forked from D-Net/dnet-hadoop
added workflow to migrate latest version of each actionset content from DM to OCEAN cluster, mapping the targetValues from the old protobuf data model to the dhp.OAF datamodel
This commit is contained in:
parent
8fe7ae1482
commit
9c84e21b87
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@ -24,6 +24,12 @@
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<groupId>eu.dnetlib.dhp</groupId>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-common</artifactId>
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<artifactId>dhp-common</artifactId>
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<version>${project.version}</version>
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<version>${project.version}</version>
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<exclusions>
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<exclusion>
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<groupId>com.sun.xml.bind</groupId>
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<artifactId>jaxb-core</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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</dependency>
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<dependency>
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<dependency>
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@ -32,6 +38,49 @@
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<version>${project.version}</version>
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<version>${project.version}</version>
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</dependency>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib</groupId>
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<artifactId>dnet-actionmanager-common</artifactId>
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<exclusions>
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<exclusion>
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<groupId>eu.dnetlib</groupId>
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<artifactId>dnet-openaireplus-mapping-utils</artifactId>
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</exclusion>
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<exclusion>
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<groupId>saxonica</groupId>
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<artifactId>saxon</artifactId>
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</exclusion>
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<exclusion>
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<groupId>saxonica</groupId>
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<artifactId>saxon-dom</artifactId>
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</exclusion>
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<exclusion>
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<groupId>jgrapht</groupId>
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<artifactId>jgrapht</artifactId>
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</exclusion>
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<exclusion>
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<groupId>net.sf.ehcache</groupId>
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<artifactId>ehcache</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.springframework</groupId>
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<artifactId>spring-test</artifactId>
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</exclusion>
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<exclusion>
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<groupId>org.apache.*</groupId>
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<artifactId>*</artifactId>
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</exclusion>
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<exclusion>
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<groupId>apache</groupId>
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<artifactId>*</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib</groupId>
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<artifactId>dnet-openaire-data-protos</artifactId>
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</dependency>
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<dependency>
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<dependency>
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<groupId>net.sf.saxon</groupId>
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<groupId>net.sf.saxon</groupId>
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<artifactId>Saxon-HE</artifactId>
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<artifactId>Saxon-HE</artifactId>
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@ -56,6 +105,11 @@
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<artifactId>mongo-java-driver</artifactId>
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<artifactId>mongo-java-driver</artifactId>
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</dependency>
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</dependency>
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<dependency>
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<groupId>org.apache.hadoop</groupId>
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<artifactId>hadoop-distcp</artifactId>
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</dependency>
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<dependency>
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<dependency>
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<groupId>org.postgresql</groupId>
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<groupId>org.postgresql</groupId>
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<artifactId>postgresql</artifactId>
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<artifactId>postgresql</artifactId>
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@ -0,0 +1,49 @@
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package eu.dnetlib.dhp.migration.actions;
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import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
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import java.util.Comparator;
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public class LicenseComparator implements Comparator<Qualifier> {
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@Override
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public int compare(Qualifier left, Qualifier right) {
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if (left == null && right == null) return 0;
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if (left == null) return 1;
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if (right == null) return -1;
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String lClass = left.getClassid();
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String rClass = right.getClassid();
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if (lClass.equals(rClass)) return 0;
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if (lClass.equals("OPEN SOURCE")) return -1;
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if (rClass.equals("OPEN SOURCE")) return 1;
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if (lClass.equals("OPEN")) return -1;
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if (rClass.equals("OPEN")) return 1;
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if (lClass.equals("6MONTHS")) return -1;
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if (rClass.equals("6MONTHS")) return 1;
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if (lClass.equals("12MONTHS")) return -1;
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if (rClass.equals("12MONTHS")) return 1;
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if (lClass.equals("EMBARGO")) return -1;
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if (rClass.equals("EMBARGO")) return 1;
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if (lClass.equals("RESTRICTED")) return -1;
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if (rClass.equals("RESTRICTED")) return 1;
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if (lClass.equals("CLOSED")) return -1;
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if (rClass.equals("CLOSED")) return 1;
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if (lClass.equals("UNKNOWN")) return -1;
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if (rClass.equals("UNKNOWN")) return 1;
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// Else (but unlikely), lexicographical ordering will do.
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return lClass.compareTo(rClass);
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}
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}
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@ -0,0 +1,170 @@
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package eu.dnetlib.dhp.migration.actions;
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import com.google.common.base.Splitter;
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import com.google.common.collect.Lists;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.hadoop.tools.DistCp;
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import org.apache.hadoop.tools.DistCpOptions;
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import org.apache.hadoop.util.ToolRunner;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.OutputStream;
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import java.util.*;
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import java.util.stream.Collectors;
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public class MigrateActionSet {
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private static final Log log = LogFactory.getLog(MigrateActionSet.class);
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private static final String SEPARATOR = "/";
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private static final String TARGET_PATHS = "target_paths";
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private static final String RAWSET_PREFIX = "rawset_";
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private static Boolean DEFAULT_TRANSFORM_ONLY = false;
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils.toString(MigrateActionSet.class.getResourceAsStream(
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"/eu/dnetlib/dhp/migration/migrate_actionsets_parameters.json")));
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parser.parseArgument(args);
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new MigrateActionSet().run(parser);
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}
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private void run(ArgumentApplicationParser parser) throws Exception {
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final String isLookupUrl = parser.get("isLookupUrl");
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final String sourceNN = parser.get("sourceNameNode");
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final String targetNN = parser.get("targetNameNode");
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final String workDir = parser.get("workingDirectory");
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final Integer distcp_num_maps = Integer.parseInt(parser.get("distcp_num_maps"));
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final String distcp_memory_mb = parser.get("distcp_memory_mb");
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final String distcp_task_timeout = parser.get("distcp_task_timeout");
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final String transform_only_s = parser.get("transform_only");
