353 lines
11 KiB
Java
353 lines
11 KiB
Java
package eu.dnetlib.ariadneplus.workflows.nodes;
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import java.net.URI;
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import java.net.URISyntaxException;
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import java.util.List;
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import java.util.Map;
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import java.util.NoSuchElementException;
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import java.util.concurrent.BlockingQueue;
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import java.util.concurrent.ExecutorService;
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import java.util.concurrent.Executors;
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import java.util.concurrent.TimeUnit;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Maps;
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import com.google.common.collect.Queues;
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import eu.dnetlib.data.collector.ThreadSafeIterator;
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import eu.dnetlib.rmi.data.CollectorServiceRuntimeException;
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import org.apache.commons.lang3.StringEscapeUtils;
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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.apache.http.client.utils.URIBuilder;
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import org.springframework.http.*;
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import org.springframework.web.client.ResourceAccessException;
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import org.springframework.web.client.RestClientException;
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import org.springframework.web.client.RestTemplate;
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/**
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* Created by Alessia Bardi on 31/01/2018.
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*
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* @author Alessia Bardi
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*/
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public class VirtuosoAriadnePlusIterator extends ThreadSafeIterator {
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private static final Log log = LogFactory.getLog(VirtuosoAriadnePlusIterator.class);
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protected static final String ANY_TIME_QUERY_MS = "1800000"; //1800000 == 3 mins
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protected static final int QUEUE_TIMEOUT_SECONDS = 600;
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public final static String TERMINATOR = "ARNOLD";
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public final static String ERROR_TERMINATOR = "SCHWARZ";
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protected final static int SLEEP_MS = 5000;
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protected final static int MAX_RETRIES = 3;
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protected final static int LIMIT = 100;
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private String datasourceName;
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private String datasourceInterface;
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private String virtuosoReaderAPIUrl;
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private boolean started = false;
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private Map<String, Integer> errors = Maps.newHashMap();
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private List<String> listForClass = Lists.newArrayList();
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private BlockingQueue<String> elements = Queues.newArrayBlockingQueue(10);
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private String currentElement = null;
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private ExecutorService executor = Executors.newSingleThreadExecutor();
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private RestTemplate restTemplate;
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private synchronized void verifyStarted(){
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if (!this.started) {
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this.started = true;
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fillQueue();
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getNextElement(MAX_RETRIES);
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}
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}
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protected void fillQueue(){
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log.info("Virtuoso reader at : " + getVirtuosoReaderAPIUrl());
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getExecutor().submit(() -> {
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try {
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int offset = 0;
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boolean again;
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do {
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List<String> subjectList = getSubjectList(offset);
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for (String subject : subjectList) {
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String xmlFile = tryGetRDF(subject, MAX_RETRIES);
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if (StringUtils.isBlank(xmlFile)) {
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log.warn("Skipping blank RDF for " + subject);
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} else {
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getElements().offer(xmlFile, QUEUE_TIMEOUT_SECONDS, TimeUnit.SECONDS);
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}
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}
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again = subjectList.size() == LIMIT;
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offset += LIMIT;
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} while(again);
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log.debug("End of subject list, adding terminator to the queue");
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getElements().offer(TERMINATOR, QUEUE_TIMEOUT_SECONDS, TimeUnit.SECONDS);
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} catch (Exception e) {
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log.error(e.getMessage());
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try {
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getElements().offer(ERROR_TERMINATOR, QUEUE_TIMEOUT_SECONDS, TimeUnit.SECONDS);
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} catch (InterruptedException e1) {
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log.error(e1.getMessage());
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}
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}
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});
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getExecutor().shutdown();
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}
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protected String tryGetRDF(final String subjectURL, int attempt) throws URISyntaxException, InterruptedException, VirtuosoAriadnePlusException {
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//this is something George said: if it has no http URI, then it is not to be considered relevant by itself
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if(!subjectURL.startsWith("http")){
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log.debug("Skipping as non-http url: "+subjectURL);
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errors.merge("Non-http URLs", 1, Integer::sum);
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return null;
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}
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log.debug("Querying Api, remaining attempts: "+attempt);
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if (attempt <= 0) {
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errors.merge("Failed tryGetRDF", 1, Integer::sum);
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return null;
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}
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ResponseEntity<String> response = null;
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try {
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response = getRDF(subjectURL);
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}catch(ResourceAccessException e){
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//request timed out --> sleep and try again
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log.warn("Request timeout for "+subjectURL+": I'll sleep and then try again");
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Thread.sleep(SLEEP_MS);
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return tryGetRDF(subjectURL, --attempt);
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}
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HttpStatus responseStatus = response.getStatusCode();
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if (responseStatus.is2xxSuccessful()) {
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String rdfFile = response.getBody();
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if(StringUtils.isBlank(rdfFile)){
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log.warn("Got blank RDF for "+subjectURL+" , let's try again...");
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Thread.sleep(SLEEP_MS);
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return tryGetRDF(subjectURL, --attempt);
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}
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else {
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final String xmlFile = completeXML(rdfFile, subjectURL);
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return xmlFile;
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}
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} else {
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if (responseStatus.is5xxServerError()) {
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//sleep for a while and re-try
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log.warn("HTTP ERROR: "+responseStatus.value() + ": " + responseStatus.getReasonPhrase()+": I'll sleep and then try again");
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Thread.sleep(SLEEP_MS);
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return tryGetRDF(subjectURL, --attempt);
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} else {
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log.error("ERROR: Can't get the RDF for " + subjectURL + " " + responseStatus.value() + ": " + responseStatus.getReasonPhrase());
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errors.merge(responseStatus.value() + ": " + responseStatus.getReasonPhrase(), 1, Integer::sum);
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}
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}
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return null;
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}
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protected URI getURIForSubjectList(final int offset) throws URISyntaxException {
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URIBuilder builder = new URIBuilder(getVirtuosoReaderAPIUrl() + "/apiSubjects");
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builder.addParameter("api", getDatasourceInterface());
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builder.addParameter("limit", Integer.toString(LIMIT));
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builder.addParameter("offset", Integer.toString(offset));
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return builder.build();
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}
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protected List<String> getSubjectList(final int offset) throws URISyntaxException, VirtuosoAriadnePlusException {
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URI uri = getURIForSubjectList(offset);
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log.debug("fillQueue -- Calling for subject list: " + uri.toString());
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List<String> subjectList;
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try {
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subjectList = getRestTemplate().getForObject(uri, getListForClass().getClass());
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}catch(RestClientException rce){
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throw new VirtuosoAriadnePlusException(rce);
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}
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return subjectList;
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}
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protected URI getURIForRDFRequest(final String subjectURL) throws URISyntaxException {
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URIBuilder builder = new URIBuilder(getVirtuosoReaderAPIUrl() + "/subject").addParameter("subjectURL", subjectURL).addParameter("timeout", ANY_TIME_QUERY_MS);
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return builder.build();
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}
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protected ResponseEntity<String> getRDF(final String subjectURL) throws URISyntaxException {
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HttpHeaders headers = new HttpHeaders();
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headers.setAccept(Lists.newArrayList(MediaType.APPLICATION_XML));
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URI uri = getURIForRDFRequest(subjectURL);
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log.debug("fillQueue -- Calling for subject RDF: " + uri.toString());
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HttpEntity<String> entity = new HttpEntity<>("parameters", headers);
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return restTemplate.exchange(uri, HttpMethod.GET, entity, String.class);
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}
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public String completeXML(final String rdfFile, final String url) {
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String xmlEscapedURL = StringEscapeUtils.escapeXml11(url);
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String rdfFileNoXmlDecl = rdfFile.replaceAll("\\<\\?xml(.+?)\\?\\>", "").trim();
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return "<?xml version=\"1.0\" encoding=\"UTF-8\"?><record xmlns=\"http://www.openarchives.org/OAI/2.0/\"><header xmlns:dri=\"http://www.driver-repository.eu/namespace/dri\"><dri:objIdentifier>"
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+ xmlEscapedURL + "</dri:objIdentifier><dri:datasourceapi>" + datasourceInterface + "</dri:datasourceapi><dri:datasourcename>" + datasourceName
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+ "</dri:datasourcename></header><metadata>" + rdfFileNoXmlDecl + "</metadata></record>";
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}
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@Override
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public boolean doHasNext() {
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try {
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verifyStarted();
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} catch (Exception e) {
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getExecutor().shutdownNow();
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throw new CollectorServiceRuntimeException(e);
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}
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switch(currentElement){
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case TERMINATOR:
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if(!executor.isTerminated()) executor.shutdownNow();
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return false;
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case ERROR_TERMINATOR:
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executor.shutdownNow();
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throw new CollectorServiceRuntimeException("Error getting elements from virtuoso");
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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 doNext() {
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if(!hasNext()) {
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log.error("Next called but hasNext is false", new NoSuchElementException());
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throw new NoSuchElementException();
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}
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switch(currentElement){
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case TERMINATOR:
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case ERROR_TERMINATOR:
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executor.shutdownNow();
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throw new NoSuchElementException();
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default:
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String res = currentElement;
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getNextElement(MAX_RETRIES);
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return res;
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}
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}
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private void getNextElement(int attempt){
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log.debug("polling from queue, remaining attempts: "+attempt);
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if(attempt <= 0) currentElement = ERROR_TERMINATOR;
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else{
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try {
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currentElement = elements.take();
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} catch (InterruptedException e) {
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//current thread interrupted. Let's end.
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currentElement = ERROR_TERMINATOR;
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executor.shutdownNow();
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}
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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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public VirtuosoAriadnePlusIterator datasourceInterface(final String datasourceInterface) {
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this.datasourceInterface = datasourceInterface;
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return this;
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}
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public VirtuosoAriadnePlusIterator virtuosoReaderAPIUrl(final String virtuosoReaderAPIUrl) {
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this.virtuosoReaderAPIUrl = virtuosoReaderAPIUrl;
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return this;
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}
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public VirtuosoAriadnePlusIterator datasourceName(final String datasourceName) {
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this.datasourceName = datasourceName;
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return this;
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}
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public VirtuosoAriadnePlusIterator errors(final Map<String, Integer> errors) {
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this.errors = errors;
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return this;
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}
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public String getDatasourceInterface() {
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return datasourceInterface;
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}
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public String getVirtuosoReaderAPIUrl() {
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return virtuosoReaderAPIUrl;
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}
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public Map<String, Integer> getErrors() {
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return errors;
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}
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public BlockingQueue<String> getElements() {
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return elements;
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}
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public RestTemplate getRestTemplate() {
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return restTemplate;
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}
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public VirtuosoAriadnePlusIterator restTemplate(final RestTemplate restTemplate) {
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this.restTemplate = restTemplate;
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return this;
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}
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public String getDatasourceName() {
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return datasourceName;
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}
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public boolean isStarted() {
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return started;
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}
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public List<String> getListForClass() {
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return listForClass;
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}
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public String getCurrentElement() {
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return currentElement;
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}
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public ExecutorService getExecutor() {
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return executor;
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}
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public void setDatasourceName(final String datasourceName) {
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this.datasourceName = datasourceName;
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}
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public void setDatasourceInterface(final String datasourceInterface) {
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this.datasourceInterface = datasourceInterface;
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}
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public void setVirtuosoReaderAPIUrl(final String virtuosoReaderAPIUrl) {
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this.virtuosoReaderAPIUrl = virtuosoReaderAPIUrl;
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}
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public void setStarted(final boolean started) {
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this.started = started;
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}
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public void setErrors(final Map<String, Integer> errors) {
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this.errors = errors;
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}
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public void setListForClass(final List<String> listForClass) {
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this.listForClass = listForClass;
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}
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public void setElements(final BlockingQueue<String> elements) {
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this.elements = elements;
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}
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public void setCurrentElement(final String currentElement) {
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this.currentElement = currentElement;
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}
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public void setExecutor(final ExecutorService executor) {
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this.executor = executor;
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}
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public void setRestTemplate(final RestTemplate restTemplate) {
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this.restTemplate = restTemplate;
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}
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}
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