244 lines
7.8 KiB
Java
244 lines
7.8 KiB
Java
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package eu.dnetlib.dhp.bulktag;
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import static eu.dnetlib.dhp.PropagationConstant.readPath;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.*;
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import java.util.function.Function;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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public class SparkEoscTag {
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private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class);
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public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static final Qualifier EOSC_QUALIFIER = OafMapperUtils
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.qualifier(
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"eosc",
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"European Open Science Cloud",
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ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES);
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public static final DataInfo EOSC_DATAINFO = OafMapperUtils
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.dataInfo(
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false, "propagation", true, false,
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OafMapperUtils
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.qualifier(
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"propagation:subject", "Inferred by OpenAIRE",
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ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
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"0.9");
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public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils
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.structuredProperty(
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"EOSC::Jupyter Notebook", EOSC_QUALIFIER, EOSC_DATAINFO);
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public final static StructuredProperty EOSC_GALAXY = OafMapperUtils
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.structuredProperty(
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"EOSC::Galaxy Workflow", EOSC_QUALIFIER, EOSC_DATAINFO);
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public final static StructuredProperty EOSC_TWITTER = OafMapperUtils
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.structuredProperty(
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"EOSC::Twitter Data", EOSC_QUALIFIER, EOSC_DATAINFO);
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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SparkEoscTag.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String workingPath = parser.get("workingPath");
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log.info("workingPath: {}", workingPath);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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execEoscTag(spark, inputPath, workingPath);
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});
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}
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private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) {
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readPath(spark, inputPath + "/software", Software.class)
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.map((MapFunction<Software, Software>) s -> {
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List<StructuredProperty> sbject;
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if (!Optional.ofNullable(s.getSubject()).isPresent())
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s.setSubject(new ArrayList<>());
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sbject = s.getSubject();
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if (containsCriteriaNotebook(s)) {
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sbject.add(EOSC_NOTEBOOK);
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}
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if (containsCriteriaGalaxy(s)) {
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sbject.add(EOSC_GALAXY);
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}
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return s;
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}, Encoders.bean(Software.class))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(workingPath + "/software");
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readPath(spark, workingPath + "/software", Software.class)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(inputPath + "/software");
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readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class)
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.map((MapFunction<OtherResearchProduct, OtherResearchProduct>) orp -> {
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List<StructuredProperty> sbject;
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if (!Optional.ofNullable(orp.getSubject()).isPresent())
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orp.setSubject(new ArrayList<>());
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sbject = orp.getSubject();
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if (containsCriteriaGalaxy(orp)) {
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sbject.add(EOSC_GALAXY);
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}
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if (containscriteriaTwitter(orp)) {
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sbject.add(EOSC_TWITTER);
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}
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return orp;
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}, Encoders.bean(OtherResearchProduct.class))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(workingPath + "/otherresearchproduct");
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readPath(spark, workingPath + "/otherresearchproduct", OtherResearchProduct.class)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(inputPath + "/otherresearchproduct");
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readPath(spark, inputPath + "/dataset", Dataset.class)
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.map((MapFunction<Dataset, Dataset>) d -> {
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List<StructuredProperty> sbject;
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if (!Optional.ofNullable(d.getSubject()).isPresent())
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d.setSubject(new ArrayList<>());
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sbject = d.getSubject();
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if (containscriteriaTwitter(d)) {
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sbject.add(EOSC_TWITTER);
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}
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return d;
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}, Encoders.bean(Dataset.class))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(workingPath + "/dataset");
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readPath(spark, workingPath + "/dataset", Dataset.class)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(inputPath + "/dataset");
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}
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private static boolean containscriteriaTwitter(Result r) {
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Set<String> words = getWordsSP(r.getTitle());
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words.addAll(getWordsF(r.getDescription()));
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if (words.contains("twitter") &&
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(words.contains("data") || words.contains("dataset")))
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return true;
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if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) &&
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r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data")))
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return true;
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return false;
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}
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private static boolean containsCriteriaGalaxy(Result r) {
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Set<String> words = getWordsSP(r.getTitle());
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words.addAll(getWordsF(r.getDescription()));
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if (words.contains("galaxy") &&
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words.contains("workflow"))
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return true;
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if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) &&
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r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow")))
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return true;
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return false;
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}
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private static boolean containsCriteriaNotebook(Software s) {
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if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter")))
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return true;
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if (s
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.getSubject()
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.stream()
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.anyMatch(
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sbj -> sbj.getValue().toLowerCase().contains("python") &&
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sbj.getValue().toLowerCase().contains("notebook")))
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return true;
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if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python")) &&
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s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("notebook")))
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return true;
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return false;
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}
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private static Set<String> getSubjects(List<StructuredProperty> s) {
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Set<String> subjects = new HashSet<>();
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s.stream().forEach(sbj -> subjects.addAll(Arrays.asList(sbj.getValue().toLowerCase().split(" "))));
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s.stream().forEach(sbj -> subjects.add(sbj.getValue().toLowerCase()));
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return subjects;
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}
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private static Set<String> getWordsSP(List<StructuredProperty> elem) {
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Set<String> words = new HashSet<>();
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Optional
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.ofNullable(elem)
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.ifPresent(
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e -> e
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.forEach(
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t -> words
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.addAll(
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Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))));
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return words;
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}
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private static Set<String> getWordsF(List<Field<String>> elem) {
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Set<String> words = new HashSet<>();
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Optional
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.ofNullable(elem)
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.ifPresent(
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e -> e
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.forEach(
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t -> words
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.addAll(
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Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))));
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// elem
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// .forEach(
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// t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))));
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return words;
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}
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}
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