase;
5
import eu.dnetlib.data.transform.xml2.DatasetToProto;
6
import org.apache.commons.lang3.time.StopWatch;
7
import org.apache.commons.logging.Log;
8
import org.apache.commons.logging.LogFactory;
9
import org.apache.commons.math.stat.descriptive.DescriptiveStatistics;
10
import org.bson.Document;
11
import org.junit.Ignore;
12
import org.junit.Test;
13
import org.junit.runner.RunWith;
14
import org.springframework.beans.factory.annotation.Autowired;
15
import org.springframework.test.context.ContextConfiguration;
16
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
17

  
18
import java.io.IOException;
19
import java.util.Objects;
20
import java.util.concurrent.atomic.AtomicInteger;
21
import java.util.stream.StreamSupport;
22

  
23
import static org.junit.Assert.assertNotNull;
24
import static org.junit.Assert.assertTrue;
25

  
26
@RunWith(SpringJUnit4ClassRunner.class)
27
@ContextConfiguration(classes = { ConfigurationTestConfig.class })
28
public class VtdParserToProtoIT {
29

  
30
	private static final Log log = LogFactory.getLog(VtdParserToProtoIT.class);
31
	public static final String COLLECTION_NAME = "datacite";
32
	private static final int BATCH_SIZE = 10000;
33
	public static final int LOG_FREQ = 5000;
34

  
35
	@Autowired
36
	private MongoDatabase db;
37

  
38
	@Test
39
	@Ignore
40
	public void testParseDatacite() throws IOException {
41

  
42
		final MongoCollection<Document> collection = db.getCollection(COLLECTION_NAME);
43

  
44
		final long collectionSize = collection.count();
45
		log.info(String.format("found %s records in collection '%s'", collectionSize, COLLECTION_NAME));
46

  
47
		final AtomicInteger read = new AtomicInteger(0);
48
		final DescriptiveStatistics stats = new DescriptiveStatistics();
49

  
50
		final StopWatch timer = new StopWatch();
51

  
52
		final DatasetToProto mapper = new DatasetToProto();
53
		StreamSupport.stream(collection.find().batchSize(BATCH_SIZE).spliterator(), false)
54
				.peek(d -> {
55
					if (read.addAndGet(1) % LOG_FREQ == 0) {
56
						log.info(String.format("records read so far %s", read.get()));
57
						log.info(String.format("stats so far %s", stats.toString()));
58
					}
59
				})
60
				.map(d -> (String) d.get("body"))
61
				.filter(Objects::nonNull)
62
				.peek(s -> timer.start())
63
				.map(mapper)
64
				.forEach(oaf -> {
65
					assertNotNull(oaf);
66
					assertTrue(oaf.hasEntity());
67

  
68
					timer.stop();
69
					stats.addValue(timer.getTime());
70
					timer.reset();
71
				});
72

  
73
		log.info(String.format("processed %s/%s records", read.get(), collectionSize));
74
	}
75

  
76

  
77
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/transform/xml/vtd/VtdUtilityParserTest.java
1
package eu.dnetlib.data.transform.xml.vtd;
2

  
3
import java.io.InputStream;
4
import java.util.List;
5

  
6
import com.ximpleware.AutoPilot;
7
import com.ximpleware.VTDGen;
8
import com.ximpleware.VTDNav;
9
import eu.dnetlib.data.transform.xml2.Node;
10
import eu.dnetlib.data.transform.xml2.VtdUtilityParser;
11
import org.apache.commons.io.IOUtils;
12
import org.junit.Assert;
13
import org.junit.Test;
14

  
15

  
16
public class VtdUtilityParserTest {
17

  
18
	@Test
19
	public void testUtils1() {
20
		String xpath = VtdUtilityParser.xpath("a", "b", "c");
21
		Assert.assertTrue("/*[local-name()='a']/*[local-name()='b']/*[local-name()='c']".equals(xpath));
22
	}
23

