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26600
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sandro.lab
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package eu.dnetlib.data.transform;
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| 3 |
39431
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claudio.at
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import java.io.*;
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import java.util.*;
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30967
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claudio.at
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import java.util.Map.Entry;
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35746
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alessia.ba
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import java.util.zip.GZIPInputStream;
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30967
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claudio.at
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import javax.xml.transform.TransformerConfigurationException;
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import javax.xml.transform.TransformerFactoryConfigurationError;
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44483
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claudio.at
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import com.google.common.base.Function;
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import com.google.common.collect.Iterables;
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31997
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claudio.at
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import com.google.common.collect.Lists;
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30967
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claudio.at
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import com.google.common.collect.Maps;
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38025
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claudio.at
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import com.google.common.collect.Sets;
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26600
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sandro.lab
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import com.google.protobuf.InvalidProtocolBufferException;
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53408
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claudio.at
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import com.googlecode.protobuf.format.JsonFormat;
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55177
|
alessia.ba
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import com.googlecode.protobuf.format.JsonFormat.ParseException;
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53408
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claudio.at
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import eu.dnetlib.actionmanager.actions.ActionFactory;
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import eu.dnetlib.actionmanager.actions.XsltInfoPackageAction;
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import eu.dnetlib.actionmanager.common.Agent;
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import eu.dnetlib.actionmanager.common.Operation;
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import eu.dnetlib.actionmanager.common.Provenance;
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39431
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claudio.at
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import eu.dnetlib.data.mapreduce.hbase.index.config.*;
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import eu.dnetlib.data.mapreduce.util.*;
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26600
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sandro.lab
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import eu.dnetlib.data.proto.KindProtos.Kind;
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import eu.dnetlib.data.proto.OafProtos.Oaf;
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30967
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claudio.at
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import eu.dnetlib.data.proto.TypeProtos.Type;
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26600
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sandro.lab
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import eu.dnetlib.miscutils.functional.xml.IndentXmlString;
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39431
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claudio.at
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang.StringUtils;
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40063
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alessia.ba
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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39431
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claudio.at
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import org.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.io.SAXReader;
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import org.json.JSONObject;
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import org.junit.Before;
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claudio.at
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import org.junit.Ignore;
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39431
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claudio.at
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import org.junit.Test;
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53408
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claudio.at
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import org.springframework.core.io.ByteArrayResource;
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import org.springframework.core.io.Resource;
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26600
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sandro.lab
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39431
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claudio.at
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import static org.junit.Assert.*;
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26600
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sandro.lab
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public class XsltRowTransformerFactoryTest {
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40063
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alessia.ba
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private static final Log log = LogFactory.getLog(XsltRowTransformerFactoryTest.class);
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| 48 |
52562
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alessia.ba
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private static String basePathProfiles = "/eu/dnetlib/test/profiles/TransformationRuleDSResources/TransformationRuleDSResourceType/2hbase/";
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26600
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sandro.lab
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private XsltRowTransformerFactory factory;
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30967
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claudio.at
