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package eu.dnetlib.data.transform;
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import java.io.*;
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import java.util.*;
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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.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.*;
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import eu.dnetlib.data.mapreduce.util.*;
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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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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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71 |
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import static org.junit.Assert.*;
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72 |
public class XsltRowTransformerFactoryTest {
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73 |
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74 |
private static final Log log = LogFactory.getLog(XsltRowTransformerFactoryTest.class);
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| ... | ... | |
| 78 |
105 |
doTest(loadFromTransformationProfile("claimRels_2_hbase.xml"), load("recordClaimRel.xml"));
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106 |
}
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| 80 |
107 |
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| 81 |
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| 82 |
108 |
@Test
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| 83 |
109 |
public void testParseFp7IctPUB() throws Exception {
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| 84 |
110 |
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| ... | ... | |
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147 |
doTest(loadFromTransformationProfile("odf2hbase.xml"), load("doecode.xml"));
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148 |
}
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149 |
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150 |
@Test
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| 126 |
151 |
public void testParseDatasetLindat() throws Exception {
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| 127 |
152 |
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| ... | ... | |
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177 |
doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("recordClaimedDedup.xml"));
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178 |
}
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| 154 |
179 |
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| 155 |
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| 156 |
180 |
@Test
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| 157 |
181 |
public void testParseClaimDataset() throws Exception {
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| 158 |
182 |
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| 159 |
183 |
doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordClaimDataset.xml"));
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184 |
}
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185 |
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| 162 |
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186 |
@Test
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187 |
public void testParseACM() throws Exception {
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| 165 |
188 |
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| ... | ... | |
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207 |
doTest(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordFCT.xml"));
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208 |
}
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| 186 |
209 |
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| 187 |
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| 188 |
210 |
@Test
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| 189 |
211 |
public void testParseOaf() throws Exception {
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| 190 |
212 |
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| ... | ... | |
| 244 |
266 |
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267 |
final List<Row> rows = Lists.newArrayList();
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| 246 |
