separate workflow to parse orcid summaries, activities and generate dataset with no doi publications; test
This commit is contained in:
parent
1729cc5cf3
commit
ca37d3427b
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@ -25,8 +25,8 @@ public class OrcidAuthorsDOIsDataGen extends OrcidDSManager {
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public void generateAuthorsDOIsData() throws Exception {
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public void generateAuthorsDOIsData() throws Exception {
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Configuration conf = initConfigurationObject();
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Configuration conf = initConfigurationObject();
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FileSystem fs = initFileSystemObject(conf);
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FileSystem fs = initFileSystemObject(conf);
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String tarGzUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(activitiesFileNameTarGz);
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String tarGzUri = hdfsServerUri.concat(workingPath).concat(activitiesFileNameTarGz);
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Path outputPath = new Path(hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(outputAuthorsDOIsPath));
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Path outputPath = new Path(hdfsServerUri.concat(workingPath).concat(outputAuthorsDOIsPath));
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ActivitiesDecompressor.parseGzActivities(conf, tarGzUri, outputPath);
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ActivitiesDecompressor.parseGzActivities(conf, tarGzUri, outputPath);
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}
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}
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@ -41,8 +41,8 @@ public class OrcidAuthorsDOIsDataGen extends OrcidDSManager {
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hdfsServerUri = parser.get("hdfsServerUri");
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hdfsServerUri = parser.get("hdfsServerUri");
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Log.info("HDFS URI: " + hdfsServerUri);
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Log.info("HDFS URI: " + hdfsServerUri);
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hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath");
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workingPath = parser.get("workingPath");
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Log.info("Default Path: " + hdfsOrcidDefaultPath);
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Log.info("Default Path: " + workingPath);
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activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz");
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activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz");
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Log.info("Activities File Name: " + activitiesFileNameTarGz);
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Log.info("Activities File Name: " + activitiesFileNameTarGz);
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outputAuthorsDOIsPath = parser.get("outputAuthorsDOIsPath");
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outputAuthorsDOIsPath = parser.get("outputAuthorsDOIsPath");
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@ -15,7 +15,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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public class OrcidDSManager {
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public class OrcidDSManager {
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protected String hdfsServerUri;
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protected String hdfsServerUri;
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protected String hdfsOrcidDefaultPath;
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protected String workingPath;
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private String summariesFileNameTarGz;
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private String summariesFileNameTarGz;
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private String outputAuthorsPath;
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private String outputAuthorsPath;
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@ -28,10 +28,10 @@ public class OrcidDSManager {
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public void generateAuthors() throws Exception {
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public void generateAuthors() throws Exception {
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Configuration conf = initConfigurationObject();
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Configuration conf = initConfigurationObject();
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FileSystem fs = initFileSystemObject(conf);
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FileSystem fs = initFileSystemObject(conf);
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String tarGzUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(summariesFileNameTarGz);
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String tarGzUri = hdfsServerUri.concat(workingPath).concat(summariesFileNameTarGz);
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Path outputPath = new Path(
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Path outputPath = new Path(
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hdfsServerUri
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hdfsServerUri
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.concat(hdfsOrcidDefaultPath)
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.concat(workingPath)
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.concat(outputAuthorsPath)
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.concat(outputAuthorsPath)
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.concat("authors.seq"));
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.concat("authors.seq"));
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SummariesDecompressor.parseGzSummaries(conf, tarGzUri, outputPath);
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SummariesDecompressor.parseGzSummaries(conf, tarGzUri, outputPath);
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@ -41,7 +41,7 @@ public class OrcidDSManager {
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// ====== Init HDFS File System Object
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// ====== Init HDFS File System Object
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Configuration conf = new Configuration();
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Configuration conf = new Configuration();
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// Set FileSystem URI
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// Set FileSystem URI
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conf.set("fs.defaultFS", hdfsServerUri.concat(hdfsOrcidDefaultPath));
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conf.set("fs.defaultFS", hdfsServerUri.concat(workingPath));
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// Because of Maven
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// Because of Maven
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conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
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conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
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conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
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conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
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@ -52,7 +52,7 @@ public class OrcidDSManager {
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// Get the filesystem - HDFS
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// Get the filesystem - HDFS
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FileSystem fs = null;
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FileSystem fs = null;
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try {
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try {
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fs = FileSystem.get(URI.create(hdfsServerUri.concat(hdfsOrcidDefaultPath)), conf);
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fs = FileSystem.get(URI.create(hdfsServerUri.concat(workingPath)), conf);
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} catch (IOException e) {
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} catch (IOException e) {
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// TODO Auto-generated catch block
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// TODO Auto-generated catch block
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e.printStackTrace();
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e.printStackTrace();
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@ -71,8 +71,8 @@ public class OrcidDSManager {
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hdfsServerUri = parser.get("hdfsServerUri");
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hdfsServerUri = parser.get("hdfsServerUri");
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Log.info("HDFS URI: " + hdfsServerUri);
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Log.info("HDFS URI: " + hdfsServerUri);
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hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath");
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workingPath = parser.get("workingPath");
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Log.info("Default Path: " + hdfsOrcidDefaultPath);
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Log.info("Working Path: " + workingPath);
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summariesFileNameTarGz = parser.get("summariesFileNameTarGz");
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summariesFileNameTarGz = parser.get("summariesFileNameTarGz");
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Log.info("Summaries File Name: " + summariesFileNameTarGz);
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Log.info("Summaries File Name: " + summariesFileNameTarGz);
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outputAuthorsPath = parser.get("outputAuthorsPath");
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outputAuthorsPath = parser.get("outputAuthorsPath");
