forked from D-Net/dnet-hadoop
sync with master branch
This commit is contained in:
commit
1b18fd4d54
|
|
@ -76,6 +76,41 @@
|
||||||
</configuration>
|
</configuration>
|
||||||
</plugin>
|
</plugin>
|
||||||
</plugins>
|
</plugins>
|
||||||
|
<pluginManagement>
|
||||||
|
<plugins>
|
||||||
|
<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
|
||||||
|
<plugin>
|
||||||
|
<groupId>org.eclipse.m2e</groupId>
|
||||||
|
<artifactId>lifecycle-mapping</artifactId>
|
||||||
|
<version>1.0.0</version>
|
||||||
|
<configuration>
|
||||||
|
<lifecycleMappingMetadata>
|
||||||
|
<pluginExecutions>
|
||||||
|
<pluginExecution>
|
||||||
|
<pluginExecutionFilter>
|
||||||
|
<groupId>
|
||||||
|
org.apache.maven.plugins
|
||||||
|
</groupId>
|
||||||
|
<artifactId>
|
||||||
|
maven-plugin-plugin
|
||||||
|
</artifactId>
|
||||||
|
<versionRange>
|
||||||
|
[3.2,)
|
||||||
|
</versionRange>
|
||||||
|
<goals>
|
||||||
|
<goal>descriptor</goal>
|
||||||
|
</goals>
|
||||||
|
</pluginExecutionFilter>
|
||||||
|
<action>
|
||||||
|
<ignore></ignore>
|
||||||
|
</action>
|
||||||
|
</pluginExecution>
|
||||||
|
</pluginExecutions>
|
||||||
|
</lifecycleMappingMetadata>
|
||||||
|
</configuration>
|
||||||
|
</plugin>
|
||||||
|
</plugins>
|
||||||
|
</pluginManagement>
|
||||||
</build>
|
</build>
|
||||||
|
|
||||||
</project>
|
</project>
|
||||||
|
|
|
||||||
|
|
@ -26,6 +26,12 @@
|
||||||
<version>${project.version}</version>
|
<version>${project.version}</version>
|
||||||
</dependency>
|
</dependency>
|
||||||
|
|
||||||
|
<dependency>
|
||||||
|
<groupId>eu.dnetlib.dhp</groupId>
|
||||||
|
<artifactId>dhp-schemas</artifactId>
|
||||||
|
<version>${project.version}</version>
|
||||||
|
</dependency>
|
||||||
|
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>net.sf.saxon</groupId>
|
<groupId>net.sf.saxon</groupId>
|
||||||
<artifactId>Saxon-HE</artifactId>
|
<artifactId>Saxon-HE</artifactId>
|
||||||
|
|
@ -45,6 +51,17 @@
|
||||||
<artifactId>jaxen</artifactId>
|
<artifactId>jaxen</artifactId>
|
||||||
</dependency>
|
</dependency>
|
||||||
|
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.mongodb</groupId>
|
||||||
|
<artifactId>mongo-java-driver</artifactId>
|
||||||
|
</dependency>
|
||||||
|
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.postgresql</groupId>
|
||||||
|
<artifactId>postgresql</artifactId>
|
||||||
|
<version>42.2.10</version>
|
||||||
|
</dependency>
|
||||||
|
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>org.mockito</groupId>
|
<groupId>org.mockito</groupId>
|
||||||
<artifactId>mockito-core</artifactId>
|
<artifactId>mockito-core</artifactId>
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,236 @@
|
||||||
|
package eu.dnetlib.dhp.migration;
|
||||||
|
|
||||||
|
import java.io.Closeable;
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.net.URI;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.Arrays;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Objects;
|
||||||
|
import java.util.concurrent.atomic.AtomicInteger;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
import org.apache.commons.logging.Log;
|
||||||
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
import org.apache.hadoop.conf.Configuration;
|
||||||
|
import org.apache.hadoop.fs.FileSystem;
|
||||||
|
import org.apache.hadoop.fs.Path;
|
||||||
|
import org.apache.hadoop.io.SequenceFile;
|
||||||
|
import org.apache.hadoop.io.Text;
|
||||||
|
import org.codehaus.jackson.map.ObjectMapper;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.ExtraInfo;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Journal;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.OAIProvenance;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.OriginDescription;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
|
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||||
|
|
||||||
|
public class AbstractMigrationExecutor implements Closeable {
|
||||||
|
|
||||||
|
private final AtomicInteger counter = new AtomicInteger(0);
|
||||||
|
|
||||||
|
private final Text key = new Text();
|
||||||
|
|
||||||
|
private final Text value = new Text();
|
||||||
|
|
||||||
|
private final ObjectMapper objectMapper = new ObjectMapper();
|
||||||
|
|
||||||
|
private final SequenceFile.Writer writer;
|
||||||
|
|
||||||
|
private static final Log log = LogFactory.getLog(AbstractMigrationExecutor.class);
|
||||||
|
|
||||||
|
public AbstractMigrationExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser) throws Exception {
|
||||||
|
|
||||||
|
log.info(String.format("Creating SequenceFile Writer, hdfsPath=%s, nameNode=%s, user=%s", hdfsPath, hdfsNameNode, hdfsUser));
|
||||||
|
|
||||||
|
this.writer = SequenceFile.createWriter(getConf(hdfsNameNode, hdfsUser), SequenceFile.Writer.file(new Path(hdfsPath)), SequenceFile.Writer
|
||||||
|
.keyClass(Text.class), SequenceFile.Writer.valueClass(Text.class));
|
||||||
|
}
|
||||||
|
|
||||||
|
private Configuration getConf(final String hdfsNameNode, final String hdfsUser) throws IOException {
|
||||||
|
final Configuration conf = new Configuration();
|
||||||
|
conf.set("fs.defaultFS", hdfsNameNode);
|
||||||
|
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
|
||||||
|
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
|
||||||
|
System.setProperty("HADOOP_USER_NAME", hdfsUser);
|
||||||
|
System.setProperty("hadoop.home.dir", "/");
|
||||||
|
FileSystem.get(URI.create(hdfsNameNode), conf);
|
||||||
|
return conf;
|
||||||
|
}
|
||||||
|
|
||||||
|
protected void emitOaf(final Oaf oaf) {
|
||||||
|
try {
|
||||||
|
key.set(counter.getAndIncrement() + ":" + oaf.getClass().getSimpleName().toLowerCase());
|
||||||
|
value.set(objectMapper.writeValueAsString(oaf));
|
||||||
|
writer.append(key, value);
|
||||||
|
} catch (final Exception e) {
|
||||||
|
throw new RuntimeException(e);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void close() throws IOException {
|
||||||
|
writer.hflush();
|
||||||
|
writer.close();
|
||||||
|
}
|
||||||
|
|
||||||
|
public static KeyValue keyValue(final String k, final String v) {
|
||||||
|
final KeyValue kv = new KeyValue();
|
||||||
|
kv.setKey(k);
|
||||||
|
kv.setValue(v);
|
||||||
|
return kv;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static List<KeyValue> listKeyValues(final String... s) {
|
||||||
|
if (s.length % 2 > 0) { throw new RuntimeException("Invalid number of parameters (k,v,k,v,....)"); }
|
||||||
|
|
||||||
|
final List<KeyValue> list = new ArrayList<>();
|
||||||
|
for (int i = 0; i < s.length; i += 2) {
|
||||||
|
list.add(keyValue(s[i], s[i + 1]));
|
||||||
|
}
|
||||||
|
return list;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static <T> Field<T> field(final T value, final DataInfo info) {
|
||||||
|
if (value == null || StringUtils.isBlank(value.toString())) { return null; }
|
||||||
|
|
||||||
|
final Field<T> field = new Field<>();
|
||||||
|
field.setValue(value);
|
||||||
|
field.setDataInfo(info);
|
||||||
|
return field;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static List<Field<String>> listFields(final DataInfo info, final String... values) {
|
||||||
|
return Arrays.stream(values).map(v -> field(v, info)).filter(Objects::nonNull).collect(Collectors.toList());
|
||||||
|
}
|
||||||
|
|
||||||
|
public static List<Field<String>> listFields(final DataInfo info, final List<String> values) {
|
||||||
|
return values.stream().map(v -> field(v, info)).filter(Objects::nonNull).collect(Collectors.toList());
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Qualifier qualifier(final String classid, final String classname, final String schemeid, final String schemename) {
|
||||||
|
final Qualifier q = new Qualifier();
|
||||||
|
q.setClassid(classid);
|
||||||
|
q.setClassname(classname);
|
||||||
|
q.setSchemeid(schemeid);
|
||||||
|
q.setSchemename(schemename);
|
||||||
|
return q;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static StructuredProperty structuredProperty(final String value,
|
||||||
|
final String classid,
|
||||||
|
final String classname,
|
||||||
|
final String schemeid,
|
||||||
|
final String schemename,
|
||||||
|
final DataInfo dataInfo) {
|
||||||
|
|
||||||
|
return structuredProperty(value, qualifier(classid, classname, schemeid, schemename), dataInfo);
|
||||||
|
}
|
||||||
|
|
||||||
|
public static StructuredProperty structuredProperty(final String value, final Qualifier qualifier, final DataInfo dataInfo) {
|
||||||
|
if (value == null) { return null; }
|
||||||
|
final StructuredProperty sp = new StructuredProperty();
|
||||||
|
sp.setValue(value);
|
||||||
|
sp.setQualifier(qualifier);
|
||||||
|
sp.setDataInfo(dataInfo);
|
||||||
|
return sp;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static ExtraInfo extraInfo(final String name, final String value, final String typology, final String provenance, final String trust) {
|
||||||
|
final ExtraInfo info = new ExtraInfo();
|
||||||
|
info.setName(name);
|
||||||
|
info.setValue(value);
|
||||||
|
info.setTypology(typology);
|
||||||
|
info.setProvenance(provenance);
|
||||||
|
info.setTrust(trust);
|
||||||
|
return info;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static OAIProvenance oaiIProvenance(final String identifier,
|
||||||
|
final String baseURL,
|
||||||
|
final String metadataNamespace,
|
||||||
|
final Boolean altered,
|
||||||
|
final String datestamp,
|
||||||
|
final String harvestDate) {
|
||||||
|
|
||||||
|
final OriginDescription desc = new OriginDescription();
|
||||||
|
desc.setIdentifier(identifier);
|
||||||
|
desc.setBaseURL(baseURL);
|
||||||
|
desc.setMetadataNamespace(metadataNamespace);
|
||||||
|
desc.setAltered(altered);
|
||||||
|
desc.setDatestamp(datestamp);
|
||||||
|
desc.setHarvestDate(harvestDate);
|
||||||
|
|
||||||
|
final OAIProvenance p = new OAIProvenance();
|
||||||
|
p.setOriginDescription(desc);
|
||||||
|
|
||||||
|
return p;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Journal journal(final String name,
|
||||||
|
final String issnPrinted,
|
||||||
|
final String issnOnline,
|
||||||
|
final String issnLinking,
|
||||||
|
final String ep,
|
||||||
|
final String iss,
|
||||||
|
final String sp,
|
||||||
|
final String vol,
|
||||||
|
final String edition,
|
||||||
|
final String conferenceplace,
|
||||||
|
final String conferencedate,
|
||||||
|
final DataInfo dataInfo) {
|
||||||
|
|
||||||
|
if (StringUtils.isNotBlank(name) || StringUtils.isNotBlank(issnPrinted) || StringUtils.isNotBlank(issnOnline) || StringUtils.isNotBlank(issnLinking)) {
|
||||||
|
final Journal j = new Journal();
|
||||||
|
j.setName(name);
|
||||||
|
j.setIssnPrinted(issnPrinted);
|
||||||
|
j.setIssnOnline(issnOnline);
|
||||||
|
j.setIssnLinking(issnLinking);
|
||||||
|
j.setEp(ep);
|
||||||
|
j.setIss(iss);
|
||||||
|
j.setSp(sp);
|
||||||
|
j.setVol(vol);
|
||||||
|
j.setEdition(edition);
|
||||||
|
j.setConferenceplace(conferenceplace);
|
||||||
|
j.setConferencedate(conferencedate);
|
||||||
|
j.setDataInfo(dataInfo);
|
||||||
|
return j;
|
||||||
|
} else {
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public static DataInfo dataInfo(final Boolean deletedbyinference,
|
||||||
|
final String inferenceprovenance,
|
||||||
|
final Boolean inferred,
|
||||||
|
final Boolean invisible,
|
||||||
|
final Qualifier provenanceaction,
|
||||||
|
final String trust) {
|
||||||
|
final DataInfo d = new DataInfo();
|
||||||
|
d.setDeletedbyinference(deletedbyinference);
|
||||||
|
d.setInferenceprovenance(inferenceprovenance);
|
||||||
|
d.setInferred(inferred);
|
||||||
|
d.setInvisible(invisible);
|
||||||
|
d.setProvenanceaction(provenanceaction);
|
||||||
|
d.setTrust(trust);
|
||||||
|
return d;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static String createOpenaireId(final int prefix, final String originalId) {
|
||||||
|
final String nsPrefix = StringUtils.substringBefore(originalId, "::");
|
||||||
|
final String rest = StringUtils.substringAfter(originalId, "::");
|
||||||
|
return String.format("%s|%s::%s", prefix, nsPrefix, DHPUtils.md5(rest));
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
public static String asString(final Object o) {
|
||||||
|
return o == null ? "" : o.toString();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,439 @@
|
||||||
|
package eu.dnetlib.dhp.migration;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.sql.SQLException;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.Arrays;
|
||||||
|
import java.util.Date;
|
||||||
|
import java.util.HashMap;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Map;
|
||||||
|
import java.util.Map.Entry;
|
||||||
|
|
||||||
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
import org.apache.commons.logging.Log;
|
||||||
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
import org.dom4j.Document;
|
||||||
|
import org.dom4j.DocumentException;
|
||||||
|
import org.dom4j.DocumentFactory;
|
||||||
|
import org.dom4j.DocumentHelper;
|
||||||
|
import org.dom4j.Node;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Author;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.GeoLocation;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Instance;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Journal;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.OAIProvenance;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Software;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
|
|
||||||
|
public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
|
||||||
|
|
||||||
|
protected final Map<String, String> code2name = new HashMap<>();
|
||||||
|
|
||||||
|
protected final MdstoreClient mdstoreClient;
|
||||||
|
|
||||||
|
protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
|
||||||
|
|
||||||
|
protected static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER =
|
||||||
|
qualifier("publication", "publication", "dnet:result_typologies", "dnet:result_typologies");
|
||||||
|
protected static final Qualifier DATASET_RESULTTYPE_QUALIFIER = qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies");
|
||||||
|
protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies");
|
||||||
|
protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER = qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies");
|
||||||
|
|
||||||
|
private static final Log log = LogFactory.getLog(AbstractMongoExecutor.class);
|
||||||
|
|
||||||
|
public AbstractMongoExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String mongoBaseUrl,
|
||||||
|
final String mongoDb, final String dbUrl, final String dbUser,
|
||||||
|
final String dbPassword) throws Exception {
|
||||||
|
|
||||||
|
super(hdfsPath, hdfsNameNode, hdfsUser);
|
||||||
|
|
||||||
|
this.mdstoreClient = new MdstoreClient(mongoBaseUrl, mongoDb);
|
||||||
|
loadClassNames(dbUrl, dbUser, dbPassword);
|
||||||
|
|
||||||
|
final Map<String, String> nsContext = new HashMap<>();
|
||||||
|
|
||||||
|
registerNamespaces(nsContext);
|
||||||
|
|
||||||
|
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
|
||||||
|
}
|
||||||
|
|
||||||
|
private void loadClassNames(final String dbUrl, final String dbUser, final String dbPassword) throws IOException {
|
||||||
|
|
||||||
|
log.info("Loading vocabulary terms from db...");
|
||||||
|
|
||||||
|
try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
|
||||||
|
code2name.clear();
|
||||||
|
dbClient.processResults("select code, name from class", rs -> {
|
||||||
|
try {
|
||||||
|
code2name.put(rs.getString("code"), rs.getString("name"));
|
||||||
|
} catch (final SQLException e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
