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package eu.dnetlib.data.transform;
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import static org.junit.Assert.assertFalse;
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import static org.junit.Assert.assertNotNull;
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import static org.junit.Assert.assertTrue;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.io.StringReader;
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import java.io.UnsupportedEncodingException;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Set;
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import java.util.zip.GZIPInputStream;
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import javax.xml.transform.TransformerConfigurationException;
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import javax.xml.transform.TransformerFactoryConfigurationError;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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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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import org.junit.Ignore;
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import org.junit.Test;
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import org.springframework.core.io.ByteArrayResource;
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import org.springframework.core.io.Resource;
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import com.google.common.base.Function;
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import com.google.common.collect.Iterables;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Maps;
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import com.google.common.collect.Sets;
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import com.google.protobuf.InvalidProtocolBufferException;
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import com.googlecode.protobuf.format.JsonFormat;
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import com.googlecode.protobuf.format.JsonFormat.ParseException;
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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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import eu.dnetlib.data.mapreduce.hbase.index.config.Context;
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import eu.dnetlib.data.mapreduce.hbase.index.config.ContextMapper;
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import eu.dnetlib.data.mapreduce.hbase.index.config.EntityConfigTable;
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import eu.dnetlib.data.mapreduce.hbase.index.config.IndexConfig;
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import eu.dnetlib.data.mapreduce.hbase.index.config.IndexConfigTest;
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import eu.dnetlib.data.mapreduce.hbase.index.config.LinkDescriptor;
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import eu.dnetlib.data.mapreduce.hbase.index.config.RelClasses;
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import eu.dnetlib.data.mapreduce.hbase.index.config.RelClassesTest;
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import eu.dnetlib.data.mapreduce.util.OafDecoder;
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import eu.dnetlib.data.mapreduce.util.OafRowKeyDecoder;
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import eu.dnetlib.data.mapreduce.util.RelDescriptor;
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import eu.dnetlib.data.mapreduce.util.UpdateMerger;
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import eu.dnetlib.data.mapreduce.util.XmlRecordFactory;
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import eu.dnetlib.data.mapreduce.util.XmlRecordFactoryTest;
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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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import eu.dnetlib.data.proto.TypeProtos.Type;
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import eu.dnetlib.miscutils.functional.xml.IndentXmlString;
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public class XsltRowTransformerFactoryTest {
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private static final Log log = LogFactory.getLog(XsltRowTransformerFactoryTest.class);
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private static String basePathProfiles = "/eu/dnetlib/test/profiles/TransformationRuleDSResources/TransformationRuleDSResourceType/2hbase/";
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private XsltRowTransformerFactory factory;
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private EntityConfigTable entityConfigTable;
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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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entityConfigTable = IndexConfig.load(IndexConfigTest.config).getConfigMap();
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}
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@Test
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@Ignore // need to reimplement because claimUpdates_2_hbase.xsl was removed
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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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@Ignore // need to reimplement because claimUpdates_2_hbase.xsl was removed
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public void testParseClaimUpdate() throws Exception {
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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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}
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@Test
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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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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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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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public void testParseDatasetPUB() throws Exception {
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordDatasetPUB.xml"));
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}
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@Test