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@ -69,12 +69,12 @@ public class OrcidDownloader extends OrcidDSManager {
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long startDownload = 0;
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long startDownload = 0;
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Configuration conf = initConfigurationObject();
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Configuration conf = initConfigurationObject();
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FileSystem fs = initFileSystemObject(conf);
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FileSystem fs = initFileSystemObject(conf);
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String lambdaFileUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(lambdaFileName);
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String lambdaFileUri = hdfsServerUri.concat(workingPath).concat(lambdaFileName);
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Path hdfsreadpath = new Path(lambdaFileUri);
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Path hdfsreadpath = new Path(lambdaFileUri);
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FSDataInputStream lambdaFileStream = fs.open(hdfsreadpath);
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FSDataInputStream lambdaFileStream = fs.open(hdfsreadpath);
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Path hdfsoutputPath = new Path(
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Path hdfsoutputPath = new Path(
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hdfsServerUri
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hdfsServerUri
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.concat(hdfsOrcidDefaultPath)
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.concat(workingPath)
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.concat(outputPath)
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.concat(outputPath)
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.concat("orcid_records.seq"));
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.concat("orcid_records.seq"));
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@ -176,8 +176,8 @@ public class OrcidDownloader extends OrcidDSManager {
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hdfsServerUri = parser.get("hdfsServerUri");
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hdfsServerUri = parser.get("hdfsServerUri");
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Log.info("HDFS URI: " + hdfsServerUri);
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Log.info("HDFS URI: " + hdfsServerUri);
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hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath");
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workingPath = parser.get("workingPath");
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Log.info("Default Path: " + hdfsOrcidDefaultPath);
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Log.info("Default Path: " + workingPath);
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lambdaFileName = parser.get("lambdaFileName");
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lambdaFileName = parser.get("lambdaFileName");
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Log.info("Lambda File Name: " + lambdaFileName);
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Log.info("Lambda File Name: " + lambdaFileName);
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outputPath = parser.get("outputPath");
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outputPath = parser.get("outputPath");
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@ -26,8 +26,8 @@ import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi;
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public class ActivitiesDumpReader {
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public class ActivitiesDumpReader {
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private static final int MAX_XML_WORKS_PARSED = 100;
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private static final int MAX_XML_WORKS_PARSED = -1;
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private static final int XML_WORKS_PARSED_COUNTER_LOG_INTERVAL = 10;
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private static final int XML_WORKS_PARSED_COUNTER_LOG_INTERVAL = 100000;
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public static void parseGzActivities(Configuration conf, String inputUri, Path outputPath)
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public static void parseGzActivities(Configuration conf, String inputUri, Path outputPath)
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throws Exception {
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throws Exception {
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@ -127,7 +127,7 @@ public class ActivitiesDumpReader {
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Log
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Log
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.warn(
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.warn(
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"Parsing work from tar archive and xml work: " + filename + " " + e.getMessage());
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"Parsing work from tar archive and xml work: " + filename + " " + e.getMessage());
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Log.warn(e);
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// Log.warn(e);
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}
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}
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if ((counter % XML_WORKS_PARSED_COUNTER_LOG_INTERVAL) == 0) {
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if ((counter % XML_WORKS_PARSED_COUNTER_LOG_INTERVAL) == 0) {
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@ -16,7 +16,7 @@ public class GenOrcidAuthorWork extends OrcidDSManager {
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private String activitiesFileNameTarGz;
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private String activitiesFileNameTarGz;
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private String outputWorksPath;
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private String outputWorksPath;
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private String workingPath;
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// private String workingPath;
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public static void main(String[] args) throws IOException, Exception {
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public static void main(String[] args) throws IOException, Exception {
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GenOrcidAuthorWork genOrcidAuthorWork = new GenOrcidAuthorWork();
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GenOrcidAuthorWork genOrcidAuthorWork = new GenOrcidAuthorWork();
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@ -45,7 +45,6 @@ public class GenOrcidAuthorWork extends OrcidDSManager {
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Log.info("HDFS URI: " + hdfsServerUri);
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Log.info("HDFS URI: " + hdfsServerUri);
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workingPath = parser.get("workingPath");
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workingPath = parser.get("workingPath");
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Log.info("Working Path: " + workingPath);
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Log.info("Working Path: " + workingPath);
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hdfsOrcidDefaultPath = workingPath;
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activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz");
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activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz");
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Log.info("Activities File Name: " + activitiesFileNameTarGz);
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Log.info("Activities File Name: " + activitiesFileNameTarGz);
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outputWorksPath = parser.get("outputWorksPath");
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outputWorksPath = parser.get("outputWorksPath");
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@ -16,6 +16,7 @@ import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.slf4j.Logger;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.slf4j.LoggerFactory;
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@ -24,9 +25,11 @@ import com.google.gson.JsonElement;
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import com.google.gson.JsonParser;
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import com.google.gson.JsonParser;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.doiboost.orcid.json.JsonHelper;
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import eu.dnetlib.doiboost.orcid.json.JsonHelper;
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import eu.dnetlib.doiboost.orcid.model.AuthorData;
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import eu.dnetlib.doiboost.orcid.model.AuthorData;
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import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
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import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
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import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf;
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import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher;
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import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher;
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import scala.Tuple2;
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import scala.Tuple2;
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@ -59,7 +62,7 @@ public class SparkGenEnrichedOrcidWorks {
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaPairRDD<Text, Text> summariesRDD = sc
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JavaPairRDD<Text, Text> summariesRDD = sc
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.sequenceFile(workingPath + "../orcid_summaries/output/authors.seq", Text.class, Text.class);
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.sequenceFile(workingPath + "summaries/output/authors.seq", Text.class, Text.class);
