Revision 57397
Added by Michele Artini over 4 years ago
| XsltRowTransformerFactoryTest.java | ||
|---|---|---|
| 1 | 1 |
package eu.dnetlib.data.transform; |
| 2 | 2 |
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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; |
| 12 | 41 |
import com.google.common.collect.Lists; |
| ... | ... | |
| 15 | 44 |
import com.google.protobuf.InvalidProtocolBufferException; |
| 16 | 45 |
import com.googlecode.protobuf.format.JsonFormat; |
| 17 | 46 |
import com.googlecode.protobuf.format.JsonFormat.ParseException; |
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|
|
| 18 | 48 |
import eu.dnetlib.actionmanager.actions.ActionFactory; |
| 19 | 49 |
import eu.dnetlib.actionmanager.actions.XsltInfoPackageAction; |
| 20 | 50 |
import eu.dnetlib.actionmanager.common.Agent; |
| 21 | 51 |
import eu.dnetlib.actionmanager.common.Operation; |
| 22 | 52 |
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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| 25 | 67 |
import eu.dnetlib.data.proto.KindProtos.Kind; |
| 26 | 68 |
import eu.dnetlib.data.proto.OafProtos.Oaf; |
| 27 | 69 |
import eu.dnetlib.data.proto.TypeProtos.Type; |
| 28 | 70 |
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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import static org.junit.Assert.*; |
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public class XsltRowTransformerFactoryTest {
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private static final Log log = LogFactory.getLog(XsltRowTransformerFactoryTest.class); |
| ... | ... | |
| 78 | 105 |
doTest(loadFromTransformationProfile("claimRels_2_hbase.xml"), load("recordClaimRel.xml"));
|
| 79 | 106 |
} |
| 80 | 107 |
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@Test |
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public void testParseFp7IctPUB() throws Exception {
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| 84 | 110 |
|
| ... | ... | |
| 121 | 147 |
doTest(loadFromTransformationProfile("odf2hbase.xml"), load("doecode.xml"));
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} |
| 123 | 149 |
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@Test |
| 126 | 151 |
public void testParseDatasetLindat() throws Exception {
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| 127 | 152 |
|
| ... | ... | |
| 152 | 177 |
doTest(loadFromTransformationProfile("oaf2hbase.xml"), load("recordClaimedDedup.xml"));
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| 153 | 178 |
} |
| 154 | 179 |
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| 156 | 180 |
@Test |
| 157 | 181 |
public void testParseClaimDataset() throws Exception {
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| 158 | 182 |
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doTest(loadFromTransformationProfile("odf2hbase.xml"), load("recordClaimDataset.xml"));
|
| 160 | 184 |
} |
| 161 | 185 |
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| 163 | 186 |
@Test |
| 164 | 187 |
public void testParseACM() throws Exception {
|
| 165 | 188 |
|
| ... | ... | |
| 184 | 207 |
doTest(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectRecordFCT.xml"));
|
| 185 | 208 |
} |
| 186 | 209 |
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| 188 | 210 |
@Test |
| 189 | 211 |
public void testParseOaf() throws Exception {
|
| 190 | 212 |
|
| ... | ... | |
| 244 | 266 |
|
| 245 | 267 |
final List<Row> rows = Lists.newArrayList(); |
| 246 | 268 |
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("odf.xml")));
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//printAll(mapAll(buildTable(rows))); |
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// printAll(mapAll(buildTable(rows)));
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|
| 248 | 270 |
} |
| 249 | 271 |
|
| 250 | 272 |
@Test |
| ... | ... | |
| 254 | 276 |
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("pangaeOAF2.xml")));
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| 255 | 277 |
printAll(mapAll(buildTable(rows))); |
| 256 | 278 |
} |
| 279 |
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@Test |
| 258 | 281 |
public void testZenodo() throws Exception {
|
| 259 | 282 |
|
| ... | ... | |
| 310 | 333 |
printAll(mapAll(buildTable(rows))); |
| 311 | 334 |
} |
| 312 | 335 |
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| 315 | 336 |
@Test |
| 316 | 337 |
public void testLinkOrganization() throws Exception {
|
| 317 | 338 |
|
| ... | ... | |
| 341 | 362 |
|
| 342 | 363 |
final Function<Row, Row> f = rowIn -> {
|
| 343 | 364 |
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| 344 |
final List<Column<String,byte[]>> cols = Lists.newArrayList(); |
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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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for (final Column<String, byte[]> col : rowIn.getColumns()) {