}
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
log.info("Found " + code2name.size() + " terms.");
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
public void processMdRecords(final String mdFormat, final String mdLayout, final String mdInterpretation) throws DocumentException {
|
||||||
|
|
||||||
|
log.info(String.format("Searching mdstores (format: %s, layout: %s, interpretation: %s)", mdFormat, mdLayout, mdInterpretation));
|
||||||
|
|
||||||
|
final Map<String, String> colls = mdstoreClient.validCollections(mdFormat, mdLayout, mdInterpretation);
|
||||||
|
log.info("Found " + colls.size() + " mdstores");
|
||||||
|
|
||||||
|
for (final Entry<String, String> entry : colls.entrySet()) {
|
||||||
|
log.info("Processing mdstore " + entry.getKey() + " (collection: " + entry.getValue() + ")");
|
||||||
|
final String currentColl = entry.getValue();
|
||||||
|
|
||||||
|
for (final String xml : mdstoreClient.listRecords(currentColl)) {
|
||||||
|
final Document doc = DocumentHelper.parseText(xml);
|
||||||
|
|
||||||
|
final String type = doc.valueOf("//dr:CobjCategory/@type");
|
||||||
|
final KeyValue collectedFrom = keyValue(doc.valueOf("//oaf:collectedFrom/@id"), doc.valueOf("//oaf:collectedFrom/@name"));
|
||||||
|
final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom
|
||||||
|
: keyValue(doc.valueOf("//oaf:hostedBy/@id"), doc.valueOf("//oaf:hostedBy/@name"));
|
||||||
|
|
||||||
|
final DataInfo info = prepareDataInfo(doc);
|
||||||
|
final long lastUpdateTimestamp = new Date().getTime();
|
||||||
|
|
||||||
|
for (final Oaf oaf : createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp)) {
|
||||||
|
emitOaf(oaf);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
log.info("All Done.");
|
||||||
|
}
|
||||||
|
|
||||||
|
protected void registerNamespaces(final Map<String, String> nsContext) {
|
||||||
|
nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
|
||||||
|
nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
|
||||||
|
nsContext.put("oaf", "http://namespace.openaire.eu/oaf");
|
||||||
|
nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/");
|
||||||
|
nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance");
|
||||||
|
}
|
||||||
|
|
||||||
|
protected List<Oaf> createOafs(final Document doc,
|
||||||
|
final String type,
|
||||||
|
final KeyValue collectedFrom,
|
||||||
|
final KeyValue hostedBy,
|
||||||
|
final DataInfo info,
|
||||||
|
final long lastUpdateTimestamp) {
|
||||||
|
|
||||||
|
final List<Oaf> oafs = new ArrayList<>();
|
||||||
|
|
||||||
|
switch (type.toLowerCase()) {
|
||||||
|
case "":
|
||||||
|
case "publication":
|
||||||
|
final Publication p = new Publication();
|
||||||
|
populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||||
|
p.setResulttype(PUBLICATION_RESULTTYPE_QUALIFIER);
|
||||||
|
p.setJournal(prepareJournal(doc, info));
|
||||||
|
oafs.add(p);
|
||||||
|
break;
|
||||||
|
case "dataset":
|
||||||
|
final Dataset d = new Dataset();
|
||||||
|
populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||||
|
d.setResulttype(DATASET_RESULTTYPE_QUALIFIER);
|
||||||
|
d.setStoragedate(prepareDatasetStorageDate(doc, info));
|
||||||
|
d.setDevice(prepareDatasetDevice(doc, info));
|
||||||
|
d.setSize(prepareDatasetSize(doc, info));
|
||||||
|
d.setVersion(prepareDatasetVersion(doc, info));
|
||||||
|
d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
|
||||||
|
d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
|
||||||
|
d.setGeolocation(prepareDatasetGeoLocations(doc, info));
|
||||||
|
oafs.add(d);
|
||||||
|
break;
|
||||||
|
case "software":
|
||||||
|
final Software s = new Software();
|
||||||
|
populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||||
|
s.setResulttype(SOFTWARE_RESULTTYPE_QUALIFIER);
|
||||||
|
s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
|
||||||
|
s.setLicense(prepareSoftwareLicenses(doc, info));
|
||||||
|
s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
|
||||||
|
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
|
||||||
|
oafs.add(s);
|
||||||
|
break;
|
||||||
|
case "otherresearchproducts":
|
||||||
|
default:
|
||||||
|
final OtherResearchProduct o = new OtherResearchProduct();
|
||||||
|
populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||||
|
o.setResulttype(OTHER_RESULTTYPE_QUALIFIER);
|
||||||
|
o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
|
||||||
|
o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
|
||||||
|
o.setTool(prepareOtherResearchProductTools(doc, info));
|
||||||
|
oafs.add(o);
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (!oafs.isEmpty()) {
|
||||||
|
oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp));
|
||||||
|
oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp));
|
||||||
|
}
|
||||||
|
|
||||||
|
return oafs;
|
||||||
|
}
|
||||||
|
|
||||||
|
private List<Oaf> addProjectRels(final Document doc,
|
||||||
|
final KeyValue collectedFrom,
|
||||||
|
final DataInfo info,
|
||||||
|
final long lastUpdateTimestamp) {
|
||||||
|
|
||||||
|
final List<Oaf> res = new ArrayList<>();
|
||||||
|
|
||||||
|
final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"));
|
||||||
|
|
||||||
|
for (final Object o : doc.selectNodes("//oaf:projectid")) {
|
||||||
|
final String projectId = createOpenaireId(40, ((Node) o).getText());
|
||||||
|
|
||||||
|
final Relation r1 = new Relation();
|
||||||
|
r1.setRelType("resultProject");
|
||||||
|
r1.setSubRelType("outcome");
|
||||||
|
r1.setRelClass("isProducedBy");
|
||||||
|
r1.setSource(docId);
|
||||||
|
r1.setTarget(projectId);
|
||||||
|
r1.setCollectedFrom(Arrays.asList(collectedFrom));
|
||||||
|
r1.setDataInfo(info);
|
||||||
|
r1.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
|
res.add(r1);
|
||||||
|
|
||||||
|
final Relation r2 = new Relation();
|
||||||
|
r2.setRelType("resultProject");
|
||||||
|
r2.setSubRelType("outcome");
|
||||||
|
r2.setRelClass("produces");
|
||||||
|
r2.setSource(projectId);
|
||||||
|
r2.setTarget(docId);
|
||||||
|
r2.setCollectedFrom(Arrays.asList(collectedFrom));
|
||||||
|
r2.setDataInfo(info);
|
||||||
|
r2.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
|
res.add(r2);
|
||||||
|
}
|
||||||
|
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
protected abstract List<Oaf> addOtherResultRels(final Document doc,
|
||||||
|
final KeyValue collectedFrom,
|
||||||
|
final DataInfo info,
|
||||||
|
final long lastUpdateTimestamp);
|
||||||
|
|
||||||
|
private void populateResultFields(final Result r,
|
||||||
|
final Document doc,
|
||||||
|
final KeyValue collectedFrom,
|
||||||
|
final KeyValue hostedBy,
|
||||||
|
final DataInfo info,
|
||||||
|
final long lastUpdateTimestamp) {
|
||||||
|
r.setDataInfo(info);
|
||||||
|
r.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
|
r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier")));
|
||||||
|
r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
|
||||||
|
r.setCollectedfrom(Arrays.asList(collectedFrom));
|
||||||
|
r.setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
|
||||||
|
r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
|
||||||
|
r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
|
||||||
|
r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||||
|
r.setOaiprovenance(prepareOAIprovenance(doc));
|
||||||
|
r.setAuthor(prepareAuthors(doc, info));
|
||||||
|
r.setLanguage(prepareLanguages(doc));
|
||||||
|
r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||||
|
r.setSubject(prepareSubjects(doc, info));
|
||||||
|
r.setTitle(prepareTitles(doc, info));
|
||||||
|
r.setRelevantdate(prepareRelevantDates(doc, info));
|
||||||
|
r.setDescription(prepareDescriptions(doc, info));
|
||||||
|
r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info));
|
||||||
|
r.setPublisher(preparePublisher(doc, info));
|
||||||
|
r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info));
|
||||||
|
r.setSource(prepareSources(doc, info));
|
||||||
|
r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||||
|
r.setFormat(prepareFormats(doc, info));
|
||||||
|
r.setContributor(prepareContributors(doc, info));
|
||||||
|
r.setResourcetype(prepareResourceType(doc, info));
|
||||||
|
r.setCoverage(prepareCoverages(doc, info));
|
||||||
|
r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||||
|
r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||||
|
r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy));
|
||||||
|
}
|
||||||
|
|
||||||
|
protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract List<Instance> prepareInstances(Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby);
|
||||||
|
|
||||||
|
protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract List<StructuredProperty> prepareRelevantDates(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract List<Field<String>> prepareCoverages(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract List<Field<String>> prepareContributors(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract List<Field<String>> prepareFormats(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract Field<String> preparePublisher(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract List<Field<String>> prepareDescriptions(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract List<StructuredProperty> prepareTitles(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract List<StructuredProperty> prepareSubjects(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract Qualifier prepareLanguages(Document doc);
|
||||||
|
|
||||||
|
protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract List<Field<String>> prepareOtherResearchProductTools(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract List<StructuredProperty> prepareSoftwareLicenses(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract Field<String> prepareDatasetMetadataVersionNumber(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract Field<String> prepareDatasetVersion(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract Field<String> prepareDatasetSize(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract Field<String> prepareDatasetDevice(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
|
||||||
|
|
||||||
|
private Journal prepareJournal(final Document doc, final DataInfo info) {
|
||||||
|
final Node n = doc.selectSingleNode("//oaf:journal");
|
||||||
|
if (n != null) {
|
||||||
|
final String name = n.getText();
|
||||||
|
final String issnPrinted = n.valueOf("@issn");
|
||||||
|
final String issnOnline = n.valueOf("@eissn");
|
||||||
|
final String issnLinking = n.valueOf("@lissn");
|
||||||
|
final String ep = n.valueOf("@ep");
|
||||||
|
final String iss = n.valueOf("@iss");
|
||||||
|
final String sp = n.valueOf("@sp");
|
||||||
|
final String vol = n.valueOf("@vol");
|
||||||
|
final String edition = n.valueOf("@edition");
|
||||||
|
if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); }
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
protected Qualifier prepareQualifier(final Node node, final String xpath, final String schemeId, final String schemeName) {
|
||||||
|
final String classId = node.valueOf(xpath);
|
||||||
|
final String className = code2name.get(classId);
|
||||||
|
return qualifier(classId, className, schemeId, schemeName);
|
||||||
|
}
|
||||||
|
|
||||||
|
protected List<StructuredProperty> prepareListStructProps(final Node node,
|
||||||
|
final String xpath,
|
||||||
|
final String xpathClassId,
|
||||||
|
final String schemeId,
|
||||||
|
final String schemeName,
|
||||||
|
final DataInfo info) {
|
||||||
|
final List<StructuredProperty> res = new ArrayList<>();
|
||||||
|
for (final Object o : node.selectNodes(xpath)) {
|
||||||
|
final Node n = (Node) o;
|
||||||
|
final String classId = n.valueOf(xpathClassId);
|
||||||
|
final String className = code2name.get(classId);
|
||||||
|
res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info));
|
||||||
|
}
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
protected List<StructuredProperty> prepareListStructProps(final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) {
|
||||||
|
final List<StructuredProperty> res = new ArrayList<>();
|
||||||
|
for (final Object o : node.selectNodes(xpath)) {
|
||||||
|
final Node n = (Node) o;
|
||||||
|
res.add(structuredProperty(n.getText(), qualifier, info));
|
||||||
|
}
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
protected List<StructuredProperty> prepareListStructProps(final Node node, final String xpath, final DataInfo info) {
|
||||||
|
final List<StructuredProperty> res = new ArrayList<>();
|
||||||
|
for (final Object o : node.selectNodes(xpath)) {
|
||||||
|
final Node n = (Node) o;
|
||||||
|
res.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n
|
||||||
|
.valueOf("@schemename"), info));
|
||||||
|
}
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
protected OAIProvenance prepareOAIprovenance(final Document doc) {
|
||||||
|
final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
|
||||||
|
|
||||||
|
if (n == null) { return null; }
|
||||||
|
|
||||||
|
final String identifier = n.valueOf("./*[local-name()='identifier']");
|
||||||
|
final String baseURL = n.valueOf("./*[local-name()='baseURL']");;
|
||||||
|
final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");;
|
||||||
|
final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
|
||||||
|
final String datestamp = n.valueOf("./*[local-name()='datestamp']");;
|
||||||
|
final String harvestDate = n.valueOf("@harvestDate");;
|
||||||
|
|
||||||
|
return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
protected DataInfo prepareDataInfo(final Document doc) {
|
||||||
|
final Node n = doc.selectSingleNode("//oaf:datainfo");
|
||||||
|
|
||||||
|
final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
|
||||||
|
final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
|
||||||
|
final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid");
|
||||||
|
final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename");
|
||||||
|
|
||||||
|
final boolean deletedbyinference = Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference"));
|
||||||
|
final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance");
|
||||||
|
final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
|
||||||
|
final String trust = n.valueOf("./oaf:trust");
|
||||||
|
|
||||||
|
return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
|
||||||
|
}
|
||||||
|
|
||||||
|
protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
|
||||||
|
return field(node.valueOf(xpath), info);
|
||||||
|
}
|
||||||
|
|
||||||
|
protected List<Field<String>> prepareListFields(final Node node, final String xpath, final DataInfo info) {
|
||||||
|
return listFields(info, prepareListString(node, xpath));
|
||||||
|
}
|
||||||
|
|
||||||
|
protected List<String> prepareListString(final Node node, final String xpath) {
|
||||||
|
final List<String> res = new ArrayList<>();
|
||||||
|
for (final Object o : node.selectNodes(xpath)) {
|
||||||
|
final String s = ((Node) o).getText().trim();
|
||||||
|
if (StringUtils.isNotBlank(s)) {
|
||||||
|
res.add(s);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void close() throws IOException {
|
||||||
|
super.close();
|
||||||
|
mdstoreClient.close();
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,63 @@
|
||||||
|
package eu.dnetlib.dhp.migration;
|
||||||
|
|
||||||
|
import java.io.Closeable;
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.sql.Connection;
|
||||||
|
import java.sql.DriverManager;
|
||||||
|