268 |
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("odf.xml")));
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//printAll(mapAll(buildTable(rows)));
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269 |
// printAll(mapAll(buildTable(rows)));
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| 248 |
270 |
}
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| 249 |
271 |
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| 250 |
272 |
@Test
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| ... | ... | |
| 254 |
276 |
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("pangaeOAF2.xml")));
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| 255 |
277 |
printAll(mapAll(buildTable(rows)));
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| 256 |
278 |
}
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279 |
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| 257 |
280 |
@Test
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| 258 |
281 |
public void testZenodo() throws Exception {
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| 259 |
282 |
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| ... | ... | |
| 310 |
333 |
printAll(mapAll(buildTable(rows)));
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| 311 |
334 |
}
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| 312 |
335 |
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| 313 |
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| 314 |
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| 315 |
336 |
@Test
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| 316 |
337 |
public void testLinkOrganization() throws Exception {
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| 317 |
338 |
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| ... | ... | |
| 341 |
362 |
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| 342 |
363 |
final Function<Row, Row> f = rowIn -> {
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| 343 |
364 |
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| 344 |
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final List<Column<String,byte[]>> cols = Lists.newArrayList();
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| 345 |
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for(Column<String,byte[]> col : rowIn.getColumns()) {
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365 |
final List<Column<String, byte[]>> cols = Lists.newArrayList();
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366 |
for (final Column<String, byte[]> col : rowIn.getColumns()) {
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367 |
if (col.getName().equals("body")) {
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368 |
cols.add(new Column(col.getName(), col.getValue()));
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| 348 |
369 |
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| ... | ... | |
| 360 |
381 |
rows.addAll(puma1);
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382 |
rows.addAll(puma2);
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| 362 |
383 |
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| 363 |
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List<Oaf> duplicates = Lists.newArrayList();
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384 |
final List<Oaf> duplicates = Lists.newArrayList();
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385 |
duplicates.add(getOafBody(puma1));
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| 365 |
386 |
duplicates.add(getOafBody(puma2));
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387 |
final Oaf.Builder oafMerge = OafEntityMerger.merge(mergeId, duplicates);
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| ... | ... | |
| 373 |
394 |
}
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| 374 |
395 |
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| 375 |
396 |
private Oaf getOafBody(final List<Row> rows) throws InvalidProtocolBufferException {
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| 376 |
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for(Row row : rows) {
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| 377 |
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if(StringUtils.startsWith(row.getKey(), "50")) {
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| 378 |
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return Oaf.parseFrom(row.getColumn("body").getValue());