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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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public void testParseSoftwareDOECODE() throws Exception {
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("doecode.xml"));
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}
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@Test
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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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@Test
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public void testParseDatasetNeuroVault() throws Exception {
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordNeuroVault.xml"));
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}
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@Test
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public void testParseDatasetNeuroVault2() throws Exception {
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordNeuroVault2.xml"));
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}
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@Test
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public void testParseClaim() throws Exception {
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doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("recordClaim.xml"));
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}
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@Test
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public void testParseClaimDedup() throws Exception {
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doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("recordClaimedDedup.xml"));
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}
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@Test
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public void testParseClaimDataset() throws Exception {
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordClaimDataset.xml"));
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}
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@Test
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public void testParseACM() throws Exception {
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doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("recordACM.xml"));
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}
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@Test
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public void testParseASB() throws Exception {
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doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("recordASB.xml"));
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}
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@Test
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public void testParseProjectCorda() throws Exception {
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doTest(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordCorda.xml"));
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}
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@Test
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public void testParseProjectFCT() throws Exception {
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doTest(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordFCT.xml"));
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}
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@Test
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public void testParseProjectWithSummaryAndAmount() throws Exception {
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doTest(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectWithSummaryAndAmount.xml"));
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}
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@Test
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public void testLinkOrganizationWithBudget() throws Exception {
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final List<Row> rows = Lists.newArrayList();
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rows.addAll(asRows(loadFromTransformationProfile("organizations_2_hbase.xsl"), load("organization.xml")));
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rows.addAll(asRows(loadFromTransformationProfile("projectorganization_2_hbase.xsl"), load("project_org_budget.xml")));
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rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectWithSummaryAndAmount.xml")));
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printAll(mapAll(buildTable(rows)));
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}
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@Test
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public void testParseOaf() throws Exception {
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doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("record.xml"));
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}
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@Test
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public void testParseOafPublication() throws Exception {
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doTest(loadFromTransformationProfile("oaf_entity2hbase.xml"), load("record.xml"));
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}
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@Test
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public void testParseLindat() throws Exception {
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordLindat.xml"));
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}
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@Test
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public void testParseDatacite() throws Exception {
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordDatacite.xml"));
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}
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@Test
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public void testParseDatacite2() throws Exception {
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordDatacite2.xml"));
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}
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@Test
