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new reports in hadoop job

This commit is contained in:
Michele Artini 2024-02-14 10:37:39 +01:00
parent 4b1ecad4e2
commit 963a2500be
3 changed files with 100 additions and 60 deletions
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99
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseAnalyzerJob.java
View File

@ -3,11 +3,14 @@ package eu.dnetlib.dhp.collection.plugin.base;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Optional;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
@ -23,6 +26,7 @@ import org.apache.spark.sql.SparkSession;
import org.dom4j.Attribute;
import org.dom4j.Document;
import org.dom4j.Element;
import org.dom4j.Node;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -65,83 +69,90 @@ public class BaseAnalyzerJob {
final SparkConf conf = new SparkConf();
runWithSparkSession(conf, isSparkSessionManaged, spark -> {
removeOutputDir(spark, outputPath);
processBaseRecords(spark, inputPath, outputPath);
});
}
private static void removeOutputDir(final SparkSession spark, final String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
runWithSparkSession(conf, isSparkSessionManaged, spark -> processBaseRecords(spark, inputPath, outputPath));
}
private static void processBaseRecords(final SparkSession spark,
final String inputPath,
final String outputPath) throws IOException {
HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
try (final FileSystem fs = FileSystem.get(new Configuration()); final AggregatorReport report = new AggregatorReport()) {
final Map<String, String> collections = new HashMap<>();
collect(fs, inputPath, outputPath + "/temp", collections, report);
finalReport(fs, outputPath + "/final", collections);
final AtomicInteger recordsCounter = new AtomicInteger(0);
final Map<String, AtomicInteger> fields = new HashMap<>();
final Map<String, AtomicInteger> types = new HashMap<>();
final Map<String, AtomicInteger> collections = new HashMap<>();
analyze(fs, inputPath, recordsCounter, fields, types, collections, report);
saveReport(fs, outputPath + "/total", Map.of("#records", recordsCounter));
saveReport(fs, outputPath + "/fields", fields);
saveReport(fs, outputPath + "/types", types);
saveReport(fs, outputPath + "/collections", collections);
} catch (final Throwable e) {
throw new RuntimeException(e);
}
}
private static void collect(final FileSystem fs,
private static void analyze(final FileSystem fs,
final String inputPath,
final String outputPath,
final Map<String, String> collections,
final AtomicInteger recordsCounter,
final Map<String, AtomicInteger> fields,
final Map<String, AtomicInteger> types,
final Map<String, AtomicInteger> collections,
final AggregatorReport report) throws JsonProcessingException, IOException {
try (final SequenceFile.Writer writer = SequenceFile
.createWriter(fs.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
.keyClass(IntWritable.class), SequenceFile.Writer
.valueClass(Text.class), SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
final BaseCollectorIterator iteraror = new BaseCollectorIterator(fs, new Path(inputPath), report);
final AtomicInteger recordsCounter = new AtomicInteger(0);
final AtomicInteger collectionsCounter = new AtomicInteger(0);
while (iteraror.hasNext()) {
final Document record = iteraror.next();
final BaseCollectorIterator iteraror = new BaseCollectorIterator(fs, new Path(inputPath), report);
final int i = recordsCounter.incrementAndGet();
if ((i % 10000) == 0) {
log.info("# Read records: " + i);
}
while (iteraror.hasNext()) {
final Document record = iteraror.next();
final List<String> recTypes = new ArrayList<>();
final int i = recordsCounter.incrementAndGet();
if ((i % 1000) == 0) {
log.info("# Read records: " + i);
}
for (final Object o : record.selectNodes("//*[local-name()='metadata']//*")) {
for (final Object o : record.selectNodes("//*[local-name() = 'collection']")) {
incrementMapCounter(fields, ((Node) o).getPath());
final String nodeName = ((Node) o).getName();
if ("collection".equals(nodeName)) {
final Element n = (Element) o;
final String collName = n.getText().trim();
if (StringUtils.isNotBlank(collName) && !collections.containsKey(collName)) {
if (StringUtils.isNotBlank(collName)) {
final Map<String, String> map = new HashMap<>();
for (final Object ao : n.attributes()) {
map.put(((Attribute) ao).getName(), ((Attribute) ao).getValue());
}
final String attrs = OBJECT_MAPPER.writeValueAsString(map);
collections.put(collName, attrs);
final IntWritable key = new IntWritable(collectionsCounter.incrementAndGet());
final Text value = new Text(collName + ": " + attrs);
try {
writer.append(key, value);
} catch (final Throwable e1) {
throw new RuntimeException(e1);
}
incrementMapCounter(collections, collName + ": " + OBJECT_MAPPER.writeValueAsString(map));
}
} else if ("type".equals(nodeName)) {
recTypes.add("TYPE: " + nodeName);
} else if ("typenorm".equals(nodeName)) {
recTypes.add("TYPE_NORM: " + nodeName);
}
}
incrementMapCounter(types, recTypes.stream().sorted().distinct().collect(Collectors.joining(", ")));
}
}
private static void incrementMapCounter(final Map<String, AtomicInteger> map, final String key) {
if (StringUtils.isNotBlank(key)) {
if (map.containsKey(key)) {
map.get(key).incrementAndGet();
} else {
map.put(key, new AtomicInteger(1));
}
}
}
private static void finalReport(final FileSystem fs, final String outputPath, final Map<String, String> collections)
private static void saveReport(final FileSystem fs, final String outputPath, final Map<String, AtomicInteger> fields)
throws JsonProcessingException, IOException {
try (final SequenceFile.Writer writer = SequenceFile
.createWriter(fs.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
@ -151,7 +162,7 @@ public class BaseAnalyzerJob {
final Text key = new Text();
final Text value = new Text();
for (final Entry<String, String> e : collections.entrySet()) {
for (final Entry<String, AtomicInteger> e : fields.entrySet()) {
key.set(e.getKey());
value.set(e.getKey() + ": " + e.getValue());
try {