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397 |
for (final Row row : rows) {
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398 |
if (StringUtils.startsWith(row.getKey(), "50")) { return Oaf.parseFrom(row.getColumn("body").getValue());
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| 379 |
399 |
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| 380 |
400 |
}
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| 381 |
401 |
}
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| ... | ... | |
| 393 |
413 |
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| 394 |
414 |
doTest(loadFromTransformationProfile("datasources_2_hbase.xsl"), load("datasourceNative.xml"));
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| 395 |
415 |
}
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|
416 |
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| 396 |
417 |
@Test
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| 397 |
418 |
public void testParseDatasourcePiwik() throws Exception {
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| 398 |
419 |
|
| ... | ... | |
| 410 |
431 |
doTestJsonGz(loadFromTransformationProfile("oaf2hbase.xml"), load("mdstore_cleaned.json.gz"));
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| 411 |
432 |
}
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| 412 |
433 |
|
| 413 |
|
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| 414 |
434 |
@Test
|
| 415 |
435 |
public void testLoadFromTransformationProfile() throws IOException {
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| 416 |
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InputStream in = loadFromTransformationProfile("oaf2hbase.xml");
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436 |
final InputStream in = loadFromTransformationProfile("oaf2hbase.xml");
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| 417 |
437 |
log.info(IOUtils.toString(in));
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| 418 |
438 |
}
|
| 419 |
439 |
|
| ... | ... | |
| 441 |
461 |
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| 442 |
462 |
doTest(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectWithFunderOriginalName.xml"));
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| 443 |
463 |
}
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|
464 |
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| 444 |
465 |
@Test
|
| 445 |
466 |
public void testLinkFunderOriginalName() throws Exception {
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| 446 |
467 |
|
| ... | ... | |
| 513 |
534 |
final List<Row> rows = Lists.newArrayList();
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| 514 |
535 |
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("oafWithCommunity.xml")));
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| 515 |
536 |
|
| 516 |
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ActionFactory actionFactory = new ActionFactory();
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|
537 |
final ActionFactory actionFactory = new ActionFactory();
|
| 517 |
538 |
|
| 518 |
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Map<String, Resource> xslts = Maps.newHashMap();
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|
539 |
final Map<String, Resource> xslts = Maps.newHashMap();
|
| 519 |
540 |
|
| 520 |
541 |
xslts.put("oaf2hbase", new ByteArrayResource(IOUtils.toString(loadFromTransformationProfile("oaf2hbase.xml")).getBytes()));
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| 521 |
542 |
actionFactory.setXslts(xslts);
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| 522 |
543 |
|
| 523 |
|
XsltInfoPackageAction pa = actionFactory.generateInfoPackageAction(
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|
544 |
final XsltInfoPackageAction pa = actionFactory.generateInfoPackageAction(
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| 524 |
545 |
"oaf2hbase",
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| 525 |
546 |
"rawset-id",
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| 526 |
547 |
new Agent("agent-id", "agent-name", Agent.AGENT_TYPE.algo),
|
| ... | ... | |
| 533 |
554 |
|
| 534 |
555 |
IOUtils.readLines(load("country_updates.json")).forEach(line -> {
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| 535 |
556 |
|
| 536 |
|
Oaf.Builder oaf = Oaf.newBuilder();
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557 |