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log.info("transform only param: " + transform_only_s);
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final Boolean transformOnly = Boolean.valueOf(parser.get("transform_only"));
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log.info("transform only: " + transformOnly);
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ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
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Configuration conf = getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps);
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FileSystem targetFS = FileSystem.get(conf);
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Configuration sourceConf = getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps);
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sourceConf.set(FileSystem.FS_DEFAULT_NAME_KEY, sourceNN);
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FileSystem sourceFS = FileSystem.get(sourceConf);
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Properties props = new Properties();
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List<Path> targetPaths = new ArrayList<>();
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final List<Path> sourcePaths = getSourcePaths(sourceNN, isLookUp);
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log.info(String.format("paths to process:\n%s", sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n"))));
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for(Path source : sourcePaths) {
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if (!sourceFS.exists(source)) {
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log.warn(String.format("skipping unexisting path: %s", source));
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} else {
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LinkedList<String> pathQ = Lists.newLinkedList(Splitter.on(SEPARATOR).split(source.toUri().getPath()));
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final String rawSet = pathQ.pollLast();
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log.info(String.format("got RAWSET: %s", rawSet));
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if (StringUtils.isNotBlank(rawSet) && rawSet.startsWith(RAWSET_PREFIX)) {
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final String actionSetDirectory = pathQ.pollLast();
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final Path targetPath = new Path(targetNN + workDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawSet);
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log.info(String.format("using TARGET PATH: %s", targetPath));
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if (!transformOnly) {
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if (targetFS.exists(targetPath)) {
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targetFS.delete(targetPath, true);
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}
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runDistcp(distcp_num_maps, distcp_memory_mb, distcp_task_timeout, conf, source, targetPath);
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}
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targetPaths.add(targetPath);
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}
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}
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}
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props.setProperty(TARGET_PATHS, targetPaths
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.stream()
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.map(p -> p.toString())
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.collect(Collectors.joining(",")));
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File file = new File(System.getProperty("oozie.action.output.properties"));
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try(OutputStream os = new FileOutputStream(file)) {
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props.store(os, "");
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}
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System.out.println(file.getAbsolutePath());
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}
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private void runDistcp(Integer distcp_num_maps, String distcp_memory_mb, String distcp_task_timeout, Configuration conf, Path source, Path targetPath) throws Exception {
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final DistCpOptions op = new DistCpOptions(source, targetPath);
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op.setMaxMaps(distcp_num_maps);
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op.preserve(DistCpOptions.FileAttribute.BLOCKSIZE);
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op.preserve(DistCpOptions.FileAttribute.REPLICATION);
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op.preserve(DistCpOptions.FileAttribute.CHECKSUMTYPE);
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int res = ToolRunner.run(new DistCp(conf, op), new String[]{
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"-Dmapred.task.timeout=" + distcp_task_timeout,
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"-Dmapreduce.map.memory.mb=" + distcp_memory_mb,
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"-pb",
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"-m " + distcp_num_maps,
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source.toString(),
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targetPath.toString()});
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if (res != 0) {
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throw new RuntimeException(String.format("distcp exited with code %s", res));
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}
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}
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private Configuration getConfiguration(String distcp_task_timeout, String distcp_memory_mb, Integer distcp_num_maps) {
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final Configuration conf = new Configuration();
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conf.set("dfs.webhdfs.socket.connect-timeout", distcp_task_timeout);
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conf.set("dfs.webhdfs.socket.read-timeout", distcp_task_timeout);
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conf.set("dfs.http.client.retry.policy.enabled", "true");
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conf.set("mapred.task.timeout", distcp_task_timeout);
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conf.set("mapreduce.map.memory.mb", distcp_memory_mb);
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conf.set("mapred.map.tasks", String.valueOf(distcp_num_maps));
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return conf;
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}
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private List<Path> getSourcePaths(String sourceNN, ISLookUpService isLookUp) throws ISLookUpException {
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String XQUERY = "distinct-values(\n" +
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"let $basePath := collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()\n" +
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"for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') \n" +
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"let $setDir := $x//SET/@directory/string()\n" +
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"let $rawSet := $x//RAW_SETS/LATEST/@id/string()\n" +
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"return concat($basePath, '/', $setDir, '/', $rawSet))";
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log.info(String.format("running xquery:\n%s", XQUERY));
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return isLookUp.quickSearchProfile(XQUERY)
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.stream()
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.map(p -> sourceNN + p)
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.map(Path::new)
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.collect(Collectors.toList());
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}
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}
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@ -0,0 +1,580 @@
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package eu.dnetlib.dhp.migration.actions;
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import com.google.common.collect.Lists;
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import com.googlecode.protobuf.format.JsonFormat;
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import eu.dnetlib.data.proto.*;
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import eu.dnetlib.dhp.schema.oaf.*;
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import org.apache.commons.lang3.StringUtils;
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import java.io.Serializable;
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import java.util.List;
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import java.util.Optional;
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import java.util.stream.Collectors;
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public class ProtoConverter implements Serializable {
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public static final String UNKNOWN = "UNKNOWN";
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public static final String NOT_AVAILABLE = "not available";
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public static final String DNET_ACCESS_MODES = "dnet:access_modes";
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public static Oaf convert(OafProtos.Oaf oaf) {
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try {
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switch (oaf.getKind()) {
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case entity:
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return convertEntity(oaf);
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case relation:
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return convertRelation(oaf);
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default:
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throw new IllegalArgumentException("invalid kind " + oaf.getKind());
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}
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} catch (Throwable e) {
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throw new RuntimeException("error on getting " + JsonFormat.printToString(oaf), e);
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}
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}
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private static Relation convertRelation(OafProtos.Oaf oaf) {
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final OafProtos.OafRel r = oaf.getRel();
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final Relation rel = new Relation();
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rel.setDataInfo(mapDataInfo(oaf.getDataInfo()));
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rel.setLastupdatetimestamp(oaf.getLastupdatetimestamp());
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rel.setSource(r.getSource());
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rel.setTarget(r.getTarget());
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rel.setRelType(r.getRelType().toString());
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rel.setSubRelType(r.getSubRelType().toString());
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rel.setRelClass(r.getRelClass());
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rel.setCollectedFrom(r.getCollectedfromCount() > 0 ?