import java.sql.ResultSet;
|
||||||
|
import java.sql.SQLException;
|
||||||
|
import java.sql.Statement;
|
||||||
|
import java.util.function.Consumer;
|
||||||
|
|
||||||
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
import org.apache.commons.logging.Log;
|
||||||
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
|
||||||
|
public class DbClient implements Closeable {
|
||||||
|
|
||||||
|
private static final Log log = LogFactory.getLog(DbClient.class);
|
||||||
|
|
||||||
|
private Connection connection;
|
||||||
|
|
||||||
|
public DbClient(final String address, final String login, final String password) {
|
||||||
|
|
||||||
|
try {
|
||||||
|
Class.forName("org.postgresql.Driver");
|
||||||
|
|
||||||
|
this.connection =
|
||||||
|
StringUtils.isNoneBlank(login, password) ? DriverManager.getConnection(address, login, password) : DriverManager.getConnection(address);
|
||||||
|
this.connection.setAutoCommit(false);
|
||||||
|
} catch (final Exception e) {
|
||||||
|
log.error(e.getClass().getName() + ": " + e.getMessage());
|
||||||
|
throw new RuntimeException(e);
|
||||||
|
}
|
||||||
|
log.info("Opened database successfully");
|
||||||
|
}
|
||||||
|
|
||||||
|
public void processResults(final String sql, final Consumer<ResultSet> consumer) {
|
||||||
|
|
||||||
|
try (final Statement stmt = connection.createStatement()) {
|
||||||
|
stmt.setFetchSize(100);
|
||||||
|
|
||||||
|
try (final ResultSet rs = stmt.executeQuery(sql)) {
|
||||||
|
while (rs.next()) {
|
||||||
|
consumer.accept(rs);
|
||||||
|
}
|
||||||
|
} catch (final SQLException e) {
|
||||||
|
throw new RuntimeException(e);
|
||||||
|
}
|
||||||
|
} catch (final SQLException e1) {
|
||||||
|
throw new RuntimeException(e1);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void close() throws IOException {
|
||||||
|
try {
|
||||||
|
connection.close();
|
||||||
|
} catch (final SQLException e) {
|
||||||
|
throw new RuntimeException(e);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,56 @@
|
||||||
|
package eu.dnetlib.dhp.migration;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
import org.apache.hadoop.io.Text;
|
||||||
|
import org.apache.spark.api.java.JavaRDD;
|
||||||
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
import scala.Tuple2;
|
||||||
|
|
||||||
|
import java.util.Arrays;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
public class ExtractEntitiesFromHDFSJob {
|
||||||
|
|
||||||
|
|
||||||
|
private static List<String> folderNames = Arrays.asList("db_entities", "oaf_entities", "odf_entities");
|
||||||
|
|
||||||
|
public static void main(String[] args) throws Exception {
|
||||||
|
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||||
|
IOUtils.toString(MigrateMongoMdstoresApplication.class.getResourceAsStream("/eu/dnetlib/dhp/migration/extract_entities_from_hdfs_parameters.json")));
|
||||||
|
parser.parseArgument(args);
|
||||||
|
|
||||||
|
final SparkSession spark = SparkSession
|
||||||
|
.builder()
|
||||||
|
.appName(ExtractEntitiesFromHDFSJob.class.getSimpleName())
|
||||||
|
.master(parser.get("master"))
|
||||||
|
.getOrCreate();
|
||||||
|
|
||||||
|
final String sourcePath = parser.get("sourcePath");
|
||||||
|
final String targetPath = parser.get("graphRawPath");
|
||||||
|
final String entity = parser.get("entity");
|
||||||
|
|
||||||
|
|
||||||
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
|
|
||||||
|
JavaRDD<String> inputRdd = sc.emptyRDD();
|
||||||
|
|
||||||
|
|
||||||
|
folderNames.forEach(p -> inputRdd.union(
|
||||||
|
sc.sequenceFile(sourcePath+"/"+p, Text.class, Text.class)
|
||||||
|
.map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
|
||||||
|
.filter(k -> isEntityType(k._1(), entity))
|
||||||
|
.map(Tuple2::_2))
|
||||||
|
);
|
||||||
|
|
||||||
|
inputRdd.saveAsTextFile(targetPath+"/"+entity);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
private static boolean isEntityType(final String item, final String entity) {
|
||||||
|
return StringUtils.substringAfter(item, ":").equalsIgnoreCase(entity);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,94 @@
|
||||||
|
package eu.dnetlib.dhp.migration;
|
||||||
|
|
||||||
|
import java.io.Closeable;
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.HashMap;
|
||||||
|
import java.util.Map;
|
||||||
|
import java.util.stream.StreamSupport;
|
||||||
|
|
||||||
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
import org.apache.commons.logging.Log;
|
||||||
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
import org.bson.Document;
|
||||||
|
|
||||||
|
import com.google.common.collect.Iterables;
|
||||||
|
import com.mongodb.MongoClient;
|
||||||
|
import com.mongodb.MongoClientURI;
|
||||||
|
import com.mongodb.client.MongoCollection;
|
||||||
|
import com.mongodb.client.MongoDatabase;
|
||||||
|
|
||||||
|
public class MdstoreClient implements Closeable {
|
||||||
|
|
||||||
|
private final MongoClient client;
|
||||||
|
private final MongoDatabase db;
|
||||||
|
|
||||||
|
private static final String COLL_METADATA = "metadata";
|
||||||
|
private static final String COLL_METADATA_MANAGER = "metadataManager";
|
||||||
|
|
||||||
|
private static final Log log = LogFactory.getLog(MdstoreClient.class);
|
||||||
|
|
||||||
|
public MdstoreClient(final String baseUrl, final String dbName) {
|
||||||
|
this.client = new MongoClient(new MongoClientURI(baseUrl));
|
||||||
|
this.db = getDb(client, dbName);
|
||||||
|
}
|
||||||
|
|
||||||
|
public Map<String, String> validCollections(final String mdFormat, final String mdLayout, final String mdInterpretation) {
|
||||||
|
|
||||||
|
final Map<String, String> transactions = new HashMap<>();
|
||||||
|
for (final Document entry : getColl(db, COLL_METADATA_MANAGER, true).find()) {
|
||||||
|
final String mdId = entry.getString("mdId");
|
||||||
|
final String currentId = entry.getString("currentId");
|
||||||
|
if (StringUtils.isNoneBlank(mdId, currentId)) {
|
||||||
|
transactions.put(mdId, currentId);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
final Map<String, String> res = new HashMap<>();
|
||||||
|
for (final Document entry : getColl(db, COLL_METADATA, true).find()) {
|
||||||
|
if (entry.getString("format").equals(mdFormat) && entry.getString("layout").equals(mdLayout)
|
||||||
|
&& entry.getString("interpretation").equals(mdInterpretation) && transactions.containsKey(entry.getString("mdId"))) {
|
||||||
|
res.put(entry.getString("mdId"), transactions.get(entry.getString("mdId")));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
private MongoDatabase getDb(final MongoClient client, final String dbName) {
|
||||||
|
if (!Iterables.contains(client.listDatabaseNames(), dbName)) {
|
||||||
|
final String err = String.format("Database '%s' not found in %s", dbName, client.getAddress());
|
||||||
|
log.warn(err);
|
||||||
|
throw new RuntimeException(err);
|
||||||
|
}
|
||||||
|
return client.getDatabase(dbName);
|
||||||
|
}
|
||||||
|
|
||||||
|
private MongoCollection<Document> getColl(final MongoDatabase db, final String collName, final boolean abortIfMissing) {
|
||||||
|
if (!Iterables.contains(db.listCollectionNames(), collName)) {
|
||||||
|
final String err = String.format(String.format("Missing collection '%s' in database '%s'", collName, db.getName()));
|
||||||
|
log.warn(err);
|
||||||
|
if (abortIfMissing) {
|
||||||
|
throw new RuntimeException(err);
|
||||||
|
} else {
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return db.getCollection(collName);
|
||||||
|
}
|
||||||
|
|
||||||
|
public Iterable<String> listRecords(final String collName) {
|
||||||
|
final MongoCollection<Document> coll = getColl(db, collName, false);
|
||||||
|
return coll == null ? new ArrayList<>()
|
||||||
|
: () -> StreamSupport.stream(coll.find().spliterator(), false)
|
||||||
|
.filter(e -> e.containsKey("body"))
|
||||||
|
.map(e -> e.getString("body"))
|
||||||
|
.iterator();
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void close() throws IOException {
|
||||||
|
client.close();
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,520 @@
|
||||||
|
package eu.dnetlib.dhp.migration;
|
||||||
|
|
||||||
|
import java.io.Closeable;
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.sql.Array;
|
||||||
|
import java.sql.ResultSet;
|
||||||
|
import java.sql.SQLException;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.Arrays;
|
||||||
|
import java.util.Date;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.function.Consumer;
|
||||||
|
|
||||||
|
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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Datasource;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Journal;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Organization;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
|
|
||||||
|
public class MigrateDbEntitiesApplication extends AbstractMigrationExecutor implements Closeable {
|
||||||
|
|
||||||
|
private static final Qualifier ENTITYREGISTRY_PROVENANCE_ACTION =
|
||||||
|
qualifier("sysimport:crosswalk:entityregistry", "sysimport:crosswalk:entityregistry", "dnet:provenance_actions", "dnet:provenance_actions");
|
||||||
|
|
||||||
|
private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class);
|
||||||
|
|
||||||
|
private final DbClient dbClient;
|
||||||
|
|
||||||
|
private final long lastUpdateTimestamp;
|
||||||
|
|
||||||
|
public static void main(final String[] args) throws Exception {
|
||||||
|
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||||
|
IOUtils.toString(MigrateDbEntitiesApplication.class.getResourceAsStream("/eu/dnetlib/dhp/migration/migrate_db_entities_parameters.json")));
|
||||||
|
|
||||||
|
parser.parseArgument(args);
|
||||||
|
|
||||||
|
final String dbUrl = parser.get("postgresUrl");
|
||||||
|
final String dbUser = parser.get("postgresUser");
|
||||||
|
final String dbPassword = parser.get("postgresPassword");
|
||||||
|
|
||||||
|
final String hdfsPath = parser.get("hdfsPath");
|
||||||
|
final String hdfsNameNode = parser.get("namenode");
|
||||||
|
final String hdfsUser = parser.get("hdfsUser");
|
||||||
|
|
||||||
|
try (final MigrateDbEntitiesApplication smdbe = new MigrateDbEntitiesApplication(hdfsPath, hdfsNameNode, hdfsUser, dbUrl, dbUser, dbPassword)) {
|
||||||
|
log.info("Processing datasources...");
|
||||||
|
smdbe.execute("queryDatasources.sql", smdbe::processDatasource);
|
||||||
|
|
||||||
|
log.info("Processing projects...");
|
||||||
|
smdbe.execute("queryProjects.sql", smdbe::processProject);
|
||||||
|
|
||||||
|
log.info("Processing orgs...");
|
||||||
|
smdbe.execute("queryOrganizations.sql", smdbe::processOrganization);
|
||||||
|
|
||||||
|
log.info("Processing relations ds <-> orgs ...");
|
||||||
|
smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization);
|
||||||
|
|
||||||
|
log.info("Processing projects <-> orgs ...");
|
||||||
|
smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization);
|
||||||
|
|
||||||
|
log.info("All done.");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public MigrateDbEntitiesApplication(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String dbUrl, final String dbUser,
|
||||||
|
final String dbPassword) throws Exception {
|
||||||
|
super(hdfsPath, hdfsNameNode, hdfsUser);
|
||||||
|
this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
|
||||||
|
this.lastUpdateTimestamp = new Date().getTime();
|
||||||
|
}
|
||||||
|
|
||||||
|
public void execute(final String sqlFile, final Consumer<ResultSet> consumer) throws Exception {
|
||||||
|
final String sql = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/migration/sql/" + sqlFile));
|
||||||
|
dbClient.processResults(sql, consumer);
|
||||||
|
}
|
||||||
|
|
||||||
|
public void processDatasource(final ResultSet rs) {
|
||||||
|
|
||||||
|
try {
|
||||||
|
|
||||||
|
final DataInfo info = prepareDataInfo(rs);
|
||||||
|
|
||||||
|
final Datasource ds = new Datasource();
|
||||||
|
|
||||||
|
ds.setId(createOpenaireId(10, rs.getString("datasourceid")));
|
||||||
|
ds.setOriginalId(Arrays.asList(rs.getString("datasourceid")));
|
||||||
|
ds.setCollectedfrom(listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname")));
|
||||||
|
ds.setPid(new ArrayList<>());
|
||||||
|
ds.setDateofcollection(asString(rs.getDate("dateofcollection")));
|
||||||
|
ds.setDateoftransformation(null); // Value not returned by the SQL query
|
||||||
|
ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB
|
||||||
|
ds.setOaiprovenance(null); // Values not present in the DB
|
||||||
|
ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype")));
|
||||||
|
ds.setOpenairecompatibility(prepareQualifierSplitting(rs.getString("openairecompatibility")));
|
||||||
|
ds.setOfficialname(field(rs.getString("officialname"), info));
|
||||||
|
ds.setEnglishname(field(rs.getString("englishname"), info));
|
||||||
|
ds.setWebsiteurl(field(rs.getString("websiteurl"), info));
|
||||||
|
ds.setLogourl(field(rs.getString("logourl"), info));
|
||||||
|
ds.setContactemail(field(rs.getString("contactemail"), info));
|
||||||
|
ds.setNamespaceprefix(field(rs.getString("namespaceprefix"), info));
|
||||||
|
ds.setLatitude(field(Double.toString(rs.getDouble("latitude")), info));
|
||||||
|
ds.setLongitude(field(Double.toString(rs.getDouble("longitude")), info));
|
||||||
|
ds.setDateofvalidation(field(asString(rs.getDate("dateofvalidation")), info));
|
||||||
|
ds.setDescription(field(rs.getString("description"), info));
|
||||||
|
ds.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info));
|
||||||
|
ds.setOdnumberofitems(field(Double.toString(rs.getInt("odnumberofitems")), info));
|
||||||
|
ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info));
|
||||||
|
ds.setOdpolicies(field(rs.getString("odpolicies"), info));
|
||||||
|
ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info));
|
||||||
|
ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info));
|
||||||
|
ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info));
|
||||||
|
ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info));
|
||||||
|
ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info));
|
||||||
|
ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info));
|
||||||
|
ds.setDataprovider(field(rs.getBoolean("dataprovider"), info));
|
||||||
|
ds.setServiceprovider(field(rs.getBoolean("serviceprovider"), info));
|
||||||
|
ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info));
|
||||||
|
ds.setDatauploadtype(field(rs.getString("datauploadtype"), info));
|
||||||
|
ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info));
|
||||||
|
ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info));
|
||||||
|
ds.setVersioning(field(rs.getBoolean("versioning"), info));
|
||||||
|
ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info));
|
||||||
|
ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info));
|
||||||
|
ds.setPidsystems(field(rs.getString("pidsystems"), info));
|
||||||
|
ds.setCertificates(field(rs.getString("certificates"), info));
|
||||||
|
ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array
|
||||||
|
ds.setJournal(prepareJournal(rs.getString("officialname"), rs.getString("journal"), info)); // Journal
|
||||||
|
ds.setDataInfo(info);
|
||||||
|
ds.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
|
|
||||||
|
// rs.getString("datasourceid");
|
||||||
|
// rs.getArray("identities");
|
||||||
|
// rs.getString("officialname");
|
||||||
|
// rs.getString("englishname");
|
||||||
|
// rs.getString("contactemail");
|
||||||
|
// rs.getString("openairecompatibility"); // COMPLEX ...@@@...
