118 lines
3.9 KiB
Java
118 lines
3.9 KiB
Java
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package eu.dnetlib.dhp.collection.plugin.base;
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import java.io.IOException;
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import java.sql.SQLException;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.Optional;
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import java.util.Set;
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import java.util.Spliterator;
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import java.util.Spliterators;
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import java.util.stream.Stream;
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import java.util.stream.StreamSupport;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.dom4j.DocumentException;
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import org.dom4j.DocumentHelper;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.collection.ApiDescriptor;
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import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.file.AbstractSplittedRecordPlugin;
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import eu.dnetlib.dhp.common.DbClient;
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import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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public class BaseCollectorPlugin implements CollectorPlugin {
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private final FileSystem fs;
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private static final Logger log = LoggerFactory.getLogger(AbstractSplittedRecordPlugin.class);
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// MAPPING AND FILTERING ARE DEFINED HERE:
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// https://docs.google.com/document/d/1Aj-ZAV11b44MCrAAUCPiS2TUlXb6PnJEu1utCMAcCOU/edit
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public BaseCollectorPlugin(final FileSystem fs) {
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this.fs = fs;
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}
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@Override
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public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report) throws CollectorException {
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// get path to file
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final Path filePath = Optional
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.ofNullable(api.getBaseUrl())
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.map(Path::new)
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.orElseThrow(() -> new CollectorException("missing baseUrl"));
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final String dbUrl = api.getParams().get("dbUrl");
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final String dbUser = api.getParams().get("dbUser");
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final String dbPassword = api.getParams().get("dbPassword");
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log.info("baseUrl: {}", filePath);
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log.info("dbUrl: {}", dbUrl);
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log.info("dbUser: {}", dbUser);
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log.info("dbPassword: {}", "***");
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try {
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if (!this.fs.exists(filePath)) { throw new CollectorException("path does not exist: " + filePath); }
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} catch (final Throwable e) {
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throw new CollectorException(e);
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}
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final Set<String> acceptedOpendoarIds = findAcceptedOpendoarIds(dbUrl, dbUser, dbPassword);
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final Iterator<String> iterator = new BaseCollectorIterator(this.fs, filePath, report);
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final Spliterator<String> spliterator = Spliterators.spliteratorUnknownSize(iterator, Spliterator.ORDERED);
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return StreamSupport
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.stream(spliterator, false)
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.filter(doc -> filterXml(doc, acceptedOpendoarIds, report));
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}
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private Set<String> findAcceptedOpendoarIds(final String dbUrl, final String dbUser, final String dbPassword)
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throws CollectorException {
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final Set<String> accepted = new HashSet<>();
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try (final DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
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final String sql = IOUtils
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.toString(BaseAnalyzerJob.class
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.getResourceAsStream("/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql"));
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dbClient.processResults(sql, row -> {
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try {
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final String dsId = row.getString("id");
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log.info("Accepted Datasource: " + dsId);
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accepted.add(dsId);
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} catch (final SQLException e) {
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log.error("Error in SQL", e);
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throw new RuntimeException("Error in SQL", e);
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}
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});
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} catch (final IOException e) {
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log.error("Error accessong SQL", e);
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throw new CollectorException("Error accessong SQL", e);
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}
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log.info("Accepted Datasources (TOTAL): " + accepted.size());
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return accepted;
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}
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private boolean filterXml(final String xml, final Set<String> acceptedOpendoarIds, final AggregatorReport report) {
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try {
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final String id = DocumentHelper.parseText(xml).valueOf("//*[local-name()='collection']/@opendoar_id").trim();
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return (StringUtils.isNotBlank(id) && acceptedOpendoarIds.contains("opendoar____::" + id.trim()));
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} catch (final DocumentException e) {
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log.error("Error parsing document", e);
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throw new RuntimeException("Error parsing document", e);
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}
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}
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}
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