package eu.dnetlib.dhp.bulktag; import static eu.dnetlib.dhp.PropagationConstant.readPath; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.*; import java.util.function.Function; import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( SparkEoscTag.class .getResourceAsStream( "/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional .ofNullable(parser.get("isSparkSessionManaged")) .map(Boolean::valueOf) .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); final String workingPath = parser.get("workingPath"); log.info("workingPath: {}", workingPath); SparkConf conf = new SparkConf(); runWithSparkSession( conf, isSparkSessionManaged, spark -> { execEoscTag(spark, inputPath, workingPath); }); } public static EoscIfGuidelines newInstance(String code, String label, String url, String semantics){ EoscIfGuidelines eig = new EoscIfGuidelines(); eig.setCode( code); eig.setLabel(label); eig.setUrl(url); eig.setSemanticRelation(semantics); return eig; } private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { readPath(spark, inputPath + "/software", Software.class) .map((MapFunction) s -> { if (containsCriteriaNotebook(s)) { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); addEIG(s.getEoscifguidelines(), "EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", "compliesWith"); } if (containsCriteriaGalaxy(s)) { if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) s.setEoscifguidelines(new ArrayList<>()); addEIG(s.getEoscifguidelines(),"EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); } return s; }, Encoders.bean(Software.class)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(workingPath + "/software"); readPath(spark, workingPath + "/software", Software.class) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(inputPath + "/software"); readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) .map((MapFunction) orp -> { if (!Optional.ofNullable(orp.getEoscifguidelines()).isPresent()) orp.setEoscifguidelines(new ArrayList<>()); if (containsCriteriaGalaxy(orp)) { addEIG(orp.getEoscifguidelines(),"EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); } if (containscriteriaTwitter(orp)) { addEIG(orp.getEoscifguidelines(),"EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return orp; }, Encoders.bean(OtherResearchProduct.class)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(workingPath + "/otherresearchproduct"); readPath(spark, workingPath + "/otherresearchproduct", OtherResearchProduct.class) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(inputPath + "/otherresearchproduct"); readPath(spark, inputPath + "/dataset", Dataset.class) .map((MapFunction) d -> { if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent()) d.setEoscifguidelines(new ArrayList<>()); if (containscriteriaTwitter(d)) { addEIG(d.getEoscifguidelines(),"EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return d; }, Encoders.bean(Dataset.class)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(workingPath + "/dataset"); readPath(spark, workingPath + "/dataset", Dataset.class) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(inputPath + "/dataset"); } private static void addEIG(List eoscifguidelines, String code, String label, String url, String sem) { if (!eoscifguidelines.stream().anyMatch(eig -> eig.getCode().equals(code))) eoscifguidelines.add(newInstance(code, label, url, sem)); } private static boolean containscriteriaTwitter(Result r) { Set words = getWordsSP(r.getTitle()); words.addAll(getWordsF(r.getDescription())); if (words.contains("twitter") && (words.contains("data") || words.contains("dataset"))) return true; if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) && r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data"))) return true; return false; } private static boolean containsCriteriaGalaxy(Result r) { Set words = getWordsSP(r.getTitle()); words.addAll(getWordsF(r.getDescription())); if (words.contains("galaxy") && words.contains("workflow")) return true; if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) && r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) return true; return false; } private static boolean containsCriteriaNotebook(Software s) { if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) return true; if (s .getSubject() .stream() .anyMatch( sbj -> sbj.getValue().toLowerCase().contains("python") && sbj.getValue().toLowerCase().contains("notebook"))) return true; if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python")) && s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("notebook"))) return true; return false; } private static Set getWordsSP(List elem) { Set words = new HashSet<>(); Optional .ofNullable(elem) .ifPresent( e -> e .forEach( t -> words .addAll( Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))))); return words; } private static Set getWordsF(List> elem) { Set words = new HashSet<>(); Optional .ofNullable(elem) .ifPresent( e -> e .forEach( t -> words .addAll( Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))))); return words; } }