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private EntityConfigTable entityConfigTable;
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26600
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sandro.lab
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@Before
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public void setUp() throws Exception {
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factory = new XsltRowTransformerFactory();
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30967
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claudio.at
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entityConfigTable = IndexConfig.load(IndexConfigTest.config).getConfigMap();
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26600
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sandro.lab
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}
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@Test
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48702
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claudio.at
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@Ignore // need to reimplement because claimUpdates_2_hbase.xsl was removed
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42534
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alessia.ba
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public void testParseOafClaimUpdate() throws Exception {
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doTest(loadFromTransformationProfile("claimUpdates_2_hbase.xsl"), load("recordClaimUpdate.xml"));
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}
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@Test
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claudio.at
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@Ignore // need to reimplement because claimUpdates_2_hbase.xsl was removed
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39616
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claudio.at
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public void testParseClaimUpdate() throws Exception {
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41468
|
claudio.at
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final List<Row> rows = Lists.newArrayList();
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rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordClaim.xml")));
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rows.addAll(asRows(loadFromTransformationProfile("claimUpdates_2_hbase.xsl"), load("recordClaimUpdate.xml")));
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printAll(mapAll(buildTable(rows)));
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39616
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claudio.at
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}
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@Test
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52543
|
alessia.ba
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public void testParseClaimRel() throws Exception {
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doTest(loadFromTransformationProfile("claimRels_2_hbase.xml"), load("recordClaimRel.xml"));
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}
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@Test
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49718
|
claudio.at
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public void testParseFp7IctPUB() throws Exception {
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doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("ec_fp7_ict.xml"));
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}
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@Test
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52524
|
claudio.at
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public void testParseRecordCrossref() throws Exception {
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doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("recordCrossref.xml"));
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}
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@Test
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claudio.at
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public void testParseDatasetPUB() throws Exception {
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40063
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alessia.ba
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordDatasetPUB.xml"));
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claudio.at
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}
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@Test
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52422
|
claudio.at
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public void testParseSoftwareEgiApp() throws Exception {
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("softwareEgiApp.xml"));
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}
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@Test
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public void testParseSoftwareEgiApp2() throws Exception {
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("softwareEgiApp2.xml"));
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}
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@Test
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public void testParseOrpEgiApp() throws Exception {
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("orpEgiApp.xml"));
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}
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@Test
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55099
|
alessia.ba
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public void testParseSoftwareDOECODE() throws Exception {
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| 120 |
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("doecode.xml"));
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}
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| 125 |
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@Test
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| 126 |
48854
|
claudio.at
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public void testParseDatasetLindat() throws Exception {
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("datasetLindat.xml"));
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}
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| 130 |
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| 131 |
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@Test
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| 132 |
53362
|
miriam.bag
|
public void testParseDatasetNeuroVault() throws Exception {
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| 133 |
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordNeuroVault.xml"));
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| 135 |
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}
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| 136 |
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| 137 |
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@Test
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| 138 |
55182
|
alessia.ba
|
public void testParseDatasetNeuroVault2() throws Exception {
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| 139 |
