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modified wf configuration; added bmuse scraping on a spark action

This commit is contained in:
Enrico Ottonello 2021-12-03 15:44:39 +01:00
parent ff530fdcb4
commit 83d5e165a7
7 changed files with 169 additions and 40 deletions
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2
dhp-workflows/dhp-bmuse/src/main/java/eu/dnetlib/dhp/bmuse/bioschema/ScrapingJob.java
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@ -70,6 +70,8 @@ public class ScrapingJob {
Elements urls = UrlParser.getSitemapList(url, sitemapURLKey);
long total = urls.size();
System.setProperty("webdriver.chrome.whitelistedIps", "");
Path output = new Path(
nameNode
.concat(workingPath)

111
dhp-workflows/dhp-bmuse/src/main/java/eu/dnetlib/dhp/bmuse/bioschema/SparkScraper.java Normal file
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@ -0,0 +1,111 @@
package eu.dnetlib.dhp.bmuse.bioschema;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Objects;
import java.util.Optional;
import java.util.stream.Stream;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.util.LongAccumulator;
import org.jsoup.nodes.Element;
import org.jsoup.select.Elements;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bmuse.utils.BMUSEScraper;
import eu.dnetlib.dhp.bmuse.utils.UrlParser;
public class SparkScraper {
static Logger logger = LoggerFactory.getLogger(SparkScraper.class);
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkScraper.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bmuse/bioschema/generate_dataset.json")));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
final String nameNode = parser.get("nameNode");
final String workingPath = parser.get("workingPath");
final String rdfOutput = parser.get("rdfOutput");
final String sitemapUrl = parser.get("sitemapUrl");
final String sitemapURLKey = parser.get("sitemapURLKey");
final String dynamic = parser.get("dynamic");
final String maxScrapedPages = parser.get("maxScrapedPages");
Boolean dynamicValue = true;
if (Objects.nonNull(dynamic)) {
dynamicValue = Boolean.parseBoolean(dynamic);
}
final boolean scrapingType = dynamicValue.booleanValue();
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
final LongAccumulator scraped = spark.sparkContext().longAccumulator("scraped");
final LongAccumulator errors = spark.sparkContext().longAccumulator("errors");
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
System.setProperty("webdriver.chrome.whitelistedIps", "");
BMUSEScraper scraper = new BMUSEScraper();
String url = sitemapUrl.toLowerCase();
Elements urls = UrlParser.getSitemapList(url, sitemapURLKey);
long total = urls.size();
Path output = new Path(
nameNode
.concat(workingPath)
.concat(rdfOutput));
try (SequenceFile.Writer writer = SequenceFile
.createWriter(
sc.hadoopConfiguration(),
SequenceFile.Writer.file(output),
SequenceFile.Writer.keyClass(Text.class),
SequenceFile.Writer.valueClass(Text.class),
SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new GzipCodec()))) {
Stream<Element> urlStream = null;
if (Objects.nonNull(maxScrapedPages)) {
urlStream = urls.stream().limit(Long.parseLong(maxScrapedPages));
} else {
urlStream = urls.stream();
}
urlStream.forEach(u -> {
try {
final Text key = new Text(u.text());
final Text value = new Text(scraper.scrapeUrl(u.text(), scrapingType));
writer.append(key, value);
scraped.add(1l);
} catch (Exception e) {
logger.error(u.text(), e);
errors.add(1l);
}
});
}
logger
.info(
"Total pages to scrape: " + total + " Scraped: " + scraped.value() +
" Errors: " + errors.value());
});
}
}

2
dhp-workflows/dhp-bmuse/src/main/java/eu/dnetlib/dhp/bmuse/utils/BMUSEScraper.java
View File

@ -53,7 +53,7 @@ public class BMUSEScraper extends ScraperFilteredCore {
logger.error(e.toString());
return e.getMessage();
}
logger.info("HTML: " + html);
DocumentSource source = new StringDocumentSource(html, url);
IRI sourceIRI = SimpleValueFactory.getInstance().createIRI(source.getDocumentIRI());

