merged from the osfPreprints_plugin branch
This commit is contained in:
commit
4e9f64e01a
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@ -1,4 +1,3 @@
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package eu.dnetlib.dhp.schema.oaf.utils;
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import java.util.*;
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@ -46,11 +46,11 @@ public class CollectorWorker extends ReportingJob {
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private final HttpClientParams clientParams;
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public CollectorWorker(
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final ApiDescriptor api,
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final FileSystem fileSystem,
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final MDStoreVersion mdStoreVersion,
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final HttpClientParams clientParams,
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final AggregatorReport report) {
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final ApiDescriptor api,
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final FileSystem fileSystem,
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final MDStoreVersion mdStoreVersion,
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final HttpClientParams clientParams,
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final AggregatorReport report) {
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super(report);
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this.api = api;
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this.fileSystem = fileSystem;
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@ -69,25 +69,22 @@ public class CollectorWorker extends ReportingJob {
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scheduleReport(counter);
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try (SequenceFile.Writer writer = SequenceFile
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.createWriter(
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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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.createWriter(this.fileSystem.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
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.keyClass(IntWritable.class), SequenceFile.Writer
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.valueClass(Text.class), 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(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 (final Throwable e) {
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throw new RuntimeException(e);
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}
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});
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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 (final Throwable e) {
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throw new RuntimeException(e);
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}
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});
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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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@ -115,36 +112,36 @@ public class CollectorWorker extends ReportingJob {
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private CollectorPlugin getCollectorPlugin() throws UnknownCollectorPluginException {
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switch (CollectorPlugin.NAME.valueOf(this.api.getProtocol())) {
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case oai:
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return new OaiCollectorPlugin(this.clientParams);
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case rest_json2xml:
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return new RestCollectorPlugin(this.clientParams);
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case file:
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return new FileCollectorPlugin(this.fileSystem);
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case fileGzip:
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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 osfPreprints:
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return new OsfPreprintsCollectorPlugin(this.clientParams);
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case other:
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final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
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case oai:
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return new OaiCollectorPlugin(this.clientParams);
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case rest_json2xml:
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return new RestCollectorPlugin(this.clientParams);
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case file:
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return new FileCollectorPlugin(this.fileSystem);
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case fileGzip:
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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 osfPreprints:
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return new OsfPreprintsCollectorPlugin(this.clientParams);
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case other:
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final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
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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(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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switch (plugin) {
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case mdstore_mongodb_dump:
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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("protocol is not managed: " + this.api.getProtocol());
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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: " + this.api.getProtocol());
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}
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}
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@ -31,19 +31,17 @@ public class OsfPreprintsCollectorPlugin implements CollectorPlugin {
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final String baseUrl = api.getBaseUrl();
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final int pageSize = Optional
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.ofNullable(api.getParams().get("pageSize"))
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.filter(StringUtils::isNotBlank)
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.map(s -> NumberUtils.toInt(s, PAGE_SIZE_VALUE_DEFAULT))
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.orElse(PAGE_SIZE_VALUE_DEFAULT);
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.ofNullable(api.getParams().get("pageSize"))
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.filter(StringUtils::isNotBlank)
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.map(s -> NumberUtils.toInt(s, PAGE_SIZE_VALUE_DEFAULT))
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.orElse(PAGE_SIZE_VALUE_DEFAULT);
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if (StringUtils.isBlank(baseUrl)) {
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throw new CollectorException("Param 'baseUrl' is null or empty");
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}
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if (StringUtils.isBlank(baseUrl)) { throw new CollectorException("Param 'baseUrl' is null or empty"); }
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final OsfPreprintsIterator it = new OsfPreprintsIterator(baseUrl, pageSize, getClientParams());
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return StreamSupport
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.stream(Spliterators.spliteratorUnknownSize(it, Spliterator.ORDERED), false);
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.stream(Spliterators.spliteratorUnknownSize(it, Spliterator.ORDERED), false);
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}
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public HttpClientParams getClientParams() {
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@ -34,9 +34,9 @@ public class OsfPreprintsIterator implements Iterator<String> {
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private final Queue<String> recordQueue = new PriorityBlockingQueue<>();
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public OsfPreprintsIterator(
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final String baseUrl,
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final int pageSize,
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final HttpClientParams clientParams) {
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final String baseUrl,
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final int pageSize,
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final HttpClientParams clientParams) {
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this.clientParams = clientParams;
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this.baseUrl = baseUrl;
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@ -54,8 +54,7 @@ public class OsfPreprintsIterator implements Iterator<String> {
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@Override
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public boolean hasNext() {
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synchronized (this.recordQueue) {
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while (this.recordQueue.isEmpty() && StringUtils.isNotBlank(this.currentUrl)
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&& this.currentUrl.startsWith("http")) {
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while (this.recordQueue.isEmpty() && StringUtils.isNotBlank(this.currentUrl) && this.currentUrl.startsWith("http")) {
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try {
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this.currentUrl = downloadPage(this.currentUrl);
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} catch (final CollectorException e) {
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@ -64,9 +63,7 @@ public class OsfPreprintsIterator implements Iterator<String> {
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}
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}
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if (!this.recordQueue.isEmpty()) {
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return true;
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}
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if (!this.recordQueue.isEmpty()) { return true; }
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return false;
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}
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@ -115,9 +112,7 @@ public class OsfPreprintsIterator implements Iterator<String> {
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}
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private Document downloadUrl(final String url, final int attempt) throws CollectorException {
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if (attempt > MAX_ATTEMPTS) {
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throw new CollectorException("Max Number of attempts reached, url:" + url);
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}
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if (attempt > MAX_ATTEMPTS) { throw new CollectorException("Max Number of attempts reached, url:" + url); }
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if (attempt > 0) {
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final int delay = (attempt * 5000);
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@ -35,18 +35,6 @@
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"paramRequired": true
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}
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,
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{
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"paramName": "wip",
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"paramLongName": "webCrawlInputPath",
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"paramDescription": "the path to get the input data from Web Crawl",
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"paramRequired": true
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},
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{
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"paramName": "pip",
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"paramLongName": "publisherInputPath",
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"paramDescription": "the path to get the input data from publishers",
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"paramRequired": true
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},
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{
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"paramName": "o",
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"paramLongName": "outputPath",
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@ -50,10 +50,9 @@ public class OsfPreprintsCollectorPluginTest {
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@Test
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@Disabled
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void test_one() throws CollectorException {
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this.plugin
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.collect(this.api, new AggregatorReport())
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.limit(1)
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.forEach(log::info);
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this.plugin.collect(this.api, new AggregatorReport())
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.limit(1)
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.forEach(log::info);
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}
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@Test
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@ -96,8 +95,7 @@ public class OsfPreprintsCollectorPluginTest {
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final HttpConnector2 connector = new HttpConnector2();
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try {
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final String res = connector
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.getInputSource("https://api.osf.io/v2/preprints/ydtzx/contributors/?format=json");
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final String res = connector.getInputSource("https://api.osf.io/v2/preprints/ydtzx/contributors/?format=json");
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System.out.println(res);
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fail();
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} catch (final Throwable e) {
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@ -29,7 +29,7 @@ class JsonPathTest {
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Assertions.assertNotNull(row);
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Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier")));
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System.out.println("row = " + row.getAs("country"));
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System.out.println("row = " + row.getAs("countrytitle"));
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}
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@Test
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