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| 140 |
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordNeuroVault2.xml"));
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| 141 |
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}
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| 142 |
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| 143 |
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@Test
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| 144 |
31997
|
claudio.at
|
public void testParseClaim() throws Exception {
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| 145 |
26600
|
sandro.lab
|
|
| 146 |
40063
|
alessia.ba
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doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("recordClaim.xml"));
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| 147 |
30967
|
claudio.at
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}
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| 148 |
26600
|
sandro.lab
|
|
| 149 |
30967
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claudio.at
|
@Test
|
| 150 |
55093
|
alessia.ba
|
public void testParseClaimDedup() throws Exception {
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| 151 |
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| 152 |
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doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("recordClaimedDedup.xml"));
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| 153 |
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}
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| 154 |
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| 155 |
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| 156 |
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@Test
|
| 157 |
42825
|
alessia.ba
|
public void testParseClaimDataset() throws Exception {
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| 158 |
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| 159 |
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordClaimDataset.xml"));
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| 160 |
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}
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| 161 |
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| 162 |
52543
|
alessia.ba
|
|
| 163 |
42825
|
alessia.ba
|
@Test
|
| 164 |
39431
|
claudio.at
|
public void testParseACM() throws Exception {
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| 165 |
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| 166 |
40063
|
alessia.ba
|
doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("recordACM.xml"));
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| 167 |
39431
|
claudio.at
|
}
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| 168 |
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| 169 |
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@Test
|
| 170 |
39616
|
claudio.at
|
public void testParseASB() throws Exception {
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| 171 |
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| 172 |
40063
|
alessia.ba
|
doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("recordASB.xml"));
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| 173 |
39616
|
claudio.at
|
}
|
| 174 |
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| 175 |
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@Test
|
| 176 |
33382
|
claudio.at
|
public void testParseProjectCorda() throws Exception {
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| 177 |
26600
|
sandro.lab
|
|
| 178 |
40205
|
claudio.at
|
doTest(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordCorda.xml"));
|
| 179 |
26600
|
sandro.lab
|
}
|
| 180 |
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| 181 |
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@Test
|
| 182 |
33382
|
claudio.at
|
public void testParseProjectFCT() throws Exception {
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| 183 |
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| 184 |
40205
|
claudio.at
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doTest(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordFCT.xml"));
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| 185 |
33382
|
claudio.at
|
}
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| 186 |
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| 187 |
46587
|
alessia.ba
|
|
| 188 |
33382
|
claudio.at
|
@Test
|
| 189 |
40205
|
claudio.at
|
public void testParseOaf() throws Exception {
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| 190 |
26600
|
sandro.lab
|
|
| 191 |
40063
|
alessia.ba
|
doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("record.xml"));
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| 192 |
30967
|
claudio.at
|
}
|
| 193 |
26600
|
sandro.lab
|
|
| 194 |
30967
|
claudio.at
|
@Test
|
| 195 |
40205
|
claudio.at
|
public void testParseOafPublication() throws Exception {
|
| 196 |
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| 197 |
52980
|
alessia.ba
|
doTest(loadFromTransformationProfile("oaf_entity2hbase.xml"), load("record.xml"));
|
| 198 |
40205
|
claudio.at
|
}
|
| 199 |
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| 200 |
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@Test
|
| 201 |
43558
|
claudio.at
|
public void testParseLindat() throws Exception {
|
| 202 |
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| 203 |
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordLindat.xml"));
|
| 204 |
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}
|
| 205 |
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| 206 |
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@Test
|
| 207 |
31997
|
claudio.at
|
public void testParseDatacite() throws Exception {
|
| 208 |
26600
|
sandro.lab
|
|
| 209 |
40063
|
alessia.ba
|
doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordDatacite.xml"));
|
| 210 |
30967
|
claudio.at
|
}
|
| 211 |
26600
|
sandro.lab
|
|
| 212 |
31997
|
claudio.at
|
@Test
|
| 213 |
33382
|
claudio.at
|
public void testParseDatacite2() throws Exception {
|
| 214 |
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| 215 |
40063
|
alessia.ba
|
doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordDatacite2.xml"));
|
| 216 |
33382
|
claudio.at
|
}
|
| 217 |
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| 218 |
|
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@Test
|
| 219 |
55263
|
alessia.ba
|
public void testParseDataciteNewES() throws Exception {
|
| 220 |
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| 221 |
|
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("dataciteNew.xml"));
|
| 222 |
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}
|
| 223 |
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|
| 224 |
|
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@Test
|
| 225 |
42495
|
alessia.ba
|
public void testParseOpenTrials() throws Exception {
|
| 226 |
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|
| 227 |
|
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("opentrials_datacite1.xml"));
|
| 228 |
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}
|
| 229 |
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|
| 230 |
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@Test
|
| 231 |
32094
|
claudio.at
|
public void testLinkPangaea() throws Exception {
|
| 232 |
26600
|
sandro.lab
|
|
| 233 |
34438
|
claudio.at
|