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Dataset<AuthorData> summariesDataset = spark
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Dataset<AuthorData> summariesDataset = spark
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.createDataset(
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.createDataset(
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summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(),
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summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(),
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@ -89,8 +92,19 @@ public class SparkGenEnrichedOrcidWorks {
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.filter(Objects::nonNull)
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.filter(Objects::nonNull)
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.toJavaRDD();
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.toJavaRDD();
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logger.info("Works enriched data created: " + enrichedWorksRDD.count());
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logger.info("Works enriched data created: " + enrichedWorksRDD.count());
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enrichedWorksRDD.repartition(10).saveAsTextFile(workingPath + outputEnrichedWorksPath);
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enrichedWorksRDD.saveAsTextFile(workingPath + outputEnrichedWorksPath);
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logger.info("Works enriched data saved");
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logger.info("Works enriched data saved");
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JavaRDD<Tuple2<String, Publication>> oafPublicationRDD = enrichedWorksRDD.map(e -> {
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JsonElement j = new JsonParser().parse(e._2());
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return new Tuple2<>(e._1(), (Publication) PublicationToOaf
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.generatePublicationActionsFromDump(j.getAsJsonObject()));
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});
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Dataset<Tuple2<String, Publication>> publicationDataset = spark
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.createDataset(
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oafPublicationRDD.repartition(1).rdd(),
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Encoders.tuple(Encoders.STRING(), Encoders.bean(Publication.class)));
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publicationDataset.write().mode(SaveMode.Overwrite).save(workingPath + "no_doi_dataset/output");
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});
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});
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}
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}
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@ -172,7 +172,7 @@ public class PublicationToOaf {
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instance.setUrl(urls);
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instance.setUrl(urls);
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}
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}
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final String pubDate = getPublicationDate(rootElement, "publication_date");
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final String pubDate = getPublicationDate(rootElement, "publicationDates");
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if (StringUtils.isNotBlank(pubDate)) {
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if (StringUtils.isNotBlank(pubDate)) {
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instance.setDateofacceptance(mapStringField(pubDate, null));
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instance.setDateofacceptance(mapStringField(pubDate, null));
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}
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}
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@ -325,7 +325,12 @@ public class PublicationToOaf {
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private static String getPublicationDate(final JsonObject rootElement,
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private static String getPublicationDate(final JsonObject rootElement,
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final String jsonKey) {
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final String jsonKey) {
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final JsonObject pubDateJson = rootElement.getAsJsonObject(jsonKey);
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JsonObject pubDateJson = null;
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try {
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pubDateJson = rootElement.getAsJsonObject(jsonKey);
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} catch (Exception e) {
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return null;
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}
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if (pubDateJson == null) {
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if (pubDateJson == null) {
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return null;
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return null;
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}
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}
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@ -1,6 +1,6 @@
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[
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[
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{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
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{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
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{"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true},
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{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true},
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{"paramName":"f", "paramLongName":"summariesFileNameTarGz", "paramDescription": "the name of the summaries orcid file", "paramRequired": true},
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{"paramName":"f", "paramLongName":"summariesFileNameTarGz", "paramDescription": "the name of the summaries orcid file", "paramRequired": true},
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{"paramName":"o", "paramLongName":"outputAuthorsPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}
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{"paramName":"o", "paramLongName":"outputAuthorsPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}
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]
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]
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@ -1,6 +1,6 @@
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[
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[
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{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
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{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
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{"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true},
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{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true},
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{"paramName":"f", "paramLongName":"activitiesFileNameTarGz", "paramDescription": "the name of the activities orcid file", "paramRequired": true},
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{"paramName":"f", "paramLongName":"activitiesFileNameTarGz", "paramDescription": "the name of the activities orcid file", "paramRequired": true},
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{"paramName":"o", "paramLongName":"outputAuthorsDOIsPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}
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{"paramName":"o", "paramLongName":"outputAuthorsDOIsPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}
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]
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]
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@ -1,6 +1,6 @@
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[
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[
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{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
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{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
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{"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true},
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{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true},
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{"paramName":"f", "paramLongName":"lambdaFileName", "paramDescription": "the name of the lambda file", "paramRequired": true},
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{"paramName":"f", "paramLongName":"lambdaFileName", "paramDescription": "the name of the lambda file", "paramRequired": true},
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{"paramName":"o", "paramLongName":"outputPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true},
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{"paramName":"o", "paramLongName":"outputPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true},
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{"paramName":"t", "paramLongName":"token", "paramDescription": "token to grant access", "paramRequired": true}
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{"paramName":"t", "paramLongName":"token", "paramDescription": "token to grant access", "paramRequired": true}
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@ -1,75 +1,9 @@
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<workflow-app name="Gen Enriched Orcid Works" xmlns="uri:oozie:workflow:0.5">
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<workflow-app name="Gen Enriched Orcid Works" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<parameters>
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<property>
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<property>
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<name>workingPath_activities</name>
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<name>workingPath</name>