final Oaf.Builder oaf = Oaf.newBuilder();
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| 537 |
558 |
|
| 538 |
559 |
try {
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| 539 |
560 |
JsonFormat.merge(line, oaf);
|
| 540 |
|
} catch (JsonFormat.ParseException e) {
|
|
561 |
} catch (final JsonFormat.ParseException e) {
|
| 541 |
562 |
throw new IllegalArgumentException(e);
|
| 542 |
563 |
}
|
| 543 |
564 |
|
| 544 |
|
Column<String, byte[]> col = new Column<>("update_" + System.nanoTime(), oaf.build().toByteArray());
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|
565 |
final Column<String, byte[]> col = new Column<>("update_" + System.nanoTime(), oaf.build().toByteArray());
|
| 545 |
566 |
rows.add(new Row("result", oaf.getEntity().getId(), Lists.newArrayList(col)));
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| 546 |
567 |
});
|
| 547 |
568 |
|
| 548 |
569 |
pa.asAtomicActions().forEach(a -> {
|
| 549 |
|
Column<String, byte[]> col = new Column<>("update_" + System.nanoTime(), a.getTargetValue());
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|
570 |
final Column<String, byte[]> col = new Column<>("update_" + System.nanoTime(), a.getTargetValue());
|
| 550 |
571 |
rows.add(new Row(a.getTargetColumnFamily(), a.getTargetRowKey(), Lists.newArrayList(col)));
|
| 551 |
572 |
});
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| 552 |
573 |
|
| 553 |
|
|
| 554 |
574 |
/*
|
| 555 |
|
rows.forEach(r -> {
|
| 556 |
|
log.info(r);
|
| 557 |
|
});
|
| 558 |
|
*/
|
|
575 |
* rows.forEach(r -> { log.info(r); });
|
|
576 |
*/
|
| 559 |
577 |
|
| 560 |
578 |
mapAll(buildTable(rows)).entrySet().forEach(b -> {
|
| 561 |
579 |
log.info(b.getKey());
|
| ... | ... | |
| 589 |
607 |
doTest(loadFromTransformationProfile("odf2hbase.xml"), load("guidelines4_qeios1.xml"));
|
| 590 |
608 |
}
|
| 591 |
609 |
|
| 592 |
|
@Test
|
| 593 |
|
public void testGuidelines4Aria() throws Exception {
|
|
610 |
@Test
|
|
611 |
public void testGuidelines4Aria() throws Exception {
|
| 594 |
612 |
|
| 595 |
|
doTest(loadFromTransformationProfile("odf2hbase.xml"), load("guidelines4_aria.xml"));
|
| 596 |
|
}
|
|
613 |
doTest(loadFromTransformationProfile("odf2hbase.xml"), load("guidelines4_aria.xml"));
|
|
614 |
}
|
| 597 |
615 |
|
| 598 |
616 |
@Test
|
| 599 |
617 |
public void testJournalRecord() throws Exception {
|
| ... | ... | |
| 610 |
628 |
printAll(mapAll(buildTable(rows)));
|
| 611 |
629 |
}
|
| 612 |
630 |
|
|
631 |
@Test
|
|
632 |
public void testOpenOrganizations() throws Exception {
|
|
633 |
|
|
634 |
final List<Row> rows = Lists.newArrayList();
|
|
635 |
rows.addAll(asRows(loadFromTransformationProfile("organizations_2_hbase.xsl"), load("openorgs_sample.xml")));
|
|
636 |
|
|
637 |
printAll(mapAll(buildTable(rows)));
|
|
638 |
}
|
|
639 |
|
| 613 |
640 |
private void doTestJsonRow(final String json) throws Exception {
|
| 614 |
|
Row row = asRowFromJson(json);
|
|
641 |
final Row row = asRowFromJson(json);
|
| 615 |
642 |
log.info(row);
|
| 616 |
|
List<Row> rows = new ArrayList<>();
|
|
643 |
final List<Row> rows = new ArrayList<>();
|
| 617 |
644 |
rows.add(row);
|
| 618 |
645 |
final Map<String, Map<String, Map<String, byte[]>>> table = buildTable(rows);
|
| 619 |
646 |
final Map<String, XmlRecordFactory> builders = mapAll(table);
|
| ... | ... | |
| 654 |
681 |
final List<Row> rows = rowsIterator.next();
|
| 655 |
682 |
i++;
|
| 656 |
683 |
|
| 657 |
|
if ((i % 10000) == 0) {
|
|
684 |
if (i % 10000 == 0) {
|
| 658 |
685 |
System.out.println(i);
|
| 659 |
686 |
}
|
| 660 |
687 |
|
| ... | ... | |
| 698 |
725 |
return asRows(xsltStream, params, recordStream, null);
|
| 699 |
726 |
}
|
| 700 |
727 |
|
| 701 |
|
private List<Row> asRows(final InputStream xsltStream, final Map<String, Object> params, final InputStream recordStream, final Function<Row, Row> p) throws Exception {
|
|
728 |
private List<Row> asRows(final InputStream xsltStream, final Map<String, Object> params, final InputStream recordStream, final Function<Row, Row> p)
|
|
729 |
throws Exception {
|
| 702 |
730 |
final String xslt = IOUtils.toString(xsltStream);
|
| 703 |
731 |
final XsltRowTransformer transformer = factory.getTransformer(xslt, params);
|
| 704 |
732 |
assertNotNull(transformer);
|
| ... | ... | |
| 804 |
832 |
if (c.getName().equals("body")) {
|
| 805 |
833 |
final String theBody = new String(c.getValue(), "UTF-8");
|
| 806 |
834 |
assertTrue(StringUtils.isNotBlank(theBody));