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r.getCollectedfromList().stream()
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.map(kv -> mapKV(kv))
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.collect(Collectors.toList()) : null);
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return rel;
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}
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private static OafEntity convertEntity(OafProtos.Oaf oaf) {
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switch (oaf.getEntity().getType()) {
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case result:
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final Result r = convertResult(oaf);
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r.setInstance(convertInstances(oaf));
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return r;
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case project:
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return convertProject(oaf);
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case datasource:
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return convertDataSource(oaf);
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case organization:
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return convertOrganization(oaf);
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default:
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throw new RuntimeException("received unknown type");
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}
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}
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|
||||||
|
private static List<Instance> convertInstances(OafProtos.Oaf oaf) {
|
||||||
|
|
||||||
|
final ResultProtos.Result r = oaf.getEntity().getResult();
|
||||||
|
if (r.getInstanceCount() > 0) {
|
||||||
|
return r.getInstanceList()
|
||||||
|
.stream()
|
||||||
|
.map(i -> convertInstance(i))
|
||||||
|
.collect(Collectors.toList());
|
||||||
|
}
|
||||||
|
return Lists.newArrayList();
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Instance convertInstance(ResultProtos.Result.Instance ri) {
|
||||||
|
final Instance i = new Instance();
|
||||||
|
i.setAccessright(mapQualifier(ri.getAccessright()));
|
||||||
|
i.setCollectedfrom(mapKV(ri.getCollectedfrom()));
|
||||||
|
i.setDateofacceptance(mapStringField(ri.getDateofacceptance()));
|
||||||
|
i.setDistributionlocation(ri.getDistributionlocation());
|
||||||
|
i.setHostedby(mapKV(ri.getHostedby()));
|
||||||
|
i.setInstancetype(mapQualifier(ri.getInstancetype()));
|
||||||
|
i.setLicense(mapStringField(ri.getLicense()));
|
||||||
|
i.setUrl(ri.getUrlList());
|
||||||
|
i.setRefereed(mapStringField(ri.getRefereed()));
|
||||||
|
i.setProcessingchargeamount(mapStringField(ri.getProcessingchargeamount()));
|
||||||
|
i.setProcessingchargecurrency(mapStringField(ri.getProcessingchargecurrency()));
|
||||||
|
return i;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Organization convertOrganization(OafProtos.Oaf oaf) {
|
||||||
|
final OrganizationProtos.Organization.Metadata m = oaf.getEntity().getOrganization().getMetadata();
|
||||||
|
final Organization org = setOaf(new Organization(), oaf);
|
||||||
|
setEntity(org, oaf);
|
||||||
|
org.setLegalshortname(mapStringField(m.getLegalshortname()));
|
||||||
|
org.setLegalname(mapStringField(m.getLegalname()));
|
||||||
|
org.setAlternativeNames(m.getAlternativeNamesList().
|
||||||
|
stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
org.setWebsiteurl(mapStringField(m.getWebsiteurl()));
|
||||||
|
org.setLogourl(mapStringField(m.getLogourl()));
|
||||||
|
org.setEclegalbody(mapStringField(m.getEclegalbody()));
|
||||||
|
org.setEclegalperson(mapStringField(m.getEclegalperson()));
|
||||||
|
org.setEcnonprofit(mapStringField(m.getEcnonprofit()));
|
||||||
|
org.setEcresearchorganization(mapStringField(m.getEcresearchorganization()));
|
||||||
|
org.setEchighereducation(mapStringField(m.getEchighereducation()));
|
||||||
|
org.setEcinternationalorganizationeurinterests(mapStringField(m.getEcinternationalorganizationeurinterests()));
|
||||||
|
org.setEcinternationalorganization(mapStringField(m.getEcinternationalorganization()));
|
||||||
|
org.setEcenterprise(mapStringField(m.getEcenterprise()));
|
||||||
|
org.setEcsmevalidated(mapStringField(m.getEcsmevalidated()));
|
||||||
|
org.setEcnutscode(mapStringField(m.getEcnutscode()));
|
||||||
|
org.setCountry(mapQualifier(m.getCountry()));
|
||||||
|
|
||||||
|
return org;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Datasource convertDataSource(OafProtos.Oaf oaf) {
|
||||||
|
final DatasourceProtos.Datasource.Metadata m = oaf.getEntity().getDatasource().getMetadata();
|
||||||
|
final Datasource datasource = setOaf(new Datasource(), oaf);
|
||||||
|
setEntity(datasource, oaf);
|
||||||
|
datasource.setAccessinfopackage(m.getAccessinfopackageList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
datasource.setCertificates(mapStringField(m.getCertificates()));
|
||||||
|
datasource.setCitationguidelineurl(mapStringField(m.getCitationguidelineurl()));
|
||||||
|
datasource.setContactemail(mapStringField(m.getContactemail()));
|
||||||
|
datasource.setDatabaseaccessrestriction(mapStringField(m.getDatabaseaccessrestriction()));
|
||||||
|
datasource.setDatabaseaccesstype(mapStringField(m.getDatabaseaccesstype()));
|
||||||
|
datasource.setDataprovider(mapBoolField(m.getDataprovider()));
|
||||||
|
datasource.setDatasourcetype(mapQualifier(m.getDatasourcetype()));
|
||||||
|
datasource.setDatauploadrestriction(mapStringField(m.getDatauploadrestriction()));
|
||||||
|
datasource.setCitationguidelineurl(mapStringField(m.getCitationguidelineurl()));
|
||||||
|
datasource.setDatauploadtype(mapStringField(m.getDatauploadtype()));
|
||||||
|
datasource.setDateofvalidation(mapStringField(m.getDateofvalidation()));
|
||||||
|
datasource.setDescription(mapStringField(m.getDescription()));
|
||||||
|
datasource.setEnglishname(mapStringField(m.getEnglishname()));
|
||||||
|
datasource.setLatitude(mapStringField(m.getLatitude()));
|
||||||
|
datasource.setLongitude(mapStringField(m.getLongitude()));
|
||||||
|
datasource.setLogourl(mapStringField(m.getLogourl()));
|
||||||
|
datasource.setMissionstatementurl(mapStringField(m.getMissionstatementurl()));
|