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<description>the working dir base path</description>
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<description>the working dir base path</description>
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</property>
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</property>
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<property>
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<name>shell_cmd_0</name>
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|
||||||
<value>wget -O /tmp/ORCID_2019_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/18017660 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_0.tar.gz /data/orcid_activities/ORCID_2019_activites_0.tar.gz ; rm -f /tmp/ORCID_2019_activites_0.tar.gz
|
|
||||||
</value>
|
|
||||||
<description>the shell command that downloads and puts to hdfs orcid activity file 0</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>shell_cmd_1</name>
|
|
||||||
<value>wget -O /tmp/ORCID_2019_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/18017675 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_1.tar.gz /data/orcid_activities/ORCID_2019_activites_1.tar.gz ; rm -f /tmp/ORCID_2019_activites_1.tar.gz
|
|
||||||
</value>
|
|
||||||
<description>the shell command that downloads and puts to hdfs orcid activity file 1</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>shell_cmd_2</name>
|
|
||||||
<value>wget -O /tmp/ORCID_2019_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/18017717 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_2.tar.gz /data/orcid_activities/ORCID_2019_activites_2.tar.gz ; rm -f /tmp/ORCID_2019_activites_2.tar.gz
|
|
||||||
</value>
|
|
||||||
<description>the shell command that downloads and puts to hdfs orcid activity file 2</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>shell_cmd_3</name>
|
|
||||||
<value>wget -O /tmp/ORCID_2019_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/18017765 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_3.tar.gz /data/orcid_activities/ORCID_2019_activites_3.tar.gz ; rm -f /tmp/ORCID_2019_activites_3.tar.gz
|
|
||||||
</value>
|
|
||||||
<description>the shell command that downloads and puts to hdfs orcid activity file 3</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>shell_cmd_4</name>
|
|
||||||
<value>wget -O /tmp/ORCID_2019_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/18017831 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_4.tar.gz /data/orcid_activities/ORCID_2019_activites_4.tar.gz ; rm -f /tmp/ORCID_2019_activites_4.tar.gz
|
|
||||||
</value>
|
|
||||||
<description>the shell command that downloads and puts to hdfs orcid activity file 4</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>shell_cmd_5</name>
|
|
||||||
<value>wget -O /tmp/ORCID_2019_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/18017987 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_5.tar.gz /data/orcid_activities/ORCID_2019_activites_5.tar.gz ; rm -f /tmp/ORCID_2019_activites_5.tar.gz
|
|
||||||
</value>
|
|
||||||
<description>the shell command that downloads and puts to hdfs orcid activity file 5</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>shell_cmd_6</name>
|
|
||||||
<value>wget -O /tmp/ORCID_2019_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/18018053 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_6.tar.gz /data/orcid_activities/ORCID_2019_activites_6.tar.gz ; rm -f /tmp/ORCID_2019_activites_6.tar.gz
|
|
||||||
</value>
|
|
||||||
<description>the shell command that downloads and puts to hdfs orcid activity file 6</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>shell_cmd_7</name>
|
|
||||||
<value>wget -O /tmp/ORCID_2019_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/18018023 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_7.tar.gz /data/orcid_activities/ORCID_2019_activites_7.tar.gz ; rm -f /tmp/ORCID_2019_activites_7.tar.gz
|
|
||||||
</value>
|
|
||||||
<description>the shell command that downloads and puts to hdfs orcid activity file 7</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>shell_cmd_8</name>
|
|
||||||
<value>wget -O /tmp/ORCID_2019_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/18018248 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_8.tar.gz /data/orcid_activities/ORCID_2019_activites_8.tar.gz ; rm -f /tmp/ORCID_2019_activites_8.tar.gz
|
|
||||||
</value>
|
|
||||||
<description>the shell command that downloads and puts to hdfs orcid activity file 8</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>shell_cmd_9</name>
|
|
||||||
<value>wget -O /tmp/ORCID_2019_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/18018029 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_9.tar.gz /data/orcid_activities/ORCID_2019_activites_9.tar.gz ; rm -f /tmp/ORCID_2019_activites_9.tar.gz
|
|
||||||
</value>
|
|
||||||
<description>the shell command that downloads and puts to hdfs orcid activity file 9</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>shell_cmd_X</name>
|
|
||||||
<value>wget -O /tmp/ORCID_2019_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/18018182 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_X.tar.gz /data/orcid_activities/ORCID_2019_activites_X.tar.gz ; rm -f /tmp/ORCID_2019_activites_X.tar.gz
|
|
||||||
</value>
|
|
||||||
<description>the shell command that downloads and puts to hdfs orcid activity file X</description>
|
|
||||||
</property>
|
|
||||||
</parameters>
|
</parameters>
|
||||||
|
|
||||||
<start to="ResetWorkingPath"/>
|
<start to="ResetWorkingPath"/>
|
||||||
|
@ -80,436 +14,11 @@
|
||||||
|
|
||||||
<action name="ResetWorkingPath">
|
<action name="ResetWorkingPath">
|
||||||
<fs>
|
<fs>
|
||||||
<delete path='${workingPath_activities}/no_doi_works/*'/>
|
<delete path='${workingPath}/no_doi_enriched_works/output'/>
|
||||||
<delete path='${workingPath_activities}/no_doi_enriched_works/*'/>
|
|
||||||
</fs>
|
</fs>
|
||||||
<ok to="fork_gen_orcid_author_work"/>
|
<ok to="Gen_Enriched_Orcid_Works"/>
|
||||||
<error to="Kill"/>
|
<error to="Kill"/>
|
||||||
</action>
|
</action>
|
||||||
|
|
||||||
<fork name = "fork_gen_orcid_author_work">
|
|
||||||
<path start = "check_exist_on_hdfs_activities_0"/>
|
|
||||||
<path start = "check_exist_on_hdfs_activities_1"/>
|
|
||||||
<path start = "check_exist_on_hdfs_activities_2"/>
|
|
||||||
<path start = "check_exist_on_hdfs_activities_3"/>
|
|
||||||
<path start = "check_exist_on_hdfs_activities_4"/>
|
|
||||||
<path start = "check_exist_on_hdfs_activities_5"/>
|
|
||||||
<path start = "check_exist_on_hdfs_activities_6"/>
|
|
||||||
<path start = "check_exist_on_hdfs_activities_7"/>
|
|
||||||
<path start = "check_exist_on_hdfs_activities_8"/>
|
|
||||||
<path start = "check_exist_on_hdfs_activities_9"/>
|
|
||||||
<path start = "check_exist_on_hdfs_activities_X"/>
|
|
||||||
</fork>
|
|
||||||
|
|
||||||
<decision name="check_exist_on_hdfs_activities_0">
|
|
||||||
<switch>
|
|
||||||
<case to="GenOrcidAuthorWork_0">
|
|
||||||
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_0.tar.gz'))}
|
|
||||||
</case>
|
|
||||||
<default to="Download_0" />
|
|
||||||
</switch>
|
|
||||||
</decision>
|
|
||||||
|
|
||||||
<action name="Download_0">
|
|
||||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<exec>bash</exec>
|
|
||||||
<argument>-c</argument>
|
|
||||||
<argument>${shell_cmd_0}</argument>
|
|
||||||
<capture-output/>
|
|
||||||
</shell>
|
|
||||||
<ok to="GenOrcidAuthorWork_0"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="GenOrcidAuthorWork_0">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
|
||||||
<arg>-w</arg><arg>${workingPath_activities}/</arg>
|
|
||||||
<arg>-n</arg><arg>${nameNode}</arg>
|
|
||||||
<arg>-f</arg><arg>ORCID_2019_activites_0.tar.gz</arg>
|
|
||||||
<arg>-ow</arg><arg>no_doi_works/works_0.seq</arg>
|
|
||||||
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
||||||
</java>
|
|
||||||
<ok to="join_node"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<decision name="check_exist_on_hdfs_activities_1">
|
|
||||||
<switch>
|
|
||||||
<case to="GenOrcidAuthorWork_1">
|
|
||||||
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_1.tar.gz'))}
|
|
||||||
</case>
|
|
||||||
<default to="Download_1" />
|
|
||||||
</switch>
|
|
||||||
</decision>
|
|
||||||
|
|
||||||
<action name="Download_1">
|
|
||||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<exec>bash</exec>
|
|
||||||
<argument>-c</argument>
|
|
||||||
<argument>${shell_cmd_1}</argument>
|
|
||||||
<capture-output/>
|
|
||||||
</shell>
|
|
||||||
<ok to="GenOrcidAuthorWork_1"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="GenOrcidAuthorWork_1">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
|
||||||
<arg>-w</arg><arg>${workingPath_activities}/</arg>
|
|
||||||
<arg>-n</arg><arg>${nameNode}</arg>
|
|
||||||
<arg>-f</arg><arg>ORCID_2019_activites_1.tar.gz</arg>
|
|
||||||
<arg>-ow</arg><arg>no_doi_works/works_1.seq</arg>
|
|
||||||
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
||||||
</java>
|
|
||||||
<ok to="join_node"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<decision name="check_exist_on_hdfs_activities_2">
|
|
||||||
<switch>
|
|
||||||
<case to="GenOrcidAuthorWork_2">
|
|
||||||
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_2.tar.gz'))}
|
|
||||||
</case>
|
|
||||||
<default to="Download_2" />
|
|
||||||
</switch>
|
|
||||||
</decision>
|
|
||||||
|
|
||||||
<action name="Download_2">
|
|
||||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<exec>bash</exec>
|
|
||||||
<argument>-c</argument>
|
|
||||||
<argument>${shell_cmd_2}</argument>
|
|
||||||
<capture-output/>
|
|
||||||
</shell>
|
|
||||||
<ok to="GenOrcidAuthorWork_2"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="GenOrcidAuthorWork_2">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
|
||||||
<arg>-w</arg><arg>${workingPath_activities}/</arg>
|
|
||||||
<arg>-n</arg><arg>${nameNode}</arg>
|
|
||||||
<arg>-f</arg><arg>ORCID_2019_activites_2.tar.gz</arg>
|
|
||||||
<arg>-ow</arg><arg>no_doi_works/works_2.seq</arg>
|
|
||||||
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
||||||
</java>
|
|
||||||
<ok to="join_node"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<decision name="check_exist_on_hdfs_activities_3">
|
|
||||||
<switch>
|
|
||||||
<case to="GenOrcidAuthorWork_3">
|
|
||||||
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_3.tar.gz'))}
|
|
||||||
</case>
|
|
||||||
<default to="Download_3" />
|
|
||||||
</switch>
|
|
||||||
</decision>
|
|
||||||
|
|
||||||
<action name="Download_3">
|
|
||||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<exec>bash</exec>
|
|
||||||
<argument>-c</argument>
|
|