|
| 807 |
|
//System.out.println(theBody);
|
|
835 |
// System.out.println(theBody);
|
| 808 |
836 |
}
|
| 809 |
837 |
}
|
| 810 |
838 |
}
|
| ... | ... | |
| 839 |
867 |
|
| 840 |
868 |
final Map<String, byte[]> familyMap = row.get(type.toString());
|
| 841 |
869 |
|
| 842 |
|
if (familyMap == null) return;
|
|
870 |
if (familyMap == null) { return; }
|
| 843 |
871 |
|
| 844 |
872 |
final byte[] bodyB = familyMap.get("body");
|
| 845 |
873 |
|
| ... | ... | |
| 857 |
885 |
final String it = ld.getRelDescriptor().getIt();
|
| 858 |
886 |
final Map<String, byte[]> cols = row.get(it);
|
| 859 |
887 |
|
| 860 |
|
if ((cols != null) && !cols.isEmpty()) {
|
|
888 |
if (cols != null && !cols.isEmpty()) {
|
| 861 |
889 |
|
| 862 |
890 |
for (final byte[] oafB : cols.values()) {
|
| 863 |
891 |
|
| ... | ... | |
| 901 |
929 |
for (final Entry<String, XmlRecordFactory> e : builders.entrySet()) {
|
| 902 |
930 |
final OafRowKeyDecoder kd = OafRowKeyDecoder.decode(e.getKey());
|
| 903 |
931 |
|
| 904 |
|
if (!e.getValue().isValid()) throw new IllegalArgumentException("invalid builder: " + e.getKey());
|
|
932 |
if (!e.getValue().isValid()) { throw new IllegalArgumentException("invalid builder: " + e.getKey()); }
|
| 905 |
933 |
if (types.contains(kd.getType())) {
|
| 906 |
934 |
final String val = IndentXmlString.apply(e.getValue().build());
|
| 907 |
935 |
|
| 908 |
|
if ((xpaths != null) && !xpaths.isEmpty() && (xpaths.get(kd.getType()) != null)) {
|
|
936 |
if (xpaths != null && !xpaths.isEmpty() && xpaths.get(kd.getType()) != null) {
|
| 909 |
937 |
final Document doc = r.read(new StringReader(val));
|
| 910 |
938 |
|
| 911 |
939 |
log.debug("\n" + e.getKey());
|
| ... | ... | |
| 937 |
965 |
|
| 938 |
966 |
private XmlRecordFactory newBuilder() throws TransformerConfigurationException, TransformerFactoryConfigurationError, DocumentException {
|
| 939 |
967 |
return new XmlRecordFactory(entityConfigTable, ContextMapper.fromXml(Context.xml),
|
| 940 |
|
RelClasses.fromJSon(RelClassesTest.relClassesJson), XmlRecordFactoryTest.SCHEMA_LOCATION, true, false, false, XmlRecordFactoryTest.specialDatasourceTypes);
|
|
968 |
RelClasses.fromJSon(RelClassesTest.relClassesJson), XmlRecordFactoryTest.SCHEMA_LOCATION, true, false, false,
|
|
969 |
XmlRecordFactoryTest.specialDatasourceTypes);
|
| 941 |
970 |
}
|
| 942 |
971 |
|
| 943 |
972 |
private InputStream load(final String fileName) {
|
| ... | ... | |
| 946 |
975 |
|
| 947 |
976 |
private InputStream loadFromTransformationProfile(final String profilePath) {
|
| 948 |
977 |
log.info("Loading xslt from: " + basePathProfiles + profilePath);
|
| 949 |
|
InputStream profile = getClass().getResourceAsStream(basePathProfiles + profilePath);
|
| 950 |
|
SAXReader saxReader = new SAXReader();
|
|
978 |
final InputStream profile = getClass().getResourceAsStream(basePathProfiles + profilePath);
|
|
979 |
final SAXReader saxReader = new SAXReader();
|
| 951 |
980 |
Document doc = null;
|
| 952 |
981 |
try {
|
| 953 |
982 |
doc = saxReader.read(profile);
|
| 954 |
|
} catch (DocumentException e) {
|
|
983 |
} catch (final DocumentException e) {
|
| 955 |
984 |
e.printStackTrace();
|
| 956 |
985 |
throw new RuntimeException(e);
|
| 957 |
986 |
}
|
| 958 |
|
String xslt = doc.selectSingleNode("//SCRIPT/CODE/*[local-name()='stylesheet']").asXML();
|
| 959 |
|
//log.info(xslt);
|
|
987 |
final String xslt = doc.selectSingleNode("//SCRIPT/CODE/*[local-name()='stylesheet']").asXML();
|
|
988 |
// log.info(xslt);
|
| 960 |
989 |
return IOUtils.toInputStream(xslt);
|
| 961 |
990 |
}
|
| 962 |
991 |
|
| 963 |
|
|
| 964 |
|
private Row asRowFromJson(String json) throws ParseException {
|
| 965 |
|
Oaf.Builder oafBuilder = Oaf.newBuilder();
|
|
992 |
private Row asRowFromJson(final String json) throws ParseException {
|
|
993 |
final Oaf.Builder oafBuilder = Oaf.newBuilder();
|
| 966 |
994 |
JsonFormat.merge(json, oafBuilder);
|
| 967 |
995 |
final Oaf oaf = oafBuilder.build();
|
| 968 |
|
Row row = new Row("result", oaf.getEntity().getId());
|
| 969 |
|
Column<String, byte[]> c = new Column<>("body", oaf.toByteArray());
|
|
996 |
final Row row = new Row("result", oaf.getEntity().getId());
|
|
997 |
final Column<String, byte[]> c = new Column<>("body", oaf.toByteArray());
|
| 970 |
998 |
row.setColumn("body", c);
|
| 971 |
999 |
return row;
|
| 972 |
1000 |
|
Added by Michele Artini about 5 years ago
(openorgs) added schemeid to pids in sql query