final List<Row> rows = Lists.newArrayList();
|
| 234 |
40205
|
claudio.at
|
rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("pangaeODF1.xml")));
|
| 235 |
|
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rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("pangaeODF2.xml")));
|
| 236 |
40063
|
alessia.ba
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("pangaeOAF.xml")));
|
| 237 |
40205
|
claudio.at
|
rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordCordaPangaea.xml")));
|
| 238 |
31997
|
claudio.at
|
|
| 239 |
38025
|
claudio.at
|
printAll(mapAll(buildTable(rows)));
|
| 240 |
31997
|
claudio.at
|
}
|
| 241 |
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|
| 242 |
33382
|
claudio.at
|
@Test
|
| 243 |
57186
|
sandro.lab
|
public void testODF() throws Exception {
|
| 244 |
|
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|
| 245 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 246 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("odf.xml")));
|
| 247 |
57193
|
sandro.lab
|
//printAll(mapAll(buildTable(rows)));
|
| 248 |
57186
|
sandro.lab
|
}
|
| 249 |
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|
| 250 |
|
|
@Test
|
| 251 |
43795
|
alessia.ba
|
public void testPangaea() throws Exception {
|
| 252 |
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|
| 253 |
|
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final List<Row> rows = Lists.newArrayList();
|
| 254 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("pangaeOAF2.xml")));
|
| 255 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 256 |
|
|
}
|
| 257 |
45034
|
alessia.ba
|
@Test
|
| 258 |
|
|
public void testZenodo() throws Exception {
|
| 259 |
43795
|
alessia.ba
|
|
| 260 |
45034
|
alessia.ba
|
final List<Row> rows = Lists.newArrayList();
|
| 261 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("zenodoData.xml")));
|
| 262 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 263 |
|
|
}
|
| 264 |
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|
| 265 |
43795
|
alessia.ba
|
@Test
|
| 266 |
52193
|
alessia.ba
|
public void testZenodoSoftware() throws Exception {
|
| 267 |
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|
| 268 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 269 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("softwareZenodo_odf.xml")));
|
| 270 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 271 |
|
|
}
|
| 272 |
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|
| 273 |
|
|
@Test
|
| 274 |
35179
|
michele.ar
|
public void testLinkCorda() throws Exception {
|
| 275 |
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|
| 276 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 277 |
40205
|
claudio.at
|
rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordCorda.xml")));
|
| 278 |
40063
|
alessia.ba
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordCorda.xml")));
|
| 279 |
35179
|
michele.ar
|
|
| 280 |
38025
|
claudio.at
|
printAll(mapAll(buildTable(rows)));
|
| 281 |
35179
|
michele.ar
|
}
|
| 282 |
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|
|
| 283 |
|
|
@Test
|
| 284 |
33382
|
claudio.at
|
public void testLinkFCT() throws Exception {
|
| 285 |
|
|
|
| 286 |
34438
|
claudio.at
|
final List<Row> rows = Lists.newArrayList();
|
| 287 |
40205
|
claudio.at
|
rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordFCT.xml")));
|
| 288 |
40063
|
alessia.ba
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordFCT.xml")));
|
| 289 |
33382
|
claudio.at
|
|
| 290 |
38025
|
claudio.at
|
printAll(mapAll(buildTable(rows)));
|
| 291 |
33382
|
claudio.at
|
}
|
| 292 |
|
|
|
| 293 |
|
|
@Test
|
| 294 |
41468
|
claudio.at
|
public void testLinkARC() throws Exception {
|
| 295 |
|
|
|
| 296 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 297 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordARC.xml")));
|
| 298 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordARC.xml")));
|
| 299 |
|
|
|
| 300 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 301 |
|
|
}
|
| 302 |
|
|
|
| 303 |
|
|
@Test
|
| 304 |
33382
|
claudio.at
|
public void testLinkWT() throws Exception {
|
| 305 |
|
|
|
| 306 |
34438
|
claudio.at
|
final List<Row> rows = Lists.newArrayList();
|
| 307 |
40205
|
claudio.at
|
rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordWT.xml")));
|
| 308 |
40063
|
alessia.ba
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordWT.xml")));
|
| 309 |
33382
|
claudio.at
|
|
| 310 |
38025
|
claudio.at
|
printAll(mapAll(buildTable(rows)));
|
| 311 |
33382
|
claudio.at
|
}
|
| 312 |
|
|
|
| 313 |
43169
|
alessia.ba
|
|
| 314 |
|
|
|
| 315 |
34438
|
claudio.at
|
@Test
|
| 316 |
|
|
public void testLinkOrganization() throws Exception {
|
| 317 |
|
|
|
| 318 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 319 |
40205
|
claudio.at
|
rows.addAll(asRows(loadFromTransformationProfile("organizations_2_hbase.xsl"), load("organization.xml")));
|
| 320 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("projectorganization_2_hbase.xsl"), load("project_organization.xml")));
|
| 321 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordCorda.xml")));
|
| 322 |
34438
|
claudio.at
|
|
| 323 |
38025
|
claudio.at
|
printAll(mapAll(buildTable(rows)));
|
| 324 |
34438
|
claudio.at
|
}
|
| 325 |
|
|
|
| 326 |
35746
|
alessia.ba
|
@Test
|
| 327 |
46587
|
alessia.ba
|
public void testLinkOrganizationAffiliation() throws Exception {
|
| 328 |
|
|
|
| 329 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 330 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("organizations_2_hbase.xsl"), load("organization.xml")));
|
| 331 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("resultorganization_2_hbase.xsl"), load("result_organization.xml")));
|
| 332 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("record.xml")));
|
| 333 |
|
|
|
| 334 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 335 |
|
|
}
|
| 336 |
|
|
|
| 337 |
|
|
@Test
|
| 338 |
44483
|
claudio.at
|
public void testDuplicates() throws Exception {
|
| 339 |
|
|
final String mergeId = "50|dedup_wf_001::08ed625d07e5738b794ff14d6773fd9f";
|
| 340 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 341 |
|
|
|
| 342 |
49029
|
claudio.at
|
final Function<Row, Row> f = rowIn -> {
|
| 343 |
44483
|
claudio.at
|
|
| 344 |
49029
|
claudio.at
|
final List<Column<String,byte[]>> cols = Lists.newArrayList();
|
| 345 |
|
|
for(Column<String,byte[]> col : rowIn.getColumns()) {
|
| 346 |
|
|
if (col.getName().equals("body")) {
|
| 347 |
|
|
cols.add(new Column(col.getName(), col.getValue()));
|
| 348 |
44483
|
claudio.at
|
|
| 349 |
|
|
}
|
| 350 |
|
|
}
|
| 351 |
49029
|
claudio.at
|
return new Row("result", rowIn.getKey(), cols);
|
| 352 |
44483
|
claudio.at
|
};
|
| 353 |
|
|
|
| 354 |
|
|
final List<Row> puma1 = asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordPuma1.xml"), f);
|
| 355 |
|
|
puma1.add(new Row("resultResult_dedup_isMergedIn", mergeId));
|
| 356 |
|
|
|
| 357 |
|
|
final List<Row> puma2 = asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordPuma2.xml"), f);
|
| 358 |
|
|
puma2.add(new Row("resultResult_dedup_isMergedIn", mergeId));
|
| 359 |
|
|
|
| 360 |
|
|
rows.addAll(puma1);
|
| 361 |
|
|
rows.addAll(puma2);
|
| 362 |
|
|
|
| 363 |
|
|
List<Oaf> duplicates = Lists.newArrayList();
|
| 364 |
|
|
duplicates.add(getOafBody(puma1));
|
| 365 |
|
|
duplicates.add(getOafBody(puma2));
|
| 366 |
|
|
final Oaf.Builder oafMerge = OafEntityMerger.merge(mergeId, duplicates);
|
| 367 |
|
|
|
| 368 |
48697