|
||||||
|
// rs.getString("websiteurl");
|
||||||
|
// rs.getString("logourl");
|
||||||
|
// rs.getArray("accessinfopackage");
|
||||||
|
// rs.getDouble("latitude");
|
||||||
|
// rs.getDouble("longitude");
|
||||||
|
// rs.getString("namespaceprefix");
|
||||||
|
// rs.getInt("odnumberofitems"); // NULL
|
||||||
|
// rs.getDate("odnumberofitemsdate"); // NULL
|
||||||
|
// rs.getArray("subjects");
|
||||||
|
// rs.getString("description");
|
||||||
|
// rs.getString("odpolicies"); // NULL
|
||||||
|
// rs.getArray("odlanguages");
|
||||||
|
// rs.getArray("odcontenttypes");
|
||||||
|
// rs.getBoolean("inferred"); // false
|
||||||
|
// rs.getBoolean("deletedbyinference");// false
|
||||||
|
// rs.getDouble("trust"); // 0.9
|
||||||
|
// rs.getString("inferenceprovenance"); // NULL
|
||||||
|
// rs.getDate("dateofcollection");
|
||||||
|
// rs.getDate("dateofvalidation");
|
||||||
|
// rs.getDate("releasestartdate");
|
||||||
|
// rs.getDate("releaseenddate");
|
||||||
|
// rs.getString("missionstatementurl");
|
||||||
|
// rs.getBoolean("dataprovider");
|
||||||
|
// rs.getBoolean("serviceprovider");
|
||||||
|
// rs.getString("databaseaccesstype");
|
||||||
|
// rs.getString("datauploadtype");
|
||||||
|
// rs.getString("databaseaccessrestriction");
|
||||||
|
// rs.getString("datauploadrestriction");
|
||||||
|
// rs.getBoolean("versioning");
|
||||||
|
// rs.getString("citationguidelineurl");
|
||||||
|
// rs.getString("qualitymanagementkind");
|
||||||
|
// rs.getString("pidsystems");
|
||||||
|
// rs.getString("certificates");
|
||||||
|
// rs.getArray("policies");
|
||||||
|
// rs.getString("collectedfromid");
|
||||||
|
// rs.getString("collectedfromname");
|
||||||
|
// rs.getString("datasourcetype"); // COMPLEX
|
||||||
|
// rs.getString("provenanceaction"); //
|
||||||
|
// 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions'
|
||||||
|
// AS provenanceaction,
|
||||||
|
// rs.getString("journal"); // CONCAT(d.issn, '@@@', d.eissn, '@@@', d.lissn) AS journal
|
||||||
|
|
||||||
|
emitOaf(ds);
|
||||||
|
} catch (final Exception e) {
|
||||||
|
throw new RuntimeException(e);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public void processProject(final ResultSet rs) {
|
||||||
|
try {
|
||||||
|
|
||||||
|
final DataInfo info = prepareDataInfo(rs);
|
||||||
|
|
||||||
|
final Project p = new Project();
|
||||||
|
|
||||||
|
p.setId(createOpenaireId(40, rs.getString("projectid")));
|
||||||
|
p.setOriginalId(Arrays.asList(rs.getString("projectid")));
|
||||||
|
p.setCollectedfrom(listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname")));
|
||||||
|
p.setPid(new ArrayList<>());
|
||||||
|
p.setDateofcollection(asString(rs.getDate("dateofcollection")));
|
||||||
|
p.setDateoftransformation(asString(rs.getDate("dateoftransformation")));
|
||||||
|
p.setExtraInfo(new ArrayList<>()); // Values not present in the DB
|
||||||
|
p.setOaiprovenance(null); // Values not present in the DB
|
||||||
|
p.setWebsiteurl(field(rs.getString("websiteurl"), info));
|
||||||
|
p.setCode(field(rs.getString("code"), info));
|
||||||
|
p.setAcronym(field(rs.getString("acronym"), info));
|
||||||
|
p.setTitle(field(rs.getString("title"), info));
|
||||||
|
p.setStartdate(field(asString(rs.getDate("startdate")), info));
|
||||||
|
p.setEnddate(field(asString(rs.getDate("enddate")), info));
|
||||||
|
p.setCallidentifier(field(rs.getString("callidentifier"), info));
|
||||||
|
p.setKeywords(field(rs.getString("keywords"), info));
|
||||||
|
p.setDuration(field(Integer.toString(rs.getInt("duration")), info));
|
||||||
|
p.setEcsc39(field(Boolean.toString(rs.getBoolean("ecsc39")), info));
|
||||||
|
p.setOamandatepublications(field(Boolean.toString(rs.getBoolean("oamandatepublications")), info));
|
||||||
|
p.setEcarticle29_3(field(Boolean.toString(rs.getBoolean("ecarticle29_3")), info));
|
||||||
|
p.setSubjects(prepareListOfStructProps(rs.getArray("subjects"), info));
|
||||||
|
p.setFundingtree(prepareListFields(rs.getArray("fundingtree"), info));
|
||||||
|
p.setContracttype(prepareQualifierSplitting(rs.getString("contracttype")));
|
||||||
|
p.setOptional1(field(rs.getString("optional1"), info));
|
||||||
|
p.setOptional2(field(rs.getString("optional2"), info));
|
||||||
|
p.setJsonextrainfo(field(rs.getString("jsonextrainfo"), info));
|
||||||
|
p.setContactfullname(field(rs.getString("contactfullname"), info));
|
||||||
|
p.setContactfax(field(rs.getString("contactfax"), info));
|
||||||
|
p.setContactphone(field(rs.getString("contactphone"), info));
|
||||||
|
p.setContactemail(field(rs.getString("contactemail"), info));
|
||||||
|
p.setSummary(field(rs.getString("summary"), info));
|
||||||
|
p.setCurrency(field(rs.getString("currency"), info));
|
||||||
|
p.setTotalcost(new Float(rs.getDouble("totalcost")));
|
||||||
|
p.setFundedamount(new Float(rs.getDouble("fundedamount")));
|
||||||
|
p.setDataInfo(info);
|
||||||
|
p.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
|
|
||||||
|
// rs.getString("projectid");
|
||||||
|
// rs.getString("code");
|
||||||
|
// rs.getString("websiteurl");
|
||||||
|
// rs.getString("acronym");
|
||||||
|
// rs.getString("title");
|
||||||
|
// rs.getDate("startdate");
|
||||||
|
// rs.getDate("enddate");
|
||||||
|
// rs.getString("callidentifier");
|
||||||
|
// rs.getString("keywords");
|
||||||
|
// rs.getInt("duration");
|
||||||
|
// rs.getBoolean("ecsc39");
|
||||||
|
// rs.getBoolean("oamandatepublications");
|
||||||
|
// rs.getBoolean("ecarticle29_3");
|
||||||
|
// rs.getDate("dateofcollection");
|
||||||
|
// rs.getDate("dateoftransformation");
|
||||||
|
// rs.getBoolean("inferred");
|
||||||
|
// rs.getBoolean("deletedbyinference");
|
||||||
|
// rs.getDouble("trust");
|
||||||
|
// rs.getString("inferenceprovenance");
|
||||||
|
// rs.getString("optional1");
|
||||||
|
// rs.getString("optional2");
|
||||||
|
// rs.getString("jsonextrainfo");
|
||||||
|
// rs.getString("contactfullname");
|
||||||
|
// rs.getString("contactfax");
|
||||||
|
// rs.getString("contactphone");
|
||||||
|
// rs.getString("contactemail");
|
||||||
|
// rs.getString("summary");
|
||||||
|
// rs.getString("currency");
|
||||||
|
// rs.getDouble("totalcost");
|
||||||
|
// rs.getDouble("fundedamount");
|
||||||
|
// rs.getString("collectedfromid");
|
||||||
|
// rs.getString("collectedfromname");
|
||||||
|
// rs.getString("contracttype"); // COMPLEX
|
||||||
|
// rs.getString("provenanceaction"); // COMPLEX
|
||||||
|
// rs.getArray("pid");
|
||||||
|
// rs.getArray("subjects");
|
||||||
|
// rs.getArray("fundingtree");
|
||||||
|
|
||||||
|
emitOaf(p);
|
||||||
|
|
||||||
|
} catch (final Exception e) {
|
||||||
|
throw new RuntimeException(e);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public void processOrganization(final ResultSet rs) {
|
||||||
|
|
||||||
|
try {
|
||||||
|
|
||||||
|
final DataInfo info = prepareDataInfo(rs);
|
||||||
|
|
||||||
|
final Organization o = new Organization();
|
||||||
|
|
||||||
|
o.setId(createOpenaireId(20, rs.getString("organizationid")));
|
||||||
|
o.setOriginalId(Arrays.asList(rs.getString("organizationid")));
|
||||||
|
o.setCollectedfrom(listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname")));
|
||||||
|
o.setPid(new ArrayList<>());
|
||||||
|
o.setDateofcollection(asString(rs.getDate("dateofcollection")));
|
||||||
|
o.setDateoftransformation(asString(rs.getDate("dateoftransformation")));
|
||||||
|
o.setExtraInfo(new ArrayList<>()); // Values not present in the DB
|
||||||
|
o.setOaiprovenance(null); // Values not present in the DB
|
||||||
|
o.setLegalshortname(field("legalshortname", info));
|
||||||
|
o.setLegalname(field("legalname", info));
|
||||||
|
o.setAlternativeNames(new ArrayList<>()); // Values not returned by the SQL query
|
||||||
|
o.setWebsiteurl(field("websiteurl", info));
|
||||||
|
o.setLogourl(field("logourl", info));
|
||||||
|
o.setEclegalbody(field(Boolean.toString(rs.getBoolean("eclegalbody")), info));
|
||||||
|
o.setEclegalperson(field(Boolean.toString(rs.getBoolean("eclegalperson")), info));
|
||||||
|
o.setEcnonprofit(field(Boolean.toString(rs.getBoolean("ecnonprofit")), info));
|
||||||
|
o.setEcresearchorganization(field(Boolean.toString(rs.getBoolean("ecresearchorganization")), info));
|
||||||
|
o.setEchighereducation(field(Boolean.toString(rs.getBoolean("echighereducation")), info));
|
||||||
|
o.setEcinternationalorganizationeurinterests(field(Boolean.toString(rs.getBoolean("ecinternationalorganizationeurinterests")), info));
|
||||||
|
o.setEcinternationalorganization(field(Boolean.toString(rs.getBoolean("ecinternationalorganization")), info));
|
||||||
|
o.setEcenterprise(field(Boolean.toString(rs.getBoolean("ecenterprise")), info));
|
||||||
|
o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info));
|
||||||
|
o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info));
|
||||||
|
o.setCountry(prepareQualifierSplitting(rs.getString("country")));
|
||||||
|
o.setDataInfo(info);
|
||||||
|
o.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
|
|
||||||
|
// rs.getString("organizationid");
|
||||||
|
// rs.getString("legalshortname");
|
||||||
|
// rs.getString("legalname");
|
||||||
|
// rs.getString("websiteurl");
|
||||||
|
// rs.getString("logourl");
|
||||||
|
// rs.getBoolean("eclegalbody");
|
||||||
|
// rs.getBoolean("eclegalperson");
|
||||||
|
// rs.getBoolean("ecnonprofit");
|
||||||
|
// rs.getBoolean("ecresearchorganization");
|
||||||
|
// rs.getBoolean("echighereducation");
|
||||||
|
// rs.getBoolean("ecinternationalorganizationeurinterests");
|
||||||
|
// rs.getBoolean("ecinternationalorganization");
|
||||||
|
// rs.getBoolean("ecenterprise");
|
||||||
|
// rs.getBoolean("ecsmevalidated");
|
||||||
|
// rs.getBoolean("ecnutscode");
|
||||||
|
// rs.getDate("dateofcollection");
|
||||||
|
// rs.getDate("dateoftransformation");
|
||||||
|
// rs.getBoolean("inferred");
|
||||||
|
// rs.getBoolean("deletedbyinference");
|
||||||
|
// rs.getDouble("trust");
|
||||||
|
// rs.getString("inferenceprovenance");
|
||||||
|
// rs.getString("collectedfromid");
|
||||||
|
// rs.getString("collectedfromname");
|
||||||
|
// rs.getString("country");
|
||||||
|
// rs.getString("provenanceaction");
|
||||||
|
// rs.getArray("pid");
|
||||||
|
|
||||||
|
emitOaf(o);
|
||||||
|
} catch (final Exception e) {
|
||||||
|
throw new RuntimeException(e);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public void processDatasourceOrganization(final ResultSet rs) {
|
||||||
|
|
||||||
|
try {
|
||||||
|
final DataInfo info = prepareDataInfo(rs);
|
||||||
|
final String orgId = createOpenaireId(20, rs.getString("organization"));
|
||||||
|
final String dsId = createOpenaireId(10, rs.getString("datasource"));
|
||||||
|
final List<KeyValue> collectedFrom = listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname"));
|
||||||
|
|
||||||
|
final Relation r1 = new Relation();
|
||||||
|
r1.setRelType("datasourceOrganization");
|
||||||
|
r1.setSubRelType("provision");
|
||||||
|
r1.setRelClass("isProvidedBy");
|
||||||
|
r1.setSource(dsId);
|
||||||
|
r1.setTarget(orgId);
|
||||||
|
r1.setCollectedFrom(collectedFrom);
|
||||||
|
r1.setDataInfo(info);
|
||||||
|
r1.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
|
emitOaf(r1);
|
||||||
|
|
||||||
|
final Relation r2 = new Relation();
|
||||||
|
r2.setRelType("datasourceOrganization");
|
||||||
|
r2.setSubRelType("provision");
|
||||||
|
r2.setRelClass("provides");
|
||||||
|
r2.setSource(orgId);
|
||||||
|
r2.setTarget(dsId);
|
||||||
|
r2.setCollectedFrom(collectedFrom);
|
||||||
|
r2.setDataInfo(info);
|
||||||
|
r1.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
|
emitOaf(r2);
|
||||||
|
|
||||||
|
// rs.getString("datasource");
|
||||||
|
// rs.getString("organization");
|
||||||
|
// rs.getDate("startdate"); // NULL
|
||||||
|
// rs.getDate("enddate"); // NULL
|
||||||
|
// rs.getBoolean("inferred"); // false
|
||||||
|
// rs.getBoolean("deletedbyinference"); // false
|
||||||
|
// rs.getDouble("trust"); // 0.9
|
||||||
|
// rs.getString("inferenceprovenance"); // NULL
|
||||||
|
// rs.getString("semantics"); // 'providedBy@@@provided
|
||||||
|
// by@@@dnet:datasources_organizations_typologies@@@dnet:datasources_organizations_typologies' AS
|
||||||
|
// semantics,
|
||||||
|
// rs.getString("provenanceaction"); // d.provenanceaction || '@@@' || d.provenanceaction ||
|
||||||
|
// '@@@dnet:provenanceActions@@@dnet:provenanceActions' AS provenanceaction
|
||||||
|
|
||||||
|
} catch (final Exception e) {
|
||||||
|
throw new RuntimeException(e);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public void processProjectOrganization(final ResultSet rs) {
|
||||||
|
|
||||||
|
try {
|
||||||
|
final DataInfo info = prepareDataInfo(rs);
|
||||||
|
final String orgId = createOpenaireId(20, rs.getString("resporganization"));
|
||||||
|
final String projectId = createOpenaireId(40, rs.getString("project"));
|
||||||
|
final List<KeyValue> collectedFrom = listKeyValues(rs.getString("collectedfromid"), rs.getString("collectedfromname"));
|
||||||
|
|
||||||
|
final Relation r1 = new Relation();
|
||||||
|
r1.setRelType("projectOrganization");
|
||||||
|
r1.setSubRelType("participation");
|
||||||
|
r1.setRelClass("isParticipant");
|
||||||
|
r1.setSource(projectId);
|
||||||
|
r1.setTarget(orgId);
|
||||||
|
r1.setCollectedFrom(collectedFrom);
|
||||||
|
r1.setDataInfo(info);
|
||||||
|
r1.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
|
emitOaf(r1);
|
||||||
|
|
||||||
|
final Relation r2 = new Relation();
|
||||||
|
r2.setRelType("projectOrganization");
|
||||||
|
r2.setSubRelType("participation");
|
||||||
|
r2.setRelClass("hasParticipant");
|
||||||
|
r2.setSource(orgId);
|
||||||
|
r2.setTarget(projectId);
|
||||||
|
r2.setCollectedFrom(collectedFrom);
|
||||||
|
r2.setDataInfo(info);
|
||||||
|
r1.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
|
emitOaf(r2);
|
||||||
|
|
||||||
|
// rs.getString("project");
|
||||||
|
// rs.getString("resporganization");
|
||||||
|
// rs.getInt("participantnumber");
|
||||||
|
// rs.getDouble("contribution");
|
||||||
|
// rs.getDate("startdate");// null
|
||||||
|
// rs.getDate("enddate");// null
|
||||||
|
// rs.getBoolean("inferred");// false
|
||||||
|
// rs.getBoolean("deletedbyinference"); // false
|
||||||
|
// rs.getDouble("trust");
|
||||||
|
// rs.getString("inferenceprovenance"); // NULL
|
||||||
|
// rs.getString("semantics"); // po.semanticclass || '@@@' || po.semanticclass ||
|
||||||
|
// '@@@dnet:project_organization_relations@@@dnet:project_organization_relations' AS semantics,
|
||||||
|
// rs.getString("provenanceaction"); //
|
||||||
|
// 'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions'
|
||||||
|
// AS provenanceaction
|
||||||
|
|
||||||
|
} catch (final Exception e) {
|
||||||
|
throw new RuntimeException(e);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private DataInfo prepareDataInfo(final ResultSet rs) throws SQLException {
|
||||||
|
final Boolean deletedbyinference = rs.getBoolean("deletedbyinference");
|
||||||
|
final String inferenceprovenance = rs.getString("inferenceprovenance");
|
||||||
|
final Boolean inferred = rs.getBoolean("inferred");
|
||||||
|
final String trust = rs.getString("trust");
|
||||||
|
return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, ENTITYREGISTRY_PROVENANCE_ACTION, trust);
|
||||||
|
}
|
||||||
|
|
||||||
|
private Qualifier prepareQualifierSplitting(final String s) {
|
||||||
|
if (StringUtils.isBlank(s)) { return null; }
|
||||||
|
final String[] arr = s.split("@@@");
|
||||||
|
return arr.length == 4 ? qualifier(arr[0], arr[1], arr[2], arr[3]) : null;
|
||||||
|
}
|
||||||
|
|
||||||
|
private List<Field<String>> prepareListFields(final Array array, final DataInfo info) {
|
||||||
|
try {
|
||||||
|
return listFields(info, (String[]) array.getArray());
|
||||||
|
} catch (final SQLException e) {
|
||||||
|
throw new RuntimeException("Invalid SQL array", e);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private StructuredProperty prepareStructProp(final String s, final DataInfo dataInfo) {
|
||||||
|
if (StringUtils.isBlank(s)) { return null; }
|
||||||
|
final String[] parts = s.split("###");
|
||||||
|
if (parts.length == 2) {
|
||||||
|
final String value = parts[0];
|
||||||
|
final String[] arr = parts[1].split("@@@");
|
||||||
|
if (arr.length == 4) { return structuredProperty(value, arr[0], arr[1], arr[2], arr[3], dataInfo); }
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
private List<StructuredProperty> prepareListOfStructProps(final Array array, final DataInfo dataInfo) throws SQLException {
|
||||||
|
final List<StructuredProperty> res = new ArrayList<>();
|
||||||
|
if (array != null) {
|
||||||
|
for (final String s : (String[]) array.getArray()) {
|
||||||
|
final StructuredProperty sp = prepareStructProp(s, dataInfo);
|
||||||
|
if (sp != null) {
|
||||||
|
res.add(sp);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
private Journal prepareJournal(final String name, final String sj, final DataInfo info) {
|
||||||
|
if (StringUtils.isNotBlank(sj)) {
|
||||||
|
final String[] arr = sj.split("@@@");
|
||||||
|
if (arr.length == 3) {
|
||||||
|
final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null;
|
||||||
|
final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null;;
|
||||||
|
final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null;;
|
||||||
|
if (issn != null || eissn != null
|
||||||
|
|| lissn != null) { return journal(name, issn, eissn, eissn, null, null, null, null, null, null, null, info); }
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void close() throws IOException {
|
||||||
|
super.close();
|
||||||
|
dbClient.close();
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,45 @@
|
||||||
|
package eu.dnetlib.dhp.migration;
|
||||||
|
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
|
||||||
|
public class MigrateMongoMdstoresApplication {
|
||||||
|
|
||||||
|
public static void main(final String[] args) throws Exception {
|
||||||
|
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||||
|
IOUtils.toString(MigrateMongoMdstoresApplication.class.getResourceAsStream("/eu/dnetlib/dhp/migration/migrate_mongo_mstores_parameters.json")));
|
||||||
|
parser.parseArgument(args);
|
||||||
|
|
||||||
|
final String mongoBaseUrl = parser.get("mongoBaseUrl");
|
||||||
|
final String mongoDb = parser.get("mongoDb");
|
||||||
|
|
||||||
|
final String mdFormat = parser.get("mdFormat");
|
||||||
|
final String mdLayout = parser.get("mdLayout");
|
||||||
|
final String mdInterpretation = parser.get("mdInterpretation");
|
||||||
|
|
||||||
|
final String hdfsPath = parser.get("hdfsPath");
|
||||||
|
final String hdfsNameNode = parser.get("namenode");
|
||||||
|
final String hdfsUser = parser.get("hdfsUser");
|
||||||
|
|
||||||
|
final String dbUrl = parser.get("postgresUrl");
|
||||||
|
final String dbUser = parser.get("postgresUser");
|
||||||
|
final String dbPassword = parser.get("postgresPassword");
|
||||||
|
|
||||||
|
