117 lines
3.4 KiB
Java
117 lines
3.4 KiB
Java
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package eu.dnetlib.dhp.oa.graph.dump;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.io.StringReader;
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import java.util.ArrayList;
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import java.util.List;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.io.SAXReader;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.Gson;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.oa.graph.dump.graph.Constants;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.Node;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation;
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import eu.dnetlib.dhp.schema.dump.pidgraph.Entity;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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public class Utils {
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public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void removeOutputDir(SparkSession spark, String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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public static <R> Dataset<R> readPath(
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SparkSession spark, String inputPath, Class<R> clazz) {
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return spark
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.read()
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.textFile(inputPath)
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.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
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}
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public static ISLookUpService getIsLookUpService(String isLookUpUrl) {
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return ISLookupClientFactory.getLookUpService(isLookUpUrl);
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}
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public static String getContextId(String id) {
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return String
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.format(
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"%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX,
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DHPUtils.md5(id));
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}
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public static CommunityMap getCommunityMap(SparkSession spark, String communityMapPath) {
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return new Gson().fromJson(spark.read().textFile(communityMapPath).collectAsList().get(0), CommunityMap.class);
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}
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public static CommunityMap readCommunityMap(FileSystem fileSystem, String communityMapPath) throws IOException {
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BufferedReader br = new BufferedReader(new InputStreamReader(fileSystem.open(new Path(communityMapPath))));
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StringBuffer sb = new StringBuffer();
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try {
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String line;
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while ((line = br.readLine()) != null) {
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sb.append(line);
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}
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} finally {
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br.close();
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}
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return new Gson().fromJson(sb.toString(), CommunityMap.class);
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}
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public static List<Relation> getRelationPair(String pid1, String pid2, String type1, String type2,
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String semtype, String rel1, String rel2) {
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List<Relation> ret = new ArrayList<>();
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ret
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.add(
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Relation
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.newInstance(
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Node.newInstance(pid1, type1),
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Node.newInstance(pid2, type2),
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RelType.newInstance(rel1, semtype),
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null));
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ret
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.add(
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Relation
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.newInstance(
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Node.newInstance(pid2, type2),
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Node.newInstance(pid1, type1),
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RelType.newInstance(rel2, semtype),
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null));
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return ret;
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}
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public static Entity getEntity(String fund, String code) throws DocumentException {
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{
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final Document doc;
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doc = new SAXReader().read(new StringReader(fund));
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String name = ((org.dom4j.Node) (doc.selectNodes("//funder/shortname").get(0))).getText();
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return Entity.newInstance(name + ":" + code);
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}
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}
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}
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