|
claudio.at
|
final Row mergeRow = new Row("result", mergeId, Lists.newArrayList(new Column("body", oafMerge.build().toByteArray())));
|
| 369 |
44483
|
claudio.at
|
|
| 370 |
|
|
rows.add(mergeRow);
|
| 371 |
|
|
|
| 372 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 373 |
|
|
}
|
| 374 |
|
|
|
| 375 |
|
|
private Oaf getOafBody(final List<Row> rows) throws InvalidProtocolBufferException {
|
| 376 |
|
|
for(Row row : rows) {
|
| 377 |
|
|
if(StringUtils.startsWith(row.getKey(), "50")) {
|
| 378 |
|
|
return Oaf.parseFrom(row.getColumn("body").getValue());
|
| 379 |
|
|
|
| 380 |
|
|
}
|
| 381 |
|
|
}
|
| 382 |
|
|
return null;
|
| 383 |
|
|
}
|
| 384 |
|
|
|
| 385 |
|
|
@Test
|
| 386 |
35746
|
alessia.ba
|
public void testParseDoajOAF() throws Exception {
|
| 387 |
|
|
|
| 388 |
40063
|
alessia.ba
|
doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("doajUniversityRecord.xml"));
|
| 389 |
35746
|
alessia.ba
|
}
|
| 390 |
|
|
|
| 391 |
39888
|
alessia.ba
|
@Test
|
| 392 |
|
|
public void testParseDatasource() throws Exception {
|
| 393 |
|
|
|
| 394 |
40205
|
claudio.at
|
doTest(loadFromTransformationProfile("datasources_2_hbase.xsl"), load("datasourceNative.xml"));
|
| 395 |
39888
|
alessia.ba
|
}
|
| 396 |
44899
|
alessia.ba
|
@Test
|
| 397 |
|
|
public void testParseDatasourcePiwik() throws Exception {
|
| 398 |
39888
|
alessia.ba
|
|
| 399 |
44899
|
alessia.ba
|
doTest(loadFromTransformationProfile("datasources_2_hbase.xsl"), load("datasourcePiwik.xml"));
|
| 400 |
|
|
}
|
| 401 |
|
|
|
| 402 |
40205
|
claudio.at
|
@Test
|
| 403 |
40341
|
alessia.ba
|
public void testParseDataDatasource() throws Exception {
|
| 404 |
|
|
|
| 405 |
|
|
doTest(loadFromTransformationProfile("datasources_2_hbase.xsl"), load("dataDatasource.xml"));
|
| 406 |
|
|
}
|
| 407 |
|
|
|
| 408 |
|
|
@Test
|
| 409 |
36164
|
claudio.at
|
public void testFromMongodbCompressedDump() throws Exception {
|
| 410 |
40063
|
alessia.ba
|
doTestJsonGz(loadFromTransformationProfile("oaf2hbase.xml"), load("mdstore_cleaned.json.gz"));
|
| 411 |
35746
|
alessia.ba
|
}
|
| 412 |
|
|
|
| 413 |
55177
|
alessia.ba
|
|
| 414 |
40205
|
claudio.at
|
@Test
|
| 415 |
|
|
public void testLoadFromTransformationProfile() throws IOException {
|
| 416 |
|
|
InputStream in = loadFromTransformationProfile("oaf2hbase.xml");
|
| 417 |
|
|
log.info(IOUtils.toString(in));
|
| 418 |
|
|
}
|
| 419 |
|
|
|
| 420 |
|
|
@Test
|
| 421 |
|
|
public void test_template() throws Exception {
|
| 422 |
|
|
final String xslt = IOUtils.toString(loadFromTransformationProfile("oaf2hbase.xml"));
|
| 423 |
|
|
final XsltRowTransformer transformer = factory.getTransformer(xslt);
|
| 424 |
|
|
assertNotNull(transformer);
|
| 425 |
|
|
|
| 426 |
|
|
final String record = IOUtils.toString(load("record.xml"));
|
| 427 |
|
|
final List<Row> rows = transformer.apply(record);
|
| 428 |
|
|
|
| 429 |
|
|
System.out.println(rows);
|
| 430 |
|
|
}
|
| 431 |
|
|
|
| 432 |
|
|
@Test
|
| 433 |
|
|
public void testWrongCharsOrganization() throws Exception {
|
| 434 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 435 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("organizations_2_hbase.xsl"), load("organizationWrongChars.xml")));
|
| 436 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 437 |
|
|
}
|
| 438 |
|
|
|
| 439 |
43169
|
alessia.ba
|
@Test
|
| 440 |
|
|
public void testParseProjectWithFunderOriginalName() throws Exception {
|
| 441 |
|
|
|
| 442 |
|
|
doTest(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectWithFunderOriginalName.xml"));
|
| 443 |
|
|
}
|
| 444 |
|
|
@Test
|
| 445 |
|
|
public void testLinkFunderOriginalName() throws Exception {
|
| 446 |
|
|
|
| 447 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 448 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectWithFunderOriginalName.xml")));
|
| 449 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordFunderOriginalName.xml")));
|
| 450 |
|
|
|
| 451 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 452 |
|
|
}
|
| 453 |
|
|
|
| 454 |
44070
|
alessia.ba
|
@Test
|
| 455 |
|
|
public void testProjectExtraInfo() throws Exception {
|
| 456 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 457 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordExtraInfo.xml")));
|
| 458 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 459 |
|
|
}
|
| 460 |
|
|
|
| 461 |
48697
|
claudio.at
|
@Test
|
| 462 |
|
|
public void testParseSoftwareFromODF() throws Exception {
|
| 463 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 464 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("softwareODF.xml")));
|
| 465 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordCorda.xml")));
|
| 466 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 467 |
|
|
}
|
| 468 |
|
|
|
| 469 |
52212
|
alessia.ba
|
@Test
|
| 470 |
48697
|
claudio.at
|
public void testParseSoftwareFromOAF() throws Exception {
|
| 471 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 472 |
52212
|
alessia.ba
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordOAFsoftwareCLOSED.xml")));
|
| 473 |
48697
|
claudio.at
|
printAll(mapAll(buildTable(rows)));
|
| 474 |
|
|
}
|
| 475 |
|
|
|
| 476 |
52212
|
alessia.ba
|
@Test
|
| 477 |
54978
|
alessia.ba
|
public void testParsePubFromODF() throws Exception {
|
| 478 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 479 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("recordODFPub.xml")));
|
| 480 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 481 |
|
|
}
|
| 482 |
|
|
|
| 483 |
|
|
@Test
|
| 484 |
52212
|
alessia.ba
|
public void testParseSoftwareFromOAFOpen() throws Exception {
|
| 485 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 486 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordOAFsoftwareOPEN.xml")));
|
| 487 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 488 |
|
|
}
|
| 489 |
|
|
|
| 490 |
52275
|
alessia.ba
|
@Test
|
| 491 |
53756
|
alessia.ba
|
public void testParseSoftwareBiotool() throws Exception {
|
| 492 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 493 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("biotoolSw.xml")));
|
| 494 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 495 |
|
|
}
|
| 496 |
|
|
|
| 497 |
|
|
@Test
|
| 498 |
52275
|
alessia.ba
|
public void testParseOafWithExternalRef() throws Exception {
|
| 499 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 500 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("oafWithExternalReference.xml")));
|
| 501 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 502 |
|
|
}
|
| 503 |
|
|
|
| 504 |
52277
|
alessia.ba
|
@Test
|
| 505 |
|
|
public void testParseOafWithCommunity() throws Exception {
|
| 506 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 507 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("oafWithCommunity.xml")));
|
| 508 |
|
|
printAll(mapAll(buildTable(rows)));
|
| 509 |
|
|
}
|
| 510 |
|
|
|
| 511 |
53408
|
claudio.at
|
@Test
|
| 512 |
|
|
public void testParseOafWithUpdates() throws Exception {
|
| 513 |
|
|
final List<Row> rows = Lists.newArrayList();
|
| 514 |
|
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("oafWithCommunity.xml")));
|
| 515 |
|
|
|
| 516 |
|
|
ActionFactory actionFactory = new ActionFactory();
|
| 517 |
|
|
|
| 518 |
|
|
Map<String, Resource> xslts = Maps.newHashMap();
|
| 519 |
|
|
|
| 520 |
|
|
xslts.put("oaf2hbase", new ByteArrayResource(IOUtils.toString(loadFromTransformationProfile("oaf2hbase.xml")).getBytes()));
|
| 521 |
|
|
actionFactory.setXslts(xslts);