  
24
    @Test
25
    public void testPartser() throws Exception {
26
        final InputStream resource = this.getClass().getResourceAsStream("/eu/dnetlib/data/transform/publication.xml");
27
        final String record =IOUtils.toString(resource);
28
        final VTDGen vg = VtdUtilityParser.parseXml(record);
29
        final VTDNav vn = vg.getNav();
30
        final AutoPilot ap = new AutoPilot(vn);
31

  
32
        List<Node> nodes = VtdUtilityParser.getNodes(ap, vn, "//*[local-name()='referenceaa']");
33

  
34
        nodes.forEach(n -> Assert.assertTrue(n.getAttributes().keySet().size()>0));
35

  
36
        System.out.println(VtdUtilityParser.countNodes(ap, vn, "count(//*[local-name()='CobjIdentifier'])"));
37

  
38

  
39

  
40

  
41
    }
42

  
43
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/transform/AuthorMergerTestIT.java
1
package eu.dnetlib.data.transform;
2

  
3
import com.google.common.base.Predicates;
4
import com.mongodb.client.FindIterable;
5
import com.mongodb.client.MongoDatabase;
6
import com.mongodb.client.MongoIterable;
7
import eu.dnetlib.data.transform.xml.vtd.ConfigurationTestConfig;
8
import org.bson.Document;
9
import org.junit.Test;
10
import org.junit.runner.RunWith;
11
import org.springframework.beans.factory.annotation.Autowired;
12
import org.springframework.test.context.ContextConfiguration;
13
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
14

  
15
import java.io.IOException;
16
import java.util.List;
17

  
18
import static java.util.stream.Collectors.toList;
19

  
20
@RunWith(SpringJUnit4ClassRunner.class)
21
@ContextConfiguration(classes = { ConfigurationTestConfig.class })
22
public class AuthorMergerTestIT extends AbstractAuthorMergerTest {
23

  
24
    @Autowired
25
    private MongoDatabase db;
26

  
27
    private String collection = "authors";
28

  
29
    @Test
30
    public void test_mergeAuthorsGroup() throws IOException {
31

  
32
        final FindIterable<Document> docs = db.getCollection(collection).find();
33

  
34
        MongoIterable<String> i = docs
35
                .map(d -> ((List<List<Document>>) d.get("authors")).stream()
36
                    .filter(Predicates.notNull())
37
                    .map(g -> g.stream()
38
                            .map(Document::toJson)
39
                            .collect(toList()))
40
                    .collect(toList()))
41
                .map(List::toString);
42

  
43
        doTestMergeAuthorGroup(i);
44

  
45
    }
46

  
47
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/transform/xml2/VtdParserToProtoTest.java
1
package eu.dnetlib.data.transform.xml2;
2

  
3
import java.io.IOException;
4
import java.util.function.Function;
5

  
6
import eu.dnetlib.data.proto.OafProtos.Oaf;
7
import org.apache.commons.io.IOUtils;
8
import org.apache.commons.logging.Log;
9
import org.apache.commons.logging.LogFactory;
10
import org.junit.Test;
11

  
12
import static org.junit.Assert.assertNotNull;
13

  
14
public class VtdParserToProtoTest {
15

  
16
	private static final Log log = LogFactory.getLog(VtdParserToProtoTest.class);
17

  
18
	@Test
19
	public void testParsePublication() throws IOException {
20
		doTest("/eu/dnetlib/data/transform/publication.xml", new PublicationToProto());
21
	}
22

  
23
	@Test
24
	public void testParseDataset() throws IOException {
25
		doTest("/eu/dnetlib/data/transform/dataset.xml", new DatasetToProto());
26
	}
27

  
28
	@Test
29
		public void testParseDataset2() throws IOException {
30
		doTest("/eu/dnetlib/data/transform/dataset2.xml", new DatasetToProto());
31
	}
32

  
33
	private void doTest(final String filePath, Function<String, Oaf> f) throws IOException {
34
		final String xml = IOUtils.toString(getClass().getResourceAsStream(filePath));
35

  
36
		assertNotNull(xml);
37

  
38
		final Oaf oaf = f.apply(xml);
39

  
40
		assertNotNull(oaf);
41

  
42
		log.info(oaf.toString());
43
	}
44

  
45
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/transform/xml2/VtdUtilityParserTest.java
1
package eu.dnetlib.data.transform.xml2;
2