8
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/oozie_app/workflow.xml
View File

@ -5,7 +5,7 @@
<description>the path of the BASE dump</description>
</property>
<property>
<name>reportsPath</name>
<name>baseReportsPath</name>
<description>path where to store the reports</description>
</property>
</parameters>
@ -18,8 +18,8 @@
<action name="deleteoutputpath">
<fs>
<delete path='${reportsPath}'/>
<mkdir path='${reportsPath}'/>
<delete path='${baseReportsPath}'/>
<mkdir path='${baseReportsPath}'/>
</fs>
<ok to="analyzeBaseRecords"/>
<error to="Kill"/>
@ -43,7 +43,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--inputPath</arg><arg>${baseInputPath}</arg>
<arg>--outputPath</arg><arg>${reportsPath}</arg>
<arg>--outputPath</arg><arg>${baseReportsPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>

53
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorIteratorTest.java
View File

@ -3,13 +3,17 @@ package eu.dnetlib.dhp.collection.plugin.base;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.concurrent.atomic.AtomicInteger;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.Attribute;
import org.dom4j.Document;
import org.dom4j.Element;
import org.dom4j.Node;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.junit.jupiter.MockitoExtension;
@ -29,6 +33,8 @@ public class BaseCollectorIteratorTest {
final BaseCollectorIterator iterator = new BaseCollectorIterator("base-sample.tar", new AggregatorReport());
final Map<String, Map<String, String>> collections = new HashMap<>();
final Map<String, AtomicInteger> fields = new HashMap<>();
final Set<String> types = new HashSet<>();
while (iterator.hasNext()) {
final Document record = iterator.next();
@ -41,21 +47,33 @@ public class BaseCollectorIteratorTest {
// System.out.println(record.asXML());
for (final Object o : record.selectNodes("//*[local-name() = 'collection']")) {
final Element n = (Element) o;
final String collName = n.getText().trim();
if (StringUtils.isNotBlank(collName) && !collections.containsKey(collName)) {
final Map<String, String> collAttrs = new HashMap<>();
for (final Object ao : n.attributes()) {
collAttrs.put(((Attribute) ao).getName(), ((Attribute) ao).getValue());
}
collections.put(collName, collAttrs);
for (final Object o : record.selectNodes("//*[local-name()='metadata']//*")) {
final String path = ((Node) o).getPath();
if (fields.containsKey(path)) {
fields.get(path).incrementAndGet();
} else {
fields.put(path, new AtomicInteger(1));
}
if ("collection".equals(((Node) o).getName())) {
final Element n = (Element) o;
final String collName = n.getText().trim();
if (StringUtils.isNotBlank(collName) && !collections.containsKey(collName)) {
final Map<String, String> collAttrs = new HashMap<>();
for (final Object ao : n.attributes()) {
collAttrs.put(((Attribute) ao).getName(), ((Attribute) ao).getValue());
}
collections.put(collName, collAttrs);
}
}
if ("type".equals(((Node) o).getName())) {
types.add(((Element) o).getText().trim());
}
}
}
final ObjectMapper mapper = new ObjectMapper();
@ -64,6 +82,17 @@ public class BaseCollectorIteratorTest {
}
for (final Entry<String, AtomicInteger> e : fields.entrySet()) {
System.out.println(e.getKey() + ": " + e.getValue().get());
}
System.out.println("TYPES: ");
for (final String s : types) {
System.out.println(s);
}
assertEquals(30000, count);
}