forked from D-Net/dnet-hadoop
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440 lines
18 KiB
Java
440 lines
18 KiB
Java
package eu.dnetlib.dhp.migration;
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import java.io.IOException;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.DocumentFactory;
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import org.dom4j.DocumentHelper;
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import org.dom4j.Node;
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import eu.dnetlib.dhp.schema.oaf.Author;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Dataset;
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import eu.dnetlib.dhp.schema.oaf.Field;
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import eu.dnetlib.dhp.schema.oaf.GeoLocation;
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import eu.dnetlib.dhp.schema.oaf.Instance;
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import eu.dnetlib.dhp.schema.oaf.Journal;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.OAIProvenance;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.Software;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
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protected final Map<String, String> code2name = new HashMap<>();
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protected final MdstoreClient mdstoreClient;
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protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
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protected static final Qualifier PUBLICATION_RESULTTYPE_QUALIFIER =
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qualifier("publication", "publication", "dnet:result_typologies", "dnet:result_typologies");
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protected static final Qualifier DATASET_RESULTTYPE_QUALIFIER = qualifier("dataset", "dataset", "dnet:result_typologies", "dnet:result_typologies");
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protected static final Qualifier SOFTWARE_RESULTTYPE_QUALIFIER = qualifier("software", "software", "dnet:result_typologies", "dnet:result_typologies");
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protected static final Qualifier OTHER_RESULTTYPE_QUALIFIER = qualifier("other", "other", "dnet:result_typologies", "dnet:result_typologies");
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private static final Log log = LogFactory.getLog(AbstractMongoExecutor.class);
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public AbstractMongoExecutor(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String mongoBaseUrl,
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final String mongoDb, final String dbUrl, final String dbUser,
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final String dbPassword) throws Exception {
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super(hdfsPath, hdfsNameNode, hdfsUser);
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this.mdstoreClient = new MdstoreClient(mongoBaseUrl, mongoDb);
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loadClassNames(dbUrl, dbUser, dbPassword);
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final Map<String, String> nsContext = new HashMap<>();
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registerNamespaces(nsContext);
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DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
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}
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private void loadClassNames(final String dbUrl, final String dbUser, final String dbPassword) throws IOException {
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log.info("Loading vocabulary terms from db...");
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try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
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code2name.clear();
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dbClient.processResults("select code, name from class", rs -> {
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try {
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code2name.put(rs.getString("code"), rs.getString("name"));
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} catch (final SQLException e) {
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e.printStackTrace();
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}
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});
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}
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log.info("Found " + code2name.size() + " terms.");
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}
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public void processMdRecords(final String mdFormat, final String mdLayout, final String mdInterpretation) throws DocumentException {
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log.info(String.format("Searching mdstores (format: %s, layout: %s, interpretation: %s)", mdFormat, mdLayout, mdInterpretation));
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final Map<String, String> colls = mdstoreClient.validCollections(mdFormat, mdLayout, mdInterpretation);
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log.info("Found " + colls.size() + " mdstores");
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for (final Entry<String, String> entry : colls.entrySet()) {
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log.info("Processing mdstore " + entry.getKey() + " (collection: " + entry.getValue() + ")");
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final String currentColl = entry.getValue();
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for (final String xml : mdstoreClient.listRecords(currentColl)) {
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final Document doc = DocumentHelper.parseText(xml);
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final String type = doc.valueOf("//dr:CobjCategory/@type");
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final KeyValue collectedFrom = keyValue(doc.valueOf("//oaf:collectedFrom/@id"), doc.valueOf("//oaf:collectedFrom/@name"));
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final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id")) ? collectedFrom
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: keyValue(doc.valueOf("//oaf:hostedBy/@id"), doc.valueOf("//oaf:hostedBy/@name"));
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final DataInfo info = prepareDataInfo(doc);
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final long lastUpdateTimestamp = new Date().getTime();
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for (final Oaf oaf : createOafs(doc, type, collectedFrom, hostedBy, info, lastUpdateTimestamp)) {
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emitOaf(oaf);
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}
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}
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}
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log.info("All Done.");
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}
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protected void registerNamespaces(final Map<String, String> nsContext) {
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nsContext.put("dr", "http://www.driver-repository.eu/namespace/dr");
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nsContext.put("dri", "http://www.driver-repository.eu/namespace/dri");
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nsContext.put("oaf", "http://namespace.openaire.eu/oaf");
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nsContext.put("oai", "http://www.openarchives.org/OAI/2.0/");
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nsContext.put("prov", "http://www.openarchives.org/OAI/2.0/provenance");
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}
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protected List<Oaf> createOafs(final Document doc,
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final String type,
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final KeyValue collectedFrom,
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final KeyValue hostedBy,
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final DataInfo info,
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final long lastUpdateTimestamp) {
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final List<Oaf> oafs = new ArrayList<>();
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switch (type.toLowerCase()) {
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case "":
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case "publication":
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final Publication p = new Publication();
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populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
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p.setResulttype(PUBLICATION_RESULTTYPE_QUALIFIER);
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p.setJournal(prepareJournal(doc, info));
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oafs.add(p);
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break;
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case "dataset":
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final Dataset d = new Dataset();
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populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
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d.setResulttype(DATASET_RESULTTYPE_QUALIFIER);
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d.setStoragedate(prepareDatasetStorageDate(doc, info));
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d.setDevice(prepareDatasetDevice(doc, info));
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d.setSize(prepareDatasetSize(doc, info));
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d.setVersion(prepareDatasetVersion(doc, info));
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d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
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d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
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d.setGeolocation(prepareDatasetGeoLocations(doc, info));
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oafs.add(d);
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break;
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case "software":
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final Software s = new Software();