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public void testParseDataciteNewES() throws Exception {
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("dataciteNew.xml"));
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}
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@Test
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public void testParseOpenTrials() throws Exception {
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266
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("opentrials_datacite1.xml"));
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268
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}
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269
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@Test
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public void testLinkPangaea() throws Exception {
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final List<Row> rows = Lists.newArrayList();
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rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("pangaeODF1.xml")));
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rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("pangaeODF2.xml")));
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rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("pangaeOAF.xml")));
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rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordCordaPangaea.xml")));
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printAll(mapAll(buildTable(rows)));
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}
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281
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282
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@Test
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283
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public void testODF() throws Exception {
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284
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285
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final List<Row> rows = Lists.newArrayList();
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286
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rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("odf.xml")));
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// printAll(mapAll(buildTable(rows)));
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288
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}
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289
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290
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@Test
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291
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public void testPangaea() throws Exception {
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292
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293
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final List<Row> rows = Lists.newArrayList();
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294
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rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("pangaeOAF2.xml")));
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295
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printAll(mapAll(buildTable(rows)));
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296
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}
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297
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298
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@Test
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299
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public void testZenodo() throws Exception {
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300
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301
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final List<Row> rows = Lists.newArrayList();
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302
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rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("zenodoData.xml")));
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303
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printAll(mapAll(buildTable(rows)));
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304
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}
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305
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306
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@Test
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307
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public void testZenodoSoftware() throws Exception {
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308
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309
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final List<Row> rows = Lists.newArrayList();
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310
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rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("softwareZenodo_odf.xml")));
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311
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printAll(mapAll(buildTable(rows)));
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312
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}
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313
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314
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@Test
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315
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public void testLinkCorda() throws Exception {
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316
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317
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final List<Row> rows = Lists.newArrayList();
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318
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rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordCorda.xml")));
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319
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rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordCorda.xml")));
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320