  
3
import java.io.InputStream;
4
import java.util.List;
5

  
6
import com.ximpleware.AutoPilot;
7
import com.ximpleware.VTDGen;
8
import com.ximpleware.VTDNav;
9
import eu.dnetlib.data.transform.xml2.Node;
10
import eu.dnetlib.data.transform.xml2.VtdUtilityParser;
11
import org.apache.commons.io.IOUtils;
12
import org.junit.Assert;
13
import org.junit.Test;
14

  
15
import static eu.dnetlib.data.transform.xml2.VtdUtilityParser.parseXml;
16

  
17
public class VtdUtilityParserTest {
18

  
19
	@Test
20
	public void testUtils1() {
21
		String xpath = VtdUtilityParser.xpath("a", "b", "c");
22
		Assert.assertTrue("/*[local-name()='a']/*[local-name()='b']/*[local-name()='c']".equals(xpath));
23
	}
24

  
25
    @Test
26
    public void testPartser() throws Exception {
27
        final InputStream resource = this.getClass().getResourceAsStream("/eu/dnetlib/data/transform/publication.xml");
28
        final String record =IOUtils.toString(resource);
29
        final VTDGen vg = parseXml(record);
30
        final VTDNav vn = vg.getNav();
31
        final AutoPilot ap = new AutoPilot(vn);
32

  
33
        List<Node> nodes = VtdUtilityParser.getNodes(ap, vn, "//*[local-name()='referenceaa']");
34

  
35
        nodes.forEach(n -> Assert.assertTrue(n.getAttributes().keySet().size()>0));
36

  
37
        System.out.println(VtdUtilityParser.countNodes(ap, vn, "count(//*[local-name()='CobjIdentifier'])"));
38

  
39

  
40

  
41

  
42
    }
43

  
44
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/transform/AuthorMergerTest.java
1
package eu.dnetlib.data.transform;
2

  
3
import org.junit.Test;
4

  
5
import java.io.BufferedReader;
6
import java.io.IOException;
7
import java.io.InputStreamReader;
8
import java.util.Iterator;
9
import java.util.zip.GZIPInputStream;
10

  
11
public class AuthorMergerTest extends AbstractAuthorMergerTest {
12

  
13
    @Test
14
    public void test_mergeAuthorsGroup() throws IOException {
15

  
16
        try(GZIPInputStream gzip = new GZIPInputStream(getClass().getResourceAsStream("author_1000.json.gz"))) {
17
            final BufferedReader br = new BufferedReader(new InputStreamReader(gzip));
18

  
19
            doTestMergeAuthorGroup(() -> new Iterator<String>() {
20

  
21
                String line = null;
22

  
23
                @Override
24
                public boolean hasNext() {
25
                    line = doNext();
26
                    return line != null;
27
                }
28

  
29
                @Override
30
                public String next() {
31
                    return line;
32
                }
33

  
34
                private String doNext() {
35
                    try {
36
                        return br.readLine();
37
                    } catch (IOException e) {
38
                        throw new RuntimeException(e);
39
                    }
40
                }
41
            });
42
        }
43
    }
44

  
45
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/transform/AbstractAuthorMergerTest.java
1
package eu.dnetlib.data.transform;
2

  
3
import com.google.common.collect.Lists;
4
import com.google.common.collect.Sets;
5
import com.google.gson.Gson;
6
import com.google.gson.JsonElement;
7
import com.google.gson.internal.StringMap;
8
import com.googlecode.protobuf.format.JsonFormat;
9
import org.apache.commons.lang3.StringUtils;
10
import org.apache.commons.math.stat.descriptive.DescriptiveStatistics;
11
import org.junit.Assert;
12

  
13
import java.io.IOException;
14
import java.util.*;
15
import java.util.concurrent.atomic.AtomicInteger;
16
import java.util.stream.Collectors;
17
import java.util.stream.StreamSupport;
18