35
dhp-workflows/dhp-bmuse/src/main/resources/eu/dnetlib/dhp/bmuse/bioschema/oozie_app/config-default.xml
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@ -2,22 +2,22 @@
<!-- OCEAN -->
<!-- <property>-->
<!-- <name>jobTracker</name>-->
<!-- <value>yarnRM</value>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>nameNode</name>-->
<!-- <value>hdfs://nameservice1</value>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>hive_metastore_uris</name>-->
<!-- <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>spark2YarnHistoryServerAddress</name>-->
<!-- <value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>jobTracker</name>-->
<!-- <value>yarnRM</value>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>nameNode</name>-->
<!-- <value>hdfs://nameservice1</value>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>hive_metastore_uris</name>-->
<!-- <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>spark2YarnHistoryServerAddress</name>-->
<!-- <value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>-->
<!-- </property>-->
<!-- GARR -->
@ -38,13 +38,10 @@
<name>spark2YarnHistoryServerAddress</name>
<value>http://hadoop-rm2.garr-pa1.d4science.org:19888</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>

49
dhp-workflows/dhp-bmuse/src/main/resources/eu/dnetlib/dhp/bmuse/bioschema/oozie_app/workflow.xml
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@ -2,17 +2,12 @@
<parameters>
<property>
<name>workingPath</name>
<value>/data/bioschema/disprot/</value>
<value>/data/bioschema/mobidb/</value>
<description>the working path</description>
</property>
<property>
<name>rdfOutput</name>
<value>nquads.seq</value>
<description>rdf output of scraping step</description>
</property>
<property>
<name>sitemapUrl</name>
<value>https://disprot.org/sitemap2.xml.gz</value>
<value>https://mobidb.org/sitemap2.xml.gz</value>
</property>
<property>
<name>sitemapURLKey</name>
@ -28,13 +23,18 @@
<value>100</value>
<description>max number of pages that will be scraped, default: no limit</description>
</property>
<property>
<name>rdfOutput</name>
<value>nquads.seq</value>
<description>rdf output of scraping step</description>
</property>
<property>
<name>oozie.launcher.mapreduce.map.java.opts</name>
<value>-Xmx4g</value>
</property>
<property>
<name>spark2RdfConversionMaxExecutors</name>
<value>50</value>
<name>spark2MaxExecutors</name>
<value>1</value>
</property>
<property>
<name>sparkDriverMemory</name>
@ -43,7 +43,7 @@
</property>
<property>
<name>sparkExecutorMemory</name>
<value>2G</value>
<value>4G</value>
<description>memory for individual executor</description>
</property>
<property>
@ -75,7 +75,7 @@
<fs>
<delete path='${workingPath}${rdfOutput}'/>
</fs>
<ok to="bmuseScraping"/>
<ok to="bmuseScrapingSpark"/>
<error to="Kill"/>
</action>
@ -94,5 +94,32 @@
<error to="Kill"/>
</action>
<action name="bmuseScrapingSpark">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>bmuseScrapingSpark</name>
<class>eu.dnetlib.dhp.bmuse.bioschema.SparkScraper</class>
<jar>dhp-bmuse-${projectVersion}.jar</jar>
<spark-opts>
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--nameNode</arg><arg>${nameNode}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--rdfOutput</arg><arg>${rdfOutput}</arg>
<arg>--sitemapUrl</arg><arg>${sitemapUrl}</arg>
<arg>--sitemapURLKey</arg><arg>${sitemapURLKey}</arg>
<arg>--dynamic</arg><arg>${dynamic}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

5
dhp-workflows/dhp-rdfconverter/src/main/resources/eu/dnetlib/dhp/rdfconverter/bioschema/oozie_app/config-default.xml
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@ -24,7 +24,7 @@
<property>
<name>jobTracker</name>
<value>yarn</value>
<value>hadoop-rm3.garr-pa1.d4science.org:8032</value>
</property>
<property>
<name>nameNode</name>
@ -38,13 +38,10 @@
<name>spark2YarnHistoryServerAddress</name>
<value>http://hadoop-rm2.garr-pa1.d4science.org:19888</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>

5
dhp-workflows/dhp-rdfconverter/src/main/resources/eu/dnetlib/dhp/rdfconverter/bioschema/oozie_app/workflow.xml
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@ -52,11 +52,6 @@
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
</global>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>