|
| 522 |
|
|
|
| 523 |
|
|
XsltInfoPackageAction pa = actionFactory.generateInfoPackageAction(
|
| 524 |
|
|
"oaf2hbase",
|
| 525 |
|
|
"rawset-id",
|
| 526 |
|
|
new Agent("agent-id", "agent-name", Agent.AGENT_TYPE.algo),
|
| 527 |
|
|
Operation.UPDATE,
|
| 528 |
|
|
IOUtils.toString(load("oafUpdateWithCommunity.xml")),
|
| 529 |
|
|
Provenance.sysimport_mining_aggregator,
|
| 530 |
|
|
"0.9");
|
| 531 |
|
|
|
| 532 |
|
|
final String qualifier = "update_" + System.nanoTime();
|
| 533 |
|
|
|
| 534 |
|
|
IOUtils.readLines(load("country_updates.json")).forEach(line -> {
|
| 535 |
|
|
|
| 536 |
|
|
Oaf.Builder oaf = Oaf.newBuilder();
|
| 537 |
|
|
|
| 538 |
|
|
try {
|
| 539 |
|
|
JsonFormat.merge(line, oaf);
|
| 540 |
|
|
} catch (JsonFormat.ParseException e) {
|
| 541 |
|
|
throw new IllegalArgumentException(e);
|
| 542 |
|
|
}
|
| 543 |
|
|
|
| 544 |
|
|
Column<String, byte[]> col = new Column<>("update_" + System.nanoTime(), oaf.build().toByteArray());
|
| 545 |
|
|
rows.add(new Row("result", oaf.getEntity().getId(), Lists.newArrayList(col)));
|
| 546 |
|
|
});
|
| 547 |
|
|
|
| 548 |
|
|
pa.asAtomicActions().forEach(a -> {
|
| 549 |
|
|
Column<String, byte[]> col = new Column<>("update_" + System.nanoTime(), a.getTargetValue());
|
| 550 |
|
|
rows.add(new Row(a.getTargetColumnFamily(), a.getTargetRowKey(), Lists.newArrayList(col)));
|
| 551 |
|
|
});
|
| 552 |
|
|
|
| 553 |
|
|
|
| 554 |
|
|
/*
|
| 555 |
|
|
rows.forEach(r -> {
|
| 556 |
|
|
log.info(r);
|
| 557 |
|
|
});
|
| 558 |
|
|
*/
|
| 559 |
|
|
|
| 560 |
|
|
mapAll(buildTable(rows)).entrySet().forEach(b -> {
|
| 561 |
|
|
log.info(b.getKey());
|
| 562 |
|
|
log.info(b.getValue());
|
| 563 |
|
|
});
|
| 564 |
|
|
}
|
| 565 |
|
|
|
| 566 |
54978
|
alessia.ba
|
@Test
|
| 567 |
|
|
public void testParseCrisPub() throws Exception {
|
| 568 |
|
|
doTest(loadFromTransformationProfile("odf2hbase.xml"), load("cris_pub1.xml"));
|
| 569 |
|
|
}
|
| 570 |
|
|
|
| 571 |
55177
|
alessia.ba
|
@Test
|
| 572 |
|
|
public void testBioToolSwRowJson() throws Exception {
|
| 573 |
|
|
doTestJsonRow(IOUtils.toString(load("biotoolSwRow.json")));
|
| 574 |
|
|
}
|
| 575 |
|
|
|
| 576 |
55887
|
alessia.ba
|
@Test
|
| 577 |
|
|
public void testParseVirta() throws Exception {
|
| 578 |
|
|
doTest(loadFromTransformationProfile("datasources_2_hbase.xsl"), load("virta.xml"));
|
| 579 |
|
|
}
|
| 580 |
|
|
|
| 581 |
|
|
@Test
|
| 582 |
|
|
public void testParseJournal() throws Exception {
|
| 583 |
|
|
doTest(loadFromTransformationProfile("datasources_2_hbase.xsl"), load("datasourceWithISSN.xml"));
|
| 584 |
|
|
}
|
| 585 |
|
|
|
| 586 |
57091
|
alessia.ba
|
@Test
|
| 587 |
57092
|
alessia.ba
|
public void testGuidelines4Qeios() throws Exception {
|
| 588 |
57091
|
alessia.ba
|
|
| 589 |
|
|
doTest(loadFromTransformationProfile("odf2hbase.xml"), load("guidelines4_qeios1.xml"));
|
| 590 |
|
|
}
|
| 591 |
|
|
|
| 592 |
57092
|
alessia.ba
|
@Test
|
| 593 |
|
|
public void testGuidelines4Aria() throws Exception {
|
| 594 |
|
|
|
| 595 |
|
|
doTest(loadFromTransformationProfile("odf2hbase.xml"), load("guidelines4_aria.xml"));
|
| 596 |
|
|
}
|
| 597 |
|
|
|
| 598 |
57162
|
alessia.ba
|
@Test
|
| 599 |
|
|
public void testJournalRecord() throws Exception {
|
| 600 |
|
|
doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("journalRecord.xml"));
|
| 601 |
|
|
}
|
| 602 |
|
|
|
| 603 |
55177
|
alessia.ba
|
private void doTestJsonRow(final String json) throws Exception {
|
| 604 |
|
|
Row row = asRowFromJson(json);
|
| 605 |
|
|
log.info(row);
|
| 606 |
|
|
List<Row> rows = new ArrayList<>();
|
| 607 |
|
|
rows.add(row);
|
| 608 |
|
|
final Map<String, Map<String, Map<String, byte[]>>> table = buildTable(rows);
|
| 609 |
|
|
final Map<String, XmlRecordFactory> builders = mapAll(table);
|
| 610 |
|
|
printAll(builders);
|
| 611 |
|
|
|
| 612 |
|
|
}
|
| 613 |
|
|
|
| 614 |
31997
|
claudio.at
|
private void doTest(final InputStream xsltStream, final InputStream recordStream) throws Exception {
|
| 615 |
|
|
try {
|
| 616 |
34438
|
claudio.at
|
final List<Row> rows = asRows(xsltStream, recordStream);
|
| 617 |
31997
|
claudio.at
|
|
| 618 |
40063
|
alessia.ba
|
log.info(rows);
|
| 619 |
26600
|
sandro.lab
|
|
| 620 |
34438
|
claudio.at
|
final Map<String, Map<String, Map<String, byte[]>>> table = buildTable(rows);
|
| 621 |
26600
|
sandro.lab
|
|
| 622 |
30967
|
claudio.at
|
// System.out.println("\n" + table.toString());
|
| 623 |
26600
|
sandro.lab
|
|
| 624 |
34438
|
claudio.at
|
final Map<String, XmlRecordFactory> builders = mapAll(table);
|
| 625 |
28094
|
claudio.at
|
|
| 626 |
38025
|
claudio.at
|
printAll(builders);
|
| 627 |
34438
|
claudio.at
|
} catch (final InvalidProtocolBufferException e) {
|
| 628 |
31997
|
claudio.at
|
throw new Exception(e);
|
| 629 |
34438
|
claudio.at
|
} catch (final TransformerConfigurationException e) {
|
| 630 |
31997
|
claudio.at
|
throw new Exception(e);
|
| 631 |
34438
|
claudio.at
|
} catch (final TransformerFactoryConfigurationError e) {
|
| 632 |
31997
|
claudio.at
|
throw new Exception(e);
|
| 633 |
34438
|
claudio.at
|
} catch (final DocumentException e) {
|
| 634 |
31997
|
claudio.at
|
throw new Exception(e);
|
| 635 |
26600
|
sandro.lab
|
}
|
| 636 |
|
|
}
|
| 637 |
|
|
|
| 638 |
35746
|
alessia.ba
|
private void doTestJsonGz(final InputStream xsltStream, final InputStream recordStream) throws Exception {
|
| 639 |
|
|
|
| 640 |
36164
|
claudio.at
|
final Iterator<List<Row>> rowsIterator = asRowsJsonGzip(xsltStream, recordStream);
|
| 641 |
35746
|
alessia.ba
|
|
| 642 |
36164
|
claudio.at
|
int i = 0;
|
| 643 |
|
|
while (rowsIterator.hasNext()) {
|
| 644 |
|
|
final List<Row> rows = rowsIterator.next();
|
| 645 |
|
|
i++;
|
| 646 |
35746
|
alessia.ba
|
|
| 647 |
36164
|
claudio.at
|
if ((i % 10000) == 0) {
|
| 648 |
|
|
System.out.println(i);
|
| 649 |
|
|
}
|
| 650 |
35746
|
alessia.ba
|
|
| 651 |
36164
|
claudio.at
|
final Map<String, Map<String, Map<String, byte[]>>> table = buildTableDoaj(rows);
|
| 652 |
35746
|
alessia.ba
|
|
| 653 |
36164
|
claudio.at
|
for (final Map<String, Map<String, byte[]>> m : table.values()) {
|
| 654 |
|
|
for (final Map<String, byte[]> mv : m.values()) {
|
| 655 |
|
|
for (final byte[] v : mv.values()) {
|
| 656 |
|
|
final OafDecoder d = OafDecoder.decode(v);
|
| 657 |
|
|
assertNotNull(d);
|
| 658 |
|
|
assertNotNull(d.getOaf());
|
| 659 |
|
|
|
| 660 |
|
|
switch (d.getKind()) {
|
| 661 |
|
|
case entity:
|
| 662 |
|
|
assertNotNull(d.getMetadata());
|
| 663 |
|
|
if (d.getOaf().getEntity().getType().equals(Type.result)) {
|
| 664 |
|
|
System.out.println(d.getOaf());
|
| 665 |
|
|
}
|
| 666 |
|
|
break;
|
| 667 |
|
|
case relation:
|
| 668 |
|
|
assertNotNull(d.getRel());
|
| 669 |
|
|
break;
|
| 670 |
|
|
default:
|
| 671 |
|
|
break;
|
| 672 |
|
|
}
|
| 673 |
|
|
}
|
| 674 |
|
|
}
|
| 675 |
35746
|
alessia.ba
|
}
|
| 676 |
|
|
}
|
| 677 |
|
|
}
|
| 678 |
|
|
|
| 679 |
44483
|
claudio.at
|
private List<Row> asRows(final InputStream xsltStream, final InputStream recordStream, final Function<Row, Row> p) throws Exception {
|
| 680 |
48697
|
claudio.at
|
return asRows(xsltStream, new HashMap<>(), recordStream, p);
|
| 681 |
44483
|
claudio.at
|
}
|
| 682 |
|
|
|
| 683 |
31997
|
claudio.at
|
private List<Row> asRows(final InputStream xsltStream, final InputStream recordStream) throws Exception {
|
| 684 |
48697
|
claudio.at
|
return asRows(xsltStream, new HashMap<>(), recordStream);
|
| 685 |
38025
|
claudio.at
|
}
|
| 686 |
|
|
|
| 687 |
|
|
