implementation of gtr2Publications plugin
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parent
8e7ef79ce0
commit
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@ -22,6 +22,7 @@ import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.base.BaseCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.file.FileCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.file.FileGZipCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.gtr2.Gtr2PublicationsCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.mongodb.MongoDbDumpCollectorPlugin;
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import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin;
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@ -58,7 +59,7 @@ public class CollectorWorker extends ReportingJob {
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public void collect() throws UnknownCollectorPluginException, CollectorException, IOException {
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final String outputPath = mdStoreVersion.getHdfsPath() + SEQUENCE_FILE_NAME;
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final String outputPath = this.mdStoreVersion.getHdfsPath() + SEQUENCE_FILE_NAME;
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log.info("outputPath path is {}", outputPath);
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final CollectorPlugin plugin = getCollectorPlugin();
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@ -68,36 +69,36 @@ public class CollectorWorker extends ReportingJob {
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try (SequenceFile.Writer writer = SequenceFile
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.createWriter(
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fileSystem.getConf(),
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SequenceFile.Writer.file(new Path(outputPath)),
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SequenceFile.Writer.keyClass(IntWritable.class),
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SequenceFile.Writer.valueClass(Text.class),
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this.fileSystem.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
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.keyClass(IntWritable.class),
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SequenceFile.Writer
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.valueClass(Text.class),
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SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
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final IntWritable key = new IntWritable(counter.get());
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final Text value = new Text();
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plugin
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.collect(api, report)
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.forEach(
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content -> {
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.collect(this.api, this.report)
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.forEach(content -> {
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key.set(counter.getAndIncrement());
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value.set(content);
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try {
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writer.append(key, value);
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} catch (Throwable e) {
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} catch (final Throwable e) {
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throw new RuntimeException(e);
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}
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});
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} catch (Throwable e) {
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report.put(e.getClass().getName(), e.getMessage());
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} catch (final Throwable e) {
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this.report.put(e.getClass().getName(), e.getMessage());
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throw new CollectorException(e);
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} finally {
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shutdown();
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report.ongoing(counter.longValue(), counter.longValue());
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this.report.ongoing(counter.longValue(), counter.longValue());
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}
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}
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private void scheduleReport(AtomicInteger counter) {
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private void scheduleReport(final AtomicInteger counter) {
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schedule(new ReporterCallback() {
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@Override
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public Long getCurrent() {
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return counter.longValue();
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@ -112,33 +113,35 @@ public class CollectorWorker extends ReportingJob {
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private CollectorPlugin getCollectorPlugin() throws UnknownCollectorPluginException {
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switch (CollectorPlugin.NAME.valueOf(api.getProtocol())) {
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switch (CollectorPlugin.NAME.valueOf(this.api.getProtocol())) {
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case oai:
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return new OaiCollectorPlugin(clientParams);
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return new OaiCollectorPlugin(this.clientParams);
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case rest_json2xml:
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return new RestCollectorPlugin(clientParams);
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return new RestCollectorPlugin(this.clientParams);
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case file:
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return new FileCollectorPlugin(fileSystem);
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return new FileCollectorPlugin(this.fileSystem);
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case fileGzip:
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return new FileGZipCollectorPlugin(fileSystem);
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return new FileGZipCollectorPlugin(this.fileSystem);
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case baseDump:
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return new BaseCollectorPlugin(this.fileSystem);
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case gtr2Publications:
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return new Gtr2PublicationsCollectorPlugin(this.clientParams);
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case other:
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final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
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.ofNullable(api.getParams().get("other_plugin_type"))
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.ofNullable(this.api.getParams().get("other_plugin_type"))
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.map(CollectorPlugin.NAME.OTHER_NAME::valueOf)
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.orElseThrow(() -> new IllegalArgumentException("invalid other_plugin_type"));
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switch (plugin) {
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case mdstore_mongodb_dump:
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return new MongoDbDumpCollectorPlugin(fileSystem);
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return new MongoDbDumpCollectorPlugin(this.fileSystem);
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case mdstore_mongodb:
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return new MDStoreCollectorPlugin();
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default:
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throw new UnknownCollectorPluginException("plugin is not managed: " + plugin);
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}
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default:
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throw new UnknownCollectorPluginException("protocol is not managed: " + api.getProtocol());
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throw new UnknownCollectorPluginException("protocol is not managed: " + this.api.getProtocol());
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}
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}
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@ -11,7 +11,7 @@ public interface CollectorPlugin {
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enum NAME {
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oai, other, rest_json2xml, file, fileGzip, baseDump;
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oai, other, rest_json2xml, file, fileGzip, baseDump, gtr2Publications;