||||||
<argument>${shell_cmd_3}</argument>
|
|
||||||
<capture-output/>
|
|
||||||
</shell>
|
|
||||||
<ok to="GenOrcidAuthorWork_3"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="GenOrcidAuthorWork_3">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
|
||||||
<arg>-w</arg><arg>${workingPath_activities}/</arg>
|
|
||||||
<arg>-n</arg><arg>${nameNode}</arg>
|
|
||||||
<arg>-f</arg><arg>ORCID_2019_activites_3.tar.gz</arg>
|
|
||||||
<arg>-ow</arg><arg>no_doi_works/works_3.seq</arg>
|
|
||||||
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
||||||
</java>
|
|
||||||
<ok to="join_node"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<decision name="check_exist_on_hdfs_activities_4">
|
|
||||||
<switch>
|
|
||||||
<case to="GenOrcidAuthorWork_4">
|
|
||||||
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_4.tar.gz'))}
|
|
||||||
</case>
|
|
||||||
<default to="Download_4" />
|
|
||||||
</switch>
|
|
||||||
</decision>
|
|
||||||
|
|
||||||
<action name="Download_4">
|
|
||||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<exec>bash</exec>
|
|
||||||
<argument>-c</argument>
|
|
||||||
<argument>${shell_cmd_4}</argument>
|
|
||||||
<capture-output/>
|
|
||||||
</shell>
|
|
||||||
<ok to="GenOrcidAuthorWork_4"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="GenOrcidAuthorWork_4">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
|
||||||
<arg>-w</arg><arg>${workingPath_activities}/</arg>
|
|
||||||
<arg>-n</arg><arg>${nameNode}</arg>
|
|
||||||
<arg>-f</arg><arg>ORCID_2019_activites_4.tar.gz</arg>
|
|
||||||
<arg>-ow</arg><arg>no_doi_works/works_4.seq</arg>
|
|
||||||
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
||||||
</java>
|
|
||||||
<ok to="join_node"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<decision name="check_exist_on_hdfs_activities_5">
|
|
||||||
<switch>
|
|
||||||
<case to="GenOrcidAuthorWork_5">
|
|
||||||
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_5.tar.gz'))}
|
|
||||||
</case>
|
|
||||||
<default to="Download_5" />
|
|
||||||
</switch>
|
|
||||||
</decision>
|
|
||||||
|
|
||||||
<action name="Download_5">
|
|
||||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<exec>bash</exec>
|
|
||||||
<argument>-c</argument>
|
|
||||||
<argument>${shell_cmd_5}</argument>
|
|
||||||
<capture-output/>
|
|
||||||
</shell>
|
|
||||||
<ok to="GenOrcidAuthorWork_5"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="GenOrcidAuthorWork_5">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
|
||||||
<arg>-w</arg><arg>${workingPath_activities}/</arg>
|
|
||||||
<arg>-n</arg><arg>${nameNode}</arg>
|
|
||||||
<arg>-f</arg><arg>ORCID_2019_activites_5.tar.gz</arg>
|
|
||||||
<arg>-ow</arg><arg>no_doi_works/works_5.seq</arg>
|
|
||||||
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
||||||
</java>
|
|
||||||
<ok to="join_node"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<decision name="check_exist_on_hdfs_activities_6">
|
|
||||||
<switch>
|
|
||||||
<case to="GenOrcidAuthorWork_6">
|
|
||||||
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_6.tar.gz'))}
|
|
||||||
</case>
|
|
||||||
<default to="Download_6" />
|
|
||||||
</switch>
|
|
||||||
</decision>
|
|
||||||
|
|
||||||
<action name="Download_6">
|
|
||||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<exec>bash</exec>
|
|
||||||
<argument>-c</argument>
|
|
||||||
<argument>${shell_cmd_6}</argument>
|
|
||||||
<capture-output/>
|
|
||||||
</shell>
|
|
||||||
<ok to="GenOrcidAuthorWork_6"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="GenOrcidAuthorWork_6">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
|
||||||
<arg>-w</arg><arg>${workingPath_activities}/</arg>
|
|
||||||
<arg>-n</arg><arg>${nameNode}</arg>
|
|
||||||
<arg>-f</arg><arg>ORCID_2019_activites_6.tar.gz</arg>
|
|
||||||
<arg>-ow</arg><arg>no_doi_works/works_6.seq</arg>
|
|
||||||
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
||||||
</java>
|
|
||||||
<ok to="join_node"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
|
|
||||||
<decision name="check_exist_on_hdfs_activities_7">
|
|
||||||
<switch>
|
|
||||||
<case to="GenOrcidAuthorWork_7">
|
|
||||||
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_7.tar.gz'))}
|
|
||||||
</case>
|
|
||||||
<default to="Download_7" />
|
|
||||||
</switch>
|
|
||||||
</decision>
|
|
||||||
|
|
||||||
<action name="Download_7">
|
|
||||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<exec>bash</exec>
|
|
||||||
<argument>-c</argument>
|
|
||||||
<argument>${shell_cmd_7}</argument>
|
|
||||||
<capture-output/>
|
|
||||||
</shell>
|
|
||||||
<ok to="GenOrcidAuthorWork_7"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="GenOrcidAuthorWork_7">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
|
||||||
<arg>-w</arg><arg>${workingPath_activities}/</arg>
|
|
||||||
<arg>-n</arg><arg>${nameNode}</arg>
|
|
||||||
<arg>-f</arg><arg>ORCID_2019_activites_7.tar.gz</arg>
|
|
||||||
<arg>-ow</arg><arg>no_doi_works/works_7.seq</arg>
|
|
||||||
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
||||||
</java>
|
|
||||||
<ok to="join_node"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<decision name="check_exist_on_hdfs_activities_8">
|
|
||||||
<switch>
|
|
||||||
<case to="GenOrcidAuthorWork_8">
|
|
||||||
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_8.tar.gz'))}
|
|
||||||
</case>
|
|
||||||
<default to="Download_8" />
|
|
||||||
</switch>
|
|
||||||
</decision>
|
|
||||||
|
|
||||||
<action name="Download_8">
|
|
||||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<exec>bash</exec>
|
|
||||||
<argument>-c</argument>
|
|
||||||
<argument>${shell_cmd_8}</argument>
|
|
||||||
<capture-output/>
|
|
||||||
</shell>
|
|
||||||
<ok to="GenOrcidAuthorWork_8"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="GenOrcidAuthorWork_8">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
|
||||||
<arg>-w</arg><arg>${workingPath_activities}/</arg>
|
|
||||||
<arg>-n</arg><arg>${nameNode}</arg>
|
|
||||||
<arg>-f</arg><arg>ORCID_2019_activites_8.tar.gz</arg>
|
|
||||||
<arg>-ow</arg><arg>no_doi_works/works_8.seq</arg>
|
|
||||||
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
||||||
</java>
|
|
||||||
<ok to="join_node"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<decision name="check_exist_on_hdfs_activities_9">
|
|
||||||
<switch>
|
|
||||||
<case to="GenOrcidAuthorWork_9">
|
|
||||||
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_9.tar.gz'))}
|
|
||||||
</case>
|
|
||||||
<default to="Download_9" />
|
|
||||||
</switch>
|
|
||||||
</decision>
|
|
||||||
|
|
||||||
<action name="Download_9">
|
|
||||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<exec>bash</exec>
|
|
||||||
<argument>-c</argument>
|
|
||||||
<argument>${shell_cmd_9}</argument>
|
|
||||||
<capture-output/>
|
|
||||||
</shell>
|
|
||||||
<ok to="GenOrcidAuthorWork_9"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="GenOrcidAuthorWork_9">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
|
||||||
<arg>-w</arg><arg>${workingPath_activities}/</arg>
|
|
||||||
<arg>-n</arg><arg>${nameNode}</arg>
|
|
||||||
<arg>-f</arg><arg>ORCID_2019_activites_9.tar.gz</arg>
|
|
||||||
<arg>-ow</arg><arg>no_doi_works/works_9.seq</arg>
|
|
||||||
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
||||||
</java>
|
|
||||||
<ok to="join_node"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<decision name="check_exist_on_hdfs_activities_X">
|
|
||||||
<switch>
|
|
||||||
<case to="GenOrcidAuthorWork_X">
|
|
||||||
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_X.tar.gz'))}
|
|
||||||
</case>
|
|
||||||
<default to="Download_X" />
|
|
||||||
</switch>
|
|
||||||
</decision>
|
|
||||||
|
|
||||||
<action name="Download_X">
|
|
||||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<exec>bash</exec>
|
|
||||||
<argument>-c</argument>
|
|
||||||
<argument>${shell_cmd_X}</argument>
|
|
||||||
<capture-output/>
|
|
||||||
</shell>
|
|
||||||
<ok to="GenOrcidAuthorWork_X"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="GenOrcidAuthorWork_X">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
|
||||||
<arg>-w</arg><arg>${workingPath_activities}/</arg>
|
|
||||||
<arg>-n</arg><arg>${nameNode}</arg>
|
|
||||||
<arg>-f</arg><arg>ORCID_2019_activites_X.tar.gz</arg>
|
|
||||||
<arg>-ow</arg><arg>no_doi_works/works_X.seq</arg>
|
|
||||||
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
|
||||||
</java>
|
|
||||||
<ok to="join_node"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<join name = "join_node" to = "Gen_Enriched_Orcid_Works"/>
|
|
||||||
|
|
||||||
<action name="Gen_Enriched_Orcid_Works">
|
<action name="Gen_Enriched_Orcid_Works">
|
||||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
|
|
@ -1,9 +1,15 @@
|
||||||
<workflow-app name="import Orcid" xmlns="uri:oozie:workflow:0.5">
|
<workflow-app name="Import Orcid Summaries" xmlns="uri:oozie:workflow:0.5">
|
||||||
<parameters>
|
<parameters>
|
||||||
<property>
|
<property>
|
||||||
<name>workingPath</name>
|
<name>workingPath</name>
|
||||||
<description>the working dir base path</description>
|
<description>the working dir base path</description>
|
||||||
</property>
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shell_cmd_0</name>
|
||||||
|
<value>wget -O /tmp/ORCID_2019_summaries.tar.gz https://orcid.figshare.com/ndownloader/files/18017633 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_summaries.tar.gz /data/orcid_activities/ORCID_2019_summaries.tar.gz ; rm -f /tmp/ORCID_2019_summaries.tar.gz
|
||||||
|
</value>
|
||||||
|
<description>the shell command that downloads and puts to hdfs orcid summaries</description>
|
||||||
|
</property>
|
||||||
</parameters>
|
</parameters>
|
||||||
|
|
||||||
<start to="ResetWorkingPath"/>
|
<start to="ResetWorkingPath"/>
|
||||||
|
@ -15,24 +21,44 @@
|
||||||
|
|
||||||
<action name="ResetWorkingPath">
|
<action name="ResetWorkingPath">
|
||||||
<fs>
|
<fs>
|
||||||
<delete path='${workingPath}/output'/>
|
<delete path='${workingPath}/summaries/output'/>
|
||||||
<mkdir path='${workingPath}/output'/>
|
<mkdir path='${workingPath}/summaries/output'/>
|
||||||
</fs>
|
</fs>
|
||||||
<ok to="ImportOrcidSummary"/>
|
<ok to="check_exist_on_hdfs_summaries"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<decision name="check_exist_on_hdfs_summaries">
|
||||||
|
<switch>
|
||||||
|
<case to="ImportOrcidSummaries">
|
||||||
|
${fs:exists(concat(workingPath,'/ORCID_2019_summaries.tar.gz'))}
|
||||||
|
</case>
|
||||||
|
<default to="DownloadSummaries" />
|
||||||
|
</switch>
|
||||||
|
</decision>
|
||||||
|
|
||||||
|
<action name="DownloadSummaries">
|
||||||
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<exec>bash</exec>
|
||||||
|
<argument>-c</argument>
