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package eu.dnetlib.data.collector.plugins.doiresolver;
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import eu.dnetlib.data.collector.plugins.filesystem.FileSystemIterator;
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import org.apache.commons.lang.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 java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Paths;
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import java.util.Iterator;
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import java.util.concurrent.ArrayBlockingQueue;
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import java.util.concurrent.TimeUnit;
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import java.util.stream.Stream;
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public class DOIResolverIterator implements Iterator<String> {
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private static final Log log = LogFactory.getLog(DOIResolverIterator.class);
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protected static final String STARTER = "FIRE";
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protected static final String TERMINATOR = "ARNOLD";
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protected static final String BAD_TERMINATOR = "BAD";
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protected static final String UNRESOLVED = "UNRESOLVED";
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protected static long TIMEOUT = 5;
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protected static TimeUnit TIMEOUT_UNIT = TimeUnit.SECONDS;
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/** Path to the dir that contains the files, each a csv with a list of DOIs, one per line. **/
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private String baseDir;
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private String fromDate;
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private ArrayBlockingQueue<String> queue;
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private CrossrefResolver crossrefResolver;
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public DOIResolverIterator(final String baseDir, final CrossrefResolver crossrefResolver, final String fromDate) {
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this.baseDir = baseDir;
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this.fromDate = fromDate;
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this.queue = new ArrayBlockingQueue<>(100);
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this.crossrefResolver = crossrefResolver;
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init();
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}
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private void init(){
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log.info("Init");
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new Thread(() -> {
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try{
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final FileSystemIterator fsi = new FileSystemIterator(baseDir, "csv", fromDate);
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// put first item in the queue
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if(queue.offer(STARTER)) {
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// read the file, ask the resolvers, put results in a shared queue
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//whatever exceptions, add terminator to the queue
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while (fsi.hasNext()) {
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String filePath = fsi.next();
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try (Stream<String> stream = Files.lines(Paths.get(filePath))) {
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stream.forEach(doi -> {
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try {
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String resolved = resolve(doi);
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if(!resolved.equals(UNRESOLVED)) queue.offer(resolved, TIMEOUT, TIMEOUT_UNIT);
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} catch (InterruptedException e) {
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log.error("DOI processing aborted, cannot offer resolved doi: "+doi+" . Did the consumer die?");
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log.error(e);
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queue.offer(BAD_TERMINATOR);
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}
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});
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} catch (IOException e) {
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log.error("DOI processing aborted");
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log.error(e);
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queue.offer(BAD_TERMINATOR);
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}
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}
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}
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} catch (Exception e) {
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log.error("DOI processing aborted");
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log.error(e);
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queue.offer(BAD_TERMINATOR);
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}
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queue.offer(TERMINATOR);
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log.info("Finished processing DOI list");
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}
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).start();
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}
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private String resolve(final String doi){
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log.debug("Resolving "+doi);
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log.debug("Crossref...");
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String record = crossrefResolver.resolve(cleanDOI(doi));
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if(StringUtils.isNotBlank(record)) return record;
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else {
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//try another resolver
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log.debug("Resolver returned blank item");
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}
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return UNRESOLVED;
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}
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/**
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* Returns the identifier part of the DOI only.
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* @param doi
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* @return the DOI
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*/
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protected String cleanDOI(final String doi){
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return doi.replace("http://dx.doi.org/", "").replace("https://dx.doi.org/", "");
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}
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@Override
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public boolean hasNext() {
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return doHasNext();
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}
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private boolean doHasNext(){
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//If I get a null value, the queue is currently empty. so we wait for something
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String element = queue.peek();
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while(element == null) {
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try {
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log.debug("Sleeping while waiting for something in the queue");
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Thread.sleep(1000);
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element = queue.peek();
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} catch (InterruptedException e) {
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e.printStackTrace();
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}
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}
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log.debug("Found in queue element: "+element);
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switch(element){
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case TERMINATOR:
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case BAD_TERMINATOR:
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return false;
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case STARTER:
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case UNRESOLVED: //although they should not be inserted at all in the queue
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queue.poll();
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return doHasNext();
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default:
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return true;
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}
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}
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@Override
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public String next() {
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return queue.poll();
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}
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public String getBaseDir() {
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return baseDir;
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}
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public void setBaseDir(String baseDir) {
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this.baseDir = baseDir;
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}
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public CrossrefResolver getCrossrefResolver() {
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return crossrefResolver;
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}
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public void setCrossrefResolver(CrossrefResolver crossrefResolver) {
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this.crossrefResolver = crossrefResolver;
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}
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}
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