  
19
import static eu.dnetlib.data.proto.FieldTypeProtos.Author;
20
import static eu.dnetlib.data.proto.FieldTypeProtos.KeyValue;
21
import static java.lang.String.format;
22
import static java.util.stream.Collectors.*;
23

  
24
public abstract class AbstractAuthorMergerTest {
25

  
26
    protected void doTestMergeAuthorGroup(final Iterable<String> input) throws IOException {
27
        final DescriptiveStatistics groupSize = new DescriptiveStatistics();
28
        final AtomicInteger authorCount = new AtomicInteger(0);
29
        final AtomicInteger authorCountMerged = new AtomicInteger(0);
30

  
31
        final AtomicInteger pidCount = new AtomicInteger(0);
32
        final AtomicInteger pidCountMerged = new AtomicInteger(0);
33
        final Map<String, Integer> pidTypes = new HashMap<>();
34
        final Map<String, Integer> pidTypesMerged = new HashMap<>();
35
        final AtomicInteger orcidCount = new AtomicInteger(0);
36

  
37
        final AtomicInteger equalGroupSizeCount = new AtomicInteger(0);
38
        final AtomicInteger lines = new AtomicInteger(0);
39

  
40
        final List<List<Author>> authorGroups = Lists.newArrayList();
41

  
42
        final Set<String> orcidIn = new HashSet<>();
43
        final Set<String> orcidOut= new HashSet<>();
44

  
45
        for(String line : input) {
46
            lines.incrementAndGet();
47
            final List<List<StringMap<Object>>> list = new Gson().fromJson(line, List.class);
48
            final List<List<Author>> groups = new ArrayList<>();
49
            groups.addAll(list.stream()
50
                    .filter(Objects::nonNull)
51
                    .map(j -> {
52
                        return j.stream().map(AbstractAuthorMergerTest::fixRank).collect(toList());
53
                    })
54
                    .map(AbstractAuthorMergerTest::asAuthors)
55
                    .filter(Objects::nonNull)
56
                    .collect(toList()));
57

  
58
            groups.stream().forEach(g -> {
59
                groupSize.addValue(g.size());
60
                g.stream().forEach(a -> {
61
                    pidCount.addAndGet(a.getPidCount());
62
                    authorCount.incrementAndGet();
63

  
64
                    countPids(pidTypes, a);
65
                    orcidIn.addAll(getOrcid(a));
66
                });
67
            });
68

  
69
            final HashSet<Integer> groupSizes = groups.stream()
70
                    .map(a -> a.size())
71
                    .collect(toCollection(HashSet::new));
72

  
73
            if (groupSizes.size() == 1) {
74
                equalGroupSizeCount.incrementAndGet();
75
            }
76

  
77
            authorGroups.addAll(groups);
78

  
79
            final List<Author> merged = AuthorMerger.merge(groups);
80

  
81
            if (!groupSizes.isEmpty()) {
82
                Assert.assertTrue(
83
                        format("the size of the merged group must be the size of one of the input groups. Merged size: %s, Sizes: %s ",
84
                                merged.size(), groupSizes),
85
                        groupSizes.contains(merged.size()));
86
            }
87

  
88
            authorCountMerged.addAndGet(merged.size());
89
            merged.forEach(a -> {
90
                pidCountMerged.addAndGet(a.getPidCount());
91
                countPids(pidTypesMerged, a);
92
                orcidOut.addAll(getOrcid(a));
93
            });
94
        }
95

  
96
        System.out.println(format("lines %s", lines.intValue()));
97
        System.out.println(format("author groups %s", authorGroups.size()));
98
        System.out.println(format("author count %s", authorCount.intValue()));
99
        System.out.println(format("avg authorGroups per group %s", authorCount.doubleValue() / authorGroups.size()));
100

  
101
        System.out.println(format("pid types %s", pidTypes));
102
        System.out.println(format("pid count %s", pidCount.intValue()));
103
        System.out.println(format("pid rate among authors %s", pidCount.doubleValue() / authorCount.intValue()));
104