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populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
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s.setResulttype(SOFTWARE_RESULTTYPE_QUALIFIER);
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s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
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s.setLicense(prepareSoftwareLicenses(doc, info));
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s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
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s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
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oafs.add(s);
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break;
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case "otherresearchproducts":
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default:
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final OtherResearchProduct o = new OtherResearchProduct();
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populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
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o.setResulttype(OTHER_RESULTTYPE_QUALIFIER);
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o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
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o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
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o.setTool(prepareOtherResearchProductTools(doc, info));
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oafs.add(o);
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break;
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}
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if (!oafs.isEmpty()) {
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oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp));
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oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp));
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}
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return oafs;
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}
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private List<Oaf> addProjectRels(final Document doc,
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final KeyValue collectedFrom,
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final DataInfo info,
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final long lastUpdateTimestamp) {
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final List<Oaf> res = new ArrayList<>();
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final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"));
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for (final Object o : doc.selectNodes("//oaf:projectid")) {
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final String projectId = createOpenaireId(40, ((Node) o).getText());
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final Relation r1 = new Relation();
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r1.setRelType("resultProject");
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r1.setSubRelType("outcome");
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r1.setRelClass("isProducedBy");
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r1.setSource(docId);
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r1.setTarget(projectId);
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r1.setCollectedFrom(Arrays.asList(collectedFrom));
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r1.setDataInfo(info);
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r1.setLastupdatetimestamp(lastUpdateTimestamp);
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res.add(r1);
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final Relation r2 = new Relation();
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r2.setRelType("resultProject");
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r2.setSubRelType("outcome");
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r2.setRelClass("produces");
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r2.setSource(projectId);
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r2.setTarget(docId);
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r2.setCollectedFrom(Arrays.asList(collectedFrom));
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r2.setDataInfo(info);
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r2.setLastupdatetimestamp(lastUpdateTimestamp);
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res.add(r2);
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}
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return res;
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}
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protected abstract List<Oaf> addOtherResultRels(final Document doc,
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final KeyValue collectedFrom,
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final DataInfo info,
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final long lastUpdateTimestamp);
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private void populateResultFields(final Result r,
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final Document doc,
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final KeyValue collectedFrom,
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final KeyValue hostedBy,
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final DataInfo info,
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final long lastUpdateTimestamp) {
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r.setDataInfo(info);
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r.setLastupdatetimestamp(lastUpdateTimestamp);
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r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier")));
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r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
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r.setCollectedfrom(Arrays.asList(collectedFrom));
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r.setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
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r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
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r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
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r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
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r.setOaiprovenance(prepareOAIprovenance(doc));
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r.setAuthor(prepareAuthors(doc, info));
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r.setLanguage(prepareLanguages(doc));
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r.setCountry(new ArrayList<>()); // NOT PRESENT IN MDSTORES
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r.setSubject(prepareSubjects(doc, info));
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r.setTitle(prepareTitles(doc, info));
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r.setRelevantdate(prepareRelevantDates(doc, info));
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r.setDescription(prepareDescriptions(doc, info));
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r.setDateofacceptance(prepareField(doc, "//oaf:dateAccepted", info));
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r.setPublisher(preparePublisher(doc, info));
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r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info));
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r.setSource(prepareSources(doc, info));
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r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
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r.setFormat(prepareFormats(doc, info));
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r.setContributor(prepareContributors(doc, info));
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r.setResourcetype(prepareResourceType(doc, info));
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r.setCoverage(prepareCoverages(doc, info));
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r.setContext(new ArrayList<>()); // NOT PRESENT IN MDSTORES
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r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
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r.setInstance(prepareInstances(doc, info, collectedFrom, hostedBy));
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}
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protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
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protected abstract List<Instance> prepareInstances(Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby);
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protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
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protected abstract List<StructuredProperty> prepareRelevantDates(Document doc, DataInfo info);
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protected abstract List<Field<String>> prepareCoverages(Document doc, DataInfo info);
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protected abstract List<Field<String>> prepareContributors(Document doc, DataInfo info);
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protected abstract List<Field<String>> prepareFormats(Document doc, DataInfo info);
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protected abstract Field<String> preparePublisher(Document doc, DataInfo info);
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protected abstract List<Field<String>> prepareDescriptions(Document doc, DataInfo info);
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protected abstract List<StructuredProperty> prepareTitles(Document doc, DataInfo info);
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protected abstract List<StructuredProperty> prepareSubjects(Document doc, DataInfo info);
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protected abstract Qualifier prepareLanguages(Document doc);
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protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
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protected abstract List<Field<String>> prepareOtherResearchProductTools(Document doc, DataInfo info);
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protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(Document doc, DataInfo info);