|
||||||
|
<argument>${shell_cmd_0}</argument>
|
||||||
|
<capture-output/>
|
||||||
|
</shell>
|
||||||
|
<ok to="ImportOrcidSummaries"/>
|
||||||
<error to="Kill"/>
|
<error to="Kill"/>
|
||||||
</action>
|
</action>
|
||||||
|
|
||||||
|
<action name="ImportOrcidSummaries">
|
||||||
|
|
||||||
<action name="ImportOrcidSummary">
|
|
||||||
<java>
|
<java>
|
||||||
<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>
|
||||||
<arg>-d</arg><arg>${workingPath}/</arg>
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
<arg>-n</arg><arg>${nameNode}</arg>
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
<arg>-f</arg><arg>ORCID_2019_summaries.tar.gz</arg>
|
<arg>-f</arg><arg>ORCID_2019_summaries.tar.gz</arg>
|
||||||
<arg>-o</arg><arg>output/</arg>
|
<arg>-o</arg><arg>summaries/output/</arg>
|
||||||
</java>
|
</java>
|
||||||
<ok to="End"/>
|
<ok to="End"/>
|
||||||
<error to="Kill"/>
|
<error to="Kill"/>
|
||||||
|
|
|
@ -0,0 +1,31 @@
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>oozie.action.sharelib.for.java</name>
|
||||||
|
<value>spark2</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.launcher.mapreduce.map.java.opts</name>
|
||||||
|
<value>-Xmx4g</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>jobTracker</name>
|
||||||
|
<value>yarnRM</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>nameNode</name>
|
||||||
|
<value>hdfs://nameservice1</value>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
<property>
|
||||||
|
<name>oozie.use.system.libpath</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.action.sharelib.for.spark</name>
|
||||||
|
<value>spark2</value>
|
||||||
|
</property>
|
||||||
|
</configuration>
|
|
@ -0,0 +1,514 @@
|
||||||
|
<workflow-app name="Import Orcid Activities" xmlns="uri:oozie:workflow:0.5">
|
||||||
|
<parameters>
|
||||||
|
<property>
|
||||||
|
<name>workingPath</name>
|
||||||
|
<description>the working dir base path</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shell_cmd_0</name>
|
||||||
|
<value>wget -O /tmp/ORCID_2019_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/18017660 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_0.tar.gz /data/orcid_activities/ORCID_2019_activites_0.tar.gz ; rm -f /tmp/ORCID_2019_activites_0.tar.gz
|
||||||
|
</value>
|
||||||
|
<description>the shell command that downloads and puts to hdfs orcid activity file 0</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shell_cmd_1</name>
|
||||||
|
<value>wget -O /tmp/ORCID_2019_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/18017675 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_1.tar.gz /data/orcid_activities/ORCID_2019_activites_1.tar.gz ; rm -f /tmp/ORCID_2019_activites_1.tar.gz
|
||||||
|
</value>
|
||||||
|
<description>the shell command that downloads and puts to hdfs orcid activity file 1</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shell_cmd_2</name>
|
||||||
|
<value>wget -O /tmp/ORCID_2019_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/18017717 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_2.tar.gz /data/orcid_activities/ORCID_2019_activites_2.tar.gz ; rm -f /tmp/ORCID_2019_activites_2.tar.gz
|
||||||
|
</value>
|
||||||
|
<description>the shell command that downloads and puts to hdfs orcid activity file 2</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shell_cmd_3</name>
|
||||||
|
<value>wget -O /tmp/ORCID_2019_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/18017765 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_3.tar.gz /data/orcid_activities/ORCID_2019_activites_3.tar.gz ; rm -f /tmp/ORCID_2019_activites_3.tar.gz
|
||||||
|
</value>
|
||||||
|
<description>the shell command that downloads and puts to hdfs orcid activity file 3</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shell_cmd_4</name>
|
||||||
|
<value>wget -O /tmp/ORCID_2019_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/18017831 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_4.tar.gz /data/orcid_activities/ORCID_2019_activites_4.tar.gz ; rm -f /tmp/ORCID_2019_activites_4.tar.gz
|
||||||
|
</value>
|
||||||
|
<description>the shell command that downloads and puts to hdfs orcid activity file 4</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shell_cmd_5</name>
|
||||||
|
<value>wget -O /tmp/ORCID_2019_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/18017987 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_5.tar.gz /data/orcid_activities/ORCID_2019_activites_5.tar.gz ; rm -f /tmp/ORCID_2019_activites_5.tar.gz
|
||||||
|
</value>
|
||||||
|
<description>the shell command that downloads and puts to hdfs orcid activity file 5</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shell_cmd_6</name>
|
||||||
|
<value>wget -O /tmp/ORCID_2019_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/18018053 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_6.tar.gz /data/orcid_activities/ORCID_2019_activites_6.tar.gz ; rm -f /tmp/ORCID_2019_activites_6.tar.gz
|
||||||
|
</value>
|
||||||
|
<description>the shell command that downloads and puts to hdfs orcid activity file 6</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shell_cmd_7</name>
|
||||||
|
<value>wget -O /tmp/ORCID_2019_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/18018023 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_7.tar.gz /data/orcid_activities/ORCID_2019_activites_7.tar.gz ; rm -f /tmp/ORCID_2019_activites_7.tar.gz
|
||||||
|
</value>
|
||||||
|
<description>the shell command that downloads and puts to hdfs orcid activity file 7</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shell_cmd_8</name>
|
||||||
|
<value>wget -O /tmp/ORCID_2019_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/18018248 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_8.tar.gz /data/orcid_activities/ORCID_2019_activites_8.tar.gz ; rm -f /tmp/ORCID_2019_activites_8.tar.gz
|
||||||
|
</value>
|
||||||
|
<description>the shell command that downloads and puts to hdfs orcid activity file 8</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shell_cmd_9</name>
|
||||||
|
<value>wget -O /tmp/ORCID_2019_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/18018029 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_9.tar.gz /data/orcid_activities/ORCID_2019_activites_9.tar.gz ; rm -f /tmp/ORCID_2019_activites_9.tar.gz
|
||||||
|
</value>
|
||||||
|
<description>the shell command that downloads and puts to hdfs orcid activity file 9</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shell_cmd_X</name>
|
||||||
|
<value>wget -O /tmp/ORCID_2019_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/18018182 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_X.tar.gz /data/orcid_activities/ORCID_2019_activites_X.tar.gz ; rm -f /tmp/ORCID_2019_activites_X.tar.gz
|
||||||
|
</value>
|
||||||
|
<description>the shell command that downloads and puts to hdfs orcid activity file X</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<start to="ResetWorkingPath"/>
|
||||||
|
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
<action name="ResetWorkingPath">
|
||||||
|
<fs>
|
||||||
|
<delete path='${workingPath}/no_doi_works/*'/>
|
||||||
|
</fs>
|
||||||
|
<ok to="fork_gen_orcid_author_work"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<fork name = "fork_gen_orcid_author_work">
|
||||||
|
<path start = "check_exist_on_hdfs_activities_0"/>
|
||||||
|
<path start = "check_exist_on_hdfs_activities_1"/>
|
||||||
|
<path start = "check_exist_on_hdfs_activities_2"/>
|
||||||
|
<path start = "check_exist_on_hdfs_activities_3"/>
|
||||||
|
<path start = "check_exist_on_hdfs_activities_4"/>
|
||||||
|
<path start = "check_exist_on_hdfs_activities_5"/>
|
||||||
|
<path start = "check_exist_on_hdfs_activities_6"/>
|
||||||
|
<path start = "check_exist_on_hdfs_activities_7"/>
|
||||||
|
<path start = "check_exist_on_hdfs_activities_8"/>
|
||||||
|
<path start = "check_exist_on_hdfs_activities_9"/>
|
||||||
|
<path start = "check_exist_on_hdfs_activities_X"/>
|
||||||
|
</fork>
|
||||||
|
|
||||||
|
<decision name="check_exist_on_hdfs_activities_0">
|
||||||
|
<switch>
|
||||||
|
<case to="GenOrcidAuthorWork_0">
|
||||||
|
${fs:exists(concat(workingPath,'/ORCID_2019_activites_0.tar.gz'))}
|
||||||
|
</case>
|
||||||
|
<default to="Download_0" />
|
||||||
|
</switch>
|
||||||
|
</decision>
|
||||||
|
|
||||||
|
<action name="Download_0">
|
||||||
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<exec>bash</exec>
|
||||||
|
<argument>-c</argument>
|
||||||
|
<argument>${shell_cmd_0}</argument>
|
||||||
|
<capture-output/>
|
||||||
|
</shell>
|
||||||
|
<ok to="GenOrcidAuthorWork_0"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="GenOrcidAuthorWork_0">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2019_activites_0.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>no_doi_works/works_0.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<decision name="check_exist_on_hdfs_activities_1">
|
||||||
|
<switch>
|
||||||
|
<case to="GenOrcidAuthorWork_1">
|
||||||
|
${fs:exists(concat(workingPath,'/ORCID_2019_activites_1.tar.gz'))}
|
||||||
|
</case>
|
||||||
|
<default to="Download_1" />
|
||||||
|
</switch>
|
||||||
|
</decision>
|
||||||
|
|
||||||
|
<action name="Download_1">
|
||||||
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<exec>bash</exec>
|
||||||
|
<argument>-c</argument>
|
||||||
|
<argument>${shell_cmd_1}</argument>
|
||||||
|
<capture-output/>
|
||||||
|
</shell>
|
||||||
|
<ok to="GenOrcidAuthorWork_1"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="GenOrcidAuthorWork_1">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2019_activites_1.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>no_doi_works/works_1.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<decision name="check_exist_on_hdfs_activities_2">
|
||||||
|
<switch>
|
||||||
|
<case to="GenOrcidAuthorWork_2">
|
||||||
|
${fs:exists(concat(workingPath,'/ORCID_2019_activites_2.tar.gz'))}
|
||||||
|
</case>
|
||||||
|
<default to="Download_2" />
|
||||||
|
</switch>
|
||||||
|
</decision>
|
||||||
|
|
||||||
|
<action name="Download_2">
|
||||||
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<exec>bash</exec>
|
||||||
|
<argument>-c</argument>
|
||||||
|
<argument>${shell_cmd_2}</argument>
|
||||||
|
<capture-output/>
|
||||||
|
</shell>
|
||||||
|
<ok to="GenOrcidAuthorWork_2"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="GenOrcidAuthorWork_2">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2019_activites_2.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>no_doi_works/works_2.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<decision name="check_exist_on_hdfs_activities_3">
|
||||||
|
<switch>
|
||||||
|