  
105
        System.out.println(format("equal group size %s", equalGroupSizeCount.incrementAndGet()));
106

  
107
        System.out.println(format("[merged] pid count %s", pidCountMerged.intValue()));
108
        System.out.println(format("[merged] avg pid per group %s", pidCountMerged.doubleValue() / authorCountMerged.intValue()));
109
        System.out.println(format("[merged] pid types %s", pidTypesMerged));
110

  
111
        System.out.println(format("ORCIDs in  %s", orcidIn.size()));
112
        System.out.println(format("ORCIDs out %s", orcidOut.size()));
113

  
114
        Sets.SetView<String> diff = Sets.difference(orcidIn, orcidOut);
115
        System.out.println(format("Difference between the number of distinct input ORCIDs and output (merged) ORCIDs: %s", diff.size()));
116

  
117
        System.out.println(format("\ngroup size %s", groupSize));
118
    }
119

  
120
    private List<String> getOrcid(Author a) {
121
        return a.getPidList().stream()
122
                .filter(p -> p.getKey().equalsIgnoreCase("orcid"))
123
                .map(KeyValue::getValue)
124
                .collect(Collectors.toList());
125
    }
126

  
127
    private void countPids(Map<String, Integer> pidTypes, Author a) {
128
        a.getPidList().stream()
129
                .collect(groupingBy(KeyValue::getKey, summingInt(e -> 1)))
130
                .forEach((k, v) -> pidTypes.merge(k, v, (v1, v2) -> v1 + v2));
131
    }
132

  
133
    private static StringMap<Object> fixRank(final StringMap<Object> j) {
134
        final StringMap<Object> m = new StringMap<>();
135

  
136
        m.putAll(j);
137

  
138
        Object rank = j.get("rank");
139
        rank = StringUtils.substringBefore(rank.toString(), ".0");
140
        m.put("rank", Integer.parseInt(rank.toString()));
141
        return m;
142
    }
143

  
144
    private static List<Author> asAuthors(Object o) {
145

  
146
        final JsonElement json = new Gson().toJsonTree(o);
147

  
148
        return StreamSupport.stream(json.getAsJsonArray().spliterator(), false)
149
                .map(j -> j.toString())
150
                .filter(Objects::nonNull)
151
                .map(AbstractAuthorMergerTest::asAuthor)
152
                .filter(Objects::nonNull)
153
                .collect(toList());
154
    }
155

  
156
    private static Author asAuthor(String json) {
157

  
158
        final Author.Builder a = Author.newBuilder();
159
        try {
160
            JsonFormat.merge(json, a);
161
        } catch (JsonFormat.ParseException e) {
162
            throw new IllegalArgumentException(e);
163
        }
164
        return a.build();
165
    }
166

  
167
}
modules/dnet-openaireplus-mapping-utils/tags/dnet-openaireplus-mapping-utils-6.3.43/src/test/java/eu/dnetlib/data/transform/SolrProtoMapperTest.java
1
package eu.dnetlib.data.transform;
2

  
3
import static org.junit.Assert.assertFalse;
4
import static org.junit.Assert.assertNotNull;
5

  
6
import java.io.IOException;
7
import java.io.StringWriter;
8

  
9
import org.apache.commons.codec.binary.Base64;
10
import org.apache.commons.io.IOUtils;
11
import org.apache.commons.logging.Log;
12
import org.apache.commons.logging.LogFactory;
13
import org.apache.solr.common.SolrInputDocument;
14
import org.apache.solr.common.SolrInputField;
15
import org.dom4j.DocumentException;
16
import org.junit.Before;
17
import org.junit.Test;
18

  
19
import com.google.protobuf.InvalidProtocolBufferException;
20
import com.googlecode.protobuf.format.JsonFormat;
21

  
22
import eu.dnetlib.data.mapreduce.util.OafTest;
23
import eu.dnetlib.data.proto.KindProtos.Kind;
24
import eu.dnetlib.data.proto.OafProtos.Oaf;
25
import eu.dnetlib.data.proto.OafProtos.OafEntity;
26
import eu.dnetlib.functionality.index.solr.feed.InputDocumentFactory;
27

  
28
public class SolrProtoMapperTest {
29

  
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