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321
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printAll(mapAll(buildTable(rows)));
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322
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}
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323
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324
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@Test
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325
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public void testLinkFCT() throws Exception {
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326
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327
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final List<Row> rows = Lists.newArrayList();
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328
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rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordFCT.xml")));
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329
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rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordFCT.xml")));
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330
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331
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printAll(mapAll(buildTable(rows)));
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332
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}
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333
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334
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@Test
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335
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public void testLinkARC() throws Exception {
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336
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337
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final List<Row> rows = Lists.newArrayList();
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338
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rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordARC.xml")));
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339
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rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordARC.xml")));
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340
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341
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printAll(mapAll(buildTable(rows)));
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342
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}
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343
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344
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@Test
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345
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public void testLinkWT() throws Exception {
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346
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347
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final List<Row> rows = Lists.newArrayList();
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348
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rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordWT.xml")));
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349
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rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordWT.xml")));
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350
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351
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printAll(mapAll(buildTable(rows)));
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352
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}
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353
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354
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@Test
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355
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public void testLinkOrganization() throws Exception {
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356
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357
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final List<Row> rows = Lists.newArrayList();
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358
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rows.addAll(asRows(loadFromTransformationProfile("organizations_2_hbase.xsl"), load("organization.xml")));
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359
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rows.addAll(asRows(loadFromTransformationProfile("projectorganization_2_hbase.xsl"), load("project_organization.xml")));
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360
|
rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordCorda.xml")));
|
|
361
|
|
|
362
|
printAll(mapAll(buildTable(rows)));
|
|
363
|
}
|
|
364
|
|
|
365
|
@Test
|
|
366
|
public void testLinkOrganizationAffiliation() throws Exception {
|
|
367
|
|
|
368
|
final List<Row> rows = Lists.newArrayList();
|
|
369
|
rows.addAll(asRows(loadFromTransformationProfile("organizations_2_hbase.xsl"), load("organization.xml")));
|
|
370
|
rows.addAll(asRows(loadFromTransformationProfile("resultorganization_2_hbase.xsl"), load("result_organization.xml")));
|
|
371
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("record.xml")));
|
|
372
|
|
|
373
|
printAll(mapAll(buildTable(rows)));
|
|
374
|
}
|
|
375
|
|
|
376
|
@Test
|
|
377
|
public void testDuplicates() throws Exception {
|
|
378
|
final String mergeId = "50|dedup_wf_001::08ed625d07e5738b794ff14d6773fd9f";
|
|
379
|
final List<Row> rows = Lists.newArrayList();
|
|
380
|
|
|
381
|
final Function<Row, Row> f = rowIn -> {
|
|
382
|
|
|
383
|
final List<Column<String, byte[]>> cols = Lists.newArrayList();
|
|
384
|
for (final Column<String, byte[]> col : rowIn.getColumns()) {
|
|
385
|
if (col.getName().equals("body")) {
|
|
386
|
cols.add(new Column(col.getName(), col.getValue()));
|
|
387
|
|
|
388
|
}
|
|
389
|
}
|
|
390
|
return new Row("result", rowIn.getKey(), cols);
|
|
391
|
};
|
|
392
|
|
|
393
|
final List<Row> puma1 = asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordPuma1.xml"), f);
|
|
394
|