private List<Row> asRows(final InputStream xsltStream, final Map<String, Object> params, final InputStream recordStream) throws Exception {
|
| 688 |
44483
|
claudio.at
|
return asRows(xsltStream, params, recordStream, null);
|
| 689 |
|
|
}
|
| 690 |
|
|
|
| 691 |
|
|
private List<Row> asRows(final InputStream xsltStream, final Map<String, Object> params, final InputStream recordStream, final Function<Row, Row> p) throws Exception {
|
| 692 |
34438
|
claudio.at
|
final String xslt = IOUtils.toString(xsltStream);
|
| 693 |
38025
|
claudio.at
|
final XsltRowTransformer transformer = factory.getTransformer(xslt, params);
|
| 694 |
31997
|
claudio.at
|
assertNotNull(transformer);
|
| 695 |
26600
|
sandro.lab
|
|
| 696 |
34438
|
claudio.at
|
final String record = IOUtils.toString(recordStream);
|
| 697 |
|
|
final List<Row> rows = transformer.apply(record);
|
| 698 |
31997
|
claudio.at
|
|
| 699 |
|
|
assertNotNull(rows);
|
| 700 |
|
|
assertFalse(rows.isEmpty());
|
| 701 |
44483
|
claudio.at
|
return p == null ? rows : Lists.newArrayList(Iterables.transform(rows, p));
|
| 702 |
31997
|
claudio.at
|
}
|
| 703 |
|
|
|
| 704 |
35746
|
alessia.ba
|
private Iterator<List<Row>> asRowsJsonGzip(final InputStream xsltStream, final InputStream recordStreamJsonGzip) throws Exception {
|
| 705 |
|
|
final String xslt = IOUtils.toString(xsltStream);
|
| 706 |
|
|
final XsltRowTransformer transformer = factory.getTransformer(xslt);
|
| 707 |
|
|
assertNotNull(transformer);
|
| 708 |
|
|
assertNotNull(recordStreamJsonGzip);
|
| 709 |
|
|
|
| 710 |
36164
|
claudio.at
|
final GZIPInputStream stream = new GZIPInputStream(recordStreamJsonGzip);
|
| 711 |
35746
|
alessia.ba
|
assertNotNull(stream);
|
| 712 |
|
|
final BufferedReader inStream = new BufferedReader(new InputStreamReader(stream));
|
| 713 |
|
|
assertNotNull(inStream);
|
| 714 |
|
|
return new Iterator<List<Row>>() {
|
| 715 |
|
|
|
| 716 |
|
|
String jsonRecord = null;
|
| 717 |
|
|
|
| 718 |
|
|
@Override
|
| 719 |
|
|
public boolean hasNext() {
|
| 720 |
|
|
try {
|
| 721 |
|
|
return (jsonRecord = inStream.readLine()) != null;
|
| 722 |
36164
|
claudio.at
|
} catch (final IOException e) {
|
| 723 |
35746
|
alessia.ba
|
throw new RuntimeException(e);
|
| 724 |
|
|
}
|
| 725 |
|
|
}
|
| 726 |
|
|
|
| 727 |
|
|
@Override
|
| 728 |
|
|
public List<Row> next() {
|
| 729 |
|
|
|
| 730 |
36164
|
claudio.at
|
final JSONObject jsonObj = new JSONObject(jsonRecord);
|
| 731 |
|
|
final String body = jsonObj.getString("body");
|
| 732 |
|
|
try {
|
| 733 |
|
|
assertTrue(StringUtils.isNotBlank(body));
|
| 734 |
|
|
// System.out.println(body);
|
| 735 |
|
|
final List<Row> rows = transformer.apply(body);
|
| 736 |
|
|
assertNotNull(rows);
|
| 737 |
|
|
assertFalse(rows.isEmpty());
|
| 738 |
|
|
return rows;
|
| 739 |
|
|
} catch (final Throwable e) {
|
| 740 |
|
|
System.err.println("error transforming document: " + body);
|
| 741 |
|
|
throw new RuntimeException(e);
|
| 742 |
|
|
}
|
| 743 |
35746
|
alessia.ba
|
}
|
| 744 |
|
|
|
| 745 |
|
|
@Override
|
| 746 |
|
|
public void remove() {
|
| 747 |
43394
|
claudio.at
|
throw new UnsupportedOperationException();
|
| 748 |
35746
|
alessia.ba
|
}
|
| 749 |
|
|
|
| 750 |
|
|
};
|
| 751 |
|
|
|
| 752 |
|
|
}
|
| 753 |
|
|
|
| 754 |
|
|
private Map<String, Map<String, Map<String, byte[]>>> buildTableDoaj(final List<Row> rows) throws UnsupportedEncodingException {
|
| 755 |
34438
|
claudio.at
|
final Map<String, Map<String, Map<String, byte[]>>> table = Maps.newHashMap();
|
| 756 |
31997
|
claudio.at
|
|
| 757 |
34438
|
claudio.at
|
for (final Row row : rows) {
|
| 758 |
|
|
final String rowKey = row.getKey();
|
| 759 |
|
|
final String cf = row.getColumnFamily();
|
| 760 |
31997
|
claudio.at
|
if (!table.containsKey(rowKey)) {
|
| 761 |
48697
|
claudio.at
|
table.put(rowKey, new HashMap<>());
|
| 762 |
31997
|
claudio.at
|
}
|
| 763 |
|
|
if (!table.get(rowKey).containsKey(cf)) {
|
| 764 |
48697
|
claudio.at
|
table.get(rowKey).put(row.getColumnFamily(), new HashMap<>());
|
| 765 |
31997
|
claudio.at
|
}
|
| 766 |
34438
|
claudio.at
|
for (final Column<String, byte[]> c : row.getColumns()) {
|
| 767 |
35746
|
alessia.ba
|
// System.out.println(String.format("ADDING K:%s CF:%s Q:%s", rowKey, cf, c.getName()));
|
| 768 |
|
|
table.get(rowKey).get(cf).put(c.getName(), c.getValue());
|
| 769 |
|
|
if (cf.equals("result") && c.getName().equals("body")) {
|
| 770 |
36164
|
claudio.at
|
// System.out.println(String.format("ADDING K:%s CF:%s Q:%s", rowKey, cf, c.getName()));
|
| 771 |
35746
|
alessia.ba
|
assertTrue(StringUtils.isNotBlank(new String(c.getValue(), "UTF-8")));
|
| 772 |
|
|
}
|
| 773 |
|
|
}
|
| 774 |
|
|
}
|
| 775 |
|
|
return table;
|
| 776 |
|
|
|
| 777 |
|
|
}
|
| 778 |
|
|
|
| 779 |
53588
|
sandro.lab
|
protected Map<String, Map<String, Map<String, byte[]>>> buildTable(final List<Row> rows) throws UnsupportedEncodingException {
|
| 780 |
35746
|
alessia.ba
|
final Map<String, Map<String, Map<String, byte[]>>> table = Maps.newHashMap();
|
| 781 |
|
|
|
| 782 |
|
|
for (final Row row : rows) {
|
| 783 |
|
|
final String rowKey = row.getKey();
|
| 784 |
|
|
final String cf = row.getColumnFamily();
|
| 785 |
|
|
if (!table.containsKey(rowKey)) {
|
| 786 |
49029
|
claudio.at
|
table.put(rowKey, new HashMap<>());
|
| 787 |
35746
|
alessia.ba
|
}
|
| 788 |
|
|
if (!table.get(rowKey).containsKey(cf)) {
|
| 789 |
49029
|
claudio.at
|
table.get(rowKey).put(row.getColumnFamily(), new HashMap<>());
|
| 790 |
35746
|
alessia.ba
|
}
|
| 791 |
|
|
for (final Column<String, byte[]> c : row.getColumns()) {
|
| 792 |
31997
|
claudio.at
|
System.out.println(String.format("ADDING K:%s CF:%s Q:%s", rowKey, cf, c.getName()));
|
| 793 |
|
|
table.get(rowKey).get(cf).put(c.getName(), c.getValue());
|
| 794 |
38586
|
claudio.at
|
if (c.getName().equals("body")) {
|
| 795 |
36164
|
claudio.at
|
final String theBody = new String(c.getValue(), "UTF-8");
|
| 796 |
35746
|
alessia.ba
|
assertTrue(StringUtils.isNotBlank(theBody));
|
| 797 |
44070
|
alessia.ba
|
//System.out.println(theBody);
|
| 798 |
35746
|
alessia.ba
|
}
|
| 799 |
31997
|
claudio.at
|
}
|
| 800 |
|
|
}
|
| 801 |
|
|
return table;
|
| 802 |
35746
|
alessia.ba
|
|
| 803 |
31997
|
claudio.at
|
}
|
| 804 |
|
|
|
| 805 |
53588
|
sandro.lab
|
protected Map<String, XmlRecordFactory> mapAll(final Map<String, Map<String, Map<String, byte[]>>> table) throws Exception {
|
| 806 |
31997
|
claudio.at
|
|
| 807 |
34438
|
claudio.at
|
final Map<String, XmlRecordFactory> builders = Maps.newHashMap();
|
| 808 |
|
|
for (final Entry<String, Map<String, Map<String, byte[]>>> e : table.entrySet()) {
|
| 809 |
31997
|
claudio.at
|
map(builders, e.getKey(), e.getValue());
|
| 810 |
|
|
}
|
| 811 |
|
|
return builders;
|
| 812 |
|
|
}
|
| 813 |
|
|
|
| 814 |
35746
|
alessia.ba
|
// private Map<String, XmlRecordFactory> mapResultsOnly(final Map<String, Map<String, Map<String, byte[]>>> table) throws Exception {
|
| 815 |
|
|
//
|
| 816 |
|
|
// final Map<String, XmlRecordFactory> builders = Maps.newHashMap();
|
| 817 |
|
|
// for (final Entry<String, Map<String, Map<String, byte[]>>> e : table.entrySet()) {
|
| 818 |
|
|
// final Type type = OafRowKeyDecoder.decode(e.getKey()).getType();
|
| 819 |
|
|
// if (type == Type.result) {
|
| 820 |
|
|
// map(builders, e.getKey(), e.getValue());
|
| 821 |
|
|
// }
|
| 822 |
|
|
// }
|
| 823 |
|
|
// return builders;
|
| 824 |
|
|
// }
|
| 825 |
|
|
|
| 826 |
31997
|
claudio.at
|
private void map(final Map<String, XmlRecordFactory> builders, final String rowKey, final Map<String, Map<String, byte[]>> row) throws Exception {