if (mdFormat.equalsIgnoreCase("oaf")) {
|
||||||
|
try (final OafMigrationExecutor mig =
|
||||||
|
new OafMigrationExecutor(hdfsPath, hdfsNameNode, hdfsUser, mongoBaseUrl, mongoDb, dbUrl, dbUser, dbPassword)) {
|
||||||
|
mig.processMdRecords(mdFormat, mdLayout, mdInterpretation);
|
||||||
|
}
|
||||||
|
} else if (mdFormat.equalsIgnoreCase("odf")) {
|
||||||
|
try (final OdfMigrationExecutor mig =
|
||||||
|
new OdfMigrationExecutor(hdfsPath, hdfsNameNode, hdfsUser, mongoBaseUrl, mongoDb, dbUrl, dbUser, dbPassword)) {
|
||||||
|
mig.processMdRecords(mdFormat, mdLayout, mdInterpretation);
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
throw new RuntimeException("Format not supported: " + mdFormat);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,251 @@
|
||||||
|
package eu.dnetlib.dhp.migration;
|
||||||
|
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.Arrays;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Map;
|
||||||
|
|
||||||
|
import org.apache.commons.logging.Log;
|
||||||
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
import org.dom4j.Document;
|
||||||
|
import org.dom4j.Node;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.migration.pace.PacePerson;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Author;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.GeoLocation;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Instance;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
|
|
||||||
|
public class OafMigrationExecutor extends AbstractMongoExecutor {
|
||||||
|
|
||||||
|
private static final Log log = LogFactory.getLog(OafMigrationExecutor.class);
|
||||||
|
|
||||||
|
public OafMigrationExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String mongoBaseUrl, final String mongoDb,
|
||||||
|
final String dbUrl, final String dbUser,
|
||||||
|
final String dbPassword) throws Exception {
|
||||||
|
super(hdfsPath, hdfsNameNode, hdfsUser, mongoBaseUrl, mongoDb, dbUrl, dbUser, dbPassword);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected void registerNamespaces(final Map<String, String> nsContext) {
|
||||||
|
super.registerNamespaces(nsContext);
|
||||||
|
nsContext.put("dc", "http://purl.org/dc/elements/1.1/");
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Author> prepareAuthors(final Document doc, final DataInfo info) {
|
||||||
|
final List<Author> res = new ArrayList<>();
|
||||||
|
int pos = 1;
|
||||||
|
for (final Object o : doc.selectNodes("//dc:creator")) {
|
||||||
|
final Node n = (Node) o;
|
||||||
|
final Author author = new Author();
|
||||||
|
author.setFullname(n.getText());
|
||||||
|
author.setRank(pos++);
|
||||||
|
final PacePerson p = new PacePerson(n.getText(), false);
|
||||||
|
if (p.isAccurate()) {
|
||||||
|
author.setName(p.getNormalisedFirstName());
|
||||||
|
author.setSurname(p.getNormalisedSurname());
|
||||||
|
}
|
||||||
|
res.add(author);
|
||||||
|
}
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Qualifier prepareLanguages(final Document doc) {
|
||||||
|
return prepareQualifier(doc, "//dc:language", "dnet:languages", "dnet:languages");
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<StructuredProperty> prepareSubjects(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListStructProps(doc, "//dc:subject", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<StructuredProperty> prepareTitles(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListStructProps(doc, "//dc:title", MAIN_TITLE_QUALIFIER, info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareDescriptions(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListFields(doc, "//dc:description", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> preparePublisher(final Document doc, final DataInfo info) {
|
||||||
|
return prepareField(doc, "//dc:publisher", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareFormats(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListFields(doc, "//dc:format", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareContributors(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListFields(doc, "//dc:contributor", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareCoverages(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListFields(doc, "//dc:coverage", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Instance> prepareInstances(final Document doc, final DataInfo info, final KeyValue collectedfrom, final KeyValue hostedby) {
|
||||||
|
final List<Instance> res = new ArrayList<>();
|
||||||
|
for (final Object o : doc.selectNodes("//dc:identifier")) {
|
||||||
|
final String url = ((Node) o).getText().trim();
|
||||||
|
if (url.startsWith("http")) {
|
||||||
|
final Instance instance = new Instance();
|
||||||
|
instance.setUrl(Arrays.asList(url));
|
||||||
|
instance.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", "dnet:publication_resource", "dnet:publication_resource"));
|
||||||
|
instance.setCollectedfrom(collectedfrom);
|
||||||
|
instance.setHostedby(hostedby);
|
||||||
|
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
|
||||||
|
instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
|
||||||
|
instance.setAccessright(prepareQualifier(doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes"));
|
||||||
|
instance.setLicense(field(doc.valueOf("//oaf:license"), info));
|
||||||
|
instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
|
||||||
|
instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
|
||||||
|
instance.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
|
||||||
|
res.add(instance);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareSources(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListFields(doc, "//dc:source", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<StructuredProperty> prepareRelevantDates(final Document doc, final DataInfo info) {
|
||||||
|
return new ArrayList<>(); // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
// SOFTWARES
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Qualifier prepareSoftwareProgrammingLanguage(final Document doc, final DataInfo info) {
|
||||||
|
return null; // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> prepareSoftwareCodeRepositoryUrl(final Document doc, final DataInfo info) {
|
||||||
|
return null; // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<StructuredProperty> prepareSoftwareLicenses(final Document doc, final DataInfo info) {
|
||||||
|
return new ArrayList<>(); // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareSoftwareDocumentationUrls(final Document doc, final DataInfo info) {
|
||||||
|
return new ArrayList<>(); // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
// DATASETS
|
||||||
|
@Override
|
||||||
|
protected List<GeoLocation> prepareDatasetGeoLocations(final Document doc, final DataInfo info) {
|
||||||
|
return new ArrayList<>(); // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> prepareDatasetMetadataVersionNumber(final Document doc, final DataInfo info) {
|
||||||
|
return null; // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> prepareDatasetLastMetadataUpdate(final Document doc, final DataInfo info) {
|
||||||
|
return null; // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> prepareDatasetVersion(final Document doc, final DataInfo info) {
|
||||||
|
return null; // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> prepareDatasetSize(final Document doc, final DataInfo info) {
|
||||||
|
return null; // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> prepareDatasetDevice(final Document doc, final DataInfo info) {
|
||||||
|
return null; // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> prepareDatasetStorageDate(final Document doc, final DataInfo info) {
|
||||||
|
return null; // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
// OTHER PRODUCTS
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareOtherResearchProductTools(final Document doc, final DataInfo info) {
|
||||||
|
return new ArrayList<>(); // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareOtherResearchProductContactGroups(final Document doc, final DataInfo info) {
|
||||||
|
return new ArrayList<>(); // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareOtherResearchProductContactPersons(final Document doc, final DataInfo info) {
|
||||||
|
return new ArrayList<>(); // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Oaf> addOtherResultRels(final Document doc,
|
||||||
|
final KeyValue collectedFrom,
|
||||||
|
final DataInfo info,
|
||||||
|
final long lastUpdateTimestamp) {
|
||||||
|
final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"));
|
||||||
|
|
||||||
|
final List<Oaf> res = new ArrayList<>();
|
||||||
|
|
||||||
|
for (final Object o : doc.selectNodes("//*[local-name()='relatedDataset']")) {
|
||||||
|
final String otherId = createOpenaireId(50, ((Node) o).getText());
|
||||||
|
|
||||||
|
final Relation r1 = new Relation();
|
||||||
|
r1.setRelType("resultResult");
|
||||||
|
r1.setSubRelType("publicationDataset");
|
||||||
|
r1.setRelClass("isRelatedTo");
|
||||||
|
r1.setSource(docId);
|
||||||
|
r1.setTarget(otherId);
|
||||||
|
r1.setCollectedFrom(Arrays.asList(collectedFrom));
|
||||||
|
r1.setDataInfo(info);
|
||||||
|
r1.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
|
res.add(r1);
|
||||||
|
|
||||||
|
final Relation r2 = new Relation();
|
||||||
|
r2.setRelType("resultResult");
|
||||||
|
r2.setSubRelType("publicationDataset");
|
||||||
|
r2.setRelClass("isRelatedTo");
|
||||||
|
r2.setSource(otherId);
|
||||||
|
r2.setTarget(docId);
|
||||||
|
r2.setCollectedFrom(Arrays.asList(collectedFrom));
|
||||||
|
r2.setDataInfo(info);
|
||||||
|
r2.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
|
res.add(r2);
|
||||||
|
}
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
|
||||||
|
return null; // NOT PRESENT IN OAF
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,273 @@
|
||||||
|
package eu.dnetlib.dhp.migration;
|
||||||
|
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.Arrays;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Map;
|
||||||
|
|
||||||
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
import org.apache.commons.logging.Log;
|
||||||
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
import org.dom4j.Document;
|
||||||
|
import org.dom4j.Node;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Author;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.GeoLocation;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Instance;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
|
|
||||||
|
public class OdfMigrationExecutor extends AbstractMongoExecutor {
|
||||||
|
|
||||||
|
private static final Log log = LogFactory.getLog(OdfMigrationExecutor.class);
|
||||||
|
|
||||||
|
public OdfMigrationExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String mongoBaseUrl, final String mongoDb,
|
||||||
|
final String dbUrl, final String dbUser,
|
||||||
|
final String dbPassword) throws Exception {
|
||||||
|
super(hdfsPath, hdfsNameNode, hdfsUser, mongoBaseUrl, mongoDb, dbUrl, dbUser, dbPassword);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected void registerNamespaces(final Map<String, String> nsContext) {
|
||||||
|
super.registerNamespaces(nsContext);
|
||||||
|
nsContext.put("dc", "http://datacite.org/schema/kernel-3");
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<StructuredProperty> prepareTitles(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListStructProps(doc, "//dc:title", MAIN_TITLE_QUALIFIER, info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Author> prepareAuthors(final Document doc, final DataInfo info) {
|
||||||
|
final List<Author> res = new ArrayList<>();
|
||||||
|
int pos = 1;
|
||||||
|
for (final Object o : doc.selectNodes("//dc:creator")) {
|
||||||
|
final Node n = (Node) o;
|
||||||
|
final Author author = new Author();
|
||||||
|
author.setFullname(n.valueOf("./dc:creatorName"));
|
||||||
|
author.setName(n.valueOf("./dc:givenName"));
|
||||||
|
author.setSurname(n.valueOf("./dc:familyName"));
|
||||||
|
author.setAffiliation(prepareListFields(doc, "./dc:affiliation", info));
|
||||||
|
author.setPid(preparePids(doc, info));
|
||||||
|
author.setRank(pos++);
|
||||||
|
res.add(author);
|
||||||
|
}
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
private List<StructuredProperty> preparePids(final Document doc, final DataInfo info) {
|
||||||
|
final List<StructuredProperty> res = new ArrayList<>();
|
||||||
|
for (final Object o : doc.selectNodes("./dc:nameIdentifier")) {
|
||||||
|
res.add(structuredProperty(((Node) o).getText(), prepareQualifier((Node) o, "./@nameIdentifierScheme", "dnet:pid_types", "dnet:pid_types"), info));
|
||||||
|
}
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Instance> prepareInstances(final Document doc, final DataInfo info, final KeyValue collectedfrom, final KeyValue hostedby) {
|
||||||
|
final List<Instance> res = new ArrayList<>();
|
||||||
|
for (final Object o : doc.selectNodes("//dc:alternateIdentifier[@alternateIdentifierType='URL']")) {
|
||||||
|
final Instance instance = new Instance();
|
||||||
|
instance.setUrl(Arrays.asList(((Node) o).getText().trim()));
|
||||||
|
instance.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", "dnet:publication_resource", "dnet:publication_resource"));
|
||||||
|
instance.setCollectedfrom(collectedfrom);
|
||||||
|
instance.setHostedby(hostedby);
|
||||||
|
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
|
||||||
|
instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
|
||||||
|
instance.setAccessright(prepareQualifier(doc, "//oaf:accessrights", "dnet:access_modes", "dnet:access_modes"));
|
||||||
|
instance.setLicense(field(doc.valueOf("//oaf:license"), info));
|
||||||
|
instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
|
||||||
|
instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
|
||||||
|
instance.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
|
||||||
|
res.add(instance);
|
||||||
|
}
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareSources(final Document doc, final DataInfo info) {
|
||||||
|
return new ArrayList<>(); // Not present in ODF ???
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<StructuredProperty> prepareRelevantDates(final Document doc, final DataInfo info) {
|
||||||
|
final List<StructuredProperty> res = new ArrayList<>();
|
||||||
|
for (final Object o : doc.selectNodes("//dc:date")) {
|
||||||
|
final String dateType = ((Node) o).valueOf("@dateType");
|
||||||
|
if (StringUtils.isBlank(dateType) && !dateType.equalsIgnoreCase("Accepted") && !dateType.equalsIgnoreCase("Issued")
|
||||||
|
&& !dateType.equalsIgnoreCase("Updated") && !dateType.equalsIgnoreCase("Available")) {
|
||||||
|
res.add(structuredProperty(((Node) o).getText(), "UNKNOWN", "UNKNOWN", "dnet:dataCite_date", "dnet:dataCite_date", info));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareCoverages(final Document doc, final DataInfo info) {
|
||||||
|
return new ArrayList<>(); // Not present in ODF ???
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareContributors(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListFields(doc, "//dc:contributorName", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareFormats(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListFields(doc, "//dc:format", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> preparePublisher(final Document doc, final DataInfo info) {
|
||||||
|
return prepareField(doc, "//dc:publisher", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareDescriptions(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListFields(doc, "//dc:description[@descriptionType='Abstract']", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<StructuredProperty> prepareSubjects(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListStructProps(doc, "//dc:subject", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Qualifier prepareLanguages(final Document doc) {
|
||||||
|
return prepareQualifier(doc, "//dc:language", "dnet:languages", "dnet:languages");
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareOtherResearchProductTools(final Document doc, final DataInfo info) {
|
||||||
|
return new ArrayList<>(); // Not present in ODF ???
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareOtherResearchProductContactGroups(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListFields(doc, "//dc:contributor[@contributorType='ContactGroup']/dc:contributorName", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareOtherResearchProductContactPersons(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListFields(doc, "//dc:contributor[@contributorType='ContactPerson']/dc:contributorName", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Qualifier prepareSoftwareProgrammingLanguage(final Document doc, final DataInfo info) {
|
||||||
|
return prepareQualifier(doc, "//dc:format", "dnet:programming_languages", "dnet:programming_languages");
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> prepareSoftwareCodeRepositoryUrl(final Document doc, final DataInfo info) {
|
||||||
|
return null; // Not present in ODF ???
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<StructuredProperty> prepareSoftwareLicenses(final Document doc, final DataInfo info) {
|
||||||
|
return new ArrayList<>(); // Not present in ODF ???
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Field<String>> prepareSoftwareDocumentationUrls(final Document doc, final DataInfo info) {
|
||||||
|
return prepareListFields(doc, "//dc:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
// DATASETS
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<GeoLocation> prepareDatasetGeoLocations(final Document doc, final DataInfo info) {
|
||||||
|
final List<GeoLocation> res = new ArrayList<>();
|
||||||
|
|
||||||
|
for (final Object o : doc.selectNodes("//dc:geoLocation")) {
|
||||||
|
final GeoLocation loc = new GeoLocation();
|
||||||
|
loc.setBox(((Node) o).valueOf("./dc:geoLocationBox"));
|
||||||
|
loc.setPlace(((Node) o).valueOf("./dc:geoLocationPlace"));
|
||||||
|
loc.setPoint(((Node) o).valueOf("./dc:geoLocationPoint"));
|
||||||
|
res.add(loc);
|
||||||
|
}
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> prepareDatasetMetadataVersionNumber(final Document doc, final DataInfo info) {
|
||||||
|
return null; // Not present in ODF ???
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> prepareDatasetLastMetadataUpdate(final Document doc, final DataInfo info) {
|
||||||
|
return prepareField(doc, "//dc:date[@dateType='Updated']", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> prepareDatasetVersion(final Document doc, final DataInfo info) {
|
||||||
|
return prepareField(doc, "//dc:version", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> prepareDatasetSize(final Document doc, final DataInfo info) {
|
||||||
|
return prepareField(doc, "//dc:size", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> prepareDatasetDevice(final Document doc, final DataInfo info) {
|
||||||
|
return null; // Not present in ODF ???