puma1.add(new Row("resultResult_dedup_isMergedIn", mergeId));
|
|
395
|
|
|
396
|
final List<Row> puma2 = asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordPuma2.xml"), f);
|
|
397
|
puma2.add(new Row("resultResult_dedup_isMergedIn", mergeId));
|
|
398
|
|
|
399
|
rows.addAll(puma1);
|
|
400
|
rows.addAll(puma2);
|
|
401
|
|
|
402
|
final List<Oaf> duplicates = Lists.newArrayList();
|
|
403
|
duplicates.add(getOafBody(puma1));
|
|
404
|
duplicates.add(getOafBody(puma2));
|
|
405
|
final Oaf.Builder oafMerge = OafEntityMerger.merge(mergeId, duplicates);
|
|
406
|
|
|
407
|
final Row mergeRow = new Row("result", mergeId, Lists.newArrayList(new Column("body", oafMerge.build().toByteArray())));
|
|
408
|
|
|
409
|
rows.add(mergeRow);
|
|
410
|
|
|
411
|
printAll(mapAll(buildTable(rows)));
|
|
412
|
}
|
|
413
|
|
|
414
|
private Oaf getOafBody(final List<Row> rows) throws InvalidProtocolBufferException {
|
|
415
|
for (final Row row : rows) {
|
|
416
|
if (StringUtils.startsWith(row.getKey(), "50")) { return Oaf.parseFrom(row.getColumn("body").getValue());
|
|
417
|
|
|
418
|
}
|
|
419
|
}
|
|
420
|
return null;
|
|
421
|
}
|
|
422
|
|
|
423
|
@Test
|
|
424
|
public void testParseDoajOAF() throws Exception {
|
|
425
|
|
|
426
|
doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("doajUniversityRecord.xml"));
|
|
427
|
}
|
|
428
|
|
|
429
|
@Test
|
|
430
|
public void testParseDatasource() throws Exception {
|
|
431
|
|
|
432
|
doTest(loadFromTransformationProfile("datasources_2_hbase.xsl"), load("datasourceNative.xml"));
|
|
433
|
}
|
|
434
|
|
|
435
|
@Test
|
|
436
|
public void testParseDatasourcePiwik() throws Exception {
|
|
437
|
|
|
438
|
doTest(loadFromTransformationProfile("datasources_2_hbase.xsl"), load("datasourcePiwik.xml"));
|
|
439
|
}
|
|
440
|
|
|
441
|
@Test
|
|
442
|
public void testParseDataDatasource() throws Exception {
|
|
443
|
|
|
444
|
doTest(loadFromTransformationProfile("datasources_2_hbase.xsl"), load("dataDatasource.xml"));
|
|
445
|
}
|
|
446
|
|
|
447
|
@Test
|
|
448
|
public void testFromMongodbCompressedDump() throws Exception {
|
|
449
|
doTestJsonGz(loadFromTransformationProfile("oaf2hbase.xml"), load("mdstore_cleaned.json.gz"));
|
|
450
|
}
|
|
451
|
|
|
452
|
@Test
|
|
453
|
public void testLoadFromTransformationProfile() throws IOException {
|
|
454
|
final InputStream in = loadFromTransformationProfile("oaf2hbase.xml");
|
|
455
|
log.info(IOUtils.toString(in));
|
|
456
|
}
|
|
457
|
|
|
458
|
@Test
|
|
459
|
public void test_template() throws Exception {
|
|
460
|
final String xslt = IOUtils.toString(loadFromTransformationProfile("oaf2hbase.xml"));
|
|
461
|
final XsltRowTransformer transformer = factory.getTransformer(xslt);
|
|
462
|
assertNotNull(transformer);
|
|
463
|
|
|
464
|
final String record = IOUtils.toString(load("record.xml"));
|
|
465
|
final List<Row> rows = transformer.apply(record);
|
|
466
|
|
|
467
|
System.out.println(rows);
|
|
468
|
}
|
|
469
|
|
|
470
|
@Test
|
|
471
|
public void testWrongCharsOrganization() throws Exception {
|
|
472
|
final List<Row> rows = Lists.newArrayList();
|
|
473
|
rows.addAll(asRows(loadFromTransformationProfile("organizations_2_hbase.xsl"), load("organizationWrongChars.xml")));
|
|
474
|
printAll(mapAll(buildTable(rows)));
|
|
475
|
}
|
|
476
|
|
|
477
|
@Test
|
|
478
|
public void testParseProjectWithFunderOriginalName() throws Exception {
|
|
479
|
|
|
480
|
doTest(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectWithFunderOriginalName.xml"));
|
|
481
|
}
|
|
482
|
|
|
483
|
@Test
|
|
484
|
public void testLinkFunderOriginalName() throws Exception {
|
|
485
|
|
|
486
|
final List<Row> rows = Lists.newArrayList();
|
|
487
|
rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectWithFunderOriginalName.xml")));
|
|
488
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordFunderOriginalName.xml")));
|
|
489
|
|
|
490
|
printAll(mapAll(buildTable(rows)));
|
|
491
|
}
|
|
492
|
|
|
493
|
@Test
|
|
494
|
public void testProjectExtraInfo() throws Exception {
|
|
495
|
final List<Row> rows = Lists.newArrayList();
|
|
496
|
rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordExtraInfo.xml")));
|
|
497
|
printAll(mapAll(buildTable(rows)));
|
|
498
|
}
|
|
499
|
|
|
500
|
@Test
|
|
501
|
public void testParseSoftwareFromODF() throws Exception {
|
|
502
|
final List<Row> rows = Lists.newArrayList();
|
|
503
|
rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("softwareODF.xml")));
|
|
504
|
rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordCorda.xml")));
|
|
505
|
printAll(mapAll(buildTable(rows)));
|
|
506
|
}
|
|
507
|
|
|
508
|
@Test
|
|
509
|
public void testParseSoftwareFromOAF() throws Exception {
|
|
510
|
final List<Row> rows = Lists.newArrayList();
|
|
511
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordOAFsoftwareCLOSED.xml")));
|
|
512
|
printAll(mapAll(buildTable(rows)));
|
|
513
|
}
|
|
514
|
|
|
515
|
@Test
|
|
516
|
public void testParsePubFromODF() throws Exception {
|
|
517
|
final List<Row> rows = Lists.newArrayList();
|
|
518
|
rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("recordODFPub.xml")));
|
|
519
|
printAll(mapAll(buildTable(rows)));
|
|
520
|
}
|
|
521
|
|
|
522
|
@Test
|
|
523
|
public void testParseSoftwareFromOAFOpen() throws Exception {
|
|
524
|
final List<Row> rows = Lists.newArrayList();
|
|
525
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("recordOAFsoftwareOPEN.xml")));
|
|
526
|
printAll(mapAll(buildTable(rows)));
|
|
527
|
}
|
|
528
|
|
|
529
|
@Test
|
|
530
|
public void testParseSoftwareBiotool() throws Exception {
|
|
531
|
final List<Row> rows = Lists.newArrayList();
|
|
532
|
rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("biotoolSw.xml")));
|
|
533
|
printAll(mapAll(buildTable(rows)));
|
|
534
|
}
|
|
535
|
|
|
536
|
@Test
|
|
537
|
public void testParseOafWithExternalRef() throws Exception {
|
|
538
|
final List<Row> rows = Lists.newArrayList();
|
|
539
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("oafWithExternalReference.xml")));
|
|
540
|
printAll(mapAll(buildTable(rows)));
|
|
541
|
}
|
|
542
|
|
|
543
|
@Test
|
|
544
|
public void testParseOafWithCommunity() throws Exception {
|
|
545
|
final List<Row> rows = Lists.newArrayList();
|
|
546
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("oafWithCommunity.xml")));
|
|
547
|
printAll(mapAll(buildTable(rows)));
|
|
548
|
}
|
|
549
|
|
|
550
|
@Test
|
|
551
|