<case to="GenOrcidAuthorWork_3">
|
||||||
|
${fs:exists(concat(workingPath,'/ORCID_2019_activites_3.tar.gz'))}
|
||||||
|
</case>
|
||||||
|
<default to="Download_3" />
|
||||||
|
</switch>
|
||||||
|
</decision>
|
||||||
|
|
||||||
|
<action name="Download_3">
|
||||||
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<exec>bash</exec>
|
||||||
|
<argument>-c</argument>
|
||||||
|
<argument>${shell_cmd_3}</argument>
|
||||||
|
<capture-output/>
|
||||||
|
</shell>
|
||||||
|
<ok to="GenOrcidAuthorWork_3"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="GenOrcidAuthorWork_3">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2019_activites_3.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>no_doi_works/works_3.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<decision name="check_exist_on_hdfs_activities_4">
|
||||||
|
<switch>
|
||||||
|
<case to="GenOrcidAuthorWork_4">
|
||||||
|
${fs:exists(concat(workingPath,'/ORCID_2019_activites_4.tar.gz'))}
|
||||||
|
</case>
|
||||||
|
<default to="Download_4" />
|
||||||
|
</switch>
|
||||||
|
</decision>
|
||||||
|
|
||||||
|
<action name="Download_4">
|
||||||
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<exec>bash</exec>
|
||||||
|
<argument>-c</argument>
|
||||||
|
<argument>${shell_cmd_4}</argument>
|
||||||
|
<capture-output/>
|
||||||
|
</shell>
|
||||||
|
<ok to="GenOrcidAuthorWork_4"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="GenOrcidAuthorWork_4">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2019_activites_4.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>no_doi_works/works_4.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<decision name="check_exist_on_hdfs_activities_5">
|
||||||
|
<switch>
|
||||||
|
<case to="GenOrcidAuthorWork_5">
|
||||||
|
${fs:exists(concat(workingPath,'/ORCID_2019_activites_5.tar.gz'))}
|
||||||
|
</case>
|
||||||
|
<default to="Download_5" />
|
||||||
|
</switch>
|
||||||
|
</decision>
|
||||||
|
|
||||||
|
<action name="Download_5">
|
||||||
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<exec>bash</exec>
|
||||||
|
<argument>-c</argument>
|
||||||
|
<argument>${shell_cmd_5}</argument>
|
||||||
|
<capture-output/>
|
||||||
|
</shell>
|
||||||
|
<ok to="GenOrcidAuthorWork_5"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="GenOrcidAuthorWork_5">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2019_activites_5.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>no_doi_works/works_5.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<decision name="check_exist_on_hdfs_activities_6">
|
||||||
|
<switch>
|
||||||
|
<case to="GenOrcidAuthorWork_6">
|
||||||
|
${fs:exists(concat(workingPath,'/ORCID_2019_activites_6.tar.gz'))}
|
||||||
|
</case>
|
||||||
|
<default to="Download_6" />
|
||||||
|
</switch>
|
||||||
|
</decision>
|
||||||
|
|
||||||
|
<action name="Download_6">
|
||||||
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<exec>bash</exec>
|
||||||
|
<argument>-c</argument>
|
||||||
|
<argument>${shell_cmd_6}</argument>
|
||||||
|
<capture-output/>
|
||||||
|
</shell>
|
||||||
|
<ok to="GenOrcidAuthorWork_6"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="GenOrcidAuthorWork_6">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2019_activites_6.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>no_doi_works/works_6.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<decision name="check_exist_on_hdfs_activities_7">
|
||||||
|
<switch>
|
||||||
|
<case to="GenOrcidAuthorWork_7">
|
||||||
|
${fs:exists(concat(workingPath,'/ORCID_2019_activites_7.tar.gz'))}
|
||||||
|
</case>
|
||||||
|
<default to="Download_7" />
|
||||||
|
</switch>
|
||||||
|
</decision>
|
||||||
|
|
||||||
|
<action name="Download_7">
|
||||||
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<exec>bash</exec>
|
||||||
|
<argument>-c</argument>
|
||||||
|
<argument>${shell_cmd_7}</argument>
|
||||||
|
<capture-output/>
|
||||||
|
</shell>
|
||||||
|
<ok to="GenOrcidAuthorWork_7"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="GenOrcidAuthorWork_7">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2019_activites_7.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>no_doi_works/works_7.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<decision name="check_exist_on_hdfs_activities_8">
|
||||||
|
<switch>
|
||||||
|
<case to="GenOrcidAuthorWork_8">
|
||||||
|
${fs:exists(concat(workingPath,'/ORCID_2019_activites_8.tar.gz'))}
|
||||||
|
</case>
|
||||||
|
<default to="Download_8" />
|
||||||
|
</switch>
|
||||||
|
</decision>
|
||||||
|
|
||||||
|
<action name="Download_8">
|
||||||
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<exec>bash</exec>
|
||||||
|
<argument>-c</argument>
|
||||||
|
<argument>${shell_cmd_8}</argument>
|
||||||
|
<capture-output/>
|
||||||
|
</shell>
|
||||||
|
<ok to="GenOrcidAuthorWork_8"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="GenOrcidAuthorWork_8">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2019_activites_8.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>no_doi_works/works_8.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<decision name="check_exist_on_hdfs_activities_9">
|
||||||
|
<switch>
|
||||||
|
<case to="GenOrcidAuthorWork_9">
|
||||||
|
${fs:exists(concat(workingPath,'/ORCID_2019_activites_9.tar.gz'))}
|
||||||
|
</case>
|
||||||
|
<default to="Download_9" />
|
||||||
|
</switch>
|
||||||
|
</decision>
|
||||||
|
|
||||||
|
<action name="Download_9">
|
||||||
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<exec>bash</exec>
|
||||||
|
<argument>-c</argument>
|
||||||
|
<argument>${shell_cmd_9}</argument>
|
||||||
|
<capture-output/>
|
||||||
|
</shell>
|
||||||
|
<ok to="GenOrcidAuthorWork_9"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="GenOrcidAuthorWork_9">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2019_activites_9.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>no_doi_works/works_9.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<decision name="check_exist_on_hdfs_activities_X">
|
||||||
|
<switch>
|
||||||
|
<case to="GenOrcidAuthorWork_X">
|
||||||
|
${fs:exists(concat(workingPath,'/ORCID_2019_activites_X.tar.gz'))}
|
||||||
|
</case>
|
||||||
|
<default to="Download_X" />
|
||||||
|
</switch>
|
||||||
|
</decision>
|
||||||
|
|
||||||
|
<action name="Download_X">
|
||||||
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<exec>bash</exec>
|
||||||
|
<argument>-c</argument>
|
||||||
|
<argument>${shell_cmd_X}</argument>
|
||||||
|
<capture-output/>
|
||||||
|
</shell>
|
||||||
|
<ok to="GenOrcidAuthorWork_X"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="GenOrcidAuthorWork_X">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2019_activites_X.tar.gz</arg>
|
||||||
|
<arg>-ow</arg><arg>no_doi_works/works_X.seq</arg>
|
||||||
|
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_node"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<join name = "join_node" to = "End"/>
|
||||||
|
|
||||||
|
<end name="End"/>
|
||||||
|
</workflow-app>
|
|
@ -0,0 +1,22 @@
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>jobTracker</name>
|
||||||
|
<value>yarnRM</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>nameNode</name>
|
||||||
|
<value>hdfs://nameservice1</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.use.system.libpath</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.action.sharelib.for.spark</name>
|
||||||
|
<value>spark2</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
</configuration>
|
|
@ -0,0 +1,68 @@
|
||||||
|
<workflow-app name="Import Orcid Summaries" xmlns="uri:oozie:workflow:0.5">
|
||||||
|
<parameters>
|
||||||
|
<property>
|
||||||
|
<name>workingPath</name>
|
||||||
|
<description>the working dir base path</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>shell_cmd_0</name>
|
||||||
|
<value>wget -O /tmp/ORCID_2019_summaries.tar.gz https://orcid.figshare.com/ndownloader/files/18017633 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_summaries.tar.gz /data/orcid_activities/ORCID_2019_summaries.tar.gz ; rm -f /tmp/ORCID_2019_summaries.tar.gz
|
||||||
|
</value>
|
||||||
|
<description>the shell command that downloads and puts to hdfs orcid summaries</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<start to="ResetWorkingPath"/>
|
||||||
|
|
||||||
|
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
<action name="ResetWorkingPath">
|
||||||
|
<fs>
|
||||||
|
<delete path='${workingPath}/summaries/output'/>
|
||||||
|
<mkdir path='${workingPath}/summaries/output'/>
|
||||||
|
</fs>
|
||||||
|
<ok to="check_exist_on_hdfs_summaries"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<decision name="check_exist_on_hdfs_summaries">
|
||||||
|
<switch>
|
||||||
|
<case to="ImportOrcidSummaries">
|
||||||
|
${fs:exists(concat(workingPath,'/ORCID_2019_summaries.tar.gz'))}
|
||||||
|
</case>
|
||||||
|
<default to="DownloadSummaries" />
|
||||||
|
</switch>
|
||||||
|
</decision>
|
||||||
|
|
||||||
|
<action name="DownloadSummaries">
|
||||||
|
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<exec>bash</exec>
|
||||||
|
<argument>-c</argument>
|
||||||
|
<argument>${shell_cmd_0}</argument>
|
||||||
|
<capture-output/>
|
||||||
|
</shell>
|
||||||
|
<ok to="ImportOrcidSummaries"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="ImportOrcidSummaries">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.doiboost.orcid.OrcidDSManager</main-class>
|
||||||
|
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-f</arg><arg>ORCID_2019_summaries.tar.gz</arg>
|
||||||
|
<arg>-o</arg><arg>summaries/output/</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="End"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<end name="End"/>
|
||||||
|
</workflow-app>
|
|
@ -3,9 +3,8 @@ package eu.dnetlib.doiboost.orcid;
|
||||||
|
|
||||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||||
|
|
||||||
import java.io.BufferedReader;
|
import java.io.*;
|
||||||
import java.io.IOException;
|
import java.nio.file.Files;
|
||||||
import java.io.InputStreamReader;
|
|
||||||
import java.text.ParseException;
|
import java.text.ParseException;
|
||||||
import java.text.SimpleDateFormat;
|
import java.text.SimpleDateFormat;
|
||||||
import java.util.Arrays;
|
import java.util.Arrays;
|
||||||
|
@ -20,6 +19,7 @@ import org.apache.http.impl.client.HttpClients;
|
||||||
import org.junit.jupiter.api.Test;
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import jdk.nashorn.internal.ir.annotations.Ignore;
|
||||||
|
|
||||||
public class OrcidClientTest {
|
public class OrcidClientTest {
|
||||||
final String orcidId = "0000-0001-7291-3210";
|
final String orcidId = "0000-0001-7291-3210";
|
||||||
|
@ -32,11 +32,20 @@ public class OrcidClientTest {