|
| 827 |
|
|
|
| 828 |
30967
|
claudio.at
|
final Type type = OafRowKeyDecoder.decode(rowKey).getType();
|
| 829 |
26600
|
sandro.lab
|
|
| 830 |
41468
|
claudio.at
|
final Map<String, byte[]> familyMap = row.get(type.toString());
|
| 831 |
26600
|
sandro.lab
|
|
| 832 |
41468
|
claudio.at
|
if (familyMap == null) return;
|
| 833 |
26600
|
sandro.lab
|
|
| 834 |
41468
|
claudio.at
|
final byte[] bodyB = familyMap.get("body");
|
| 835 |
26600
|
sandro.lab
|
|
| 836 |
30967
|
claudio.at
|
if (bodyB != null) {
|
| 837 |
|
|
ensureBuilder(builders, rowKey);
|
| 838 |
41468
|
claudio.at
|
|
| 839 |
|
|
final Oaf oaf = UpdateMerger.mergeBodyUpdates(familyMap);
|
| 840 |
|
|
|
| 841 |
|
|
final OafDecoder mainEntity = OafDecoder.decode(oaf);
|
| 842 |
|
|
|
| 843 |
30967
|
claudio.at
|
builders.get(rowKey).setMainEntity(mainEntity);
|
| 844 |
28094
|
claudio.at
|
|
| 845 |
34438
|
claudio.at
|
for (final LinkDescriptor ld : entityConfigTable.getDescriptors(type)) {
|
| 846 |
26600
|
sandro.lab
|
|
| 847 |
34438
|
claudio.at
|
final String it = ld.getRelDescriptor().getIt();
|
| 848 |
|
|
final Map<String, byte[]> cols = row.get(it);
|
| 849 |
26600
|
sandro.lab
|
|
| 850 |
35746
|
alessia.ba
|
if ((cols != null) && !cols.isEmpty()) {
|
| 851 |
26600
|
sandro.lab
|
|
| 852 |
34438
|
claudio.at
|
for (final byte[] oafB : cols.values()) {
|
| 853 |
26600
|
sandro.lab
|
|
| 854 |
41468
|
claudio.at
|
final Oaf.Builder relBuilder = Oaf.newBuilder(Oaf.parseFrom(oafB));
|
| 855 |
26600
|
sandro.lab
|
|
| 856 |
30967
|
claudio.at
|
if (ld.isSymmetric()) {
|
| 857 |
34438
|
claudio.at
|
final RelDescriptor rd = ld.getRelDescriptor();
|
| 858 |
40205
|
claudio.at
|
|
| 859 |
|
|
relBuilder.getRelBuilder().setCachedTarget(mainEntity.getEntity()).setRelType(rd.getRelType()).setSubRelType(rd.getSubRelType());
|
| 860 |
30967
|
claudio.at
|
}
|
| 861 |
26600
|
sandro.lab
|
|
| 862 |
40205
|
claudio.at
|
relBuilder.getRelBuilder().setChild(ld.isChild());
|
| 863 |
26600
|
sandro.lab
|
|
| 864 |
40314
|
claudio.at
|
final Oaf.Builder oafBuilder = Oaf.newBuilder().setKind(Kind.relation).setLastupdatetimestamp(System.currentTimeMillis());
|
| 865 |
40205
|
claudio.at
|
oafBuilder.mergeFrom(relBuilder.build());
|
| 866 |
26600
|
sandro.lab
|
|
| 867 |
40205
|
claudio.at
|
final String targetId = ld.isSymmetric() ? oafBuilder.getRel().getTarget() : oafBuilder.getRel().getSource();
|
| 868 |
30967
|
claudio.at
|
ensureBuilder(builders, targetId);
|
| 869 |
34438
|
claudio.at
|
final OafDecoder decoder = OafDecoder.decode(oafBuilder.build());
|
| 870 |
37334
|
claudio.at
|
|
| 871 |
30967
|
claudio.at
|
if (ld.isChild()) {
|
| 872 |
37334
|
claudio.at
|
builders.get(targetId).addChild(type, decoder);
|
| 873 |
30967
|
claudio.at
|
} else {
|
| 874 |
37334
|
claudio.at
|
builders.get(targetId).addRelation(type, decoder);
|
| 875 |
30967
|
claudio.at
|
}
|
| 876 |
37334
|
claudio.at
|
}
|
| 877 |
26600
|
sandro.lab
|
|
| 878 |
30967
|
claudio.at
|
}
|
| 879 |
|
|
}
|
| 880 |
26600
|
sandro.lab
|
}
|
| 881 |
|
|
|
| 882 |
|
|
}
|
| 883 |
|
|
|
| 884 |
38025
|
claudio.at
|
private void printAll(final Map<String, XmlRecordFactory> builders) throws DocumentException {
|
| 885 |
|
|
print(Sets.newHashSet(Type.values()), builders, null);
|
| 886 |
|
|
}
|
| 887 |
|
|
|
| 888 |
|
|
private void print(final Set<Type> types, final Map<String, XmlRecordFactory> builders, final Map<Type, Set<String>> xpaths) throws DocumentException {
|
| 889 |
|
|
final SAXReader r = new SAXReader();
|
| 890 |
|
|
|
| 891 |
34438
|
claudio.at
|
for (final Entry<String, XmlRecordFactory> e : builders.entrySet()) {
|
| 892 |
38025
|
claudio.at
|
final OafRowKeyDecoder kd = OafRowKeyDecoder.decode(e.getKey());
|
| 893 |
|
|
|
| 894 |
|
|
if (!e.getValue().isValid()) throw new IllegalArgumentException("invalid builder: " + e.getKey());
|
| 895 |
|
|
if (types.contains(kd.getType())) {
|
| 896 |
|
|
final String val = IndentXmlString.apply(e.getValue().build());
|
| 897 |
|
|
|
| 898 |
|
|
if ((xpaths != null) && !xpaths.isEmpty() && (xpaths.get(kd.getType()) != null)) {
|
| 899 |
|
|
final Document doc = r.read(new StringReader(val));
|
| 900 |
|
|
|
| 901 |
40063
|
alessia.ba
|
log.debug("\n" + e.getKey());
|
| 902 |
38025
|
claudio.at
|
for (final String xpath : xpaths.get(kd.getType())) {
|
| 903 |
40063
|
alessia.ba
|
log.debug(doc.valueOf(xpath));
|
| 904 |
38025
|
claudio.at
|
}
|
| 905 |
|
|
} else {
|
| 906 |
40063
|
alessia.ba
|
log.info(val);
|
| 907 |
38025
|
claudio.at
|
}
|
| 908 |
31997
|
claudio.at
|
}
|
| 909 |
|
|
}
|
| 910 |
|
|
}
|
| 911 |
|
|
|
| 912 |
35746
|
alessia.ba
|
private void printNoIndent(final Map<String, XmlRecordFactory> builders) {
|
| 913 |
|
|
for (final Entry<String, XmlRecordFactory> e : builders.entrySet()) {
|
| 914 |
|
|
if (e.getValue().isValid()) {
|
| 915 |
40063
|
alessia.ba
|
log.debug(e.getValue().build());
|
| 916 |
35746
|
alessia.ba
|
} else {
|
| 917 |
40063
|
alessia.ba
|
log.debug("invalid builder: " + e.getKey());
|
| 918 |
35746
|
alessia.ba
|
}
|
| 919 |
|
|
}
|
| 920 |
|
|
}
|
| 921 |
|
|
|
| 922 |
31997
|
claudio.at
|
private void ensureBuilder(final Map<String, XmlRecordFactory> builders, final String rowKey) throws Exception {
|
| 923 |
30967
|
claudio.at
|
if (!builders.containsKey(rowKey)) {
|
| 924 |
|
|
builders.put(rowKey, newBuilder());
|
| 925 |
26600
|
sandro.lab
|
}
|
| 926 |
|
|
}
|
| 927 |
|
|
|
| 928 |
30967
|
claudio.at
|
private XmlRecordFactory newBuilder() throws TransformerConfigurationException, TransformerFactoryConfigurationError, DocumentException {
|
| 929 |
46587
|
alessia.ba
|
return new XmlRecordFactory(entityConfigTable, ContextMapper.fromXml(Context.xml),
|
| 930 |
|
|
RelClasses.fromJSon(RelClassesTest.relClassesJson), XmlRecordFactoryTest.SCHEMA_LOCATION, true, false, false, XmlRecordFactoryTest.specialDatasourceTypes);
|
| 931 |
30967
|
claudio.at
|
}
|
| 932 |
|
|
|
| 933 |
33382
|
claudio.at
|
private InputStream load(final String fileName) {
|
| 934 |
|
|
return getClass().getResourceAsStream(fileName);
|
| 935 |
|
|
}
|
| 936 |
|
|
|
| 937 |
40063
|
alessia.ba
|
private InputStream loadFromTransformationProfile(final String profilePath) {
|
| 938 |
|
|
log.info("Loading xslt from: " + basePathProfiles + profilePath);
|
| 939 |
|
|
InputStream profile = getClass().getResourceAsStream(basePathProfiles + profilePath);
|
| 940 |
|
|
SAXReader saxReader = new SAXReader();
|
| 941 |
|
|
Document doc = null;
|
| 942 |
|
|
try {
|
| 943 |
|
|
doc = saxReader.read(profile);
|
| 944 |
|
|
} catch (DocumentException e) {
|
| 945 |
|
|
e.printStackTrace();
|
| 946 |
|
|
throw new RuntimeException(e);
|
| 947 |
|
|
}
|
| 948 |
|
|
String xslt = doc.selectSingleNode("//SCRIPT/CODE/*[local-name()='stylesheet']").asXML();
|
| 949 |
52422
|
claudio.at
|
//log.info(xslt);
|
| 950 |
40063
|
alessia.ba
|
return IOUtils.toInputStream(xslt);
|
| 951 |
|
|
}
|
| 952 |
|
|
|
| 953 |
55177
|
alessia.ba
|
|
| 954 |
|
|
private Row asRowFromJson(String json) throws ParseException {
|
| 955 |
|
|
Oaf.Builder oafBuilder = Oaf.newBuilder();
|
| 956 |
|
|
JsonFormat.merge(json, oafBuilder);
|
| 957 |
|
|
final Oaf oaf = oafBuilder.build();
|
| 958 |
|
|
Row row = new Row("result", oaf.getEntity().getId());
|
| 959 |
|
|
Column<String, byte[]> c = new Column<>("body", oaf.toByteArray());
|
| 960 |
|
|
row.setColumn("body", c);
|
| 961 |
|
|
return row;
|
| 962 |
|
|
|
| 963 |
|
|
}
|
| 964 |
|
|
|
| 965 |
26600
|
sandro.lab
|
}
|