public void testParseOafWithUpdates() throws Exception {
|
|
552
|
final List<Row> rows = Lists.newArrayList();
|
|
553
|
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("oafWithCommunity.xml")));
|
|
554
|
|
|
555
|
final ActionFactory actionFactory = new ActionFactory();
|
|
556
|
|
|
557
|
final Map<String, Resource> xslts = Maps.newHashMap();
|
|
558
|
|
|
559
|
xslts.put("oaf2hbase", new ByteArrayResource(IOUtils.toString(loadFromTransformationProfile("oaf2hbase.xml")).getBytes()));
|
|
560
|
actionFactory.setXslts(xslts);
|
|
561
|
|
|
562
|
final XsltInfoPackageAction pa = actionFactory.generateInfoPackageAction(
|
|
563
|
"oaf2hbase",
|
|
564
|
"rawset-id",
|
|
565
|
new Agent("agent-id", "agent-name", Agent.AGENT_TYPE.algo),
|
|
566
|
Operation.UPDATE,
|
|
567
|
IOUtils.toString(load("oafUpdateWithCommunity.xml")),
|
|
568
|
Provenance.sysimport_mining_aggregator,
|
|
569
|
"0.9");
|
|
570
|
|
|
571
|
final String qualifier = "update_" + System.nanoTime();
|
|
572
|
|
|
573
|
IOUtils.readLines(load("country_updates.json")).forEach(line -> {
|
|
574
|
|
|
575
|
final Oaf.Builder oaf = Oaf.newBuilder();
|
|
576
|
|
|
577
|
try {
|
|
578
|
JsonFormat.merge(line, oaf);
|
|
579
|
} catch (final JsonFormat.ParseException e) {
|
|
580
|
throw new IllegalArgumentException(e);
|
|
581
|
}
|
|
582
|
|
|
583
|
final Column<String, byte[]> col = new Column<>("update_" + System.nanoTime(), oaf.build().toByteArray());
|
|
584
|
rows.add(new Row("result", oaf.getEntity().getId(), Lists.newArrayList(col)));
|
|
585
|
});
|
|
586
|
|
|
587
|
pa.asAtomicActions().forEach(a -> {
|
|
588
|
final Column<String, byte[]> col = new Column<>("update_" + System.nanoTime(), a.getTargetValue());
|
|
589
|
rows.add(new Row(a.getTargetColumnFamily(), a.getTargetRowKey(), Lists.newArrayList(col)));
|
|
590
|
});
|
|
591
|
|
|
592
|
/*
|
|
593
|
* rows.forEach(r -> { log.info(r); });
|
|
594
|
*/
|
|
595
|
|
|
596
|
mapAll(buildTable(rows)).entrySet().forEach(b -> {
|
|
597
|
log.info(b.getKey());
|
|
598
|
log.info(b.getValue());
|
|
599
|
});
|
|
600
|
}
|
|
601
|
|
|
602
|
@Test
|
|
603
|
public void testParseCrisPub() throws Exception {
|
|
604
|
doTest(loadFromTransformationProfile("odf2hbase.xml"), load("cris_pub1.xml"));
|
|
605
|
}
|
|
606
|
|
|
607
|
@Test
|
|
608
|
public void testBioToolSwRowJson() throws Exception {
|
|
609
|
doTestJsonRow(IOUtils.toString(load("biotoolSwRow.json")));
|
|
610
|
}
|
|
611
|
|
|
612
|
@Test
|
|
613
|
public void testParseVirta() throws Exception {
|
|
614
|
doTest(loadFromTransformationProfile("datasources_2_hbase.xsl"), load("virta.xml"));
|
|
615
|
}
|
|
616
|
|
|
617
|
@Test
|
|
618
|
public void testParseJournal() throws Exception {
|
|
619
|
doTest(loadFromTransformationProfile("datasources_2_hbase.xsl"), load("datasourceWithISSN.xml"));
|
|
620
|
}
|
|
621
|
|
|
622
|
@Test
|
|
623
|
public void testGuidelines4Qeios() throws Exception {
|
|
624
|
|
|
625
|
doTest(loadFromTransformationProfile("odf2hbase.xml"), load("guidelines4_qeios1.xml"));
|
|
626
|
}
|
|
627
|
|
|
628
|
@Test
|
|
629
|
public void testGuidelines4Aria() throws Exception {
|
|
630
|
|
|
631
|
doTest(loadFromTransformationProfile("odf2hbase.xml"), load("guidelines4_aria.xml"));
|
|
632
|
}
|
|
633
|
|
|
634
|
@Test
|
|
635
|
public void testJournalRecord() throws Exception {
|
|
636
|
doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("journalRecord.xml"));
|
|
637
|
}
|
|
638
|
|
|
639
|
@Test
|
|
640
|
public void testSygmaDatacite() throws Exception {
|
|
641
|
|
|
642
|
final List<Row> rows = Lists.newArrayList();
|
|
643
|
rows.addAll(asRows(loadFromTransformationProfile("odf2hbase.xml"), load("sygma_datacite.xml")));
|
|
644
|
rows.addAll(asRows(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordCorda.xml")));
|
|
645
|
|
|
646
|
printAll(mapAll(buildTable(rows)));
|
|
647
|
}
|
|
648
|
|
|
649
|
@Test
|
|
650
|
public void testOpenOrganizations() throws Exception {
|
|
651
|
|
|
652
|
final List<Row> rows = Lists.newArrayList();
|
|
653
|
rows.addAll(asRows(loadFromTransformationProfile("organizations_2_hbase.xsl"), load("openorgs_sample.xml")));
|
|
654
|
|
|
655
|
printAll(mapAll(buildTable(rows)));
|
|
656
|
}
|
|
657
|
|
|
658
|
private void doTestJsonRow(final String json) throws Exception {
|
|
659
|
final Row row = asRowFromJson(json);
|
|
660
|
log.info(row);
|
|
661
|
final List<Row> rows = new ArrayList<>();
|
|
662
|
rows.add(row);
|
|
663
|
final Map<String, Map<String, Map<String, byte[]>>> table = buildTable(rows);
|
|
664
|
final Map<String, XmlRecordFactory> builders = mapAll(table);
|
|
665
|
printAll(builders);
|
|
666
|
|
|
667
|
}
|
|
668
|
|
|
669
|
private void doTest(final InputStream xsltStream, final InputStream recordStream) throws Exception {
|
|
670
|
try {
|
|
671
|
final List<Row> rows = asRows(xsltStream, recordStream);
|
|
672
|
|
|
673
|
log.info(rows);
|
|
674
|
|
|
675
|
final Map<String, Map<String, Map<String, byte[]>>> table = buildTable(rows);
|
|
676
|
|
|
677
|
// System.out.println("\n" + table.toString());
|
|
678
|
|
|
679
|
final Map<String, XmlRecordFactory> builders = mapAll(table);
|
|
680
|
|
|
681
|
printAll(builders);
|
|
682
|
} catch (final InvalidProtocolBufferException e) {
|
|
683
|
throw new Exception(e);
|
|
684
|
} catch (final TransformerConfigurationException e) {
|
|
685
|
throw new Exception(e);
|
|
686
|
} catch (final TransformerFactoryConfigurationError e) {
|
|
687
|
throw new Exception(e);
|
|
688
|
} catch (final DocumentException e) {
|
|
689
|
throw new Exception(e);
|
|
690
|
}
|
|
691
|
}
|
|
692
|
|
|
693
|
private void doTestJsonGz(final InputStream xsltStream, final InputStream recordStream) throws Exception {
|
|
694
|
|
|
695
|
final Iterator<List<Row>> rowsIterator = asRowsJsonGzip(xsltStream, recordStream);
|
|
696
|
|
|
697
|
int i = 0;
|
|
698
|
while (rowsIterator.hasNext()) {
|
|
699
|
final List<Row> rows = rowsIterator.next();
|
|
700
|
i++;
|
|
701
|
|
|
702
|
if (i % 10000 == 0) {
|
|
703
|
System.out.println(i);
|
|
704
|
}
|
|
705
|
|
|
706
|
final Map<String, Map<String, Map<String, byte[]>>> table = buildTableDoaj(rows);
|
|
707
|
|
|
708
|
for (final Map<String, Map<String, byte[]>> m : table.values()) {
|
|
709
|
for (final Map<String, byte[]> mv : m.values()) {
|
|
710
|
for (final byte[] v : mv.values()) {
|
|
711
|
final OafDecoder d = OafDecoder.decode(v);
|
|
712
|
assertNotNull(d);
|
|
713
|
assertNotNull(d.getOaf());