|
||||||
String lastUpdate = "2019-09-30 00:00:00";
|
String lastUpdate = "2019-09-30 00:00:00";
|
||||||
String shortDate = "2020-05-06 16:06:11";
|
String shortDate = "2020-05-06 16:06:11";
|
||||||
|
|
||||||
// curl -i -H "Accept: application/vnd.orcid+xml"
|
// curl -i -H "Accept: application/vnd.orcid+xml"
|
||||||
// -H 'Authorization: Bearer 78fdb232-7105-4086-8570-e153f4198e3d'
|
// -H 'Authorization: Bearer 78fdb232-7105-4086-8570-e153f4198e3d'
|
||||||
// 'https://api.orcid.org/v3.0/0000-0001-7291-3210/record'
|
// 'https://api.orcid.org/v3.0/0000-0001-7291-3210/record'
|
||||||
|
|
||||||
public String testDownloadRecord(String orcidId) throws Exception {
|
@Test
|
||||||
|
public void downloadTest() throws Exception {
|
||||||
|
String record = testDownloadRecord("0000-0002-2536-4498");
|
||||||
|
File f = new File("/tmp/downloaded_0000-0002-2536-4498.xml");
|
||||||
|
OutputStream outStream = new FileOutputStream(f);
|
||||||
|
IOUtils.write(record.getBytes(), outStream);
|
||||||
|
System.out.println("saved to tmp");
|
||||||
|
}
|
||||||
|
|
||||||
|
private String testDownloadRecord(String orcidId) throws Exception {
|
||||||
try (CloseableHttpClient client = HttpClients.createDefault()) {
|
try (CloseableHttpClient client = HttpClients.createDefault()) {
|
||||||
HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record");
|
HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record");
|
||||||
httpGet.addHeader("Accept", "application/vnd.orcid+xml");
|
httpGet.addHeader("Accept", "application/vnd.orcid+xml");
|
||||||
|
@ -100,7 +109,7 @@ public class OrcidClientTest {
|
||||||
}
|
}
|
||||||
|
|
||||||
// @Test
|
// @Test
|
||||||
public void getRecordDatestamp() throws ParseException {
|
private void getRecordDatestamp() throws ParseException {
|
||||||
Date toRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toRetrieveDate);
|
Date toRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toRetrieveDate);
|
||||||
Date toNotRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toNotRetrieveDate);
|
Date toNotRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toNotRetrieveDate);
|
||||||
Date lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate);
|
Date lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate);
|
||||||
|
@ -108,7 +117,7 @@ public class OrcidClientTest {
|
||||||
assertTrue(!toNotRetrieveDateDt.after(lastUpdateDt));
|
assertTrue(!toNotRetrieveDateDt.after(lastUpdateDt));
|
||||||
}
|
}
|
||||||
|
|
||||||
public void testDate(String value) throws ParseException {
|
private void testDate(String value) throws ParseException {
|
||||||
System.out.println(value.toString());
|
System.out.println(value.toString());
|
||||||
if (value.length() != 19) {
|
if (value.length() != 19) {
|
||||||
value = value.substring(0, 19);
|
value = value.substring(0, 19);
|
||||||
|
@ -118,14 +127,16 @@ public class OrcidClientTest {
|
||||||
}
|
}
|
||||||
|
|
||||||
// @Test
|
// @Test
|
||||||
public void testModifiedDate() throws ParseException {
|
@Ignore
|
||||||
|
private void testModifiedDate() throws ParseException {
|
||||||
testDate(toRetrieveDate);
|
testDate(toRetrieveDate);
|
||||||
testDate(toNotRetrieveDate);
|
testDate(toNotRetrieveDate);
|
||||||
testDate(shortDate);
|
testDate(shortDate);
|
||||||
}
|
}
|
||||||
|
|
||||||
// @Test
|
// @Test
|
||||||
public void testReadBase64CompressedRecord() throws Exception {
|
@Ignore
|
||||||
|
private void testReadBase64CompressedRecord() throws Exception {
|
||||||
final String base64CompressedRecord = IOUtils
|
final String base64CompressedRecord = IOUtils
|
||||||
.toString(getClass().getResourceAsStream("0000-0001-6645-509X.compressed.base64"));
|
.toString(getClass().getResourceAsStream("0000-0001-6645-509X.compressed.base64"));
|
||||||
final String recordFromSeqFile = ArgumentApplicationParser.decompressValue(base64CompressedRecord);
|
final String recordFromSeqFile = ArgumentApplicationParser.decompressValue(base64CompressedRecord);
|
||||||
|
|
|
@ -13,14 +13,15 @@ import com.google.gson.JsonParser;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf;
|
import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf;
|
||||||
|
import jdk.nashorn.internal.ir.annotations.Ignore;
|
||||||
|
|
||||||
public class PublicationToOafTest {
|
public class PublicationToOafTest {
|
||||||
|
|
||||||
private static final Logger logger = LoggerFactory.getLogger(PublicationToOafTest.class);
|
private static final Logger logger = LoggerFactory.getLogger(PublicationToOafTest.class);
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
// @Ignore
|
@Ignore
|
||||||
public void convertOafPublicationTest() throws Exception {
|
private void convertOafPublicationTest() throws Exception {
|
||||||
String jsonPublication = IOUtils
|
String jsonPublication = IOUtils
|
||||||
.toString(
|
.toString(
|
||||||
PublicationToOafTest.class.getResourceAsStream("publication.json"));
|
PublicationToOafTest.class.getResourceAsStream("publication.json"));
|
||||||
|
|
|
@ -42,12 +42,12 @@ public class OrcidNoDoiTest {
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
@Ignore
|
@Ignore
|
||||||
private void readPublicationFieldsTest()
|
public void readPublicationFieldsTest()
|
||||||
throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException {
|
throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException {
|
||||||
logger.info("running loadPublicationFieldsTest ....");
|
logger.info("running loadPublicationFieldsTest ....");
|
||||||
String xml = IOUtils
|
String xml = IOUtils
|
||||||
.toString(
|
.toString(
|
||||||
OrcidNoDoiTest.class.getResourceAsStream("activity_work_0000-0003-2760-1191.xml"));
|
OrcidNoDoiTest.class.getResourceAsStream("activity_work_0000-0002-2536-4498.xml"));
|
||||||
|
|
||||||
if (xml == null) {
|
if (xml == null) {
|
||||||
logger.info("Resource not found");
|
logger.info("Resource not found");
|
||||||
|
|
|
@ -0,0 +1,72 @@
|
||||||
|
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
|
||||||
|
<work:work xmlns:address="http://www.orcid.org/ns/address"
|
||||||
|
xmlns:email="http://www.orcid.org/ns/email" xmlns:history="http://www.orcid.org/ns/history"
|
||||||
|
xmlns:employment="http://www.orcid.org/ns/employment"
|
||||||
|
xmlns:education="http://www.orcid.org/ns/education"
|
||||||
|
xmlns:other-name="http://www.orcid.org/ns/other-name"
|
||||||
|
xmlns:deprecated="http://www.orcid.org/ns/deprecated"
|
||||||
|
xmlns:funding="http://www.orcid.org/ns/funding"
|
||||||
|
xmlns:research-resource="http://www.orcid.org/ns/research-resource"
|
||||||
|
xmlns:service="http://www.orcid.org/ns/service"
|
||||||
|
xmlns:researcher-url="http://www.orcid.org/ns/researcher-url"
|
||||||
|
xmlns:distinction="http://www.orcid.org/ns/distinction"
|
||||||
|
xmlns:internal="http://www.orcid.org/ns/internal"
|
||||||
|
xmlns:membership="http://www.orcid.org/ns/membership"
|
||||||
|
xmlns:person="http://www.orcid.org/ns/person"
|
||||||
|
xmlns:personal-details="http://www.orcid.org/ns/personal-details"
|
||||||
|
xmlns:bulk="http://www.orcid.org/ns/bulk" xmlns:common="http://www.orcid.org/ns/common"
|
||||||
|
xmlns:record="http://www.orcid.org/ns/record" xmlns:keyword="http://www.orcid.org/ns/keyword"
|
||||||
|
xmlns:activities="http://www.orcid.org/ns/activities"
|
||||||
|
xmlns:qualification="http://www.orcid.org/ns/qualification"
|
||||||
|
xmlns:external-identifier="http://www.orcid.org/ns/external-identifier"
|
||||||
|
xmlns:error="http://www.orcid.org/ns/error"
|
||||||
|
xmlns:preferences="http://www.orcid.org/ns/preferences"
|
||||||
|
xmlns:invited-position="http://www.orcid.org/ns/invited-position"
|
||||||
|
xmlns:work="http://www.orcid.org/ns/work"
|
||||||
|
xmlns:peer-review="http://www.orcid.org/ns/peer-review" put-code="63461376"
|
||||||
|
path="/0000-0002-2536-4498/work/63461376" visibility="public">
|
||||||
|
<common:created-date>2019-10-22T03:18:13.755Z</common:created-date>
|
||||||
|
<common:last-modified-date>2020-06-17T11:07:13.703Z</common:last-modified-date>
|
||||||
|
<common:source>
|
||||||
|
<common:source-client-id>
|
||||||
|
<common:uri>https://orcid.org/client/0000-0001-8607-8906</common:uri>
|
||||||
|
<common:path>0000-0001-8607-8906</common:path>
|
||||||
|
<common:host>orcid.org</common:host>
|
||||||
|
</common:source-client-id>
|
||||||
|
<common:source-name>INSPIRE-HEP</common:source-name>
|
||||||
|
</common:source>
|
||||||
|
<work:title>
|
||||||
|
<common:title>Measurement of the $t\bar{t}$ production cross-section and lepton differential distributions in $e\mu$ dilepton events from $pp$ collisions at $\sqrt{s}=13$ TeV with the ATLAS detector</common:title>
|
||||||
|
</work:title>
|
||||||
|
<common:external-ids>
|
||||||
|
<common:external-id>
|
||||||
|
<common:external-id-type>other-id</common:external-id-type>
|
||||||
|
<common:external-id-value>1759875</common:external-id-value>
|
||||||
|
<common:external-id-normalized transient="true">1759875</common:external-id-normalized>
|
||||||
|
<common:external-id-url>http://inspirehep.net/record/1759875</common:external-id-url>
|
||||||
|
<common:external-id-relationship>self</common:external-id-relationship>
|
||||||
|
</common:external-id>
|
||||||
|
<common:external-id>
|
||||||
|
<common:external-id-type>doi</common:external-id-type>
|
||||||
|
<common:external-id-value>10.1140/epjc/s10052-020-7907-9</common:external-id-value>
|
||||||
|
<common:external-id-normalized transient="true">10.1140/epjc/s10052-020-7907-9</common:external-id-normalized>
|
||||||
|
<common:external-id-url>http://dx.doi.org/10.1140/epjc/s10052-020-7907-9</common:external-id-url>
|
||||||
|
<common:external-id-relationship>self</common:external-id-relationship>
|
||||||
|
</common:external-id>
|
||||||
|
<common:external-id>
|
||||||
|
<common:external-id-type>arxiv</common:external-id-type>
|
||||||
|
<common:external-id-value>1910.08819</common:external-id-value>
|
||||||
|
<common:external-id-normalized transient="true">arXiv:1910.08819</common:external-id-normalized>
|
||||||
|
<common:external-id-url>http://arxiv.org/abs/1910.08819</common:external-id-url>
|
||||||
|
<common:external-id-relationship>self</common:external-id-relationship>
|
||||||
|
</common:external-id>
|
||||||
|
</common:external-ids>
|
||||||
|
<common:url>http://inspirehep.net/record/1759875</common:url>
|
||||||
|
<work:type>journal-article</work:type>
|
||||||
|
<common:publication-date>
|
||||||
|
<common:year>2020</common:year>
|
||||||
|
<common:month>06</common:month>
|
||||||
|
<common:day>12</common:day>
|
||||||
|
</common:publication-date>
|
||||||
|
<work:journal-title>Eur.Phys.J.C</work:journal-title>
|
||||||
|
</work:work>
|
Loading…
Reference in New Issue