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added workflow parameters

This commit is contained in:
Enrico Ottonello 2020-04-20 12:00:04 +02:00
parent eef60bb9f4
commit 4ae55e3891
4 changed files with 30 additions and 48 deletions
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62
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java
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@ -1,35 +1,30 @@
package eu.dnetlib.doiboost.orcid; package eu.dnetlib.doiboost.orcid;
import java.io.FileNotFoundException;
import java.io.IOException; import java.io.IOException;
import java.net.URI; import java.net.URI;
import java.util.Properties; import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path; import org.apache.hadoop.fs.Path;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class OrcidDSManager { public class OrcidDSManager {
private static final Logger logger = LoggerFactory.getLogger(OrcidDSManager.class); private static final Logger logger = LoggerFactory.getLogger(OrcidDSManager.class);
private String hdfsServerUri; private String hdfsServerUri;
private String hadoopUsername;
private String hdfsOrcidDefaultPath; private String hdfsOrcidDefaultPath;
private String summariesFileNameTarGz; private String summariesFileNameTarGz;
private String outputAuthorsPath; private String outputAuthorsPath;
public static void main(String[] args) { public static void main(String[] args) throws IOException, Exception {
logger.info("OrcidDSManager started"); logger.info("OrcidDSManager started");
OrcidDSManager orcidDSManager = new OrcidDSManager(); OrcidDSManager orcidDSManager = new OrcidDSManager();
try { orcidDSManager.loadArgs(args);
orcidDSManager.initGARRProperties(); orcidDSManager.generateAuthors();
orcidDSManager.generateAuthors();
} catch (Exception e) {
logger.error("Generating authors data: "+e.getMessage());
}
} }
public void generateAuthors() throws Exception { public void generateAuthors() throws Exception {
@ -49,9 +44,6 @@ public class OrcidDSManager {
// Because of Maven // Because of Maven
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
// Set HADOOP user
System.setProperty("HADOOP_USER_NAME", hadoopUsername);
System.setProperty("hadoop.home.dir", "/");
return conf; return conf;
} }
@ -66,34 +58,18 @@ public class OrcidDSManager {
} }
return fs; return fs;
} }
private void loadProperties() throws FileNotFoundException, IOException { private void loadArgs(String[] args) throws IOException, Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(OrcidDSManager.class.getResourceAsStream("/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json")));
Properties appProps = new Properties(); parser.parseArgument(args);
ClassLoader classLoader = ClassLoader.getSystemClassLoader();
appProps.load(classLoader.getResourceAsStream("orciddsmanager/props/app.properties")); final String hdfsServerUri = parser.get("hdfsServerUri");
hdfsServerUri = appProps.getProperty("hdfs.server.uri"); logger.info("HDFS URI: "+hdfsServerUri);
hadoopUsername = appProps.getProperty("hdfs.hadoopusername"); Path hdfsOrcidDefaultPath = new Path(parser.get("hdfsOrcidDefaultPath"));
hdfsOrcidDefaultPath = appProps.getProperty("hdfs.orcid.defaultpath"); logger.info("Default Path: "+hdfsOrcidDefaultPath);
summariesFileNameTarGz = appProps.getProperty("hdfs.orcid.summariesfilename.tar.gz"); final String summariesFileNameTarGz = parser.get("summariesFileNameTarGz");
outputAuthorsPath = appProps.getProperty("hdfs.orcid.output.authorspath"); logger.info("Summaries File Name: "+summariesFileNameTarGz);
} final String outputAuthorsPath = parser.get("summariesFileNameTarGz");
logger.info("Output Authors Data: "+outputAuthorsPath);
private void initDefaultProperties() throws FileNotFoundException, IOException {
hdfsServerUri = "hdfs://localhost:9000";
hadoopUsername = "enrico.ottonello";
hdfsOrcidDefaultPath = "/user/enrico.ottonello/orcid/";
summariesFileNameTarGz = "ORCID_2019_summaries.tar.gz";
outputAuthorsPath = "output/";
}
private void initGARRProperties() throws FileNotFoundException, IOException {
hdfsServerUri = "hdfs://hadoop-rm1.garr-pa1.d4science.org:8020";
hadoopUsername = "root";
hdfsOrcidDefaultPath = "/data/orcid_summaries/";
summariesFileNameTarGz = "ORCID_2019_summaries.tar.gz";
outputAuthorsPath = "output/";
} }
} }

4
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java
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@ -122,14 +122,14 @@ public class SummariesDecompressor {
} }
} }
if ((counter % 1000) == 0) { if ((counter % 100000) == 0) {
logger.info("Current xml records parsed: "+counter); logger.info("Current xml records parsed: "+counter);
} }
} }
} }
} catch (IOException e) { } catch (IOException e) {
logger.error("Parsing record from gzip archive: "+e.getMessage()); logger.error("Parsing record from gzip archive: "+e.getMessage());
e.printStackTrace(); throw new RuntimeException(e);
} }
logger.info("Summaries parse completed"); logger.info("Summaries parse completed");
logger.info("Total XML records parsed: "+counter); logger.info("Total XML records parsed: "+counter);

6
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json Normal file
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@ -0,0 +1,6 @@
[
{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
{"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true},
{"paramName":"f", "paramLongName":"summariesFileNameTarGz", "paramDescription": "the name of the summaries orcid file", "paramRequired": true},
{"paramName":"o", "paramLongName":"outputAuthorsPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}
]

6
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid.oozie_app/workflow.xml
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@ -29,10 +29,10 @@
<job-tracker>${jobTracker}</job-tracker> <job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node> <name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidDSManager</main-class> <main-class>eu.dnetlib.doiboost.orcid.OrcidDSManager</main-class>
<!-- ENRICO FILL THE RIGHT ARG SECTION --> <arg>-d</arg><arg>${workingPath}/</arg>
<arg>-t</arg><arg>${workingPath}/input/crossref/index_dump</arg>
<arg>-n</arg><arg>${nameNode}</arg> <arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_summaries.tar.gz</arg>
<arg>-o</arg><arg>output/</arg>
</java> </java>
<ok to="End"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>