|
|
714
|
|
|
715
|
switch (d.getKind()) {
|
|
716
|
case entity:
|
|
717
|
assertNotNull(d.getMetadata());
|
|
718
|
if (d.getOaf().getEntity().getType().equals(Type.result)) {
|
|
719
|
System.out.println(d.getOaf());
|
|
720
|
}
|
|
721
|
break;
|
|
722
|
case relation:
|
|
723
|
assertNotNull(d.getRel());
|
|
724
|
break;
|
|
725
|
default:
|
|
726
|
break;
|
|
727
|
}
|
|
728
|
}
|
|
729
|
}
|
|
730
|
}
|
|
731
|
}
|
|
732
|
}
|
|
733
|
|
|
734
|
private List<Row> asRows(final InputStream xsltStream, final InputStream recordStream, final Function<Row, Row> p) throws Exception {
|
|
735
|
return asRows(xsltStream, new HashMap<>(), recordStream, p);
|
|
736
|
}
|
|
737
|
|
|
738
|
private List<Row> asRows(final InputStream xsltStream, final InputStream recordStream) throws Exception {
|
|
739
|
return asRows(xsltStream, new HashMap<>(), recordStream);
|
|
740
|
}
|
|
741
|
|
|
742
|
private List<Row> asRows(final InputStream xsltStream, final Map<String, Object> params, final InputStream recordStream) throws Exception {
|
|
743
|
return asRows(xsltStream, params, recordStream, null);
|
|
744
|
}
|
|
745
|
|
|
746
|
private List<Row> asRows(final InputStream xsltStream, final Map<String, Object> params, final InputStream recordStream, final Function<Row, Row> p)
|
|
747
|
throws Exception {
|
|
748
|
final String xslt = IOUtils.toString(xsltStream);
|
|
749
|
final XsltRowTransformer transformer = factory.getTransformer(xslt, params);
|
|
750
|
assertNotNull(transformer);
|
|
751
|
|
|
752
|
final String record = IOUtils.toString(recordStream);
|
|
753
|
final List<Row> rows = transformer.apply(record);
|
|
754
|
|
|
755
|
assertNotNull(rows);
|
|
756
|
assertFalse(rows.isEmpty());
|
|
757
|
return p == null ? rows : Lists.newArrayList(Iterables.transform(rows, p));
|
|
758
|
}
|
|
759
|
|
|
760
|
private Iterator<List<Row>> asRowsJsonGzip(final InputStream xsltStream, final InputStream recordStreamJsonGzip) throws Exception {
|
|
761
|
final String xslt = IOUtils.toString(xsltStream);
|
|
762
|
final XsltRowTransformer transformer = factory.getTransformer(xslt);
|
|
763
|
assertNotNull(transformer);
|
|
764
|
assertNotNull(recordStreamJsonGzip);
|
|
765
|
|
|
766
|
final GZIPInputStream stream = new GZIPInputStream(recordStreamJsonGzip);
|
|
767
|
assertNotNull(stream);
|
|
768
|
final BufferedReader inStream = new BufferedReader(new InputStreamReader(stream));
|
|
769
|
assertNotNull(inStream);
|
|
770
|
return new Iterator<List<Row>>() {
|
|
771
|
|
|
772
|
String jsonRecord = null;
|
|
773
|
|
|
774
|
@Override
|
|
775
|
public boolean hasNext() {
|
|
776
|
try {
|
|
777
|
return (jsonRecord = inStream.readLine()) != null;
|
|
778
|
} catch (final IOException e) {
|
|
779
|
throw new RuntimeException(e);
|
|
780
|
}
|
|
781
|
}
|
|
782
|
|
|
783
|
@Override
|
|
784
|
public List<Row> next() {
|
|
785
|
|
|
786
|
final JSONObject jsonObj = new JSONObject(jsonRecord);
|
|
787
|
final String body = jsonObj.getString("body");
|
|
788
|
try {
|
|
789
|
assertTrue(StringUtils.isNotBlank(body));
|
|
790
|
// System.out.println(body);
|
|
791
|
final List<Row> rows = transformer.apply(body);
|
|
792
|
assertNotNull(rows);
|
|
793
|
assertFalse(rows.isEmpty());
|
|
794
|
return rows;
|
|
795
|
} catch (final Throwable e) {
|
|
796
|
System.err.println("error transforming document: " + body);
|
|
797
|
throw new RuntimeException(e);
|
|
798
|
}
|
|
799
|
}
|
|
800
|
|
|
801
|
@Override
|
|
802
|
public void remove() {
|
|
803
|
throw new UnsupportedOperationException();
|
|
804
|
}
|
|
805
|
|
|
806
|
};
|
|
807
|
|
|
808
|
}
|
|
809
|
|
|
810
|
private Map<String, Map<String, Map<String, byte[]>>> buildTableDoaj(final List<Row> rows) throws UnsupportedEncodingException {
|
|
811
|
final Map<String, Map<String, Map<String, byte[]>>> table = Maps.newHashMap();
|
|
812
|
|
|
813
|
for (final Row row : rows) {
|
|
814
|
final String rowKey = row.getKey();
|
|
815
|
final String cf = row.getColumnFamily();
|
|
816
|
if (!table.containsKey(rowKey)) {
|
|
817
|
table.put(rowKey, new HashMap<>());
|
|
818
|
}
|
|
819
|
if (!table.get(rowKey).containsKey(cf)) {
|
|
820
|
table.get(rowKey).put(row.getColumnFamily(), new HashMap<>());
|
|
821
|
}
|
|
822
|
for (final Column<String, byte[]> c : row.getColumns()) {
|
|
823
|
// System.out.println(String.format("ADDING K:%s CF:%s Q:%s", rowKey, cf, c.getName()));
|
|
824
|
table.get(rowKey).get(cf).put(c.getName(), c.getValue());
|
|
825
|
if (cf.equals("result") && c.getName().equals("body")) {
|
|
826
|
// System.out.println(String.format("ADDING K:%s CF:%s Q:%s", rowKey, cf, c.getName()));
|
|
827
|
assertTrue(StringUtils.isNotBlank(new String(c.getValue(), "UTF-8")));
|
|
828
|
}
|
|
829
|
}
|
|
830
|
}
|
|
831
|
return table;
|
|
832
|
|
|
833
|
}
|
|
834
|
|
|
835
|
protected Map<String, Map<String, Map<String, byte[]>>> buildTable(final List<Row> rows) throws UnsupportedEncodingException {
|
|
836
|
final Map<String, Map<String, Map<String, byte[]>>> table = Maps.newHashMap();
|
|
837
|
|
|
838
|
for (final Row row : rows) {
|
|
839
|
final String rowKey = row.getKey();
|
|
840
|
final String cf = row.getColumnFamily();
|
|
841
|
if (!table.containsKey(rowKey)) {
|
|
842
|
table.put(rowKey, new HashMap<>());
|
|
843
|
}
|
|
844
|
if (!table.get(rowKey).containsKey(cf)) {
|
|
845
|
table.get(rowKey).put(row.getColumnFamily(), new HashMap<>());
|
|
846
|
}
|
|
847
|
for (final Column<String, byte[]> c : row.getColumns()) {
|
|
848
|
System.out.println(String.format("ADDING K:%s CF:%s Q:%s", rowKey, cf, c.getName()));
|
|
849
|
table.get(rowKey).get(cf).put(c.getName(), c.getValue());
|
|
850
|
if (c.getName().equals("body")) {
|
|
851
|
final String theBody = new String(c.getValue(), "UTF-8");
|
|
852
|
assertTrue(StringUtils.isNotBlank(theBody));
|
|
853
|
// System.out.println(theBody);
|
|
854
|
}
|
|
855
|
}
|
|
856
|
}
|
|
857
|
return table;
|
|
858
|
|
|
859
|
}
|
|
860
|
|
|
861
|
protected Map<String, XmlRecordFactory> mapAll(final Map<String, Map<String, Map<String, byte[]>>> table) throws Exception {
|
|
862
|
|
|
863
|
final Map<String, XmlRecordFactory> builders = Maps.newHashMap();
|
|
864
|
for (final Entry<String, Map<String, Map<String, byte[]>>> e : table.entrySet()) {
|
|
865
|
map(builders, e.getKey(), e.getValue());
|
|
866
|
}
|
|
867
|
return builders;
|
|
868
|
}
|
|
869
|
|
|
870
|