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Field<String> prepareDatasetStorageDate(final Document doc, final DataInfo info) {
|
||||||
|
return prepareField(doc, "//dc:date[@dateType='Issued']", info);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected List<Oaf> addOtherResultRels(final Document doc, final KeyValue collectedFrom, final DataInfo info, final long lastUpdateTimestamp) {
|
||||||
|
|
||||||
|
final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"));
|
||||||
|
|
||||||
|
final List<Oaf> res = new ArrayList<>();
|
||||||
|
|
||||||
|
for (final Object o : doc.selectNodes("//*[local-name() = 'resource']//*[local-name()='relatedIdentifier' and ./@relatedIdentifierType='OPENAIRE']")) {
|
||||||
|
final String otherId = createOpenaireId(50, ((Node) o).getText());
|
||||||
|
final String type = ((Node) o).valueOf("@relationType");
|
||||||
|
|
||||||
|
if (type.equals("IsSupplementTo")) {
|
||||||
|
res.add(prepareOtherResultRel(collectedFrom, info, lastUpdateTimestamp, docId, otherId, "supplement", "isSupplementTo"));
|
||||||
|
res.add(prepareOtherResultRel(collectedFrom, info, lastUpdateTimestamp, otherId, docId, "supplement", "isSupplementedBy"));
|
||||||
|
} else if (type.equals("IsPartOf")) {
|
||||||
|
res.add(prepareOtherResultRel(collectedFrom, info, lastUpdateTimestamp, docId, otherId, "part", "IsPartOf"));
|
||||||
|
res.add(prepareOtherResultRel(collectedFrom, info, lastUpdateTimestamp, otherId, docId, "part", "HasParts"));
|
||||||
|
} else {}
|
||||||
|
}
|
||||||
|
return res;
|
||||||
|
}
|
||||||
|
|
||||||
|
private Relation prepareOtherResultRel(final KeyValue collectedFrom,
|
||||||
|
final DataInfo info,
|
||||||
|
final long lastUpdateTimestamp,
|
||||||
|
final String source,
|
||||||
|
final String target,
|
||||||
|
final String subRelType,
|
||||||
|
final String relClass) {
|
||||||
|
final Relation r = new Relation();
|
||||||
|
r.setRelType("resultResult");
|
||||||
|
r.setSubRelType(subRelType);
|
||||||
|
r.setRelClass(relClass);
|
||||||
|
r.setSource(source);
|
||||||
|
r.setTarget(target);
|
||||||
|
r.setCollectedFrom(Arrays.asList(collectedFrom));
|
||||||
|
r.setDataInfo(info);
|
||||||
|
r.setLastupdatetimestamp(lastUpdateTimestamp);
|
||||||
|
return r;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
|
||||||
|
return prepareQualifier(doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", "dnet:dataCite_resource", "dnet:dataCite_resource");
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,176 @@
|
||||||
|
package eu.dnetlib.dhp.migration.pace;
|
||||||
|
|
||||||
|
import java.nio.charset.Charset;
|
||||||
|
import java.text.Normalizer;
|
||||||
|
import java.util.HashSet;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Set;
|
||||||
|
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.commons.lang3.text.WordUtils;
|
||||||
|
|
||||||
|
import com.google.common.base.Joiner;
|
||||||
|
import com.google.common.base.Splitter;
|
||||||
|
import com.google.common.collect.Iterables;
|
||||||
|
import com.google.common.collect.Lists;
|
||||||
|
import com.google.common.hash.Hashing;
|
||||||
|
|
||||||
|
public class PacePerson {
|
||||||
|
|
||||||
|
private static final String UTF8 = "UTF-8";
|
||||||
|
private List<String> name = Lists.newArrayList();
|
||||||
|
private List<String> surname = Lists.newArrayList();
|
||||||
|
private List<String> fullname = Lists.newArrayList();
|
||||||
|
private final String original;
|
||||||
|
|
||||||
|
private static Set<String> particles = null;
|
||||||
|
|
||||||
|
public static final String capitalize(final String s) {
|
||||||
|
return WordUtils.capitalize(s.toLowerCase(), ' ', '-');
|
||||||
|
}
|
||||||
|
|
||||||
|
public static final String dotAbbreviations(final String s) {
|
||||||
|
return s.length() == 1 ? s + "." : s;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Set<String> loadFromClasspath(final String classpath) {
|
||||||
|
final Set<String> h = new HashSet<>();
|
||||||
|
try {
|
||||||
|
for (final String s : IOUtils.readLines(PacePerson.class.getResourceAsStream(classpath))) {
|
||||||
|
h.add(s);
|
||||||
|
}
|
||||||
|
} catch (final Throwable e) {
|
||||||
|
return new HashSet<>();
|
||||||
|
}
|
||||||
|
return h;
|
||||||
|
}
|
||||||
|
|
||||||
|
public PacePerson(String s, final boolean aggressive) {
|
||||||
|
original = s;
|
||||||
|
s = Normalizer.normalize(s, Normalizer.Form.NFD);
|
||||||
|
s = s.replaceAll("\\(.+\\)", "");
|
||||||
|
s = s.replaceAll("\\[.+\\]", "");
|
||||||
|
s = s.replaceAll("\\{.+\\}", "");
|
||||||
|
s = s.replaceAll("\\s+-\\s+", "-");
|
||||||
|
s = s.replaceAll("[\\p{Punct}&&[^,-]]", " ");
|
||||||
|
s = s.replaceAll("\\d", " ");
|
||||||
|
s = s.replaceAll("\\n", " ");
|
||||||
|
s = s.replaceAll("\\.", " ");
|
||||||
|
s = s.replaceAll("\\s+", " ");
|
||||||
|
|
||||||
|
if (aggressive) {
|
||||||
|
s = s.replaceAll("[\\p{InCombiningDiacriticalMarks}&&[^,-]]", "");
|
||||||
|
// s = s.replaceAll("[\\W&&[^,-]]", "");
|
||||||
|
}
|
||||||
|
|
||||||
|
if (s.contains(",")) {
|
||||||
|
final String[] arr = s.split(",");
|
||||||
|
if (arr.length == 1) {
|
||||||
|
fullname = splitTerms(arr[0]);
|
||||||
|
} else if (arr.length > 1) {
|
||||||
|
surname = splitTerms(arr[0]);
|
||||||
|
name = splitTerms(arr[1]);
|
||||||
|
fullname.addAll(surname);
|
||||||
|
fullname.addAll(name);
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
fullname = splitTerms(s);
|
||||||
|
|
||||||
|
int lastInitialPosition = fullname.size();
|
||||||
|
boolean hasSurnameInUpperCase = false;
|
||||||
|
|
||||||
|
for (int i = 0; i < fullname.size(); i++) {
|
||||||
|
final String term = fullname.get(i);
|
||||||
|
if (term.length() == 1) {
|
||||||
|
lastInitialPosition = i;
|
||||||
|
} else if (term.equals(term.toUpperCase())) {
|
||||||
|
hasSurnameInUpperCase = true;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (lastInitialPosition < fullname.size() - 1) { // Case: Michele G. Artini
|
||||||
|
name = fullname.subList(0, lastInitialPosition + 1);
|
||||||
|
surname = fullname.subList(lastInitialPosition + 1, fullname.size());
|
||||||
|
} else if (hasSurnameInUpperCase) { // Case: Michele ARTINI
|
||||||
|
for (final String term : fullname) {
|
||||||
|
if (term.length() > 1 && term.equals(term.toUpperCase())) {
|
||||||
|
surname.add(term);
|
||||||
|
} else {
|
||||||
|
name.add(term);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private List<String> splitTerms(final String s) {
|
||||||
|
if (particles == null) {
|
||||||
|
particles = loadFromClasspath("/eu/dnetlib/dhp/migration/pace/name_particles.txt");
|
||||||
|
}
|
||||||
|
|
||||||
|
final List<String> list = Lists.newArrayList();
|
||||||
|
for (final String part : Splitter.on(" ").omitEmptyStrings().split(s)) {
|
||||||
|
if (!particles.contains(part.toLowerCase())) {
|
||||||
|
list.add(part);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return list;
|
||||||
|
}
|
||||||
|
|
||||||
|
public List<String> getName() {
|
||||||
|
return name;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getNameString() {
|
||||||
|
return Joiner.on(" ").join(getName());
|
||||||
|
}
|
||||||
|
|
||||||
|
public List<String> getSurname() {
|
||||||
|
return surname;
|
||||||
|
}
|
||||||
|
|
||||||
|
public List<String> getFullname() {
|
||||||
|
return fullname;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getOriginal() {
|
||||||
|
return original;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String hash() {
|
||||||
|
return Hashing.murmur3_128().hashString(getNormalisedFullname(), Charset.forName(UTF8)).toString();
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getNormalisedFirstName() {
|
||||||
|
return Joiner.on(" ").join(getCapitalFirstnames());
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getNormalisedSurname() {
|
||||||
|
return Joiner.on(" ").join(getCapitalSurname());
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getSurnameString() {
|
||||||
|
return Joiner.on(" ").join(getSurname());
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getNormalisedFullname() {
|
||||||
|
return isAccurate() ? getNormalisedSurname() + ", " + getNormalisedFirstName() : Joiner.on(" ").join(fullname);
|
||||||
|
}
|
||||||
|
|
||||||
|
public List<String> getCapitalFirstnames() {
|
||||||
|
return Lists.newArrayList(Iterables.transform(getNameWithAbbreviations(), PacePerson::capitalize));
|
||||||
|
}
|
||||||
|
|
||||||
|
public List<String> getCapitalSurname() {
|
||||||
|
return Lists.newArrayList(Iterables.transform(surname, PacePerson::capitalize));
|
||||||
|
}
|
||||||
|
|
||||||
|
public List<String> getNameWithAbbreviations() {
|
||||||
|
return Lists.newArrayList(Iterables.transform(name, PacePerson::dotAbbreviations));
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean isAccurate() {
|
||||||
|
return name != null && surname != null && !name.isEmpty() && !surname.isEmpty();
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,26 @@
|
||||||
|
[
|
||||||
|
{
|
||||||
|
"paramName": "s",
|
||||||
|
"paramLongName": "sourcePath",
|
||||||
|
"paramDescription": "the HDFS source path which contains the sequential file",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "mt",
|
||||||
|
"paramLongName": "master",
|
||||||
|
"paramDescription": "should be local or yarn",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "g",
|
||||||
|
"paramLongName": "graphRawPath",
|
||||||
|
"paramDescription": "the path of the graph Raw in hdfs",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "e",
|
||||||
|
"paramLongName": "entity",
|
||||||
|
"paramDescription": "The entity to extract",
|
||||||
|
"paramRequired": true
|
||||||
|
}
|
||||||
|
]
|
||||||
|
|
@ -0,0 +1,38 @@
|
||||||
|
[
|
||||||
|
{
|
||||||
|
"paramName": "p",
|
||||||
|
"paramLongName": "hdfsPath",
|
||||||
|
"paramDescription": "the path where storing the sequential file",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "n",
|
||||||
|
"paramLongName": "namenode",
|
||||||
|
"paramDescription": "the Name Node URI",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "u",
|
||||||
|
"paramLongName": "hdfsUser",
|
||||||
|
"paramDescription": "the user wich create the hdfs seq file",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "dburl",
|
||||||
|
"paramLongName": "postgresUrl",
|
||||||
|
"paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "dbuser",
|
||||||
|
"paramLongName": "postgresUser",
|
||||||
|
"paramDescription": "postgres user",
|
||||||
|
"paramRequired": false
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "dbpasswd",
|
||||||
|
"paramLongName": "postgresPassword",
|
||||||
|
"paramDescription": "postgres password",
|
||||||
|
"paramRequired": false
|
||||||
|
}
|
||||||
|
]
|
||||||
|
|
@ -0,0 +1,68 @@
|
||||||
|
[
|
||||||
|
{
|
||||||
|
"paramName": "p",
|
||||||
|
"paramLongName": "hdfsPath",
|
||||||
|
"paramDescription": "the path where storing the sequential file",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "n",
|
||||||
|
"paramLongName": "namenode",
|
||||||
|
"paramDescription": "the Name Node URI",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "u",
|
||||||
|
"paramLongName": "hdfsUser",
|
||||||
|
"paramDescription": "the user wich create the hdfs seq file",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "mongourl",
|
||||||
|
"paramLongName": "mongoBaseUrl",
|
||||||
|
"paramDescription": "mongoDB url, example: mongodb://[username:password@]host[:port]",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "db",
|
||||||
|
"paramLongName": "mongoDb",
|
||||||
|
"paramDescription": "mongo database",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "f",
|
||||||
|
"paramLongName": "mdFormat",
|
||||||
|
"paramDescription": "metadata format",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "l",
|
||||||
|
"paramLongName": "mdLayout",
|
||||||
|
"paramDescription": "metadata layout",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "i",
|
||||||
|
"paramLongName": "mdInterpretation",
|
||||||
|
"paramDescription": "metadata interpretation",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "pgurl",
|
||||||
|
"paramLongName": "postgresUrl",
|
||||||
|
"paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "pguser",
|
||||||
|
"paramLongName": "postgresUser",
|
||||||
|
"paramDescription": "postgres user",
|
||||||
|
"paramRequired": false
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "pgpasswd",
|
||||||
|
"paramLongName": "postgresPassword",
|
||||||
|
"paramDescription": "postgres password",
|
||||||
|
"paramRequired": false
|
||||||
|
}
|
||||||
|
]
|
||||||
|
|
@ -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>hdfsUser</name>
|
||||||
|
<value>dnet</value>
|
||||||
|
</property>
|
||||||
|
</configuration>
|
||||||
|
|
@ -0,0 +1,282 @@
|
||||||
|
<workflow-app name="import Entities from aggretor to HDFS" xmlns="uri:oozie:workflow:0.5">
|
||||||
|
<parameters>
|
||||||
|
<property>
|
||||||
|
<name>workingPath</name>
|
||||||
|
<description>the base path to store hdfs file</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>graphRawPath</name>
|
||||||
|
<description>the graph Raw base path</description>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
<property>
|
||||||
|
<name>postgresURL</name>
|
||||||
|
<description>the postgres URL to access to the database</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>postgresUser</name>
|
||||||
|
<description>the user postgres</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>postgresPassword</name>
|
||||||
|
<description>the password postgres</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>mongourl</name>
|
||||||
|
<description>mongoDB url, example: mongodb://[username:password@]host[:port]</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>mongoDb</name>
|
||||||
|
<description>mongo database</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>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<start to="ResetWorkingPath"/>
|
||||||
|
|
||||||
|
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
<action name="ResetWorkingPath">
|
||||||
|
<fs>
|
||||||
|
<delete path='${workingPath}'/>
|
||||||
|
<mkdir path='${workingPath}'/>
|
||||||
|
</fs>
|
||||||
|
<ok to="ImportEntitiesFromPostgres"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="ImportEntitiesFromPostgres">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.dhp.migration.MigrateDbEntitiesApplication</main-class>
|
||||||
|
<arg>-p</arg><arg>${workingPath}/db_entities</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-u</arg><arg>${hdfsUser}</arg>
|
||||||
|
<arg>-dburl</arg><arg>${postgresURL}</arg>
|
||||||
|
<arg>-dbuser</arg><arg>${postgresUser}</arg>
|
||||||
|
<arg>-dbpasswd</arg><arg>${postgresPassword}</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="ImportODFEntitiesFromMongoDB"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="ImportODFEntitiesFromMongoDB">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.dhp.migration.MigrateMongoMdstoresApplication</main-class>
|
||||||
|
<arg>-p</arg><arg>${workingPath}/odf_entities</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-u</arg><arg>${hdfsUser}</arg>
|
||||||
|
<arg>-mongourl</arg><arg>${mongourl}</arg>
|
||||||
|
<arg>-db</arg><arg>${mongoDb}</arg>
|
||||||
|
<arg>-f</arg><arg>ODF</arg>