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public enum OTHER_NAME {
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mdstore_mongodb_dump, mdstore_mongodb
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@ -0,0 +1,40 @@
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package eu.dnetlib.dhp.collection.plugin.gtr2;
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import java.util.Iterator;
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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 eu.dnetlib.dhp.collection.ApiDescriptor;
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import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
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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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import eu.dnetlib.dhp.common.collection.HttpClientParams;
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public class Gtr2PublicationsCollectorPlugin implements CollectorPlugin {
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private final HttpClientParams clientParams;
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public Gtr2PublicationsCollectorPlugin(final HttpClientParams clientParams) {
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this.clientParams = clientParams;
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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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final String baseUrl = api.getBaseUrl();
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final String startPage = api.getParams().get("startPage");
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final String endPage = api.getParams().get("endPage");
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final String fromDate = api.getParams().get("fromDate");
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if ((fromDate != null) && !fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) { throw new CollectorException("Invalid date (YYYY-MM-DD): " + fromDate); }
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final Iterator<String> iterator = new Gtr2PublicationsIterator(baseUrl, fromDate, startPage, endPage, this.clientParams);
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final Spliterator<String> spliterator = Spliterators.spliteratorUnknownSize(iterator, Spliterator.ORDERED);
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return StreamSupport.stream(spliterator, false);
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}
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}
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@ -0,0 +1,210 @@
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package eu.dnetlib.dhp.collection.plugin.gtr2;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.Iterator;
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import java.util.LinkedList;
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import java.util.List;
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import java.util.Map;
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import java.util.Queue;
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import java.util.function.Function;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.math.NumberUtils;
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import org.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.DocumentHelper;
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import org.dom4j.Element;
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import org.joda.time.DateTime;
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import org.joda.time.format.DateTimeFormat;
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import org.joda.time.format.DateTimeFormatter;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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import eu.dnetlib.dhp.common.collection.HttpClientParams;
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import eu.dnetlib.dhp.common.collection.HttpConnector2;
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public class Gtr2PublicationsIterator implements Iterator<String> {
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public static final int PAGE_SIZE = 20;
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private static final Logger log = LoggerFactory.getLogger(Gtr2PublicationsIterator.class);
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private final HttpConnector2 connector;
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private static final DateTimeFormatter simpleDateTimeFormatter = DateTimeFormat.forPattern("yyyy-MM-dd");
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private static final int MAX_ATTEMPTS = 10;
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private final String baseUrl;
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private int currPage;
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private int endPage;
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private boolean incremental = false;
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private DateTime fromDate;
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private final Map<String, String> cache = new HashMap<>();
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private final Queue<String> queue = new LinkedList<>();
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private String nextElement;
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public Gtr2PublicationsIterator(final String baseUrl, final String fromDate, final String startPage, final String endPage,
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final HttpClientParams clientParams)
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throws CollectorException {
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this.baseUrl = baseUrl;
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this.currPage = NumberUtils.toInt(startPage, 1);
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this.endPage = NumberUtils.toInt(endPage, Integer.MAX_VALUE);
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this.incremental = StringUtils.isNotBlank(fromDate);
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this.connector = new HttpConnector2(clientParams);
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if (this.incremental) {
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this.fromDate = parseDate(fromDate);
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}
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prepareNextElement();
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}
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@Override
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public boolean hasNext() {
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return this.nextElement != null;
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}
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@Override
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public String next() {
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try {
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return this.nextElement;
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} finally {
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prepareNextElement();
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}
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}
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@Override
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public void remove() {
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throw new UnsupportedOperationException();
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}
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private void prepareNextElement() {
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while ((this.currPage <= this.endPage) && this.queue.isEmpty()) {
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log.debug("FETCHING PAGE + " + this.currPage + "/" + this.endPage);
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this.queue.addAll(fetchPage(this.currPage++));
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}
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this.nextElement = this.queue.poll();
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}
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private List<String> fetchPage(final int pageNumber) {
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final List<String> res = new ArrayList<>();
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try {
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final Document doc = loadURL(cleanURL(this.baseUrl + "/outcomes/publications?p=" + pageNumber), 0);
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if (this.endPage == Integer.MAX_VALUE) {
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this.endPage = NumberUtils.toInt(doc.valueOf("/*/@*[local-name() = 'totalPages']"));
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}
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for (final Object po : doc.selectNodes("//*[local-name() = 'publication']")) {
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final Element mainEntity = (Element) ((Element) po).detach();