// private Map<String, XmlRecordFactory> mapResultsOnly(final Map<String, Map<String, Map<String, byte[]>>> table) throws Exception {
|
|
871
|
//
|
|
872
|
// final Map<String, XmlRecordFactory> builders = Maps.newHashMap();
|
|
873
|
// for (final Entry<String, Map<String, Map<String, byte[]>>> e : table.entrySet()) {
|
|
874
|
// final Type type = OafRowKeyDecoder.decode(e.getKey()).getType();
|
|
875
|
// if (type == Type.result) {
|
|
876
|
// map(builders, e.getKey(), e.getValue());
|
|
877
|
// }
|
|
878
|
// }
|
|
879
|
// return builders;
|
|
880
|
// }
|
|
881
|
|
|
882
|
private void map(final Map<String, XmlRecordFactory> builders, final String rowKey, final Map<String, Map<String, byte[]>> row) throws Exception {
|
|
883
|
|
|
884
|
final Type type = OafRowKeyDecoder.decode(rowKey).getType();
|
|
885
|
|
|
886
|
final Map<String, byte[]> familyMap = row.get(type.toString());
|
|
887
|
|
|
888
|
if (familyMap == null) { return; }
|
|
889
|
|
|
890
|
final byte[] bodyB = familyMap.get("body");
|
|
891
|
|
|
892
|
if (bodyB != null) {
|
|
893
|
ensureBuilder(builders, rowKey);
|
|
894
|
|
|
895
|
final Oaf oaf = UpdateMerger.mergeBodyUpdates(familyMap);
|
|
896
|
|
|
897
|
final OafDecoder mainEntity = OafDecoder.decode(oaf);
|
|
898
|
|
|
899
|
builders.get(rowKey).setMainEntity(mainEntity);
|
|
900
|
|
|
901
|
for (final LinkDescriptor ld : entityConfigTable.getDescriptors(type)) {
|
|
902
|
|
|
903
|
final String it = ld.getRelDescriptor().getIt();
|
|
904
|
final Map<String, byte[]> cols = row.get(it);
|
|
905
|
|
|
906
|
if (cols != null && !cols.isEmpty()) {
|
|
907
|
|
|
908
|
for (final byte[] oafB : cols.values()) {
|
|
909
|
|
|
910
|
final Oaf.Builder relBuilder = Oaf.newBuilder(Oaf.parseFrom(oafB));
|
|
911
|
|
|
912
|
if (ld.isSymmetric()) {
|
|
913
|
final RelDescriptor rd = ld.getRelDescriptor();
|
|
914
|
|
|
915
|
relBuilder.getRelBuilder().setCachedTarget(mainEntity.getEntity()).setRelType(rd.getRelType()).setSubRelType(rd.getSubRelType());
|
|
916
|
}
|
|
917
|
|
|
918
|
relBuilder.getRelBuilder().setChild(ld.isChild());
|
|
919
|
|
|
920
|
final Oaf.Builder oafBuilder = Oaf.newBuilder().setKind(Kind.relation).setLastupdatetimestamp(System.currentTimeMillis());
|
|
921
|
oafBuilder.mergeFrom(relBuilder.build());
|
|
922
|
|
|
923
|
final String targetId = ld.isSymmetric() ? oafBuilder.getRel().getTarget() : oafBuilder.getRel().getSource();
|
|
924
|
ensureBuilder(builders, targetId);
|
|
925
|
final OafDecoder decoder = OafDecoder.decode(oafBuilder.build());
|
|
926
|
|
|
927
|
if (ld.isChild()) {
|
|
928
|
builders.get(targetId).addChild(type, decoder);
|
|
929
|
} else {
|
|
930
|
builders.get(targetId).addRelation(type, decoder);
|
|
931
|
}
|
|
932
|
}
|
|
933
|
|
|
934
|
}
|
|
935
|
}
|
|
936
|
}
|
|
937
|
|
|
938
|
}
|
|
939
|
|
|
940
|
private void printAll(final Map<String, XmlRecordFactory> builders) throws DocumentException {
|
|
941
|
print(Sets.newHashSet(Type.values()), builders, null);
|
|
942
|
}
|
|
943
|
|
|
944
|
private void print(final Set<Type> types, final Map<String, XmlRecordFactory> builders, final Map<Type, Set<String>> xpaths) throws DocumentException {
|
|
945
|
final SAXReader r = new SAXReader();
|
|
946
|
|
|
947
|
for (final Entry<String, XmlRecordFactory> e : builders.entrySet()) {
|
|
948
|
final OafRowKeyDecoder kd = OafRowKeyDecoder.decode(e.getKey());
|
|
949
|
|
|
950
|
if (!e.getValue().isValid()) { throw new IllegalArgumentException("invalid builder: " + e.getKey()); }
|
|
951
|
if (types.contains(kd.getType())) {
|
|
952
|
final String val = IndentXmlString.apply(e.getValue().build());
|
|
953
|
|
|
954
|
if (xpaths != null && !xpaths.isEmpty() && xpaths.get(kd.getType()) != null) {
|
|
955
|
final Document doc = r.read(new StringReader(val));
|
|
956
|
|
|
957
|
log.debug("\n" + e.getKey());
|
|
958
|
for (final String xpath : xpaths.get(kd.getType())) {
|
|
959
|
log.debug(doc.valueOf(xpath));
|
|
960
|
}
|
|
961
|
} else {
|
|
962
|
log.info(val);
|
|
963
|
}
|
|
964
|
}
|
|
965
|
}
|
|
966
|
}
|
|
967
|
|
|
968
|
private void printNoIndent(final Map<String, XmlRecordFactory> builders) {
|
|
969
|
for (final Entry<String, XmlRecordFactory> e : builders.entrySet()) {
|
|
970
|
if (e.getValue().isValid()) {
|
|
971
|
log.debug(e.getValue().build());
|
|
972
|
} else {
|
|
973
|
log.debug("invalid builder: " + e.getKey());
|
|
974
|
}
|
|
975
|
}
|
|
976
|
}
|
|
977
|
|
|
978
|
private void ensureBuilder(final Map<String, XmlRecordFactory> builders, final String rowKey) throws Exception {
|
|
979
|
if (!builders.containsKey(rowKey)) {
|
|
980
|
builders.put(rowKey, newBuilder());
|
|
981
|
}
|
|
982
|
}
|
|
983
|
|
|
984
|
private XmlRecordFactory newBuilder() throws TransformerConfigurationException, TransformerFactoryConfigurationError, DocumentException {
|
|
985
|
return new XmlRecordFactory(entityConfigTable, ContextMapper.fromXml(Context.xml),
|
|
986
|
RelClasses.fromJSon(RelClassesTest.relClassesJson), XmlRecordFactoryTest.SCHEMA_LOCATION, true, false, false,
|
|
987
|
XmlRecordFactoryTest.specialDatasourceTypes);
|
|
988
|
}
|
|
989
|
|
|
990
|
private InputStream load(final String fileName) {
|
|
991
|
return getClass().getResourceAsStream(fileName);
|
|
992
|
}
|
|
993
|
|
|
994
|
private InputStream loadFromTransformationProfile(final String profilePath) {
|
|
995
|
log.info("Loading xslt from: " + basePathProfiles + profilePath);
|
|
996
|
final InputStream profile = getClass().getResourceAsStream(basePathProfiles + profilePath);
|
|
997
|
final SAXReader saxReader = new SAXReader();
|
|
998
|
Document doc = null;
|
|
999
|
try {
|
|
1000
|
doc = saxReader.read(profile);
|
|
1001
|
} catch (final DocumentException e) {
|
|
1002
|
e.printStackTrace();
|
|
1003
|
throw new RuntimeException(e);
|
|
1004
|
}
|
|
1005
|
final String xslt = doc.selectSingleNode("//SCRIPT/CODE/*[local-name()='stylesheet']").asXML();
|
|
1006
|
// log.info(xslt);
|
|
1007
|
return IOUtils.toInputStream(xslt);
|
|
1008
|
}
|
|
1009
|
|
|
1010
|
private Row asRowFromJson(final String json) throws ParseException {
|
|
1011
|
final Oaf.Builder oafBuilder = Oaf.newBuilder();
|
|
1012
|
JsonFormat.merge(json, oafBuilder);
|
|
1013
|
final Oaf oaf = oafBuilder.build();
|
|
1014
|
final Row row = new Row("result", oaf.getEntity().getId());
|
|
1015
|
final Column<String, byte[]> c = new Column<>("body", oaf.toByteArray());
|
|
1016
|
row.setColumn("body", c);
|
|
1017
|
return row;
|
|
1018
|
|
|
1019
|
}
|
|
1020
|
|
|
1021
|
}
|