|
||||||
|
<arg>-l</arg><arg>store</arg>
|
||||||
|
<arg>-i</arg><arg>cleaned</arg>
|
||||||
|
<arg>-pgurl</arg><arg>${postgresURL}</arg>
|
||||||
|
<arg>-pguser</arg><arg>${postgresUser}</arg>
|
||||||
|
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="ImportOAFEntitiesFromMongoDB"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="ImportOAFEntitiesFromMongoDB">
|
||||||
|
<java>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<main-class>eu.dnetlib.dhp.migration.MigrateMongoMdstoresApplication</main-class>
|
||||||
|
<arg>-p</arg><arg>${workingPath}/oaf_entities</arg>
|
||||||
|
<arg>-n</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>-u</arg><arg>${hdfsUser}</arg>
|
||||||
|
<arg>-mongourl</arg><arg>${mongourl}</arg>
|
||||||
|
<arg>-db</arg><arg>${mongoDb}</arg>
|
||||||
|
<arg>-f</arg><arg>OAF</arg>
|
||||||
|
<arg>-l</arg><arg>store</arg>
|
||||||
|
<arg>-i</arg><arg>cleaned</arg>
|
||||||
|
<arg>-pgurl</arg><arg>${postgresURL}</arg>
|
||||||
|
<arg>-pguser</arg><arg>${postgresUser}</arg>
|
||||||
|
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="End"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<action name="ExtractPublication">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn-cluster</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>ExtractEntities: publication</name>
|
||||||
|
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
|
||||||
|
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
|
||||||
|
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingPath}</arg>
|
||||||
|
<arg>-g</arg><arg>${graphRawPath}/publication</arg>
|
||||||
|
<arg>-e</arg><arg>publication</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="ExtractDataset"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<action name="ExtractDataset">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn-cluster</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>ExtractEntities: dataset</name>
|
||||||
|
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
|
||||||
|
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
|
||||||
|
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingPath}</arg>
|
||||||
|
<arg>-g</arg><arg>${graphRawPath}/dataset</arg>
|
||||||
|
<arg>-e</arg><arg>dataset</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="ExtractSoftware"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<action name="ExtractSoftware">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn-cluster</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>ExtractEntities: software</name>
|
||||||
|
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
|
||||||
|
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
|
||||||
|
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingPath}</arg>
|
||||||
|
<arg>-g</arg><arg>${graphRawPath}/software</arg>
|
||||||
|
<arg>-e</arg><arg>software</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="ExtractORP"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<action name="ExtractORP">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn-cluster</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>ExtractEntities: otherresearchproduct</name>
|
||||||
|
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
|
||||||
|
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
|
||||||
|
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingPath}</arg>
|
||||||
|
<arg>-g</arg><arg>${graphRawPath}/otherresearchproduct</arg>
|
||||||
|
<arg>-e</arg><arg>otherresearchproduct</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="ExtractDatasource"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<action name="ExtractDatasource">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn-cluster</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>ExtractEntities: datasource</name>
|
||||||
|
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
|
||||||
|
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
|
||||||
|
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingPath}</arg>
|
||||||
|
<arg>-g</arg><arg>${graphRawPath}/datasource</arg>
|
||||||
|
<arg>-e</arg><arg>datasource</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="ExtractOrganization"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<action name="ExtractOrganization">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn-cluster</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>ExtractEntities: organization</name>
|
||||||
|
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
|
||||||
|
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
|
||||||
|
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingPath}</arg>
|
||||||
|
<arg>-g</arg><arg>${graphRawPath}/organization</arg>
|
||||||
|
<arg>-e</arg><arg>organization</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="ExtractProject"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<action name="ExtractProject">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn-cluster</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>ExtractEntities: project</name>
|
||||||
|
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
|
||||||
|
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
|
||||||
|
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingPath}</arg>
|
||||||
|
<arg>-g</arg><arg>${graphRawPath}/project</arg>
|
||||||
|
<arg>-e</arg><arg>project</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="ExtractRelation"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<action name="ExtractRelation">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn-cluster</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>ExtractEntities: relation</name>
|
||||||
|
<class>eu.dnetlib.dhp.migration.ExtractEntitiesFromHDFSJob</class>
|
||||||
|
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf spark.sql.warehouse.dir="/user/hive/warehouse"</spark-opts>
|
||||||
|
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingPath}</arg>
|
||||||
|
<arg>-g</arg><arg>${graphRawPath}/relation</arg>
|
||||||
|
<arg>-e</arg><arg>relation</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="End"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<end name="End"/>
|
||||||
|
</workflow-app>
|
||||||
|
|
@ -0,0 +1,7 @@
|
||||||
|
van
|
||||||
|
der
|
||||||
|
de
|
||||||
|
dell
|
||||||
|
sig
|
||||||
|
mr
|
||||||
|
mrs
|
||||||
|
|
@ -0,0 +1,17 @@
|
||||||
|
SELECT
|
||||||
|
dor.datasource AS datasource,
|
||||||
|
dor.organization AS organization,
|
||||||
|
NULL AS startdate,
|
||||||
|
NULL AS enddate,
|
||||||
|
false AS inferred,
|
||||||
|
false AS deletedbyinference,
|
||||||
|
0.9 AS trust,
|
||||||
|
NULL AS inferenceprovenance,
|
||||||
|
dc.id AS collectedfromid,
|
||||||
|
dc.officialname AS collectedfromname,
|
||||||
|
'providedBy@@@provided by@@@dnet:datasources_organizations_typologies@@@dnet:datasources_organizations_typologies' AS semantics,
|
||||||
|
d.provenanceaction || '@@@' || d.provenanceaction || '@@@dnet:provenanceActions@@@dnet:provenanceActions' AS provenanceaction
|
||||||
|
|
||||||
|
FROM dsm_datasource_organization dor
|
||||||
|
LEFT OUTER JOIN dsm_datasources d ON (dor.datasource = d.id)
|
||||||
|
LEFT OUTER JOIN dsm_datasources dc ON (dc.id = d.collectedfrom)
|
||||||
|
|
@ -0,0 +1,147 @@
|
||||||
|
SELECT
|
||||||
|
d.id AS datasourceid,
|
||||||
|
d.id || array_agg(distinct di.pid) AS identities,
|
||||||
|
d.officialname AS officialname,
|
||||||
|
d.englishname AS englishname,
|
||||||
|
d.contactemail AS contactemail,
|
||||||
|
CASE
|
||||||
|
WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['openaire-cris_1.1'])
|
||||||
|
THEN
|
||||||
|
'openaire-cris_1.1@@@OpenAIRE CRIS v1.1@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel'
|
||||||
|
WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['driver', 'openaire2.0'])
|
||||||
|
THEN
|
||||||
|
'driver-openaire2.0@@@OpenAIRE 2.0+ (DRIVER OA, EC funding)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel'
|
||||||
|
WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['driver'])
|
||||||
|
THEN
|
||||||
|
'driver@@@OpenAIRE Basic (DRIVER OA)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel'
|
||||||
|
WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['openaire2.0'])
|
||||||
|
THEN
|
||||||
|
'openaire2.0@@@OpenAIRE 2.0 (EC funding)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel'
|
||||||
|
WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['openaire3.0'])
|
||||||
|
THEN
|
||||||
|
'openaire3.0@@@OpenAIRE 3.0 (OA, funding)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel'
|
||||||
|
WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['openaire2.0_data'])
|
||||||
|
THEN
|
||||||
|
'openaire2.0_data@@@OpenAIRE Data (funded, referenced datasets)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel'
|
||||||
|
WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['native'])
|
||||||
|
THEN
|
||||||
|
'native@@@proprietary@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel'
|
||||||
|
WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['hostedBy'])
|
||||||
|
THEN
|
||||||
|
'hostedBy@@@collected from a compatible aggregator@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel'
|
||||||
|
WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility) :: TEXT) @> ARRAY ['notCompatible'])
|
||||||
|
THEN
|
||||||
|
'notCompatible@@@under validation@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel'
|
||||||
|
ELSE
|
||||||
|
'UNKNOWN@@@not available@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel'
|
||||||
|
END AS openairecompatibility,
|
||||||
|
d.websiteurl AS websiteurl,
|
||||||
|
d.logourl AS logourl,
|
||||||
|
array_agg(DISTINCT CASE WHEN a.protocol = 'oai' and last_aggregation_date is not null THEN a.baseurl ELSE NULL END) AS accessinfopackage,
|
||||||
|
d.latitude AS latitude,
|
||||||
|
d.longitude AS longitude,
|
||||||
|
d.namespaceprefix AS namespaceprefix,
|
||||||
|
NULL AS odnumberofitems,
|
||||||
|
NULL AS odnumberofitemsdate,
|
||||||
|
|
||||||
|
(SELECT array_agg(s|| '###keywords@@@keywords@@@dnet:subject_classification_typologies@@@dnet:subject_classification_typologies')
|
||||||
|
FROM UNNEST(
|
||||||
|
ARRAY(
|
||||||
|
SELECT trim(s)
|
||||||
|
FROM unnest(string_to_array(d.subjects, '@@')) AS s)) AS s) AS subjects,
|
||||||
|
|
||||||
|
d.description AS description,
|
||||||
|
NULL AS odpolicies,
|
||||||
|
ARRAY(SELECT trim(s)
|
||||||
|
FROM unnest(string_to_array(d.languages, ',')) AS s) AS odlanguages,
|
||||||
|
ARRAY(SELECT trim(s)
|
||||||
|
FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes,
|
||||||
|
false AS inferred,
|
||||||
|
false AS deletedbyinference,
|
||||||
|
0.9 AS trust,
|
||||||
|
NULL AS inferenceprovenance,
|
||||||
|
d.dateofcollection AS dateofcollection,
|
||||||
|
d.dateofvalidation AS dateofvalidation,
|
||||||
|
-- re3data fields
|
||||||
|
d.releasestartdate AS releasestartdate,
|
||||||
|
d.releaseenddate AS releaseenddate,
|
||||||
|
d.missionstatementurl AS missionstatementurl,
|
||||||
|
d.dataprovider AS dataprovider,
|
||||||
|
d.serviceprovider AS serviceprovider,
|
||||||
|
d.databaseaccesstype AS databaseaccesstype,
|
||||||
|
d.datauploadtype AS datauploadtype,
|
||||||
|
d.databaseaccessrestriction AS databaseaccessrestriction,
|
||||||
|
d.datauploadrestriction AS datauploadrestriction,
|
||||||
|
d.versioning AS versioning,
|
||||||
|
d.citationguidelineurl AS citationguidelineurl,
|
||||||
|
d.qualitymanagementkind AS qualitymanagementkind,
|
||||||
|
d.pidsystems AS pidsystems,
|
||||||
|
d.certificates AS certificates,
|
||||||
|
ARRAY[]::text[] AS policies,
|
||||||
|
dc.id AS collectedfromid,
|
||||||
|
dc.officialname AS collectedfromname,
|
||||||
|
d.typology || '@@@' || CASE
|
||||||
|
WHEN (d.typology = 'crissystem') THEN 'CRIS System'
|
||||||
|
WHEN (d.typology = 'datarepository::unknown') THEN 'Data Repository'
|
||||||
|
WHEN (d.typology = 'aggregator::datarepository') THEN 'Data Repository Aggregator'
|
||||||
|
WHEN (d.typology = 'infospace') THEN 'Information Space'
|
||||||
|
WHEN (d.typology = 'pubsrepository::institutional') THEN 'Institutional Repository'
|
||||||
|
WHEN (d.typology = 'aggregator::pubsrepository::institutional') THEN 'Institutional Repository Aggregator'
|
||||||
|
WHEN (d.typology = 'pubsrepository::journal') THEN 'Journal'
|
||||||
|
WHEN (d.typology = 'aggregator::pubsrepository::journals') THEN 'Journal Aggregator/Publisher'
|
||||||
|
WHEN (d.typology = 'pubsrepository::mock') THEN 'Other'
|
||||||
|
WHEN (d.typology = 'pubscatalogue::unknown') THEN 'Publication Catalogue'
|
||||||
|
WHEN (d.typology = 'pubsrepository::unknown') THEN 'Publication Repository'
|
||||||
|
WHEN (d.typology = 'aggregator::pubsrepository::unknown') THEN 'Publication Repository Aggregator'
|
||||||
|
WHEN (d.typology = 'entityregistry') THEN 'Registry'
|
||||||
|
WHEN (d.typology = 'scholarcomminfra') THEN 'Scholarly Comm. Infrastructure'
|
||||||
|
WHEN (d.typology = 'pubsrepository::thematic') THEN 'Thematic Repository'
|
||||||
|
WHEN (d.typology = 'websource') THEN 'Web Source'
|
||||||
|
WHEN (d.typology = 'entityregistry::projects') THEN 'Funder database'
|
||||||
|
WHEN (d.typology = 'entityregistry::repositories') THEN 'Registry of repositories'
|
||||||
|
WHEN (d.typology = 'softwarerepository') THEN 'Software Repository'
|
||||||
|
WHEN (d.typology = 'aggregator::softwarerepository') THEN 'Software Repository Aggregator'
|
||||||
|
WHEN (d.typology = 'orprepository') THEN 'Repository'
|
||||||
|
ELSE 'Other'
|
||||||
|
END || '@@@dnet:datasource_typologies@@@dnet:datasource_typologies' AS datasourcetype,
|
||||||
|
'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction,
|
||||||
|
CONCAT(d.issn, '@@@', d.eissn, '@@@', d.lissn) AS journal
|
||||||
|
|
||||||
|
FROM dsm_datasources d
|
||||||
|
|
||||||
|
LEFT OUTER JOIN dsm_datasources dc on (d.collectedfrom = dc.id)
|
||||||
|
LEFT OUTER JOIN dsm_api a ON (d.id = a.datasource)
|
||||||
|
LEFT OUTER JOIN dsm_datasourcepids di ON (d.id = di.datasource)
|
||||||
|
|
||||||
|
GROUP BY
|
||||||
|
d.id,
|
||||||
|
d.officialname,
|
||||||
|
d.englishname,
|
||||||
|
d.websiteurl,
|
||||||
|
d.logourl,
|
||||||
|
d.contactemail,
|
||||||
|
d.namespaceprefix,
|
||||||
|
d.description,
|
||||||
|
d.latitude,
|
||||||
|
d.longitude,
|
||||||
|
d.dateofcollection,
|
||||||
|
d.dateofvalidation,
|
||||||
|
d.releasestartdate,
|
||||||
|
d.releaseenddate,
|
||||||
|
d.missionstatementurl,
|
||||||
|
d.dataprovider,
|
||||||
|
d.serviceprovider,
|
||||||
|
d.databaseaccesstype,
|
||||||
|
d.datauploadtype,
|
||||||
|
d.databaseaccessrestriction,
|
||||||
|
d.datauploadrestriction,
|
||||||
|
d.versioning,
|
||||||
|
d.citationguidelineurl,
|
||||||
|
d.qualitymanagementkind,
|
||||||
|
d.pidsystems,
|
||||||
|
d.certificates,
|
||||||
|
dc.id,
|
||||||
|
dc.officialname,
|
||||||
|
d.issn,
|
||||||
|
d.eissn,
|
||||||
|
d.lissn
|
||||||
|
|
@ -0,0 +1,36 @@
|
||||||
|
SELECT
|
||||||
|
o.id AS organizationid,
|
||||||
|
o.legalshortname AS legalshortname,
|
||||||
|
o.legalname AS legalname,
|
||||||
|
o.websiteurl AS websiteurl,
|
||||||
|
o.logourl AS logourl,
|
||||||
|
o.ec_legalbody AS eclegalbody,
|
||||||
|
o.ec_legalperson AS eclegalperson,
|
||||||
|
o.ec_nonprofit AS ecnonprofit,
|
||||||
|