||||||
|
datasource.setNamespaceprefix(mapStringField(m.getNamespaceprefix()));
|
||||||
|
datasource.setOdcontenttypes(m.getOdcontenttypesList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
datasource.setOdlanguages(m.getOdlanguagesList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
datasource.setOdnumberofitems(mapStringField(m.getOdnumberofitems()));
|
||||||
|
datasource.setOdnumberofitemsdate(mapStringField(m.getOdnumberofitemsdate()));
|
||||||
|
datasource.setOdpolicies(mapStringField(m.getOdpolicies()));
|
||||||
|
datasource.setOfficialname(mapStringField(m.getOfficialname()));
|
||||||
|
datasource.setOpenairecompatibility(mapQualifier(m.getOpenairecompatibility()));
|
||||||
|
datasource.setPidsystems(mapStringField(m.getPidsystems()));
|
||||||
|
datasource.setPolicies(m.getPoliciesList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapKV)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
datasource.setQualitymanagementkind(mapStringField(m.getQualitymanagementkind()));
|
||||||
|
datasource.setReleaseenddate(mapStringField(m.getReleaseenddate()));
|
||||||
|
datasource.setServiceprovider(mapBoolField(m.getServiceprovider()));
|
||||||
|
datasource.setReleasestartdate(mapStringField(m.getReleasestartdate()));
|
||||||
|
datasource.setSubjects(m.getSubjectsList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStructuredProperty)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
datasource.setVersioning(mapBoolField(m.getVersioning()));
|
||||||
|
datasource.setWebsiteurl(mapStringField(m.getWebsiteurl()));
|
||||||
|
datasource.setJournal(mapJournal(m.getJournal()));
|
||||||
|
|
||||||
|
|
||||||
|
return datasource;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Project convertProject(OafProtos.Oaf oaf) {
|
||||||
|
final ProjectProtos.Project.Metadata m = oaf.getEntity().getProject().getMetadata();
|
||||||
|
final Project project = setOaf(new Project(), oaf);
|
||||||
|
setEntity(project, oaf);
|
||||||
|
project.setAcronym(mapStringField(m.getAcronym()));
|
||||||
|
project.setCallidentifier(mapStringField(m.getCallidentifier()));
|
||||||
|
project.setCode(mapStringField(m.getCode()));
|
||||||
|
project.setContactemail(mapStringField(m.getContactemail()));
|
||||||
|
project.setContactfax(mapStringField(m.getContactfax()));
|
||||||
|
project.setContactfullname(mapStringField(m.getContactfullname()));
|
||||||
|
project.setContactphone(mapStringField(m.getContactphone()));
|
||||||
|
project.setContracttype(mapQualifier(m.getContracttype()));
|
||||||
|
project.setCurrency(mapStringField(m.getCurrency()));
|
||||||
|
project.setDuration(mapStringField(m.getDuration()));
|
||||||
|
project.setEcarticle29_3(mapStringField(m.getEcarticle293()));
|
||||||
|
project.setEcsc39(mapStringField(m.getEcsc39()));
|
||||||
|
project.setOamandatepublications(mapStringField(m.getOamandatepublications()));
|
||||||
|
project.setStartdate(mapStringField(m.getStartdate()));
|
||||||
|
project.setEnddate(mapStringField(m.getEnddate()));
|
||||||
|
project.setFundedamount(m.getFundedamount());
|
||||||
|
project.setTotalcost(m.getTotalcost());
|
||||||
|
project.setKeywords(mapStringField(m.getKeywords()));
|
||||||
|
project.setSubjects(m.getSubjectsList().stream()
|
||||||
|
.map(sp -> mapStructuredProperty(sp))
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
project.setTitle(mapStringField(m.getTitle()));
|
||||||
|
project.setWebsiteurl(mapStringField(m.getWebsiteurl()));
|
||||||
|
project.setFundingtree(m.getFundingtreeList().stream()
|
||||||
|
.map(f -> mapStringField(f))
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
project.setJsonextrainfo(mapStringField(m.getJsonextrainfo()));
|
||||||
|
project.setSummary(mapStringField(m.getSummary()));
|
||||||
|
project.setOptional1(mapStringField(m.getOptional1()));
|
||||||
|
project.setOptional2(mapStringField(m.getOptional2()));
|
||||||
|
return project;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Result convertResult(OafProtos.Oaf oaf) {
|
||||||
|
switch (oaf.getEntity().getResult().getMetadata().getResulttype().getClassid()) {
|
||||||
|
case "dataset":
|
||||||
|
return createDataset(oaf);
|
||||||
|
case "publication":
|
||||||
|
return createPublication(oaf);
|
||||||
|
case "software":
|
||||||
|
return createSoftware(oaf);
|
||||||
|
case "other":
|
||||||
|
return createORP(oaf);
|
||||||
|
default:
|
||||||
|
Result result = setOaf(new Result(), oaf);
|
||||||
|
setEntity(result, oaf);
|
||||||
|
return setResult(result, oaf);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Software createSoftware(OafProtos.Oaf oaf) {
|
||||||
|
ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata();
|
||||||
|
Software software = setOaf(new Software(), oaf);
|
||||||
|
setEntity(software, oaf);
|
||||||
|
setResult(software, oaf);
|
||||||
|
|
||||||
|
software.setDocumentationUrl(m.getDocumentationUrlList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
software.setLicense(m.getLicenseList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStructuredProperty)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
software.setCodeRepositoryUrl(mapStringField(m.getCodeRepositoryUrl()));
|
||||||
|
software.setProgrammingLanguage(mapQualifier(m.getProgrammingLanguage()));
|
||||||
|
return software;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static OtherResearchProduct createORP(OafProtos.Oaf oaf) {
|
||||||
|
ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata();
|
||||||
|
OtherResearchProduct otherResearchProducts = setOaf(new OtherResearchProduct(), oaf);
|
||||||
|
setEntity(otherResearchProducts, oaf);
|
||||||
|
setResult(otherResearchProducts, oaf);
|
||||||
|
otherResearchProducts.setContactperson(m.getContactpersonList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
otherResearchProducts.setContactgroup(m.getContactgroupList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
otherResearchProducts.setTool(m.getToolList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
|
||||||
|
return otherResearchProducts;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Publication createPublication(OafProtos.Oaf oaf) {
|
||||||
|
|
||||||
|
ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata();
|
||||||
|
Publication publication = setOaf(new Publication(), oaf);
|
||||||
|
setEntity(publication, oaf);
|
||||||
|