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if (filterIncremental(mainEntity)) {
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res.add(expandMainEntity(mainEntity));
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} else {
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log.debug("Skipped entity");
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}
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}
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} catch (final Throwable e) {
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log.error("Exception fetching page " + pageNumber, e);
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throw new RuntimeException("Exception fetching page " + pageNumber, e);
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}
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return res;
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}
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private void addLinkedEntities(final Element master, final String relType, final Element newRoot, final Function<Document, Element> mapper) {
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for (final Object o : master.selectNodes(".//*[local-name()='link']")) {
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final String rel = ((Element) o).valueOf("@*[local-name()='rel']");
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final String href = ((Element) o).valueOf("@*[local-name()='href']");
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if (relType.equals(rel) && StringUtils.isNotBlank(href)) {
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final String cacheKey = relType + "#" + href;
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if (this.cache.containsKey(cacheKey)) {
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try {
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log.debug(" * from cache (" + relType + "): " + href);
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newRoot.add(DocumentHelper.parseText(this.cache.get(cacheKey)).getRootElement());
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} catch (final DocumentException e) {
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log.error("Error retrieving cache element: " + cacheKey, e);
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throw new RuntimeException("Error retrieving cache element: " + cacheKey, e);
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}
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} else {
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final Document doc = loadURL(cleanURL(href), 0);
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final Element elem = mapper.apply(doc);
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newRoot.add(elem);
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this.cache.put(cacheKey, elem.asXML());
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}
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}
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}
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}
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private boolean filterIncremental(final Element e) {
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if (!this.incremental || isAfter(e.valueOf("@*[local-name() = 'created']"), this.fromDate)
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|| isAfter(e.valueOf("@*[local-name() = 'updated']"), this.fromDate)) {
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return true;
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}
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return false;
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}
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private String expandMainEntity(final Element mainEntity) {
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final Element newRoot = DocumentHelper.createElement("doc");
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newRoot.add(mainEntity);
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addLinkedEntities(mainEntity, "PROJECT", newRoot, this::asProjectElement);
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return DocumentHelper.createDocument(newRoot).asXML();
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}
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private Element asProjectElement(final Document doc) {
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final Element newOrg = DocumentHelper.createElement("project");
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newOrg.addElement("id").setText(doc.valueOf("/*/@*[local-name()='id']"));
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newOrg.addElement("code").setText(doc.valueOf("//*[local-name()='identifier' and @*[local-name()='type'] = 'RCUK']"));
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newOrg.addElement("title").setText(doc.valueOf("//*[local-name()='title']"));
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return newOrg;
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}
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private static String cleanURL(final String url) {
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String cleaned = url;
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if (cleaned.contains("gtr.gtr")) {
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cleaned = cleaned.replace("gtr.gtr", "gtr");
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}
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if (cleaned.startsWith("http://")) {
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cleaned = cleaned.replaceFirst("http://", "https://");
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}
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return cleaned;
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}
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private Document loadURL(final String cleanUrl, final int attempt) {
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try {
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log.debug(" * Downloading Url: " + cleanUrl);
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final byte[] bytes = this.connector.getInputSource(cleanUrl).getBytes("UTF-8");
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return DocumentHelper.parseText(new String(bytes));
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} catch (final Throwable e) {
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log.error("Error dowloading url: " + cleanUrl + ", attempt = " + attempt, e);
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if (attempt >= MAX_ATTEMPTS) { throw new RuntimeException("Error dowloading url: " + cleanUrl, e); }
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try {
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Thread.sleep(60000); // I wait for a minute
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} catch (final InterruptedException e1) {
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throw new RuntimeException("Error dowloading url: " + cleanUrl, e);
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}
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return loadURL(cleanUrl, attempt + 1);
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}
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}
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private DateTime parseDate(final String s) {
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// I expect dates in the format 'yyyy-MM-dd'. See class
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// eu.dnetlib.msro.workflows.nodes.collect.FindDateRangeForIncrementalHarvestingJobNode
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return DateTime.parse(s.substring(0, s.indexOf("T")), simpleDateTimeFormatter);
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}
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private boolean isAfter(final String d, final DateTime fromDate) {
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return parseDate(d).isAfter(fromDate);
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}
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}
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@ -20,7 +20,6 @@ import javax.xml.transform.*;
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import javax.xml.transform.dom.DOMSource;
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import javax.xml.transform.stream.StreamResult;
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import eu.dnetlib.dhp.oa.provision.model.*;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.tuple.ImmutablePair;
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import org.apache.commons.lang3.tuple.Pair;
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@ -42,6 +41,7 @@ import com.google.common.collect.Sets;
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import com.mycila.xmltool.XMLDoc;
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import com.mycila.xmltool.XMLTag;
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import eu.dnetlib.dhp.oa.provision.model.*;
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import eu.dnetlib.dhp.schema.common.*;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.Result;
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