diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java
index 05e280d41..daff69623 100644
--- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java
+++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java
@@ -1,35 +1,30 @@
package eu.dnetlib.doiboost.orcid;
-import java.io.FileNotFoundException;
import java.io.IOException;
import java.net.URI;
-import java.util.Properties;
-
+import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+
public class OrcidDSManager {
private static final Logger logger = LoggerFactory.getLogger(OrcidDSManager.class);
private String hdfsServerUri;
- private String hadoopUsername;
private String hdfsOrcidDefaultPath;
private String summariesFileNameTarGz;
private String outputAuthorsPath;
- public static void main(String[] args) {
+ public static void main(String[] args) throws IOException, Exception {
logger.info("OrcidDSManager started");
OrcidDSManager orcidDSManager = new OrcidDSManager();
- try {
- orcidDSManager.initGARRProperties();
- orcidDSManager.generateAuthors();
- } catch (Exception e) {
- logger.error("Generating authors data: "+e.getMessage());
- }
+ orcidDSManager.loadArgs(args);
+ orcidDSManager.generateAuthors();
}
public void generateAuthors() throws Exception {
@@ -49,9 +44,6 @@ public class OrcidDSManager {
// Because of Maven
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.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;
}
@@ -66,34 +58,18 @@ public class OrcidDSManager {
}
return fs;
}
-
- private void loadProperties() throws FileNotFoundException, IOException {
-
- Properties appProps = new Properties();
- ClassLoader classLoader = ClassLoader.getSystemClassLoader();
- appProps.load(classLoader.getResourceAsStream("orciddsmanager/props/app.properties"));
- hdfsServerUri = appProps.getProperty("hdfs.server.uri");
- hadoopUsername = appProps.getProperty("hdfs.hadoopusername");
- hdfsOrcidDefaultPath = appProps.getProperty("hdfs.orcid.defaultpath");
- summariesFileNameTarGz = appProps.getProperty("hdfs.orcid.summariesfilename.tar.gz");
- outputAuthorsPath = appProps.getProperty("hdfs.orcid.output.authorspath");
- }
-
- 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/";
+
+ 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")));
+ parser.parseArgument(args);
+
+ final String hdfsServerUri = parser.get("hdfsServerUri");
+ logger.info("HDFS URI: "+hdfsServerUri);
+ Path hdfsOrcidDefaultPath = new Path(parser.get("hdfsOrcidDefaultPath"));
+ logger.info("Default Path: "+hdfsOrcidDefaultPath);
+ final String summariesFileNameTarGz = parser.get("summariesFileNameTarGz");
+ logger.info("Summaries File Name: "+summariesFileNameTarGz);
+ final String outputAuthorsPath = parser.get("summariesFileNameTarGz");
+ logger.info("Output Authors Data: "+outputAuthorsPath);
}
}
diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java
index d8eb49013..2a8d6d6de 100644
--- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java
+++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java
@@ -122,14 +122,14 @@ public class SummariesDecompressor {
}
}
- if ((counter % 1000) == 0) {
+ if ((counter % 100000) == 0) {
logger.info("Current xml records parsed: "+counter);
}
}
}
} catch (IOException e) {
logger.error("Parsing record from gzip archive: "+e.getMessage());
- e.printStackTrace();
+ throw new RuntimeException(e);
}
logger.info("Summaries parse completed");
logger.info("Total XML records parsed: "+counter);
diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json
new file mode 100644
index 000000000..bf992b508
--- /dev/null
+++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json
@@ -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}
+]
\ No newline at end of file
diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid.oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid.oozie_app/workflow.xml
index 5fb25a696..36e0cdf1b 100644
--- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid.oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid.oozie_app/workflow.xml
@@ -29,10 +29,10 @@
${jobTracker}
${nameNode}
eu.dnetlib.doiboost.orcid.OrcidDSManager
-
- -t${workingPath}/input/crossref/index_dump
+ -d${workingPath}/
-n${nameNode}
-
+ -fORCID_2019_summaries.tar.gz
+ -ooutput/