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protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(Document doc, DataInfo info);
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protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
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protected abstract Field<String> prepareSoftwareCodeRepositoryUrl(Document doc, DataInfo info);
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protected abstract List<StructuredProperty> prepareSoftwareLicenses(Document doc, DataInfo info);
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protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(Document doc, DataInfo info);
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protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
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protected abstract Field<String> prepareDatasetMetadataVersionNumber(Document doc, DataInfo info);
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protected abstract Field<String> prepareDatasetLastMetadataUpdate(Document doc, DataInfo info);
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protected abstract Field<String> prepareDatasetVersion(Document doc, DataInfo info);
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protected abstract Field<String> prepareDatasetSize(Document doc, DataInfo info);
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protected abstract Field<String> prepareDatasetDevice(Document doc, DataInfo info);
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protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
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private Journal prepareJournal(final Document doc, final DataInfo info) {
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final Node n = doc.selectSingleNode("//oaf:journal");
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if (n != null) {
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final String name = n.getText();
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final String issnPrinted = n.valueOf("@issn");
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final String issnOnline = n.valueOf("@eissn");
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final String issnLinking = n.valueOf("@lissn");
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final String ep = n.valueOf("@ep");
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final String iss = n.valueOf("@iss");
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final String sp = n.valueOf("@sp");
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final String vol = n.valueOf("@vol");
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final String edition = n.valueOf("@edition");
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if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); }
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}
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return null;
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}
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protected Qualifier prepareQualifier(final Node node, final String xpath, final String schemeId, final String schemeName) {
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final String classId = node.valueOf(xpath);
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final String className = code2name.get(classId);
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return qualifier(classId, className, schemeId, schemeName);
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}
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protected List<StructuredProperty> prepareListStructProps(final Node node,
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final String xpath,
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final String xpathClassId,
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final String schemeId,
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final String schemeName,
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final DataInfo info) {
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final List<StructuredProperty> res = new ArrayList<>();
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for (final Object o : node.selectNodes(xpath)) {
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final Node n = (Node) o;
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final String classId = n.valueOf(xpathClassId);
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final String className = code2name.get(classId);
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res.add(structuredProperty(n.getText(), classId, className, schemeId, schemeName, info));
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}
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return res;
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}
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protected List<StructuredProperty> prepareListStructProps(final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) {
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final List<StructuredProperty> res = new ArrayList<>();
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for (final Object o : node.selectNodes(xpath)) {
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final Node n = (Node) o;
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res.add(structuredProperty(n.getText(), qualifier, info));
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}
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return res;
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}
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protected List<StructuredProperty> prepareListStructProps(final Node node, final String xpath, final DataInfo info) {
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final List<StructuredProperty> res = new ArrayList<>();
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for (final Object o : node.selectNodes(xpath)) {
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final Node n = (Node) o;
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res.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n
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.valueOf("@schemename"), info));
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}
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return res;
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}
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protected OAIProvenance prepareOAIprovenance(final Document doc) {
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final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
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if (n == null) { return null; }
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final String identifier = n.valueOf("./*[local-name()='identifier']");
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final String baseURL = n.valueOf("./*[local-name()='baseURL']");;
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final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");;
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final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
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final String datestamp = n.valueOf("./*[local-name()='datestamp']");;
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final String harvestDate = n.valueOf("@harvestDate");;
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return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
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}
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protected DataInfo prepareDataInfo(final Document doc) {
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final Node n = doc.selectSingleNode("//oaf:datainfo");
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final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
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final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
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final String paSchemeId = n.valueOf("./oaf:provenanceaction/@schemeid");
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final String paSchemeName = n.valueOf("./oaf:provenanceaction/@schemename");
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final boolean deletedbyinference = Boolean.parseBoolean(n.valueOf("./oaf:deletedbyinference"));
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final String inferenceprovenance = n.valueOf("./oaf:inferenceprovenance");
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final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
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final String trust = n.valueOf("./oaf:trust");
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return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
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}
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protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
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return field(node.valueOf(xpath), info);
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}
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protected List<Field<String>> prepareListFields(final Node node, final String xpath, final DataInfo info) {
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return listFields(info, prepareListString(node, xpath));
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}
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protected List<String> prepareListString(final Node node, final String xpath) {
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final List<String> res = new ArrayList<>();
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for (final Object o : node.selectNodes(xpath)) {
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final String s = ((Node) o).getText().trim();
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if (StringUtils.isNotBlank(s)) {
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res.add(s);
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}
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}
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return res;
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}
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@Override
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public void close() throws IOException {
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super.close();
|
|
mdstoreClient.close();
|
|
}
|
|
|
|
}
|