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|
| 346 | 367 |
if (col.getName().equals("body")) {
|
| 347 | 368 |
cols.add(new Column(col.getName(), col.getValue())); |
| 348 | 369 |
|
| ... | ... | |
| 360 | 381 |
rows.addAll(puma1); |
| 361 | 382 |
rows.addAll(puma2); |
| 362 | 383 |
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List<Oaf> duplicates = Lists.newArrayList(); |
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final List<Oaf> duplicates = Lists.newArrayList();
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| 364 | 385 |
duplicates.add(getOafBody(puma1)); |
| 365 | 386 |
duplicates.add(getOafBody(puma2)); |
| 366 | 387 |
final Oaf.Builder oafMerge = OafEntityMerger.merge(mergeId, duplicates); |
| ... | ... | |
| 373 | 394 |
} |
| 374 | 395 |
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| 375 | 396 |
private Oaf getOafBody(final List<Row> rows) throws InvalidProtocolBufferException {
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for(Row row : rows) {
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| 377 |
if(StringUtils.startsWith(row.getKey(), "50")) {
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return Oaf.parseFrom(row.getColumn("body").getValue());
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for (final Row row : rows) {
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if (StringUtils.startsWith(row.getKey(), "50")) { return Oaf.parseFrom(row.getColumn("body").getValue());
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| 379 | 399 |
|
| 380 | 400 |
} |
| 381 | 401 |
} |
| ... | ... | |
| 393 | 413 |
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| 394 | 414 |
doTest(loadFromTransformationProfile("datasources_2_hbase.xsl"), load("datasourceNative.xml"));
|
| 395 | 415 |
} |
| 416 |
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| 396 | 417 |
@Test |
| 397 | 418 |
public void testParseDatasourcePiwik() throws Exception {
|
| 398 | 419 |
|
| ... | ... | |
| 410 | 431 |
doTestJsonGz(loadFromTransformationProfile("oaf2hbase.xml"), load("mdstore_cleaned.json.gz"));
|
| 411 | 432 |
} |
| 412 | 433 |
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| 413 |
|
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| 414 | 434 |
@Test |
| 415 | 435 |
public void testLoadFromTransformationProfile() throws IOException {
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InputStream in = loadFromTransformationProfile("oaf2hbase.xml");
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final InputStream in = loadFromTransformationProfile("oaf2hbase.xml");
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|
| 417 | 437 |
log.info(IOUtils.toString(in)); |
| 418 | 438 |
} |
| 419 | 439 |
|
| ... | ... | |
| 441 | 461 |
|
| 442 | 462 |
doTest(loadFromTransformationProfile("projects_2_hbase.xsl"), load("projectWithFunderOriginalName.xml"));
|
| 443 | 463 |
} |
| 464 |
|
|
| 444 | 465 |
@Test |
| 445 | 466 |
public void testLinkFunderOriginalName() throws Exception {
|
| 446 | 467 |
|
| ... | ... | |
| 513 | 534 |
final List<Row> rows = Lists.newArrayList(); |
| 514 | 535 |
rows.addAll(asRows(loadFromTransformationProfile("oaf2hbase.xml"), load("oafWithCommunity.xml")));
|
| 515 | 536 |
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| 516 |
ActionFactory actionFactory = new ActionFactory(); |
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| 537 |
final ActionFactory actionFactory = new ActionFactory();
|
|
| 517 | 538 |
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| 518 |
Map<String, Resource> xslts = Maps.newHashMap(); |
|
| 539 |
final Map<String, Resource> xslts = Maps.newHashMap();
|
|
| 519 | 540 |
|
| 520 | 541 |
xslts.put("oaf2hbase", new ByteArrayResource(IOUtils.toString(loadFromTransformationProfile("oaf2hbase.xml")).getBytes()));
|
| 521 | 542 |
actionFactory.setXslts(xslts); |
| 522 | 543 |
|
| 523 |
XsltInfoPackageAction pa = actionFactory.generateInfoPackageAction( |
|
| 544 |
final XsltInfoPackageAction pa = actionFactory.generateInfoPackageAction(
|
|
| 524 | 545 |
"oaf2hbase", |
| 525 | 546 |
"rawset-id", |
| 526 | 547 |
new Agent("agent-id", "agent-name", Agent.AGENT_TYPE.algo),
|
| ... | ... | |
| 533 | 554 |
|
| 534 | 555 |
IOUtils.readLines(load("country_updates.json")).forEach(line -> {
|
| 535 | 556 |
|
| 536 |
Oaf.Builder oaf = Oaf.newBuilder(); |
|
| 557 |
final Oaf.Builder oaf = Oaf.newBuilder();
|
|
| 537 | 558 |
|
| 538 | 559 |
try {
|
| 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());
|
|
| 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)));
|
| 546 | 567 |
}); |
| 547 | 568 |
|
| 548 | 569 |
pa.asAtomicActions().forEach(a -> {
|
| 549 |
Column<String, byte[]> col = new Column<>("update_" + System.nanoTime(), a.getTargetValue());
|
|
| 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 |
}); |
| 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 |
|
Also available in: Unified diff
(openorgs) added schemeid to pids in sql query