o.ec_researchorganization AS ecresearchorganization,
|
||||||
|
o.ec_highereducation AS echighereducation,
|
||||||
|
o.ec_internationalorganizationeurinterests AS ecinternationalorganizationeurinterests,
|
||||||
|
o.ec_internationalorganization AS ecinternationalorganization,
|
||||||
|
o.ec_enterprise AS ecenterprise,
|
||||||
|
o.ec_smevalidated AS ecsmevalidated,
|
||||||
|
o.ec_nutscode AS ecnutscode,
|
||||||
|
o.dateofcollection AS dateofcollection,
|
||||||
|
o.lastupdate AS dateoftransformation,
|
||||||
|
false AS inferred,
|
||||||
|
false AS deletedbyinference,
|
||||||
|
o.trust AS trust,
|
||||||
|
'' AS inferenceprovenance,
|
||||||
|
d.id AS collectedfromid,
|
||||||
|
d.officialname AS collectedfromname,
|
||||||
|
|
||||||
|
o.country || '@@@dnet:countries' AS country,
|
||||||
|
'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction,
|
||||||
|
|
||||||
|
ARRAY[]::text[] AS pid
|
||||||
|
FROM dsm_organizations o
|
||||||
|
LEFT OUTER JOIN dsm_datasources d ON (d.id = o.collectedfrom)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -0,0 +1,53 @@
|
||||||
|
SELECT
|
||||||
|
o.id AS organizationid,
|
||||||
|
coalesce((array_agg(a.acronym))[1], o.name) AS legalshortname,
|
||||||
|
o.name AS legalname,
|
||||||
|
array_agg(DISTINCT n.name) AS "alternativeNames",
|
||||||
|
(array_agg(u.url))[1] AS websiteurl,
|
||||||
|
o.modification_date AS dateoftransformation,
|
||||||
|
false AS inferred,
|
||||||
|
false AS deletedbyinference,
|
||||||
|
0.95 AS trust,
|
||||||
|
'' AS inferenceprovenance,
|
||||||
|
'openaire____::openorgs' AS collectedfromid,
|
||||||
|
'OpenOrgs Database' AS collectedfromname,
|
||||||
|
o.country || '@@@dnet:countries' AS country,
|
||||||
|
'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction,
|
||||||
|
array_agg(DISTINCT i.otherid || '###' || i.type || '@@@dnet:pid_types') AS pid
|
||||||
|
FROM organizations o
|
||||||
|
LEFT OUTER JOIN acronyms a ON (a.id = o.id)
|
||||||
|
LEFT OUTER JOIN urls u ON (u.id = o.id)
|
||||||
|
LEFT OUTER JOIN other_ids i ON (i.id = o.id)
|
||||||
|
LEFT OUTER JOIN other_names n ON (n.id = o.id)
|
||||||
|
GROUP BY
|
||||||
|
o.id,
|
||||||
|
o.name,
|
||||||
|
o.modification_date,
|
||||||
|
o.country
|
||||||
|
|
||||||
|
UNION ALL
|
||||||
|
|
||||||
|
SELECT
|
||||||
|
'openorgsmesh'||substring(o.id, 13)||'-'||md5(n.name) AS organizationid,
|
||||||
|
n.name AS legalshortname,
|
||||||
|
n.name AS legalname,
|
||||||
|
ARRAY[]::text[] AS "alternativeNames",
|
||||||
|
(array_agg(u.url))[1] AS websiteurl,
|
||||||
|
o.modification_date AS dateoftransformation,
|
||||||
|
false AS inferred,
|
||||||
|
false AS deletedbyinference,
|
||||||
|
0.88 AS trust,
|
||||||
|
'' AS inferenceprovenance,
|
||||||
|
'openaire____::openorgs' AS collectedfromid,
|
||||||
|
'OpenOrgs Database' AS collectedfromname,
|
||||||
|
o.country || '@@@dnet:countries' AS country,
|
||||||
|
'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction,
|
||||||
|
array_agg(DISTINCT i.otherid || '###' || i.type || '@@@dnet:pid_types') AS pid
|
||||||
|
FROM other_names n
|
||||||
|
LEFT OUTER JOIN organizations o ON (n.id = o.id)
|
||||||
|
LEFT OUTER JOIN urls u ON (u.id = o.id)
|
||||||
|
LEFT OUTER JOIN other_ids i ON (i.id = o.id)
|
||||||
|
GROUP BY
|
||||||
|
o.id, o.modification_date, o.country, n.name
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -0,0 +1,19 @@
|
||||||
|
SELECT
|
||||||
|
po.project AS project,
|
||||||
|
po.resporganization AS resporganization,
|
||||||
|
po.participantnumber AS participantnumber,
|
||||||
|
po.contribution AS contribution,
|
||||||
|
NULL AS startdate,
|
||||||
|
NULL AS enddate,
|
||||||
|
false AS inferred,
|
||||||
|
false AS deletedbyinference,
|
||||||
|
po.trust AS trust,
|
||||||
|
NULL AS inferenceprovenance,
|
||||||
|
dc.id AS collectedfromid,
|
||||||
|
dc.officialname AS collectedfromname,
|
||||||
|
po.semanticclass || '@@@' || po.semanticclass || '@@@dnet:project_organization_relations@@@dnet:project_organization_relations' AS semantics,
|
||||||
|
'sysimport:crosswalk:entityregistry@@@sysimport:crosswalk:entityregistry@@@dnet:provenance_actions@@@dnet:provenance_actions' AS provenanceaction
|
||||||
|
|
||||||
|
FROM project_organization po
|
||||||
|
LEFT OUTER JOIN projects p ON (p.id = po.project)
|
||||||
|
LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom)
|
||||||
|
|
@ -0,0 +1,90 @@
|
||||||
|
SELECT
|
||||||
|
p.id AS projectid,
|
||||||
|
p.code AS code,
|
||||||
|
p.websiteurl AS websiteurl,
|
||||||
|
p.acronym AS acronym,
|
||||||
|
p.title AS title,
|
||||||
|
p.startdate AS startdate,
|
||||||
|
p.enddate AS enddate,
|
||||||
|
p.call_identifier AS callidentifier,
|
||||||
|
p.keywords AS keywords,
|
||||||
|
p.duration AS duration,
|
||||||
|
p.ec_sc39 AS ecsc39,
|
||||||
|
p.oa_mandate_for_publications AS oamandatepublications,
|
||||||
|
p.ec_article29_3 AS ecarticle29_3,
|
||||||
|
p.dateofcollection AS dateofcollection,
|
||||||
|
p.lastupdate AS dateoftransformation,
|
||||||
|
p.inferred AS inferred,
|
||||||
|
p.deletedbyinference AS deletedbyinference,
|
||||||
|
p.trust AS trust,
|
||||||
|
p.inferenceprovenance AS inferenceprovenance,
|
||||||
|
p.optional1 AS optional1,
|
||||||
|
p.optional2 AS optional2,
|
||||||
|
p.jsonextrainfo AS jsonextrainfo,
|
||||||
|
p.contactfullname AS contactfullname,
|
||||||
|
p.contactfax AS contactfax,
|
||||||
|
p.contactphone AS contactphone,
|
||||||
|
p.contactemail AS contactemail,
|
||||||
|
p.summary AS summary,
|
||||||
|
p.currency AS currency,
|
||||||
|
p.totalcost AS totalcost,
|
||||||
|
p.fundedamount AS fundedamount,
|
||||||
|
dc.id AS collectedfromid,
|
||||||
|
dc.officialname AS collectedfromname,
|
||||||
|
ctc.code || '@@@' || ctc.name || '@@@' || cts.code || '@@@' || cts.name AS contracttype,
|
||||||
|
pac.code || '@@@' || pac.name || '@@@' || pas.code || '@@@' || pas.name AS provenanceaction,
|
||||||
|
array_agg(DISTINCT i.pid || '###' || i.issuertype) AS pid,
|
||||||
|
array_agg(DISTINCT s.name || '###' || sc.code || '@@@' || sc.name || '@@@' || ss.code || '@@@' || ss.name) AS subjects,
|
||||||
|
array_agg(DISTINCT fp.path) AS fundingtree
|
||||||
|
FROM projects p
|
||||||
|
LEFT OUTER JOIN class pac ON (pac.code = p.provenanceactionclass)
|
||||||
|
LEFT OUTER JOIN scheme pas ON (pas.code = p.provenanceactionscheme)
|
||||||
|
|
||||||
|
LEFT OUTER JOIN projectpids pp ON (pp.project = p.id)
|
||||||
|
LEFT OUTER JOIN dsm_identities i ON (i.pid = pp.pid)
|
||||||
|
|
||||||
|
LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom)
|
||||||
|
|
||||||
|
LEFT OUTER JOIN project_fundingpath pf ON (pf.project = p.id)
|
||||||
|
LEFT OUTER JOIN fundingpaths fp ON (fp.id = pf.funding)
|
||||||
|
|
||||||
|
LEFT OUTER JOIN project_subject ps ON (ps.project = p.id)
|
||||||
|
LEFT OUTER JOIN subjects s ON (s.id = ps.subject)
|
||||||
|
|
||||||
|
LEFT OUTER JOIN class sc ON (sc.code = s.semanticclass)
|
||||||
|
LEFT OUTER JOIN scheme ss ON (ss.code = s.semanticscheme)
|
||||||
|
|
||||||
|
LEFT OUTER JOIN class ctc ON (ctc.code = p.contracttypeclass)
|
||||||
|
LEFT OUTER JOIN scheme cts ON (cts.code = p.contracttypescheme)
|
||||||
|
|
||||||
|
GROUP BY
|
||||||
|
p.id,
|
||||||
|
p.code,
|
||||||
|
p.websiteurl,
|
||||||
|
p.acronym,
|
||||||
|
p.title,
|
||||||
|
p.startdate,
|
||||||
|
p.enddate,
|
||||||
|
p.call_identifier,
|
||||||
|
p.keywords,
|
||||||
|
p.duration,
|
||||||
|
p.ec_sc39,
|
||||||
|
p.oa_mandate_for_publications,
|
||||||
|
p.ec_article29_3,
|
||||||
|
p.dateofcollection,
|
||||||
|
p.inferred,
|
||||||
|
p.deletedbyinference,
|
||||||
|
p.trust,
|
||||||
|
p.inferenceprovenance,
|
||||||
|
p.contactfullname,
|
||||||
|
p.contactfax,
|
||||||
|
p.contactphone,
|
||||||
|
p.contactemail,
|
||||||
|
p.summary,
|
||||||
|
p.currency,
|
||||||
|
p.totalcost,
|
||||||
|
p.fundedamount,
|
||||||
|
dc.id,
|
||||||
|
dc.officialname,
|
||||||
|
pac.code, pac.name, pas.code, pas.name,
|
||||||
|
ctc.code, ctc.name, cts.code, cts.name;
|
||||||
|
|
@ -0,0 +1,17 @@
|
||||||
|
SELECT local_id AS id1, oa_original_id AS id2 FROM openaire_simrels WHERE reltype = 'is_similar'
|
||||||
|
|
||||||
|
UNION ALL
|
||||||
|
|
||||||
|
SELECT
|
||||||
|
o.id AS id1,
|
||||||
|
'openorgsmesh'||substring(o.id, 13)||'-'||md5(a.acronym) AS id2
|
||||||
|
FROM acronyms a
|
||||||
|
LEFT OUTER JOIN organizations o ON (a.id = o.id)
|
||||||
|
|
||||||
|
UNION ALL
|
||||||
|
|
||||||
|
SELECT
|
||||||
|
o.id AS id1,
|
||||||
|
'openorgsmesh'||substring(o.id, 13)||'-'||md5(n.name) AS id2
|
||||||
|
FROM other_names n
|
||||||
|
LEFT OUTER JOIN organizations o ON (n.id = o.id)
|
||||||
|
|
@ -0,0 +1,9 @@
|
||||||
|
# Set root logger level to DEBUG and its only appender to A1.
|
||||||
|
log4j.rootLogger=INFO, A1
|
||||||
|
|
||||||
|
# A1 is set to be a ConsoleAppender.
|
||||||
|
log4j.appender.A1=org.apache.log4j.ConsoleAppender
|
||||||
|
|
||||||
|
# A1 uses PatternLayout.
|
||||||
|
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
|
||||||
|
log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
|
||||||
|
|
@ -9,6 +9,37 @@
|
||||||
|
|
||||||
<artifactId>dhp-dedup</artifactId>
|
<artifactId>dhp-dedup</artifactId>
|
||||||
|
|
||||||
|
<build>
|
||||||
|
<plugins>
|
||||||
|
<plugin>
|
||||||
|
<groupId>net.alchim31.maven</groupId>
|
||||||
|
<artifactId>scala-maven-plugin</artifactId>
|
||||||
|
<version>4.0.1</version>
|
||||||
|
<executions>
|
||||||
|
<execution>
|
||||||
|
<id>scala-compile-first</id>
|
||||||
|
<phase>initialize</phase>
|
||||||
|
<goals>
|
||||||
|
<goal>add-source</goal>
|
||||||
|
<goal>compile</goal>
|
||||||
|
</goals>
|
||||||
|
</execution>
|
||||||
|
<execution>
|
||||||
|
<id>scala-test-compile</id>
|
||||||
|
<phase>process-test-resources</phase>
|
||||||
|
<goals>
|
||||||
|
<goal>testCompile</goal>
|
||||||
|
</goals>
|
||||||
|
</execution>
|
||||||
|
</executions>
|
||||||
|
<configuration>
|
||||||
|
<scalaVersion>${scala.version}</scalaVersion>
|
||||||
|
</configuration>
|
||||||
|
</plugin>
|
||||||
|
</plugins>
|
||||||
|
|
||||||
|
</build>
|
||||||
|
|
||||||
<dependencies>
|
<dependencies>
|
||||||
|
|
||||||
<dependency>
|
<dependency>
|
||||||
|
|
|
||||||
|
|
@ -1,10 +1,18 @@
|
||||||
package eu.dnetlib.dhp.graph;
|
package eu.dnetlib.dhp.graph;
|
||||||
|
|
||||||
import com.google.common.collect.Maps;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
|
||||||
|
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
|
|
||||||
|
import com.google.common.collect.Maps;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Datasource;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Organization;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Project;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Software;
|
||||||
|
|
||||||
public class GraphMappingUtils {
|
public class GraphMappingUtils {
|
||||||
|
|
||||||
public final static Map<String, Class> types = Maps.newHashMap();
|
public final static Map<String, Class> types = Maps.newHashMap();
|
||||||
|
|
|
||||||
|
|
@ -4,12 +4,10 @@ import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.apache.hadoop.io.Text;
|
import org.apache.hadoop.io.Text;
|
||||||
import org.apache.spark.api.java.JavaRDD;
|
|
||||||
import org.apache.spark.api.java.JavaSparkContext;
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
import org.apache.spark.sql.Encoders;
|
import org.apache.spark.sql.Encoders;
|
||||||
import org.apache.spark.sql.SaveMode;
|
import org.apache.spark.sql.SaveMode;
|
||||||
import org.apache.spark.sql.SparkSession;
|
import org.apache.spark.sql.SparkSession;
|
||||||
import scala.Tuple2;
|
|
||||||
|
|
||||||
public class SparkGraphImporterJob {
|
public class SparkGraphImporterJob {
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -10,9 +10,8 @@ This module is automatically executed when running:
|
||||||
on module having set:
|
on module having set:
|
||||||
|
|
||||||
<parent>
|
<parent>
|
||||||
<groupId>eu.dnetlib</groupId>
|
<groupId>eu.dnetlib.dhp</groupId>
|
||||||
<artifactId>dhp-wf</artifactId>
|
<artifactId>dhp-workflows</artifactId>
|
||||||
<version>1.0.0-SNAPSHOT</version>
|
|
||||||
</parent>
|
</parent>
|
||||||
|
|
||||||
in `pom.xml` file. `oozie-package` profile initializes oozie workflow packaging, `workflow.source.dir` property points to a workflow (notice: this is not a relative path but a classpath to directory usually holding `oozie_app` subdirectory).
|
in `pom.xml` file. `oozie-package` profile initializes oozie workflow packaging, `workflow.source.dir` property points to a workflow (notice: this is not a relative path but a classpath to directory usually holding `oozie_app` subdirectory).
|
||||||
|
|
|
||||||
36
pom.xml
36
pom.xml
|
|
@ -1,4 +1,6 @@
|
||||||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
|
<project xmlns="http://maven.apache.org/POM/4.0.0"
|
||||||
|
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||||
|
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
|
||||||
|
|
||||||
<modelVersion>4.0.0</modelVersion>
|
<modelVersion>4.0.0</modelVersion>
|
||||||
<groupId>eu.dnetlib.dhp</groupId>
|
<groupId>eu.dnetlib.dhp</groupId>
|
||||||
|
|
@ -296,6 +298,11 @@
|
||||||
<artifactId>secondstring</artifactId>
|
<artifactId>secondstring</artifactId>
|
||||||
<version>1.0.0</version>
|
<version>1.0.0</version>
|
||||||
</dependency>
|
</dependency>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.mongodb</groupId>
|
||||||
|
<artifactId>mongo-java-driver</artifactId>
|
||||||
|
<version>${mongodb.driver.version}</version>
|
||||||
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>org.antlr</groupId>
|
<groupId>org.antlr</groupId>
|
||||||
<artifactId>stringtemplate</artifactId>
|
<artifactId>stringtemplate</artifactId>
|
||||||
|
|
@ -419,31 +426,7 @@
|
||||||
</execution>
|
</execution>
|
||||||
</executions>
|
</executions>
|
||||||
</plugin>
|
</plugin>
|
||||||
<plugin>
|
|
||||||
<groupId>net.alchim31.maven</groupId>
|
|
||||||
<artifactId>scala-maven-plugin</artifactId>
|
|
||||||
<version>4.0.1</version>
|
|
||||||
<executions>
|
|
||||||
<execution>
|
|
||||||
<id>scala-compile-first</id>
|
|
||||||
<phase>initialize</phase>
|
|
||||||
<goals>
|
|
||||||
<goal>add-source</goal>
|
|
||||||
<goal>compile</goal>
|
|
||||||
</goals>
|
|
||||||
</execution>
|
|
||||||
<execution>
|
|
||||||
<id>scala-test-compile</id>
|
|
||||||
<phase>process-test-resources</phase>
|
|
||||||
<goals>
|
|
||||||
<goal>testCompile</goal>
|
|
||||||
</goals>
|
|
||||||
</execution>
|
|
||||||
</executions>
|
|
||||||
<configuration>
|
|
||||||
<scalaVersion>${scala.version}</scalaVersion>
|
|
||||||
</configuration>
|
|
||||||
</plugin>
|
|
||||||
</plugins>
|
</plugins>
|
||||||
|
|
||||||
<extensions>
|
<extensions>
|
||||||
|
|
@ -491,6 +474,7 @@
|
||||||
<dhp.jackson.version>2.9.6</dhp.jackson.version>
|
<dhp.jackson.version>2.9.6</dhp.jackson.version>
|
||||||
<dhp.commons.lang.version>3.5</dhp.commons.lang.version>
|
<dhp.commons.lang.version>3.5</dhp.commons.lang.version>
|
||||||
<scala.version>2.11.12</scala.version>
|
<scala.version>2.11.12</scala.version>
|
||||||
|
<mongodb.driver.version>3.4.2</mongodb.driver.version>
|
||||||
</properties>
|
</properties>
|
||||||
</project>
|
</project>
|
||||||
|
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue