Revision 63300
Added by Michele Artini about 2 months ago
| modules/dnet-collector-plugins/branches/gtr2_michele/src/test/java/eu/dnetlib/data/collector/plugins/projects/gtr2/Gtr2Test.java | ||
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package eu.dnetlib.data.collector.plugins.projects.gtr2; |
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import static org.junit.Assert.assertEquals; |
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import static org.junit.Assert.assertNotNull; |
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import java.util.Iterator; |
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import org.junit.Before; |
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import org.junit.Ignore; |
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import org.junit.Test; |
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import com.ximpleware.VTDGen; |
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import eu.dnetlib.data.collector.plugins.HttpConnector; |
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import eu.dnetlib.miscutils.functional.xml.TryIndentXmlString; |
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@Ignore |
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public class Gtr2Test {
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private final String baseURL = "https://gtr.ukri.org/gtr/api"; |
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private Gtr2Helper helper; |
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private Gtr2ProjectsIterator iterator; |
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private HttpConnector connector; |
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@Before |
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public void prepare() {
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helper = new Gtr2Helper(); |
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// System.setProperty("jsse.enableSNIExtension","false");
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} |
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@Test |
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public void testOne() throws Exception {
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System.out.println("one project");
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final String url = "http://gtr.ukri.org/gtr/api/projects/0AE039A7-9A84-4943-AA36-001DB5763245"; |
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final VTDGen vg_tmp = new VTDGen(); |
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connector = new HttpConnector(); |
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final String tmp = connector.getInputSource(url); |
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final byte[] bytes = tmp.getBytes("UTF-8");
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vg_tmp.setDoc(bytes); |
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vg_tmp.parse(false); |
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final String s = helper.processProject(vg_tmp.getNav(), "xmlns:ns=\"http:///afgshs\"", url); |
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System.out.println(s); |
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} |
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@Test |
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public void testPaging() throws Exception {
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iterator = new Gtr2ProjectsIterator(baseURL, null, 2, 2); |
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final TryIndentXmlString indenter = new TryIndentXmlString(); |
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while (iterator.hasNext()) {
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Thread.sleep(300); |
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final String res = iterator.next(); |
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assertNotNull(res); |
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indenter.evaluate(res); |
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System.out.println(res); |
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} |
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} |
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@Test |
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public void testOnePage() throws Exception {
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iterator = new Gtr2ProjectsIterator(baseURL, null, 12, 12); |
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final int count = iterateAndCount(iterator); |
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assertEquals(21, count); |
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} |
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@Test |
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public void testIncrementalHarvestingNoRecords() throws Exception {
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System.out.println("incremental Harvesting");
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iterator = new Gtr2ProjectsIterator(baseURL, "2050-12-12", 11, 13); |
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final int count = iterateAndCount(iterator); |
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assertEquals(1, count); |
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} |
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@Test |
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public void testIncrementalHarvesting() throws Exception {
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System.out.println("incremental Harvesting");
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iterator = new Gtr2ProjectsIterator(baseURL, "2016-11-30", 11, 11); |
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final int count = iterateAndCount(iterator); |
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assertEquals(21, count); |
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} |
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@Test |
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@Ignore |
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public void testCompleteHarvesting() throws Exception {
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System.out.println("testing complete harvesting");
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iterator = new Gtr2ProjectsIterator(baseURL, null); |
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// TryIndentXmlString indenter = new TryIndentXmlString(); |
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// it.setEndAtPage(3); |
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while (iterator.hasNext()) {
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final String res = iterator.next(); |
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assertNotNull(res); |
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// System.out.println(res); |
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// Scanner keyboard = new Scanner(System.in); |
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// System.out.println("press enter for next record");
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// keyboard.nextLine(); |
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} |
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} |
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private int iterateAndCount(final Iterator<String> iterator) throws Exception {
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int i = 0; |
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while (iterator.hasNext()) {
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assertNotNull(iterator.next()); |
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i++; |
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} |
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System.out.println("Got " + i + " projects");
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return i; |
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} |
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} |
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| modules/dnet-collector-plugins/branches/gtr2_michele/src/main/java/eu/dnetlib/data/collector/plugins/projects/gtr2/Gtr2Helper.java | ||
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package eu.dnetlib.data.collector.plugins.projects.gtr2; |
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import java.io.ByteArrayOutputStream; |
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import java.io.StringWriter; |
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import org.apache.commons.lang3.StringEscapeUtils; |
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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.DocumentHelper; |
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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 com.ximpleware.AutoPilot; |
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import com.ximpleware.VTDGen; |
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import com.ximpleware.VTDNav; |
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import eu.dnetlib.data.collector.plugins.HttpConnector; |
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import eu.dnetlib.data.collector.rmi.CollectorServiceRuntimeException; |
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public class Gtr2Helper {
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private static final Log log = LogFactory.getLog(Gtr2Helper.class); // NOPMD by marko on 11/24/08 5:02 PM |
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private VTDNav mainVTDNav; |
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private AutoPilot mainAutoPilot; |
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private StringWriter writer; |
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private HttpConnector connector; |
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// private BlockingQueue<String> fragment = new ArrayBlockingQueue<String>(20); |
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private static final HttpConnector connector = new HttpConnector(); |
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private static final DateTimeFormatter simpleDateTimeFormatter = DateTimeFormat.forPattern("yyyy-MM-dd");
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private static final int MAX_ATTEMPTS = 3; |
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public 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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| ... | ... | |
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return cleaned; |
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} |
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public String processProject(final VTDNav vn, final String namespaces, final String projectUrl) throws Exception {
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writer = new StringWriter(); |
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mainVTDNav = vn; |
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mainAutoPilot = new AutoPilot(mainVTDNav); |
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writer.write("<doc " + namespaces + ">");
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writeFragment(mainVTDNav); |
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mainAutoPilot.selectXPath("//link[@rel='FUND']");
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while (mainAutoPilot.evalXPath() != -1) {
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processFunder(mainVTDNav.toNormalizedString(mainVTDNav.getAttrVal("href")), projectUrl);
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public static Document loadURL(final String url) {
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try {
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final String cleanUrl = cleanURL(url); |
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final String xml = loadURL(cleanUrl, 0); |
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return DocumentHelper.parseText(xml); |
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} catch (final Exception e) {
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log.error("Error parsing xml", e);
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throw new CollectorServiceRuntimeException("Error parsing xml", e);
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} |
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mainAutoPilot.resetXPath(); |
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mainAutoPilot.selectXPath(".//link[@rel='LEAD_ORG']");
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while (mainAutoPilot.evalXPath() != -1) {
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processOrg(mainVTDNav.toNormalizedString(mainVTDNav.getAttrVal("href")), new String[] {
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"<ld-org>", "</ld-org>" |
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}, projectUrl); |
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} |
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mainAutoPilot.resetXPath(); |
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mainAutoPilot.selectXPath(".//link[@rel='PP_ORG']");
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while (mainAutoPilot.evalXPath() != -1) {
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processOrg(mainVTDNav.toNormalizedString(mainVTDNav.getAttrVal("href")), new String[] {
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"<pp-org>", "</pp-org>" |
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}, projectUrl); |
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} |
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// mainAutoPilot.resetXPath(); |
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// mainAutoPilot.selectXPath(".//link[@rel='PARTICIPANT_ORG']");
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// while (mainAutoPilot.evalXPath() != -1) {
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// processOrg(mainVTDNav.toNormalizedString(mainVTDNav.getAttrVal("href")),
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// new String[]{"<pp-org>", "</pp-org>"}, projectUrl);
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// } |
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mainAutoPilot.resetXPath(); |
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mainAutoPilot.selectXPath(".//link[@rel='PI_PER']");
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while (mainAutoPilot.evalXPath() != -1) {
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processPerson(mainVTDNav.toNormalizedString(mainVTDNav.getAttrVal("href")), projectUrl);
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} |
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writer.write("</doc>");
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writer.close(); |
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return writer.toString(); |
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} |
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private VTDNav setNavigator(final String httpUrl) {
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final VTDGen vg_tmp = new VTDGen(); |
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connector = new HttpConnector(); |
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private static String loadURL(final String cleanUrl, final int attempt) {
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try {
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final byte[] bytes = connector.getInputSource(cleanURL(httpUrl)).getBytes("UTF-8");
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vg_tmp.setDoc(bytes); |
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vg_tmp.parse(false); |
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// vg_tmp.parseHttpUrl(httpUrl, false); |
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return vg_tmp.getNav(); |
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} catch (final Throwable e) {
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return null; |
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} |
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} |
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private int evalXpath(final VTDNav fragmentVTDNav, final String xPath) throws Exception {
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final AutoPilot ap_tmp = new AutoPilot(fragmentVTDNav); |
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ap_tmp.selectXPath(xPath); |
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return ap_tmp.evalXPath(); |
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} |
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private void writeFragment(final VTDNav nav) throws Exception {
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final ByteArrayOutputStream b = new ByteArrayOutputStream(); |
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nav.dumpFragment(b); |
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final String ret = b.toString(); |
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b.reset(); |
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writer.write(ret); |
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} |
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private void writeNewTagAndInfo(final VTDNav vn, final String xPath, final String xmlOpenTag, final String xmlCloseTag, final String attrName) |
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throws Exception {
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final int nav_res = evalXpath(vn, xPath); |
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if (nav_res != -1) {
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String tmp = xmlOpenTag; |
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if (attrName != null) {
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tmp += vn.toNormalizedString(vn.getAttrVal(attrName)); |
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log.debug(" * Downloading Url: " + cleanUrl);
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final byte[] bytes = connector.getInputSource(cleanUrl).getBytes("UTF-8");
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return new String(bytes); |
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} catch (final Exception e) {
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log.error("Error dowloading url: " + cleanUrl, e);
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if (attempt < MAX_ATTEMPTS) {
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return loadURL(cleanUrl, attempt + 1); |
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} else {
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tmp += StringEscapeUtils.escapeXml11(vn.toNormalizedString(vn.getText()));
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throw new CollectorServiceRuntimeException("Error dowloading url: " + cleanUrl, e);
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} |
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tmp += xmlCloseTag; |
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writer.write(tmp); |
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} |
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} |
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private void processPerson(final String httpUrl, final String projectUrl) {
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log.debug(String.format("Getting person %s for project %s", httpUrl, projectUrl));
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final VTDNav vn = setNavigator(cleanURL(httpUrl)); |
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try {
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writeFragment(vn); |
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} catch (final Throwable e) {
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log.debug(String.format("Exception in processPerson from %s \n Error message: \n %s", httpUrl, e.getMessage()));
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} |
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public static 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 void processOrg(final String httpUrl, final String[] tags, final String projectUrl) {
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log.debug(String.format("Getting org %s for project %s", httpUrl, projectUrl));
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final VTDNav vn = setNavigator(cleanURL(httpUrl)); |
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try {
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writeNewTagAndInfo(vn, "//name", tags[0] + "<name>", "</name>", null); |
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vn.toElement(VTDNav.ROOT); |
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writeNewTagAndInfo(vn, "//country", "<country>", "</country>", null); |
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vn.toElement(VTDNav.ROOT); |
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writeNewTagAndInfo(vn, ".", "<id>", "</id>" + tags[1], "id"); |
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} catch (final Throwable e) {
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log.debug(String.format("Exception in processOrg from %s \n Error message: \n %s", httpUrl, e.getMessage()));
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} |
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public static boolean isAfter(final String d, final DateTime fromDate) {
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return Gtr2Helper.parseDate(d).isAfter(fromDate); |
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} |
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private void processFunder(final String httpUrl, final String projectUrl) {
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log.debug(String.format("Getting funder %s for project %s", httpUrl, projectUrl));
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final VTDNav vn = setNavigator(cleanURL(httpUrl)); |
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try {
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final AutoPilot ap = new AutoPilot(vn); |
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writeFragment(vn); |
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ap.selectXPath(".//link[@rel='FUNDER']");
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VTDNav tmp_vn; |
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while (ap.evalXPath() != -1) {
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tmp_vn = setNavigator(vn.toNormalizedString(vn.getAttrVal("href")));
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writeNewTagAndInfo(tmp_vn, "//name", "<funder> <name>", "</name></funder>", null); |
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} |
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} catch (final Throwable e) {
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log.debug(String.format("Exception in processFunder from %s \n Error message: \n %s", httpUrl, e.getMessage()));
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} |
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} |
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| 169 | 69 |
} |
| modules/dnet-collector-plugins/branches/gtr2_michele/src/main/java/eu/dnetlib/data/collector/plugins/projects/gtr2/Gtr2ProjectsIterator.java | ||
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| 1 | 1 |
package eu.dnetlib.data.collector.plugins.projects.gtr2; |
| 2 | 2 |
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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.concurrent.ArrayBlockingQueue; |
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import java.util.concurrent.TimeUnit; |
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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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| 6 | 11 |
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import org.apache.commons.lang.math.NumberUtils; |
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| 7 | 13 |
import org.apache.commons.lang3.StringUtils; |
| 8 | 14 |
import org.apache.commons.logging.Log; |
| 9 | 15 |
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.DocumentHelper; |
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import org.dom4j.Element; |
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import org.dom4j.Node; |
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| 10 | 21 |
import org.joda.time.DateTime; |
| 11 |
import org.joda.time.format.DateTimeFormat; |
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import org.joda.time.format.DateTimeFormatter; |
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| 13 | 22 |
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| 14 |
import com.ximpleware.AutoPilot; |
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import com.ximpleware.VTDGen; |
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import com.ximpleware.VTDNav; |
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|
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import eu.dnetlib.data.collector.plugins.HttpConnector; |
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| 19 | 23 |
import eu.dnetlib.data.collector.rmi.CollectorServiceException; |
| 20 | 24 |
import eu.dnetlib.data.collector.rmi.CollectorServiceRuntimeException; |
| 21 | 25 |
|
| ... | ... | |
| 24 | 28 |
*/ |
| 25 | 29 |
public class Gtr2ProjectsIterator implements Iterator<String> {
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| 26 | 30 |
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public static final String TERMINATOR = "ARNOLD"; |
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public static final int WAIT_END_SECONDS = 600; |
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public static final int PAGE_SZIE = 20; |
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public static final int PAGE_SIZE = 20; |
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| 30 | 32 |
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| 31 | 33 |
private static final Log log = LogFactory.getLog(Gtr2ProjectsIterator.class); |
| 32 | 34 |
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| 33 |
private String queryURL; |
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private int total = -1; |
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private int startFromPage = 1; |
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private int endAtPage; |
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private VTDGen vg; |
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private VTDNav vn; |
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private AutoPilot ap; |
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private String namespaces; |
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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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| 41 | 38 |
private boolean incremental = false; |
| 42 | 39 |
private DateTime fromDate; |
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private final DateTimeFormatter simpleDateTimeFormatter = DateTimeFormat.forPattern("yyyy-MM-dd");
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private final ArrayBlockingQueue<String> projects = new ArrayBlockingQueue<>(200); |
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// private boolean finished = false; |
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private String nextElement = "<doc></doc>"; |
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private HttpConnector connector; |
|
| 48 | 40 |
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| 41 |
private final Map<String, String> cache = new HashMap<>(); |
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| 42 |
|
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| 43 |
private final Queue<String> queue = new LinkedList<>(); |
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private String nextElement; |
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|
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public Gtr2ProjectsIterator(final String baseUrl, final String fromDate, final String startPage, final String endPage) |
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throws CollectorServiceException {
|
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|
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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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| 54 |
|
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| 55 |
if (this.incremental) {
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|
| 56 |
this.fromDate = Gtr2Helper.parseDate(fromDate); |
|
| 57 |
} |
|
| 58 |
|
|
| 59 |
prepareNextElement(); |
|
| 60 |
} |
|
| 61 |
|
|
| 49 | 62 |
@Override |
| 50 | 63 |
public boolean hasNext() {
|
| 51 |
return !TERMINATOR.equals(nextElement);
|
|
| 64 |
return nextElement != null;
|
|
| 52 | 65 |
} |
| 53 | 66 |
|
| 54 | 67 |
@Override |
| ... | ... | |
| 56 | 69 |
try {
|
| 57 | 70 |
return nextElement; |
| 58 | 71 |
} finally {
|
| 59 |
try {
|
|
| 60 |
nextElement = projects.poll(WAIT_END_SECONDS, TimeUnit.SECONDS); |
|
| 61 |
} catch (final InterruptedException e) {
|
|
| 62 |
throw new RuntimeException(e); |
|
| 63 |
} |
|
| 72 |
prepareNextElement(); |
|
| 64 | 73 |
} |
| 65 |
|
|
| 66 | 74 |
} |
| 67 | 75 |
|
| 68 | 76 |
@Override |
| ... | ... | |
| 70 | 78 |
throw new UnsupportedOperationException(); |
| 71 | 79 |
} |
| 72 | 80 |
|
| 73 |
public Gtr2ProjectsIterator(final String baseUrl, final String fromDate) throws CollectorServiceException {
|
|
| 74 |
prepare(baseUrl, fromDate); |
|
| 75 |
fillInfo(true); |
|
| 76 |
} |
|
| 77 |
|
|
| 78 |
public Gtr2ProjectsIterator(final String baseUrl, final String fromDate, final int startFromPage, final int endAtPage) throws CollectorServiceException {
|
|
| 79 |
prepare(baseUrl, fromDate); |
|
| 80 |
this.setStartFromPage(startFromPage); |
|
| 81 |
this.setEndAtPage(endAtPage); |
|
| 82 |
fillInfo(false); |
|
| 83 |
} |
|
| 84 |
|
|
| 85 |
public Gtr2ProjectsIterator(final String baseUrl, final String fromDate, final String startFromPage, final String endAtPage) |
|
| 86 |
throws CollectorServiceException {
|
|
| 87 |
prepare(baseUrl, fromDate); |
|
| 88 |
if (StringUtils.isNotBlank(startFromPage)) {
|
|
| 89 |
this.setStartFromPage(Integer.parseInt(startFromPage)); |
|
| 81 |
private void prepareNextElement() {
|
|
| 82 |
while (this.currPage <= this.endPage && queue.isEmpty()) {
|
|
| 83 |
log.debug("FETCHING PAGE + " + currPage + "/" + endPage);
|
|
| 84 |
this.queue.addAll(fetchPage(currPage++)); |
|
| 90 | 85 |
} |
| 91 |
if (StringUtils.isNotBlank(endAtPage)) {
|
|
| 92 |
this.setEndAtPage(Integer.parseInt(endAtPage)); |
|
| 93 |
} |
|
| 94 |
fillInfo(false); |
|
| 86 |
this.nextElement = this.queue.poll(); |
|
| 95 | 87 |
} |
| 96 | 88 |
|
| 97 |
private void prepare(final String baseUrl, final String fromDate) {
|
|
| 98 |
connector = new HttpConnector(); |
|
| 99 |
queryURL = baseUrl + "/projects"; |
|
| 100 |
vg = new VTDGen(); |
|
| 101 |
this.incremental = StringUtils.isNotBlank(fromDate); |
|
| 102 |
if (incremental) {
|
|
| 103 |
// I expect fromDate in the format 'yyyy-MM-dd'. See class |
|
| 104 |
// eu.dnetlib.msro.workflows.nodes.collect.FindDateRangeForIncrementalHarvestingJobNode |
|
| 105 |
this.fromDate = DateTime.parse(fromDate, simpleDateTimeFormatter); |
|
| 106 |
log.debug("fromDate string: " + fromDate + " -- parsed: " + this.fromDate.toString());
|
|
| 107 |
} |
|
| 108 |
} |
|
| 89 |
private List<String> fetchPage(final int pageNumber) {
|
|
| 109 | 90 |
|
| 110 |
private void fillInfo(final boolean all) throws CollectorServiceException {
|
|
| 91 |
final List<String> res = new ArrayList<>();
|
|
| 111 | 92 |
try {
|
| 112 |
// log.debug("Getting hit count from: " + queryURL);
|
|
| 113 |
final byte[] bytes = connector.getInputSource(queryURL).getBytes("UTF-8");
|
|
| 114 |
vg.setDoc(bytes); |
|
| 115 |
vg.parse(false); |
|
| 116 |
// vg.parseHttpUrl(queryURL, false); |
|
| 117 |
initParser(); |
|
| 118 |
final String hitCount = vn.toNormalizedString(vn.getAttrVal("totalSize"));
|
|
| 119 |
final String totalPages = vn.toNormalizedString(vn.getAttrVal("totalPages"));
|
|
| 120 |
namespaces = "xmlns:ns1=\"" + vn.toNormalizedString(vn.getAttrVal("ns1")) + "\" ";
|
|
| 121 |
namespaces += "xmlns:ns2=\"" + vn.toNormalizedString(vn.getAttrVal("ns2")) + "\" ";
|
|
| 122 |
namespaces += "xmlns:ns3=\"" + vn.toNormalizedString(vn.getAttrVal("ns3")) + "\" ";
|
|
| 123 |
namespaces += "xmlns:ns4=\"" + vn.toNormalizedString(vn.getAttrVal("ns4")) + "\" ";
|
|
| 124 |
namespaces += "xmlns:ns5=\"" + vn.toNormalizedString(vn.getAttrVal("ns5")) + "\" ";
|
|
| 125 |
namespaces += "xmlns:ns6=\"" + vn.toNormalizedString(vn.getAttrVal("ns6")) + "\" ";
|
|
| 126 |
if (all) {
|
|
| 127 |
setEndAtPage(Integer.parseInt(totalPages)); |
|
| 128 |
total = Integer.parseInt(hitCount); |
|
| 93 |
final Document doc = Gtr2Helper.loadURL(baseUrl + "/projects?p=" + pageNumber); |
|
| 94 |
|
|
| 95 |
if (endPage == Integer.MAX_VALUE) {
|
|
| 96 |
this.endPage = NumberUtils.toInt(doc.valueOf("/*[local-name()='projects']/@*[local-name() = 'totalPages']"));
|
|
| 129 | 97 |
} |
| 130 |
final Thread ft = new Thread(new FillProjectList()); |
|
| 131 |
ft.start(); |
|
| 132 |
log.debug("Expected number of pages: " + (endAtPage - startFromPage + 1));
|
|
| 133 |
} catch (final NumberFormatException e) {
|
|
| 134 |
log.error("Cannot set the total count or the number of pages");
|
|
| 135 |
throw new CollectorServiceException(e); |
|
| 136 |
} catch (final Throwable e) {
|
|
| 137 |
throw new CollectorServiceException(e); |
|
| 138 |
} |
|
| 139 |
} |
|
| 140 | 98 |
|
| 141 |
private void initParser() {
|
|
| 142 |
vn = vg.getNav(); |
|
| 143 |
ap = new AutoPilot(vn); |
|
| 144 |
} |
|
| 99 |
for (final Object po : doc.selectNodes("//*[local-name() = 'project']")) {
|
|
| 100 |
final Element master = (Element) po; |
|
| 145 | 101 |
|
| 146 |
public String getQueryURL() {
|
|
| 147 |
return queryURL; |
|
| 148 |
} |
|
| 102 |
final String href = master.valueOf("@*[local-name() = 'href']");
|
|
| 149 | 103 |
|
| 150 |
public void setQueryURL(final String queryURL) {
|
|
| 151 |
this.queryURL = queryURL; |
|
| 152 |
} |
|
| 104 |
if (filterIncremental(master)) {
|
|
| 105 |
res.add(expandProject(href, master).asXML()); |
|
| 106 |
} else {
|
|
| 107 |
log.debug("Skipped project: " + href);
|
|
| 108 |
} |
|
| 153 | 109 |
|
| 154 |
public int getTotal() {
|
|
| 155 |
return total; |
|
| 156 |
} |
|
| 110 |
} |
|
| 111 |
} catch (final Throwable e) {
|
|
| 112 |
log.error("Exception fetching page " + pageNumber, e);
|
|
| 113 |
throw new CollectorServiceRuntimeException("Exception fetching page " + pageNumber, e);
|
|
| 114 |
} |
|
| 115 |
return res; |
|
| 157 | 116 |
|
| 158 |
public void setTotal(final int total) {
|
|
| 159 |
this.total = total; |
|
| 160 | 117 |
} |
| 161 | 118 |
|
| 162 |
public int getEndAtPage() {
|
|
| 163 |
return endAtPage; |
|
| 164 |
} |
|
| 119 |
private Document expandProject(final String href, final Element masterProject) {
|
|
| 120 |
log.debug("Expanding project: " + href);
|
|
| 165 | 121 |
|
| 166 |
public void setEndAtPage(final int endAtPage) {
|
|
| 167 |
this.endAtPage = endAtPage; |
|
| 168 |
log.debug("Overriding endAtPage to " + endAtPage);
|
|
| 169 |
} |
|
| 122 |
final Element newRoot = DocumentHelper.createElement("doc");
|
|
| 170 | 123 |
|
| 171 |
public VTDGen getVg() {
|
|
| 172 |
return vg; |
|
| 173 |
} |
|
| 124 |
newRoot.add(Gtr2Helper.loadURL(href).getRootElement()); |
|
| 174 | 125 |
|
| 175 |
public void setVg(final VTDGen vg) {
|
|
| 176 |
this.vg = vg; |
|
| 177 |
} |
|
| 126 |
addFragments(masterProject, "FUND", newRoot, o -> {
|
|
| 127 |
final Element fundNode = o.getRootElement(); |
|
| 178 | 128 |
|
| 179 |
public VTDNav getVn() {
|
|
| 180 |
return vn; |
|
| 181 |
} |
|
| 129 |
final Node funderLinkNode = fundNode.selectSingleNode("//*[local-name()='link' and @*[local-name()='rel']='FUNDER']");
|
|
| 182 | 130 |
|
| 183 |
public void setVn(final VTDNav vn) {
|
|
| 184 |
this.vn = vn;
|
|
| 185 |
}
|
|
| 131 |
if (funderLinkNode != null) {
|
|
| 132 |
final String funderHref = funderLinkNode.valueOf("@*[local-name() = 'href']");
|
|
| 133 |
final Element funderNode = Gtr2Helper.loadURL(funderHref).getRootElement();
|
|
| 186 | 134 |
|
| 187 |
public AutoPilot getAp() {
|
|
| 188 |
return ap; |
|
| 189 |
} |
|
| 135 |
final Element newFunderNode = DocumentHelper.createElement("funder");
|
|
| 136 |
newFunderNode.addElement("name").setText(funderNode.valueOf("//*[local-name()='name']"));
|
|
| 190 | 137 |
|
| 191 |
public void setAp(final AutoPilot ap) {
|
|
| 192 |
this.ap = ap; |
|
| 193 |
} |
|
| 194 |
|
|
| 195 |
public String getNamespaces() {
|
|
| 196 |
return namespaces; |
|
| 197 |
} |
|
| 198 |
|
|
| 199 |
public void setNamespaces(final String namespaces) {
|
|
| 200 |
this.namespaces = namespaces; |
|
| 201 |
} |
|
| 202 |
|
|
| 203 |
public int getStartFromPage() {
|
|
| 204 |
return startFromPage; |
|
| 205 |
} |
|
| 206 |
|
|
| 207 |
public void setStartFromPage(final int startFromPage) {
|
|
| 208 |
this.startFromPage = startFromPage; |
|
| 209 |
log.debug("Overriding startFromPage to " + startFromPage);
|
|
| 210 |
} |
|
| 211 |
|
|
| 212 |
private class FillProjectList implements Runnable {
|
|
| 213 |
|
|
| 214 |
private boolean morePages = true; |
|
| 215 |
private int pageNumber = startFromPage; |
|
| 216 |
|
|
| 217 |
@Override |
|
| 218 |
public void run() {
|
|
| 219 |
String resultPageUrl = ""; |
|
| 220 |
try {
|
|
| 221 |
do {
|
|
| 222 |
resultPageUrl = getNextPageUrl(); |
|
| 223 |
log.debug("Page: " + resultPageUrl);
|
|
| 224 |
// clear VGen before processing the next file |
|
| 225 |
vg.clear(); |
|
| 226 |
final byte[] bytes = connector.getInputSource(resultPageUrl).getBytes("UTF-8");
|
|
| 227 |
vg.setDoc(bytes); |
|
| 228 |
vg.parse(false); |
|
| 229 |
// vg.parseHttpUrl(resultPageUrl, false); |
|
| 230 |
initParser(); |
|
| 231 |
ap.selectXPath("//project");
|
|
| 232 |
while (ap.evalXPath() != -1) {
|
|
| 233 |
final String projectHref = vn.toNormalizedString(vn.getAttrVal("href"));
|
|
| 234 |
final ParseProject p = new ParseProject(projectHref); |
|
| 235 |
p.execute(); |
|
| 236 |
} |
|
| 237 |
ap.resetXPath(); |
|
| 238 |
|
|
| 239 |
} while (morePages); |
|
| 240 |
projects.put(TERMINATOR); |
|
| 241 |
|
|
| 242 |
} catch (final Throwable e) {
|
|
| 243 |
log.error("Exception processing " + resultPageUrl + "\n" + e.getMessage());
|
|
| 138 |
return newFunderNode; |
|
| 139 |
} else {
|
|
| 140 |
return null; |
|
| 244 | 141 |
} |
| 245 |
} |
|
| 142 |
}); |
|
| 143 |
addFragments(masterProject, "LEAD_ORG", newRoot, o -> asOrgElement("ld-org", o));
|
|
| 144 |
addFragments(masterProject, "PP_ORG", newRoot, o -> asOrgElement("pp-org", o));
|
|
| 145 |
addFragments(masterProject, "PI_PER", newRoot, Document::getRootElement); |
|
| 246 | 146 |
|
| 247 |
private String getNextPageUrl() {
|
|
| 248 |
final String url = queryURL + "?p=" + pageNumber; |
|
| 249 |
if (pageNumber == endAtPage) {
|
|
| 250 |
morePages = false; |
|
| 251 |
} |
|
| 252 |
pageNumber++; |
|
| 253 |
return url; |
|
| 254 |
} |
|
| 255 |
|
|
| 147 |
return DocumentHelper.createDocument(newRoot); |
|
| 256 | 148 |
} |
| 257 | 149 |
|
| 258 |
private class ParseProject {
|
|
| 150 |
private void addFragments(final Element master, final String relType, final Element newRoot, final Function<Document, Element> mapper) {
|
|
| 259 | 151 |
|
| 260 |
VTDNav vn1;
|
|
| 261 |
VTDGen vg1;
|
|
| 262 |
private final String projectRef;
|
|
| 152 |
for (final Object o : master.selectNodes(".//*[local-name()='link']")) {
|
|
| 153 |
final String rel = ((Element) o).valueOf("@*[local-name()='rel']");
|
|
| 154 |
final String href = ((Element) o).valueOf("@*[local-name()='href']");
|
|
| 263 | 155 |
|
| 264 |
public ParseProject(final String projectHref) {
|
|
| 265 |
projectRef = Gtr2Helper.cleanURL(projectHref); |
|
| 266 |
vg1 = new VTDGen(); |
|
| 267 |
try {
|
|
| 268 |
final byte[] bytes = connector.getInputSource(projectRef).getBytes("UTF-8");
|
|
| 269 |
vg1.setDoc(bytes); |
|
| 270 |
vg1.parse(false); |
|
| 271 |
vn1 = vg1.getNav(); |
|
| 272 |
} catch (final Throwable e) {
|
|
| 273 |
log.error("Exception processing " + projectRef + "\n" + e.getMessage());
|
|
| 274 |
} |
|
| 275 |
} |
|
| 276 |
|
|
| 277 |
private int projectsUpdate(final String attr) throws CollectorServiceException {
|
|
| 278 |
try {
|
|
| 279 |
final int index = vn1.getAttrVal(attr); |
|
| 280 |
if (index != -1) {
|
|
| 281 |
final String d = vn1.toNormalizedString(index); |
|
| 282 |
final DateTime recordDate = DateTime.parse(d.substring(0, d.indexOf("T")), simpleDateTimeFormatter);
|
|
| 283 |
// updated or created after the last time it was collected |
|
| 284 |
if (recordDate.isAfter(fromDate)) {
|
|
| 285 |
log.debug("New project to collect");
|
|
| 286 |
return index; |
|
| 156 |
if (relType.equals(rel) && StringUtils.isNotBlank(href)) {
|
|
| 157 |
final String cacheKey = relType + "#" + href; |
|
| 158 |
if (cache.containsKey(cacheKey)) {
|
|
| 159 |
try {
|
|
| 160 |
log.debug(" * from cache (" + relType + "): " + href);
|
|
| 161 |
newRoot.add(DocumentHelper.parseText(cache.get(cacheKey)).getRootElement()); |
|
| 162 |
} catch (final DocumentException e) {
|
|
| 163 |
log.error("Error retrieving cache element: " + cacheKey, e);
|
|
| 164 |
throw new CollectorServiceRuntimeException("Error retrieving cache element: " + cacheKey, e);
|
|
| 287 | 165 |
} |
| 288 |
return -1; |
|
| 166 |
} else {
|
|
| 167 |
final Document doc = Gtr2Helper.loadURL(href); |
|
| 168 |
final Element elem = mapper.apply(doc); |
|
| 169 |
newRoot.add(elem); |
|
| 170 |
cache.put(cacheKey, elem.asXML()); |
|
| 289 | 171 |
} |
| 290 |
return index; |
|
| 291 |
} catch (final Throwable e) {
|
|
| 292 |
throw new CollectorServiceException(e); |
|
| 293 |
} |
|
| 294 |
} |
|
| 295 | 172 |
|
| 296 |
private String collectProject() throws CollectorServiceException {
|
|
| 297 |
try {
|
|
| 298 |
final int p = vn1.getAttrVal("href");
|
|
| 299 |
final String projectHref = vn1.toNormalizedString(p); |
|
| 300 |
log.debug("Collecting project at " + projectHref);
|
|
| 301 |
final Gtr2Helper gtr2Helper = new Gtr2Helper(); |
|
| 302 |
return gtr2Helper.processProject(vn1, namespaces, projectHref); |
|
| 303 |
} catch (final Throwable e) {
|
|
| 304 |
throw new CollectorServiceException(e); |
|
| 305 | 173 |
} |
| 306 | 174 |
} |
| 175 |
} |
|
| 307 | 176 |
|
| 308 |
private boolean add(final String attr) throws CollectorServiceException {
|
|
| 309 |
return projectsUpdate(attr) != -1; |
|
| 310 |
} |
|
| 177 |
private Element asOrgElement(final String nodeName, final Document doc) {
|
|
| 178 |
final Element newOrg = DocumentHelper.createElement(nodeName); |
|
| 179 |
newOrg.addElement("name").setText(doc.valueOf("//*[local-name()='name']"));
|
|
| 180 |
newOrg.addElement("country").setText(doc.valueOf("//*[local-name()='country']"));
|
|
| 181 |
newOrg.addElement("id").setText(doc.valueOf("/*[local-name()='organisation']/@*[local-name()='id']"));
|
|
| 182 |
return newOrg; |
|
| 183 |
} |
|
| 311 | 184 |
|
| 312 |
public void execute() {
|
|
| 313 |
try {
|
|
| 314 |
if (!incremental || incremental && (add("created") || add("updated"))) {
|
|
| 315 |
projects.put(collectProject());
|
|
| 316 |
}
|
|
| 317 |
} catch (final Throwable e) {
|
|
| 318 |
log.error("Error on ParseProject " + e.getMessage());
|
|
| 319 |
throw new CollectorServiceRuntimeException(e);
|
|
| 320 |
}
|
|
| 185 |
private boolean filterIncremental(final Element e) {
|
|
| 186 |
if (!incremental) {
|
|
| 187 |
return true;
|
|
| 188 |
} else if (Gtr2Helper.isAfter(e.valueOf("@*[local-name() = 'created']"), fromDate)) {
|
|
| 189 |
return true;
|
|
| 190 |
} else if (Gtr2Helper.isAfter(e.valueOf("@*[local-name() = 'updated']"), fromDate)) {
|
|
| 191 |
return true;
|
|
| 192 |
} else {
|
|
| 193 |
return false;
|
|
| 321 | 194 |
} |
| 322 |
|
|
| 323 | 195 |
} |
| 324 | 196 |
|
| 325 | 197 |
} |
| modules/dnet-collector-plugins/branches/gtr2_michele/src/test/java/eu/dnetlib/data/collector/plugins/projects/gtr2/Gtr2ProjectsIteratorTest.java | ||
|---|---|---|
| 1 |
package eu.dnetlib.data.collector.plugins.projects.gtr2; |
|
| 2 |
|
|
| 3 |
import static org.junit.Assert.assertEquals; |
|
| 4 |
import static org.junit.Assert.assertNotNull; |
|
| 5 |
|
|
| 6 |
import java.util.Iterator; |
|
| 7 |
|
|
| 8 |
import org.junit.Ignore; |
|
| 9 |
import org.junit.Test; |
|
| 10 |
|
|
| 11 |
import eu.dnetlib.miscutils.functional.xml.TryIndentXmlString; |
|
| 12 |
|
|
| 13 |
public class Gtr2ProjectsIteratorTest {
|
|
| 14 |
|
|
| 15 |
private static final String baseURL = "https://gtr.ukri.org/gtr/api"; |
|
| 16 |
|
|
| 17 |
private Gtr2ProjectsIterator iterator; |
|
| 18 |
|
|
| 19 |
@Test |
|
| 20 |
@Ignore |
|
| 21 |
public void testOne() throws Exception {
|
|
| 22 |
System.out.println("one project");
|
|
| 23 |
|
|
| 24 |
iterator = new Gtr2ProjectsIterator(baseURL, null, null, null); |
|
| 25 |
|
|
| 26 |
while (iterator.hasNext()) {
|
|
| 27 |
final String res = iterator.next(); |
|
| 28 |
assertNotNull(res); |
|
| 29 |
System.out.println(res); |
|
| 30 |
return; |
|
| 31 |
} |
|
| 32 |
} |
|
| 33 |
|
|
| 34 |
@Test |
|
| 35 |
@Ignore |
|
| 36 |
public void testPaging() throws Exception {
|
|
| 37 |
iterator = new Gtr2ProjectsIterator(baseURL, null, "2", "2"); |
|
| 38 |
final TryIndentXmlString indenter = new TryIndentXmlString(); |
|
| 39 |
|
|
| 40 |
while (iterator.hasNext()) {
|
|
| 41 |
Thread.sleep(300); |
|
| 42 |
final String res = iterator.next(); |
|
| 43 |
assertNotNull(res); |
|
| 44 |
indenter.evaluate(res); |
|
| 45 |
System.out.println(res); |
|
| 46 |
} |
|
| 47 |
} |
|
| 48 |
|
|
| 49 |
@Test |
|
| 50 |
@Ignore |
|
| 51 |
public void testOnePage() throws Exception {
|
|
| 52 |
iterator = new Gtr2ProjectsIterator(baseURL, null, "12", "12"); |
|
| 53 |
final int count = iterateAndCount(iterator); |
|
| 54 |
assertEquals(21, count); |
|
| 55 |
} |
|
| 56 |
|
|
| 57 |
@Test |
|
| 58 |
@Ignore |
|
| 59 |
public void testIncrementalHarvestingNoRecords() throws Exception {
|
|
| 60 |
System.out.println("incremental Harvesting");
|
|
| 61 |
iterator = new Gtr2ProjectsIterator(baseURL, "2050-12-12", "11", "13"); |
|
| 62 |
final int count = iterateAndCount(iterator); |
|
| 63 |
assertEquals(1, count); |
|
| 64 |
} |
|
| 65 |
|
|
| 66 |
@Test |
|
| 67 |
@Ignore |
|
| 68 |
public void testIncrementalHarvesting() throws Exception {
|
|
| 69 |
System.out.println("incremental Harvesting");
|
|
| 70 |
iterator = new Gtr2ProjectsIterator(baseURL, "2016-11-30", "11", "11"); |
|
| 71 |
final int count = iterateAndCount(iterator); |
|
| 72 |
assertEquals(21, count); |
|
| 73 |
} |
|
| 74 |
|
|
| 75 |
@Test |
|
| 76 |
@Ignore |
|
| 77 |
public void testCompleteHarvesting() throws Exception {
|
|
| 78 |
System.out.println("testing complete harvesting");
|
|
| 79 |
iterator = new Gtr2ProjectsIterator(baseURL, null, null, null); |
|
| 80 |
// TryIndentXmlString indenter = new TryIndentXmlString(); |
|
| 81 |
// it.setEndAtPage(3); |
|
| 82 |
|
|
| 83 |
while (iterator.hasNext()) {
|
|
| 84 |
final String res = iterator.next(); |
|
| 85 |
assertNotNull(res); |
|
| 86 |
// System.out.println(res); |
|
| 87 |
// Scanner keyboard = new Scanner(System.in); |
|
| 88 |
// System.out.println("press enter for next record");
|
|
| 89 |
// keyboard.nextLine(); |
|
| 90 |
|
|
| 91 |
} |
|
| 92 |
} |
|
| 93 |
|
|
| 94 |
private int iterateAndCount(final Iterator<String> iterator) throws Exception {
|
|
| 95 |
int i = 0; |
|
| 96 |
while (iterator.hasNext()) {
|
|
| 97 |
assertNotNull(iterator.next()); |
|
| 98 |
i++; |
|
| 99 |
} |
|
| 100 |
System.out.println("Got " + i + " projects");
|
|
| 101 |
return i; |
|
| 102 |
} |
|
| 103 |
} |
|
Also available in: Unified diff
first implementation