setResult(publication, oaf);
|
||||||
|
publication.setJournal(mapJournal(m.getJournal()));
|
||||||
|
return publication;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Dataset createDataset(OafProtos.Oaf oaf) {
|
||||||
|
|
||||||
|
ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata();
|
||||||
|
Dataset dataset = setOaf(new Dataset(), oaf);
|
||||||
|
setEntity(dataset, oaf);
|
||||||
|
setResult(dataset, oaf);
|
||||||
|
dataset.setStoragedate(mapStringField(m.getStoragedate()));
|
||||||
|
dataset.setDevice(mapStringField(m.getDevice()));
|
||||||
|
dataset.setSize(mapStringField(m.getSize()));
|
||||||
|
dataset.setVersion(mapStringField(m.getVersion()));
|
||||||
|
dataset.setLastmetadataupdate(mapStringField(m.getLastmetadataupdate()));
|
||||||
|
dataset.setMetadataversionnumber(mapStringField(m.getMetadataversionnumber()));
|
||||||
|
dataset.setGeolocation(m.getGeolocationList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapGeolocation)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
return dataset;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
public static <T extends Oaf> T setOaf(T oaf, OafProtos.Oaf o) {
|
||||||
|
oaf.setDataInfo(mapDataInfo(o.getDataInfo()));
|
||||||
|
oaf.setLastupdatetimestamp(o.getLastupdatetimestamp());
|
||||||
|
return oaf;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static <T extends OafEntity> T setEntity(T entity, OafProtos.Oaf oaf) {
|
||||||
|
//setting Entity fields
|
||||||
|
final OafProtos.OafEntity e = oaf.getEntity();
|
||||||
|
entity.setId(e.getId());
|
||||||
|
entity.setOriginalId(e.getOriginalIdList());
|
||||||
|
entity.setCollectedfrom(e.getCollectedfromList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapKV)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
entity.setPid(e.getPidList().stream()
|
||||||
|
.map(ProtoConverter::mapStructuredProperty)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
entity.setDateofcollection(e.getDateofcollection());
|
||||||
|
entity.setDateoftransformation(e.getDateoftransformation());
|
||||||
|
entity.setExtraInfo(e.getExtraInfoList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapExtraInfo)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
return entity;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static <T extends Result> T setResult(T entity, OafProtos.Oaf oaf) {
|
||||||
|
//setting Entity fields
|
||||||
|
final ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata();
|
||||||
|
entity.setAuthor(m.getAuthorList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapAuthor)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
entity.setResulttype(mapQualifier(m.getResulttype()));
|
||||||
|
entity.setLanguage(mapQualifier(m.getLanguage()));
|
||||||
|
entity.setCountry(m.getCountryList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapQualifierAsCountry)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
entity.setSubject(m.getSubjectList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStructuredProperty)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
entity.setTitle(m.getTitleList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStructuredProperty)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
entity.setRelevantdate(m.getRelevantdateList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStructuredProperty)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
entity.setDescription(m.getDescriptionList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
entity.setDateofacceptance(mapStringField(m.getDateofacceptance()));
|
||||||
|
entity.setPublisher(mapStringField(m.getPublisher()));
|
||||||
|
entity.setEmbargoenddate(mapStringField(m.getEmbargoenddate()));
|
||||||
|
entity.setSource(m.getSourceList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
entity.setFulltext(m.getFulltextList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
entity.setFormat(m.getFormatList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
entity.setContributor(m.getContributorList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
entity.setResourcetype(mapQualifier(m.getResourcetype()));
|
||||||
|
entity.setCoverage(m.getCoverageList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
entity.setContext(m.getContextList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapContext)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
|
||||||
|
entity.setBestaccessright(getBestAccessRights(oaf.getEntity().getResult().getInstanceList()));
|
||||||
|
|
||||||
|
return entity;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Qualifier getBestAccessRights(List<ResultProtos.Result.Instance> instanceList) {
|
||||||
|
if (instanceList != null) {
|
||||||
|
final Optional<FieldTypeProtos.Qualifier> min = instanceList.stream()
|
||||||
|
.map(i -> i.getAccessright()).min(new LicenseComparator());
|
||||||
|
|
||||||
|
final Qualifier rights = min.isPresent() ? mapQualifier(min.get()) : new Qualifier();
|
||||||
|
|
||||||
|
if (StringUtils.isBlank(rights.getClassid())) {
|
||||||
|
rights.setClassid(UNKNOWN);
|
||||||
|
}
|
||||||
|
if (StringUtils.isBlank(rights.getClassname()) || UNKNOWN.equalsIgnoreCase(rights.getClassname())) {
|
||||||
|
rights.setClassname(NOT_AVAILABLE);
|
||||||
|
}
|
||||||
|
if (StringUtils.isBlank(rights.getSchemeid())) {
|
||||||
|
rights.setSchemeid(DNET_ACCESS_MODES);
|
||||||
|
}
|
||||||
|
if (StringUtils.isBlank(rights.getSchemename())) {
|
||||||
|
rights.setSchemename(DNET_ACCESS_MODES);
|
||||||
|
}
|
||||||
|
|
||||||
|
return rights;
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Context mapContext(ResultProtos.Result.Context context) {
|
||||||
|
|
||||||
|
final Context entity = new Context();
|
||||||
|
entity.setId(context.getId());
|
||||||
|
entity.setDataInfo(context.getDataInfoList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapDataInfo)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
return entity;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
public static KeyValue mapKV(FieldTypeProtos.KeyValue kv) {
|
||||||
|
final KeyValue keyValue = new KeyValue();
|
||||||
|
keyValue.setKey(kv.getKey());
|
||||||
|
keyValue.setValue(kv.getValue());
|
||||||
|
keyValue.setDataInfo(mapDataInfo(kv.getDataInfo()));
|
||||||
|
return keyValue;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static DataInfo mapDataInfo(FieldTypeProtos.DataInfo d) {
|
||||||
|
final DataInfo dataInfo = new DataInfo();
|
||||||
|
dataInfo.setDeletedbyinference(d.getDeletedbyinference());
|
||||||
|
dataInfo.setInferenceprovenance(d.getInferenceprovenance());
|
||||||
|
dataInfo.setInferred(d.getInferred());
|
||||||
|
dataInfo.setInvisible(d.getInvisible());
|
||||||
|
dataInfo.setProvenanceaction(mapQualifier(d.getProvenanceaction()));
|
||||||
|
dataInfo.setTrust(d.getTrust());
|
||||||
|
return dataInfo;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Qualifier mapQualifier(FieldTypeProtos.Qualifier q) {
|
||||||
|
final Qualifier qualifier = new Qualifier();
|
||||||
|
qualifier.setClassid(q.getClassid());
|
||||||
|
qualifier.setClassname(q.getClassname());
|
||||||
|
qualifier.setSchemeid(q.getSchemeid());
|
||||||
|
qualifier.setSchemename(q.getSchemename());
|
||||||
|
return qualifier;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Country mapQualifierAsCountry(FieldTypeProtos.Qualifier q) {
|
||||||
|
final Country c = new Country();
|
||||||
|
c.setClassid(q.getClassid());
|
||||||
|
c.setClassname(q.getClassname());
|
||||||
|
c.setSchemeid(q.getSchemeid());
|
||||||
|
c.setSchemename(q.getSchemename());
|
||||||
|
c.setDataInfo(mapDataInfo(q.getDataInfo()));
|
||||||
|
return c;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static StructuredProperty mapStructuredProperty(FieldTypeProtos.StructuredProperty sp) {
|
||||||
|
final StructuredProperty structuredProperty = new StructuredProperty();
|
||||||
|
structuredProperty.setValue(sp.getValue());
|
||||||
|
structuredProperty.setQualifier(mapQualifier(sp.getQualifier()));
|
||||||
|
structuredProperty.setDataInfo(mapDataInfo(sp.getDataInfo()));
|
||||||
|
return structuredProperty;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static ExtraInfo mapExtraInfo(FieldTypeProtos.ExtraInfo extraInfo) {
|
||||||
|
final ExtraInfo entity = new ExtraInfo();
|
||||||
|
entity.setName(extraInfo.getName());
|
||||||
|
entity.setTypology(extraInfo.getTypology());
|
||||||
|
entity.setProvenance(extraInfo.getProvenance());
|
||||||
|
entity.setTrust(extraInfo.getTrust());
|
||||||
|
entity.setValue(extraInfo.getValue());
|
||||||
|
return entity;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static OAIProvenance mapOAIProvenance(FieldTypeProtos.OAIProvenance oaiProvenance) {
|
||||||
|
final OAIProvenance entity = new OAIProvenance();
|
||||||
|
entity.setOriginDescription(mapOriginalDescription(oaiProvenance.getOriginDescription()));
|
||||||
|
return entity;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static OriginDescription mapOriginalDescription(FieldTypeProtos.OAIProvenance.OriginDescription originDescription) {
|
||||||
|
final OriginDescription originDescriptionResult = new OriginDescription();
|
||||||
|
originDescriptionResult.setHarvestDate(originDescription.getHarvestDate());
|
||||||
|
originDescriptionResult.setAltered(originDescription.getAltered());
|
||||||
|
originDescriptionResult.setBaseURL(originDescription.getBaseURL());
|
||||||
|
originDescriptionResult.setIdentifier(originDescription.getIdentifier());
|
||||||
|
originDescriptionResult.setDatestamp(originDescription.getDatestamp());
|
||||||
|
originDescriptionResult.setMetadataNamespace(originDescription.getMetadataNamespace());
|
||||||
|
return originDescriptionResult;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Field<String> mapStringField(FieldTypeProtos.StringField s) {
|
||||||
|
final Field<String> stringField = new Field<>();
|
||||||
|
stringField.setValue(s.getValue());
|
||||||
|
stringField.setDataInfo(mapDataInfo(s.getDataInfo()));
|
||||||
|
return stringField;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Field<Boolean> mapBoolField(FieldTypeProtos.BoolField b) {
|
||||||
|
final Field<Boolean> booleanField = new Field<>();
|
||||||
|
booleanField.setValue(b.getValue());
|
||||||
|
booleanField.setDataInfo(mapDataInfo(b.getDataInfo()));
|
||||||
|
return booleanField;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Field<Integer> mapIntField(FieldTypeProtos.IntField b) {
|
||||||
|
final Field<Integer> entity = new Field<>();
|
||||||
|
entity.setValue(b.getValue());
|
||||||
|
entity.setDataInfo(mapDataInfo(b.getDataInfo()));
|
||||||
|
return entity;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Journal mapJournal(FieldTypeProtos.Journal j) {
|
||||||
|
final Journal journal = new Journal();
|
||||||
|
journal.setConferencedate(j.getConferencedate());
|
||||||
|
journal.setConferenceplace(j.getConferenceplace());
|
||||||
|
journal.setEdition(j.getEdition());
|
||||||
|
journal.setEp(j.getEp());
|
||||||
|
journal.setIss(j.getIss());
|
||||||
|
journal.setIssnLinking(j.getIssnLinking());
|
||||||
|
journal.setIssnOnline(j.getIssnOnline());
|
||||||
|
journal.setIssnPrinted(j.getIssnPrinted());
|
||||||
|
journal.setName(j.getName());
|
||||||
|
journal.setSp(j.getSp());
|
||||||
|
journal.setVol(j.getVol());
|
||||||
|
journal.setDataInfo(mapDataInfo(j.getDataInfo()));
|
||||||
|
return journal;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Author mapAuthor(FieldTypeProtos.Author author) {
|
||||||
|
final Author entity = new Author();
|
||||||
|
entity.setFullname(author.getFullname());
|
||||||
|
entity.setName(author.getName());
|
||||||
|
entity.setSurname(author.getSurname());
|
||||||
|
entity.setRank(author.getRank());
|
||||||
|
entity.setPid(author.getPidList()
|
||||||
|
.stream()
|
||||||
|
.map(kv -> {
|
||||||
|
final StructuredProperty sp = new StructuredProperty();
|
||||||
|
sp.setValue(kv.getValue());
|
||||||
|
final Qualifier q = new Qualifier();
|
||||||
|
q.setClassid(kv.getKey());
|
||||||
|
q.setClassname(kv.getKey());
|
||||||
|
sp.setQualifier(q);
|
||||||
|
return sp;
|
||||||
|
})
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
entity.setAffiliation(author.getAffiliationList()
|
||||||
|
.stream()
|
||||||
|
.map(ProtoConverter::mapStringField)
|
||||||
|
.collect(Collectors.toList()));
|
||||||
|
return entity;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
public static GeoLocation mapGeolocation(ResultProtos.Result.GeoLocation geoLocation) {
|
||||||
|
final GeoLocation entity = new GeoLocation();
|
||||||
|
entity.setPoint(geoLocation.getPoint());
|
||||||
|
entity.setBox(geoLocation.getBox());
|
||||||
|
entity.setPlace(geoLocation.getPlace());
|
||||||
|
return entity;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,120 @@
|
||||||
|
package eu.dnetlib.dhp.migration.actions;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.core.JsonProcessingException;
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
import com.google.common.base.Splitter;
|
||||||
|
import com.google.common.collect.Lists;
|
||||||
|
import com.google.protobuf.InvalidProtocolBufferException;
|
||||||
|
import eu.dnetlib.actionmanager.actions.AtomicAction;
|
||||||
|
import eu.dnetlib.data.proto.OafProtos;
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||||
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||||
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||||
|
import org.apache.commons.codec.binary.Base64;
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
import org.apache.commons.logging.Log;
|
||||||
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
import org.apache.hadoop.fs.FileSystem;
|
||||||
|
import org.apache.hadoop.fs.Path;
|
||||||
|
import org.apache.hadoop.io.Text;
|
||||||
|
import org.apache.hadoop.io.compress.GzipCodec;
|
||||||
|
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
|
||||||
|
import org.apache.spark.SparkConf;
|
||||||
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
import scala.Tuple2;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.io.Serializable;
|
||||||
|
import java.util.LinkedList;
|
||||||
|
|
||||||
|
public class TransformActions implements Serializable {
|
||||||
|
|
||||||
|
private static final Log log = LogFactory.getLog(TransformActions.class);
|
||||||
|
private static final String SEPARATOR = "/";
|
||||||
|
|
||||||
|
public static void main(String[] args) throws Exception {
|
||||||
|
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||||
|
IOUtils.toString(MigrateActionSet.class.getResourceAsStream(
|
||||||
|
"/eu/dnetlib/dhp/migration/transform_actionsets_parameters.json")));
|
||||||
|
parser.parseArgument(args);
|
||||||
|
|
||||||
|
new TransformActions().run(parser);
|
||||||
|
}
|
||||||
|
|
||||||
|
private void run(ArgumentApplicationParser parser) throws ISLookUpException, IOException {
|
||||||
|
|
||||||
|
final String isLookupUrl = parser.get("isLookupUrl");
|
||||||
|
log.info("isLookupUrl: " + isLookupUrl);
|
||||||
|
|
||||||
|
final String inputPaths = parser.get("inputPaths");
|
||||||
|
|
||||||
|
if (StringUtils.isBlank(inputPaths)) {
|
||||||
|
throw new RuntimeException("empty inputPaths");
|
||||||
|
}
|
||||||
|
log.info("inputPaths: " + inputPaths);
|
||||||
|
|
||||||
|
final String targetBaseDir = getTargetBaseDir(isLookupUrl);
|
||||||
|
|
||||||
|
try(SparkSession spark = getSparkSession(parser)) {
|
||||||
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration());
|
||||||
|
|
||||||
|
for(String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) {
|
||||||
|
|
||||||
|
LinkedList<String> pathQ = Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath));
|
||||||
|
|
||||||
|
final String rawset = pathQ.pollLast();
|
||||||
|
final String actionSetDirectory = pathQ.pollLast();
|
||||||
|
|
||||||
|
final Path targetDirectory = new Path(targetBaseDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawset);
|
||||||
|
|
||||||
|
if (fs.exists(targetDirectory)) {
|
||||||
|
log.info(String.format("found target directory '%s", targetDirectory));
|
||||||
|
fs.delete(targetDirectory, true);
|
||||||
|
log.info(String.format("deleted target directory '%s", targetDirectory));
|
||||||
|
}
|
||||||
|
|
||||||
|
log.info(String.format("transforming actions from '%s' to '%s'", sourcePath, targetDirectory));
|
||||||
|
|
||||||
|
sc.sequenceFile(sourcePath, Text.class, Text.class)
|
||||||
|
.mapToPair(a -> new Tuple2<>(a._1(), AtomicAction.fromJSON(a._2().toString())))
|
||||||
|
.mapToPair(a -> new Tuple2<>(a._1(), transformAction(a._2())))
|
||||||
|
|
||||||
|
.saveAsHadoopFile(targetDirectory.toString(), Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private Text transformAction(AtomicAction aa) throws InvalidProtocolBufferException, JsonProcessingException {
|
||||||
|
|
||||||
|
final ObjectMapper mapper = new ObjectMapper();
|
||||||
|
if (aa.getTargetValue() != null && aa.getTargetValue().length > 0) {
|
||||||
|
Oaf oaf = ProtoConverter.convert(OafProtos.Oaf.parseFrom(aa.getTargetValue()));
|
||||||
|
aa.setTargetValue(mapper.writeValueAsString(oaf).getBytes());
|
||||||
|
}
|
||||||
|
|
||||||
|
return new Text(mapper.writeValueAsString(aa));
|
||||||
|
}
|
||||||
|
|
||||||
|
private String getTargetBaseDir(String isLookupUrl) throws ISLookUpException {
|
||||||
|
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
|
||||||
|
String XQUERY = "collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()";
|
||||||
|
return isLookUp.getResourceProfileByQuery(XQUERY);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static SparkSession getSparkSession(ArgumentApplicationParser parser) {
|
||||||
|
SparkConf conf = new SparkConf();
|
||||||
|
|
||||||
|
return SparkSession
|
||||||
|
.builder()
|
||||||
|
.appName(TransformActions.class.getSimpleName())
|
||||||
|
.master(parser.get("master"))
|
||||||
|
.config(conf)
|
||||||
|
.enableHiveSupport()
|
||||||
|
.getOrCreate();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,10 @@
|
||||||
|
[
|
||||||
|
{"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true},
|
||||||
|
{"paramName":"sn", "paramLongName":"sourceNameNode", "paramDescription": "nameNode of the source cluster", "paramRequired": true},
|
||||||
|
{"paramName":"tn", "paramLongName":"targetNameNode", "paramDescription": "namoNode of the target cluster", "paramRequired": true},
|
||||||
|
{"paramName":"w", "paramLongName":"workingDirectory", "paramDescription": "working directory", "paramRequired": true},
|
||||||
|
{"paramName":"nm", "paramLongName":"distcp_num_maps", "paramDescription": "maximum number of map tasks used in the distcp process", "paramRequired": true},
|
||||||
|
{"paramName":"mm", "paramLongName":"distcp_memory_mb", "paramDescription": "memory for distcp action copying actionsets from remote cluster", "paramRequired": true},
|
||||||
|
{"paramName":"tt", "paramLongName":"distcp_task_timeout", "paramDescription": "timeout for distcp copying actions from remote cluster", "paramRequired": true},
|
||||||
|
{"paramName":"tr", "paramLongName":"transform_only", "paramDescription": "activate tranform-only mode. Only apply transformation step", "paramRequired": true}
|
||||||
|
]
|
||||||
|
|
@ -0,0 +1,5 @@
|
||||||
|
[
|
||||||
|
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||||
|
{"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true},
|
||||||
|
{"paramName":"i", "paramLongName":"inputPaths", "paramDescription": "URL of the isLookUp Service", "paramRequired": true}
|
||||||
|
]
|
||||||
|
|
@ -0,0 +1,30 @@
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>jobTracker</name>
|
||||||
|
<value>yarnRM</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>nameNode</name>
|
||||||
|
<value>hdfs://nameservice1</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sourceNN</name>
|
||||||
|
<value>webhdfs://namenode2.hadoop.dm.openaire.eu:50071</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>spark2YarnHistoryServerAddress</name>
|
||||||
|
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18088</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2EventLogDir</name>
|
||||||
|
<value>/user/spark/applicationHistory</value>
|
||||||
|
</property>
|
||||||
|
</configuration>
|
||||||
|
|
@ -0,0 +1,111 @@
|
||||||
|
<workflow-app xmlns='uri:oozie:workflow:0.5' name='migrate_actions'>
|
||||||
|
<parameters>
|
||||||
|
<property>
|
||||||
|
<name>sourceNN</name>
|
||||||
|
<description>the source name node</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>isLookupUrl</name>
|
||||||
|
<description>the isLookup service endpoint</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>workingDirectory</name>
|
||||||
|
<value>/tmp/actionsets</value>
|
||||||
|
<description>working directory</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>distcp_memory_mb</name>
|
||||||
|
<value>6144</value>
|
||||||
|
<description>memory for distcp copying actionsets from remote cluster</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>distcp_task_timeout</name>
|
||||||
|
<value>60000000</value>
|
||||||
|
<description>timeout for distcp copying actions from remote cluster</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>distcp_num_maps</name>
|
||||||
|
<value>1</value>
|
||||||
|
<description>mmaximum number of map tasks used in the distcp process</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>transform_only</name>
|
||||||
|
<description>activate tranform-only mode. Only apply transformation step</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkDriverMemory</name>
|
||||||
|
<description>memory for driver process</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkExecutorMemory</name>
|
||||||
|
<description>memory for individual executor</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkExecutorCores</name>
|
||||||
|
<description>number of cores used by single executor</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2YarnHistoryServerAddress</name>
|
||||||
|
<description>spark 2.* yarn history server address</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2EventLogDir</name>
|
||||||
|
<description>spark 2.* event log dir location</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<start to='migrate_actionsets' />
|
||||||
|
|
||||||
|
<action name='migrate_actionsets'>
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.dhp.migration.actions.MigrateActionSet</main-class>
|
||||||
|
<java-opt>-Dmapred.task.timeout=${distcp_task_timeout}</java-opt>
|
||||||
|
<arg>-is</arg><arg>${isLookupUrl}</arg>
|
||||||
|
<arg>-sn</arg><arg>${sourceNN}</arg>
|
||||||
|
<arg>-tn</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-w</arg><arg>${workingDirectory}</arg>
|
||||||
|
<arg>-nm</arg><arg>${distcp_num_maps}</arg>
|
||||||
|
<arg>-mm</arg><arg>${distcp_memory_mb}</arg>
|
||||||
|
<arg>-tt</arg><arg>${distcp_task_timeout}</arg>
|
||||||
|
<arg>-tr</arg><arg>${transform_only}</arg>
|
||||||
|
<capture-output/>
|
||||||
|
</java>
|
||||||
|
<ok to="transform_actions" />
|
||||||
|
<error to="fail" />
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="transform_actions">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>transform_actions</name>
|
||||||
|
<class>eu.dnetlib.dhp.migration.actions.TransformActions</class>
|
||||||
|
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-cores ${sparkExecutorCores}
|
||||||
|
--executor-memory ${sparkExecutorMemory}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
|
||||||
|
--conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>-mt</arg><arg>yarn</arg>
|
||||||
|
<arg>-is</arg><arg>${isLookupUrl}</arg>
|
||||||
|
<arg>--inputPaths</arg><arg>${wf:actionData('migrate_actionsets')['target_paths']}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="end"/>
|
||||||
|
<error to="fail"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<kill name="fail">
|
||||||
|
<message>migrate_actions failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
<end name="end" />
|
||||||
|
|
||||||
|
</workflow-app>
|
||||||
16
pom.xml
16
pom.xml
|
|
@ -110,6 +110,12 @@
|
||||||
<version>${dhp.hadoop.version}</version>
|
<version>${dhp.hadoop.version}</version>
|
||||||
<scope>provided</scope>
|
<scope>provided</scope>
|
||||||
</dependency>
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.apache.hadoop</groupId>
|
||||||
|
<artifactId>hadoop-distcp</artifactId>
|
||||||
|
<version>${dhp.hadoop.version}</version>
|
||||||
|
<scope>provided</scope>
|
||||||
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>org.apache.spark</groupId>
|
<groupId>org.apache.spark</groupId>
|
||||||
<artifactId>spark-core_2.11</artifactId>
|
<artifactId>spark-core_2.11</artifactId>
|
||||||
|
|
@ -262,6 +268,16 @@
|
||||||
<scope>provided</scope>
|
<scope>provided</scope>
|
||||||
</dependency>
|
</dependency>
|
||||||
|
|
||||||
|
<dependency>
|
||||||
|
<groupId>eu.dnetlib</groupId>
|
||||||
|
<artifactId>dnet-actionmanager-common</artifactId>
|
||||||
|
<version>6.0.5</version>
|
||||||
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>eu.dnetlib</groupId>
|
||||||
|
<artifactId>dnet-openaire-data-protos</artifactId>
|
||||||
|
<version>3.9.8-proto250</version>
|
||||||
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>eu.dnetlib</groupId>
|
<groupId>eu.dnetlib</groupId>
|
||||||
<artifactId>dnet-pace-core</artifactId>
|
<artifactId>dnet-pace-core</artifactId>
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue